+
+
+
+
+ Export to new record
+
+ Export to existing draft record
+
+
+
+
+
diff --git a/client/src/components/Common/FilterMenu.test.js b/client/src/components/Common/FilterMenu.test.js
new file mode 100644
index 000000000000..5f7598ece3fd
--- /dev/null
+++ b/client/src/components/Common/FilterMenu.test.js
@@ -0,0 +1,293 @@
+import { mount } from "@vue/test-utils";
+import { HistoryFilters } from "components/History/HistoryFilters";
+import { getLocalVue } from "tests/jest/helpers";
+import Filtering, { compare, contains, equals, toBool, toDate } from "utils/filtering";
+
+import FilterMenu from "./FilterMenu";
+
+const localVue = getLocalVue();
+const options = [
+ { text: "Any", value: "any" },
+ { text: "Yes", value: true },
+ { text: "No", value: false },
+];
+const validTestFilters = {
+ /** A basic name filter (with same placeholder as the key) */
+ name: { placeholder: "name", type: String, handler: contains("name"), menuItem: true },
+ /** A filter with different key and placeholder */
+ filter_key: { placeholder: "item", type: String, handler: contains("filter_key"), menuItem: true },
+ /** A filter with help component */
+ has_help: {
+ placeholder: "value",
+ type: String,
+ handler: equals("has_help"),
+ helpInfo: "Some test help info",
+ menuItem: true,
+ },
+ /** A filter with datalist */
+ list_item: {
+ placeholder: "list item",
+ type: Number,
+ handler: equals("list_item"),
+ datalist: ["option1", "option2"],
+ menuItem: true,
+ },
+ /** A ranged date filter */
+ create_time: {
+ placeholder: "creation time",
+ type: Date,
+ handler: compare("create_time", "le", toDate),
+ isRangeInput: true,
+ menuItem: true,
+ },
+ /** A ranged number filter */
+ number: { placeholder: "index", type: Number, handler: equals("number"), isRangeInput: true, menuItem: true },
+ /** A boolean filter with default boolType */
+ bool_def: {
+ placeholder: "Filter by option (any/yes/no)",
+ type: Boolean,
+ handler: equals("bool_def", "bool_def", toBool),
+ menuItem: true,
+ },
+ /** A boolean filter with is:filter boolType */
+ bool_is: {
+ placeholder: "Filter by option (yes/no)",
+ type: Boolean,
+ handler: equals("bool_is", "bool_is", toBool),
+ menuItem: true,
+ boolType: "is",
+ },
+ /** A valid filter, just not included in menu */
+ not_included: { handler: contains("not_included"), menuItem: false },
+};
+const TestFilters = new Filtering(validTestFilters, false);
+
+describe("FilterMenu", () => {
+ let wrapper;
+
+ function setUpWrapper(name, placeholder, filterClass) {
+ wrapper = mount(FilterMenu, {
+ propsData: {
+ name: name,
+ placeholder: placeholder,
+ filterClass: filterClass,
+ filterText: "",
+ showAdvanced: false,
+ },
+ localVue,
+ stubs: {
+ icon: { template: "" },
+ },
+ });
+ }
+
+ async function performSearch() {
+ // Test: search button (should toggle the view out)
+ const searchButton = wrapper.find("[data-description='apply filters']");
+ await searchButton.trigger("click");
+ }
+
+ async function expectCorrectEmits(showAdvanced, filterText, filterClass) {
+ const filterEmit = wrapper.emitted()["update:filter-text"].length - 1;
+ const toggleEmit = wrapper.emitted()["update:show-advanced"].length - 1;
+ expect(wrapper.emitted()["update:show-advanced"][toggleEmit][0]).toEqual(showAdvanced);
+ await wrapper.setProps({ showAdvanced: wrapper.emitted()["update:show-advanced"][toggleEmit][0] });
+ const receivedText = wrapper.emitted()["update:filter-text"][filterEmit][0];
+ const receivedDict = filterClass.getQueryDict(receivedText);
+ const parsedDict = filterClass.getQueryDict(filterText);
+ expect(receivedDict).toEqual(parsedDict);
+ }
+
+ it("test generic test items filter panel search", async () => {
+ setUpWrapper("Test Items", "search test items", TestFilters);
+ const validFilters = wrapper.vm.$props.filterClass.validFilters;
+
+ await wrapper.setProps({ showAdvanced: true });
+
+ const expectedFilters = [
+ {
+ label: "Filter by name:",
+ placeholder: "any name",
+ value: "name-filter",
+ },
+ {
+ label: "Filter by item:",
+ placeholder: "any item",
+ value: "item-filter",
+ },
+ {
+ label: "Filter by value:",
+ placeholder: "any value",
+ value: "has-help-filter",
+ },
+ {
+ label: "Filter by list item:",
+ placeholder: "any list item",
+ value: "1234",
+ },
+ ];
+
+ expect(Object.keys(validFilters).length).toBe(13);
+ // find all labels for the filters
+ const labels = wrapper.findAll("small");
+ expect(labels.length).toBe(8);
+ // 8 labels, but 15 valid filters
+ // more valid filters than labels because not all all `menuItem:true`
+
+ /**
+ * Now add filters in all input fields in the advanced menu
+ * and check that the correct query is emitted
+ * */
+
+ // First 4 filters are normal, non ranged input fields
+ expectedFilters.forEach((expectedFilter, i) => {
+ const label = labels.at(i);
+ expect(label.text()).toBe(expectedFilter.label);
+ if (i < 4) {
+ const filterInput = wrapper.find(`[placeholder='${expectedFilter.placeholder}']`);
+ expect(filterInput.exists()).toBe(true);
+ filterInput.setValue(expectedFilter.value);
+ }
+ });
+ // `has_help` filter should have help modal button
+ expect(wrapper.find("[title='Value Help']").classes().includes("btn")).toBe(true);
+ // ranged time field (has 2 datepickers)
+ const createdGtInput = wrapper.find("[placeholder='creation time after']");
+ const createdLtInput = wrapper.find("[placeholder='creation time before']");
+ createdGtInput.setValue("January 1, 2022");
+ createdLtInput.setValue("January 1, 2023");
+ expect(wrapper.findAll(".b-form-datepicker").length).toBe(2);
+ // ranged number field (has different placeholder: greater instead of after...)
+ const indexGtInput = wrapper.find("[placeholder='index greater']");
+ const indexLtInput = wrapper.find("[placeholder='index lower']");
+ indexGtInput.setValue("1234");
+ indexLtInput.setValue("5678");
+ // default bool filter
+ const radioBtnGrp = wrapper.find("[data-description='filter bool_def']").findAll(".btn-secondary");
+ expect(radioBtnGrp.length).toBe(options.length);
+ for (let i = 0; i < options.length; i++) {
+ expect(radioBtnGrp.at(i).text()).toBe(options[i].text);
+ expect(radioBtnGrp.at(i).props().value).toBe(options[i].value);
+ expect(radioBtnGrp.at(i).props().checked).toBe(null);
+ }
+ await radioBtnGrp.at(1).find("input").setChecked(); // click "Yes"
+ // boolean filter
+ const boolBtnGrp = wrapper.find("[data-description='filter bool_is']").findAll(".btn-secondary");
+ expect(boolBtnGrp.length).toBe(2);
+ expect(boolBtnGrp.at(0).text()).toBe("Yes");
+ expect(boolBtnGrp.at(0).props().value).toBe(true);
+ expect(boolBtnGrp.at(1).text()).toBe("No");
+ expect(boolBtnGrp.at(1).props().value).toBe("any");
+ await boolBtnGrp.at(1).find("input").setChecked(); // click "No"
+
+ // perform search
+ await performSearch();
+ await expectCorrectEmits(
+ false,
+ "create_time>'January 1, 2022' create_time<'January 1, 2023' " +
+ "filter_key:item-filter has_help:has-help-filter list_item:1234 " +
+ "number>1234 number<5678 name:name-filter radio:true bool_def:true",
+ TestFilters
+ );
+ });
+
+ it("test buttons that navigate menu and keyup.enter/esc events", async () => {
+ setUpWrapper("Test Items", "search test items", TestFilters);
+
+ expect(wrapper.find("[data-description='advanced filters']").exists()).toBe(false);
+ await wrapper.setProps({ showAdvanced: true });
+ expect(wrapper.find("[data-description='advanced filters']").exists()).toBe(true);
+
+ // only add name filter in the advanced menu
+ let filterName = wrapper.find("[placeholder='any name']");
+ if (filterName.vm && filterName.props().type == "text") {
+ await filterName.setValue("sample name");
+ }
+
+ // -------- Test keyup.enter key: ---------
+ // toggles view out and performs a search
+ await filterName.trigger("keyup.enter");
+ await expectCorrectEmits(false, "name:'sample name'", TestFilters);
+
+ // Test: clearing the filterText
+ const clearButton = wrapper.find("[data-description='reset query']");
+ await clearButton.trigger("click");
+ await expectCorrectEmits(false, "", TestFilters);
+
+ // Test: toggling view back in
+ const toggleButton = wrapper.find("[data-description='toggle advanced search']");
+ await toggleButton.trigger("click");
+ await expectCorrectEmits(true, "", TestFilters);
+
+ // -------- Test keyup.esc key: ---------
+ // toggles view out only (doesn't cause a new search / doesn't emulate enter)
+
+ // find name field again (destroyed because of toggling out) and set value
+ filterName = wrapper.find("[placeholder='any name']");
+ if (filterName.vm && filterName.props().type == "text") {
+ filterName.setValue("newnamefilter");
+ }
+
+ // press esc key from name field (should not change emitted filterText unlike enter key)
+ await filterName.trigger("keyup.esc");
+ await expectCorrectEmits(false, "", TestFilters);
+ });
+
+ /**
+ * Testing the default values of the filters defined in the HistoryFilters: Filtering
+ * class, ensuring the default values are reflected in the radio-group buttons
+ */
+ it("test radio-group default filters on HistoryFilters", async () => {
+ setUpWrapper("History Items", "search datasets", HistoryFilters);
+ // -------- Testing deleted filter first: ---------
+
+ await wrapper.setProps({ showAdvanced: true });
+ const deletedFilterBtnGrp = wrapper.find("[data-description='filter deleted']");
+ const deletedFilterAnyBtn = deletedFilterBtnGrp.find(".btn-secondary");
+ expect(deletedFilterAnyBtn.text()).toBe("Any");
+
+ // current active button for deleted filter should be "No"
+ let deletedFilterActiveBtn = deletedFilterBtnGrp.find(".btn-secondary.active");
+ expect(deletedFilterActiveBtn.text()).toBe("No");
+
+ await deletedFilterAnyBtn.find("input").setChecked();
+
+ // now active button for deleted filter should be "Any"
+ deletedFilterActiveBtn = deletedFilterBtnGrp.find(".btn-secondary.active");
+ expect(deletedFilterActiveBtn.text()).toBe("Any");
+
+ // expect "deleted = any" filter to be applied
+ await performSearch();
+ await expectCorrectEmits(false, "visible:true", HistoryFilters);
+
+ // -------- Testing visible filter now: ---------
+
+ const toggleButton = wrapper.find("[data-description='toggle advanced search']");
+ await toggleButton.trigger("click");
+ await expectCorrectEmits(true, "visible:true", HistoryFilters);
+ const visibleFilterBtnGrp = wrapper.find("[data-description='filter visible']");
+ const visibleFilterAnyBtn = visibleFilterBtnGrp.find(".btn-secondary");
+ expect(visibleFilterAnyBtn.text()).toBe("Any");
+
+ // current active button for visible filter should be "Yes"
+ let visibleFilterActiveBtn = visibleFilterBtnGrp.find(".btn-secondary.active");
+ expect(visibleFilterActiveBtn.text()).toBe("Yes");
+
+ await visibleFilterAnyBtn.find("input").setChecked();
+
+ // now active button for visible filter should be "Any"
+ visibleFilterActiveBtn = visibleFilterBtnGrp.find(".btn-secondary.active");
+ expect(visibleFilterActiveBtn.text()).toBe("Any");
+
+ // expect "visible = any" filter to be applied
+ await performSearch();
+ await expectCorrectEmits(false, "deleted:any visible:any", HistoryFilters);
+
+ // -------- Testing repeated search if it prevents bug: ---------
+ // (bug reported here: https://github.com/galaxyproject/galaxy/issues/16211)
+ await toggleButton.trigger("click");
+ await expectCorrectEmits(true, "deleted:any visible:any", HistoryFilters);
+ await performSearch();
+ await expectCorrectEmits(false, "deleted:any visible:any", HistoryFilters);
+ });
+});
diff --git a/client/src/components/Common/FilterMenu.vue b/client/src/components/Common/FilterMenu.vue
new file mode 100644
index 000000000000..b418d1ca2355
--- /dev/null
+++ b/client/src/components/Common/FilterMenu.vue
@@ -0,0 +1,245 @@
+
+
+
+
+
+
+
+
+ Export to this record
+
+
+
+ + {{ newEntry.name }} + draft record has been created in the repository. +
+
+ You can preview the record in the repository, further edit its metadata and decide when to
+ publish it at
+
Please use the button below to upload the exported {{ props.what }} to the record.
+
+
+
+
+
+
+ Create new record
+
+
+ + You need to create the new record in a repository before exporting the {{ props.what }} to it. +
+
+
+
+
+ Export to existing record
+
+
+
+
+
+
+
diff --git a/client/src/components/Common/FilterMenuBoolean.vue b/client/src/components/Common/FilterMenuBoolean.vue
new file mode 100644
index 000000000000..8c54665d8a9b
--- /dev/null
+++ b/client/src/components/Common/FilterMenuBoolean.vue
@@ -0,0 +1,55 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ {{ props.filter.placeholder }}:
+
+
+
+
diff --git a/client/src/components/Common/FilterMenuInput.vue b/client/src/components/Common/FilterMenuInput.vue
new file mode 100644
index 000000000000..3c889a1800c9
--- /dev/null
+++ b/client/src/components/Common/FilterMenuInput.vue
@@ -0,0 +1,99 @@
+
+
+
+
+ Filter by {{ props.filter.placeholder }}:
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/client/src/components/Common/FilterMenuMultiTags.vue b/client/src/components/Common/FilterMenuMultiTags.vue
new file mode 100644
index 000000000000..8434837470ef
--- /dev/null
+++ b/client/src/components/Common/FilterMenuMultiTags.vue
@@ -0,0 +1,47 @@
+
+
+
+
+
+ {{ props.filter.helpInfo }}
+
+ Filter by {{ props.filter.placeholder }}:
+
+
+
+
diff --git a/client/src/components/Common/FilterMenuRanged.vue b/client/src/components/Common/FilterMenuRanged.vue
new file mode 100644
index 000000000000..25308df252f5
--- /dev/null
+++ b/client/src/components/Common/FilterMenuRanged.vue
@@ -0,0 +1,108 @@
+
+
+
+
+ Filter by {{ props.filter.placeholder }}:
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/client/src/components/Common/Published.vue b/client/src/components/Common/Published.vue
deleted file mode 100644
index dff84be865ce..000000000000
--- a/client/src/components/Common/Published.vue
+++ /dev/null
@@ -1,79 +0,0 @@
-
-
-
-
-
-
-
-
diff --git a/client/src/components/Common/PublishedItem.vue b/client/src/components/Common/PublishedItem.vue
new file mode 100644
index 000000000000..246cae7db0b4
--- /dev/null
+++ b/client/src/components/Common/PublishedItem.vue
@@ -0,0 +1,84 @@
+
+
+
+
-
-
- ![user avatar]()
-
-
-
- About this {{ modelTitle }}
-{{ item.title || item.name }}
--
Author
-{{ owner }}
- -
Related Pages
-
- All published {{ plural }}.
-
-
- Published {{ plural }} by {{ owner }}.
-
-
+
+
+
+
+
+
diff --git a/client/src/components/Common/models/exportRecordModel.ts b/client/src/components/Common/models/exportRecordModel.ts
index edb03290e1df..82a4458c5e3b 100644
--- a/client/src/components/Common/models/exportRecordModel.ts
+++ b/client/src/components/Common/models/exportRecordModel.ts
@@ -5,10 +5,11 @@ import type { components } from "@/schema";
type ExportObjectRequestMetadata = components["schemas"]["ExportObjectRequestMetadata"];
export type StoreExportPayload = components["schemas"]["StoreExportPayload"];
+export type ModelStoreFormat = components["schemas"]["ModelStoreFormat"];
export type ObjectExportTaskResponse = components["schemas"]["ObjectExportTaskResponse"];
export interface ExportParams {
- readonly modelStoreFormat: string;
+ readonly modelStoreFormat: ModelStoreFormat;
readonly includeFiles: boolean;
readonly includeDeleted: boolean;
readonly includeHidden: boolean;
diff --git a/client/src/components/DataDialog/DataDialog.vue b/client/src/components/DataDialog/DataDialog.vue
index 6ace81eecc13..8f4874b67df2 100644
--- a/client/src/components/DataDialog/DataDialog.vue
+++ b/client/src/components/DataDialog/DataDialog.vue
@@ -94,13 +94,22 @@ export default {
optionsShow: false,
undoShow: false,
hasValue: false,
+ urlTracker: null,
};
},
+ watch: {
+ history: async function () {
+ this.urlTracker = new UrlTracker(this.getHistoryUrl());
+ this.load();
+ },
+ },
created: function () {
this.services = new Services();
- this.urlTracker = new UrlTracker(this.getHistoryUrl());
this.model = new Model({ multiple: this.multiple, format: this.format });
- this.load();
+ if (this.history) {
+ this.urlTracker = new UrlTracker(this.getHistoryUrl());
+ this.load();
+ }
},
methods: {
/** Returns the default url i.e. the url of the current history **/
@@ -142,6 +151,7 @@ export default {
};
this.openGlobalUploadModal(propsData);
this.modalShow = false;
+ this.$emit("onUpload");
},
/** Called when selection is complete, values are formatted and parsed to external callback **/
onOk() {
diff --git a/client/src/components/Dataset/DatasetLink/DatasetLink.vue b/client/src/components/Dataset/DatasetLink/DatasetLink.vue
index 7fb1d5974d44..273d76318294 100644
--- a/client/src/components/Dataset/DatasetLink/DatasetLink.vue
+++ b/client/src/components/Dataset/DatasetLink/DatasetLink.vue
@@ -5,9 +5,10 @@
+
-
+
+
+ ![user avatar]()
+
+
+
+ About this {{ modelTitle }}
+{{ props.item?.title ?? props.item?.name }}
++
Author
+{{ owner }}
+ +
Related Pages
+
+ All published {{ plural }}.
+
+
+ Published {{ plural }} by {{ owner }}.
+
+ If you are signed-in to Galaxy using a third-party identity and you do not have a Galaxy password please use the reset password option in the login form with your email to create a password for your account. -
+
+
diff --git a/client/src/components/Form/Elements/FormData/types.ts b/client/src/components/Form/Elements/FormData/types.ts
new file mode 100644
index 000000000000..46929c8b876d
--- /dev/null
+++ b/client/src/components/Form/Elements/FormData/types.ts
@@ -0,0 +1,10 @@
+export interface DataOption {
+ id: string;
+ hid: number;
+ is_dataset?: boolean;
+ keep: boolean;
+ map_over_type?: string;
+ name: string;
+ src: string;
+ tags: Array
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/client/src/components/Form/Elements/FormDirectory.test.js b/client/src/components/Form/Elements/FormDirectory.test.js
index b878bc68d89f..c12171e233bc 100644
--- a/client/src/components/Form/Elements/FormDirectory.test.js
+++ b/client/src/components/Form/Elements/FormDirectory.test.js
@@ -2,6 +2,7 @@ import { mount } from "@vue/test-utils";
import FilesDialog from "components/FilesDialog/FilesDialog";
import { rootResponse } from "components/FilesDialog/testingData";
import flushPromises from "flush-promises";
+import { createPinia } from "pinia";
import { getLocalVue } from "tests/jest/helpers";
import { mockFetcher } from "@/schema/__mocks__";
@@ -52,12 +53,16 @@ describe("DirectoryPathEditableBreadcrumb", () => {
spyOnUpdateURL = jest.spyOn(FormDirectory.methods, "updateURL");
mockFetcher.path("/api/remote_files/plugins").method("get").mock({ data: rootResponse });
+ mockFetcher.path("/api/configuration").method("get").mock({ data: {} });
+
+ const pinia = createPinia();
wrapper = mount(FormDirectory, {
propsData: {
callback: () => {},
},
localVue: localVue,
+ pinia,
});
await flushPromises();
await init();
diff --git a/client/src/components/Form/Elements/FormNumber.vue b/client/src/components/Form/Elements/FormNumber.vue
index efdd9bfbd935..a616bd3d8706 100644
--- a/client/src/components/Form/Elements/FormNumber.vue
+++ b/client/src/components/Form/Elements/FormNumber.vue
@@ -8,16 +8,16 @@
-
-
-
-
-
-
-
-
-
+
-
- {{ input.title }}
- {{ input.help }}
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/client/src/components/Form/parameterTypes.d.ts b/client/src/components/Form/parameterTypes.d.ts
index 93f1a5406a5b..84ac11756c97 100644
--- a/client/src/components/Form/parameterTypes.d.ts
+++ b/client/src/components/Form/parameterTypes.d.ts
@@ -23,7 +23,6 @@ export type FormParameterTypes =
| "data_collection"
| "drill_down"
| "group_tag"
- | "library_data"
| "ftpfile"
| "upload"
| "rules"
diff --git a/client/src/components/GDateTime.test.ts b/client/src/components/GDateTime.test.ts
new file mode 100644
index 000000000000..e1303991b752
--- /dev/null
+++ b/client/src/components/GDateTime.test.ts
@@ -0,0 +1,43 @@
+import { getLocalVue } from "@tests/jest/helpers";
+import { mount } from "@vue/test-utils";
+
+import GDateTime from "./GDateTime.vue";
+
+const localVue = getLocalVue(true);
+
+async function mountGDateTime(props: object) {
+ const wrapper = mount(GDateTime as object, {
+ propsData: {
+ ...props,
+ },
+ localVue,
+ });
+
+ return wrapper;
+}
+
+describe("GDateTime.vue", () => {
+ it("emits updated date when input changes", async () => {
+ const wrapper = await mountGDateTime({
+ value: new Date("1970-01-01T00:00:00"),
+ });
+
+ const dateInput = wrapper.find('input[type="date"]');
+ await dateInput.setValue("2023-08-30");
+
+ expect(wrapper.emitted()).toHaveProperty("input");
+ expect(wrapper.emitted()?.["input"]?.[0]?.[0]).toEqual(new Date("2023-08-30T00:00:00"));
+ });
+
+ it("emits updated time when input changes", async () => {
+ const wrapper = await mountGDateTime({
+ value: new Date("1970-01-01T00:00:00"),
+ });
+
+ const timeInput = wrapper.find('input[type="time"]');
+ await timeInput.setValue("12:30");
+
+ expect(wrapper.emitted()).toHaveProperty("input");
+ expect(wrapper.emitted()?.["input"]?.[0]?.[0]).toEqual(new Date("1970-01-01T12:30:00"));
+ });
+});
diff --git a/client/src/components/GDateTime.vue b/client/src/components/GDateTime.vue
new file mode 100644
index 000000000000..616bc8322684
--- /dev/null
+++ b/client/src/components/GDateTime.vue
@@ -0,0 +1,71 @@
+
+
+
+
+
+
+ {{ props.input.title }}
+ {{ props.input.help }}
+
+
+
-
+
-
diff --git a/client/src/components/History/HistoryView.test.js b/client/src/components/History/HistoryView.test.js
index 5e2f559c96f2..ad880b5792ca 100644
--- a/client/src/components/History/HistoryView.test.js
+++ b/client/src/components/History/HistoryView.test.js
@@ -13,13 +13,14 @@ import HistoryView from "./HistoryView";
const localVue = getLocalVue();
jest.mock("stores/services/history.services");
-function create_history(historyId, userId, purged = false) {
+function create_history(historyId, userId, purged = false, archived = false) {
const historyName = `${userId}'s History ${historyId}`;
return {
model_class: "History",
id: historyId,
name: historyName,
purged: purged,
+ archived: archived,
count: 10,
annotation: "This is a history",
tags: ["tag_1", "tag_2"],
@@ -164,13 +165,43 @@ describe("History center panel View", () => {
const wrapper = await createWrapper(localVue, "user_1", history);
expect(wrapper.vm.history).toEqual(history);
- // switch/import buttons: purged they don't exist
+ // history purged, not switchable and not importable
const switchButton = wrapper.find("[data-description='switch to history button']");
const importButton = wrapper.find("[data-description='import history button']");
- expect(switchButton.exists()).toBe(false);
+ expect(switchButton.attributes("disabled")).toBeTruthy();
expect(importButton.exists()).toBe(false);
// instead we have an alert
expect(wrapper.find("[data-description='history state info']").text()).toBe("This history has been purged.");
});
+
+ it("should not display archived message and should be importable when user is not owner and history is archived", async () => {
+ const history = create_history("history_2", "user_2", false, true);
+ const wrapper = await createWrapper(localVue, "user_1", history);
+ expect(wrapper.vm.history).toEqual(history);
+
+ const switchButton = wrapper.find("[data-description='switch to history button']");
+ const importButton = wrapper.find("[data-description='import history button']");
+ expect(switchButton.exists()).toBe(false);
+ expect(importButton.exists()).toBe(true);
+ expect(importButton.attributes("disabled")).toBeFalsy();
+
+ expectCorrectLayout(wrapper);
+ expect(wrapper.find("[data-description='history state info']").exists()).toBe(false);
+ });
+
+ it("should display archived message and should not be importable when user is owner and history is archived", async () => {
+ const history = create_history("history_2", "user_1", false, true);
+ const wrapper = await createWrapper(localVue, "user_1", history);
+ expect(wrapper.vm.history).toEqual(history);
+
+ const switchButton = wrapper.find("[data-description='switch to history button']");
+ const importButton = wrapper.find("[data-description='import history button']");
+ expect(switchButton.exists()).toBe(true);
+ expect(switchButton.attributes("disabled")).toBeTruthy();
+ expect(importButton.exists()).toBe(false);
+
+ expectCorrectLayout(wrapper);
+ expect(wrapper.find("[data-description='history state info']").text()).toBe("This history has been archived.");
+ });
});
diff --git a/client/src/components/History/HistoryView.vue b/client/src/components/History/HistoryView.vue
index 4a43f6ce624e..f03c02e718d8 100644
--- a/client/src/components/History/HistoryView.vue
+++ b/client/src/components/History/HistoryView.vue
@@ -3,19 +3,19 @@
{{ historyStateInfoMessage }}
-
{{ stateText }}
@@ -81,40 +122,9 @@
class="dataset-peek p-1">| Dataset peek loading... |
+
Switch to this history
- As an anonymous user, unless you login or register, you will lose your current history after copying
+ As an anonymous user, unless you log in or register, you will lose your current history after copying
this history. You can log in here or register here.
@@ -36,7 +36,7 @@
Cancel
-
+
{{ saveTitle | localize }}
@@ -62,7 +62,7 @@ export default {
};
},
computed: {
- ...mapState(useUserStore, ["isAnonymous"]),
+ ...mapState(useUserStore, ["currentUser", "isAnonymous"]),
title() {
return `Copying History: ${this.history.name}`;
},
@@ -72,9 +72,12 @@ export default {
saveVariant() {
return this.loading ? "info" : this.formValid ? "primary" : "secondary";
},
+ userOwnsHistory() {
+ return this.currentUser.id == this.history.user_id;
+ },
newNameValid() {
- if (this.name == this.history.name) {
- return null;
+ if (this.userOwnsHistory && this.name == this.history.name) {
+ return false;
}
return this.name.length > 0;
},
diff --git a/client/src/components/History/Modals/SelectorModal.vue b/client/src/components/History/Modals/SelectorModal.vue
index 7d960c501fd3..400dc12bc743 100644
--- a/client/src/components/History/Modals/SelectorModal.vue
+++ b/client/src/components/History/Modals/SelectorModal.vue
@@ -4,16 +4,7 @@ import { faListAlt } from "@fortawesome/free-regular-svg-icons";
import { faArrowDown, faColumns, faSignInAlt } from "@fortawesome/free-solid-svg-icons";
import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
import { useInfiniteScroll } from "@vueuse/core";
-import {
- BBadge,
- BButton,
- BButtonGroup,
- BFormGroup,
- BFormInput,
- BListGroup,
- BListGroupItem,
- BModal,
-} from "bootstrap-vue";
+import { BBadge, BButton, BButtonGroup, BFormGroup, BListGroup, BListGroupItem, BModal } from "bootstrap-vue";
import isEqual from "lodash.isequal";
import { storeToRefs } from "pinia";
import { computed, onMounted, onUnmounted, type PropType, type Ref, ref, watch } from "vue";
@@ -22,19 +13,29 @@ import { useRouter } from "vue-router/composables";
import type { components } from "@/schema";
import { useHistoryStore } from "@/stores/historyStore";
import { useUserStore } from "@/stores/userStore";
-import Filtering, { contains, expandNameTag } from "@/utils/filtering";
+import Filtering, { compare, contains, expandNameTag, toDate } from "@/utils/filtering";
import localize from "@/utils/localization";
+import FilterMenu from "@/components/Common/FilterMenu.vue";
import Heading from "@/components/Common/Heading.vue";
import StatelessTags from "@/components/TagsMultiselect/StatelessTags.vue";
import UtcDate from "@/components/UtcDate.vue";
const validFilters = {
- name: contains("name"),
- tag: contains("tags", "tag", expandNameTag),
- annotation: contains("annotation"),
+ name: { placeholder: "name", type: String, handler: contains("name"), menuItem: true },
+ tag: { placeholder: "tag", type: String, handler: contains("tags", "tag", expandNameTag), menuItem: true },
+ annotation: { placeholder: "annotation", type: String, handler: contains("annotation"), menuItem: true },
+ update_time: {
+ placeholder: "updated time",
+ type: Date,
+ handler: compare("update_time", "le", toDate),
+ isRangeInput: true,
+ menuItem: true,
+ },
+ update_time_ge: { handler: compare("update_time", "ge", toDate), menuItem: false },
+ update_time_le: { handler: compare("update_time", "le", toDate), menuItem: false },
};
-const HistoriesFilters = new Filtering(validFilters, false);
+const HistoriesFilters = new Filtering(validFilters);
type AdditionalOptions = "set-current" | "multi" | "center";
type HistorySummary = components["schemas"]["HistorySummary"];
@@ -60,7 +61,7 @@ const propShowModal = computed({
get: () => {
return props.showModal;
},
- set: (val) => {
+ set: (val: boolean) => {
emit("update:show-modal", val);
},
});
@@ -68,6 +69,7 @@ const propShowModal = computed({
const selectedHistories: Ref<{ id: string }[]> = ref([]);
const filter = ref("");
const busy = ref(false);
+const showAdvanced = ref(false);
const modal: Ref = ref(null);
const scrollableDiv: Ref = ref(null);
@@ -87,7 +89,7 @@ onMounted(async () => {
// retain previously selected histories when you reopen the modal in multi view
watch(
() => propShowModal.value,
- (show) => {
+ (show: boolean) => {
if (props.multiple && show) {
selectedHistories.value = [...pinnedHistories.value];
}
@@ -104,7 +106,7 @@ onUnmounted(() => {
watch(
() => filter.value,
- async (newVal, oldVal) => {
+ async (newVal: string, oldVal: string) => {
if (newVal !== "" && validFilter.value && newVal !== oldVal) {
await loadMore(true);
}
@@ -117,7 +119,7 @@ watch(
const historiesProxy: Ref = ref([]);
watch(
() => props.histories as HistoryDetailed[],
- (h) => {
+ (h: HistoryDetailed[]) => {
historiesProxy.value = h.filter(
(h) => !h.user_id || (!currentUser.value?.isAnonymous && h.user_id === currentUser.value?.id)
);
@@ -133,7 +135,7 @@ const filtered: Ref = computed(() => {
filteredHistories = historiesProxy.value;
} else {
const filters = HistoriesFilters.getFiltersForText(filter.value);
- filteredHistories = historiesProxy.value.filter((history) => {
+ filteredHistories = historiesProxy.value.filter((history: HistorySummary) => {
if (!HistoriesFilters.testFilters(filters, history)) {
return false;
}
@@ -187,6 +189,10 @@ function setCenterPanelHistory(history: HistorySummary) {
modal.value?.hide();
}
+function setFilterValue(newFilter: string, newValue: string) {
+ filter.value = HistoriesFilters.setFilterValue(filter.value, newFilter, newValue);
+}
+
function openInMulti(history: HistorySummary) {
router.push("/histories/view_multiple");
historyStore.pinHistory(history.id);
@@ -221,13 +227,20 @@ async function loadMore(noScroll = false) {
-
Search string too short!
No histories found.
-
+
+
+
+
diff --git a/client/src/components/Panels/testToolsList.json b/client/src/components/Panels/testToolsList.json
deleted file mode 100644
index c5a3f965240c..000000000000
--- a/client/src/components/Panels/testToolsList.json
+++ /dev/null
@@ -1,72 +0,0 @@
-[
- {
- "model_class": "ToolSection",
- "id": "group_1",
- "name": "Group 1",
- "elems": [
- {
- "model_class": "Tool",
- "name": "Join",
- "id": "join1",
- "description": "two files",
- "panel_section_id": "group_1",
- "panel_section_name": "Group 1"
- },
- {
- "model_class": "Tool",
- "name": "Remove",
- "id": "remove1",
- "description": "lines",
- "panel_section_id": "group_1",
- "panel_section_name": "Group 1"
- },
- {
- "model_class": "Tool",
- "name": "Cut",
- "id": "cut1",
- "description": "lines",
- "panel_section_id": "group_1",
- "panel_section_name": "Group 1"
- },
- {
- "model_class": "Tool",
- "name": "Find",
- "id": "find1",
- "description": "joined dataset",
- "panel_section_id": "group_1",
- "panel_section_name": "Group 1"
- }
- ]
- },
- {
- "model_class": "ToolSection",
- "id": "group_2",
- "name": "Group 2",
- "elems": [
- {
- "model_class": "Tool",
- "name": "Join Collections",
- "id": "join_collections",
- "description": "",
- "panel_section_id": "group_2",
- "panel_section_name": "Group 2"
- },
- {
- "model_class": "Tool",
- "name": "Create Collections",
- "id": "create_collections",
- "description": "from datasets",
- "panel_section_id": "group_2",
- "panel_section_name": "Group 2"
- }
- ]
- },
- {
- "model_class": "Tool",
- "name": "Remove duplicate",
- "id": "remove_duplicate",
- "description": "lines from dataset",
- "panel_section_id": "remove_duplicate",
- "panel_section_name": "Remove duplicate"
- }
-]
diff --git a/client/src/components/Panels/toolSearch.worker.js b/client/src/components/Panels/toolSearch.worker.js
index 83e3663ad4cd..1b70b4b084c8 100644
--- a/client/src/components/Panels/toolSearch.worker.js
+++ b/client/src/components/Panels/toolSearch.worker.js
@@ -8,10 +8,16 @@ import { searchToolsByKeys } from "./utilities";
self.addEventListener("message", (event) => {
const { type, payload } = event.data;
if (type === "searchToolsByKeys") {
- const { tools, keys, query } = payload;
- const { results, closestTerm } = searchToolsByKeys(tools, keys, query);
+ const { tools, keys, query, panelView, currentPanel } = payload;
+ const { results, resultPanel, closestTerm } = searchToolsByKeys(tools, keys, query, panelView, currentPanel);
// send the result back to the main thread
- self.postMessage({ type: "searchToolsByKeysResult", payload: results, query: query, closestTerm: closestTerm });
+ self.postMessage({
+ type: "searchToolsByKeysResult",
+ payload: results,
+ sectioned: resultPanel,
+ query: query,
+ closestTerm: closestTerm,
+ });
} else if (type === "clearFilter") {
self.postMessage({ type: "clearFilterResult" });
} else if (type === "favoriteTools") {
diff --git a/client/src/components/Panels/utilities.js b/client/src/components/Panels/utilities.js
deleted file mode 100644
index 8bbc5385f68d..000000000000
--- a/client/src/components/Panels/utilities.js
+++ /dev/null
@@ -1,345 +0,0 @@
-/**
- * Utilities file for Panel Searches (panel/client search + advanced/backend search)
- */
-import { orderBy } from "lodash";
-import levenshteinDistance from "utils/levenshtein";
-
-const TOOLS_RESULTS_SORT_LABEL = "apiSort";
-const TOOLS_RESULTS_SECTIONS_HIDE = ["Expression Tools"];
-const STRING_REPLACEMENTS = [" ", "-", "(", ")", "'", ":"];
-
-// Converts filterSettings { key: value } to query = "key:value"
-export function createWorkflowQuery(filterSettings) {
- let query = "";
- query = Object.entries(filterSettings)
- .filter(([filter, value]) => value)
- .map(([filter, value]) => {
- if (value === true) {
- return `is:${filter}`;
- }
- return `${filter}:${value}`;
- })
- .join(" ");
- if (Object.keys(filterSettings).length == 1 && filterSettings.name) {
- return filterSettings.name;
- }
- return query;
-}
-
-/** Converts filters into tool search backend whoosh query.
- * @param {Object} filterSettings e.g.: {"name": "Tool Name", "section": "Collection", ...}
- * @param {String} panelView (if not `default`, does ontology search at backend)
- * @param {Array} toolbox (to find ontology id if given ontology name)
- * @returns parsed Whoosh `query`
- * @example
- * createWhooshQuery(filterSettings, 'ontology:edam_topics', toolbox)
- * return query = "(name:(skew) name_exact:(skew) description:(skew)) AND (edam_topics:(topic_0797) AND )"
- */
-export function createWhooshQuery(filterSettings, panelView, toolbox) {
- let query = "(";
- // add description+name_exact fields = name, to do a combined OrGroup at backend
- const name = filterSettings["name"];
- if (name) {
- query += "name:(" + name + ") ";
- query += "name_exact:(" + name + ") ";
- query += "description:(" + name + ")";
- }
- query += ") AND (";
- for (const [key, filterValue] of Object.entries(filterSettings)) {
- // get ontology keys if view is not default
- if (key === "section" && panelView !== "default") {
- const ontology = toolbox.find(({ name }) => name && name.toLowerCase().match(filterValue.toLowerCase()));
- if (ontology) {
- let ontologyKey = "";
- if (panelView === "ontology:edam_operations") {
- ontologyKey = "edam_operations";
- } else if (panelView === "ontology:edam_topics") {
- ontologyKey = "edam_topics";
- }
- query += ontologyKey + ":(" + ontology.id + ") AND ";
- } else {
- query += key + ":(" + filterValue + ") AND ";
- }
- } else if (key == "id") {
- query += "id_exact:(" + filterValue + ") AND ";
- } else if (key != "name") {
- query += key + ":(" + filterValue + ") AND ";
- }
- }
- query += ")";
- return query;
-}
-
-// Determines width given the root and draggable element, smallest and largest size and the current position
-export function determineWidth(rectRoot, rectDraggable, minWidth, maxWidth, direction, positionX) {
- let newWidth = null;
- if (direction === "right") {
- const offset = rectRoot.left - rectDraggable.left;
- newWidth = rectRoot.right - positionX - offset;
- } else {
- const offset = rectRoot.right - rectDraggable.left;
- newWidth = positionX - rectRoot.left + offset;
- }
- return Math.max(minWidth, Math.min(maxWidth, newWidth));
-}
-
-// Given toolbox and search results, returns filtered tool results
-export function filterTools(tools, results) {
- let toolsResults = [];
- tools = flattenTools(tools);
- toolsResults = mapToolsResults(tools, results);
- toolsResults = sortToolsResults(toolsResults);
- toolsResults = removeDuplicateResults(toolsResults);
- return toolsResults;
-}
-
-// Given toolbox and search results, returns filtered tool results by sections
-export function filterToolSections(tools, results) {
- let toolsResults = [];
- let toolsResultsSection = [];
- if (hasResults(results)) {
- toolsResults = tools.map((section) => {
- tools = flattenToolsSection(section);
- toolsResultsSection = mapToolsResults(tools, results);
- toolsResultsSection = sortToolsResults(toolsResultsSection);
- return {
- ...section,
- elems: toolsResultsSection,
- };
- });
- toolsResults = deleteEmptyToolsSections(toolsResults, results);
- } else {
- toolsResults = tools;
- }
- return toolsResults;
-}
-
-export function hasResults(results) {
- return Array.isArray(results) && results.length > 0;
-}
-
-/**
- * Given toolbox, keys to sort/search results by and a search query,
- * Does a direct string.match() comparison to find results,
- * If that produces nothing, runs DL distance alg to allow misspells
- *
- * @param {Array} tools - toolbox
- * @param {Object} keys - keys to sort and search results by
- * @param {String} query - a search query
- * @param {Boolean} usesDL - Optional: used for recursive call with DL if no string.match()
- * @returns tool ids sorted by order of keys that are being searched (+ closest matching term if DL)
- */
-export function searchToolsByKeys(tools, keys, query, usesDL = false) {
- let returnedTools = [];
- let closestTerm = null;
- const queryValue = sanitizeString(query.trim().toLowerCase(), STRING_REPLACEMENTS);
- const minimumQueryLength = 5; // for DL
- for (const tool of tools) {
- for (const key of Object.keys(keys)) {
- if (tool[key] || key === "combined") {
- let actualValue = "";
- if (key === "combined") {
- actualValue = (tool.name + tool.description).trim().toLowerCase();
- } else {
- actualValue = tool[key].trim().toLowerCase();
- }
- const actualValueWords = actualValue.split(" ");
- actualValue = sanitizeString(actualValue, STRING_REPLACEMENTS);
- // do we care for exact matches && is it an exact match ?
- const order = keys.exact && actualValue === queryValue ? keys.exact : keys[key];
- if (!usesDL && actualValue.match(queryValue)) {
- returnedTools.push({ id: tool.id, order });
- break;
- } else if (usesDL) {
- let substring = null;
- if ((key == "name" || key == "description") && queryValue.length >= minimumQueryLength) {
- substring = closestSubstring(queryValue, actualValue);
- }
- // there is a closestSubstring: matching tool found
- if (substring) {
- // get the closest matching term for substring
- const foundTerm = matchingTerm(actualValueWords, substring);
- if (foundTerm && (!closestTerm || (closestTerm && foundTerm.length < closestTerm.length))) {
- closestTerm = foundTerm;
- }
- returnedTools.push({ id: tool.id, order, closestTerm });
- break;
- }
- }
- }
- }
- }
- // no results with string.match(): recursive call with usesDL
- if (!usesDL && returnedTools.length == 0) {
- return searchToolsByKeys(tools, keys, query, true);
- }
- // sorting results by indexed order of keys
- returnedTools = orderBy(returnedTools, ["order"], ["desc"]).map((tool) => tool.id);
- return { results: returnedTools, closestTerm: closestTerm };
-}
-
-export function flattenTools(tools) {
- let normalizedTools = [];
- tools.forEach((section) => {
- normalizedTools = normalizedTools.concat(flattenToolsSection(section));
- });
- return normalizedTools;
-}
-
-export function hideToolsSection(tools) {
- return tools.filter((section) => !TOOLS_RESULTS_SECTIONS_HIDE.includes(section.name));
-}
-
-export function removeDisabledTools(tools) {
- return tools.filter((section) => {
- if (section.model_class === "ToolSectionLabel") {
- return true;
- } else if (!section.elems && section.disabled) {
- return false;
- } else if (section.elems) {
- section.elems = section.elems.filter((el) => !el.disabled);
- if (!section.elems.length) {
- return false;
- }
- }
- return true;
- });
-}
-
-/**
- *
- * @param {String} query
- * @param {String} actualStr
- * @returns substring with smallest DL distance, or null
- */
-function closestSubstring(query, actualStr) {
- // Max distance a query and substring can be apart
- const maxDistance = 1;
- // Create an array of all actualStr substrings that are query length, query length -1, and query length + 1
- const substrings = Array.from({ length: actualStr.length - query.length + 1 }, (_, i) =>
- actualStr.substr(i, query.length)
- );
- if (query.length > 1) {
- substrings.push(
- ...Array.from({ length: actualStr.length - query.length + 2 }, (_, i) =>
- actualStr.substr(i, query.length - 1)
- )
- );
- }
- if (actualStr.length > query.length) {
- substrings.push(
- ...Array.from({ length: actualStr.length - query.length }, (_, i) => actualStr.substr(i, query.length + 1))
- );
- }
- // check to see if any substrings have a levenshtein distance less than the max distance
- for (const substring of substrings) {
- if (levenshteinDistance(query, substring, true) <= maxDistance) {
- return substring;
- }
- }
- return null;
-}
-
-function isToolObject(tool) {
- // toolbox overhaul with typing will simplify this dramatically...
- // Right now, our shorthand is that tools have no 'text', and don't match
- // the model_class of the section/label.
- if (!tool.text && tool.model_class !== "ToolSectionLabel" && tool.model_class !== "ToolSection") {
- return true;
- }
- return false;
-}
-
-// given array and a substring, get the closest matching term for substring
-function matchingTerm(termArray, substring) {
- const sanitized = sanitizeString(substring);
-
- for (const i in termArray) {
- const term = termArray[i];
- if (term.match(sanitized)) {
- return term;
- }
- }
- return null;
-}
-
-/**
- *
- * @param {String} value - to be sanitized
- * @param {Array} targets - Optional: characters to replace
- * @param {String} substitute - Optional: replacement character
- * @returns sanitized string
- */
-function sanitizeString(value, targets = [], substitute = "") {
- let sanitized = value;
- targets.forEach((rep) => {
- sanitized = sanitized.replaceAll(rep, substitute);
- });
-
- return sanitized.replace(/[.*+?^${}()|[\]\\]/g, "\\$&");
-}
-
-function flattenToolsSection(section) {
- const flattenTools = [];
- if (section.elems) {
- section.elems.forEach((tool) => {
- if (isToolObject(tool)) {
- flattenTools.push(tool);
- }
- });
- } else if (isToolObject(section)) {
- // This might be a top-level section-less tool and not actually a
- // section.
- flattenTools.push(section);
- }
- return flattenTools;
-}
-
-function mapToolsResults(tools, results) {
- const toolsResults = tools
- .filter((tool) => !tool.text && results.includes(tool.id))
- .map((tool) => {
- Object.assign(tool, setSort(tool, results));
- return tool;
- });
- return toolsResults;
-}
-
-function removeDuplicateResults(results) {
- const uniqueTools = [];
- return results.filter((tool) => {
- if (!uniqueTools.includes(tool.id)) {
- uniqueTools.push(tool.id);
- return true;
- } else {
- return false;
- }
- });
-}
-
-function setSort(tool, results) {
- return { [TOOLS_RESULTS_SORT_LABEL]: results.indexOf(tool.id) };
-}
-
-function sortToolsResults(toolsResults) {
- return orderBy(toolsResults, [TOOLS_RESULTS_SORT_LABEL], ["asc"]);
-}
-
-function deleteEmptyToolsSections(tools, results) {
- let isSection = false;
- let isMatchedTool = false;
- tools = tools
- .filter((section) => {
- isSection = section.elems && section.elems.length > 0;
- isMatchedTool = !section.text && results.includes(section.id);
- return isSection || isMatchedTool;
- })
- .sort((sectionPrevious, sectionCurrent) => {
- if (sectionPrevious.elems.length == 0 || sectionCurrent.elems.length == 0) {
- return 0;
- }
- return results.indexOf(sectionPrevious.elems[0].id) - results.indexOf(sectionCurrent.elems[0].id);
- });
-
- return tools;
-}
diff --git a/client/src/components/Panels/utilities.test.js b/client/src/components/Panels/utilities.test.js
index 6564fb7bf737..dcf5e39c53a0 100644
--- a/client/src/components/Panels/utilities.test.js
+++ b/client/src/components/Panels/utilities.test.js
@@ -1,12 +1,11 @@
import toolsList from "components/ToolsView/testData/toolsList";
+import toolsListInPanel from "components/ToolsView/testData/toolsListInPanel";
import {
+ createSortedResultObject,
createWhooshQuery,
- createWorkflowQuery,
determineWidth,
filterTools,
- filterToolSections,
- flattenTools,
searchToolsByKeys,
} from "./utilities";
@@ -19,27 +18,35 @@ describe("test helpers in tool searching utilities and panel handling", () => {
});
});
-const tempToolsList = [
- {
- elems: [
- {
- panel_section_name: "FASTA/FASTQ",
- description: "Extract UMI from fastq files",
- id: "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2",
- name: "UMI-tools extract",
- },
- {
- panel_section_name: "FASTA/FASTQ",
- description: "Extract UMI from (fasta files)",
- id: "umi_tools_reduplicate",
- name: "UMI-tools reduplicate",
- },
- ],
- model_class: "ToolSection",
- id: "fasta/fastq",
- name: "FASTA/FASTQ",
+const tempToolPanel = {
+ default: {
+ "fasta/fastq": {
+ tools: [
+ "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2",
+ "umi_tools_reduplicate",
+ ],
+ model_class: "ToolSection",
+ id: "fasta/fastq",
+ name: "FASTA/FASTQ",
+ },
},
-];
+};
+const tempToolsList = {
+ tools: {
+ "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2": {
+ panel_section_name: "FASTA/FASTQ",
+ description: "Extract UMI from fastq files",
+ id: "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2",
+ name: "UMI-tools extract",
+ },
+ umi_tools_reduplicate: {
+ panel_section_name: "FASTA/FASTQ",
+ description: "Extract UMI from (fasta files)",
+ id: "umi_tools_reduplicate",
+ name: "UMI-tools reduplicate",
+ },
+ },
+};
describe("test helpers in tool searching utilities", () => {
it("test parsing helper that converts settings to whoosh query", async () => {
@@ -73,7 +80,8 @@ describe("test helpers in tool searching utilities", () => {
"__ZIP_COLLECTION__",
],
keys: { description: 1, name: 0 },
- list: toolsList,
+ tools: Object.values(toolsList.tools),
+ panel: toolsListInPanel.default,
},
{
// name prioritized
@@ -85,32 +93,71 @@ describe("test helpers in tool searching utilities", () => {
"__FILTER_EMPTY_DATASETS__",
],
keys: { description: 0, name: 1 },
- list: toolsList,
+ tools: Object.values(toolsList.tools),
+ panel: toolsListInPanel.default,
},
{
// whitespace precedes to ensure query.trim() works
q: " filter empty datasets",
expectedResults: ["__FILTER_EMPTY_DATASETS__"],
keys: { description: 1, name: 2, combined: 0 },
- list: toolsList,
+ tools: Object.values(toolsList.tools),
+ panel: toolsListInPanel.default,
},
{
// hyphenated tool-name is searchable
q: "uMi tools extract ",
expectedResults: ["toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2"],
keys: { description: 1, name: 2 },
- list: tempToolsList,
+ tools: Object.values(tempToolsList.tools),
+ panel: tempToolPanel.default,
},
{
- // parenthesis is searchable
- q: "from FASTA files",
+ // parenthesis (and other chars) are searchable
+ q: "from FASTA:files",
expectedResults: ["umi_tools_reduplicate"],
keys: { description: 1, name: 2 },
- list: tempToolsList,
+ tools: Object.values(tempToolsList.tools),
+ panel: tempToolPanel.default,
+ },
+ {
+ // id is not searchable if not identified by colon
+ q: "__ZIP_COLLECTION__",
+ expectedResults: [],
+ keys: { description: 1, name: 2 },
+ tools: Object.values(toolsList.tools),
+ panel: toolsListInPanel.default,
+ },
+ {
+ // id is searchable if provided "id:"
+ q: "id:__ZIP_COLLECTION__",
+ expectedResults: ["__ZIP_COLLECTION__"],
+ keys: { description: 1, name: 2 },
+ tools: Object.values(toolsList.tools),
+ panel: toolsListInPanel.default,
+ },
+ {
+ // id is searchable if provided "tool_id:"
+ q: "tool_id:umi_tools",
+ expectedResults: [
+ "toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/1.1.2+galaxy2",
+ "umi_tools_reduplicate",
+ ],
+ keys: { description: 1, name: 2 },
+ tools: Object.values(tempToolsList.tools),
+ panel: tempToolPanel.default,
+ },
+ // if at least couple words match, return results
+ {
+ q: "filter datasets",
+ expectedResults: ["__FILTER_FAILED_DATASETS__", "__FILTER_EMPTY_DATASETS__"],
+ keys: { combined: 1, wordMatch: 0 },
+ tools: Object.values(toolsList.tools),
+ panel: toolsListInPanel.default,
},
];
searches.forEach((search) => {
- const { results } = searchToolsByKeys(flattenTools(search.list), search.keys, search.q);
+ const { results } = searchToolsByKeys(search.tools, search.keys, search.q, "default", search.panel);
expect(results).toEqual(search.expectedResults);
});
});
@@ -118,15 +165,41 @@ describe("test helpers in tool searching utilities", () => {
it("test tool fuzzy search", async () => {
const expectedResults = ["__FILTER_FAILED_DATASETS__", "__FILTER_EMPTY_DATASETS__"];
const keys = { description: 1, name: 2, combined: 0 };
+ // Testing if just names work with DL search
const filterQueries = ["Fillter", "FILYER", " Fitler", " filtr"];
filterQueries.forEach((q) => {
- const { results, closestTerm } = searchToolsByKeys(flattenTools(toolsList), keys, q);
+ const { results, closestTerm } = searchToolsByKeys(
+ Object.values(toolsList.tools),
+ keys,
+ q,
+ "default",
+ toolsListInPanel.default
+ );
expect(results).toEqual(expectedResults);
expect(closestTerm).toEqual("filter");
});
- const queries = ["datases from a collection", "from a colleection"];
+ // Testing if names and description function with DL search
+ let queries = ["datases from a collection", "from a colleection", "from a colleection"];
+ queries.forEach((q) => {
+ const { results } = searchToolsByKeys(
+ Object.values(toolsList.tools),
+ keys,
+ q,
+ "default",
+ toolsListInPanel.default
+ );
+ expect(results).toEqual(expectedResults);
+ });
+ // Testing if different length queries correctly trigger changes in max DL distance
+ queries = ["datae", "ppasetsfrom", "datass from a cppollection"];
queries.forEach((q) => {
- const { results } = searchToolsByKeys(flattenTools(toolsList), keys, q);
+ const { results } = searchToolsByKeys(
+ Object.values(toolsList.tools),
+ keys,
+ q,
+ "default",
+ toolsListInPanel.default
+ );
expect(results).toEqual(expectedResults);
});
});
@@ -134,26 +207,16 @@ describe("test helpers in tool searching utilities", () => {
it("test tool filtering helpers on toolsList given list of ids", async () => {
const ids = ["__FILTER_FAILED_DATASETS__", "liftOver1"];
// check length of first section from imported const toolsList
- expect(toolsList.find((section) => section.id == "collection_operations").elems).toHaveLength(4);
+ expect(toolsListInPanel.default["collection_operations"].tools).toHaveLength(4);
// check length of same section from filtered toolsList
- expect(
- filterToolSections(toolsList, ids).find((section) => section.id == "collection_operations").elems
- ).toHaveLength(1);
- // check length of filtered tools without sections
- expect(filterTools(toolsList, ids)).toHaveLength(2);
- });
-});
-
-describe("test helpers in workflow searching utilities", () => {
- it("test helper that creates workflow query given filters", async () => {
- const settings = {
- name: "extract",
- tag: "Genomic",
- published: null,
- shared_with_me: true,
- deleted: false,
- };
- const q = createWorkflowQuery(settings);
- expect(q).toEqual("name:extract tag:Genomic is:shared_with_me");
+ const matchedTools = ids.map((id) => {
+ return { id: id, sections: [], order: 0 };
+ });
+ const toolResultsPanel = createSortedResultObject(matchedTools, toolsListInPanel.default);
+ const toolResultsSection = toolResultsPanel.resultPanel["collection_operations"];
+ expect(toolResultsSection.tools).toHaveLength(1);
+ // check length of filtered tools (regardless of sections)
+ const filteredToolIds = Object.keys(filterTools(toolsList.tools, ids));
+ expect(filteredToolIds).toHaveLength(2);
});
});
diff --git a/client/src/components/Panels/utilities.ts b/client/src/components/Panels/utilities.ts
new file mode 100644
index 000000000000..ff75e194b13d
--- /dev/null
+++ b/client/src/components/Panels/utilities.ts
@@ -0,0 +1,542 @@
+/**
+ * Utilities file for Panel Searches (panel/client search + advanced/backend search)
+ * Note: Any mention of "DL" in this file refers to the Demerau-Levenshtein distance algorithm
+ */
+import { orderBy } from "lodash";
+
+import {
+ type FilterSettings as ToolFilters,
+ type Tool,
+ type ToolSection,
+ type ToolSectionLabel,
+} from "@/stores/toolStore";
+import levenshteinDistance from "@/utils/levenshtein";
+
+const TOOL_ID_KEYS = ["id", "tool_id"];
+const STRING_REPLACEMENTS: string[] = [" ", "-", "\\(", "\\)", "'", ":", `"`];
+const MINIMUM_DL_LENGTH = 5; // for Demerau-Levenshtein distance
+const MINIMUM_WORD_MATCH = 2; // for word match
+const UNSECTIONED_SECTION = {
+ // to return a section for unsectioned tools
+ model_class: "ToolSection",
+ id: "unsectioned",
+ name: "Unsectioned Tools",
+ description: "Tools that don't appear under any section in the unsearched panel",
+};
+const VALID_SECTION_TYPES = ["edam_operations", "edam_topics"]; // other than `default`
+
+/** These are keys used to order/sort results in `ToolSearch`.
+ * The value for each is the sort order, higher number = higher rank.
+ * Must include some `Tool` properties (like name, description, id etc.)
+ * to check against query, and any other keys below are special, used for
+ * specific cases (like `combined` for name+description).
+ */
+export interface ToolSearchKeys {
+ [key: string | keyof Tool]: number | undefined;
+ /** property has exact match with query */
+ exact?: number;
+ /** property starts with query */
+ startsWith?: number;
+ /** query contains matches `Tool.name + Tool.description` */
+ combined?: number;
+ /** property matches */
+ wordMatch?: number;
+}
+
+interface SearchMatch {
+ id: string;
+ sections: (string | undefined)[];
+ order: number;
+}
+
+// Converts filterSettings { key: value } to query = "key:value"
+export function createWorkflowQuery(filterSettings: Record) {
+ let query = "";
+ query = Object.entries(filterSettings)
+ .filter(([, value]) => value)
+ .map(([filter, value]) => {
+ if (value === true) {
+ return `is:${filter}`;
+ }
+ return `${filter}:${value}`;
+ })
+ .join(" ");
+ if (Object.keys(filterSettings).length == 1 && filterSettings.name) {
+ return filterSettings.name as string;
+ }
+ return query;
+}
+
+/** Converts filters into tool search backend whoosh query.
+ * @param filterSettings e.g.: {"name": "Tool Name", "section": "Collection", ...}
+ * @returns parsed Whoosh `query`
+ * @example
+ * createWhooshQuery(filterSettings = {"name": "skew", "ontology": "topic_0797"})
+ * return query = "(name:(skew) name_exact:(skew) description:(skew)) AND (edam_topics:(topic_0797) AND )"
+ */
+export function createWhooshQuery(filterSettings: ToolFilters) {
+ let query = "(";
+ // add description+name_exact fields = name, to do a combined OrGroup at backend
+ const name = filterSettings["name"];
+ if (name) {
+ query += "name:(" + name + ") ";
+ query += "name_exact:(" + name + ") ";
+ query += "description:(" + name + ")";
+ }
+ query += ") AND (";
+ for (const [key, filterValue] of Object.entries(filterSettings)) {
+ if (filterValue) {
+ if (key === "ontology" && filterValue.includes("operation")) {
+ query += "edam_operations:(" + filterValue + ") AND ";
+ } else if (key === "ontology" && filterValue.includes("topic")) {
+ query += "edam_topics:(" + filterValue + ") AND ";
+ } else if (key == "id") {
+ query += "id_exact:(" + filterValue + ") AND ";
+ } else if (key != "name") {
+ query += key + ":(" + filterValue + ") AND ";
+ }
+ }
+ }
+ query += ")";
+ return query;
+}
+
+// Determines width given the root and draggable element, smallest and largest size and the current position
+export function determineWidth(
+ rectRoot: { left: number; right: number },
+ rectDraggable: { left: number },
+ minWidth: number,
+ maxWidth: number,
+ direction: string,
+ positionX: number
+) {
+ let newWidth = null;
+ if (direction === "right") {
+ const offset = rectRoot.left - rectDraggable.left;
+ newWidth = rectRoot.right - positionX - offset;
+ } else {
+ const offset = rectRoot.right - rectDraggable.left;
+ newWidth = positionX - rectRoot.left + offset;
+ }
+ return Math.max(minWidth, Math.min(maxWidth, newWidth));
+}
+
+/**
+ * @param toolsById - all tools, keyed by id
+ * @param results - list of result tool ids
+ * @returns filtered tool results (by id)
+ */
+export function filterTools(toolsById: Record, results: string[]) {
+ const filteredTools: Record = {};
+ for (const id of results) {
+ const localTool = toolsById[id];
+ if (localTool !== undefined) {
+ filteredTools[id] = localTool;
+ }
+ }
+ return filteredTools;
+}
+
+/** Returns a `toolsById` object containing tools that meet required conditions
+ * based on params.
+ * @param toolsById - object of tools, keyed by id
+ * @param isWorkflowPanel - whether or not the ToolPanel is in Workflow Editor
+ * @param excludedSectionIds - ids for sections whose tools will be excluded
+ */
+export function getValidToolsInCurrentView(
+ toolsById: Record,
+ isWorkflowPanel = false,
+ excludedSectionIds: string[] = []
+) {
+ const addedToolTexts: string[] = [];
+ const toolEntries = Object.entries(toolsById).filter(([, tool]) => {
+ // filter out duplicate tools (different ids, same exact name+description)
+ // related ticket: https://github.com/galaxyproject/galaxy/issues/16145
+ const toolText = tool.name + tool.description;
+ if (addedToolTexts.includes(toolText)) {
+ return false;
+ } else {
+ addedToolTexts.push(toolText);
+ }
+ // filter on non-hidden, non-disabled, and workflow compatibile (based on props.workflow)
+ return (
+ !tool.hidden &&
+ tool.disabled !== true &&
+ !(isWorkflowPanel && !tool.is_workflow_compatible) &&
+ !excludedSectionIds.includes(tool.panel_section_id || "")
+ );
+ });
+ return Object.fromEntries(toolEntries);
+}
+
+/** Looks in each section of `currentPanel` and filters `section.tools` on `validToolIdsInCurrentView` */
+export function getValidToolsInEachSection(
+ validToolIdsInCurrentView: string[],
+ currentPanel: Record
+) {
+ return Object.entries(currentPanel).map(([id, section]) => {
+ const validatedSection = { ...section } as ToolSection;
+ if (validatedSection.tools && Array.isArray(validatedSection.tools)) {
+ // filter on valid tools and panel labels in this section
+ validatedSection.tools = validatedSection.tools.filter((toolId) => {
+ if (typeof toolId === "string" && validToolIdsInCurrentView.includes(toolId)) {
+ return true;
+ } else if (typeof toolId !== "string") {
+ // is a special case where there is a label within a section
+ return true;
+ }
+ });
+ }
+ return [id, validatedSection];
+ });
+}
+
+/**
+ * @param items - `[id, PanelItem]` entries (from the `currentPanel` object)
+ * @param validToolIdsInCurrentView - tool ids that are valid in current view
+ * @param excludedSectionIds - any section ids to exclude
+ * @returns a `currentPanel` object containing sections/tools/labels that meet required conditions
+ */
+export function getValidPanelItems(
+ items: (string | ToolSection)[][],
+ validToolIdsInCurrentView: string[],
+ excludedSectionIds: string[] = []
+) {
+ const validEntries = items.filter(([id, item]) => {
+ id = id as string;
+ item = item as Tool | ToolSection;
+ if (isToolObject(item as Tool) && validToolIdsInCurrentView.includes(id)) {
+ // is a `Tool` and is in `localToolsById`
+ return true;
+ } else if (item.tools === undefined) {
+ // is neither a `Tool` nor a `ToolSection`, maybe a `ToolSectionLabel`
+ return true;
+ } else if (item.tools && item.tools.length > 0 && !excludedSectionIds.includes(id)) {
+ // is a `ToolSection` with tools; is not an excluded section
+ return true;
+ } else {
+ return false;
+ }
+ });
+ return Object.fromEntries(validEntries);
+}
+
+/**
+ * Given toolbox, keys to sort/search results by and a search query,
+ * Does a direct string.match() comparison to find results,
+ * If that produces nothing, runs DL distance alg to allow misspells
+ *
+ * @param tools - toolbox
+ * @param keys - keys to sort and search results by
+ * @param query - a search query
+ * @param panelView - panel view, to find section_id for each tool
+ * @param currentPanel - current ToolPanel with { section_id: { tools: [tool ids] }, ... }
+ * @param usesDL - Optional: used for recursive call with DL if no string.match()
+ * @returns an object containing
+ * - results: array of tool ids that match the query
+ * - resultPanel: a ToolPanel with only the results for the current panelView
+ * - closestTerm: Optional: closest matching term for DL (in case no match with query)
+ *
+ * all sorted by order of keys that are being searched (+ closest matching term if DL)
+ */
+export function searchToolsByKeys(
+ tools: Tool[],
+ keys: ToolSearchKeys,
+ query: string,
+ panelView = "default",
+ currentPanel: Record,
+ usesDL = false
+): {
+ results: string[];
+ resultPanel: Record;
+ closestTerm: string | null;
+} {
+ const matchedTools: SearchMatch[] = [];
+ let closestTerm = null;
+ // if user's query = "id:1234" or "tool_id:1234", only search for id
+ const id = processForId(query, TOOL_ID_KEYS);
+ if (id) {
+ query = id;
+ keys = { id: 1 };
+ }
+
+ const queryWords = query.trim().toLowerCase().split(" ");
+ const queryValue = sanitizeString(query.trim().toLowerCase(), STRING_REPLACEMENTS);
+ for (const tool of tools) {
+ for (const key of Object.keys(keys)) {
+ if (tool[key as keyof Tool] || key === "combined") {
+ let actualValue = "";
+ // key = "combined" is a special case for searching name + description
+ if (key === "combined") {
+ actualValue = `${tool.name.trim()} ${tool.description.trim()}`.toLowerCase();
+ } else {
+ actualValue = (tool[key as keyof Tool] as string)?.trim().toLowerCase();
+ }
+
+ // get all (space separated) words in actualValue for tool (for DL)
+ const actualValueWords = actualValue.split(" ");
+ actualValue = sanitizeString(actualValue, STRING_REPLACEMENTS);
+
+ // do we care for exact matches && is it an exact match ?
+ let order =
+ keys.exact !== undefined && actualValue === queryValue
+ ? (keys.exact as number)
+ : (keys[key] as number);
+ // do we care for startsWith && does it actualValue start with query ?
+ order =
+ keys.startsWith !== undefined &&
+ order !== keys.exact &&
+ key === "name" &&
+ actualValue.startsWith(queryValue)
+ ? keys.startsWith
+ : order;
+
+ const wordMatches = actualValueWords.filter((word) => queryWords.includes(word));
+ if (!usesDL) {
+ if (actualValue.match(queryValue)) {
+ // if string.match() returns true, matching tool found
+ matchedTools.push({ id: tool.id, sections: getPanelSectionsForTool(tool, panelView), order });
+ break;
+ } else if (
+ key === "combined" &&
+ keys.wordMatch !== undefined &&
+ wordMatches.length >= MINIMUM_WORD_MATCH
+ ) {
+ // we are looking at combined name+description, and there are enough word matches
+ matchedTools.push({
+ id: tool.id,
+ sections: getPanelSectionsForTool(tool, panelView),
+ order: keys.wordMatch,
+ });
+ break;
+ }
+ } else if (usesDL) {
+ // if string.match() returns false, try DL distance once to see if there is a closestSubstring
+ let substring = null;
+ if ((key == "name" || key == "description") && queryValue.length >= MINIMUM_DL_LENGTH) {
+ substring = closestSubstring(queryValue, actualValue);
+ }
+ // there is a closestSubstring: matching tool found
+ if (substring) {
+ // get the closest matching term for substring
+ const foundTerm = matchingTerm(actualValueWords, substring);
+ if (foundTerm && (!closestTerm || (closestTerm && foundTerm.length < closestTerm.length))) {
+ closestTerm = foundTerm;
+ }
+ matchedTools.push({
+ id: tool.id,
+ sections: getPanelSectionsForTool(tool, panelView),
+ order,
+ });
+ break;
+ }
+ }
+ }
+ }
+ }
+ // no results with string.match(): recursive call with usesDL
+ if (!id && !usesDL && matchedTools.length == 0) {
+ return searchToolsByKeys(tools, keys, query, panelView, currentPanel, true);
+ }
+ const { idResults, resultPanel } = createSortedResultObject(matchedTools, currentPanel);
+ return { results: idResults, resultPanel: resultPanel, closestTerm: closestTerm };
+}
+
+/**
+ * Orders the matchedTools by order of keys that are being searched, and creates a resultPanel
+ * @param matchedTools containing { id: tool id, sections: [section ids], order: order }
+ * @param currentPanel current ToolPanel for current view
+ * @returns an object containing
+ * - idResults: array of tool ids that match the query
+ * - resultPanel: a ToolPanel with only the results
+ */
+export function createSortedResultObject(
+ matchedTools: SearchMatch[],
+ currentPanel: Record
+) {
+ const idResults: string[] = [];
+ // creating a sectioned results object ({section_id: [tool ids], ...}), keeping
+ // track of the best version of each tool, and also sorting by indexed order of keys
+ const resultPanel = orderBy(matchedTools, ["order"], ["desc"]).reduce(
+ (acc: Record, match: SearchMatch) => {
+ // we either found specific section(s) for tool, or we need to search all sections
+ const sections: (string | undefined)[] =
+ match.sections.length !== 0 ? match.sections : Object.keys(currentPanel);
+ for (const section of sections) {
+ let toolAdded = false;
+ const existingPanelItem = section ? currentPanel[section] : undefined;
+ if (existingPanelItem && section) {
+ if (
+ (existingPanelItem as ToolSection).tools &&
+ (existingPanelItem as ToolSection).tools?.includes(match.id)
+ ) {
+ // it has tools so is a section, and it has the tool we're looking for
+
+ // if we haven't seen this section yet, create it in the resultPanel
+ let existingSection = acc[section] as ToolSection;
+ if (!existingSection) {
+ existingSection = { ...existingPanelItem };
+ existingSection.tools = [];
+ }
+ existingSection.tools?.push(match.id);
+ acc[section] = existingSection;
+ toolAdded = true;
+ } else if (isToolObject(existingPanelItem as Tool) && existingPanelItem.id === match.id) {
+ // it is a tool, and it is the tool we're looking for
+
+ // put in it the "Unsectioned Tools" section (if it doesn't exist, create it)
+ const unsectionedId = UNSECTIONED_SECTION.id;
+ let unsectionedSection = acc[unsectionedId] as ToolSection;
+ if (!unsectionedSection) {
+ unsectionedSection = { ...UNSECTIONED_SECTION };
+ unsectionedSection.tools = [];
+ }
+ unsectionedSection.tools?.push(match.id);
+ acc[unsectionedId] = unsectionedSection;
+ toolAdded = true;
+ }
+ if (toolAdded && !idResults.includes(match.id)) {
+ idResults.push(match.id);
+ }
+ }
+ }
+ return acc;
+ },
+ {}
+ );
+ return { idResults, resultPanel };
+}
+
+/**
+ * Gets the section(s) a tool belongs to for a given panelView.
+ * Unless view=`default`, all other views must be of format `class:view_type`,
+ * where `Tool` object has a `view_name` key containing an array of section ids.
+ * e.g.: view = `ontology:edam_operations` => `Tool.edam_operations = [section ids]`.
+ *
+ * Therefore, this would not handle the case where view = `ontology:edam_merged`, since
+ * Tool.edam_merged is not a valid key, and we would just return `[uncategorized]`.
+ *
+ * Just prevents looking through whole panel to find section id for tool,
+ * we still end up doing that (in `createSortedResultObject`) in case we return [] here
+ * @param tool
+ * @param panelView
+ * @returns Array of section ids
+ */
+function getPanelSectionsForTool(tool: Tool, panelView: string) {
+ if (panelView === "default" && tool.panel_section_id) {
+ if (tool.panel_section_id.startsWith("tool_")) {
+ return [tool.panel_section_id.split("tool_")[1]];
+ } else {
+ return [tool.panel_section_id];
+ }
+ } else if (panelView !== "default") {
+ const sectionType = panelView.split(":")[1] as keyof Tool;
+ if (
+ sectionType &&
+ VALID_SECTION_TYPES.includes(sectionType as string) &&
+ (tool[sectionType] as string[])?.length !== 0
+ ) {
+ return tool[sectionType] as string[];
+ } else {
+ return ["uncategorized"];
+ }
+ }
+ return [];
+}
+
+/**
+ *
+ * @param query
+ * @param actualStr
+ * @returns substring with smallest DL distance, or null
+ */
+function closestSubstring(query: string, actualStr: string) {
+ // Create max distance
+ // Max distance a query and substring can be apart
+ const maxDistance = Math.floor(query.length / 5);
+ // Create an array of all actualStr substrings that are query length, query length -1, and query length + 1
+ const substrings = Array.from({ length: actualStr.length - query.length + maxDistance }, (_, i) =>
+ actualStr.substr(i, query.length)
+ );
+ if (query.length > 1) {
+ substrings.push(
+ ...Array.from({ length: actualStr.length - query.length + maxDistance + 1 }, (_, i) =>
+ actualStr.substr(i, query.length - maxDistance)
+ )
+ );
+ }
+ if (actualStr.length > query.length) {
+ substrings.push(
+ ...Array.from({ length: actualStr.length - query.length }, (_, i) =>
+ actualStr.substr(i, query.length + maxDistance)
+ )
+ );
+ }
+ // check to see if any substrings have a levenshtein distance less than the max distance
+ for (const substring of substrings) {
+ if (levenshteinDistance(query, substring, true) <= maxDistance) {
+ return substring;
+ }
+ }
+ return null;
+}
+
+export function isToolObject(tool: Tool | ToolSection | ToolSectionLabel) {
+ // toolbox overhaul with typing will simplify this dramatically...
+ // Right now, our shorthand is that tools have no 'text', and don't match
+ // the model_class of the section/label.
+ if (
+ !(tool as ToolSectionLabel).text &&
+ tool.model_class !== "ToolSectionLabel" &&
+ tool.model_class !== "ToolSection" &&
+ (tool as ToolSection).tools === undefined
+ ) {
+ return true;
+ }
+ return false;
+}
+
+// given array and a substring, get the closest matching term for substring
+function matchingTerm(termArray: string[], substring: string) {
+ const sanitized = sanitizeString(substring);
+
+ for (const i in termArray) {
+ const term = termArray[i];
+ if (term?.match(sanitized)) {
+ return term;
+ }
+ }
+ return null;
+}
+
+/**
+ *
+ * @param value - to be sanitized
+ * @param targets - Optional: characters to replace
+ * @param substitute - Optional: replacement character
+ * @returns sanitized string
+ */
+function sanitizeString(value: string, targets: string[] = [], substitute = "") {
+ let sanitized = value;
+ targets.forEach((rep) => {
+ sanitized = sanitized.replace(new RegExp(rep, "g"), substitute);
+ });
+
+ return sanitized.replace(/[.*+?^${}()|[\]\\]/g, "\\$&");
+}
+
+/**
+ * If the query is of the form "id:1234" (or "tool_id:1234"), return the id.
+ * Otherwise, return null.
+ * @param query - the raw query
+ * @param keys - Optional: keys to check for (default: ["id"])
+ * @returns id or null
+ */
+function processForId(query: string, keys = ["id"]) {
+ for (const key of keys) {
+ if (query.includes(`${key}:`)) {
+ return query.split(`${key}:`)[1]?.trim();
+ }
+ }
+ return null;
+}
diff --git a/client/src/components/Popper/Popper.vue b/client/src/components/Popper/Popper.vue
index 0ad88fa106d9..edd74cddd609 100644
--- a/client/src/components/Popper/Popper.vue
+++ b/client/src/components/Popper/Popper.vue
@@ -1,5 +1,5 @@
-
+
+
+
diff --git a/client/src/components/Upload/UploadBox.vue b/client/src/components/Upload/UploadBox.vue
new file mode 100644
index 000000000000..bf620e6be8a3
--- /dev/null
+++ b/client/src/components/Upload/UploadBox.vue
@@ -0,0 +1,32 @@
+
+
+
+
+import { BTab, BTabs } from "bootstrap-vue";
+import { getDatatypesMapper } from "components/Datatypes";
+import LoadingSpan from "components/LoadingSpan";
+import {
+ AUTO_EXTENSION,
+ DEFAULT_DBKEY,
+ DEFAULT_EXTENSION,
+ getUploadDatatypes,
+ getUploadDbKeys,
+} from "components/Upload/utils";
+import { computed, onMounted, ref } from "vue";
+
+import { eventHub } from "@/components/plugins/eventHub.js";
+import { uploadPayload } from "@/utils/upload-payload.js";
+
+import CompositeBox from "./CompositeBox";
+import DefaultBox from "./DefaultBox";
+import RulesInput from "./RulesInput";
+
+const props = defineProps({
+ auto: {
+ type: Object,
+ default: () => AUTO_EXTENSION,
+ },
+ chunkUploadSize: {
+ type: Number,
+ default: 1024,
+ },
+ currentHistoryId: {
+ type: String,
+ required: true,
+ },
+ currentUserId: {
+ type: String,
+ default: "",
+ },
+ datatypesDisableAuto: {
+ type: Boolean,
+ default: false,
+ },
+ defaultDbKey: {
+ type: String,
+ default: DEFAULT_DBKEY,
+ },
+ defaultExtension: {
+ type: String,
+ default: DEFAULT_EXTENSION,
+ },
+ fileSourcesConfigured: {
+ type: Boolean,
+ default: false,
+ },
+ ftpUploadSite: {
+ type: String,
+ default: "",
+ },
+ formats: {
+ type: Array,
+ default: null,
+ },
+ // Return uploads when done if supplied.
+ hasCallback: {
+ type: Boolean,
+ default: false,
+ },
+ // Restrict the forms to a single dataset upload if false
+ multiple: {
+ type: Boolean,
+ default: true,
+ },
+});
+
+const extensionsSet = ref(false);
+const datatypesMapper = ref(null);
+const datatypesMapperReady = ref(false);
+const dbKeysSet = ref(false);
+const listExtensions = ref([]);
+const listDbKeys = ref([]);
+const regular = ref(null);
+
+const effectiveExtensions = computed(() => {
+ if (props.formats === null || !datatypesMapperReady.value) {
+ return listExtensions.value;
+ } else {
+ const result = [];
+ listExtensions.value.forEach((extension) => {
+ if (extension && extension.id == "auto") {
+ result.push(extension);
+ } else if (datatypesMapper.value.isSubTypeOfAny(extension.id, props.formats)) {
+ result.push(extension);
+ }
+ });
+ return result;
+ }
+});
+
+const hasCompositeExtension = computed(() =>
+ effectiveExtensions.value.some((extension) => !!extension.composite_files)
+);
+const hasRegularExtension = computed(() => effectiveExtensions.value.some((extension) => !extension.composite_files));
+const historyAvailable = computed(() => Boolean(props.currentHistoryId));
+const ready = computed(
+ () => dbKeysSet.value && extensionsSet.value && historyAvailable.value && datatypesMapperReady.value
+);
+const showCollection = computed(() => !props.formats && props.multiple);
+const showComposite = computed(() => !props.formats || hasCompositeExtension);
+const showRegular = computed(() => !props.formats || hasRegularExtension);
+const showRules = computed(() => !props.formats || props.multiple);
+
+function immediateUpload(files) {
+ regular.value?.addFiles(files);
+}
+
+function toData(items, history_id, composite = false) {
+ return uploadPayload(items, history_id, composite);
+}
+
+async function loadExtensions() {
+ listExtensions.value = await getUploadDatatypes(props.datatypesDisableAuto, props.auto);
+ extensionsSet.value = true;
+}
+
+async function loadDbKeys() {
+ listDbKeys.value = await getUploadDbKeys(props.defaultDbKey);
+ dbKeysSet.value = true;
+}
+
+async function loadMappers() {
+ if (props.formats !== null) {
+ datatypesMapper.value = await getDatatypesMapper();
+ }
+ datatypesMapperReady.value = true;
+}
+
+function progress(percentage, status = null) {
+ if (percentage !== null) {
+ eventHub.$emit(`upload:percentage`, percentage);
+ }
+ if (status !== null) {
+ eventHub.$emit(`upload:status`, status);
+ }
+}
+
+onMounted(() => {
+ loadExtensions();
+ loadDbKeys();
+ loadMappers();
+});
+
+defineExpose({
+ immediateUpload,
+ listDbKeys,
+ listExtensions,
+ toData,
+});
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/client/src/components/Upload/UploadModal.test.js b/client/src/components/Upload/UploadModal.test.js
index 9422e481fba7..3943f69ea8f5 100644
--- a/client/src/components/Upload/UploadModal.test.js
+++ b/client/src/components/Upload/UploadModal.test.js
@@ -2,18 +2,25 @@ import { mount } from "@vue/test-utils";
import axios from "axios";
import MockAdapter from "axios-mock-adapter";
import { createPinia } from "pinia";
-import { configStore } from "store/configStore";
import { useHistoryStore } from "stores/historyStore";
import { useUserStore } from "stores/userStore";
-import { getLocalVue, mockModule } from "tests/jest/helpers";
-import Vuex from "vuex";
+import { getLocalVue } from "tests/jest/helpers";
-import { getDatatypes, getGenomes } from "./services";
-import UploadModal from "./UploadModal";
-import UploadModalContent from "./UploadModalContent";
+import { getDatatypes, getDbKeys } from "./services";
+
+import UploadContainer from "./UploadContainer.vue";
+import UploadModal from "./UploadModal.vue";
jest.mock("app");
jest.mock("./services");
+jest.mock("@/schema");
+
+jest.mock("@/composables/config", () => ({
+ useConfig: jest.fn(() => ({
+ config: {},
+ isConfigLoaded: true,
+ })),
+}));
const fastaResponse = {
description_url: "https://wiki.galaxyproject.org/Learn/Datatypes#Fasta",
@@ -30,22 +37,13 @@ const genomesResponse = [
];
getDatatypes.mockReturnValue({ data: [fastaResponse] });
-getGenomes.mockReturnValue({ data: genomesResponse });
+getDbKeys.mockReturnValue({ data: genomesResponse });
const propsData = {
chunkUploadSize: 1024,
- uploadPath: "/api/tools",
fileSourcesConfigured: true,
};
-const createStore = () => {
- return new Vuex.Store({
- modules: {
- config: mockModule(configStore, { config: {} }),
- },
- });
-};
-
describe("UploadModal.vue", () => {
let wrapper;
let axiosMock;
@@ -58,11 +56,8 @@ describe("UploadModal.vue", () => {
const localVue = getLocalVue();
const pinia = createPinia();
- const store = createStore();
wrapper = mount(UploadModal, {
- store,
- provide: { store },
propsData,
localVue,
stubs: {
@@ -91,14 +86,13 @@ describe("UploadModal.vue", () => {
});
it("should load with correct defaults", async () => {
- const contentWrapper = wrapper.findComponent(UploadModalContent);
+ const contentWrapper = wrapper.findComponent(UploadContainer);
expect(contentWrapper.vm.auto.id).toBe("auto");
expect(contentWrapper.vm.datatypesDisableAuto).toBe(false);
});
it("should fetch datatypes and parse them", async () => {
- // lists are one layer deeper now, it won't matter after refactoring
- const contentWrapper = wrapper.findComponent(UploadModalContent);
+ const contentWrapper = wrapper.findComponent(UploadContainer);
expect(contentWrapper.exists()).toBe(true);
expect(contentWrapper.vm.listExtensions.length).toBe(2);
expect(contentWrapper.vm.listExtensions[0].id).toBe("auto");
@@ -106,8 +100,7 @@ describe("UploadModal.vue", () => {
});
it("should fetch genomes and parse them", async () => {
- // lists are one yaer deeper now, it won't matter after refactoring
- const contentWrapper = wrapper.findComponent(UploadModalContent);
- expect(contentWrapper.vm.listGenomes.length).toBe(3);
+ const contentWrapper = wrapper.findComponent(UploadContainer);
+ expect(contentWrapper.vm.listDbKeys.length).toBe(3);
});
});
diff --git a/client/src/components/Upload/UploadModal.vue b/client/src/components/Upload/UploadModal.vue
index e7c284ee2a34..59239a7347da 100644
--- a/client/src/components/Upload/UploadModal.vue
+++ b/client/src/components/Upload/UploadModal.vue
@@ -1,35 +1,30 @@
diff --git a/client/src/components/Upload/UploadOption.vue b/client/src/components/Upload/UploadOption.vue
new file mode 100644
index 000000000000..d9c2925a42f7
--- /dev/null
+++ b/client/src/components/Upload/UploadOption.vue
@@ -0,0 +1,33 @@
+
+
+
+
+
+
+
+ {{ title }}
+
+
+
diff --git a/client/src/components/Upload/UploadSelect.vue b/client/src/components/Upload/UploadSelect.vue
new file mode 100644
index 000000000000..847fc160f4d0
--- /dev/null
+++ b/client/src/components/Upload/UploadSelect.vue
@@ -0,0 +1,106 @@
+
+
+
+
+ No matching {{ what }}s found.
+
+ {{ option.text }}
+
+
+
+
+
diff --git a/client/src/components/Upload/UploadSelectExtension.vue b/client/src/components/Upload/UploadSelectExtension.vue
new file mode 100644
index 000000000000..0f75026b5349
--- /dev/null
+++ b/client/src/components/Upload/UploadSelectExtension.vue
@@ -0,0 +1,63 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/client/src/components/Upload/UploadWrapper.vue b/client/src/components/Upload/UploadWrapper.vue
deleted file mode 100644
index 3d05a61b9e8a..000000000000
--- a/client/src/components/Upload/UploadWrapper.vue
+++ /dev/null
@@ -1,49 +0,0 @@
-
-
-
-
-
-
-
+
+
+
@@ -124,7 +130,6 @@
import { getGalaxyInstance } from "app";
import axios from "axios";
import BootstrapVue from "bootstrap-vue";
-import ConfigProvider from "components/providers/ConfigProvider";
import { getUserPreferencesModel } from "components/User/UserPreferencesModel";
import { mapState } from "pinia";
import _l from "utils/localization";
@@ -133,6 +138,7 @@ import QueryStringParsing from "utils/query-string-parsing";
import { withPrefix } from "utils/redirect";
import Vue from "vue";
+import { useConfig } from "@/composables/config";
import { useUserStore } from "@/stores/userStore";
import UserActivityBarSettings from "./UserActivityBarSettings";
@@ -147,7 +153,6 @@ Vue.use(BootstrapVue);
export default {
components: {
- ConfigProvider,
UserActivityBarSettings,
UserDeletion,
UserPreferencesElement,
@@ -165,6 +170,10 @@ export default {
required: true,
},
},
+ setup() {
+ const { config, isConfigLoaded } = useConfig(true);
+ return { config, isConfigLoaded };
+ },
data() {
return {
email: "",
@@ -172,6 +181,8 @@ export default {
diskQuota: "",
messageVariant: null,
message: null,
+ showLogoutModal: false,
+ showDataPrivateModal: false,
toggleActivityBar: false,
toggleTheme: false,
};
@@ -187,13 +198,15 @@ export default {
},
hasLogout() {
const Galaxy = getGalaxyInstance();
- return !!Galaxy.session_csrf_token && !Galaxy.config.single_user;
+ return !!Galaxy.session_csrf_token && !this.config.single_user;
},
hasThemes() {
- const Galaxy = getGalaxyInstance();
- const themes = Object.keys(Galaxy.config.themes);
+ const themes = Object.keys(this.config.themes);
return themes?.length > 1 ?? false;
},
+ userPermissionsUrl() {
+ return withPrefix("/user/permissions");
+ },
},
created() {
const message = QueryStringParsing.get("message");
@@ -210,7 +223,6 @@ export default {
},
methods: {
makeDataPrivate() {
- const Galaxy = getGalaxyInstance();
if (
confirm(
_l(
@@ -224,33 +236,13 @@ export default {
)
)
) {
- axios.post(withPrefix(`/history/make_private?all_histories=true`)).then((response) => {
- Galaxy.modal.show({
- title: _l("Datasets are now private"),
- body: `All of your histories and datsets have been made private. If you'd like to make all *future* histories private please use the User Permissions interface.`,
- buttons: {
- Close: () => {
- Galaxy.modal.hide();
- },
- },
- });
+ axios.post(withPrefix(`/history/make_private?all_histories=true`)).then(() => {
+ this.showDataPrivateModal = true;
});
}
},
signOut() {
- const Galaxy = getGalaxyInstance();
- Galaxy.modal.show({
- title: _l("Sign out"),
- body: "Do you want to continue and sign out of all active sessions?",
- buttons: {
- Cancel: function () {
- Galaxy.modal.hide();
- },
- "Sign out": userLogoutAll,
- },
- });
+ userLogoutAll();
},
},
};
diff --git a/client/src/components/Visualizations/VisualizationPublished.vue b/client/src/components/Visualizations/VisualizationPublished.vue
index 9ed33e20e9e9..1b562347a08d 100644
--- a/client/src/components/Visualizations/VisualizationPublished.vue
+++ b/client/src/components/Visualizations/VisualizationPublished.vue
@@ -1,20 +1,21 @@
-
+
+
+
+
diff --git a/client/src/components/Workflow/Editor/Draggable.vue b/client/src/components/Workflow/Editor/Draggable.vue
index 6be9f539e40c..79634948bdcd 100644
--- a/client/src/components/Workflow/Editor/Draggable.vue
+++ b/client/src/components/Workflow/Editor/Draggable.vue
@@ -1,7 +1,7 @@
+
+
diff --git a/client/src/components/Workflow/Editor/NodeInput.vue b/client/src/components/Workflow/Editor/NodeInput.vue
index 48fc498ee0a2..63ce71806384 100644
--- a/client/src/components/Workflow/Editor/NodeInput.vue
+++ b/client/src/components/Workflow/Editor/NodeInput.vue
@@ -1,21 +1,225 @@
+
+
-
+
@@ -63,6 +116,9 @@ const scrolledRight = computed(() => !isScrollable.value || arrived.right);
.history-picker {
border: dotted lightgray;
cursor: pointer;
+ width: 15rem;
+ position: relative;
+ justify-content: center;
}
position: relative;
diff --git a/client/src/components/Indices/SharingIndicators.test.js b/client/src/components/Indices/SharingIndicators.test.js
index bf06e1ad58ec..2faa1013934b 100644
--- a/client/src/components/Indices/SharingIndicators.test.js
+++ b/client/src/components/Indices/SharingIndicators.test.js
@@ -48,13 +48,13 @@ describe("SharingIndicators.vue", () => {
it("should fire a is:published filter on published click", async () => {
await wrapper.find(".sharing-indicator-published").trigger("click");
const emitted = wrapper.emitted("filter");
- expect(emitted[0][0]).toBe("is:published");
+ expect(emitted[0][0]).toBe("published");
});
it("should fire a is:shared_with_me filter on shared click", async () => {
await wrapper.find(".sharing-indicator-shared").trigger("click");
const emitted = wrapper.emitted("filter");
- expect(emitted[0][0]).toBe("is:shared_with_me");
+ expect(emitted[0][0]).toBe("shared_with_me");
});
});
});
diff --git a/client/src/components/Indices/SharingIndicators.vue b/client/src/components/Indices/SharingIndicators.vue
index ee34342592b5..b2f1cd3fdae2 100644
--- a/client/src/components/Indices/SharingIndicators.vue
+++ b/client/src/components/Indices/SharingIndicators.vue
@@ -16,32 +16,32 @@ const props = defineProps();
+ @click.prevent="$emit('filter', 'published')">
+ @click.prevent="$emit('filter', 'importable')">
+ @click.prevent="$emit('filter', 'shared_with_me')">
diff --git a/client/src/components/JobParameters/JobParameters.test.js b/client/src/components/JobParameters/JobParameters.test.ts
similarity index 71%
rename from client/src/components/JobParameters/JobParameters.test.js
rename to client/src/components/JobParameters/JobParameters.test.ts
index 0ef46b16ab24..e0f6c04e669b 100644
--- a/client/src/components/JobParameters/JobParameters.test.js
+++ b/client/src/components/JobParameters/JobParameters.test.ts
@@ -1,17 +1,17 @@
-import { createLocalVue, mount } from "@vue/test-utils";
+import { mount, Wrapper } from "@vue/test-utils";
import axios from "axios";
import MockAdapter from "axios-mock-adapter";
-import raw from "components/providers/test/json/Dataset.json";
import flushPromises from "flush-promises";
import { createPinia } from "pinia";
-import { configStore } from "store/configStore";
-import Vuex from "vuex";
-import JobParameters from "./JobParameters";
+import raw from "@/components/providers/test/json/Dataset.json";
+
import paramResponse from "./parameters-response.json";
+import JobParameters from "./JobParameters.vue";
+
const JOB_ID = "foo";
-const DatasetProvider = {
+const DatasetProvider: any = {
render() {
return this.$scopedSlots.default({
loading: false,
@@ -19,31 +19,18 @@ const DatasetProvider = {
});
},
};
-const localVue = createLocalVue();
const pinia = createPinia();
-localVue.use(Vuex);
describe("JobParameters/JobParameters.vue", () => {
- let actions;
- let state;
- let store;
-
- const linkParam = paramResponse.parameters.find((element) => Array.isArray(element.value));
- let axiosMock;
+ const linkParam = paramResponse.parameters.find((element) => Array.isArray(element.value)) ?? {
+ text: "Test Parameter not found",
+ value: "NOT FOUND",
+ };
+ let axiosMock: MockAdapter;
beforeEach(() => {
axiosMock = new MockAdapter(axios);
axiosMock.onGet(`/api/jobs/${JOB_ID}/parameters_display`).reply(200, paramResponse);
- store = new Vuex.Store({
- modules: {
- config: {
- state,
- actions,
- getters: configStore.getters,
- namespaced: true,
- },
- },
- });
});
afterEach(() => {
@@ -57,7 +44,6 @@ describe("JobParameters/JobParameters.vue", () => {
const wrapper = mount(JobParameters, {
propsData,
- store,
stubs: {
DatasetProvider: DatasetProvider,
},
@@ -65,7 +51,12 @@ describe("JobParameters/JobParameters.vue", () => {
});
await flushPromises();
- const checkTableParameter = (element, expectedTitle, expectedValue, link) => {
+ const checkTableParameter = (
+ element: Wrapper,
+ expectedTitle: string,
+ expectedValue: string,
+ link?: string
+ ) => {
const tds = element.findAll("td");
expect(tds.at(0).text()).toBe(expectedTitle);
expect(tds.at(1).text()).toContain(expectedValue);
@@ -82,9 +73,9 @@ describe("JobParameters/JobParameters.vue", () => {
const elements = tbody.findAll("tr");
expect(elements.length).toBe(3);
- checkTableParameter(elements.at(0), "Add this value", "22");
- checkTableParameter(elements.at(1), linkParam.text, `${raw.hid}: ${raw.name}`);
- checkTableParameter(elements.at(2), "Iterate?", "NO");
+ checkTableParameter(elements.at(0), "Add this value", "22", undefined);
+ checkTableParameter(elements.at(1), linkParam.text, `${raw.hid}: ${raw.name}`, undefined);
+ checkTableParameter(elements.at(2), "Iterate?", "NO", undefined);
});
it("should show only single parameter", async () => {
@@ -93,7 +84,7 @@ describe("JobParameters/JobParameters.vue", () => {
param: "Iterate?",
};
- const getSingleParam = async (propsData) => {
+ const getSingleParam = async (propsData: { jobId: string; param: string }) => {
const wrapper = mount(JobParameters, {
propsData,
stubs: {
diff --git a/client/src/components/Login/RegisterForm.vue b/client/src/components/Login/RegisterForm.vue
index cd3b3cb192bf..478917fc269e 100644
--- a/client/src/components/Login/RegisterForm.vue
+++ b/client/src/components/Login/RegisterForm.vue
@@ -3,7 +3,8 @@
- {{ registrationWarningMessage }}
+
+
{{ messageText }}
@@ -64,19 +65,18 @@
dashes ('.', '_', '-').
-
-
+
- Create
+
+ Create
+
@@ -93,8 +93,9 @@
-
@@ -204,3 +205,26 @@ export default {
},
};
+
diff --git a/client/src/components/Markdown/Elements/HistoryDatasetCollection/CollectionDisplay.vue b/client/src/components/Markdown/Elements/HistoryDatasetCollection/CollectionDisplay.vue
index b6283c487e33..134483634555 100644
--- a/client/src/components/Markdown/Elements/HistoryDatasetCollection/CollectionDisplay.vue
+++ b/client/src/components/Markdown/Elements/HistoryDatasetCollection/CollectionDisplay.vue
@@ -86,9 +86,7 @@ export default {
return collection && collection.name;
},
itemUrl() {
- const collectionId = this.args.history_dataset_collection_id;
- const collection = this.collections[collectionId];
- return collection.url;
+ return `${getAppRoot()}api/dataset_collections/${this.args.history_dataset_collection_id}`;
},
downloadUrl() {
return `${getAppRoot()}api/dataset_collections/${this.args.history_dataset_collection_id}/download`;
diff --git a/client/src/components/Markdown/Elements/InvocationTime.vue b/client/src/components/Markdown/Elements/InvocationTime.vue
index 63355884e82d..b335bb377974 100644
--- a/client/src/components/Markdown/Elements/InvocationTime.vue
+++ b/client/src/components/Markdown/Elements/InvocationTime.vue
@@ -19,7 +19,7 @@ export default {
computed: {
content() {
const invocation = this.invocations[this.args.invocation_id];
- return invocation && invocation["create_time"];
+ return invocation && new Date(invocation["create_time"]).toUTCString();
},
},
};
diff --git a/client/src/components/Markdown/Markdown.vue b/client/src/components/Markdown/Markdown.vue
index 57a794b2b554..065d601b4a3a 100644
--- a/client/src/components/Markdown/Markdown.vue
+++ b/client/src/components/Markdown/Markdown.vue
@@ -138,8 +138,13 @@ export default {
return this.enable_beta_markdown_export ? this.exportLink : null;
},
time() {
- const generateTime = this.markdownConfig.generate_time;
+ let generateTime = this.markdownConfig.generate_time;
if (generateTime) {
+ if (!generateTime.endsWith("Z")) {
+ // We don't have tzinfo, but this will always be UTC coming
+ // from Galaxy so append Z to assert that prior to parsing
+ generateTime += "Z";
+ }
const date = new Date(generateTime);
return date.toLocaleString("default", {
day: "numeric",
@@ -147,6 +152,8 @@ export default {
year: "numeric",
minute: "numeric",
hour: "numeric",
+ timeZone: "UTC",
+ timeZoneName: "short",
});
}
return "unavailable";
diff --git a/client/src/components/Masthead/Masthead.test.js b/client/src/components/Masthead/Masthead.test.js
index 851b80bfbf70..25908fedb015 100644
--- a/client/src/components/Masthead/Masthead.test.js
+++ b/client/src/components/Masthead/Masthead.test.js
@@ -2,10 +2,10 @@ import { createTestingPinia } from "@pinia/testing";
import { mount } from "@vue/test-utils";
import { WindowManager } from "layout/window-manager";
import { PiniaVuePlugin, setActivePinia } from "pinia";
-import { configStore } from "store/configStore";
import { useEntryPointStore } from "stores/entryPointStore";
-import { getLocalVue, mockModule } from "tests/jest/helpers";
-import Vuex from "vuex";
+import { getLocalVue } from "tests/jest/helpers";
+
+import { mockFetcher } from "@/schema/__mocks__";
import { loadWebhookMenuItems } from "./_webhooks";
import { getActiveTab } from "./utilities";
@@ -17,13 +17,13 @@ jest.mock("./_webhooks");
jest.mock("vue-router/composables", () => ({
useRoute: jest.fn(() => ({ name: "Home" })),
}));
+jest.mock("@/schema");
describe("Masthead.vue", () => {
let wrapper;
let localVue;
let windowManager;
let tabs;
- let store;
let testPinia;
function stubLoadWebhooks(items) {
@@ -41,11 +41,7 @@ describe("Masthead.vue", () => {
localVue = getLocalVue();
localVue.use(PiniaVuePlugin);
testPinia = createTestingPinia();
- store = new Vuex.Store({
- modules: {
- config: mockModule(configStore),
- },
- });
+ mockFetcher.path("/api/configuration").method("get").mock({ data: {} });
tabs = [
// Main Analysis Tab..
@@ -79,8 +75,6 @@ describe("Masthead.vue", () => {
windowTab,
initialActiveTab,
},
- store,
- provide: { store },
localVue,
pinia: testPinia,
});
diff --git a/client/src/components/Masthead/Masthead.vue b/client/src/components/Masthead/Masthead.vue
index 3f67213fc70f..21f44f39fe72 100644
--- a/client/src/components/Masthead/Masthead.vue
+++ b/client/src/components/Masthead/Masthead.vue
@@ -19,7 +19,7 @@ import NotificationsBell from "@/components/Notifications/NotificationsBell.vue"
const { isAnonymous, showActivityBar } = storeToRefs(useUserStore());
const route = useRoute();
-const { config } = useConfig();
+const { config, isConfigLoaded } = useConfig();
const emit = defineEmits(["open-url"]);
@@ -139,7 +139,7 @@ onMounted(() => {
@open-url="emit('open-url', $event)" />
diff --git a/client/src/components/Masthead/QuotaMeter.test.js b/client/src/components/Masthead/QuotaMeter.test.ts
similarity index 60%
rename from client/src/components/Masthead/QuotaMeter.test.js
rename to client/src/components/Masthead/QuotaMeter.test.ts
index 71e71601113c..fb32389fe0fa 100644
--- a/client/src/components/Masthead/QuotaMeter.test.js
+++ b/client/src/components/Masthead/QuotaMeter.test.ts
@@ -1,37 +1,28 @@
+import { createTestingPinia } from "@pinia/testing";
import { mount } from "@vue/test-utils";
-import { createPinia } from "pinia";
-import { configStore } from "store/configStore";
-import { useUserStore } from "stores/userStore";
+import flushPromises from "flush-promises";
import { getLocalVue } from "tests/jest/helpers";
-import Vuex from "vuex";
+
+import { mockFetcher } from "@/schema/__mocks__";
+import { useUserStore } from "@/stores/userStore";
import QuotaMeter from "./QuotaMeter.vue";
+jest.mock("@/schema");
+
const localVue = getLocalVue();
-const createStore = (config) => {
- return new Vuex.Store({
- modules: {
- config: {
- state: {
- config,
- },
- getters: configStore.getters,
- namespaced: true,
- },
- },
- });
-};
+async function createQuotaMeterWrapper(config: any, userData: any) {
+ mockFetcher.path("/api/configuration").method("get").mock({ data: config });
+ const pinia = createTestingPinia();
+ const userStore = useUserStore();
+ userStore.currentUser = { ...userStore.currentUser, ...userData };
-async function createWrapper(component, localVue, store, userData) {
- const pinia = createPinia();
- const wrapper = mount(component, {
+ const wrapper = mount(QuotaMeter, {
localVue,
pinia,
- store,
});
- const userStore = useUserStore();
- userStore.currentUser = { ...userStore.currentUser, ...userData };
+ await flushPromises();
return wrapper;
}
@@ -43,8 +34,7 @@ describe("QuotaMeter.vue", () => {
};
const config = { enable_quotas: true };
- const store = createStore(config);
- const wrapper = await createWrapper(QuotaMeter, localVue, store, user);
+ const wrapper = await createQuotaMeterWrapper(config, user);
expect(wrapper.find(".quota-progress > span").text()).toBe("Using 50%");
});
@@ -54,24 +44,21 @@ describe("QuotaMeter.vue", () => {
{
const user = { quota_percent: 30 };
- const store = createStore(config);
- const wrapper = await createWrapper(QuotaMeter, localVue, store, user);
+ const wrapper = await createQuotaMeterWrapper(config, user);
expect(wrapper.find(".quota-progress .progress-bar").classes()).toContain("bg-success");
}
{
const user = { quota_percent: 80 };
- const store = createStore(config);
- const wrapper = await createWrapper(QuotaMeter, localVue, store, user);
+ const wrapper = await createQuotaMeterWrapper(config, user);
expect(wrapper.find(".quota-progress .progress-bar").classes()).toContain("bg-warning");
}
{
const user = { quota_percent: 95 };
- const store = createStore(config);
- const wrapper = await createWrapper(QuotaMeter, localVue, store, user);
+ const wrapper = await createQuotaMeterWrapper(config, user);
expect(wrapper.find(".quota-progress .progress-bar").classes()).toContain("bg-danger");
}
@@ -79,8 +66,7 @@ describe("QuotaMeter.vue", () => {
it("prompts user to log in", async () => {
const config = { enable_quotas: true };
- const store = createStore(config);
- const wrapper = await createWrapper(QuotaMeter, localVue, store, {});
+ const wrapper = await createQuotaMeterWrapper(config, {});
expect(wrapper.find(".quota-meter > a").attributes("title")).toContain("Log in");
});
@@ -88,8 +74,7 @@ describe("QuotaMeter.vue", () => {
it("shows total usage in title", async () => {
const user = { total_disk_usage: 9216 };
const config = { enable_quotas: true };
- const store = createStore(config);
- const wrapper = await createWrapper(QuotaMeter, localVue, store, user);
+ const wrapper = await createQuotaMeterWrapper(config, user);
expect(wrapper.find(".quota-progress").attributes("title")).toContain("9 KB");
});
@@ -98,8 +83,7 @@ describe("QuotaMeter.vue", () => {
{
const user = { total_disk_usage: 7168 };
const config = { enable_quotas: false };
- const store = createStore(config);
- const wrapper = await createWrapper(QuotaMeter, localVue, store, user);
+ const wrapper = await createQuotaMeterWrapper(config, user);
expect(wrapper.find(".quota-text > a").text()).toBe("Using 7 KB");
expect(wrapper.find(".quota-text > a").attributes("title")).not.toContain("7 KB");
@@ -112,8 +96,7 @@ describe("QuotaMeter.vue", () => {
};
const config = { enable_quotas: true };
- const store = createStore(config);
- const wrapper = await createWrapper(QuotaMeter, localVue, store, user);
+ const wrapper = await createQuotaMeterWrapper(config, user);
expect(wrapper.find(".quota-text > a").text()).toBe("Using 21 KB");
expect(wrapper.find(".quota-text > a").attributes("title")).not.toContain("21 KB");
diff --git a/client/src/components/Masthead/QuotaMeter.vue b/client/src/components/Masthead/QuotaMeter.vue
index e9b750b88fb1..c2ddf28525c1 100644
--- a/client/src/components/Masthead/QuotaMeter.vue
+++ b/client/src/components/Masthead/QuotaMeter.vue
@@ -31,8 +31,8 @@
+
+
+
+
+
+
+
+
+
+ {{ props.options.broadcast.content.subject }}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/client/src/components/Notifications/Broadcasts/BroadcastsOverlay.test.ts b/client/src/components/Notifications/Broadcasts/BroadcastsOverlay.test.ts
index 3fac9f5966a6..210707179ffe 100644
--- a/client/src/components/Notifications/Broadcasts/BroadcastsOverlay.test.ts
+++ b/client/src/components/Notifications/Broadcasts/BroadcastsOverlay.test.ts
@@ -1,6 +1,6 @@
import { createTestingPinia } from "@pinia/testing";
import { getLocalVue } from "@tests/jest/helpers";
-import { shallowMount } from "@vue/test-utils";
+import { mount } from "@vue/test-utils";
import flushPromises from "flush-promises";
import { setActivePinia } from "pinia";
@@ -46,9 +46,12 @@ async function mountBroadcastsOverlayWith(broadcasts: BroadcastNotification[] =
broadcastsStore.broadcasts = broadcastsStore.broadcasts.filter((b) => b.id !== broadcast.id);
});
- const wrapper = shallowMount(BroadcastsOverlay, {
+ const wrapper = mount(BroadcastsOverlay, {
localVue,
pinia,
+ stubs: {
+ BroadcastContainer: true,
+ },
});
await flushPromises();
diff --git a/client/src/components/Notifications/Broadcasts/BroadcastsOverlay.vue b/client/src/components/Notifications/Broadcasts/BroadcastsOverlay.vue
index e1af53357fb4..de9b6a1c8791 100644
--- a/client/src/components/Notifications/Broadcasts/BroadcastsOverlay.vue
+++ b/client/src/components/Notifications/Broadcasts/BroadcastsOverlay.vue
@@ -1,135 +1,26 @@
> {
+async function mountComponent(component: object, propsData: object = {}): Promise> {
const pinia = createTestingPinia();
setActivePinia(pinia);
@@ -38,7 +35,9 @@ describe("Notifications categories", () => {
notification.content.message = "This is a **markdown** message to test _rendering_";
const wrapper = await mountComponent(MessageNotification, {
- notification,
+ options: {
+ notification,
+ },
});
expect(wrapper.find("#notification-message").html()).toContain(
diff --git a/client/src/components/Notifications/Categories/MessageNotification.vue b/client/src/components/Notifications/Categories/MessageNotification.vue
index 8f79f19e57cf..880c625aa2a9 100644
--- a/client/src/components/Notifications/Categories/MessageNotification.vue
+++ b/client/src/components/Notifications/Categories/MessageNotification.vue
@@ -5,7 +5,7 @@ import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
import { BCol, BRow } from "bootstrap-vue";
import { computed } from "vue";
-import type { MessageNotification } from "@/components/Notifications";
+import { type MessageNotification } from "@/components/Notifications";
import { useMarkdown } from "@/composables/markdown";
import Heading from "@/components/Common/Heading.vue";
@@ -13,20 +13,30 @@ import NotificationActions from "@/components/Notifications/NotificationActions.
library.add(faInbox);
-interface Props {
- notification: MessageNotification;
-}
+type PartialNotification = Partial & { content: MessageNotification["content"] };
-const { renderMarkdown } = useMarkdown({ openLinksInNewPage: true });
+type Options =
+ | {
+ previewMode?: false;
+ notification: MessageNotification;
+ }
+ | {
+ previewMode: true;
+ notification: PartialNotification;
+ };
+
+const props = defineProps<{
+ options: Options;
+}>();
-const props = defineProps();
+const { renderMarkdown } = useMarkdown({ openLinksInNewPage: true });
const notificationVariant = computed(() => {
- switch (props.notification.variant) {
+ switch (props.options.notification.variant) {
case "urgent":
return "danger";
default:
- return props.notification.variant;
+ return props.options.notification.variant;
}
});
@@ -34,14 +44,14 @@ const notificationVariant = computed(() => {
-
+
-
-
+
diff --git a/client/src/components/Notifications/Categories/SharedItemNotification.vue b/client/src/components/Notifications/Categories/SharedItemNotification.vue
index 1740583ba8ab..42e919c1f722 100644
--- a/client/src/components/Notifications/Categories/SharedItemNotification.vue
+++ b/client/src/components/Notifications/Categories/SharedItemNotification.vue
@@ -7,6 +7,7 @@ import { computed } from "vue";
import type { SharedItemNotification } from "@/components/Notifications";
import { useNotificationsStore } from "@/stores/notificationsStore";
+import { absPath } from "@/utils/redirect";
import Heading from "@/components/Common/Heading.vue";
import NotificationActions from "@/components/Notifications/NotificationActions.vue";
@@ -43,9 +44,12 @@ const notificationVariant = computed(() => {
}
});
-function onClick(link: string) {
+const sharedItemUrl = computed(() => {
+ return absPath(content.value.slug);
+});
+
+function markNotificationAsSeen() {
notificationsStore.updateNotification(props.notification, { seen: true });
- window.open(link, "_blank");
}
@@ -67,7 +71,9 @@ function onClick(link: string) {
v-b-tooltip.bottom
:title="`View ${content.item_type} in new tab`"
class="text-primary"
- @click="onClick(content.slug)">
+ :href="sharedItemUrl"
+ target="_blank"
+ @click="markNotificationAsSeen()">
{{ content.item_name }}
,
+ wrapper: Wrapper,
notification: UserNotification,
newSeenTime: string | undefined = undefined
) {
@@ -80,7 +81,8 @@ describe("NotificationActions.vue", () => {
await wrapper.vm.$nextTick();
- expect(spyOnUpdateNotification).toHaveBeenCalled();
+ expect(spyOnUpdateNotification).toHaveBeenCalledTimes(1);
+
expect(wrapper.find("#expiration-time-button").exists()).toBe(true);
});
diff --git a/client/src/components/Notifications/NotificationItem.vue b/client/src/components/Notifications/NotificationItem.vue
index 23ab3053b73c..edcf6e4e5bb6 100644
--- a/client/src/components/Notifications/NotificationItem.vue
+++ b/client/src/components/Notifications/NotificationItem.vue
@@ -1,26 +1,18 @@
- {{ message }}
-
+
+
+
+
-
-
diff --git a/client/src/components/Panels/ToolBoxWorkflow.vue b/client/src/components/Panels/ToolBoxWorkflow.vue
deleted file mode 100644
index 0c66d78de495..000000000000
--- a/client/src/components/Panels/ToolBoxWorkflow.vue
+++ /dev/null
@@ -1,194 +0,0 @@
-
- , filterText?: string, query?: string) {
+ const path = "/workflows/list";
+ const routerParams = query ? { path, query: { query } } : { path };
+ router.push(routerParams);
+}
+
function userTitle(title: string) {
if (isAnonymous.value == true) {
return `Log in to ${title}`;
@@ -69,7 +79,17 @@ function userTitle(title: string) {
Please log in or register to create workflows.
-
const scrolledLeft = computed(() => !isScrollable.value || arrived.left);
const scrolledRight = computed(() => !isScrollable.value || arrived.right);
+
+const showDropZone = ref(false);
+const historyPickerText = computed(() =>
+ showDropZone.value ? localize("Create new history with this item") : localize("Select histories")
+);
+const processingDrop = ref(false);
+async function onDrop(evt: any) {
+ if (processingDrop.value) {
+ showDropZone.value = false;
+ return;
+ }
+ processingDrop.value = true;
+ showDropZone.value = false;
+ let data: any;
+ try {
+ data = JSON.parse(evt.dataTransfer.getData("text"))[0];
+ } catch (error) {
+ // this was not a valid object for this dropzone, ignore
+ }
+ if (data) {
+ await historyStore.createNewHistory();
+ const currentHistoryId = historyStore.currentHistoryId;
+ const dataSource = data.history_content_type === "dataset" ? "hda" : "hdca";
+ if (currentHistoryId) {
+ await copyDataset(data.id, currentHistoryId, data.history_content_type, dataSource)
+ .then(() => {
+ if (data.history_content_type === "dataset") {
+ Toast.info(localize("Dataset copied to new history"));
+ } else {
+ Toast.info(localize("Collection copied to new history"));
+ }
+ historyStore.loadHistoryById(currentHistoryId);
+ })
+ .catch((error) => {
+ Toast.error(error);
+ });
+ historyStore.pinHistory(currentHistoryId);
+ }
+ processingDrop.value = false;
+ }
+}
@@ -50,9 +98,14 @@ const scrolledRight = computed(() => !isScrollable.value || arrived.right);
- Select histories
+ class="history-picker text-primary d-flex m-3 align-items-center text-nowrap"
+ @click.stop="$emit('update:show-modal', true)"
+ @drop.prevent="onDrop"
+ @dragenter.prevent="showDropZone = true"
+ @dragover.prevent
+ @dragleave.prevent="showDropZone = false">
+ {{ historyPickerText }}
+
-
+
+ {{ actionLink.action_name }}
+
+
+
+ {{ remainingBroadcastsCountText }}...
+
+
-
-
-
-
-
-
- {{ currentBroadcast.content.subject }}
-
-
-
-
-
-
-
-
-
-
-
-
-
+
-
-
diff --git a/client/src/components/Notifications/Categories/Categories.test.ts b/client/src/components/Notifications/Categories/Categories.test.ts
index 359d67b118c0..f471dbaa6149 100644
--- a/client/src/components/Notifications/Categories/Categories.test.ts
+++ b/client/src/components/Notifications/Categories/Categories.test.ts
@@ -11,10 +11,7 @@ import SharedItemNotification from "@/components/Notifications/Categories/Shared
const localVue = getLocalVue(true);
-async function mountComponent(
- component: typeof MessageNotification | typeof SharedItemNotification,
- propsData: object = {}
-): Promise
-
- {{ actionLink.action_name }}
-
-
-
- {{ remainingBroadcastsCountText }}...
-
-
- No matching entries found for: {{ filter }}
+ No matching entries found for: {{ filterText }}.
No pages found. You may create a new page.
@@ -35,24 +47,25 @@
-
-
-
-
diff --git a/client/src/components/Panels/ToolPanel.vue b/client/src/components/Panels/ToolPanel.vue
new file mode 100644
index 000000000000..ed166d8fc29b
--- /dev/null
+++ b/client/src/components/Panels/ToolPanel.vue
@@ -0,0 +1,140 @@
+
+
+
+
-
-
-
-
-
-
-
- Search string too short!
-
-
- No results found!
-
-
-
-
-
-
+
+
diff --git a/client/src/components/Panels/WorkflowBox.vue b/client/src/components/Panels/WorkflowBox.vue
index a26197a184b4..e36a3b018227 100644
--- a/client/src/components/Panels/WorkflowBox.vue
+++ b/client/src/components/Panels/WorkflowBox.vue
@@ -3,17 +3,27 @@ import { library } from "@fortawesome/fontawesome-svg-core";
import { faGlobe, faUpload } from "@fortawesome/free-solid-svg-icons";
import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
import { computed } from "vue";
+import { useRouter } from "vue-router/composables";
+import { helpHtml, WorkflowFilters } from "@/components/Workflow/WorkflowFilters";
import { useUserStore } from "@/stores/userStore";
import { withPrefix } from "@/utils/redirect";
-import WorkflowSearch from "@/components/Workflow/WorkflowSearch.vue";
+import FilterMenu from "@/components/Common/FilterMenu.vue";
+
+const router = useRouter();
// @ts-ignore bad library types
library.add(faUpload, faGlobe);
const isAnonymous = computed(() => useUserStore().isAnonymous);
+function onSearch(filters: Record
+
+
+
+
+
+
+
+
+
+
@@ -9,21 +9,32 @@
v-bind="popperProps"
ref="popper"
class="popper-element mt-1"
- :class="{ 'popper-element-dark': darkMode, 'popper-element-light': !darkMode }">
-
+ :class="`popper-element-${mode}`">
+
+
+
+
+
+ {{ title }}
+
+
+
+ {{ filterCount }}
+ {{ filterCount === 1 ? "filter" : "filters" }}.
+
+
+ Filters
+
+
+
+
+
+ No filters applied. Please add filters to the Advanced Tool Search in the Tool Panel.
+
+
+
+ Search Results
+ + + Found {{ itemsLoaded.length }} tools for +
+ {{ filter }}: {{ value }}
+
+
+
+
+
+ No tools found for the entered filters.
+
+
+
+
+
+
+
+
+
diff --git a/client/src/components/Upload/UploadBoxMixin.js b/client/src/components/Upload/UploadBoxMixin.js
deleted file mode 100644
index b74ddf6607e4..000000000000
--- a/client/src/components/Upload/UploadBoxMixin.js
+++ /dev/null
@@ -1,370 +0,0 @@
-import axios from "axios";
-import Select2 from "components/Select2";
-import $ from "jquery";
-import Popover from "mvc/ui/ui-popover";
-import UploadExtension from "mvc/upload/upload-extension";
-import UploadFtp from "mvc/upload/upload-ftp";
-import UploadModel from "mvc/upload/upload-model";
-import { getAppRoot } from "onload";
-import { filesDialog, refreshContentsWrapper } from "utils/data";
-import _l from "utils/localization";
-import { UploadQueue } from "utils/uploadbox";
-
-import { defaultNewFileName, uploadModelsToPayload } from "./helpers";
-import LazyLimited from "./lazy-limited";
-import UploadWrapper from "./UploadWrapper";
-import { findExtension } from "./utils";
-
-const localize = _l;
-
-export default {
- components: {
- UploadWrapper,
- Select2,
- },
- props: {
- lazyLoadMax: {
- type: Number,
- default: null,
- },
- selectable: {
- type: Boolean,
- default: false,
- },
- hasCallback: {
- type: Boolean,
- default: false,
- },
- details: {
- type: Object,
- required: true,
- },
- },
- computed: {
- btnFilesTitle() {
- if (this.fileSourcesConfigured) {
- return localize("Choose remote files");
- } else {
- return localize("Choose FTP files");
- }
- },
- remoteFiles() {
- // this needs to be true for the tests to pass
- return !!this.fileSourcesConfigured || !!this.ftpUploadSite;
- },
- btnCloseTitle() {
- return this.hasCallback ? "Cancel" : "Close";
- },
- history_id() {
- return this.details.history_id;
- },
- },
- methods: {
- $uploadBox() {
- return $(this.$refs.wrapper.$refs.uploadBox);
- },
- initUploadbox(options) {
- const $uploadBox = this.$uploadBox();
- options.$uploadBox = $uploadBox;
- this.uploadbox = new UploadQueue(options);
- if (this.lazyLoadMax !== null) {
- const $uploadBox = this.$uploadBox();
- this.loader = new LazyLimited({
- $container: $uploadBox,
- collection: this.collection,
- max: this.lazyLoadMax,
- new_content: (model) => {
- return this.renderNewModel(model);
- },
- });
- }
- },
- uploadSelect: function () {
- this.uploadbox.select();
- },
-
- /** Start upload process */
- _eventStart: function () {
- if (this.counterAnnounce == 0 || this.counterRunning > 0) {
- return;
- }
- this.uploadSize = 0;
- this.uploadCompleted = 0;
- this.collection.each((model) => {
- if (model.get("status") == "init") {
- model.set("status", "queued");
- this.uploadSize += model.get("file_size");
- }
- });
- this.appModel.set({ percentage: 0, status: "success" });
- this.counterRunning = this.counterAnnounce;
-
- // package ftp files separately, and remove them from queue
- this._uploadFtp();
- this.uploadbox.start();
- this._updateStateForCounters();
- },
-
- /** Package and upload ftp files in a single request */
- _uploadFtp: function () {
- const list = [];
- this.collection.each((model) => {
- if (model.get("status") == "queued" && model.get("file_mode") == "ftp") {
- this.uploadbox.remove(model.id);
- list.push(model);
- }
- });
- if (list.length > 0) {
- const data = uploadModelsToPayload(list, this.details.history_id);
- axios
- .post(`${getAppRoot()}api/tools/fetch`, data)
- .then((message) => {
- list.forEach((model) => {
- this._eventSuccess(model.id, message);
- });
- })
- .catch((message) => {
- list.forEach((model) => {
- this._eventError(model.id, message);
- });
- });
- }
- },
- renderNewModel: function (model) {
- // Turn backbone upload model into row model and place in table,
- // render in next tick so table can respond first and dynamic
- // sizing works.
- var uploadRow = new this.rowUploadModel(this, { model: model });
- this.$uploadTable().find("tbody:first").append(uploadRow.$el);
- this._updateStateForCounters();
- this.$nextTick(() => {
- uploadRow.render();
- });
- return uploadRow;
- },
- _updateStateForCounters: function () {
- this.setTopInfoBasedOnCounters();
- const counterNonRunning = this.counterAnnounce + this.counterSuccess + this.counterError;
- this.enableReset = this.counterRunning == 0 && counterNonRunning > 0;
- this.enableStart = this.counterRunning == 0 && this.counterAnnounce > 0;
- this.enableBuild =
- this.counterRunning == 0 &&
- this.counterAnnounce == 0 &&
- this.counterSuccess > 0 &&
- this.counterError == 0;
- this.enableSources = this.counterRunning == 0 && (this.multiple || counterNonRunning == 0);
- var show_table = this.counterAnnounce + this.counterSuccess + this.counterError > 0;
- this.showHelper = !show_table;
- },
- setTopInfoBasedOnCounters: function () {
- var message = "";
- if (this.counterAnnounce == 0) {
- if (this.uploadbox.compatible()) {
- message = " ";
- } else {
- message =
- "Browser does not support Drag & Drop. Try Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+.";
- }
- } else {
- if (this.counterRunning == 0) {
- message = `You added ${this.counterAnnounce} file(s) to the queue. Add more files or click 'Start' to proceed.`;
- } else {
- message = `Please wait...${this.counterAnnounce} out of ${this.counterRunning} remaining.`;
- }
- }
- this.topInfo = message;
- },
- /** Progress */
- _eventProgress: function (index, percentage) {
- var it = this.collection.get(index);
- it.set("percentage", percentage);
- this.appModel.set("percentage", this._uploadPercentage(percentage, it.get("file_size")));
- },
- /** Calculate percentage of all queued uploads */
- _uploadPercentage: function (percentage, size) {
- return (this.uploadCompleted + percentage * size) / this.uploadSize;
- },
- _updateStateForSuccess: function (model) {
- this.appModel.set("percentage", this._uploadPercentage(100, model.get("file_size")));
- this.uploadCompleted += model.get("file_size") * 100;
- this.counterAnnounce--;
- this.counterSuccess++;
- this._updateStateForCounters();
- refreshContentsWrapper();
- },
- /** A new file has been dropped/selected through the uploadbox plugin */
- _eventAnnounce: function (index, file) {
- this.counterAnnounce++;
- const modelProps = this._newUploadModelProps(index, file);
- var newModel = new UploadModel.Model(modelProps);
- this.collection.add(newModel);
- // if using lazyLoader, let it handle it - else render directly
- if (this.loader) {
- this._updateStateForCounters();
- } else {
- this.renderNewModel(newModel);
- }
- },
- /** Error */
- _eventError: function (index, message) {
- var it = this.collection.get(index);
- it.set({ percentage: 100, status: "error", info: message });
- this.appModel.set({
- percentage: this._uploadPercentage(100, it.get("file_size")),
- status: "danger",
- });
- this.uploadCompleted += it.get("file_size") * 100;
- this.counterAnnounce--;
- this.counterError++;
- this._updateStateForCounters();
- },
- /** Queue is done */
- _eventComplete: function () {
- this.collection.each((model) => {
- model.get("status") == "queued" && model.set("status", "init");
- });
- this.counterRunning = 0;
- this._updateStateForCounters();
- },
- /** Remove model from upload list */
- _eventRemove: function (model) {
- var status = model.get("status");
- if (status == "success") {
- this.counterSuccess--;
- } else if (status == "error") {
- this.counterError--;
- } else {
- this.counterAnnounce--;
- }
- this.uploadbox.remove(model.id);
- this._updateStateForCounters();
- },
- /** Show remote files dialog or FTP files */
- _eventRemoteFiles: function () {
- if (this.fileSourcesConfigured) {
- filesDialog(
- (items) => {
- this.uploadbox.add(
- items.map((item) => {
- const rval = {
- mode: "ftp",
- name: item.label,
- size: item.size,
- path: item.url,
- };
- return rval;
- })
- );
- },
- { multiple: true }
- );
- } else {
- this.ftp.show(
- new UploadFtp({
- collection: this.collection,
- ftp_upload_site: this.ftpUploadSite,
- onadd: (ftp_file) => {
- return this.uploadbox.add([
- {
- mode: "ftp",
- name: ftp_file.path,
- size: ftp_file.size,
- path: ftp_file.path,
- uri: ftp_file.uri,
- },
- ]);
- },
- onremove: function (model_index) {
- this.collection.remove(model_index);
- },
- }).$el
- );
- }
- },
- /** Create a new file */
- _eventCreate: function () {
- this.uploadbox.add([{ name: defaultNewFileName, size: 0, mode: "new" }]);
- },
- addFiles: function (files) {
- this.uploadbox.add(files);
- },
- /** Pause upload process */
- _eventStop: function () {
- if (this.counterRunning > 0) {
- this.appModel.set("status", "info");
- this.topInfo = "Queue will pause after completing the current file...";
- this.uploadbox.stop();
- }
- },
- _eventWarning: function (index, message) {
- var it = this.collection.get(index);
- it.set({ status: "warning", info: message });
- },
- $uploadTable() {
- return $(this.$refs.uploadTable);
- },
- extensionDetails(extension) {
- return findExtension(this.details.effectiveExtensions, extension);
- },
- initExtensionInfo() {
- $(this.$refs.footerExtensionInfo)
- .on("click", (e) => {
- const details = this.extensionDetails(this.extension);
- if (details) {
- new UploadExtension({
- $el: $(e.target),
- title: details && details.text,
- extension: details && details.id,
- list: this.listExtensions,
- placement: "top",
- });
- }
- })
- .on("mousedown", (e) => {
- e.preventDefault();
- });
- },
- initCollection() {
- this.collection = new UploadModel.Collection();
- },
- initAppProperties() {
- this.listExtensions = this.details.effectiveExtensions;
- this.listGenomes = this.details.listGenomes;
- this.ftpUploadSite = this.details.currentFtp;
- this.fileSourcesConfigured = this.details.fileSourcesConfigured;
- },
- initFtpPopover() {
- // add ftp file viewer
- this.ftp = new Popover({
- title: _l("FTP files"),
- class: "ftp-upload",
- container: $(this.$refs.btnFtp),
- });
- },
- /* walk collection and update un-modified default values when globals
- change */
- updateExtension(extension, defaults_only) {
- this.collection.each((model) => {
- if (
- model.get("status") == "init" &&
- (model.get("extension") == this.details.defaultExtension || !defaults_only)
- ) {
- model.set("extension", extension);
- }
- });
- },
- updateGenome: function (genome, defaults_only) {
- this.collection.each((model) => {
- if (
- model.get("status") == "init" &&
- (model.get("genome") == this.details.defaultDbKey || !defaults_only)
- ) {
- model.set("genome", genome);
- }
- });
- },
- getRequestUrl: function (items, history_id) {
- return `${getAppRoot()}api/tools/fetch`;
- },
- },
-};
diff --git a/client/src/components/Upload/UploadButton.vue b/client/src/components/Upload/UploadButton.vue
index b890877bd40a..ade8abee45b5 100644
--- a/client/src/components/Upload/UploadButton.vue
+++ b/client/src/components/Upload/UploadButton.vue
@@ -1,7 +1,7 @@
+
+
diff --git a/client/src/components/Upload/UploadExtension.vue b/client/src/components/Upload/UploadExtension.vue
new file mode 100644
index 000000000000..38fffdccbea0
--- /dev/null
+++ b/client/src/components/Upload/UploadExtension.vue
@@ -0,0 +1,42 @@
+
+
+
+
+
+
+ {{ details.description }}
+
+
+ (read more)
+
+ There is no description available for this file extension.
+
+ {{ warnText }}
+
+
+
+
+
+
+
+
-
-
-
-
diff --git a/client/src/components/Upload/builders.js b/client/src/components/Upload/builders.js
new file mode 100644
index 000000000000..5253a8ba6b97
--- /dev/null
+++ b/client/src/components/Upload/builders.js
@@ -0,0 +1,27 @@
+/*
+ * Interface with rule builder
+ */
+import { getGalaxyInstance } from "app";
+
+/** Populates collection builder with uploaded files */
+export function collectionBuilder(historyId, type, uploadValues) {
+ const Galaxy = getGalaxyInstance();
+ const models = {};
+ uploadValues.forEach((model) => {
+ const outputs = model.outputs;
+ if (outputs) {
+ Object.entries(outputs).forEach((output) => {
+ const outputDetails = output[1];
+ models[outputDetails.id] = outputDetails;
+ });
+ } else {
+ console.debug("Warning, upload response does not contain outputs.", model);
+ }
+ });
+ // Build selection object
+ const selection = {
+ models: Object.values(models),
+ historyId: historyId,
+ };
+ Galaxy.currHistoryPanel.buildCollection(type, selection);
+}
diff --git a/client/src/components/Upload/helpers.js b/client/src/components/Upload/helpers.js
deleted file mode 100644
index c39ca5369bfc..000000000000
--- a/client/src/components/Upload/helpers.js
+++ /dev/null
@@ -1,120 +0,0 @@
-export const defaultNewFileName = "New File";
-
-const URI_PREFIXES = [
- "http://",
- "https://",
- "ftp://",
- "file://",
- "gxfiles://",
- "gximport://",
- "gxuserimport://",
- "gxftp://",
- "drs://",
-];
-function itemIsUrl(item) {
- return URI_PREFIXES.some((prefix) => item.get("url_paste").startsWith(prefix));
-}
-
-export function uploadModelsToPayload(items, history_id, composite = false) {
- const files = [];
- const elements = items
- .map((item) => {
- if (item.get("optional")) {
- return null;
- }
- let src;
- let pasteContent = null;
- let fileName = item.get("file_name");
- if (fileName === defaultNewFileName) {
- fileName = null;
- }
- const url = (item.get("file_uri") || item.get("file_path") || item.get("url_paste")).trim();
- const elem = {
- dbkey: item.get("genome", "?"),
- ext: item.get("extension", "auto"),
- space_to_tab: item.get("space_to_tab"),
- to_posix_lines: item.get("to_posix_lines"),
- deferred: item.get("deferred"),
- };
- switch (item.get("file_mode")) {
- case "new":
- if (itemIsUrl(item)) {
- src = "url";
- /* Could be multiple URLs pasted in.
- TODO: eliminate backbone models,
- then suggest to split multiple URLs
- across multiple uploads directly in upload modal,
- instead of this intransparent magic. */
- return url.split("\n").map((splitUrl) => {
- return {
- src: src,
- url: splitUrl,
- name: fileName,
- ...elem,
- };
- });
- } else {
- pasteContent = item.get("url_paste");
- src = "pasted";
- }
- break;
- case "ftp":
- if (url.indexOf("://") >= 0) {
- src = "url";
- }
- break;
- case "local":
- src = "files";
- files.push(item.get("file_data"));
- break;
- default:
- console.error("Unknown file_mode", item);
- }
- if (src == "pasted") {
- return {
- src: src,
- paste_content: pasteContent,
- name: fileName,
- ...elem,
- };
- } else if (src == "url") {
- return {
- src: src,
- name: fileName,
- url: url,
- ...elem,
- };
- } else {
- return {
- src: src,
- name: fileName,
- ...elem,
- };
- }
- })
- .filter((item) => item)
- .flat();
- const target = {
- destination: { type: "hdas" },
- elements: elements,
- };
- if (composite) {
- const compositeItems = [
- {
- src: "composite",
- ext: elements[0].ext,
- composite: {
- items: target.elements,
- },
- },
- ];
- delete target["elements"];
- target["items"] = compositeItems;
- }
- return {
- history_id: history_id,
- targets: [target],
- auto_decompress: true,
- files: files,
- };
-}
diff --git a/client/src/components/Upload/index.js b/client/src/components/Upload/index.js
deleted file mode 100644
index c63d3b27fb8f..000000000000
--- a/client/src/components/Upload/index.js
+++ /dev/null
@@ -1,4 +0,0 @@
-/**
- * External entry point for Upload components (currently only the modal).
- */
-export { default as UploadModal } from "./UploadModal";
diff --git a/client/src/components/Upload/lazy-limited.js b/client/src/components/Upload/lazy-limited.js
deleted file mode 100644
index 11af61185a20..000000000000
--- a/client/src/components/Upload/lazy-limited.js
+++ /dev/null
@@ -1,66 +0,0 @@
-/** Contains helpers to limit/lazy load views for backbone views */
-import Backbone from "backbone";
-import $ from "jquery";
-import _ from "underscore";
-
-export default Backbone.View.extend({
- initialize: function (options) {
- this.$container = options.$container;
- this.collection = options.collection;
- this.new_content = options.new_content;
- this.max = options.max || 50;
- this.content_list = {};
- this.$message = $("")
- .addClass("ui-limitloader")
- .append(`...only the first ${this.max} entries are visible.`)
- .hide();
- this.$container.append(this.$message);
- this.listenTo(this.collection, "reset", this._reset, this);
- this.listenTo(this.collection, "add", this._refresh, this);
- this.listenTo(this.collection, "remove", this._remove, this);
- },
-
- /** Checks if the limit has been reached */
- _done: function () {
- var done = _.size(this.content_list) >= this.max;
- this.$message[done ? "show" : "hide"]();
- return done;
- },
-
- /** Remove all content */
- _reset: function () {
- _.each(this.content_list, (content) => {
- content.remove();
- });
- this.content_list = {};
- this.$message.hide();
- },
-
- /** Remove content */
- _remove: function (model) {
- var model_id = model.id;
- var content = this.content_list[model_id];
- if (content) {
- content.remove();
- delete this.content_list[model_id];
- }
- this._refresh();
- },
-
- /** Refreshes container content by adding new views if visible */
- _refresh: function () {
- if (!this._done()) {
- for (var i in this.collection.models) {
- var model = this.collection.models[i];
- // TODO: View is unused here.
- //var view = this.content_list[model.id];
- if (!this.content_list[model.id]) {
- this.content_list[model.id] = this.new_content(model);
- if (this._done()) {
- break;
- }
- }
- }
- }
- },
-});
diff --git a/client/src/components/Upload/model.js b/client/src/components/Upload/model.js
new file mode 100644
index 000000000000..55080954e1f2
--- /dev/null
+++ b/client/src/components/Upload/model.js
@@ -0,0 +1,20 @@
+export const defaultModel = {
+ dbKey: "?",
+ deferred: false,
+ enabled: true,
+ extension: "auto",
+ fileContent: "",
+ fileData: null,
+ fileMode: "",
+ fileName: "",
+ filePath: "",
+ fileSize: 0,
+ fileUri: null,
+ info: null,
+ optional: false,
+ outputs: null,
+ percentage: 0,
+ spaceToTab: false,
+ status: "init",
+ toPosixLines: true,
+};
diff --git a/client/src/components/Upload/services.ts b/client/src/components/Upload/services.ts
index 8c3a3019fd66..a77613b55ea8 100644
--- a/client/src/components/Upload/services.ts
+++ b/client/src/components/Upload/services.ts
@@ -1,5 +1,5 @@
import { fetcher } from "@/schema/fetcher";
export const getDatatypes = fetcher.path("/api/datatypes").method("get").create();
-export const getGenomes = fetcher.path("/api/genomes").method("get").create();
+export const getDbKeys = fetcher.path("/api/genomes").method("get").create();
export const getRemoteFiles = fetcher.path("/api/remote_files").method("get").create();
diff --git a/client/src/components/Upload/testHelpers.js b/client/src/components/Upload/testHelpers.js
deleted file mode 100644
index 7568a3e7da9a..000000000000
--- a/client/src/components/Upload/testHelpers.js
+++ /dev/null
@@ -1,53 +0,0 @@
-import "utils/uploadbox";
-
-import { createLocalVue, mount } from "@vue/test-utils";
-import Backbone from "backbone";
-import BootstrapVue from "bootstrap-vue";
-import _ from "underscore";
-
-export const createMockDetails = (options = {}) => {
- return _.defaults(options, {
- defaultExtension: "auto",
- currentFtp: "ftp://localhost",
- model: new Backbone.Model(),
- effectiveExtensions: [
- { id: "ab1", text: "ab1", description: "A binary sequence file in 'ab1' format with a '.ab1'" },
- {
- id: "affybatch",
- text: "affybatch",
- description: null,
- composite_files: [
- {
- name: "%s.pheno",
- optional: false,
- description: "Phenodata tab text file",
- },
- {
- name: "%s.affybatch",
- optional: false,
- description: "AffyBatch R object saved to file",
- },
- ],
- },
- ],
- });
-};
-
-export function mountWithDetails(component, options = {}, propsData_ = {}) {
- const details = createMockDetails(options);
- const propsData = _.defaults(propsData_, { details });
-
- const localVue = createLocalVue();
- localVue.use(BootstrapVue);
-
- const wrapper = mount(component, {
- propsData,
- localVue,
- attachTo: document.body,
- stubs: {
- select2: true,
- },
- });
-
- return { wrapper, localVue };
-}
diff --git a/client/src/components/Upload/utils.js b/client/src/components/Upload/utils.js
index 41b77b8bc129..e9bcbcaeeb3a 100644
--- a/client/src/components/Upload/utils.js
+++ b/client/src/components/Upload/utils.js
@@ -3,7 +3,7 @@
*/
import { errorMessageAsString, rethrowSimple } from "utils/simple-error";
-import { getDatatypes, getGenomes, getRemoteFiles } from "./services";
+import { getDatatypes, getDbKeys, getRemoteFiles } from "./services";
export const AUTO_EXTENSION = {
id: "auto",
@@ -11,8 +11,18 @@ export const AUTO_EXTENSION = {
description:
"This system will try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed.",
};
+export const COLLECTION_TYPES = [
+ { id: "list", text: "List" },
+ { id: "paired", text: "Pair" },
+ { id: "list:paired", text: "List of Pairs" },
+];
export const DEFAULT_DBKEY = "?";
export const DEFAULT_EXTENSION = "auto";
+export const DEFAULT_FILE_NAME = "New File";
+export const RULES_TYPES = [
+ { id: "collections", text: "Collections" },
+ { id: "datasets", text: "Datasets" },
+];
/**
* Local cache.
@@ -39,7 +49,7 @@ async function loadDbKeys() {
if (_cachedDbKeys) {
return _cachedDbKeys;
}
- const { data: dbKeys } = await getGenomes();
+ const { data: dbKeys } = await getDbKeys();
const dbKeyList = [];
for (var key in dbKeys) {
dbKeyList.push({
@@ -64,6 +74,7 @@ async function loadUploadDatatypes() {
description: datatypes[key].description,
description_url: datatypes[key].description_url,
composite_files: datatypes[key].composite_files,
+ upload_warning: datatypes[key].upload_warning,
});
}
listExtensions.sort((a, b) => {
@@ -79,7 +90,7 @@ async function loadUploadDatatypes() {
* Exported utilities.
*/
export function findExtension(extensions, id) {
- return extensions.find((extension) => extension.id == id);
+ return extensions.find((extension) => extension.id == id) || {};
}
export async function getUploadDatatypes(datatypesDisableAuto, auto) {
@@ -116,6 +127,10 @@ export async function getRemoteEntriesAt(target) {
}
}
+export function hasBrowserSupport() {
+ return window.File && window.FormData && window.XMLHttpRequest && window.FileList;
+}
+
export default {
AUTO_EXTENSION,
DEFAULT_DBKEY,
diff --git a/client/src/components/User/DiskUsage/DiskUsageSummary.test.ts b/client/src/components/User/DiskUsage/DiskUsageSummary.test.ts
index 510b65a9fc04..35a54c467b05 100644
--- a/client/src/components/User/DiskUsage/DiskUsageSummary.test.ts
+++ b/client/src/components/User/DiskUsage/DiskUsageSummary.test.ts
@@ -1,61 +1,129 @@
import { mount } from "@vue/test-utils";
+import axios from "axios";
+import MockAdapter from "axios-mock-adapter";
import flushPromises from "flush-promises";
import { createPinia } from "pinia";
import { getLocalVue } from "tests/jest/helpers";
-import MockConfigProvider from "@/components/providers/MockConfigProvider";
-import MockCurrentUser from "@/components/providers/MockCurrentUser";
-import MockProvider from "@/components/providers/MockProvider";
+import { mockFetcher } from "@/schema/__mocks__";
+import { getCurrentUser } from "@/stores/users/queries";
import { useUserStore } from "@/stores/userStore";
+import { UserQuotaUsageData } from "./Quota/model";
+
import DiskUsageSummary from "./DiskUsageSummary.vue";
+jest.mock("@/schema");
+jest.mock("@/stores/users/queries");
+
const localVue = getLocalVue();
-const quotaUsageSummaryComponentId = "quota-usage-summary";
-const basicDiskUsageSummaryId = "basic-disk-usage-summary";
+const quotaUsageClassSelector = ".quota-usage";
+const basicDiskUsageSummaryId = "#basic-disk-usage-summary";
-const fakeUser = {
- total_disk_usage: 1054068,
+const fakeUserWithQuota = {
+ id: "fakeUser",
+ email: "fakeUserEmail",
+ tags_used: [],
+ isAnonymous: false,
+ total_disk_usage: 1048576,
+ quota_bytes: 104857600,
+ quota_percent: 1,
+ quota_source_label: "Default",
};
-const CurrentUserMock = MockCurrentUser(fakeUser);
-const QuotaUsageProviderMock = MockProvider({
- result: [],
-});
-const QuotaUsageSummaryMock = { template: `` };
+
+// TODO: Replace this with a mockFetcher when #16608 is merged
+const mockGetCurrentUser = getCurrentUser as jest.Mock;
+mockGetCurrentUser.mockImplementation(() => Promise.resolve(fakeUserWithQuota));
+
+const fakeQuotaUsages: UserQuotaUsageData[] = [
+ {
+ quota_source_label: "Default",
+ quota_bytes: 104857600,
+ total_disk_usage: 1048576,
+ },
+];
+
+const FAKE_TASK_ID = "fakeTaskId";
async function mountDiskUsageSummaryWrapper(enableQuotas: boolean) {
+ mockFetcher
+ .path("/api/configuration")
+ .method("get")
+ .mock({ data: { enable_quotas: enableQuotas } });
+ mockFetcher.path("/api/users/{user_id}/usage").method("get").mock({ data: fakeQuotaUsages });
+ mockFetcher
+ .path("/api/users/current/recalculate_disk_usage")
+ .method("put")
+ .mock({ status: 200, data: { id: FAKE_TASK_ID } });
+
const pinia = createPinia();
const wrapper = mount(DiskUsageSummary, {
- stubs: {
- ConfigProvider: MockConfigProvider({
- enable_quotas: enableQuotas,
- }),
- CurrentUser: CurrentUserMock,
- QuotaUsageProvider: QuotaUsageProviderMock,
- QuotaUsageSummary: QuotaUsageSummaryMock,
- },
localVue,
pinia,
});
const userStore = useUserStore();
- userStore.currentUser = { id: "fakeUser", email: "fakeUserEmail", tags_used: [], isAnonymous: false };
+ userStore.currentUser = fakeUserWithQuota;
await flushPromises();
return wrapper;
}
describe("DiskUsageSummary.vue", () => {
+ let axiosMock: MockAdapter;
+
+ beforeEach(async () => {
+ axiosMock = new MockAdapter(axios);
+ });
+
+ afterEach(async () => {
+ axiosMock.reset();
+ });
+
it("should display basic disk usage summary if quotas are NOT enabled", async () => {
const enableQuotasInConfig = false;
const wrapper = await mountDiskUsageSummaryWrapper(enableQuotasInConfig);
- expect(wrapper.find(`#${basicDiskUsageSummaryId}`).exists()).toBe(true);
- expect(wrapper.find(`#${quotaUsageSummaryComponentId}`).exists()).toBe(false);
+ expect(wrapper.find(basicDiskUsageSummaryId).exists()).toBe(true);
+ const quotaUsages = wrapper.findAll(quotaUsageClassSelector);
+ expect(quotaUsages.length).toBe(0);
});
it("should display quota usage summary if quotas are enabled", async () => {
const enableQuotasInConfig = true;
const wrapper = await mountDiskUsageSummaryWrapper(enableQuotasInConfig);
- expect(wrapper.find(`#${basicDiskUsageSummaryId}`).exists()).toBe(false);
- expect(wrapper.find(`#${quotaUsageSummaryComponentId}`).exists()).toBe(true);
+ expect(wrapper.find(basicDiskUsageSummaryId).exists()).toBe(false);
+ const quotaUsages = wrapper.findAll(quotaUsageClassSelector);
+ expect(quotaUsages.length).toBe(1);
+ });
+
+ it("should display the correct quota usage", async () => {
+ const enableQuotasInConfig = true;
+ const wrapper = await mountDiskUsageSummaryWrapper(enableQuotasInConfig);
+ const quotaUsage = wrapper.find(quotaUsageClassSelector);
+ expect(quotaUsage.text()).toContain("1 MB");
+ });
+
+ it("should refresh the quota usage when the user clicks the refresh button", async () => {
+ const enableQuotasInConfig = true;
+ const wrapper = await mountDiskUsageSummaryWrapper(enableQuotasInConfig);
+ const quotaUsage = wrapper.find(quotaUsageClassSelector);
+ expect(quotaUsage.text()).toContain("1 MB");
+ const updatedFakeQuotaUsages: UserQuotaUsageData[] = [
+ {
+ quota_source_label: "Default",
+ quota_bytes: 104857600,
+ total_disk_usage: 2097152,
+ },
+ ];
+ mockFetcher.path("/api/users/{user_id}/usage").method("get").mock({ data: updatedFakeQuotaUsages });
+ axiosMock.onGet(`/api/tasks/${FAKE_TASK_ID}/state`).reply(200, "SUCCESS");
+ const refreshButton = wrapper.find("#refresh-disk-usage");
+ await refreshButton.trigger("click");
+ const refreshingAlert = wrapper.find(".refreshing-alert");
+ expect(refreshingAlert.exists()).toBe(true);
+ // Make sure the refresh has finished before checking the quota usage
+ await flushPromises();
+ // The refreshing alert should disappear and the quota usage should be updated
+ expect(refreshingAlert.exists()).toBe(false);
+ expect(quotaUsage.text()).toContain("2 MB");
});
});
diff --git a/client/src/components/User/DiskUsage/DiskUsageSummary.vue b/client/src/components/User/DiskUsage/DiskUsageSummary.vue
index f0e7fa5f4224..2aca40bb11e8 100644
--- a/client/src/components/User/DiskUsage/DiskUsageSummary.vue
+++ b/client/src/components/User/DiskUsage/DiskUsageSummary.vue
@@ -1,112 +1,123 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- Recalculating disk usage... this may take some time, please check back later.
-
-
-
- {{ errorMessageTitle }}
- {{ errorMessage }} -- You're using {{ getTotalDiskUsage(currentUser) }} of disk space. -
-
+
+
+
+
+
+
+
+
+
+ Recalculating disk usage... this may take some time, please check back later.
+
+
+
+
diff --git a/client/src/components/User/DiskUsage/Quota/model/QuotaUsage.test.ts b/client/src/components/User/DiskUsage/Quota/model/QuotaUsage.test.ts
index 134aaa510b06..006440faf1a2 100644
--- a/client/src/components/User/DiskUsage/Quota/model/QuotaUsage.test.ts
+++ b/client/src/components/User/DiskUsage/Quota/model/QuotaUsage.test.ts
@@ -1,20 +1,20 @@
-import { DEFAULT_QUOTA_SOURCE_LABEL, QuotaUsage, type QuotaUsageResponse } from "./QuotaUsage";
+import { DEFAULT_QUOTA_SOURCE_LABEL, QuotaUsage, type UserQuotaUsageData } from "./QuotaUsage";
-const RAW_DEFAULT_QUOTA_USAGE: QuotaUsageResponse = {
+const RAW_DEFAULT_QUOTA_USAGE: UserQuotaUsageData = {
quota_source_label: undefined,
quota_bytes: 68468436,
total_disk_usage: 4546654,
quota_percent: 20,
};
-const RAW_LIMITED_SOURCE_QUOTA_USAGE: QuotaUsageResponse = {
+const RAW_LIMITED_SOURCE_QUOTA_USAGE: UserQuotaUsageData = {
quota_source_label: "The source",
quota_bytes: 68468436,
total_disk_usage: 4546654,
quota_percent: 20,
};
-const RAW_UNLIMITED_SOURCE_QUOTA_USAGE: QuotaUsageResponse = {
+const RAW_UNLIMITED_SOURCE_QUOTA_USAGE: UserQuotaUsageData = {
quota_source_label: "The unlimited source",
quota_bytes: undefined,
total_disk_usage: 4546654,
diff --git a/client/src/components/User/DiskUsage/Quota/model/QuotaUsage.ts b/client/src/components/User/DiskUsage/Quota/model/QuotaUsage.ts
index 28ce5dfb1b84..9f0c2577bf11 100644
--- a/client/src/components/User/DiskUsage/Quota/model/QuotaUsage.ts
+++ b/client/src/components/User/DiskUsage/Quota/model/QuotaUsage.ts
@@ -1,21 +1,17 @@
+import type { components } from "@/schema";
import { bytesToString } from "@/utils/utils";
export const DEFAULT_QUOTA_SOURCE_LABEL = "Default";
-export interface QuotaUsageResponse {
- quota_source_label?: string;
- quota_bytes?: number;
- total_disk_usage: number;
- quota_percent?: number;
-}
+export type UserQuotaUsageData = components["schemas"]["UserQuotaUsage"];
/**
* Contains information about quota usage for a particular ObjectStore.
*/
export class QuotaUsage {
- private _data: QuotaUsageResponse;
+ private _data: UserQuotaUsageData;
- constructor(data: QuotaUsageResponse) {
+ constructor(data: UserQuotaUsageData) {
this._data = data;
}
diff --git a/client/src/components/User/DiskUsage/Quota/model/index.js b/client/src/components/User/DiskUsage/Quota/model/index.js
deleted file mode 100644
index 43c68fd60b0b..000000000000
--- a/client/src/components/User/DiskUsage/Quota/model/index.js
+++ /dev/null
@@ -1 +0,0 @@
-export { QuotaUsage } from "./QuotaUsage";
diff --git a/client/src/components/User/DiskUsage/Quota/model/index.ts b/client/src/components/User/DiskUsage/Quota/model/index.ts
new file mode 100644
index 000000000000..c5818f3a191e
--- /dev/null
+++ b/client/src/components/User/DiskUsage/Quota/model/index.ts
@@ -0,0 +1 @@
+export { QuotaUsage, UserQuotaUsageData } from "./QuotaUsage";
diff --git a/client/src/components/User/DiskUsage/Visualizations/Charts/BarChart.vue b/client/src/components/User/DiskUsage/Visualizations/Charts/BarChart.vue
index 24ccfa28e99d..c45717d6f1f4 100644
--- a/client/src/components/User/DiskUsage/Visualizations/Charts/BarChart.vue
+++ b/client/src/components/User/DiskUsage/Visualizations/Charts/BarChart.vue
@@ -184,6 +184,17 @@ function createLegend() {
.attr("fill", "black")
.text((d) => props.labelFormatter(d));
+ // Set the width of the SVG to the width of the widest entry
+ let maxWidth = 0;
+ for (const node of entries.nodes()) {
+ const width = (node as HTMLElement).getBoundingClientRect().width;
+ maxWidth = Math.max(maxWidth, width);
+ }
+ const svg = container.node()?.closest("svg");
+ if (svg) {
+ svg.setAttribute("width", `${maxWidth}`);
+ }
+
return entries;
}
@@ -294,7 +305,7 @@ function setTooltipPosition(mouseX: number, mouseY: number): void {
- Failed to access disk usage details.
+ {{ errorMessage }} ++ You're using {{ niceTotalDiskUsage }} of disk space. +
+
@@ -337,7 +348,7 @@ function setTooltipPosition(mouseX: number, mouseY: number): void {
}
.bar-chart {
- float: right;
+ float: left;
&:deep(svg) {
overflow: visible;
@@ -349,12 +360,9 @@ function setTooltipPosition(mouseX: number, mouseY: number): void {
}
.legend {
- float: left;
+ float: right;
height: 400px;
-
- &:deep(svg) {
- overflow: visible;
- }
+ overflow: auto;
&:deep(.legend-item) {
font-size: 14px;
diff --git a/client/src/components/User/ThemeSelector.vue b/client/src/components/User/ThemeSelector.vue
index 8b2f2b4a9c91..46f0948e9c98 100644
--- a/client/src/components/User/ThemeSelector.vue
+++ b/client/src/components/User/ThemeSelector.vue
@@ -6,7 +6,7 @@ import { useCurrentTheme } from "@/composables/user";
import { withPrefix } from "@/utils/redirect";
const { currentTheme, setCurrentTheme } = useCurrentTheme();
-const { config, isLoaded } = useConfig();
+const { config, isConfigLoaded } = useConfig();
const show = ref(false);
const currentValue = computed({
@@ -23,7 +23,7 @@ function getLogo(themeDetails) {
}
watch(
- () => isLoaded.value,
+ () => isConfigLoaded.value,
() => {
const themes = Object.keys(config.value.themes);
show.value = themes?.length > 1 ?? false;
diff --git a/client/src/components/User/UserPreferences.vue b/client/src/components/User/UserPreferences.vue
index edd3651fa793..327a2c17ff46 100644
--- a/client/src/components/User/UserPreferences.vue
+++ b/client/src/components/User/UserPreferences.vue
@@ -47,15 +47,13 @@
title="Manage Cloud Authorization"
description="Add or modify the configuration that grants Galaxy to access your cloud-based resources."
to="/user/cloud_auth" />
-
-
+
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+ All of your histories and datasets have been made private. If you'd like to make all *future* histories
+ private please use the
+
+ User Permissions
+ interface.
+
+
+ Do you want to continue and sign out of all active sessions?
+
@@ -124,7 +130,6 @@
import { getGalaxyInstance } from "app";
import axios from "axios";
import BootstrapVue from "bootstrap-vue";
-import ConfigProvider from "components/providers/ConfigProvider";
import { getUserPreferencesModel } from "components/User/UserPreferencesModel";
import { mapState } from "pinia";
import _l from "utils/localization";
@@ -133,6 +138,7 @@ import QueryStringParsing from "utils/query-string-parsing";
import { withPrefix } from "utils/redirect";
import Vue from "vue";
+import { useConfig } from "@/composables/config";
import { useUserStore } from "@/stores/userStore";
import UserActivityBarSettings from "./UserActivityBarSettings";
@@ -147,7 +153,6 @@ Vue.use(BootstrapVue);
export default {
components: {
- ConfigProvider,
UserActivityBarSettings,
UserDeletion,
UserPreferencesElement,
@@ -165,6 +170,10 @@ export default {
required: true,
},
},
+ setup() {
+ const { config, isConfigLoaded } = useConfig(true);
+ return { config, isConfigLoaded };
+ },
data() {
return {
email: "",
@@ -172,6 +181,8 @@ export default {
diskQuota: "",
messageVariant: null,
message: null,
+ showLogoutModal: false,
+ showDataPrivateModal: false,
toggleActivityBar: false,
toggleTheme: false,
};
@@ -187,13 +198,15 @@ export default {
},
hasLogout() {
const Galaxy = getGalaxyInstance();
- return !!Galaxy.session_csrf_token && !Galaxy.config.single_user;
+ return !!Galaxy.session_csrf_token && !this.config.single_user;
},
hasThemes() {
- const Galaxy = getGalaxyInstance();
- const themes = Object.keys(Galaxy.config.themes);
+ const themes = Object.keys(this.config.themes);
return themes?.length > 1 ?? false;
},
+ userPermissionsUrl() {
+ return withPrefix("/user/permissions");
+ },
},
created() {
const message = QueryStringParsing.get("message");
@@ -210,7 +223,6 @@ export default {
},
methods: {
makeDataPrivate() {
- const Galaxy = getGalaxyInstance();
if (
confirm(
_l(
@@ -224,33 +236,13 @@ export default {
)
)
) {
- axios.post(withPrefix(`/history/make_private?all_histories=true`)).then((response) => {
- Galaxy.modal.show({
- title: _l("Datasets are now private"),
- body: `All of your histories and datsets have been made private. If you'd like to make all *future* histories private please use the User Permissions interface.`,
- buttons: {
- Close: () => {
- Galaxy.modal.hide();
- },
- },
- });
+ axios.post(withPrefix(`/history/make_private?all_histories=true`)).then(() => {
+ this.showDataPrivateModal = true;
});
}
},
signOut() {
- const Galaxy = getGalaxyInstance();
- Galaxy.modal.show({
- title: _l("Sign out"),
- body: "Do you want to continue and sign out of all active sessions?",
- buttons: {
- Cancel: function () {
- Galaxy.modal.hide();
- },
- "Sign out": userLogoutAll,
- },
- });
+ userLogoutAll();
},
},
};
diff --git a/client/src/components/Visualizations/VisualizationPublished.vue b/client/src/components/Visualizations/VisualizationPublished.vue
index 9ed33e20e9e9..1b562347a08d 100644
--- a/client/src/components/Visualizations/VisualizationPublished.vue
+++ b/client/src/components/Visualizations/VisualizationPublished.vue
@@ -1,20 +1,21 @@
-
+
+
;
let stepStore: ReturnType;
+ let connectionStore: ReturnType;
beforeEach(() => {
pinia = createPinia();
setActivePinia(pinia);
- stepStore = useWorkflowStepStore();
+ stepStore = useWorkflowStepStore("mock-workflow");
+ connectionStore = useConnectionStore("mock-workflow");
Object.values(advancedSteps).map((step) => stepStore.addStep(step));
});
it("does not display multiple icon if not mapped over", async () => {
const simpleDataStep = stepForLabel("simple data", stepStore.steps);
const propsData = propsForStep(simpleDataStep);
- const wrapper = shallowMount(NodeOutput, {
+ const wrapper = shallowMount(NodeOutput as any, {
propsData: propsData,
localVue,
pinia,
- provide: { transform },
+ provide: { transform, workflowId: "mock-workflow" },
});
expect(wrapper.find(".multiple").exists()).toBe(false);
});
+
it("displays multiple icon if not mapped over", async () => {
const simpleDataStep = stepForLabel("simple data", stepStore.steps);
const listInputStep = stepForLabel("list input", stepStore.steps);
- const inputTerminal = terminalFactory(simpleDataStep.id, simpleDataStep.inputs[0]!, testDatatypesMapper);
- const outputTerminal = terminalFactory(listInputStep.id, listInputStep.outputs[0]!, testDatatypesMapper);
+ const inputTerminal = terminalFactory(
+ simpleDataStep.id,
+ simpleDataStep.inputs[0]!,
+ testDatatypesMapper,
+ connectionStore,
+ stepStore
+ );
+ const outputTerminal = terminalFactory(
+ listInputStep.id,
+ listInputStep.outputs[0]!,
+ testDatatypesMapper,
+ connectionStore,
+ stepStore
+ );
const propsData = propsForStep(simpleDataStep);
- const wrapper = shallowMount(NodeOutput, {
+ const wrapper = shallowMount(NodeOutput as any, {
propsData: propsData,
localVue,
pinia,
- provide: { transform },
+ provide: { transform, workflowId: "mock-workflow" },
});
- expect(wrapper.find(".multiple").exists()).toBe(false);
+ expect(wrapper.find(".mapped-over").exists()).toBe(false);
inputTerminal.connect(outputTerminal);
await nextTick();
- expect(wrapper.find(".multiple").exists()).toBe(true);
+ expect(wrapper.find(".mapped-over").exists()).toBe(true);
inputTerminal.disconnect(outputTerminal);
await nextTick();
- expect(wrapper.find(".multiple").exists()).toBe(false);
+ expect(wrapper.find(".mapped-over").exists()).toBe(false);
});
});
diff --git a/client/src/components/Workflow/Editor/NodeOutput.vue b/client/src/components/Workflow/Editor/NodeOutput.vue
index e5cefe525a1f..3ade4881f3aa 100644
--- a/client/src/components/Workflow/Editor/NodeOutput.vue
+++ b/client/src/components/Workflow/Editor/NodeOutput.vue
@@ -1,24 +1,33 @@
-
-
+
+ {{ reason }}
+
+
-
+ class="delete-terminal-button"
+ @click="onRemove">
+
+
-
-
-
+
- {{ label }}
+ {
-
+
+
diff --git a/client/src/components/Workflow/Editor/Recommendations.vue b/client/src/components/Workflow/Editor/Recommendations.vue
index 0c43186059ef..5d1153cb5744 100644
--- a/client/src/components/Workflow/Editor/Recommendations.vue
+++ b/client/src/components/Workflow/Editor/Recommendations.vue
@@ -21,7 +21,7 @@
import LoadingSpan from "components/LoadingSpan";
import _l from "utils/localization";
-import { useWorkflowStepStore } from "@/stores/workflowStepStore";
+import { useWorkflowStores } from "@/composables/workflowStores";
import { getToolPredictions } from "./modules/services";
import { getCompatibleRecommendations } from "./modules/utilities";
@@ -41,7 +41,7 @@ export default {
},
},
setup() {
- const stepStore = useWorkflowStepStore();
+ const { stepStore } = useWorkflowStores();
return { stepStore };
},
data() {
@@ -131,3 +131,17 @@ export default {
},
};
+
+
diff --git a/client/src/components/Workflow/Editor/SVGConnection.vue b/client/src/components/Workflow/Editor/SVGConnection.vue
index 17120890ba66..2b84f4ec56b1 100644
--- a/client/src/components/Workflow/Editor/SVGConnection.vue
+++ b/client/src/components/Workflow/Editor/SVGConnection.vue
@@ -2,10 +2,9 @@
import { curveBasis, line } from "d3";
import { computed, type PropType } from "vue";
+import { useWorkflowStores } from "@/composables/workflowStores";
import { type Connection, getConnectionId } from "@/stores/workflowConnectionStore";
-import { useConnectionStore } from "@/stores/workflowConnectionStore";
-import { type TerminalPosition, useWorkflowStateStore } from "@/stores/workflowEditorStateStore";
-import { useWorkflowStepStore } from "@/stores/workflowStepStore";
+import type { TerminalPosition } from "@/stores/workflowEditorStateStore";
const props = defineProps({
id: String,
@@ -23,9 +22,7 @@ const ribbonMargin = 4;
const curve = line().curve(curveBasis);
-const stateStore = useWorkflowStateStore();
-const connectionStore = useConnectionStore();
-const stepStore = useWorkflowStepStore();
+const { connectionStore, stateStore, stepStore } = useWorkflowStores();
const outputPos = computed(() => {
if (props.terminalPosition) {
diff --git a/client/src/components/Workflow/Editor/WorkflowEdges.vue b/client/src/components/Workflow/Editor/WorkflowEdges.vue
index f7a070a341a6..be9ff1d89b34 100644
--- a/client/src/components/Workflow/Editor/WorkflowEdges.vue
+++ b/client/src/components/Workflow/Editor/WorkflowEdges.vue
@@ -2,7 +2,8 @@
import { storeToRefs } from "pinia";
import { computed, type Ref } from "vue";
-import { type Connection, type OutputTerminal, useConnectionStore } from "@/stores/workflowConnectionStore";
+import { useWorkflowStores } from "@/composables/workflowStores";
+import type { Connection, OutputTerminal } from "@/stores/workflowConnectionStore";
import type { TerminalPosition } from "@/stores/workflowEditorStateStore";
import type { OutputTerminals } from "./modules/terminals";
@@ -15,7 +16,7 @@ const props = defineProps<{
transform: { x: number; y: number; k: number };
}>();
-const connectionStore = useConnectionStore();
+const { connectionStore } = useWorkflowStores();
const { connections } = storeToRefs(connectionStore);
const draggingConnection: Ref<[Connection, TerminalPosition] | null> = computed(() => {
diff --git a/client/src/components/Workflow/Editor/WorkflowGraph.vue b/client/src/components/Workflow/Editor/WorkflowGraph.vue
index 15d007fcd123..f72ce29e6de5 100644
--- a/client/src/components/Workflow/Editor/WorkflowGraph.vue
+++ b/client/src/components/Workflow/Editor/WorkflowGraph.vue
@@ -1,12 +1,7 @@
-
+ @click="toggleChildComponent">
+
+
+
, required: true },
datatypesMapper: { type: DatatypesMapperModel, required: true },
- highlightId: { type: null as unknown as PropType, default: null },
- scrollToId: { type: null as unknown as PropType, default: null },
+ highlightId: { type: Number as PropType, default: null },
+ scrollToId: { type: Number as PropType, default: null },
+ readonly: { type: Boolean, default: false },
});
-const stateStore = useWorkflowStateStore();
-const stepStore = useWorkflowStepStore();
+const { stateStore, stepStore } = useWorkflowStores();
const { scale, activeNodeId, draggingPosition, draggingTerminal } = storeToRefs(stateStore);
const canvas: Ref = ref(null);
const elementBounding = useElementBounding(canvas, { windowResize: false, windowScroll: false });
const scroll = useScroll(canvas);
-const { transform, panBy, setZoom, moveTo } = useD3Zoom(1, minZoom, maxZoom, canvas, scroll, { x: 20, y: 20 });
+const { transform, panBy, setZoom, moveTo } = useD3Zoom(scale.value, minZoom, maxZoom, canvas, scroll, {
+ x: 20,
+ y: 20,
+});
const { viewportBoundingBox } = useViewportBoundingBox(elementBounding, scale, transform);
const isDragging = ref(false);
@@ -156,3 +155,27 @@ const canvasStyle = computed(() => {
return { transform: `translate(${transform.value.x}px, ${transform.value.y}px) scale(${transform.value.k})` };
});
+
+
diff --git a/client/src/components/Workflow/Editor/WorkflowMinimap.vue b/client/src/components/Workflow/Editor/WorkflowMinimap.vue
index ef17b40c14fe..969fd3460c66 100644
--- a/client/src/components/Workflow/Editor/WorkflowMinimap.vue
+++ b/client/src/components/Workflow/Editor/WorkflowMinimap.vue
@@ -5,7 +5,7 @@ import { computed, onMounted, ref, unref, watch } from "vue";
import { useAnimationFrame } from "@/composables/sensors/animationFrame";
import { useAnimationFrameThrottle } from "@/composables/throttle";
-import { useWorkflowStateStore } from "@/stores/workflowEditorStateStore";
+import { useWorkflowStores } from "@/composables/workflowStores";
import type { Step, Steps } from "@/stores/workflowStepStore";
import { AxisAlignedBoundingBox, Transform } from "./modules/geometry";
@@ -21,7 +21,7 @@ const emit = defineEmits<{
(e: "moveTo", position: { x: number; y: number }): void;
}>();
-const stateStore = useWorkflowStateStore();
+const { stateStore } = useWorkflowStores();
/** reference to the main canvas element */
const canvas: Ref = ref(null);
@@ -305,11 +305,53 @@ useDraggable(canvas, {
@import "~bootstrap/scss/_functions.scss";
@import "theme/blue.scss";
-.workflow-overview-body {
- --node-color: #{$brand-primary};
- --error-color: #{$state-danger-bg};
- --selected-outline-color: #{$brand-primary};
- --view-color: #{fade-out($brand-dark, 0.8)};
- --view-outline-color: #{$brand-info};
+.workflow-overview {
+ --workflow-overview-size: 150px;
+ --workflow-overview-min-size: 50px;
+ --workflow-overview-max-size: 300px;
+ --workflow-overview-padding: 7px;
+ --workflow-overview-border: 1px;
+
+ border-top-left-radius: 0.3rem;
+ cursor: nwse-resize;
+ position: absolute;
+ width: var(--workflow-overview-size);
+ height: var(--workflow-overview-size);
+ right: 0px;
+ bottom: 0px;
+ border-top: solid $border-color var(--workflow-overview-border);
+ border-left: solid $border-color var(--workflow-overview-border);
+ background: $workflow-overview-bg no-repeat url("assets/images/resizable.png");
+ z-index: 20000;
+ overflow: hidden;
+ padding: var(--workflow-overview-padding) 0 0 var(--workflow-overview-padding);
+
+ // account for padding and border
+ max-width: calc(
+ var(--workflow-overview-max-size) + var(--workflow-overview-padding) + var(--workflow-overview-border)
+ );
+ max-height: calc(
+ var(--workflow-overview-max-size) + var(--workflow-overview-padding) + var(--workflow-overview-border)
+ );
+ min-width: calc(
+ var(--workflow-overview-min-size) + var(--workflow-overview-padding) + var(--workflow-overview-border)
+ );
+ min-height: calc(
+ var(--workflow-overview-min-size) + var(--workflow-overview-padding) + var(--workflow-overview-border)
+ );
+
+ .workflow-overview-body {
+ cursor: pointer;
+ position: relative;
+ overflow: hidden;
+ width: 100%;
+ height: 100%;
+
+ --node-color: #{$brand-primary};
+ --error-color: #{$state-danger-bg};
+ --selected-outline-color: #{$brand-primary};
+ --view-color: #{fade-out($brand-dark, 0.8)};
+ --view-outline-color: #{$brand-info};
+ }
}
diff --git a/client/src/components/Workflow/Editor/_nodeTerminalStyle.scss b/client/src/components/Workflow/Editor/_nodeTerminalStyle.scss
new file mode 100644
index 000000000000..77ab4b8351e6
--- /dev/null
+++ b/client/src/components/Workflow/Editor/_nodeTerminalStyle.scss
@@ -0,0 +1,36 @@
+@mixin node-terminal-style($side) {
+ position: absolute;
+ #{$side}: -0.65rem;
+ border-radius: 50%;
+ background-color: $white;
+ display: grid;
+ place-items: center;
+ width: 11px;
+ height: 11px;
+ margin-top: 0.25rem;
+
+ color: $brand-primary;
+
+ &.mapped-over {
+ width: 20px;
+ height: 20px;
+ margin-top: 0;
+ #{$side}: -0.8rem;
+
+ .terminal-icon {
+ top: -1px;
+ left: -1px;
+ width: 22px;
+ height: 22px;
+ }
+ }
+
+ .terminal-icon {
+ position: absolute;
+ top: -1px;
+ left: -1px;
+ width: 13px;
+ height: 13px;
+ pointer-events: none;
+ }
+}
diff --git a/client/src/components/Workflow/Editor/composables/useTerminal.ts b/client/src/components/Workflow/Editor/composables/useTerminal.ts
index fad0aee5b2f8..482c9dfcbe0e 100644
--- a/client/src/components/Workflow/Editor/composables/useTerminal.ts
+++ b/client/src/components/Workflow/Editor/composables/useTerminal.ts
@@ -2,8 +2,8 @@ import { computed, type Ref, ref, watch } from "vue";
import type { DatatypesMapperModel } from "@/components/Datatypes/model";
import { terminalFactory } from "@/components/Workflow/Editor/modules/terminals";
+import { useWorkflowStores } from "@/composables/workflowStores";
import type { Step, TerminalSource } from "@/stores/workflowStepStore";
-import { useWorkflowStepStore } from "@/stores/workflowStepStore";
export function useTerminal(
stepId: Ref,
@@ -11,7 +11,7 @@ export function useTerminal(
datatypesMapper: Ref
) {
const terminal: Ref | null> = ref(null);
- const stepStore = useWorkflowStepStore();
+ const { connectionStore, stepStore } = useWorkflowStores();
const step = computed(() => stepStore.getStep(stepId.value));
const isMappedOver = computed(() => stepStore.stepMapOver[stepId.value]?.isCollection ?? false);
@@ -19,7 +19,13 @@ export function useTerminal(
[step, terminalSource, datatypesMapper],
() => {
// rebuild terminal if any of the tracked dependencies change
- const newTerminal = terminalFactory(stepId.value, terminalSource.value, datatypesMapper.value);
+ const newTerminal = terminalFactory(
+ stepId.value,
+ terminalSource.value,
+ datatypesMapper.value,
+ connectionStore,
+ stepStore
+ );
newTerminal.getInvalidConnectedTerminals();
terminal.value = newTerminal;
},
diff --git a/client/src/components/Workflow/Editor/modules/layout.ts b/client/src/components/Workflow/Editor/modules/layout.ts
index 08d15ae088c3..3a4882e6a53b 100644
--- a/client/src/components/Workflow/Editor/modules/layout.ts
+++ b/client/src/components/Workflow/Editor/modules/layout.ts
@@ -33,9 +33,9 @@ interface NewGraph {
edges: GraphEdge[];
}
-export async function autoLayout(steps: { [index: string]: Step }) {
- const stateStore = useWorkflowStateStore();
- const connectionStore = useConnectionStore();
+export async function autoLayout(id: string, steps: { [index: string]: Step }) {
+ const connectionStore = useConnectionStore(id);
+ const stateStore = useWorkflowStateStore(id);
// Convert this to ELK compat.
const newGraph: NewGraph = {
diff --git a/client/src/components/Workflow/Editor/modules/linting.ts b/client/src/components/Workflow/Editor/modules/linting.ts
index 169fdc13fa52..86f700e70436 100644
--- a/client/src/components/Workflow/Editor/modules/linting.ts
+++ b/client/src/components/Workflow/Editor/modules/linting.ts
@@ -1,6 +1,7 @@
import type { DatatypesMapperModel } from "@/components/Datatypes/model";
import type { UntypedParameters } from "@/components/Workflow/Editor/modules/parameters";
-import type { Step, Steps } from "@/stores/workflowStepStore";
+import type { useConnectionStore } from "@/stores/workflowConnectionStore";
+import type { Step, Steps, useWorkflowStepStore } from "@/stores/workflowStepStore";
import { assertDefined } from "@/utils/assertions";
import { terminalFactory } from "./terminals";
@@ -14,11 +15,16 @@ interface LintState {
autofix?: boolean;
}
-export function getDisconnectedInputs(steps: Steps = {}, datatypesMapper: DatatypesMapperModel) {
+export function getDisconnectedInputs(
+ steps: Steps = {},
+ datatypesMapper: DatatypesMapperModel,
+ connectionStore: ReturnType,
+ stepStore: ReturnType
+) {
const inputs: LintState[] = [];
Object.values(steps).forEach((step) => {
step.inputs.map((inputSource) => {
- const inputTerminal = terminalFactory(step.id, inputSource, datatypesMapper);
+ const inputTerminal = terminalFactory(step.id, inputSource, datatypesMapper, connectionStore, stepStore);
if (!inputTerminal.optional && inputTerminal.connections.length === 0) {
const inputLabel = inputSource.label || inputSource.name;
inputs.push({
@@ -114,7 +120,13 @@ export function getUntypedParameters(untypedParameters: UntypedParameters) {
return items;
}
-export function fixAllIssues(steps: Steps, parameters: UntypedParameters, datatypesMapper: DatatypesMapperModel) {
+export function fixAllIssues(
+ steps: Steps,
+ parameters: UntypedParameters,
+ datatypesMapper: DatatypesMapperModel,
+ connectionStore: ReturnType,
+ stepStore: ReturnType
+) {
const actions = [];
const untypedParameters = getUntypedParameters(parameters);
for (const untypedParameter of untypedParameters) {
@@ -122,7 +134,7 @@ export function fixAllIssues(steps: Steps, parameters: UntypedParameters, dataty
actions.push(fixUntypedParameter(untypedParameter));
}
}
- const disconnectedInputs = getDisconnectedInputs(steps, datatypesMapper);
+ const disconnectedInputs = getDisconnectedInputs(steps, datatypesMapper, connectionStore, stepStore);
for (const disconnectedInput of disconnectedInputs) {
if (disconnectedInput.autofix) {
actions.push(fixDisconnectedInput(disconnectedInput));
diff --git a/client/src/components/Workflow/Editor/modules/model.ts b/client/src/components/Workflow/Editor/modules/model.ts
index 75f38b690160..36c5eff4e1ad 100644
--- a/client/src/components/Workflow/Editor/modules/model.ts
+++ b/client/src/components/Workflow/Editor/modules/model.ts
@@ -10,8 +10,21 @@ interface Workflow {
steps: Steps;
}
-export async function fromSimple(data: Workflow, appendData = false, defaultPosition = { top: 0, left: 0 }) {
- const stepStore = useWorkflowStepStore();
+/**
+ * Loads a workflow into the editor
+ *
+ * @param id ID of workflow to load data *into*
+ * @param data Workflow data to load from
+ * @param appendData if true appends data to current workflow, making sure to create new uuids
+ * @param defaultPosition where to position workflow in the editor
+ */
+export async function fromSimple(
+ id: string,
+ data: Workflow,
+ appendData = false,
+ defaultPosition = { top: 0, left: 0 }
+) {
+ const stepStore = useWorkflowStepStore(id);
const stepIdOffset = stepStore.getStepIndex + 1;
Object.values(data.steps).forEach((step) => {
// If workflow being copied into another, wipe UUID and let
diff --git a/client/src/components/Workflow/Editor/modules/terminals.test.ts b/client/src/components/Workflow/Editor/modules/terminals.test.ts
index b425e63b9774..1c49c1513aa6 100644
--- a/client/src/components/Workflow/Editor/modules/terminals.test.ts
+++ b/client/src/components/Workflow/Editor/modules/terminals.test.ts
@@ -24,15 +24,31 @@ import {
function setupAdvanced() {
const terminals: { [index: string]: { [index: string]: ReturnType } } = {};
+
+ const connectionStore = useConnectionStore("mock-workflow");
+ const stepStore = useWorkflowStepStore("mock-workflow");
+
Object.values(advancedSteps).map((step) => {
const stepLabel = step.label;
if (stepLabel) {
terminals[stepLabel] = {};
step.inputs?.map((input) => {
- terminals[stepLabel]![input.name] = terminalFactory(step.id, input, testDatatypesMapper);
+ terminals[stepLabel]![input.name] = terminalFactory(
+ step.id,
+ input,
+ testDatatypesMapper,
+ connectionStore,
+ stepStore
+ );
});
step.outputs?.map((output) => {
- terminals[stepLabel]![output.name] = terminalFactory(step.id, output, testDatatypesMapper);
+ terminals[stepLabel]![output.name] = terminalFactory(
+ step.id,
+ output,
+ testDatatypesMapper,
+ connectionStore,
+ stepStore
+ );
});
}
});
@@ -42,12 +58,16 @@ function setupAdvanced() {
function rebuildTerminal>(terminal: T): T {
let terminalSource: TerminalSource;
const step = terminal.stepStore.getStep(terminal.stepId);
+
+ const connectionStore = useConnectionStore("mock-workflow");
+ const stepStore = useWorkflowStepStore("mock-workflow");
+
if (terminal.terminalType === "input") {
terminalSource = step!.inputs.find((input) => input.name == terminal.name)!;
} else {
terminalSource = step!.outputs.find((output) => output.name == terminal.name)!;
}
- return terminalFactory(terminal.stepId, terminalSource, testDatatypesMapper) as T;
+ return terminalFactory(terminal.stepId, terminalSource, testDatatypesMapper, connectionStore, stepStore) as T;
}
describe("terminalFactory", () => {
@@ -83,7 +103,10 @@ describe("terminalFactory", () => {
expect(terminals["filter_failed"]?.["output"]).toBeInstanceOf(OutputCollectionTerminal);
});
it("throws error on invalid terminalSource", () => {
- const invalidFactory = () => terminalFactory(1, {} as any, testDatatypesMapper);
+ const connectionStore = useConnectionStore("mock-workflow");
+ const stepStore = useWorkflowStepStore("mock-workflow");
+
+ const invalidFactory = () => terminalFactory(1, {} as any, testDatatypesMapper, connectionStore, stepStore);
expect(invalidFactory).toThrow();
});
});
@@ -95,8 +118,8 @@ describe("canAccept", () => {
beforeEach(() => {
setActivePinia(createPinia());
terminals = setupAdvanced();
- stepStore = useWorkflowStepStore();
- connectionStore = useConnectionStore();
+ stepStore = useWorkflowStepStore("mock-workflow");
+ connectionStore = useConnectionStore("mock-workflow");
Object.values(JSON.parse(JSON.stringify(advancedSteps)) as Steps).map((step) => {
stepStore.addStep(step);
});
@@ -542,18 +565,30 @@ describe("Input terminal", () => {
let terminals: { [index: number]: { [index: string]: ReturnType } };
beforeEach(() => {
setActivePinia(createPinia());
- stepStore = useWorkflowStepStore();
- connectionStore = useConnectionStore();
+ stepStore = useWorkflowStepStore("mock-workflow");
+ connectionStore = useConnectionStore("mock-workflow");
terminals = {};
Object.values(simpleSteps).map((step) => {
stepStore.addStep(step);
terminals[step.id] = {};
const stepTerminals = terminals[step.id]!;
step.inputs?.map((input) => {
- stepTerminals[input.name] = terminalFactory(step.id, input, testDatatypesMapper);
+ stepTerminals[input.name] = terminalFactory(
+ step.id,
+ input,
+ testDatatypesMapper,
+ connectionStore,
+ stepStore
+ );
});
step.outputs?.map((output) => {
- stepTerminals[output.name] = terminalFactory(step.id, output, testDatatypesMapper);
+ stepTerminals[output.name] = terminalFactory(
+ step.id,
+ output,
+ testDatatypesMapper,
+ connectionStore,
+ stepStore
+ );
});
});
});
diff --git a/client/src/components/Workflow/Editor/modules/terminals.ts b/client/src/components/Workflow/Editor/modules/terminals.ts
index 2821748a5df6..7aab6d3e5e48 100644
--- a/client/src/components/Workflow/Editor/modules/terminals.ts
+++ b/client/src/components/Workflow/Editor/modules/terminals.ts
@@ -5,7 +5,7 @@ import {
type Connection,
type ConnectionId,
getConnectionId,
- useConnectionStore,
+ type useConnectionStore,
} from "@/stores/workflowConnectionStore";
import type {
CollectionOutput,
@@ -15,8 +15,8 @@ import type {
ParameterOutput,
ParameterStepInput,
TerminalSource,
+ useWorkflowStepStore,
} from "@/stores/workflowStepStore";
-import { useWorkflowStepStore } from "@/stores/workflowStepStore";
import { assertDefined } from "@/utils/assertions";
import {
@@ -39,6 +39,8 @@ interface BaseTerminalArgs {
name: string;
stepId: number;
datatypesMapper: DatatypesMapperModel;
+ connectionStore: ReturnType;
+ stepStore: ReturnType;
}
interface InputTerminalInputs {
@@ -64,8 +66,8 @@ class Terminal extends EventEmitter {
constructor(attr: BaseTerminalArgs) {
super();
- this.connectionStore = useConnectionStore();
- this.stepStore = useWorkflowStepStore();
+ this.connectionStore = attr.connectionStore;
+ this.stepStore = attr.stepStore;
this.stepId = attr.stepId;
this.name = attr.name;
this.multiple = false;
@@ -244,12 +246,24 @@ class BaseInputTerminal extends Terminal {
// step must have an output, since it is or was connected to this step
const terminalSource = step.outputs[0];
if (terminalSource) {
- const terminal = terminalFactory(step.id, terminalSource, this.datatypesMapper);
+ const terminal = terminalFactory(
+ step.id,
+ terminalSource,
+ this.datatypesMapper,
+ this.connectionStore,
+ this.stepStore
+ );
// drop mapping restrictions
terminal.resetMappingIfNeeded();
// re-establish map over through inputs
step.inputs.forEach((input) => {
- terminalFactory(step.id, input, this.datatypesMapper).getStepMapOver();
+ terminalFactory(
+ step.id,
+ input,
+ this.datatypesMapper,
+ this.connectionStore,
+ this.stepStore
+ ).getStepMapOver();
});
}
} else {
@@ -356,6 +370,8 @@ class BaseInputTerminal extends Terminal {
name: connection.output.name,
valid: false,
datatypesMapper: this.datatypesMapper,
+ connectionStore: this.connectionStore,
+ stepStore: this.stepStore,
});
}
let terminalSource = outputStep.outputs.find((output) => output.name === connection.output.name);
@@ -367,6 +383,8 @@ class BaseInputTerminal extends Terminal {
name: connection.output.name,
valid: false,
datatypesMapper: this.datatypesMapper,
+ connectionStore: this.connectionStore,
+ stepStore: this.stepStore,
});
}
const postJobActionKey = `ChangeDatatypeAction${connection.output.name}`;
@@ -383,7 +401,13 @@ class BaseInputTerminal extends Terminal {
};
}
- return terminalFactory(outputStep.id, terminalSource, this.datatypesMapper);
+ return terminalFactory(
+ outputStep.id,
+ terminalSource,
+ this.datatypesMapper,
+ this.connectionStore,
+ this.stepStore
+ );
});
}
@@ -658,9 +682,17 @@ class BaseOutputTerminal extends Terminal {
optional: false,
multiple: false,
},
+ connectionStore: this.connectionStore,
+ stepStore: this.stepStore,
});
}
- return terminalFactory(inputStep.id, terminalSource, this.datatypesMapper);
+ return terminalFactory(
+ inputStep.id,
+ terminalSource,
+ this.datatypesMapper,
+ this.connectionStore,
+ this.stepStore
+ );
});
}
@@ -689,7 +721,13 @@ class BaseOutputTerminal extends Terminal {
const validInputTerminals: InputTerminals[] = [];
Object.values(this.stepStore.steps).map((step) => {
step.inputs?.forEach((input) => {
- const inputTerminal = terminalFactory(step.id, input, this.datatypesMapper);
+ const inputTerminal = terminalFactory(
+ step.id,
+ input,
+ this.datatypesMapper,
+ this.connectionStore,
+ this.stepStore
+ );
if (inputTerminal.canAccept(this).canAccept) {
validInputTerminals.push(inputTerminal);
}
@@ -738,8 +776,20 @@ export class OutputCollectionTerminal extends BaseOutputTerminal {
const stepOutput = outputStep.outputs.find((output) => output.name == connection.output.name);
const stepInput = inputStep.inputs.find((input) => input.name === this.collectionTypeSource);
if (stepInput && stepOutput) {
- const outputTerminal = terminalFactory(connection.output.stepId, stepOutput, this.datatypesMapper);
- const inputTerminal = terminalFactory(connection.output.stepId, stepInput, this.datatypesMapper);
+ const outputTerminal = terminalFactory(
+ connection.output.stepId,
+ stepOutput,
+ this.datatypesMapper,
+ this.connectionStore,
+ this.stepStore
+ );
+ const inputTerminal = terminalFactory(
+ connection.output.stepId,
+ stepInput,
+ this.datatypesMapper,
+ this.connectionStore,
+ this.stepStore
+ );
// otherCollectionType is the mapped over output collection as it would appear at the input terminal
const otherCollectionType = inputTerminal._otherCollectionType(outputTerminal);
// we need to find which of the possible input collection types is connected
@@ -885,7 +935,9 @@ type TerminalOf = T extends InvalidInputTerm
export function terminalFactory(
stepId: number,
terminalSource: T,
- datatypesMapper: DatatypesMapperModel
+ datatypesMapper: DatatypesMapperModel,
+ connectionStore: ReturnType,
+ stepStore: ReturnType
): TerminalOf {
if ("input_type" in terminalSource) {
const terminalArgs = {
@@ -893,6 +945,8 @@ export function terminalFactory(
input_type: terminalSource.input_type,
name: terminalSource.name,
stepId: stepId,
+ connectionStore,
+ stepStore,
};
if ("valid" in terminalSource) {
return new InvalidInputTerminal({
@@ -902,7 +956,7 @@ export function terminalFactory(
multiple: false,
optional: false,
},
- valid: terminalSource.valid,
+ valid: terminalSource.valid as false,
}) as TerminalOf;
} else {
const inputArgs = {
@@ -940,6 +994,8 @@ export function terminalFactory(
optional: terminalSource.optional,
stepId: stepId,
datatypesMapper: datatypesMapper,
+ connectionStore,
+ stepStore,
};
if (isOutputParameterArg(terminalSource)) {
return new OutputParameterTerminal({
diff --git a/client/src/components/Workflow/InvocationReport.vue b/client/src/components/Workflow/InvocationReport.vue
index a5b787559c32..ad227d183c9e 100644
--- a/client/src/components/Workflow/InvocationReport.vue
+++ b/client/src/components/Workflow/InvocationReport.vue
@@ -1,29 +1,27 @@
-
-
+
-
+
+
+
+
+
+
+
diff --git a/client/src/components/Workflow/Run/WorkflowRunFormSimple.vue b/client/src/components/Workflow/Run/WorkflowRunFormSimple.vue
index c2730aeb03aa..77621c6d74de 100644
--- a/client/src/components/Workflow/Run/WorkflowRunFormSimple.vue
+++ b/client/src/components/Workflow/Run/WorkflowRunFormSimple.vue
@@ -1,61 +1,59 @@
-
+
+
+
+
+
+
+ Failed to load published Workflow
+
+
+ {{ errorMessage }}
+
+ Unknown Error
+
+
+
+
+
+ Workflow Preview
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
-
- Workflow: {{ model.name }}
-
-
-
-
-
- Send results to a new history
- Attempt to re-use jobs with identical parameters?
- Send outputs and intermediate to different object stores?
-
-
-
-
-
-
+
diff --git a/client/src/components/Workflow/WorkflowSearch.vue b/client/src/components/Workflow/WorkflowSearch.vue
deleted file mode 100644
index 25a7f5d1bfe5..000000000000
--- a/client/src/components/Workflow/WorkflowSearch.vue
+++ /dev/null
@@ -1,78 +0,0 @@
-
-
-
+ Workflow: {{ model.name }}
+
+
+
+
+
+
+ Send results to a new history
+
+
+ Attempt to re-use jobs with identical parameters?
+
+
+ Send outputs and intermediate to different object stores?
+
+
+
+
+
-
+
-
-
diff --git a/client/src/components/WorkflowInvocationState/InvocationMessage.vue b/client/src/components/WorkflowInvocationState/InvocationMessage.vue
index 6bf5dd2d966c..a65bf5a7c96c 100644
--- a/client/src/components/WorkflowInvocationState/InvocationMessage.vue
+++ b/client/src/components/WorkflowInvocationState/InvocationMessage.vue
@@ -149,6 +149,9 @@ const infoString = computed(() => {
invocationMessage.workflow_step_id + 1
} is a conditional step and the result of the when expression is not a boolean type.`;
} else if (reason === "unexpected_failure") {
+ if (invocationMessage.details) {
+ return `${failFragment} an unexpected failure occurred: '${invocationMessage.details}'`;
+ }
return `${failFragment} an unexpected failure occurred.`;
} else if (reason === "workflow_output_not_found") {
return `Defined workflow output '${invocationMessage.output_name}' was not found in step ${
diff --git a/client/src/components/WorkflowInvocationState/WorkflowInvocationState.test.js b/client/src/components/WorkflowInvocationState/WorkflowInvocationState.test.js
index eee535348b66..8425829db8f4 100644
--- a/client/src/components/WorkflowInvocationState/WorkflowInvocationState.test.js
+++ b/client/src/components/WorkflowInvocationState/WorkflowInvocationState.test.js
@@ -11,7 +11,7 @@ useConfig.mockReturnValue({
config: {
enable_celery_tasks: true,
},
- isLoaded: true,
+ isConfigLoaded: true,
});
const invocationJobsSummaryById = {
diff --git a/client/src/components/WorkflowInvocationState/WorkflowInvocationStep.vue b/client/src/components/WorkflowInvocationState/WorkflowInvocationStep.vue
index fb9500063b81..ea5da90e8b45 100644
--- a/client/src/components/WorkflowInvocationState/WorkflowInvocationStep.vue
+++ b/client/src/components/WorkflowInvocationState/WorkflowInvocationStep.vue
@@ -1,11 +1,12 @@
- Filter by name:
-
-
- Search shared workflows:
-
-
- Search deleted workflows:
-
-
-
-
-
-
-
-
-
+
+
+
+ , enabled: boolean) {
+ expect(wrapper.find(SUBMIT_BUTTON_SELECTOR).exists()).toBeTruthy();
+ expect(wrapper.find(SUBMIT_BUTTON_SELECTOR).attributes("disabled")).toBe(enabled ? undefined : "disabled");
+ expect(wrapper.find(SUBMIT_BUTTON_SELECTOR).attributes("title")).toBe(
+ enabled ? "" : "Please fill all required fields"
+ );
+ }
+
+ it("should render form with empty fields and submit button disabled", async () => {
+ const { wrapper } = await mountNotificationForm();
+
+ expectSubmitButton(wrapper, false);
+ });
+});
diff --git a/client/src/components/admin/Notifications/NotificationForm.vue b/client/src/components/admin/Notifications/NotificationForm.vue
new file mode 100644
index 000000000000..ded986f90e33
--- /dev/null
+++ b/client/src/components/admin/Notifications/NotificationForm.vue
@@ -0,0 +1,251 @@
+
+
+
+ {
+ const { data } = await getBroadcast({ notification_id: id });
+ return data;
+}
+
+const getBroadcasts = fetcher.path("/api/notifications/broadcast").method("get").create();
+export async function loadBroadcasts(): Promise {
+ const { data } = await getBroadcasts({});
+ return data;
+}
+
+const postBroadcast = fetcher.path("/api/notifications/broadcast").method("post").create();
+type BroadcastNotificationCreateRequest = components["schemas"]["BroadcastNotificationCreateRequest"];
+export async function createBroadcast(broadcast: BroadcastNotificationCreateRequest) {
+ const { data } = await postBroadcast(broadcast);
+ return data;
+}
+
+const putBroadcast = fetcher.path("/api/notifications/broadcast/{notification_id}").method("put").create();
+type NotificationBroadcastUpdateRequest = components["schemas"]["NotificationBroadcastUpdateRequest"];
+export async function updateBroadcast(id: string, broadcast: NotificationBroadcastUpdateRequest) {
+ const { data } = await putBroadcast({ notification_id: id, ...broadcast });
+ return data;
+}
diff --git a/client/src/components/admin/Notifications/notifications.services.ts b/client/src/components/admin/Notifications/notifications.services.ts
new file mode 100644
index 000000000000..fd115d2e81f6
--- /dev/null
+++ b/client/src/components/admin/Notifications/notifications.services.ts
@@ -0,0 +1,42 @@
+import axios from "axios";
+
+import { type components, fetcher } from "@/schema";
+
+const getNotification = fetcher.path("/api/notifications/{notification_id}").method("get").create();
+type NotificationResponse = components["schemas"]["NotificationResponse"];
+export async function loadNotification(id: string): Promise {
+ const { data } = await getNotification({ notification_id: id });
+ return data;
+}
+
+const postNotification = fetcher.path("/api/notifications").method("post").create();
+type NotificationCreateRequest = components["schemas"]["NotificationCreateRequest"];
+export async function sendNotification(notification: NotificationCreateRequest) {
+ const { data } = await postNotification(notification);
+ return data;
+}
+
+const putNotification = fetcher.path("/api/notifications/{notification_id}").method("put").create();
+type UserNotificationUpdateRequest = components["schemas"]["UserNotificationUpdateRequest"];
+export async function updateNotification(id: string, notification: UserNotificationUpdateRequest) {
+ const { data } = await putNotification({ notification_id: id, ...notification });
+ return data;
+}
+
+const getRolesReq = fetcher.path("/api/roles").method("get").create();
+export async function getRoles() {
+ const { data } = await getRolesReq({});
+ return data;
+}
+
+const getUsersReq = fetcher.path("/api/users").method("get").create();
+export async function getUsers() {
+ const { data } = await getUsersReq({});
+ return data;
+}
+
+type GroupModel = components["schemas"]["GroupModel"];
+export async function getGroups(): Promise {
+ const { data } = await axios.get("/api/groups");
+ return data;
+}
diff --git a/client/src/components/admin/Notifications/test.utils.ts b/client/src/components/admin/Notifications/test.utils.ts
new file mode 100644
index 000000000000..6b137aa636b2
--- /dev/null
+++ b/client/src/components/admin/Notifications/test.utils.ts
@@ -0,0 +1,51 @@
+import { type components } from "@/schema";
+
+type NotificationVariants = components["schemas"]["NotificationVariant"];
+type BroadcastNotificationResponse = components["schemas"]["BroadcastNotificationResponse"];
+
+export function generateRandomString() {
+ return Math.random().toString(36).substring(7) as string;
+}
+
+export function generateRandomVariant() {
+ const variants: NotificationVariants[] = ["info", "warning", "urgent"];
+ const randomIndex = Math.floor(Math.random() * variants.length);
+ return variants[randomIndex] as NotificationVariants;
+}
+
+export function generateNewBroadcast({ actionLink = false, published = false }): BroadcastNotificationResponse {
+ let baseDate;
+
+ if (published) {
+ baseDate = Date.now() - 100000;
+ } else {
+ baseDate = Date.now() + 100000;
+ }
+
+ const tmp: BroadcastNotificationResponse = {
+ id: "broadcast-" + Math.floor(Math.random() * 1000000),
+ source: generateRandomString(),
+ category: "broadcast",
+ variant: generateRandomVariant(),
+ create_time: new Date(baseDate + 1).toISOString(),
+ update_time: new Date(baseDate + 2000).toISOString(),
+ publication_time: new Date(baseDate + 3000).toISOString(),
+ expiration_time: new Date(baseDate + 86400000).toISOString(),
+ content: {
+ subject: generateRandomString(),
+ message: generateRandomString(),
+ category: "broadcast",
+ },
+ };
+
+ if (actionLink) {
+ tmp.content.action_links = [
+ {
+ link: "https://test.link",
+ action_name: generateRandomString(),
+ },
+ ];
+ }
+
+ return tmp;
+}
diff --git a/client/src/components/providers/ConfigProvider.js b/client/src/components/providers/ConfigProvider.js
deleted file mode 100644
index cfbd987980d4..000000000000
--- a/client/src/components/providers/ConfigProvider.js
+++ /dev/null
@@ -1,26 +0,0 @@
-/**
- * ConfigProvider ensures that the configs have been loaded from the server and
- * delivers all the config values onto the slotProps. Basically it just exists
- * to house the load method in a lifecycle handler because Vuex can't do that
- * for itself.
- */
-
-import Vue from "vue"; // this module's Vue is different from store/index.js' Vue
-import Vuex, { mapActions, mapGetters } from "vuex";
-
-Vue.use(Vuex);
-
-export default {
- computed: {
- ...mapGetters("config", ["config"]),
- },
- methods: {
- ...mapActions("config", ["loadConfigs"]),
- },
- created() {
- this.loadConfigs();
- },
- render() {
- return this.$scopedSlots.default({ config: this.config, loading: this.config === undefined });
- },
-};
diff --git a/client/src/components/providers/DatasetProvider.js b/client/src/components/providers/DatasetProvider.js
index 826a9fff4162..bf643f51aac7 100644
--- a/client/src/components/providers/DatasetProvider.js
+++ b/client/src/components/providers/DatasetProvider.js
@@ -1,19 +1,11 @@
import axios from "axios";
-import { SingleQueryProvider } from "components/providers/SingleQueryProvider";
import { getAppRoot } from "onload/loadConfig";
-import { rethrowSimple } from "utils/simple-error";
-import { stateIsTerminal } from "./utils";
+import { SingleQueryProvider } from "@/components/providers/SingleQueryProvider";
+import { fetchDatasetDetails } from "@/stores/services/dataset.service";
+import { rethrowSimple } from "@/utils/simple-error";
-async function getDataset({ id }) {
- const url = `${getAppRoot()}api/datasets/${id}`;
- try {
- const { data } = await axios.get(url);
- return data;
- } catch (e) {
- rethrowSimple(e);
- }
-}
+import { stateIsTerminal } from "./utils";
async function getDatasetAttributes({ id }) {
const url = `${getAppRoot()}dataset/get_edit?dataset_id=${id}`;
@@ -26,4 +18,4 @@ async function getDatasetAttributes({ id }) {
}
export const DatasetAttributesProvider = SingleQueryProvider(getDatasetAttributes);
-export default SingleQueryProvider(getDataset, stateIsTerminal);
+export default SingleQueryProvider(fetchDatasetDetails, stateIsTerminal);
diff --git a/client/src/components/providers/MockConfigProvider.js b/client/src/components/providers/MockConfigProvider.js
deleted file mode 100644
index 0126446102b9..000000000000
--- a/client/src/components/providers/MockConfigProvider.js
+++ /dev/null
@@ -1,9 +0,0 @@
-const MockConfigProvider = (fakeConfig) => ({
- render() {
- return this.$scopedSlots.default({
- config: fakeConfig,
- });
- },
-});
-
-export default MockConfigProvider;
diff --git a/client/src/components/providers/ToolPanelViewProvider.js b/client/src/components/providers/ToolPanelViewProvider.js
deleted file mode 100644
index 0be49d3e6d9f..000000000000
--- a/client/src/components/providers/ToolPanelViewProvider.js
+++ /dev/null
@@ -1,40 +0,0 @@
-import { mapActions, mapGetters } from "vuex";
-
-export default {
- props: {
- panelView: {
- type: String,
- required: true,
- },
- setDefault: {
- type: Boolean,
- required: false,
- default: true,
- },
- },
- computed: {
- ...mapGetters("panels", ["currentPanel", "currentPanelView", "panel"]),
- localPanelView() {
- return this.setDefault ? this.currentPanelView : this.panelView;
- },
- localPanel() {
- return this.setDefault ? this.currentPanel : this.panel(this.panelView);
- },
- },
- methods: {
- ...mapActions("panels", ["initCurrentPanelView", "fetchPanel"]),
- },
- created() {
- if (this.setDefault) {
- this.initCurrentPanelView(this.panelView);
- } else {
- this.fetchPanel(this.panelView);
- }
- },
- render() {
- return this.$scopedSlots.default({
- currentPanel: this.localPanel,
- currentPanelView: this.localPanelView,
- });
- },
-};
diff --git a/client/src/components/providers/storeProviders.js b/client/src/components/providers/storeProviders.js
index 62fef970457a..2c2531d5149b 100644
--- a/client/src/components/providers/storeProviders.js
+++ b/client/src/components/providers/storeProviders.js
@@ -145,9 +145,8 @@ export const DatasetCollectionElementProvider = {
* Provider component interface to the actual stores i.e. history items and collection elements stores.
* @param {String} storeAction The store action is executed when the consuming component e.g. the history panel, changes the provider props.
* @param {String} storeGetter The store getter passes its result to the slot of the corresponding provider.
- * @param {String} storeCountGetter The query stats store getter passes its matches counts to the slot of the corresponding provider.
*/
-export const StoreProvider = (storeAction, storeGetter, storeCountGetter = undefined) => {
+export const StoreProvider = (storeAction, storeGetter) => {
return {
mixins: [HasAttributesMixin],
watch: {
@@ -167,20 +166,16 @@ export const StoreProvider = (storeAction, storeGetter, storeCountGetter = undef
this.load();
},
computed: {
- ...mapGetters([storeGetter, storeCountGetter]),
+ ...mapGetters([storeGetter]),
result() {
return this[storeGetter](this.attributes);
},
- count() {
- return storeCountGetter ? this[storeCountGetter]() : undefined;
- },
},
render() {
return this.$scopedSlots.default({
error: this.error,
loading: this.loading,
result: this.result,
- count: this.count,
});
},
methods: {
@@ -199,7 +194,3 @@ export const StoreProvider = (storeAction, storeGetter, storeCountGetter = undef
},
};
};
-
-export const DatasetProvider = StoreProvider("fetchDataset", "getDataset");
-export const CollectionElementsProvider = StoreProvider("fetchCollectionElements", "getCollectionElements");
-export const ToolsProvider = StoreProvider("fetchAllTools", "getTools");
diff --git a/client/src/components/providers/test/json/DatasetCollection.error.json b/client/src/components/providers/test/json/DatasetCollection.error.json
index 4765b3b67952..71e6a8864546 100644
--- a/client/src/components/providers/test/json/DatasetCollection.error.json
+++ b/client/src/components/providers/test/json/DatasetCollection.error.json
@@ -11,7 +11,7 @@
"name": "abcdef",
"create_time": "2020-07-02T17:33:56.567412",
"populated_state": "new",
- "collection_id": 44,
+ "collection_id": "b887d74393f85b6d",
"hid": 2,
"job_source_id": "3da1fe6d8d16a505",
"type_id": "dataset_collection-ba03619785539f8c",
diff --git a/client/src/components/providers/test/json/DatasetCollection.json b/client/src/components/providers/test/json/DatasetCollection.json
index 85b9cada9fd6..83957be08738 100644
--- a/client/src/components/providers/test/json/DatasetCollection.json
+++ b/client/src/components/providers/test/json/DatasetCollection.json
@@ -35,5 +35,5 @@
"deleted": false,
"populated": true,
"update_time": "2020-06-26T14:22:58.435348",
- "collection_id": 23
-}
\ No newline at end of file
+ "collection_id": "f09437b8822035f7"
+}
diff --git a/client/src/components/providers/test/json/DatasetCollection.processing.json b/client/src/components/providers/test/json/DatasetCollection.processing.json
index 890176225d11..423cca99d161 100644
--- a/client/src/components/providers/test/json/DatasetCollection.processing.json
+++ b/client/src/components/providers/test/json/DatasetCollection.processing.json
@@ -19,7 +19,7 @@
"tags": [],
"hid": 2,
"url": "/api/histories/f7bb1edd6b95db62/contents/dataset_collections/ba03619785539f8c",
- "collection_id": 44,
+ "collection_id": "b887d74393f85b6d",
"job_state_summary": {
"running": 3,
"waiting": 0,
@@ -36,4 +36,4 @@
"new": 0
},
"name": "Unzip on data 1"
-}
\ No newline at end of file
+}
diff --git a/client/src/composables/config.js b/client/src/composables/config.js
deleted file mode 100644
index 0464f48e2908..000000000000
--- a/client/src/composables/config.js
+++ /dev/null
@@ -1,18 +0,0 @@
-import { computed, inject, onMounted } from "vue";
-
-/* composable config wrapper */
-export function useConfig(fetchOnce = false) {
- const store = inject("store");
-
- const config = computed(() => store.getters["config/config"]);
- const isLoaded = computed(() => store.getters["config/configIsLoaded"]);
-
- // Anytime we mount this (for now), make sure to load.
- onMounted(() => {
- if (!(fetchOnce && isLoaded)) {
- store.dispatch("config/loadConfigs");
- }
- });
-
- return { config, isLoaded };
-}
diff --git a/client/src/composables/config.ts b/client/src/composables/config.ts
new file mode 100644
index 000000000000..2ead6f16a302
--- /dev/null
+++ b/client/src/composables/config.ts
@@ -0,0 +1,20 @@
+import { computed, onMounted } from "vue";
+
+import { useConfigStore } from "@/stores/configurationStore";
+
+/* composable config wrapper */
+export function useConfig(fetchOnce = false) {
+ const store = useConfigStore();
+
+ const config = computed(() => store.config);
+ const isConfigLoaded = computed(() => store.isLoaded);
+
+ // Anytime we mount this (for now), make sure to load.
+ onMounted(() => {
+ if (!(fetchOnce && isConfigLoaded)) {
+ store.loadConfig();
+ }
+ });
+
+ return { config, isConfigLoaded };
+}
diff --git a/client/src/composables/fileSources.ts b/client/src/composables/fileSources.ts
index 67eb3d635676..1ed12e79f05c 100644
--- a/client/src/composables/fileSources.ts
+++ b/client/src/composables/fileSources.ts
@@ -1,17 +1,23 @@
import { onMounted, readonly, ref } from "vue";
-import { FilesSourcePlugin, getFileSources } from "@/components/FilesDialog/services";
+import {
+ BrowsableFilesSourcePlugin,
+ FilterFileSourcesOptions,
+ getFileSources,
+} from "@/components/FilesDialog/services";
/**
* Composable for accessing and working with file sources.
+ *
+ * @param options - The options to filter the file sources.
*/
-export function useFileSources() {
+export function useFileSources(options: FilterFileSourcesOptions = {}) {
const isLoading = ref(true);
const hasWritable = ref(false);
- const fileSources = ref([]);
+ const fileSources = ref([]);
onMounted(async () => {
- fileSources.value = await getFileSources();
+ fileSources.value = await getFileSources(options);
hasWritable.value = fileSources.value.some((fs) => fs.writable);
isLoading.value = false;
});
diff --git a/client/src/composables/keyedObjects.test.ts b/client/src/composables/keyedObjects.test.ts
new file mode 100644
index 000000000000..2321e5d62327
--- /dev/null
+++ b/client/src/composables/keyedObjects.test.ts
@@ -0,0 +1,50 @@
+import { useKeyedObjects } from "./keyedObjects";
+
+describe("useKeyedObjects", () => {
+ it("returns the same id for the same object", () => {
+ const { keyObject } = useKeyedObjects();
+
+ const obj = {
+ a: 1,
+ b: 2,
+ } as {
+ a: number;
+ b: number;
+ c?: number;
+ };
+
+ const keyA = keyObject(obj);
+ expect(keyObject(obj)).toBe(keyA);
+
+ obj.a += 5;
+ obj["c"] = 6;
+
+ expect(keyObject(obj)).toBe(keyA);
+ });
+
+ it("returns different ids for different objects", () => {
+ const { keyObject } = useKeyedObjects();
+
+ const objA = {
+ a: 1,
+ };
+
+ const objB = {
+ b: 2,
+ };
+
+ const keyA = keyObject(objA);
+ const keyB = keyObject(objB);
+ expect(keyA).not.toBe(keyB);
+
+ const objD = {
+ d: 3,
+ };
+ const objE = structuredClone(objD);
+ const keyD = keyObject(objD);
+ const keyE = keyObject(objE);
+ expect(keyD).not.toBe(keyE);
+
+ expect(keyObject({})).not.toBe(keyObject({}));
+ });
+});
diff --git a/client/src/composables/keyedObjects.ts b/client/src/composables/keyedObjects.ts
new file mode 100644
index 000000000000..097ca8d51231
--- /dev/null
+++ b/client/src/composables/keyedObjects.ts
@@ -0,0 +1,34 @@
+import { unref } from "vue";
+
+import { useUid } from "./utils/uid";
+
+/**
+ * Allows for keying objects by their internal ids.
+ * Returns a function which takes an object and returns a string uid.
+ * Passing the same object to this function twice, will return the same id.
+ *
+ * Passing the same object to a function created by another
+ * `useKeyedObjects` composable will not produce the same ids.
+ *
+ * A cloned object will not have the same id as the object it was cloned from.
+ * Modifying an objects properties will not affect its id.
+ *
+ * @returns A function which allows for keying objects
+ */
+export function useKeyedObjects() {
+ const keyCache = new WeakMap();
+
+ function keyObject(object: object) {
+ const cachedKey = keyCache.get(object);
+
+ if (cachedKey) {
+ return cachedKey;
+ } else {
+ const key = unref(useUid("object-"));
+ keyCache.set(object, key);
+ return key;
+ }
+ }
+
+ return { keyObject };
+}
diff --git a/client/src/composables/shortTermStorage.js b/client/src/composables/shortTermStorage.js
deleted file mode 100644
index fdb6ff72fde8..000000000000
--- a/client/src/composables/shortTermStorage.js
+++ /dev/null
@@ -1,155 +0,0 @@
-import axios from "axios";
-import { withPrefix } from "utils/redirect";
-import { rethrowSimple } from "utils/simple-error";
-import { readonly, ref } from "vue";
-
-export const DEFAULT_EXPORT_PARAMS = {
- modelStoreFormat: "rocrate.zip",
- includeFiles: true,
- includeDeleted: false,
- includeHidden: false,
-};
-
-const DEFAULT_POLL_DELAY = 1000;
-const DEFAULT_OPTIONS = { exportParams: DEFAULT_EXPORT_PARAMS, pollDelayInMs: DEFAULT_POLL_DELAY };
-
-/**
- * Composable to simplify and reuse the logic for downloading objects using Galaxy's Short Term Storage system.
- */
-export function useShortTermStorage() {
- let timeout = null;
- let pollDelay = DEFAULT_POLL_DELAY;
-
- const isPreparing = ref(false);
-
- async function prepareHistoryDownload(historyId, options = DEFAULT_OPTIONS) {
- return prepareObjectDownload(historyId, "histories", options, false);
- }
-
- async function downloadHistory(historyId, options = DEFAULT_OPTIONS) {
- return prepareObjectDownload(historyId, "histories", options, true);
- }
-
- async function prepareWorkflowInvocationDownload(invocationId, options = DEFAULT_OPTIONS) {
- return prepareObjectDownload(invocationId, "invocations", options, false);
- }
-
- async function downloadWorkflowInvocation(invocationId, options = DEFAULT_OPTIONS) {
- return prepareObjectDownload(invocationId, "invocations", options, true);
- }
-
- function getDownloadObjectUrl(storageRequestId) {
- const url = withPrefix(`/api/short_term_storage/${storageRequestId}`);
- return url;
- }
-
- function downloadObjectByRequestId(storageRequestId) {
- const url = getDownloadObjectUrl(storageRequestId);
- window.location.assign(url);
- }
-
- async function prepareObjectDownload(object_id, object_api, options = DEFAULT_OPTIONS, downloadWhenReady = true) {
- const finalOptions = Object.assign(DEFAULT_OPTIONS, options);
- resetTimeout();
- isPreparing.value = true;
- pollDelay = finalOptions.pollDelayInMs;
- const url = withPrefix(`/api/${object_api}/${object_id}/prepare_store_download`);
- const exportParams = {
- model_store_format: finalOptions.exportParams.modelStoreFormat,
- include_files: finalOptions.exportParams.includeFiles,
- include_deleted: finalOptions.exportParams.includeDeleted,
- include_hidden: finalOptions.exportParams.includeHidden,
- };
-
- const response = await axios.post(url, exportParams).catch(handleError);
- handleInitialize(response, downloadWhenReady);
- }
-
- function handleInitialize(response, downloadWhenReady) {
- const storageRequestId = response.data.storage_request_id;
- pollStorageRequestId(storageRequestId, downloadWhenReady);
- }
-
- function pollStorageRequestId(storageRequestId, downloadWhenReady) {
- const url = withPrefix(`/api/short_term_storage/${storageRequestId}/ready`);
- axios
- .get(url)
- .then((r) => {
- handlePollResponse(r, storageRequestId, downloadWhenReady);
- })
- .catch(handleError);
- }
-
- function handlePollResponse(response, storageRequestId, downloadWhenReady) {
- const ready = response.data;
- if (ready) {
- isPreparing.value = false;
- if (downloadWhenReady) {
- downloadObjectByRequestId(storageRequestId);
- }
- } else {
- pollAfterDelay(storageRequestId);
- }
- }
-
- function handleError(err) {
- rethrowSimple(err);
- isPreparing.value = false;
- }
-
- function pollAfterDelay(storageRequestId) {
- resetTimeout();
- timeout = setTimeout(() => {
- pollStorageRequestId(storageRequestId);
- }, pollDelay);
- }
-
- function resetTimeout() {
- if (timeout) {
- clearTimeout(timeout);
- timeout = null;
- }
- }
-
- return {
- /**
- * Starts preparing a history download file in the short term storage.
- * @param {String} historyId The ID of the history to be prepared for download
- * @param {Object} options Options for the download preparation
- */
- prepareHistoryDownload,
- /**
- * Prepares a history download file in the short term storage and starts the download when ready.
- * @param {String} historyId The ID of the history to be downloaded
- * @param {Object} options Options for the download preparation
- */
- downloadHistory,
- /**
- * Starts preparing a workflow invocation download file in the short term storage.
- * @param {String} invocationId The ID of the workflow invocation to be prepared for download
- * @param {Object} options Options for the download preparation
- */
- prepareWorkflowInvocationDownload,
- /**
- * Starts preparing a workflow invocation download file in the short term storage and starts the download when ready.
- * @param {String} invocationId The ID of the workflow invocation to be downloaded
- * @param {Object} options Options for the download preparation
- */
- downloadWorkflowInvocation,
- /**
- * Starts a direct download of the object associated with the given `storageRequestId`.
- * For the download to succeed, the associated `storageRequestId` must be `ready` and not in failure state.
- * @param {String} storageRequestId The storage request ID associated to the object to be downloaded
- */
- downloadObjectByRequestId,
- /**
- * Whether the download is still being prepared.
- */
- isPreparing: readonly(isPreparing),
- /**
- * Given a storageRequestId it returns the download URL for that object.
- * @param {String} storageRequestId The storage request ID associated to the object to be downloaded
- */
- getDownloadObjectUrl,
- };
-}
diff --git a/client/src/composables/shortTermStorage.ts b/client/src/composables/shortTermStorage.ts
new file mode 100644
index 000000000000..f760fea8872e
--- /dev/null
+++ b/client/src/composables/shortTermStorage.ts
@@ -0,0 +1,186 @@
+import { readonly, ref } from "vue";
+
+import { ExportParams, StoreExportPayload } from "@/components/Common/models/exportRecordModel";
+import { fetcher } from "@/schema";
+import { withPrefix } from "@/utils/redirect";
+
+export const DEFAULT_EXPORT_PARAMS: ExportParams = {
+ modelStoreFormat: "rocrate.zip",
+ includeFiles: true,
+ includeDeleted: false,
+ includeHidden: false,
+};
+
+interface Options {
+ exportParams: ExportParams;
+ pollDelayInMs: number;
+}
+
+interface StorageRequestResponse {
+ storage_request_id: string;
+}
+
+type StartPreparingDownloadCallback = (objectId: string, params: StoreExportPayload) => Promise;
+
+const DEFAULT_POLL_DELAY = 1000;
+const DEFAULT_OPTIONS: Options = { exportParams: DEFAULT_EXPORT_PARAMS, pollDelayInMs: DEFAULT_POLL_DELAY };
+
+const startPreparingHistoryDownload = fetcher
+ .path("/api/histories/{history_id}/prepare_store_download")
+ .method("post")
+ .create();
+const startPreparingInvocationDownload = fetcher
+ .path("/api/invocations/{invocation_id}/prepare_store_download")
+ .method("post")
+ .create();
+const getTempStorageRequestReady = fetcher
+ .path("/api/short_term_storage/{storage_request_id}/ready")
+ .method("get")
+ .create();
+
+/**
+ * Composable to simplify and reuse the logic for downloading objects using Galaxy's Short Term Storage system.
+ */
+export function useShortTermStorage() {
+ let timeout: NodeJS.Timeout | null = null;
+ let pollDelay = DEFAULT_POLL_DELAY;
+
+ const isPreparing = ref(false);
+
+ const forHistory: StartPreparingDownloadCallback = async (id: string, params: StoreExportPayload) => {
+ const { data } = await startPreparingHistoryDownload({ history_id: id, ...params });
+ return data;
+ };
+
+ const forInvocation: StartPreparingDownloadCallback = async (id: string, params: StoreExportPayload) => {
+ const { data } = await startPreparingInvocationDownload({ invocation_id: id, ...params });
+ return data;
+ };
+
+ async function prepareHistoryDownload(historyId: string, options = DEFAULT_OPTIONS) {
+ return prepareObjectDownload(forHistory, historyId, options, false);
+ }
+ async function downloadHistory(historyId: string, options = DEFAULT_OPTIONS) {
+ return prepareObjectDownload(forHistory, historyId, options, true);
+ }
+
+ async function prepareWorkflowInvocationDownload(invocationId: string, options = DEFAULT_OPTIONS) {
+ return prepareObjectDownload(forInvocation, invocationId, options, false);
+ }
+
+ async function downloadWorkflowInvocation(invocationId: string, options = DEFAULT_OPTIONS) {
+ return prepareObjectDownload(forInvocation, invocationId, options, true);
+ }
+
+ function getDownloadObjectUrl(storageRequestId: string) {
+ const url = withPrefix(`/api/short_term_storage/${storageRequestId}`);
+ return url;
+ }
+
+ function downloadObjectByRequestId(storageRequestId: string) {
+ const url = getDownloadObjectUrl(storageRequestId);
+ window.location.assign(url);
+ }
+
+ async function prepareObjectDownload(
+ startPreparingDownloadAsync: StartPreparingDownloadCallback,
+ objectId: string,
+ options = DEFAULT_OPTIONS,
+ downloadWhenReady = true
+ ) {
+ resetTimeout();
+ isPreparing.value = true;
+ const finalOptions = Object.assign(DEFAULT_OPTIONS, options);
+ pollDelay = finalOptions.pollDelayInMs;
+ const exportParams: StoreExportPayload = {
+ model_store_format: finalOptions.exportParams.modelStoreFormat,
+ include_files: finalOptions.exportParams.includeFiles,
+ include_deleted: finalOptions.exportParams.includeDeleted,
+ include_hidden: finalOptions.exportParams.includeHidden,
+ };
+
+ try {
+ const response = await startPreparingDownloadAsync(objectId, exportParams);
+ const storageRequestId = response.storage_request_id;
+ pollStorageRequestId(storageRequestId, downloadWhenReady);
+ } catch (err) {
+ stopPreparing();
+ }
+ }
+
+ async function pollStorageRequestId(storageRequestId: string, downloadWhenReady: boolean) {
+ try {
+ const { data: ready } = await getTempStorageRequestReady({ storage_request_id: storageRequestId });
+ if (ready) {
+ isPreparing.value = false;
+ if (downloadWhenReady) {
+ downloadObjectByRequestId(storageRequestId);
+ }
+ } else {
+ pollAfterDelay(storageRequestId, downloadWhenReady);
+ }
+ } catch (err) {
+ stopPreparing();
+ }
+ }
+
+ function stopPreparing() {
+ isPreparing.value = false;
+ }
+
+ function pollAfterDelay(storageRequestId: string, downloadWhenReady: boolean) {
+ resetTimeout();
+ timeout = setTimeout(() => {
+ pollStorageRequestId(storageRequestId, downloadWhenReady);
+ }, pollDelay);
+ }
+
+ function resetTimeout() {
+ if (timeout) {
+ clearTimeout(timeout);
+ timeout = null;
+ }
+ }
+
+ return {
+ /**
+ * Starts preparing a history download file in the short term storage.
+ * @param {String} historyId The ID of the history to be prepared for download
+ * @param {Object} options Options for the download preparation
+ */
+ prepareHistoryDownload,
+ /**
+ * Prepares a history download file in the short term storage and starts the download when ready.
+ * @param {String} historyId The ID of the history to be downloaded
+ * @param {Object} options Options for the download preparation
+ */
+ downloadHistory,
+ /**
+ * Starts preparing a workflow invocation download file in the short term storage.
+ * @param {String} invocationId The ID of the workflow invocation to be prepared for download
+ * @param {Object} options Options for the download preparation
+ */
+ prepareWorkflowInvocationDownload,
+ /**
+ * Starts preparing a workflow invocation download file in the short term storage and starts the download when ready.
+ * @param {String} invocationId The ID of the workflow invocation to be downloaded
+ * @param {Object} options Options for the download preparation
+ */
+ downloadWorkflowInvocation,
+ /**
+ * Starts a direct download of the object associated with the given `storageRequestId`.
+ * For the download to succeed, the associated `storageRequestId` must be `ready` and not in failure state.
+ * @param {String} storageRequestId The storage request ID associated to the object to be downloaded
+ */
+ downloadObjectByRequestId,
+ /**
+ * Whether the download is still being prepared.
+ */
+ isPreparing: readonly(isPreparing),
+ /**
+ * Given a storageRequestId it returns the download URL for that object.
+ * @param {String} storageRequestId The storage request ID associated to the object to be downloaded
+ */
+ getDownloadObjectUrl,
+ };
+}
diff --git a/client/src/composables/taskMonitor.test.js b/client/src/composables/taskMonitor.test.ts
similarity index 70%
rename from client/src/composables/taskMonitor.test.js
rename to client/src/composables/taskMonitor.test.ts
index 596fcfdad687..ad3f3a446204 100644
--- a/client/src/composables/taskMonitor.test.js
+++ b/client/src/composables/taskMonitor.test.ts
@@ -1,26 +1,38 @@
-import axios from "axios";
-import MockAdapter from "axios-mock-adapter";
-import { useTaskMonitor } from "composables/taskMonitor";
import flushPromises from "flush-promises";
+import { useTaskMonitor } from "@/composables/taskMonitor";
+import { mockFetcher } from "@/schema/__mocks__";
+
+jest.mock("@/schema");
+
const PENDING_TASK_ID = "pending-fake-task-id";
const COMPLETED_TASK_ID = "completed-fake-task-id";
const FAILED_TASK_ID = "failed-fake-task-id";
const REQUEST_FAILED_TASK_ID = "request-failed-fake-task-id";
-describe("useTaskMonitor", () => {
- let axiosMock;
+function getMockedTaskStatus({ task_id }: { task_id: string }) {
+ switch (task_id) {
+ case PENDING_TASK_ID:
+ return { data: "PENDING", status: 200 };
- beforeEach(async () => {
- axiosMock = new MockAdapter(axios);
- });
+ case COMPLETED_TASK_ID:
+ return { data: "SUCCESS", status: 200 };
- afterEach(async () => {
- axiosMock.reset();
- });
+ case FAILED_TASK_ID:
+ return { data: "FAILURE", status: 200 };
+ case REQUEST_FAILED_TASK_ID:
+ throw new Error("Request failed");
+
+ default:
+ return { data: "UNKNOWN", status: 404 };
+ }
+}
+
+mockFetcher.path("/api/tasks/{task_id}/state").method("get").mock(getMockedTaskStatus);
+
+describe("useTaskMonitor", () => {
it("should indicate the task is running when it is still pending", async () => {
- axiosMock.onGet(`/api/tasks/${PENDING_TASK_ID}/state`).reply(200, "PENDING");
const { waitForTask, isRunning } = useTaskMonitor();
expect(isRunning.value).toBe(false);
@@ -30,7 +42,6 @@ describe("useTaskMonitor", () => {
});
it("should indicate the task is successfully completed when the state is SUCCESS", async () => {
- axiosMock.onGet(`/api/tasks/${COMPLETED_TASK_ID}/state`).reply(200, "SUCCESS");
const { waitForTask, isRunning, isCompleted } = useTaskMonitor();
expect(isCompleted.value).toBe(false);
@@ -41,7 +52,6 @@ describe("useTaskMonitor", () => {
});
it("should indicate the task has failed when the state is FAILED", async () => {
- axiosMock.onGet(`/api/tasks/${FAILED_TASK_ID}/state`).reply(200, "FAILURE");
const { waitForTask, isRunning, hasFailed } = useTaskMonitor();
expect(hasFailed.value).toBe(false);
@@ -52,7 +62,6 @@ describe("useTaskMonitor", () => {
});
it("should indicate the task status request failed when the request failed", async () => {
- axiosMock.onGet(`/api/tasks/${REQUEST_FAILED_TASK_ID}/state`).reply(400, "UNKNOWN");
const { waitForTask, requestHasFailed } = useTaskMonitor();
expect(requestHasFailed.value).toBe(false);
diff --git a/client/src/composables/taskMonitor.js b/client/src/composables/taskMonitor.ts
similarity index 67%
rename from client/src/composables/taskMonitor.js
rename to client/src/composables/taskMonitor.ts
index 01a5a591a4b0..6b94e9c9e05b 100644
--- a/client/src/composables/taskMonitor.js
+++ b/client/src/composables/taskMonitor.ts
@@ -1,57 +1,61 @@
-import axios from "axios";
import { computed, readonly, ref } from "vue";
+import { fetcher } from "@/schema";
+import { errorMessageAsString } from "@/utils/simple-error";
+
const SUCCESS_STATE = "SUCCESS";
const FAILURE_STATE = "FAILURE";
const TASK_READY_STATES = [SUCCESS_STATE, FAILURE_STATE];
const DEFAULT_POLL_DELAY = 10000;
+const getTaskStatus = fetcher.path("/api/tasks/{task_id}/state").method("get").create();
+
/**
* Composable for waiting on Galaxy background tasks.
*/
export function useTaskMonitor() {
- let timeout = null;
+ let timeout: NodeJS.Timeout | null = null;
let pollDelay = DEFAULT_POLL_DELAY;
const isRunning = ref(false);
- const status = ref(null);
- const currentTaskId = ref(null);
+ const status = ref();
+ const currentTaskId = ref();
const requestHasFailed = ref(false);
const isCompleted = computed(() => status.value === SUCCESS_STATE);
const hasFailed = computed(() => status.value === FAILURE_STATE);
- const queryStateUrl = computed(() => `/api/tasks/${currentTaskId.value}/state`);
- function waitForTask(taskId, pollDelayInMs = DEFAULT_POLL_DELAY) {
+ async function waitForTask(taskId: string, pollDelayInMs = DEFAULT_POLL_DELAY) {
pollDelay = pollDelayInMs;
resetState();
currentTaskId.value = taskId;
isRunning.value = true;
- fetchTaskStatus();
- }
-
- function fetchTaskStatus() {
- axios.get(queryStateUrl.value).then(handleStatusResponse).catch(handleError);
+ return fetchTaskStatus(taskId);
}
- function handleStatusResponse(response) {
- status.value = response.data;
- const isReady = TASK_READY_STATES.includes(status.value);
- if (isReady) {
- isRunning.value = false;
- } else {
- pollAfterDelay();
+ async function fetchTaskStatus(taskId: string) {
+ try {
+ const { data } = await getTaskStatus({ task_id: taskId });
+ status.value = data;
+ const isReady = TASK_READY_STATES.includes(status.value);
+ if (isReady) {
+ isRunning.value = false;
+ } else {
+ pollAfterDelay(taskId);
+ }
+ } catch (err) {
+ handleError(errorMessageAsString(err));
}
}
- function pollAfterDelay(taskId) {
+ function pollAfterDelay(taskId: string) {
resetTimeout();
timeout = setTimeout(() => {
fetchTaskStatus(taskId);
}, pollDelay);
}
- function handleError(err) {
+ function handleError(err: string) {
status.value = err;
requestHasFailed.value = true;
isRunning.value = false;
@@ -66,7 +70,7 @@ export function useTaskMonitor() {
function resetState() {
resetTimeout();
- status.value = null;
+ status.value = undefined;
}
return {
diff --git a/client/src/composables/toolTrainingMaterial.ts b/client/src/composables/toolTrainingMaterial.ts
index 03ff57f2461d..d72613256bbb 100644
--- a/client/src/composables/toolTrainingMaterial.ts
+++ b/client/src/composables/toolTrainingMaterial.ts
@@ -25,12 +25,6 @@ type TrainingMaterialResponse = {
[id: string]: TrainingDetails;
};
-type Config = {
- tool_training_recommendations: boolean;
- tool_training_recommendations_api_url: string;
- tool_training_recommendations_link: string;
-};
-
export type TutorialDetails = {
category: string;
title: string;
@@ -61,10 +55,10 @@ function mapToolIds() {
/** Training information about given tool */
export function useToolTrainingMaterial(id: string, name: string, version: string, owner?: string) {
- const { config, isLoaded }: { config: Ref; isLoaded: Ref } = useConfig();
+ const { config, isConfigLoaded } = useConfig();
const apiEnabled = computed(() => {
return Boolean(
- isLoaded.value &&
+ isConfigLoaded.value &&
config.value.tool_training_recommendations &&
config.value.tool_training_recommendations_api_url
);
@@ -73,9 +67,9 @@ export function useToolTrainingMaterial(id: string, name: string, version: strin
const cacheLoaded = ref(false);
watch(
- () => isLoaded.value,
+ () => isConfigLoaded.value,
async () => {
- if (!isLoaded.value) {
+ if (!isConfigLoaded.value) {
return;
}
diff --git a/client/src/composables/usePanels.ts b/client/src/composables/usePanels.ts
new file mode 100644
index 000000000000..46f6f334cc68
--- /dev/null
+++ b/client/src/composables/usePanels.ts
@@ -0,0 +1,26 @@
+import { computed } from "vue";
+import { useRoute } from "vue-router/composables";
+
+import { useUserStore } from "@/stores/userStore";
+
+export function usePanels() {
+ const userStore = useUserStore();
+ const route = useRoute();
+
+ const showPanels = computed(() => {
+ const panels = route.query.hide_panels;
+ if (panels !== undefined && panels !== null && typeof panels === "string") {
+ return panels.toLowerCase() != "true";
+ }
+ return true;
+ });
+
+ const showActivityBar = computed(() => showPanels.value && userStore.showActivityBar && !userStore.isAnonymous);
+ const showToolbox = computed(() => showPanels.value && !showActivityBar.value);
+
+ return {
+ showPanels,
+ showActivityBar,
+ showToolbox,
+ };
+}
diff --git a/client/src/composables/workflowStores.ts b/client/src/composables/workflowStores.ts
new file mode 100644
index 000000000000..40893840e5b0
--- /dev/null
+++ b/client/src/composables/workflowStores.ts
@@ -0,0 +1,63 @@
+import { inject, onScopeDispose, provide } from "vue";
+
+import { useConnectionStore } from "@/stores/workflowConnectionStore";
+import { useWorkflowStateStore } from "@/stores/workflowEditorStateStore";
+import { useWorkflowStepStore } from "@/stores/workflowStepStore";
+
+/**
+ * Creates stores scoped to a specific workflowId, and manages their lifetime.
+ * In child components, use `useWorkflowStores` instead.
+ *
+ * Provides `workflowId` to all child components.
+ *
+ * @param workflowId the workflow to scope to
+ * @returns workflow Stores
+ */
+export function provideScopedWorkflowStores(workflowId: string) {
+ provide("workflowId", workflowId);
+
+ const connectionStore = useConnectionStore(workflowId);
+ const stateStore = useWorkflowStateStore(workflowId);
+ const stepStore = useWorkflowStepStore(workflowId);
+
+ onScopeDispose(() => {
+ connectionStore.$dispose();
+ stateStore.$dispose();
+ stepStore.$dispose();
+ });
+
+ return {
+ connectionStore,
+ stateStore,
+ stepStore,
+ };
+}
+
+/**
+ * Uses all workflow related stores scoped to the workflow defined by a parent component.
+ * Does not manage lifetime.
+ *
+ * `provideScopedWorkflowStores` needs to be called by a parent component,
+ * or this composable will throw an error.
+ *
+ * @returns workflow stores
+ */
+export function useWorkflowStores() {
+ const workflowId = inject("workflowId");
+
+ if (typeof workflowId !== "string") {
+ throw new Error(
+ "Workflow ID not provided by parent component. Use `setupWorkflowStores` on a parent component."
+ );
+ }
+
+ const connectionStore = useConnectionStore(workflowId);
+ const stateStore = useWorkflowStateStore(workflowId);
+ const stepStore = useWorkflowStepStore(workflowId);
+
+ return {
+ connectionStore,
+ stateStore,
+ stepStore,
+ };
+}
diff --git a/client/src/entry/analysis/menu.js b/client/src/entry/analysis/menu.js
index 1f75398d3560..7badb524ee39 100644
--- a/client/src/entry/analysis/menu.js
+++ b/client/src/entry/analysis/menu.js
@@ -166,7 +166,7 @@ export function fetchMenu(options = {}) {
if (options.allow_user_creation) {
userTab = {
id: "user",
- title: _l("Login or Register"),
+ title: _l("Log in or Register"),
cls: "loggedout-only",
url: "/login",
tooltip: _l("Log in or register a new account"),
diff --git a/client/src/entry/analysis/modules/Admin.vue b/client/src/entry/analysis/modules/Admin.vue
index 7f67d9f11d63..33d9abf634d4 100644
--- a/client/src/entry/analysis/modules/Admin.vue
+++ b/client/src/entry/analysis/modules/Admin.vue
@@ -6,7 +6,7 @@ import { useConfig } from "@/composables/config";
import AdminPanel from "@/components/admin/AdminPanel.vue";
import FlexPanel from "@/components/Panels/FlexPanel.vue";
-const { config, isLoaded } = useConfig();
+const { config, isConfigLoaded } = useConfig();
const panelProperties = computed(() => {
return {
@@ -18,7 +18,7 @@ const panelProperties = computed(() => {
-
{{ stepLabel }}
+
+ {{ title }}
+
+
+
+
+
+
diff --git a/client/src/components/admin/Notifications/BroadcastsList.vue b/client/src/components/admin/Notifications/BroadcastsList.vue
new file mode 100644
index 000000000000..969d1eb25246
--- /dev/null
+++ b/client/src/components/admin/Notifications/BroadcastsList.vue
@@ -0,0 +1,260 @@
+
+
+
+
+
+ This broadcast has already been published. Some users may have already seen it and changing it now will
+ not affect them.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Preview
+
+
+
+
+ Update Broadcast
+ Create Broadcast
+
+
+
+
+ Broadcasts list
+
+
+
+
+
+ No broadcasts to show. Use the button above to create a new broadcast.
+
+
+
+
+
+
+
+
diff --git a/client/src/components/admin/Notifications/NotificationForm.test.ts b/client/src/components/admin/Notifications/NotificationForm.test.ts
new file mode 100644
index 000000000000..e2d26ac3856d
--- /dev/null
+++ b/client/src/components/admin/Notifications/NotificationForm.test.ts
@@ -0,0 +1,50 @@
+import { createTestingPinia } from "@pinia/testing";
+import { getLocalVue } from "@tests/jest/helpers";
+import { mount, type Wrapper } from "@vue/test-utils";
+import flushPromises from "flush-promises";
+import { setActivePinia } from "pinia";
+import Vue from "vue";
+
+import NotificationForm from "./NotificationForm.vue";
+
+jest.mock("@/schema");
+
+const SUBMIT_BUTTON_SELECTOR = "#notification-submit";
+
+const localVue = getLocalVue(true);
+
+async function mountNotificationForm(props?: object) {
+ const pinia = createTestingPinia();
+ setActivePinia(pinia);
+
+ const wrapper = mount(NotificationForm as object, {
+ propsData: {
+ ...props,
+ },
+ localVue,
+ pinia,
+ stubs: {
+ FontAwesomeIcon: true,
+ },
+ });
+
+ await flushPromises();
+
+ return { wrapper };
+}
+
+describe("NotificationForm.vue", () => {
+ function expectSubmitButton(wrapper: Wrapper
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ created
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ {{ actionLink.action_name }}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ New Notification
+
+
+
+
+
+
diff --git a/client/src/components/admin/Notifications/NotificationsManagement.vue b/client/src/components/admin/Notifications/NotificationsManagement.vue
new file mode 100644
index 000000000000..0863aeae64bb
--- /dev/null
+++ b/client/src/components/admin/Notifications/NotificationsManagement.vue
@@ -0,0 +1,42 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Preview
+
+
+
+
+
+
+
+
+
+
+ Send Notification
+
+
+
+
+
+
diff --git a/client/src/components/admin/Notifications/broadcasts.services.ts b/client/src/components/admin/Notifications/broadcasts.services.ts
new file mode 100644
index 000000000000..a62dbb267363
--- /dev/null
+++ b/client/src/components/admin/Notifications/broadcasts.services.ts
@@ -0,0 +1,29 @@
+import { type components, fetcher } from "@/schema";
+
+type BroadcastNotificationResponse = components["schemas"]["BroadcastNotificationResponse"];
+
+const getBroadcast = fetcher.path("/api/notifications/broadcast/{notification_id}").method("get").create();
+export async function loadBroadcast(id: string): Promise
+
+ Notifications and Broadcasts
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/client/src/entry/analysis/modules/Analysis.vue b/client/src/entry/analysis/modules/Analysis.vue
index d904b6069bba..e865276d6f5f 100644
--- a/client/src/entry/analysis/modules/Analysis.vue
+++ b/client/src/entry/analysis/modules/Analysis.vue
@@ -1,34 +1,19 @@
+
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w.ajax({url:e,type:"GET",dataType:"script",cache:!0,async:!1,global:!1,throws:!0})},w.fn.extend({wrapAll:function(e){var t;return this[0]&&(v(e)&&(e=e.call(this[0])),t=w(e,this[0].ownerDocument).eq(0).clone(!0),this[0].parentNode&&t.insertBefore(this[0]),t.map(function(){for(var e=this;e.firstElementChild;)e=e.firstElementChild;return e}).append(this)),this},wrapInner:function(e){return v(e)?this.each(function(t){w(this).wrapInner(e.call(this,t))}):this.each(function(){var t=w(this),n=t.contents();n.length?n.wrapAll(e):t.append(e)})},wrap:function(e){var t=v(e);return this.each(function(n){w(this).wrapAll(t?e.call(this,n):e)})},unwrap:function(e){return this.parent(e).not("body").each(function(){w(this).replaceWith(this.childNodes)}),this}}),w.expr.pseudos.hidden=function(e){return!w.expr.pseudos.visible(e)},w.expr.pseudos.visible=function(e){return!!(e.offsetWidth||e.offsetHeight||e.getClientRects().length)},w.ajaxSettings.xhr=function(){try{return new t.XMLHttpRequest}catch(e){}};var $t={0:200,1223:204},Bt=w.ajaxSettings.xhr();g.cors=!!Bt&&"withCredentials"in Bt,g.ajax=Bt=!!Bt,w.ajaxTransport(function(e){var n,r;if(g.cors||Bt&&!e.crossDomain)return{send:function(i,o){var a,s=e.xhr();if(s.open(e.type,e.url,e.async,e.username,e.password),e.xhrFields)for(a in e.xhrFields)s[a]=e.xhrFields[a];for(a in e.mimeType&&s.overrideMimeType&&s.overrideMimeType(e.mimeType),e.crossDomain||i["X-Requested-With"]||(i["X-Requested-With"]="XMLHttpRequest"),i)s.setRequestHeader(a,i[a]);n=function(e){return function(){n&&(n=r=s.onload=s.onerror=s.onabort=s.ontimeout=s.onreadystatechange=null,"abort"===e?s.abort():"error"===e?"number"!=typeof s.status?o(0,"error"):o(s.status,s.statusText):o($t[s.status]||s.status,s.statusText,"text"!==(s.responseType||"text")||"string"!=typeof s.responseText?{binary:s.response}:{text:s.responseText},s.getAllResponseHeaders()))}},s.onload=n(),r=s.onerror=s.ontimeout=n("error"),void 0!==s.onabort?s.onabort=r:s.onreadystatechange=function(){4===s.readyState&&t.setTimeout(function(){n&&r()})},n=n("abort");try{s.send(e.hasContent&&e.data||null)}catch(u){if(n)throw u}},abort:function(){n&&n()}}}),w.ajaxPrefilter(function(e){e.crossDomain&&(e.contents.script=!1)}),w.ajaxSetup({accepts:{script:"text/javascript, application/javascript, application/ecmascript, application/x-ecmascript"},contents:{script:/\b(?:java|ecma)script\b/},converters:{"text script":function(e){return w.globalEval(e),e}}}),w.ajaxPrefilter("script",function(e){void 0===e.cache&&(e.cache=!1),e.crossDomain&&(e.type="GET")}),w.ajaxTransport("script",function(e){var t,n;if(e.crossDomain)return{send:function(r,o){t=w("""",
+ f"""""",
+ )
+ else:
+ index = FRONTEND_DIST / "index.html"
+ index_html = index.read_text()
+ ensure_valid_session(trans)
+ cookie = trans.session_csrf_token
+ r: HTMLResponse = cast(HTMLResponse, trans.response)
+ r.set_cookie("session_csrf_token", cookie)
+ return index_html
+
+ return app, index
+
+
+def redirect_route(app, from_url: str, to_url: str):
+ @app.get(from_url)
+ def redirect():
+ return RedirectResponse(to_url)
+
+
+def frontend_route(controller, path):
+ app, index = controller
+ app.get(path, response_class=HTMLResponse)(index)
+
+
+def mount_graphql(app: FastAPI, tool_shed_app: ToolShedApp):
+ context = {
+ "session": tool_shed_app.model.context,
+ "security": tool_shed_app.security,
+ }
+ g_app = GraphQLApp(schema, on_get=make_graphiql_handler(), context_value=context, root_value=context)
+ app.mount("/graphql", g_app)
+ app.mount("/api/graphql", g_app)
+
+
+FRONT_END_ROUTES = [
+ "/",
+ "/admin",
+ "/login",
+ "/register",
+ "/logout_success",
+ "/login_success",
+ "/registration_success",
+ "/help",
+ "/repositories_by_search",
+ "/repositories_by_category",
+ "/repositories_by_category/{category_id}",
+ "/repositories_by_owner",
+ "/repositories_by_owner/{username}",
+ "/repositories/{repository_id}",
+ "/repositories_search",
+ "/_component_showcase",
+ "/user/api_key",
+ "/user/change_password",
+ "/view/{username}",
+ "/view/{username}/{repository_name}",
+ "/view/{username}/{repository_name}/{changeset_revision}",
+]
+LEGACY_ROUTES = {
+ "/user/create": "/register", # for twilltestcase
+ "/user/login": "/login", # for twilltestcase
+}
def initialize_fast_app(gx_webapp, tool_shed_app):
- app = FastAPI(
- title="Galaxy Tool Shed API",
- description=("This API allows you to manage the Tool Shed repositories."),
- docs_url="/api/docs",
- redoc_url="/api/redoc",
- )
+ app = get_fastapi_instance()
add_exception_handler(app)
add_request_id_middleware(app)
- include_all_package_routers(app, "tool_shed.webapp.api")
+ from .buildapp import SHED_API_VERSION
+
+ def mount_static(directory: Path):
+ name = directory.name
+ if directory.exists():
+ app.mount(f"/{name}", StaticFiles(directory=directory), name=name)
+
+ if SHED_API_VERSION == "v2":
+ controller = frontend_controller(app)
+ for route in FRONT_END_ROUTES:
+ frontend_route(controller, route)
+
+ for from_route, to_route in LEGACY_ROUTES.items():
+ redirect_route(app, from_route, to_route)
+
+ mount_graphql(app, tool_shed_app)
+
+ mount_static(FRONTEND / "static")
+ if TOOL_SHED_USE_HMR:
+ mount_static(FRONTEND / "node_modules")
+ else:
+ mount_static(FRONTEND_DIST / "assets")
+
+ routes_package = "tool_shed.webapp.api" if SHED_API_VERSION == "v1" else "tool_shed.webapp.api2"
+ include_all_package_routers(app, routes_package)
wsgi_handler = WSGIMiddleware(gx_webapp)
tool_shed_app.haltables.append(("WSGI Middleware threadpool", wsgi_handler.executor.shutdown))
app.mount("/", wsgi_handler)
return app
+def get_fastapi_instance() -> FastAPI:
+ return FastAPI(
+ title="Galaxy Tool Shed API",
+ description=("This API allows you to manage the Tool Shed repositories."),
+ docs_url="/api/docs",
+ redoc_url="/api/redoc",
+ tags=api_tags_metadata,
+ license_info={"name": "MIT", "url": "https://github.com/galaxyproject/galaxy/blob/dev/LICENSE.txt"},
+ )
+
+
+def get_openapi_schema() -> Dict[str, Any]:
+ """
+ Dumps openAPI schema without starting a full app and webserver.
+ """
+ app = get_fastapi_instance()
+ include_all_package_routers(app, "tool_shed.webapp.api2")
+ return get_openapi(
+ title=app.title,
+ version=app.version,
+ openapi_version="3.1.0",
+ description=app.description,
+ routes=app.routes,
+ license_info=app.license_info,
+ )
+
+
__all__ = (
"add_request_id_middleware",
+ "get_openapi_schema",
"initialize_fast_app",
)
diff --git a/lib/tool_shed/webapp/frontend/.eslintignore b/lib/tool_shed/webapp/frontend/.eslintignore
new file mode 100644
index 000000000000..b22c816bfd5e
--- /dev/null
+++ b/lib/tool_shed/webapp/frontend/.eslintignore
@@ -0,0 +1,7 @@
+# don't ever lint node_modules
+node_modules
+# don't lint build output (make sure it's set to your correct build folder name)
+dist
+
+# Ignore codegen aritfacts
+src/gql/*.ts
diff --git a/lib/tool_shed/webapp/frontend/.eslintrc.js b/lib/tool_shed/webapp/frontend/.eslintrc.js
new file mode 100644
index 000000000000..7343e0cc14e1
--- /dev/null
+++ b/lib/tool_shed/webapp/frontend/.eslintrc.js
@@ -0,0 +1,29 @@
+module.exports = {
+ root: true,
+ parser: "vue-eslint-parser",
+ parserOptions: {
+ parser: "@typescript-eslint/parser",
+ // project: ['./tsconfig.json'],
+ },
+ extends: [
+ "plugin:vue/strongly-recommended",
+ "eslint:recommended",
+ "@vue/typescript/recommended",
+ "prettier",
+ "plugin:vuejs-accessibility/recommended",
+ "plugin:@typescript-eslint/eslint-recommended",
+ "plugin:@typescript-eslint/recommended",
+ // More goodies..
+ // "plugin:@typescript-eslint/recommended-requiring-type-checking",
+ ],
+ plugins: ["@typescript-eslint", "prettier", "vuejs-accessibility"],
+ rules: {
+ "prettier/prettier": "error",
+ // not needed for vue 3
+ "vue/no-multiple-template-root": "off",
+ // upgrade warnings for common John problems
+ "@typescript-eslint/no-unused-vars": "error",
+ "vue/require-default-prop": "error",
+ "vue/v-slot-style": "error",
+ },
+}
diff --git a/lib/tool_shed/webapp/frontend/.prettierrc b/lib/tool_shed/webapp/frontend/.prettierrc
new file mode 100644
index 000000000000..0fe7f46213c9
--- /dev/null
+++ b/lib/tool_shed/webapp/frontend/.prettierrc
@@ -0,0 +1,5 @@
+{
+ "tabWidth": 4,
+ "printWidth": 120,
+ "semi": false
+}
diff --git a/lib/tool_shed/webapp/frontend/Makefile b/lib/tool_shed/webapp/frontend/Makefile
new file mode 100644
index 000000000000..b520b0be6844
--- /dev/null
+++ b/lib/tool_shed/webapp/frontend/Makefile
@@ -0,0 +1,22 @@
+GALAXY_ROOT=../../../..
+
+client:
+ yarn build
+
+dev:
+ yarn dev-all
+
+format:
+ yarn format
+
+lint:
+ yarn typecheck && yarn lint
+
+# These next two tasks don't really belong here, but they do demonstrate
+# how to get a test server running and populated with some initial data
+# for the new tool shed frontend.
+run_test_backend:
+ cd $(GALAXY_ROOT); TOOL_SHED_CONFIG_OVERRIDE_BOOTSTRAP_ADMIN_API_KEY=tsadminkey TOOL_SHED_VITE_PORT=4040 TOOL_SHED_API_VERSION=v2 ./run_tool_shed.sh
+
+bootstrap_test_backend:
+ cd $(GALAXY_ROOT); . .venv/bin/activate; python scripts/bootstrap_test_shed.py
diff --git a/lib/tool_shed/webapp/frontend/codegen.ts b/lib/tool_shed/webapp/frontend/codegen.ts
new file mode 100644
index 000000000000..116794231c76
--- /dev/null
+++ b/lib/tool_shed/webapp/frontend/codegen.ts
@@ -0,0 +1,16 @@
+import type { CodegenConfig } from '@graphql-codegen/cli'
+
+const config: CodegenConfig = {
+ schema: 'http://localhost:9009/graphql/',
+ documents: ['src/**/*.vue', 'src/**/*.ts'],
+ generates: {
+ './src/gql/': {
+ preset: 'client',
+ plugins: [],
+ config: {
+ useTypeImport: true
+ }
+ }
+ }
+}
+export default config
diff --git a/lib/tool_shed/webapp/frontend/index.html b/lib/tool_shed/webapp/frontend/index.html
new file mode 100644
index 000000000000..ab7c301efc7d
--- /dev/null
+++ b/lib/tool_shed/webapp/frontend/index.html
@@ -0,0 +1,13 @@
+
+
+
+
+
+
+ Galaxy Tool Shed
+
+
+
+
+
+
diff --git a/lib/tool_shed/webapp/frontend/package.json b/lib/tool_shed/webapp/frontend/package.json
new file mode 100644
index 000000000000..ab8b86cc6b26
--- /dev/null
+++ b/lib/tool_shed/webapp/frontend/package.json
@@ -0,0 +1,54 @@
+{
+ "name": "galaxy-tool-shed",
+ "license": "MIT",
+ "version": "0.2.0",
+ "scripts": {
+ "dev": "vite --port 4040 --strict-port",
+ "build": "vue-tsc --noEmit && vite build",
+ "graphql": "graphql-codegen --watch",
+ "dev-all": "concurrently --kill-others \"npm run dev\" \"npm run graphql\"",
+ "format": "prettier --write src",
+ "typecheck": "vue-tsc --noEmit",
+ "lint": "eslint src --ext .ts,.vue"
+ },
+ "devDependencies": {
+ "@graphql-codegen/cli": "^2.16.1",
+ "@graphql-codegen/client-preset": "^1.2.3",
+ "@quasar/vite-plugin": "^1.0.4",
+ "@types/node": "^16.6.1",
+ "@typescript-eslint/eslint-plugin": "^5.47.1",
+ "@typescript-eslint/parser": "^5.47.1",
+ "@vitejs/plugin-vue": "^1.6.0",
+ "@vue/compiler-sfc": "^3.2.6",
+ "@vue/eslint-config-typescript": "^11.0.2",
+ "concurrently": "^7.6.0",
+ "eslint": "^8.30.0",
+ "eslint-config-prettier": "^8.5.0",
+ "eslint-plugin-prettier": "^4.2.1",
+ "eslint-plugin-vue": "^9.8.0",
+ "eslint-plugin-vuejs-accessibility": "^2.0.0",
+ "prettier": "^2.8.1",
+ "sass": "^1.32.0",
+ "typescript": "^4.3.2",
+ "vite": "^4.4.9",
+ "vue-eslint-parser": "^9.1.0",
+ "vue-tsc": "^1.0.16"
+ },
+ "dependencies": {
+ "@apollo/client": "^3.7.3",
+ "@quasar/extras": "^1.12.4",
+ "@vue/apollo-composable": "^4.0.0-beta.1",
+ "@vue/apollo-option": "^4.0.0-alpha.20",
+ "axios": "^1.2.1",
+ "date-fns": "^2.29.3",
+ "date-fns-tz": "^1.3.7",
+ "e": "^0.2.2",
+ "graphql": "^16.6.0",
+ "graphql-tag": "^2.12.6",
+ "openapi-typescript-fetch": "^1.1.3",
+ "pinia": "^2.0.28",
+ "quasar": "^2.5.0",
+ "vue": "^3.2.6",
+ "vue-router": "4"
+ }
+}
diff --git a/lib/tool_shed/webapp/frontend/src/App.vue b/lib/tool_shed/webapp/frontend/src/App.vue
new file mode 100644
index 000000000000..a11ce54f175e
--- /dev/null
+++ b/lib/tool_shed/webapp/frontend/src/App.vue
@@ -0,0 +1,51 @@
+
+ {
+ const conf: RawAxiosRequestConfig = {}
+ conf.validateStatus = (status: number) => {
+ const valid = status == 200 || status == 404
+ return valid
+ }
+ const { data: user, status } = await axios.get
-
-
+
@@ -73,7 +73,7 @@ ${h.javascript_link(app_root + "dist/script.js")}
$(document).ready(function (){
var config = {
dbkey: '${hda.get_metadata().dbkey}',
- href: document.location.origin,
+ href: document.location.origin + '${h.url_for( "/" )}'.replace(/\/$/, ''),
dataName: '${hda.name}',
historyID: '${trans.security.encode_id( hda.history_id )}',
datasetID: '${trans.security.encode_id( hda.id )}',
diff --git a/config/plugins/visualizations/nvd3/nvd3_bar/package.json b/config/plugins/visualizations/nvd3/nvd3_bar/package.json
index f3a30d2f9948..fc0090764f97 100644
--- a/config/plugins/visualizations/nvd3/nvd3_bar/package.json
+++ b/config/plugins/visualizations/nvd3/nvd3_bar/package.json
@@ -1,6 +1,6 @@
{
"name": "nvd3",
- "version": "0.1.0",
+ "version": "0.2.0",
"description": "NVD3 visualization plugin.",
"keywords": [
"galaxy",
@@ -9,7 +9,7 @@
],
"license": "AFL-3.0",
"dependencies": {
- "@galaxyproject/charts": "^0.0.6",
+ "@galaxyproject/charts": "^0.1.0",
"babel-preset-env": "^1.6.1",
"backbone": "^1.3.3",
"bootstrap": "^3.3.7",
diff --git a/config/plugins/visualizations/openlayers/src/script.js b/config/plugins/visualizations/openlayers/src/script.js
index 48b1dcf9faab..90922403fa7f 100644
--- a/config/plugins/visualizations/openlayers/src/script.js
+++ b/config/plugins/visualizations/openlayers/src/script.js
@@ -215,8 +215,7 @@ var MapViewer = (function(mv) {
const sourceVec = new Vector({ format: formatType, url: filePath, wrapX: false });
mv.createMap(filePath, sourceVec, options, chart, styleFunction, target);
} else if (fileType === "shp") {
- const fileUrl = prefixedDownloadUrl(options.root, filePath);
- axios.get(fileUrl, { responseType: "arraybuffer" }).then(shpfile => {
+ axios.get(filePath, { responseType: "arraybuffer" }).then(shpfile => {
console.debug(shpfile);
shp(shpfile.data).then(
geojson => {
diff --git a/config/plugins/visualizations/scatterplot/src/scatterplot.js b/config/plugins/visualizations/scatterplot/src/scatterplot.js
index 8124b8e6b580..c167d1369991 100644
--- a/config/plugins/visualizations/scatterplot/src/scatterplot.js
+++ b/config/plugins/visualizations/scatterplot/src/scatterplot.js
@@ -821,7 +821,7 @@ var ScatterplotDisplay = Backbone.View.extend({
var view = this,
config = this.model.get("config"),
//TODO: very tied to datasets - should be generalized eventually
- baseUrl = window.parent && window.parent.galaxy_config ? window.parent.galaxy_config.root : "/",
+ baseUrl = window.parent && window.parent.options ? window.parent.options.root : "/",
xhr = $.getJSON(baseUrl + "api/datasets/" + this.dataset.id, {
data_type: "raw_data",
provider: "dataset-column",
@@ -986,7 +986,7 @@ var ScatterplotDisplay = Backbone.View.extend({
}
var view = this;
var config = this.model.get("config");
- var meanWorker = new window.Worker("worker-stats.js");
+ var meanWorker = new window.Worker("./static/worker-stats.js");
meanWorker.postMessage({
data: this.data,
keys: [config.xColumn, config.yColumn]
diff --git a/config/plugins/visualizations/scatterplot/src/numeric-column-stats.js b/config/plugins/visualizations/scatterplot/static/numeric-column-stats.js
similarity index 100%
rename from config/plugins/visualizations/scatterplot/src/numeric-column-stats.js
rename to config/plugins/visualizations/scatterplot/static/numeric-column-stats.js
diff --git a/config/plugins/visualizations/scatterplot/static/scatterplot.js b/config/plugins/visualizations/scatterplot/static/scatterplot.js
index 523503e467dd..5d5f56081db4 100644
--- a/config/plugins/visualizations/scatterplot/static/scatterplot.js
+++ b/config/plugins/visualizations/scatterplot/static/scatterplot.js
@@ -1,58 +1,376 @@
-parcelRequire=function(e,r,n,t){var i="function"==typeof parcelRequire&&parcelRequire,o="function"==typeof require&&require;function u(n,t){if(!r[n]){if(!e[n]){var f="function"==typeof parcelRequire&&parcelRequire;if(!t&&f)return f(n,!0);if(i)return i(n,!0);if(o&&"string"==typeof n)return o(n);var c=new Error("Cannot find module '"+n+"'");throw c.code="MODULE_NOT_FOUND",c}p.resolve=function(r){return e[n][1][r]||r},p.cache={};var l=r[n]=new u.Module(n);e[n][0].call(l.exports,p,l,l.exports,this)}return r[n].exports;function p(e){return u(p.resolve(e))}}u.isParcelRequire=!0,u.Module=function(e){this.id=e,this.bundle=u,this.exports={}},u.modules=e,u.cache=r,u.parent=i,u.register=function(r,n){e[r]=[function(e,r){r.exports=n},{}]};for(var f=0;f
-
`;
- },
-
- /** Row Template */
- _templateRow: function (options) {
- return `
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- `;
- },
-});
diff --git a/client/src/mvc/upload/default/default-row.js b/client/src/mvc/upload/default/default-row.js
deleted file mode 100644
index 88621d805eab..000000000000
--- a/client/src/mvc/upload/default/default-row.js
+++ /dev/null
@@ -1,241 +0,0 @@
-/** Renders the default uploader rows */
-import Backbone from "backbone";
-import $ from "jquery";
-import Select from "mvc/ui/ui-select";
-import UploadExtension from "mvc/upload/upload-extension";
-import UploadBoxRow from "mvc/upload/uploadbox-row";
-import _ from "underscore";
-import Utils from "utils/utils";
-
-export default UploadBoxRow.extend({
- initialize: function (app, options) {
- var self = this;
- this.app = app;
- this.list_extensions = app.listExtensions;
- this.model = options.model;
- this.setElement(this._template(options.model));
- this.$mode = this.$(".upload-mode");
- this.$title = this.$(".upload-title");
- this.$text = this.$(".upload-text");
- this.$size = this.$(".upload-size");
- this.$info_text = this.$(".upload-info-text");
- this.$info_progress = this.$(".upload-info-progress");
- this.$text_content = this.$(".upload-text-content");
- this.$settings = this.$(".upload-settings");
- this.$symbol = this.$(".upload-symbol");
- this.$progress_bar = this.$(".upload-progress-bar");
- this.$percentage = this.$(".upload-percentage");
-
- this._setupSettings();
-
- // identify default genome and extension values
- var default_genome = this.app.genome;
- var default_extension = this.app.extension;
-
- // create select genomes
- this.select_genome = new Select.View({
- css: "upload-genome",
- data: self.app.listGenomes,
- container: this.$(".upload-genome"),
- value: default_genome,
- onchange: function (genome) {
- self.model.set("genome", genome);
- },
- });
-
- // create select extension
- this.select_extension = new Select.View({
- css: "upload-extension",
- data: self.app.extensions,
- container: this.$(".upload-extension"),
- value: default_extension,
- onchange: function (extension) {
- self.model.set("extension", extension);
- },
- });
-
- // initialize genome and extension values
- this.model.set({
- genome: default_genome,
- extension: default_extension,
- });
-
- // handle click event
- this.$symbol.on("click", () => {
- self._removeRow();
- });
-
- // handle extension info popover
- this.$(".upload-extension-info")
- .on("click", (e) => {
- const upload_ext = this.upload_extension;
- if (upload_ext) {
- if (upload_ext.extension_popup.visible) {
- upload_ext.extension_popup.hide();
- } else {
- upload_ext.extension_popup.remove();
- this._makeUploadExtensionsPopover(e);
- }
- } else {
- this._makeUploadExtensionsPopover(e);
- }
- })
- .on("mousedown", (e) => {
- e.preventDefault();
- });
-
- // handle settings popover
- this.$settings
- .on("click", (e) => {
- self._showSettings();
- })
- .on("mousedown", (e) => {
- e.preventDefault();
- });
-
- // handle text editing event
- this.$text_content.on("change input", (e) => {
- self.model.set({
- url_paste: $(e.target).val(),
- file_size: $(e.target).val().length,
- });
- });
-
- // handle text editing event
- this.$title.on("change input", (e) => {
- self.model.set({ file_name: $(e.target).val() });
- });
-
- // model events
- this._setupUploadBoxListeners();
- this.listenTo(this.model, "change:genome", () => {
- self._refreshGenome();
- });
- this.listenTo(this.model, "change:extension", () => {
- self._refreshExtension();
- });
- },
-
- render: function () {
- this._refreshType();
- this._refreshPercentage();
- this._refreshStatus();
- this._refreshInfo();
- this._refreshGenome();
- this._refreshExtension();
- this._refreshFileSize();
- },
-
- /** Remove view */
- remove: function () {
- this.select_genome.remove();
- this.select_extension.remove();
- Backbone.View.prototype.remove.apply(this);
- },
-
- /** Render type */
- _refreshType: function () {
- var options = this.model.attributes;
- this.$title.val(_.escape(options.file_name));
- this.$title.select();
- this.$size.html(Utils.bytesToString(options.file_size));
- this.$mode.removeClass().addClass("upload-mode").addClass("text-primary");
- if (options.file_mode == "new") {
- this.$text
- .css({
- width: `${this.$el.width() - 16}px`,
- top: `${this.$el.height() - 8}px`,
- })
- .show();
- this.$el.height(this.$el.height() - 8 + this.$text.height() + 16);
- this.$mode.addClass("fa fa-edit");
- } else if (options.file_mode == "local") {
- this.$mode.addClass("fa fa-laptop");
- } else if (options.file_mode == "ftp") {
- this.$mode.addClass("fa fa-folder-open-o");
- }
- },
-
- /** Update extension */
- _refreshExtension: function () {
- this.select_extension.value(this.model.get("extension"));
- },
-
- /** Update genome */
- _refreshGenome: function () {
- this.select_genome.value(this.model.get("genome"));
- },
-
- /** Refresh status */
- _refreshStatus: function () {
- var status = this.model.get("status");
- this.$symbol.removeClass().addClass("upload-symbol").addClass(this.status_classes[status]);
- this.model.set("enabled", status == "init");
- var enabled = this.model.get("enabled");
- this.$text_content.attr("disabled", !enabled);
- this.$title.attr("disabled", !enabled);
- if (enabled) {
- this.select_genome.enable();
- this.select_extension.enable();
- } else {
- this.select_genome.disable();
- this.select_extension.disable();
- }
- this.$info_progress.show();
- this.$el.removeClass().addClass("upload-row");
- this._renderStatusType(status);
- },
-
- /** Make extension popover */
- _makeUploadExtensionsPopover: function (e) {
- this.upload_extension = new UploadExtension({
- $el: $(e.target),
- title: this.select_extension.text(),
- extension: this.select_extension.value(),
- list: this.list_extensions,
- });
- },
-
- /** View template */
- _template: function (options) {
- return `
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- `;
- },
-});
diff --git a/client/src/mvc/upload/upload-extension.js b/client/src/mvc/upload/upload-extension.js
deleted file mode 100644
index 73f6095bf461..000000000000
--- a/client/src/mvc/upload/upload-extension.js
+++ /dev/null
@@ -1,39 +0,0 @@
-/** This renders a popover with extension details **/
-import Backbone from "backbone";
-import Popover from "mvc/ui/ui-popover";
-import _ from "underscore";
-
-export default Backbone.View.extend({
- initialize: function (options) {
- this.model = new Backbone.Model(options);
- this.setElement("");
- this.render();
- },
-
- render: function () {
- var options = this.model.attributes;
- var description = _.findWhere(options.list, {
- id: options.extension,
- });
- this.extension_popup && this.extension_popup.remove();
- this.extension_popup = new Popover({
- title: options.title,
- placement: options.placement || "bottom",
- container: options.$el,
- });
- this.extension_popup.show(this._templateDescription(description));
- },
-
- /** Template for extensions description */
- _templateDescription: function (options) {
- if (options.description) {
- var tmpl = options.description;
- if (options.description_url) {
- tmpl += ` (read more)`;
- }
- return tmpl;
- } else {
- return "There is no description available for this file extension.";
- }
- },
-});
diff --git a/client/src/mvc/upload/upload-ftp.js b/client/src/mvc/upload/upload-ftp.js
deleted file mode 100644
index 64468339df45..000000000000
--- a/client/src/mvc/upload/upload-ftp.js
+++ /dev/null
@@ -1,220 +0,0 @@
-/** This renders the content of the ftp popup **/
-import { getGalaxyInstance } from "app";
-import Backbone from "backbone";
-import UploadUtils from "components/Upload/utils";
-import $ from "jquery";
-import _ from "underscore";
-import Utils from "utils/utils";
-
-export default Backbone.View.extend({
- initialize: function (options) {
- this.model = new Backbone.Model({
- cls: "upload-ftp",
- class_add: "upload-icon-button fa fa-square-o",
- class_remove: "upload-icon-button fa fa-check-square-o",
- class_partial: "upload-icon-button fa fa-minus-square-o",
- help_enabled: true,
- oidc_text: `
If you are signed-in to Galaxy using a third-party identity and you do not have a Galaxy password please use the reset password option in the login form with your email to create a password for your account.`, - help_text: `This Galaxy server allows you to upload files via FTP. To upload some files, log in to the FTP server at ${options.ftp_upload_site} using your Galaxy credentials. - For help visit the tutorial.`, - collection: null, - onchange: function () {}, - onadd: function () {}, - onremove: function () {}, - }).set(options); - - this.collection = this.model.get("collection"); - const Galaxy = getGalaxyInstance(); - if (Galaxy.config.enable_oidc) { - this.model.set("help_text", this.model.get("help_text") + this.model.get("oidc_text")); - } - this.setElement(this._template()); - this.$content = this.$(".upload-ftp-content"); - this.$wait = this.$(".upload-ftp-wait"); - this.$help = this.$(".upload-ftp-help"); - this.$number = this.$(".upload-ftp-number"); - this.$disk = this.$(".upload-ftp-disk"); - this.$body = this.$(".upload-ftp-body"); - this.$warning = this.$(".upload-ftp-warning"); - this.$select = this.$(".upload-ftp-select-all"); - this.render(); - }, - - render: function () { - var self = this; - this.$wait.show(); - this.$content.hide(); - this.$warning.hide(); - this.$help.hide(); - UploadUtils.getRemoteEntries( - function (ftp_files) { - self.model.set("ftp_files", ftp_files); - self._index(); - self._renderTable(); - }, - function () { - self._renderTable(); - } - ); - }, - - /** Fill table with ftp entries */ - _renderTable: function () { - var self = this; - var ftp_files = this.model.get("ftp_files"); - this.rows = []; - if (ftp_files && ftp_files.length > 0) { - this.$body.empty(); - var size = 0; - _.each(ftp_files, (ftp_file) => { - self.rows.push(self._renderRow(ftp_file)); - size += ftp_file.size; - }); - this.$number.html(`${ftp_files.length} files`); - this.$disk.html(Utils.bytesToString(size, true)); - if (this.collection) { - this.$("._has_collection").show(); - this.$select - .addClass(this.model.get("class_add")) - .off() - .on("click", () => { - self._all(); - }); - this._refresh(); - } - this.$content.show(); - } else { - this.$warning.show(); - } - this.model.get("help_enabled") && this.$help.show(); - this.$wait.hide(); - }, - - /** Add row */ - _renderRow: function (ftp_file) { - var self = this; - var options = this.model.attributes; - var $it = $(this._templateRow(ftp_file)); - var $icon = $it.find(".icon"); - this.$body.append($it); - if (this.collection) { - var model_index = this.ftp_index[ftp_file.path]; - $icon.addClass(model_index === undefined ? options.class_add : options.class_remove); - $it.on("click", () => { - self._switch($icon, ftp_file); - self._refresh(); - }); - } else { - $it.on("click", () => { - options.onchange(ftp_file); - }); - } - return $icon; - }, - - /** Create ftp index */ - _index: function () { - var self = this; - this.ftp_index = {}; - this.collection && - this.collection.each((model) => { - if (model.get("file_mode") == "ftp") { - self.ftp_index[model.get("file_path")] = model.id; - } - }); - }, - - /** Select all event handler */ - _all: function () { - var options = this.model.attributes; - var ftp_files = this.model.get("ftp_files"); - var add = this.$select.hasClass(options.class_add); - for (var index in ftp_files) { - var ftp_file = ftp_files[index]; - var model_index = this.ftp_index[ftp_file.path]; - if ((model_index === undefined && add) || (model_index !== undefined && !add)) { - this._switch(this.rows[index], ftp_file); - } - } - this._refresh(); - }, - - /** Handle collection changes */ - _switch: function ($icon, ftp_file) { - $icon.removeClass(); - var options = this.model.attributes; - var model_index = this.ftp_index[ftp_file.path]; - if (model_index === undefined) { - var new_index = options.onadd(ftp_file); - $icon.addClass(options.class_remove); - this.ftp_index[ftp_file.path] = new_index; - } else { - options.onremove(model_index); - $icon.addClass(options.class_add); - delete this.ftp_index[ftp_file.path]; - } - }, - - /** Refresh select all button state */ - _refresh: function () { - var counts = _.reduce( - this.ftp_index, - (memo, element) => { - element !== undefined && memo++; - return memo; - }, - 0 - ); - this.$select.removeClass(); - if (counts == 0) { - this.$select.addClass(this.model.get("class_add")); - } else { - this.$select.addClass( - counts == this.rows.length ? this.model.get("class_remove") : this.model.get("class_partial") - ); - } - }, - - /** Template of row */ - _templateRow: function (options) { - return `
-
- ${_.escape(options.path)}
- ${Utils.bytesToString(options.size)}
- ${options.ctime}
- `;
- },
-
- /** Template of main view */
- _template: function () {
- return `
").addClass("upload-settings-table grid").append(""));
- this.$cover = this.$(".upload-settings-cover");
- this.$table = this.$(".upload-settings-table > tbody");
- this.listenTo(this.model, "change", this.render, this);
- this.model.trigger("change");
- },
-
- render: function () {
- var self = this;
- this.$table.empty();
- _.each(this.options.parameters, (parameter) => {
- var $checkbox = $("")
- .addClass(`upload-${parameter.id} fa`)
- .addClass((self.model.get(parameter.id) && self.options.class_check) || self.options.class_uncheck);
- const $row = $(";
+ /**
+ * Total disk usage
+ * @description Size of all non-purged, unique datasets of the user in bytes.
+ */
+ total_disk_usage: number;
+ };
/**
* ArchiveHistoryRequestPayload
* @description Base model definition with common configuration used by all derived models.
@@ -2132,6 +2212,63 @@ export interface components {
*/
variant: components["schemas"]["NotificationVariant"];
};
+ /**
+ * BrowsableFilesSourcePlugin
+ * @description Base model definition with common configuration used by all derived models.
+ */
+ BrowsableFilesSourcePlugin: {
+ /**
+ * Browsable
+ * @enum {boolean}
+ */
+ browsable: true;
+ /**
+ * Documentation
+ * @description Documentation or extended description for this plugin.
+ * @example Galaxy's library import directory
+ */
+ doc: string;
+ /**
+ * ID
+ * @description The `FilesSource` plugin identifier
+ * @example _import
+ */
+ id: string;
+ /**
+ * Label
+ * @description The display label for this plugin.
+ * @example Library Import Directory
+ */
+ label: string;
+ /**
+ * Requires groups
+ * @description Only users belonging to the groups specified here can access this files source.
+ */
+ requires_groups?: string;
+ /**
+ * Requires roles
+ * @description Only users with the roles specified here can access this files source.
+ */
+ requires_roles?: string;
+ /**
+ * Type
+ * @description The type of the plugin.
+ * @example gximport
+ */
+ type: string;
+ /**
+ * URI root
+ * @description The URI root used by this type of plugin.
+ * @example gximport://
+ */
+ uri_root: string;
+ /**
+ * Writeable
+ * @description Whether this files source plugin allows write access.
+ * @example false
+ */
+ writable: boolean;
+ };
/**
* BulkOperationItemError
* @description Base model definition with common configuration used by all derived models.
@@ -2522,6 +2659,23 @@ export interface components {
ConvertedDatasetsMap: {
[key: string]: string | undefined;
};
+ /**
+ * CreateEntryPayload
+ * @description Base model definition with common configuration used by all derived models.
+ */
+ CreateEntryPayload: {
+ /**
+ * Name
+ * @description The name of the entry to create.
+ * @example my_new_entry
+ */
+ name: string;
+ /**
+ * Target
+ * @description The target file source to create the entry in.
+ */
+ target: string;
+ };
/**
* CreateHistoryContentFromStore
* @description Base model definition with common configuration used by all derived models.
@@ -2554,8 +2708,8 @@ export interface components {
content?: string | string;
/**
* Copy Elements
- * @description If the source is a collection, whether to copy child HDAs into the target history as well, defaults to False but this is less than ideal and may be changed in future releases.
- * @default false
+ * @description If the source is a collection, whether to copy child HDAs into the target history as well. Prior to the galaxy release 23.1 this defaulted to false.
+ * @default true
*/
copy_elements?: boolean;
/**
@@ -2725,7 +2879,7 @@ export interface components {
/**
* Copy Elements
* @description Whether to create a copy of the source HDAs for the new collection.
- * @default false
+ * @default true
*/
copy_elements?: boolean;
/**
@@ -2893,6 +3047,159 @@ export interface components {
*/
url: string;
};
+ /**
+ * CreatedEntryResponse
+ * @description Base model definition with common configuration used by all derived models.
+ */
+ CreatedEntryResponse: {
+ /**
+ * External link
+ * @description An optional external link to the created entry if available.
+ */
+ external_link?: string;
+ /**
+ * Name
+ * @description The name of the created entry.
+ * @example my_new_entry
+ */
+ name: string;
+ /**
+ * URI
+ * @description The URI of the created entry.
+ * @example gxfiles://my_new_entry
+ */
+ uri: string;
+ };
+ /**
+ * CreatedUserModel
+ * @description User in a transaction context.
+ */
+ CreatedUserModel: {
+ /**
+ * Active
+ * @description User is active
+ */
+ active: boolean;
+ /**
+ * Deleted
+ * @description User is deleted
+ */
+ deleted: boolean;
+ /**
+ * Email
+ * @description Email of the user
+ */
+ email: string;
+ /**
+ * ID
+ * @description Encoded ID of the user
+ * @example 0123456789ABCDEF
+ */
+ id: string;
+ /**
+ * Last password change
+ * Format: date-time
+ */
+ last_password_change?: string;
+ /**
+ * Model class
+ * @description The name of the database model class.
+ * @default User
+ * @enum {string}
+ */
+ model_class: "User";
+ /**
+ * Nice total disc usage
+ * @description Size of all non-purged, unique datasets of the user in a nice format.
+ */
+ nice_total_disk_usage: string;
+ /**
+ * Preferred Object Store ID
+ * @description The ID of the object store that should be used to store new datasets in this history.
+ */
+ preferred_object_store_id?: string;
+ /**
+ * Total disk usage
+ * @description Size of all non-purged, unique datasets of the user in bytes.
+ */
+ total_disk_usage: number;
+ /**
+ * user_name
+ * @description The name of the user.
+ */
+ username: string;
+ };
+ /**
+ * CustomBuildCreationPayload
+ * @description Base model definition with common configuration used by all derived models.
+ */
+ CustomBuildCreationPayload: {
+ /**
+ * Length type
+ * @description The type of the len file.
+ */
+ "len|type": components["schemas"]["CustomBuildLenType"];
+ /**
+ * Length value
+ * @description The content of the length file.
+ */
+ "len|value": string;
+ /**
+ * Name
+ * @description The name of the custom build.
+ */
+ name: string;
+ };
+ /**
+ * CustomBuildLenType
+ * @description An enumeration.
+ * @enum {string}
+ */
+ CustomBuildLenType: "file" | "fasta" | "text";
+ /**
+ * CustomBuildModel
+ * @description Base model definition with common configuration used by all derived models.
+ */
+ CustomBuildModel: {
+ /**
+ * Count
+ * @description The number of chromosomes/contigs.
+ */
+ count?: string;
+ /**
+ * Fasta
+ * @description The primary id of the fasta file from a history.
+ * @example 0123456789ABCDEF
+ */
+ fasta?: string;
+ /**
+ * ID
+ * @description The ID of the custom build.
+ */
+ id: string;
+ /**
+ * Length
+ * @description The primary id of the len file.
+ * @example 0123456789ABCDEF
+ */
+ len: string;
+ /**
+ * Line count
+ * @description The primary id of a linecount dataset.
+ * @example 0123456789ABCDEF
+ */
+ linecount?: string;
+ /**
+ * Name
+ * @description The name of the custom build.
+ */
+ name: string;
+ };
+ /**
+ * CustomBuildsCollection
+ * @description The custom builds associated with the user.
+ */
+ CustomBuildsCollection: components["schemas"]["CustomBuildModel"][];
/**
* CustomBuildsMetadataResponse
* @description Base model definition with common configuration used by all derived models.
@@ -3426,6 +3733,11 @@ export interface components {
* @example bed
*/
extension: string;
+ /**
+ * Upload warning
+ * @description End-user information regarding potential pitfalls with this upload type.
+ */
+ upload_warning?: string;
};
/** DatatypeEDAMDetails */
DatatypeEDAMDetails: {
@@ -3635,65 +3947,153 @@ export interface components {
purge?: boolean;
};
/**
- * DisplayApp
- * @description Basic linked information about an application that can display certain datatypes.
+ * DeletedCustomBuild
+ * @description Base model definition with common configuration used by all derived models.
*/
- DisplayApp: {
- /**
- * Label
- * @description The label or title of the Display Application.
- */
- label: string;
+ DeletedCustomBuild: {
/**
- * Links
- * @description The collection of link details for this Display Application.
+ * Deletion message
+ * @description Confirmation of the custom build deletion.
*/
- links: components["schemas"]["Hyperlink"][];
- };
- /** DisplayApplication */
- DisplayApplication: {
- /** Filename */
- filename_: string;
- /** Id */
- id: string;
- /** Links */
- links: components["schemas"]["Link"][];
- /** Name */
- name: string;
- /** Version */
- version: string;
+ message: string;
};
/**
- * ElementsFromType
- * @description An enumeration.
- * @enum {string}
- */
- ElementsFromType: "archive" | "bagit" | "bagit_archive" | "directory";
- /**
- * EncodedDatasetSourceId
+ * DetailedUserModel
* @description Base model definition with common configuration used by all derived models.
*/
- EncodedDatasetSourceId: {
+ DetailedUserModel: {
+ /**
+ * Deleted
+ * @description User is deleted
+ */
+ deleted: boolean;
+ /**
+ * Email
+ * @description Email of the user
+ */
+ email: string;
/**
* ID
- * @description The encoded ID of this entity.
+ * @description Encoded ID of the user
* @example 0123456789ABCDEF
*/
id: string;
/**
- * Source
- * @description The source of this dataset, either `hda` or `ldda` depending of its origin.
+ * Is admin
+ * @description User is admin
*/
- src: components["schemas"]["DatasetSourceType"];
- };
- /**
- * EncodedHistoryContentItem
- * @description Identifies a dataset or collection contained in a History.
- */
- EncodedHistoryContentItem: {
+ is_admin: boolean;
/**
- * Content Type
- * @description The type of this item.
+ * Nice total disc usage
+ * @description Size of all non-purged, unique datasets of the user in a nice format.
+ */
+ nice_total_disk_usage: string;
+ /**
+ * Preferences
+ * @description Preferences of the user
+ */
+ preferences: Record;
+ /**
+ * Preferred Object Store ID
+ * @description The ID of the object store that should be used to store new datasets in this history.
+ */
+ preferred_object_store_id?: string;
+ /**
+ * Purged
+ * @description User is purged
+ */
+ purged: boolean;
+ /**
+ * Quota
+ * @description Quota applicable to the user
+ */
+ quota: string;
+ /**
+ * Quota in bytes
+ * @description Quota applicable to the user in bytes.
+ */
+ quota_bytes: Record;
+ /**
+ * Quota percent
+ * @description Percentage of the storage quota applicable to the user.
+ */
+ quota_percent?: Record;
+ /**
+ * Tags used
+ * @description Tags used by the user
+ */
+ tags_used: string[];
+ /**
+ * Total disk usage
+ * @description Size of all non-purged, unique datasets of the user in bytes.
+ */
+ total_disk_usage: number;
+ /**
+ * user_name
+ * @description The name of the user.
+ */
+ username: string;
+ };
+ /**
+ * DisplayApp
+ * @description Basic linked information about an application that can display certain datatypes.
+ */
+ DisplayApp: {
+ /**
+ * Label
+ * @description The label or title of the Display Application.
+ */
+ label: string;
+ /**
+ * Links
+ * @description The collection of link details for this Display Application.
+ */
+ links: components["schemas"]["Hyperlink"][];
+ };
+ /** DisplayApplication */
+ DisplayApplication: {
+ /** Filename */
+ filename_: string;
+ /** Id */
+ id: string;
+ /** Links */
+ links: components["schemas"]["Link"][];
+ /** Name */
+ name: string;
+ /** Version */
+ version: string;
+ };
+ /**
+ * ElementsFromType
+ * @description An enumeration.
+ * @enum {string}
+ */
+ ElementsFromType: "archive" | "bagit" | "bagit_archive" | "directory";
+ /**
+ * EncodedDatasetSourceId
+ * @description Base model definition with common configuration used by all derived models.
+ */
+ EncodedDatasetSourceId: {
+ /**
+ * ID
+ * @description The encoded ID of this entity.
+ * @example 0123456789ABCDEF
+ */
+ id: string;
+ /**
+ * Source
+ * @description The source of this dataset, either `hda` or `ldda` depending of its origin.
+ */
+ src: components["schemas"]["DatasetSourceType"];
+ };
+ /**
+ * EncodedHistoryContentItem
+ * @description Identifies a dataset or collection contained in a History.
+ */
+ EncodedHistoryContentItem: {
+ /**
+ * Content Type
+ * @description The type of this item.
*/
history_content_type: components["schemas"]["HistoryContentType"];
/**
@@ -3836,6 +4236,34 @@ export interface components {
items_from?: string;
src: components["schemas"]["Src"];
};
+ /**
+ * FavoriteObject
+ * @description Base model definition with common configuration used by all derived models.
+ */
+ FavoriteObject: {
+ /**
+ * Object ID
+ * @description The id of an object the user wants to favorite.
+ */
+ object_id: string;
+ };
+ /**
+ * FavoriteObjectType
+ * @description An enumeration.
+ * @enum {string}
+ */
+ FavoriteObjectType: "tools";
+ /**
+ * FavoriteObjectsSummary
+ * @description Base model definition with common configuration used by all derived models.
+ */
+ FavoriteObjectsSummary: {
+ /**
+ * Favorite tools
+ * @description The name of the tools the user favored.
+ */
+ tools: string[];
+ };
/**
* FetchDataPayload
* @description Base model definition with common configuration used by all derived models.
@@ -3961,8 +4389,7 @@ export interface components {
* @description The current state of this dataset.
*/
state: components["schemas"]["DatasetState"];
- /** Tags */
- tags: string;
+ tags: components["schemas"]["TagCollection"];
/**
* Type
* @enum {string}
@@ -3980,6 +4407,11 @@ export interface components {
* @description Base model definition with common configuration used by all derived models.
*/
FilesSourcePlugin: {
+ /**
+ * Browsable
+ * @description Whether this file source plugin can list items.
+ */
+ browsable: boolean;
/**
* Documentation
* @description Documentation or extended description for this plugin.
@@ -4014,12 +4446,6 @@ export interface components {
* @example gximport
*/
type: string;
- /**
- * URI root
- * @description The URI root used by this type of plugin.
- * @example gximport://
- */
- uri_root?: string;
/**
* Writeable
* @description Whether this files source plugin allows write access.
@@ -4043,7 +4469,10 @@ export interface components {
* }
* ]
*/
- FilesSourcePluginList: components["schemas"]["FilesSourcePlugin"][];
+ FilesSourcePluginList: (
+ | components["schemas"]["BrowsableFilesSourcePlugin"]
+ | components["schemas"]["FilesSourcePlugin"]
+ )[];
/**
* FolderLibraryFolderItem
* @description Base model definition with common configuration used by all derived models.
@@ -4378,10 +4807,11 @@ export interface components {
*/
hid: number;
/**
- * Content Type
- * @description The type of this item.
+ * History Content Type
+ * @description This is always `dataset` for datasets.
+ * @enum {string}
*/
- history_content_type: components["schemas"]["HistoryContentType"];
+ history_content_type: "dataset";
/**
* History ID
* @description The encoded ID of the history associated with this item.
@@ -4592,10 +5022,11 @@ export interface components {
*/
hid: number;
/**
- * Content Type
- * @description The type of this item.
+ * History Content Type
+ * @description This is always `dataset` for datasets.
+ * @enum {string}
*/
- history_content_type: components["schemas"]["HistoryContentType"];
+ history_content_type: "dataset";
/**
* History ID
* @description The encoded ID of the history associated with this item.
@@ -4707,10 +5138,11 @@ export interface components {
*/
hid: number;
/**
- * Content Type
- * @description The type of this item.
+ * History Content Type
+ * @description This is always `dataset_collection` for dataset collections.
+ * @enum {string}
*/
- history_content_type: components["schemas"]["HistoryContentType"];
+ history_content_type: "dataset_collection";
/**
* History ID
* @description The encoded ID of the history associated with this item.
@@ -4841,10 +5273,11 @@ export interface components {
*/
hid: number;
/**
- * Content Type
- * @description The type of this item.
+ * History Content Type
+ * @description This is always `dataset_collection` for dataset collections.
+ * @enum {string}
*/
- history_content_type: components["schemas"]["HistoryContentType"];
+ history_content_type: "dataset_collection";
/**
* History ID
* @description The encoded ID of the history associated with this item.
@@ -6430,11 +6863,40 @@ export interface components {
*/
url: string;
};
+ /**
+ * LimitedUserModel
+ * @description This is used when config options (expose_user_name and expose_user_email) are in place.
+ */
+ LimitedUserModel: {
+ /** Email */
+ email?: string;
+ /**
+ * ID
+ * @description Encoded ID of the user
+ * @example 0123456789ABCDEF
+ */
+ id: string;
+ /** Username */
+ username?: string;
+ };
/** Link */
Link: {
/** Name */
name: string;
};
+ /**
+ * ListJstreeResponse
+ * @deprecated
+ * @description List of files in Jstree format.
+ * @default []
+ */
+ ListJstreeResponse: Record[];
+ /**
+ * ListUriResponse
+ * @description List of directories and files.
+ * @default []
+ */
+ ListUriResponse: (components["schemas"]["RemoteFile"] | components["schemas"]["RemoteDirectory"])[];
/**
* MandatoryNotificationCategory
* @description These notification categories cannot be opt-out by the user.
@@ -6452,7 +6914,7 @@ export interface components {
* Content
* @description Depending on the `source` it can be:
* - The encoded id of the source library dataset
- * - The encoded id of the the HDA
+ * - The encoded id of the HDA
*
* @example 0123456789ABCDEF
*/
@@ -7366,6 +7828,12 @@ export interface components {
* @enum {string}
*/
PersonalNotificationCategory: "message" | "new_shared_item";
+ /**
+ * PluginKind
+ * @description Enum to distinguish between different kinds or categories of plugins.
+ * @enum {string}
+ */
+ PluginKind: "rfs" | "drs" | "rdm" | "stock";
/**
* PrepareStoreDownloadPayload
* @description Base model definition with common configuration used by all derived models.
@@ -7558,6 +8026,68 @@ export interface components {
/** Reloaded */
reloaded: string[];
};
+ /**
+ * RemoteDirectory
+ * @description Base model definition with common configuration used by all derived models.
+ */
+ RemoteDirectory: {
+ /**
+ * Class
+ * @enum {string}
+ */
+ class: "Directory";
+ /**
+ * Name
+ * @description The name of the entry.
+ */
+ name: string;
+ /**
+ * Path
+ * @description The path of the entry.
+ */
+ path: string;
+ /**
+ * URI
+ * @description The URI of the entry.
+ */
+ uri: string;
+ };
+ /**
+ * RemoteFile
+ * @description Base model definition with common configuration used by all derived models.
+ */
+ RemoteFile: {
+ /**
+ * Class
+ * @enum {string}
+ */
+ class: "File";
+ /**
+ * Creation time
+ * @description The creation time of the file.
+ */
+ ctime: string;
+ /**
+ * Name
+ * @description The name of the entry.
+ */
+ name: string;
+ /**
+ * Path
+ * @description The path of the entry.
+ */
+ path: string;
+ /**
+ * Size
+ * @description The size of the file in bytes.
+ */
+ size: number;
+ /**
+ * URI
+ * @description The URI of the entry.
+ */
+ uri: string;
+ };
/**
* RemoteFilesDisableMode
* @description An enumeration.
@@ -7570,6 +8100,17 @@ export interface components {
* @enum {string}
*/
RemoteFilesFormat: "flat" | "jstree" | "uri";
+ /**
+ * RemoteUserCreationPayload
+ * @description Base model definition with common configuration used by all derived models.
+ */
+ RemoteUserCreationPayload: {
+ /**
+ * Email
+ * @description Email of the user
+ */
+ remote_user_email: string;
+ };
/**
* RequestDataType
* @description Particular pieces of information that can be requested for a dataset.
@@ -8126,6 +8667,11 @@ export interface components {
/**
* TagCollection
* @description The collection of tags associated with an item.
+ * @example [
+ * "COVID-19",
+ * "#myFancyTag",
+ * "covid19.galaxyproject.org"
+ * ]
*/
TagCollection: string[];
/**
@@ -8146,14 +8692,17 @@ export interface components {
TaggableItemClass:
| "History"
| "HistoryDatasetAssociation"
+ | "HistoryDatasetCollectionAssociation"
| "LibraryDatasetDatasetAssociation"
| "Page"
- | "WorkflowStep"
| "StoredWorkflow"
- | "Visualization"
- | "HistoryDatasetCollection"
- | "LibraryDatasetCollection"
- | "Tool";
+ | "Visualization";
+ /**
+ * TaskState
+ * @description Enum representing the possible states of a task.
+ * @enum {string}
+ */
+ TaskState: "PENDING" | "STARTED" | "RETRY" | "FAILURE" | "SUCCESS";
/** ToolDataDetails */
ToolDataDetails: {
/**
@@ -8623,6 +9172,38 @@ export interface components {
*/
enabled: boolean;
};
+ /**
+ * UserCreationPayload
+ * @description Base model definition with common configuration used by all derived models.
+ */
+ UserCreationPayload: {
+ /**
+ * Email
+ * @description Email of the user
+ */
+ email: string;
+ /**
+ * user_password
+ * @description The password of the user.
+ */
+ password: string;
+ /**
+ * user_name
+ * @description The name of the user.
+ */
+ username: string;
+ };
+ /**
+ * UserDeletionPayload
+ * @description Base model definition with common configuration used by all derived models.
+ */
+ UserDeletionPayload: {
+ /**
+ * Purge user
+ * @description Purge the user
+ */
+ purge: boolean;
+ };
/**
* UserEmail
* @description Base model definition with common configuration used by all derived models.
@@ -8652,17 +9233,17 @@ export interface components {
active: boolean;
/**
* Deleted
- * @description User is deleted
+ * @description User is deleted
*/
deleted: boolean;
/**
* Email
- * @description User email
+ * @description Email of the user
*/
email: string;
/**
* ID
- * @description User ID
+ * @description Encoded ID of the user
* @example 0123456789ABCDEF
*/
id: string;
@@ -8679,8 +9260,8 @@ export interface components {
*/
model_class: "User";
/**
- * Username
- * @description User username
+ * user_name
+ * @description The name of the user.
*/
username: string;
};
@@ -9387,7 +9968,7 @@ export interface operations {
/** @description Successful Response */
200: {
content: {
- "application/json": components["schemas"]["HDCADetailed"] | components["schemas"]["HDCASummary"];
+ "application/json": components["schemas"]["HDCADetailed"];
};
};
/** @description Validation Error */
@@ -10671,11 +11252,13 @@ export interface operations {
/** @description The requested format of returned data. Either `flat` to simply list all the files, `jstree` to get a tree representation of the files, or the default `uri` to list files and directories by their URI. */
/** @description Wether to recursively lists all sub-directories. This will be `True` by default depending on the `target`. */
/** @description (This only applies when `format` is `jstree`) The value can be either `folders` or `files` and it will disable the corresponding nodes of the tree. */
+ /** @description Whether the query is made with the intention of writing to the source. If set to True, only entries that can be written to will be returned. */
query?: {
target?: string;
format?: components["schemas"]["RemoteFilesFormat"];
recursive?: boolean;
disable?: components["schemas"]["RemoteFilesDisableMode"];
+ writeable?: boolean;
};
/** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
header?: {
@@ -10686,7 +11269,9 @@ export interface operations {
/** @description Successful Response */
200: {
content: {
- "application/json": Record[];
+ "application/json":
+ | components["schemas"]["ListUriResponse"]
+ | components["schemas"]["ListJstreeResponse"];
};
};
/** @description Validation Error */
@@ -12976,7 +13561,7 @@ export interface operations {
header?: {
"run-as"?: string;
};
- /** @description The ID of the History. */
+ /** @description History ID or any string. */
/** @description The ID of the item (`HDA`/`HDCA`) contained in the history. */
/**
* @description The type of the target history element.
@@ -15628,11 +16213,13 @@ export interface operations {
/** @description The requested format of returned data. Either `flat` to simply list all the files, `jstree` to get a tree representation of the files, or the default `uri` to list files and directories by their URI. */
/** @description Wether to recursively lists all sub-directories. This will be `True` by default depending on the `target`. */
/** @description (This only applies when `format` is `jstree`) The value can be either `folders` or `files` and it will disable the corresponding nodes of the tree. */
+ /** @description Whether the query is made with the intention of writing to the source. If set to True, only entries that can be written to will be returned. */
query?: {
target?: string;
format?: components["schemas"]["RemoteFilesFormat"];
recursive?: boolean;
disable?: components["schemas"]["RemoteFilesDisableMode"];
+ writeable?: boolean;
};
/** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
header?: {
@@ -15643,7 +16230,9 @@ export interface operations {
/** @description A list with details about the remote files available to the user. */
200: {
content: {
- "application/json": Record[];
+ "application/json":
+ | components["schemas"]["ListUriResponse"]
+ | components["schemas"]["ListJstreeResponse"];
};
};
/** @description Validation Error */
@@ -15654,26 +16243,27 @@ export interface operations {
};
};
};
- plugins_api_remote_files_plugins_get: {
+ create_entry_api_remote_files_post: {
/**
- * Display plugin information for each of the gxfiles:// URI targets available.
- * @description Display plugin information for each of the gxfiles:// URI targets available.
+ * Creates a new entry (directory/record) on the remote files source.
+ * @description Creates a new entry on the remote files source.
*/
parameters?: {
- /** @description Whether to return browsable filesources only. The default is `True`, which will omit filesourceslike `http` and `base64` that do not implement a list method. */
- query?: {
- browsable_only?: boolean;
- };
/** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
header?: {
"run-as"?: string;
};
};
+ requestBody: {
+ content: {
+ "application/json": components["schemas"]["CreateEntryPayload"];
+ };
+ };
responses: {
- /** @description A list with details about each plugin. */
+ /** @description Successful Response */
200: {
content: {
- "application/json": components["schemas"]["FilesSourcePluginList"];
+ "application/json": components["schemas"]["CreatedEntryResponse"];
};
};
/** @description Validation Error */
@@ -15684,12 +16274,46 @@ export interface operations {
};
};
};
- index_api_roles_get: {
- /** Index */
- parameters?: {
- /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
- header?: {
- "run-as"?: string;
+ plugins_api_remote_files_plugins_get: {
+ /**
+ * Display plugin information for each of the gxfiles:// URI targets available.
+ * @description Display plugin information for each of the gxfiles:// URI targets available.
+ */
+ parameters?: {
+ /** @description Whether to return browsable filesources only. The default is `True`, which will omit filesourceslike `http` and `base64` that do not implement a list method. */
+ /** @description Whether to return **only** filesources of the specified kind. The default is `None`, which will return all filesources. Multiple values can be specified by repeating the parameter. */
+ /** @description Whether to exclude filesources of the specified kind from the list. The default is `None`, which will return all filesources. Multiple values can be specified by repeating the parameter. */
+ query?: {
+ browsable_only?: boolean;
+ include_kind?: components["schemas"]["PluginKind"][];
+ exclude_kind?: components["schemas"]["PluginKind"][];
+ };
+ /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+ header?: {
+ "run-as"?: string;
+ };
+ };
+ responses: {
+ /** @description A list with details about each plugin. */
+ 200: {
+ content: {
+ "application/json": components["schemas"]["FilesSourcePluginList"];
+ };
+ };
+ /** @description Validation Error */
+ 422: {
+ content: {
+ "application/json": components["schemas"]["HTTPValidationError"];
+ };
+ };
+ };
+ };
+ index_api_roles_get: {
+ /** Index */
+ parameters?: {
+ /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+ header?: {
+ "run-as"?: string;
};
};
responses: {
@@ -16068,7 +16692,7 @@ export interface operations {
/** @description String indicating task state. */
200: {
content: {
- "application/json": string;
+ "application/json": components["schemas"]["TaskState"];
};
};
/** @description Validation Error */
@@ -16485,6 +17109,75 @@ export interface operations {
};
};
};
+ get_users_api_users_get: {
+ /**
+ * Get Users
+ * @description Return a collection of users. Filters will only work if enabled in config or user is admin.
+ */
+ parameters?: {
+ /** @description Indicates if the collection will be about deleted users */
+ /** @description An email address to filter on */
+ /** @description An username address to filter on */
+ /** @description Filter on username OR email */
+ query?: {
+ deleted?: boolean;
+ f_email?: string;
+ f_name?: string;
+ f_any?: string;
+ };
+ /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+ header?: {
+ "run-as"?: string;
+ };
+ };
+ responses: {
+ /** @description Successful Response */
+ 200: {
+ content: {
+ "application/json": (
+ | components["schemas"]["UserModel"]
+ | components["schemas"]["LimitedUserModel"]
+ )[];
+ };
+ };
+ /** @description Validation Error */
+ 422: {
+ content: {
+ "application/json": components["schemas"]["HTTPValidationError"];
+ };
+ };
+ };
+ };
+ create_user_api_users_post: {
+ /** Create a new Galaxy user. Only admins can create users for now. */
+ parameters?: {
+ /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+ header?: {
+ "run-as"?: string;
+ };
+ };
+ requestBody: {
+ content: {
+ "application/json":
+ | components["schemas"]["UserCreationPayload"]
+ | components["schemas"]["RemoteUserCreationPayload"];
+ };
+ };
+ responses: {
+ /** @description Successful Response */
+ 200: {
+ content: {
+ "application/json": components["schemas"]["CreatedUserModel"];
+ };
+ };
+ /** @description Validation Error */
+ 422: {
+ content: {
+ "application/json": components["schemas"]["HTTPValidationError"];
+ };
+ };
+ };
+ };
recalculate_disk_usage_api_users_current_recalculate_disk_usage_put: {
/**
* Triggers a recalculation of the current user disk usage.
@@ -16515,6 +17208,99 @@ export interface operations {
};
};
};
+ get_deleted_users_api_users_deleted_get: {
+ /**
+ * Get Deleted Users
+ * @description Return a collection of deleted users. Only admins can see deleted users.
+ */
+ parameters?: {
+ /** @description An email address to filter on */
+ /** @description An username address to filter on */
+ /** @description Filter on username OR email */
+ query?: {
+ f_email?: string;
+ f_name?: string;
+ f_any?: string;
+ };
+ /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+ header?: {
+ "run-as"?: string;
+ };
+ };
+ responses: {
+ /** @description Successful Response */
+ 200: {
+ content: {
+ "application/json": (
+ | components["schemas"]["UserModel"]
+ | components["schemas"]["LimitedUserModel"]
+ )[];
+ };
+ };
+ /** @description Validation Error */
+ 422: {
+ content: {
+ "application/json": components["schemas"]["HTTPValidationError"];
+ };
+ };
+ };
+ };
+ get_deleted_user_api_users_deleted__user_id__get: {
+ /** Return information about a deleted user. Only admins can see deleted users. */
+ parameters: {
+ /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+ header?: {
+ "run-as"?: string;
+ };
+ /** @description The ID of the user to get. */
+ path: {
+ user_id: string;
+ };
+ };
+ responses: {
+ /** @description Successful Response */
+ 200: {
+ content: {
+ "application/json":
+ | components["schemas"]["DetailedUserModel"]
+ | components["schemas"]["AnonUserModel"];
+ };
+ };
+ /** @description Validation Error */
+ 422: {
+ content: {
+ "application/json": components["schemas"]["HTTPValidationError"];
+ };
+ };
+ };
+ };
+ undelete_user_api_users_deleted__user_id__undelete_post: {
+ /** Restore a deleted user. Only admins can restore users. */
+ parameters: {
+ /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+ header?: {
+ "run-as"?: string;
+ };
+ /** @description The ID of the user to get. */
+ path: {
+ user_id: string;
+ };
+ };
+ responses: {
+ /** @description Successful Response */
+ 200: {
+ content: {
+ "application/json": components["schemas"]["DetailedUserModel"];
+ };
+ };
+ /** @description Validation Error */
+ 422: {
+ content: {
+ "application/json": components["schemas"]["HTTPValidationError"];
+ };
+ };
+ };
+ };
recalculate_disk_usage_api_users_recalculate_disk_usage_put: {
/**
* Triggers a recalculation of the current user disk usage.
@@ -16546,6 +17332,107 @@ export interface operations {
};
};
};
+ get_user_api_users__user_id__get: {
+ /** Return information about a specified or the current user. Only admin can see deleted or other users */
+ parameters: {
+ /** @description Indicates if the user is deleted */
+ query?: {
+ deleted?: boolean;
+ };
+ /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+ header?: {
+ "run-as"?: string;
+ };
+ /** @description The ID of the user to get or 'current'. */
+ path: {
+ user_id: string | "current";
+ };
+ };
+ responses: {
+ /** @description Successful Response */
+ 200: {
+ content: {
+ "application/json":
+ | components["schemas"]["DetailedUserModel"]
+ | components["schemas"]["AnonUserModel"];
+ };
+ };
+ /** @description Validation Error */
+ 422: {
+ content: {
+ "application/json": components["schemas"]["HTTPValidationError"];
+ };
+ };
+ };
+ };
+ update_user_api_users__user_id__put: {
+ /** Update the values of a user. Only admin can update others. */
+ parameters: {
+ /** @description Indicates if the user is deleted */
+ query?: {
+ deleted?: boolean;
+ };
+ /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+ header?: {
+ "run-as"?: string;
+ };
+ /** @description The ID of the user to get or 'current'. */
+ path: {
+ user_id: string | "current";
+ };
+ };
+ requestBody: {
+ content: {
+ "application/json": Record;
+ };
+ };
+ responses: {
+ /** @description Successful Response */
+ 200: {
+ content: {
+ "application/json": components["schemas"]["DetailedUserModel"];
+ };
+ };
+ /** @description Validation Error */
+ 422: {
+ content: {
+ "application/json": components["schemas"]["HTTPValidationError"];
+ };
+ };
+ };
+ };
+ delete_user_api_users__user_id__delete: {
+ /** Delete a user. Only admins can delete others or purge users. */
+ parameters: {
+ /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+ header?: {
+ "run-as"?: string;
+ };
+ /** @description The ID of the user to get. */
+ path: {
+ user_id: string;
+ };
+ };
+ requestBody?: {
+ content: {
+ "application/json": components["schemas"]["UserDeletionPayload"];
+ };
+ };
+ responses: {
+ /** @description Successful Response */
+ 200: {
+ content: {
+ "application/json": components["schemas"]["DetailedUserModel"];
+ };
+ };
+ /** @description Validation Error */
+ 422: {
+ content: {
+ "application/json": components["schemas"]["HTTPValidationError"];
+ };
+ };
+ };
+ };
get_or_create_api_key_api_users__user_id__api_key_get: {
/** Return the user's API key */
parameters: {
@@ -16574,7 +17461,7 @@ export interface operations {
};
};
create_api_key_api_users__user_id__api_key_post: {
- /** Creates a new API key for the user */
+ /** Create a new API key for the user */
parameters: {
/** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
header?: {
@@ -16652,9 +17539,9 @@ export interface operations {
};
};
};
- get_beacon_api_users__user_id__beacon_get: {
+ get_beacon_settings_api_users__user_id__beacon_get: {
/**
- * Returns information about beacon share settings
+ * Return information about beacon share settings
* @description **Warning**: This endpoint is experimental and might change or disappear in future versions.
*/
parameters: {
@@ -16682,9 +17569,9 @@ export interface operations {
};
};
};
- set_beacon_api_users__user_id__beacon_post: {
+ set_beacon_settings_api_users__user_id__beacon_post: {
/**
- * Changes beacon setting
+ * Change beacon setting
* @description **Warning**: This endpoint is experimental and might change or disappear in future versions.
*/
parameters: {
@@ -16717,6 +17604,190 @@ export interface operations {
};
};
};
+ get_custom_builds_api_users__user_id__custom_builds_get: {
+ /** Returns collection of custom builds. */
+ parameters: {
+ /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+ header?: {
+ "run-as"?: string;
+ };
+ /** @description The ID of the user to get. */
+ path: {
+ user_id: string;
+ };
+ };
+ responses: {
+ /** @description Successful Response */
+ 200: {
+ content: {
+ "application/json": components["schemas"]["CustomBuildsCollection"];
+ };
+ };
+ /** @description Validation Error */
+ 422: {
+ content: {
+ "application/json": components["schemas"]["HTTPValidationError"];
+ };
+ };
+ };
+ };
+ add_custom_builds_api_users__user_id__custom_builds__key__put: {
+ /** Add new custom build. */
+ parameters: {
+ /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+ header?: {
+ "run-as"?: string;
+ };
+ /** @description The key of the custom build to be deleted. */
+ /** @description The ID of the user to get. */
+ path: {
+ key: string;
+ user_id: string;
+ };
+ };
+ requestBody: {
+ content: {
+ "application/json": components["schemas"]["CustomBuildCreationPayload"];
+ };
+ };
+ responses: {
+ /** @description Successful Response */
+ 200: {
+ content: {
+ "application/json": Record;
+ };
+ };
+ /** @description Validation Error */
+ 422: {
+ content: {
+ "application/json": components["schemas"]["HTTPValidationError"];
+ };
+ };
+ };
+ };
+ delete_custom_build_api_users__user_id__custom_builds__key__delete: {
+ /** Delete a custom build */
+ parameters: {
+ /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+ header?: {
+ "run-as"?: string;
+ };
+ /** @description The key of the custom build to be deleted. */
+ /** @description The ID of the user to get. */
+ path: {
+ key: string;
+ user_id: string;
+ };
+ };
+ responses: {
+ /** @description Successful Response */
+ 200: {
+ content: {
+ "application/json": components["schemas"]["DeletedCustomBuild"];
+ };
+ };
+ /** @description Validation Error */
+ 422: {
+ content: {
+ "application/json": components["schemas"]["HTTPValidationError"];
+ };
+ };
+ };
+ };
+ set_favorite_api_users__user_id__favorites__object_type__put: {
+ /** Add the object to user's favorites */
+ parameters: {
+ /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+ header?: {
+ "run-as"?: string;
+ };
+ /** @description The ID of the user to get. */
+ /** @description The object type the user wants to favorite */
+ path: {
+ user_id: string;
+ object_type: components["schemas"]["FavoriteObjectType"];
+ };
+ };
+ requestBody: {
+ content: {
+ "application/json": components["schemas"]["FavoriteObject"];
+ };
+ };
+ responses: {
+ /** @description Successful Response */
+ 200: {
+ content: {
+ "application/json": components["schemas"]["FavoriteObjectsSummary"];
+ };
+ };
+ /** @description Validation Error */
+ 422: {
+ content: {
+ "application/json": components["schemas"]["HTTPValidationError"];
+ };
+ };
+ };
+ };
+ remove_favorite_api_users__user_id__favorites__object_type___object_id__delete: {
+ /** Remove the object from user's favorites */
+ parameters: {
+ /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+ header?: {
+ "run-as"?: string;
+ };
+ /** @description The ID of the user to get. */
+ /** @description The object type the user wants to favorite */
+ /** @description The ID of an object the user wants to remove from favorites */
+ path: {
+ user_id: string;
+ object_type: components["schemas"]["FavoriteObjectType"];
+ object_id: string;
+ };
+ };
+ responses: {
+ /** @description Successful Response */
+ 200: {
+ content: {
+ "application/json": components["schemas"]["FavoriteObjectsSummary"];
+ };
+ };
+ /** @description Validation Error */
+ 422: {
+ content: {
+ "application/json": components["schemas"]["HTTPValidationError"];
+ };
+ };
+ };
+ };
+ set_theme_api_users__user_id__theme__theme__put: {
+ /** Set the user's theme choice */
+ parameters: {
+ /** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
+ header?: {
+ "run-as"?: string;
+ };
+ /** @description The ID of the user to get. */
+ /** @description The theme of the GUI */
+ path: {
+ user_id: string;
+ theme: string;
+ };
+ };
+ responses: {
+ /** @description Successful Response */
+ 200: {
+ content: {
+ "application/json": string;
+ };
+ };
+ /** @description Validation Error */
+ 422: {
+ content: {
+ "application/json": components["schemas"]["HTTPValidationError"];
+ };
+ };
+ };
+ };
get_user_usage_api_users__user_id__usage_get: {
/** Return the user's quota usage summary broken down by quota source */
parameters: {
@@ -17069,10 +18140,10 @@ export interface operations {
* : The stored workflow's owner's username. (The tag `u` can be used a short hand alias for this tag to filter on this attribute.)
*
* `is:published`
- * : Include only published workflows in the final result. Be sure the the query parameter `show_published` is set to `true` if to include all published workflows and not just the requesting user's.
+ * : Include only published workflows in the final result. Be sure the query parameter `show_published` is set to `true` if to include all published workflows and not just the requesting user's.
*
* `is:share_with_me`
- * : Include only workflows shared with the requesting user. Be sure the the query parameter `show_shared` is set to `true` if to include shared workflows.
+ * : Include only workflows shared with the requesting user. Be sure the query parameter `show_shared` is set to `true` if to include shared workflows.
*
* ## Free Text
*
diff --git a/client/src/store/collectionAttributesStore.js b/client/src/store/collectionAttributesStore.js
deleted file mode 100644
index e80c5c2bc632..000000000000
--- a/client/src/store/collectionAttributesStore.js
+++ /dev/null
@@ -1,33 +0,0 @@
-import axios from "axios";
-import { prependPath } from "utils/redirect";
-import Vue from "vue";
-
-export const state = {
- collectionAttributes: {},
-};
-
-const getters = {
- getCollectionAttributes: (state) => (collectionId) => {
- return state.collectionAttributes[collectionId] || null;
- },
-};
-
-const actions = {
- fetchCollectionAttributes: async ({ commit }, collectionId) => {
- const { data } = await axios.get(prependPath("api/dataset_collections/" + collectionId + "/attributes"));
- commit("saveCollectionAttributes", { collectionId, collectionAttributes: data });
- },
-};
-
-const mutations = {
- saveCollectionAttributes: (state, { collectionId, collectionAttributes }) => {
- Vue.set(state.collectionAttributes, collectionId, collectionAttributes);
- },
-};
-
-export const collectionAttributesStore = {
- state,
- getters,
- actions,
- mutations,
-};
diff --git a/client/src/store/configStore/configStore.js b/client/src/store/configStore/configStore.js
deleted file mode 100644
index a16e15ac8a0c..000000000000
--- a/client/src/store/configStore/configStore.js
+++ /dev/null
@@ -1,42 +0,0 @@
-import { getConfig } from "./queries";
-
-const state = {
- config: null,
-};
-
-const getters = {
- config(state) {
- return state?.config || {};
- },
- configIsLoaded(state) {
- return state?.config !== null;
- },
-};
-
-const mutations = {
- setConfigs(state, newConfigs = {}) {
- state.config = Object.assign({}, state.config || {}, newConfigs);
- },
-};
-
-// Holds promise for in-flight loads
-let loadPromise;
-
-const actions = {
- loadConfigs({ commit }) {
- if (!loadPromise) {
- loadPromise = getConfig()
- .then((configs) => commit("setConfigs", configs))
- .catch((err) => console.warn("loadConfigs error", err))
- .finally(() => (loadPromise = null));
- }
- },
-};
-
-export const configStore = {
- namespaced: true,
- getters,
- state,
- mutations,
- actions,
-};
diff --git a/client/src/store/configStore/index.js b/client/src/store/configStore/index.js
deleted file mode 100644
index 4f7427f7d7a8..000000000000
--- a/client/src/store/configStore/index.js
+++ /dev/null
@@ -1,2 +0,0 @@
-export { configStore } from "./configStore";
-export { syncConfigToGalaxy } from "./syncConfigToGalaxy";
diff --git a/client/src/store/configStore/queries.js b/client/src/store/configStore/queries.js
deleted file mode 100644
index 773f18fd1df8..000000000000
--- a/client/src/store/configStore/queries.js
+++ /dev/null
@@ -1,11 +0,0 @@
-import axios from "axios";
-import { prependPath } from "utils/redirect";
-
-export async function getConfig() {
- const url = prependPath("/api/configuration");
- const response = await axios.get(url);
- if (response.status != 200) {
- throw new Error(response);
- }
- return response.data;
-}
diff --git a/client/src/store/configStore/syncConfigToGalaxy.js b/client/src/store/configStore/syncConfigToGalaxy.js
deleted file mode 100644
index 7208ddf1310d..000000000000
--- a/client/src/store/configStore/syncConfigToGalaxy.js
+++ /dev/null
@@ -1,16 +0,0 @@
-import { map, pluck } from "rxjs/operators";
-
-export function syncConfigToGalaxy(galaxy$, store) {
- const cfg$ = galaxy$.pipe(
- pluck("config"),
- // make sure we're not operating on that config by reference.
- // we want a unique copy to stick into Vuex
- map((config) => Object.assign({}, config))
- );
-
- return cfg$.subscribe(
- (cfg) => store.commit("config/setConfigs", cfg),
- (err) => console.log("syncConfigToGalaxy error", err),
- () => console.log("syncConfigToGalaxy complete")
- );
-}
diff --git a/client/src/store/historyStore/collectionElementsStore.js b/client/src/store/historyStore/collectionElementsStore.js
deleted file mode 100644
index 264df2f55447..000000000000
--- a/client/src/store/historyStore/collectionElementsStore.js
+++ /dev/null
@@ -1,73 +0,0 @@
-/**
- * Requests collection elements by reacting to changes of props passed to the collection elements
- * provider used in the collection panel e.g. changes of the offset prop when scrolling. This store
- * attached to the changed history items store, but could also use the getter of the dataset store
- * instead, particularly after a collection store has been added if required.
- */
-
-import { LastQueue } from "utils/promise-queue";
-import { urlData } from "utils/url";
-import Vue from "vue";
-
-import { mergeArray } from "./model/utilities";
-
-const limit = 100;
-const queue = new LastQueue();
-
-const getObjectId = (elementObject) => {
- return `${elementObject.model_class}-${elementObject.id}`;
-};
-
-const state = {
- items: {},
- itemKey: "element_index",
- objectIndex: {},
-};
-
-const getters = {
- getCollectionElements:
- (state) =>
- ({ id }) => {
- const itemArray = state.items[id] || [];
- const filtered = itemArray.filter((item) => !!item);
- return filtered.map((item) => {
- const objectId = getObjectId(item.object);
- const objectData = state.objectIndex[objectId];
- const objectResult = { ...item.object };
- if (objectData) {
- Object.keys(objectResult).forEach((key) => {
- objectResult[key] = objectData[key];
- });
- }
- return { ...item, object: objectResult };
- });
- },
-};
-
-const actions = {
- fetchCollectionElements: async ({ commit }, { id, contentsUrl, offset }) => {
- const url = `/${contentsUrl}?offset=${offset}&limit=${limit}`;
- await queue.enqueue(urlData, { url }).then((payload) => {
- commit("saveCollectionElements", { id, payload });
- });
- },
-};
-
-const mutations = {
- saveCollectionElements: (state, { id, payload }) => {
- mergeArray(id, payload, state.items, state.itemKey);
- },
- saveCollectionObjects: (state, { payload }) => {
- payload.forEach((item) => {
- const objectId = getObjectId(item);
- Vue.set(state.objectIndex, objectId, item);
- });
- },
-};
-
-export const collectionElementsStore = {
- state,
- getters,
- actions,
- mutations,
-};
diff --git a/client/src/store/historyStore/datasetStore.js b/client/src/store/historyStore/datasetStore.js
deleted file mode 100644
index b3d4d127a0d9..000000000000
--- a/client/src/store/historyStore/datasetStore.js
+++ /dev/null
@@ -1,58 +0,0 @@
-import { urlData } from "utils/url";
-import Vue from "vue";
-
-const state = {
- items: {},
-};
-
-const getters = {
- getDataset:
- (state) =>
- ({ id }) => {
- return state.items[id] || { hid: 0, name: "Wait..." };
- },
-};
-
-const actions = {
- fetchDataset: async ({ state, commit }, { id }) => {
- if (!state.items[id]) {
- const url = `/api/datasets/${id}`;
- const dataset = await urlData({ url });
- commit("saveDataset", { id, dataset });
- }
- },
-};
-
-const mutations = {
- /**
- * Adds a new dataset.
- * @param {Array} dataset as returned by the datasets api (detailed serialization)
- */
- saveDataset: (state, { id, dataset }) => {
- Vue.set(state.items, id, dataset);
- },
- /**
- * Updates existing datasets. This is called by the history changed items store.
- * @param {Array} payload as returned by the history contents api (detailed serialization)
- */
- saveDatasets: (state, { payload }) => {
- payload.forEach((item) => {
- if (item.history_content_type == "dataset") {
- const id = item.id;
- if (state.items[id]) {
- const localItem = state.items[id];
- Object.keys(localItem).forEach((key) => {
- localItem[key] = item[key];
- });
- }
- }
- });
- },
-};
-
-export const datasetStore = {
- state,
- getters,
- actions,
- mutations,
-};
diff --git a/client/src/store/historyStore/index.js b/client/src/store/historyStore/index.js
deleted file mode 100644
index 980e5767e4a2..000000000000
--- a/client/src/store/historyStore/index.js
+++ /dev/null
@@ -1,2 +0,0 @@
-export { collectionElementsStore } from "./collectionElementsStore";
-export { datasetStore } from "./datasetStore";
diff --git a/client/src/store/historyStore/model/watchHistory.js b/client/src/store/historyStore/model/watchHistory.js
index d42df79de948..97c87c7c1919 100644
--- a/client/src/store/historyStore/model/watchHistory.js
+++ b/client/src/store/historyStore/model/watchHistory.js
@@ -13,6 +13,9 @@ import { getCurrentHistoryFromServer } from "stores/services/history.services";
import { loadSet } from "utils/setCache";
import { urlData } from "utils/url";
+import { useCollectionElementsStore } from "@/stores/collectionElementsStore";
+import { useDatasetStore } from "@/stores/datasetStore";
+
const limit = 1000;
let throttlePeriod = 3000;
@@ -41,6 +44,8 @@ function setVisibilityThrottle() {
export async function watchHistoryOnce(store) {
const historyStore = useHistoryStore();
const historyItemsStore = useHistoryItemsStore();
+ const datasetStore = useDatasetStore();
+ const collectionElementsStore = useCollectionElementsStore();
// "Reset" watchTimeout so we don't queue up watchHistory calls in rewatchHistory.
watchTimeout = null;
// get current history
@@ -77,9 +82,9 @@ export async function watchHistoryOnce(store) {
}
// pass changed items to attached stores
historyStore.setHistory(history);
- store.commit("saveDatasets", { payload });
+ datasetStore.saveDatasets(payload);
historyItemsStore.saveHistoryItems(historyId, payload);
- store.commit("saveCollectionObjects", { payload });
+ collectionElementsStore.saveCollections(payload);
// trigger changes in legacy handler
const Galaxy = getGalaxyInstance();
if (Galaxy) {
diff --git a/client/src/store/historyStore/model/watchHistory.test.js b/client/src/store/historyStore/model/watchHistory.test.js
index a82dcace8e1f..d986a7060f5a 100644
--- a/client/src/store/historyStore/model/watchHistory.test.js
+++ b/client/src/store/historyStore/model/watchHistory.test.js
@@ -2,11 +2,8 @@ import { createLocalVue, mount } from "@vue/test-utils";
import axios from "axios";
import MockAdapter from "axios-mock-adapter";
import { createPinia, mapState } from "pinia";
-import { collectionElementsStore } from "store/historyStore/collectionElementsStore";
-import { datasetStore } from "store/historyStore/datasetStore";
import { useHistoryItemsStore } from "stores/history/historyItemsStore";
import { useHistoryStore } from "stores/historyStore";
-import Vuex from "vuex";
import { watchHistoryOnce } from "./watchHistory";
@@ -51,16 +48,9 @@ describe("watchHistory", () => {
beforeEach(() => {
axiosMock = new MockAdapter(axios);
const localVue = createLocalVue();
- localVue.use(Vuex);
useHistoryItemsStore(pinia);
wrapper = mount(testApp, {
- store: new Vuex.Store({
- modules: {
- collectionElements: collectionElementsStore,
- dataset: datasetStore,
- },
- }),
localVue,
pinia,
});
diff --git a/client/src/store/index.js b/client/src/store/index.js
index 34553b161256..8ce43f061f30 100644
--- a/client/src/store/index.js
+++ b/client/src/store/index.js
@@ -9,18 +9,13 @@ import Vuex from "vuex";
import createCache from "vuex-cache";
import VuexPersistence from "vuex-persist";
-import { collectionAttributesStore } from "./collectionAttributesStore";
-import { configStore } from "./configStore";
import { datasetExtFilesStore } from "./datasetExtFilesStore";
import { datasetPathDestinationStore } from "./datasetPathDestinationStore";
import { gridSearchStore } from "./gridSearchStore";
-import { collectionElementsStore, datasetStore } from "./historyStore";
import { invocationStore } from "./invocationStore";
import { jobDestinationParametersStore } from "./jobDestinationParametersStore";
-import { panelStore } from "./panelStore";
import { syncVuextoGalaxy } from "./syncVuextoGalaxy";
import { tagStore } from "./tagStore";
-import { toolStore } from "./toolStore";
Vue.use(Vuex);
@@ -47,18 +42,12 @@ export function createStore() {
const storeConfig = {
plugins: [createCache(), panelsPersistence.plugin],
modules: {
- collectionAttributesStore: collectionAttributesStore,
- collectionElements: collectionElementsStore,
- config: configStore,
destinationParameters: jobDestinationParametersStore,
- dataset: datasetStore,
datasetExtFiles: datasetExtFilesStore,
datasetPathDestination: datasetPathDestinationStore,
invocations: invocationStore,
gridSearch: gridSearchStore,
- panels: panelStore,
tags: tagStore,
- tools: toolStore,
},
};
diff --git a/client/src/store/panelStore.js b/client/src/store/panelStore.js
deleted file mode 100644
index 93dea90d221f..000000000000
--- a/client/src/store/panelStore.js
+++ /dev/null
@@ -1,66 +0,0 @@
-import axios from "axios";
-import { getAppRoot } from "onload/loadConfig";
-import Vue from "vue";
-
-export const state = {
- panel: {},
- currentPanelView: null,
-};
-
-const getters = {
- panel: (state) => (panelView) => {
- return state.panel[panelView] || [];
- },
- currentPanel: (state) => {
- const effectiveView = state.currentPanelView || "default";
- const val = state.panel[effectiveView] || [];
- return val;
- },
- currentPanelView: (state) => {
- return state.currentPanelView;
- },
-};
-
-const actions = {
- initCurrentPanelView: async ({ commit, state, dispatch }, siteDefaultPanelView) => {
- const panelView = state.currentPanelView || siteDefaultPanelView;
- if (state.currentPanelView == null) {
- commit("setCurrentPanelView", { panelView });
- }
- const response = await axios.get(`${getAppRoot()}api/tools?in_panel=true&view=${panelView}`).catch((error) => {
- if (error.response && error.response.status == 400) {
- // Assume the stored panelView disappeared, revert to the panel default for this site.
- dispatch("setCurrentPanelView", siteDefaultPanelView);
- }
- });
- if (response !== undefined) {
- commit("savePanelView", { panelView, panel: response.data });
- }
- },
- setCurrentPanelView: async ({ commit }, panelView) => {
- commit("setCurrentPanelView", { panelView });
- const { data } = await axios.get(`${getAppRoot()}api/tools?in_panel=true&view=${panelView}`);
- commit("savePanelView", { panelView, panel: data });
- },
- fetchPanel: async ({ commit }, panelView) => {
- const { data } = await axios.get(`${getAppRoot()}api/tools?in_panel=true&view=${panelView}`);
- commit("savePanelView", { panelView, panel: data });
- },
-};
-
-const mutations = {
- savePanelView: (state, { panelView, panel }) => {
- Vue.set(state.panel, panelView, panel);
- },
- setCurrentPanelView: (state, { panelView }) => {
- state.currentPanelView = panelView;
- },
-};
-
-export const panelStore = {
- namespaced: true,
- state,
- getters,
- actions,
- mutations,
-};
diff --git a/client/src/store/syncVuextoGalaxy.js b/client/src/store/syncVuextoGalaxy.js
index e3201080c52b..acec636dfcfa 100644
--- a/client/src/store/syncVuextoGalaxy.js
+++ b/client/src/store/syncVuextoGalaxy.js
@@ -7,10 +7,10 @@
import { getGalaxyInstance } from "app";
import { defer } from "rxjs";
import { shareReplay } from "rxjs/operators";
-import { syncConfigToGalaxy } from "store/configStore";
-import { syncUserToGalaxy } from "stores/users/syncUserToGalaxy";
import { waitForInit } from "utils/observable";
+import { syncUserToGalaxy } from "@/stores/users/syncUserToGalaxy";
+
// store subscriptions
export const syncVuextoGalaxy = (store) => {
@@ -18,9 +18,6 @@ export const syncVuextoGalaxy = (store) => {
return waitForInit(() => getGalaxyInstance()).pipe(shareReplay(1));
});
- // sets current user when glaaxy changes
- syncUserToGalaxy(globalGalaxy$, store);
-
- // configuration
- syncConfigToGalaxy(globalGalaxy$, store);
+ // sets current user when galaxy changes
+ syncUserToGalaxy(globalGalaxy$);
};
diff --git a/client/src/store/toolStore.js b/client/src/store/toolStore.js
deleted file mode 100644
index 67b938963127..000000000000
--- a/client/src/store/toolStore.js
+++ /dev/null
@@ -1,71 +0,0 @@
-import axios from "axios";
-import { createWhooshQuery, filterTools } from "components/Panels/utilities";
-import { getAppRoot } from "onload/loadConfig";
-import Vue from "vue";
-
-export const state = {
- toolById: {},
- toolResults: [],
- allTools: [],
-};
-
-const getters = {
- getToolForId: (state) => (toolId) => {
- return state.toolById[toolId];
- },
- getToolNameById: (state) => (toolId) => {
- const details = state.toolById[toolId];
- if (details && details.name) {
- return details.name;
- } else {
- return "...";
- }
- },
- getTools:
- (state) =>
- ({ filterSettings, toolbox }) => {
- if (Object.keys(filterSettings).length === 0) {
- return state.allTools;
- } else {
- return filterTools(toolbox, state.toolResults);
- }
- },
-};
-
-const actions = {
- fetchToolForId: async ({ commit }, toolId) => {
- console.log("fetching tool");
- const { data } = await axios.get(`${getAppRoot()}api/tools/${toolId}`);
- commit("saveToolForId", { toolId, toolData: data });
- },
- fetchAllTools: async ({ commit }, { filterSettings, panelView, toolbox }) => {
- if (Object.keys(filterSettings).length !== 0) {
- // Parsing filterSettings to Whoosh query
- const q = createWhooshQuery(filterSettings, panelView, toolbox);
- const { data } = await axios.get(`${getAppRoot()}api/tools`, { params: { q } });
- commit("saveToolResults", { toolsData: data });
- } else if (state.allTools.length === 0) {
- const { data } = await axios.get(`${getAppRoot()}api/tools?in_panel=False`);
- commit("saveAllTools", { toolsData: data });
- }
- },
-};
-
-const mutations = {
- saveToolForId: (state, { toolId, toolData }) => {
- Vue.set(state.toolById, toolId, toolData);
- },
- saveToolResults: (state, { toolsData }) => {
- state.toolResults = toolsData;
- },
- saveAllTools: (state, { toolsData }) => {
- state.allTools = toolsData;
- },
-};
-
-export const toolStore = {
- state,
- getters,
- actions,
- mutations,
-};
diff --git a/client/src/stores/collectionAttributesStore.test.ts b/client/src/stores/collectionAttributesStore.test.ts
new file mode 100644
index 000000000000..5afcfccbe812
--- /dev/null
+++ b/client/src/stores/collectionAttributesStore.test.ts
@@ -0,0 +1,55 @@
+import flushPromises from "flush-promises";
+import { createPinia, setActivePinia } from "pinia";
+
+import { mockFetcher } from "@/schema/__mocks__";
+import { DatasetCollectionAttributes } from "@/stores/services";
+
+import { useCollectionAttributesStore } from "./collectionAttributesStore";
+
+jest.mock("@/schema");
+
+const FAKE_HDCA_ID = "123";
+
+const FAKE_ATTRIBUTES: DatasetCollectionAttributes = {
+ dbkey: "hg19",
+ extension: "bed",
+ model_class: "HistoryDatasetCollectionAssociation",
+ dbkeys: ["hg19", "hg38"],
+ extensions: ["bed", "vcf"],
+ tags: ["tag1", "tag2"],
+};
+
+const fetchCollectionAttributes = jest.fn().mockResolvedValue({ data: FAKE_ATTRIBUTES });
+
+describe("collectionAttributesStore", () => {
+ beforeEach(() => {
+ setActivePinia(createPinia());
+ mockFetcher.path("/api/dataset_collections/{id}/attributes").method("get").mock(fetchCollectionAttributes);
+ });
+
+ it("should fetch attributes and store them", async () => {
+ const store = useCollectionAttributesStore();
+ expect(store.storedAttributes[FAKE_HDCA_ID]).toBeUndefined();
+ expect(store.isLoadingAttributes(FAKE_HDCA_ID)).toBeFalsy();
+
+ store.getAttributes(FAKE_HDCA_ID);
+ // getAttributes will trigger a fetch if the attributes are not stored
+ expect(store.isLoadingAttributes(FAKE_HDCA_ID)).toBeTruthy();
+ await flushPromises();
+ expect(store.isLoadingAttributes(FAKE_HDCA_ID)).toBeFalsy();
+
+ expect(store.storedAttributes[FAKE_HDCA_ID]).toEqual(FAKE_ATTRIBUTES);
+ expect(fetchCollectionAttributes).toHaveBeenCalled();
+ });
+
+ it("should not fetch attributes if already stored", async () => {
+ const store = useCollectionAttributesStore();
+
+ store.storedAttributes[FAKE_HDCA_ID] = FAKE_ATTRIBUTES;
+
+ const result = store.getAttributes(FAKE_HDCA_ID);
+
+ expect(result).toEqual(FAKE_ATTRIBUTES);
+ expect(fetchCollectionAttributes).not.toHaveBeenCalled();
+ });
+});
diff --git a/client/src/stores/collectionAttributesStore.ts b/client/src/stores/collectionAttributesStore.ts
new file mode 100644
index 000000000000..96b31d0c03da
--- /dev/null
+++ b/client/src/stores/collectionAttributesStore.ts
@@ -0,0 +1,43 @@
+import { defineStore } from "pinia";
+import { computed, del, ref, set } from "vue";
+
+import { DatasetCollectionAttributes } from "./services";
+import { fetchCollectionAttributes } from "./services/datasetCollection.service";
+
+export const useCollectionAttributesStore = defineStore("collectionAttributesStore", () => {
+ const storedAttributes = ref<{ [key: string]: DatasetCollectionAttributes }>({});
+ const loadingAttributes = ref<{ [key: string]: boolean }>({});
+
+ const getAttributes = computed(() => {
+ return (hdcaId: string) => {
+ if (!storedAttributes.value[hdcaId]) {
+ set(storedAttributes.value, hdcaId, {});
+ fetchAttributes({ hdcaId });
+ }
+ return storedAttributes.value[hdcaId];
+ };
+ });
+
+ const isLoadingAttributes = computed(() => {
+ return (hdcaId: string) => {
+ return loadingAttributes.value[hdcaId] ?? false;
+ };
+ });
+
+ async function fetchAttributes(params: { hdcaId: string }) {
+ set(loadingAttributes.value, params.hdcaId, true);
+ try {
+ const attributes = await fetchCollectionAttributes(params);
+ set(storedAttributes.value, params.hdcaId, attributes);
+ return attributes;
+ } finally {
+ del(loadingAttributes.value, params.hdcaId);
+ }
+ }
+
+ return {
+ storedAttributes,
+ getAttributes,
+ isLoadingAttributes,
+ };
+});
diff --git a/client/src/stores/collectionElementsStore.test.ts b/client/src/stores/collectionElementsStore.test.ts
new file mode 100644
index 000000000000..475da2cf7668
--- /dev/null
+++ b/client/src/stores/collectionElementsStore.test.ts
@@ -0,0 +1,180 @@
+import flushPromises from "flush-promises";
+import { createPinia, setActivePinia } from "pinia";
+
+import { mockFetcher } from "@/schema/__mocks__";
+import { DCEEntry, useCollectionElementsStore } from "@/stores/collectionElementsStore";
+import { DCESummary, HDCASummary } from "@/stores/services";
+
+jest.mock("@/schema");
+
+describe("useCollectionElementsStore", () => {
+ beforeEach(() => {
+ setActivePinia(createPinia());
+ mockFetcher
+ .path("/api/dataset_collections/{hdca_id}/contents/{parent_id}")
+ .method("get")
+ .mock(fetchCollectionElements);
+ });
+
+ it("should save collections", async () => {
+ const collection1: HDCASummary = mockCollection("1");
+ const collection2: HDCASummary = mockCollection("2");
+ const collections: HDCASummary[] = [collection1, collection2];
+ const store = useCollectionElementsStore();
+ expect(store.storedCollections).toEqual({});
+
+ store.saveCollections(collections);
+
+ expect(store.storedCollections).toEqual({
+ "1": collection1,
+ "2": collection2,
+ });
+ });
+
+ it("should fetch collection elements if they are not yet in the store", async () => {
+ const totalElements = 10;
+ const collection: HDCASummary = mockCollection("1", totalElements);
+ const store = useCollectionElementsStore();
+ expect(store.storedCollectionElements).toEqual({});
+ expect(store.isLoadingCollectionElements(collection)).toEqual(false);
+
+ const offset = 0;
+ const limit = 5;
+ // Getting collection elements should trigger a fetch and change the loading state
+ store.getCollectionElements(collection, offset, limit);
+ expect(store.isLoadingCollectionElements(collection)).toEqual(true);
+ await flushPromises();
+ expect(store.isLoadingCollectionElements(collection)).toEqual(false);
+ expect(fetchCollectionElements).toHaveBeenCalled();
+
+ const collectionKey = store.getCollectionKey(collection);
+ const elements = store.storedCollectionElements[collectionKey];
+ expect(elements).toBeDefined();
+ // The total number of elements (including placeholders) is 10, but only the first 5 are fetched (real elements)
+ expect(elements).toHaveLength(totalElements);
+ const nonPlaceholderElements = getRealElements(elements);
+ expect(nonPlaceholderElements).toHaveLength(limit);
+ });
+
+ it("should not fetch collection elements if they are already in the store", async () => {
+ const totalElements = 10;
+ const collection: HDCASummary = mockCollection("1", totalElements);
+ const store = useCollectionElementsStore();
+ // Prefill the store with the first 5 elements
+ const storedCount = 5;
+ const expectedStoredElements = Array.from({ length: storedCount }, (_, i) => mockElement(collection.id, i));
+ const collectionKey = store.getCollectionKey(collection);
+ store.storedCollectionElements[collectionKey] = expectedStoredElements;
+ expect(store.storedCollectionElements[collectionKey]).toHaveLength(storedCount);
+
+ const offset = 0;
+ const limit = storedCount;
+ // Getting the same collection elements range should not trigger a fetch
+ store.getCollectionElements(collection, offset, limit);
+ expect(store.isLoadingCollectionElements(collection)).toEqual(false);
+ expect(fetchCollectionElements).not.toHaveBeenCalled();
+ });
+
+ it("should fetch only missing elements if the requested range is not already stored", async () => {
+ const totalElements = 10;
+ const collection: HDCASummary = mockCollection("1", totalElements);
+ const store = useCollectionElementsStore();
+
+ const initialElements = 3;
+ store.getCollectionElements(collection, 0, initialElements);
+ await flushPromises();
+ expect(fetchCollectionElements).toHaveBeenCalled();
+ const collectionKey = store.getCollectionKey(collection);
+ let elements = store.storedCollectionElements[collectionKey];
+ // The first call will initialize the 10 placeholders and fetch the first 3 elements out of 10
+ expect(elements).toHaveLength(totalElements);
+ expect(getRealElements(elements)).toHaveLength(initialElements);
+
+ const offset = 2;
+ const limit = 5;
+ // Getting collection elements should trigger a fetch in this case
+ store.getCollectionElements(collection, offset, limit);
+ expect(store.isLoadingCollectionElements(collection)).toEqual(true);
+ await flushPromises();
+ expect(store.isLoadingCollectionElements(collection)).toEqual(false);
+ expect(fetchCollectionElements).toHaveBeenCalled();
+
+ elements = store.storedCollectionElements[collectionKey];
+ expect(elements).toBeDefined();
+ expect(elements).toHaveLength(10);
+ // The offset was overlapping with the stored elements, so it was increased by the number of stored elements
+ // and it fetches the next "limit" number of elements
+ expect(getRealElements(elements)).toHaveLength(initialElements + limit);
+ });
+});
+
+function mockCollection(id: string, numElements = 10): HDCASummary {
+ return {
+ id: id,
+ element_count: numElements,
+ collection_type: "list",
+ populated_state: "ok",
+ populated_state_message: "",
+ collection_id: `DC_ID_${id}`,
+ name: `collection ${id}`,
+ deleted: false,
+ contents_url: "",
+ hid: 1,
+ history_content_type: "dataset_collection",
+ history_id: "1",
+ model_class: "HistoryDatasetCollectionAssociation",
+ tags: [],
+ visible: true,
+ create_time: "2021-05-25T14:00:00.000Z",
+ update_time: "2021-05-25T14:00:00.000Z",
+ type_id: "dataset_collection",
+ url: "",
+ };
+}
+
+function mockElement(collectionId: string, i: number): DCESummary {
+ const fakeID = `${collectionId}-${i}`;
+ return {
+ id: fakeID,
+ element_index: i,
+ element_identifier: `element ${i}`,
+ element_type: "hda",
+ model_class: "DatasetCollectionElement",
+ object: {
+ id: fakeID,
+ model_class: "HistoryDatasetAssociation",
+ state: "ok",
+ hda_ldda: "hda",
+ history_id: "1",
+ tags: [],
+ },
+ };
+}
+
+interface ApiRequest {
+ hdca_id: string;
+ parent_id: string;
+ offset: number;
+ limit: number;
+}
+
+const fetchCollectionElements = jest.fn(fakeCollectionElementsApiResponse);
+
+function fakeCollectionElementsApiResponse(params: ApiRequest) {
+ const elements: DCESummary[] = [];
+ const startIndex = params.offset ?? 0;
+ const endIndex = startIndex + (params.limit ?? 10);
+ for (let i = startIndex; i < endIndex; i++) {
+ elements.push(mockElement(params.hdca_id, i));
+ }
+ return {
+ data: elements,
+ };
+}
+
+/**
+ * Filter out the placeholder elements from the given array.
+ */
+function getRealElements(elements?: DCEEntry[]): DCESummary[] | undefined {
+ return elements?.filter((element) => "id" in element === true) as DCESummary[];
+}
diff --git a/client/src/stores/collectionElementsStore.ts b/client/src/stores/collectionElementsStore.ts
new file mode 100644
index 000000000000..8f97ad319745
--- /dev/null
+++ b/client/src/stores/collectionElementsStore.ts
@@ -0,0 +1,157 @@
+import { defineStore } from "pinia";
+import { computed, del, ref, set } from "vue";
+
+import { CollectionEntry, DCESummary, HDCASummary, HistoryContentItemBase, isHDCA } from "./services";
+import { fetchCollectionDetails, fetchElementsFromCollection } from "./services/datasetCollection.service";
+
+/**
+ * Represents an element in a collection that has not been fetched yet.
+ */
+export interface ContentPlaceholder {
+ /**
+ * The index of the element in the containing collection.
+ *
+ * This is used to determine the offset to fetch the element from when
+ * scrolling through the collection.
+ */
+ element_index: number;
+ /**
+ * Whether the element is currently being fetched.
+ *
+ * This is used to prevent fetching the same element multiple times.
+ */
+ fetching?: boolean;
+}
+
+export type DCEEntry = ContentPlaceholder | DCESummary;
+
+const FETCH_LIMIT = 50;
+
+export const useCollectionElementsStore = defineStore("collectionElementsStore", () => {
+ const storedCollections = ref<{ [key: string]: HDCASummary }>({});
+ const loadingCollectionElements = ref<{ [key: string]: boolean }>({});
+ const storedCollectionElements = ref<{ [key: string]: DCEEntry[] }>({});
+
+ /**
+ * Returns a key that can be used to store or retrieve the elements of a collection in the store.
+ *
+ * It consistently returns a DatasetCollection ID for (top level) HDCAs or sub-collections.
+ */
+ function getCollectionKey(collection: CollectionEntry): string {
+ if (isHDCA(collection)) {
+ return collection.collection_id;
+ }
+ return collection.id;
+ }
+
+ const getCollectionElements = computed(() => {
+ return (collection: CollectionEntry, offset = 0, limit = FETCH_LIMIT) => {
+ const storedElements =
+ storedCollectionElements.value[getCollectionKey(collection)] ?? initWithPlaceholderElements(collection);
+ fetchMissingElements({ collection, storedElements, offset, limit });
+ return storedElements;
+ };
+ });
+
+ const isLoadingCollectionElements = computed(() => {
+ return (collection: CollectionEntry) => {
+ return loadingCollectionElements.value[getCollectionKey(collection)] ?? false;
+ };
+ });
+
+ async function fetchMissingElements(params: {
+ collection: CollectionEntry;
+ storedElements: DCEEntry[];
+ offset: number;
+ limit: number;
+ }) {
+ const collectionKey = getCollectionKey(params.collection);
+ try {
+ // We should fetch only missing (placeholder) elements from the range
+ const firstMissingIndexInRange = params.storedElements
+ .slice(params.offset, params.offset + params.limit)
+ .findIndex((element) => isPlaceholder(element) && !element.fetching);
+
+ if (firstMissingIndexInRange === -1) {
+ // All elements in the range are already stored or being fetched
+ return;
+ }
+ // Adjust the offset to the first missing element
+ params.offset += firstMissingIndexInRange;
+
+ set(loadingCollectionElements.value, collectionKey, true);
+ // Mark all elements in the range as fetching
+ params.storedElements
+ .slice(params.offset, params.offset + params.limit)
+ .forEach((element) => isPlaceholder(element) && (element.fetching = true));
+ const fetchedElements = await fetchElementsFromCollection({
+ entry: params.collection,
+ offset: params.offset,
+ limit: params.limit,
+ });
+ // Update only the elements that were fetched
+ params.storedElements.splice(params.offset, fetchedElements.length, ...fetchedElements);
+ set(storedCollectionElements.value, collectionKey, params.storedElements);
+ } finally {
+ del(loadingCollectionElements.value, collectionKey);
+ }
+ }
+
+ async function loadCollectionElements(collection: CollectionEntry) {
+ const elements = await fetchElementsFromCollection({ entry: collection });
+ set(storedCollectionElements.value, getCollectionKey(collection), elements);
+ }
+
+ function saveCollections(historyContentsPayload: HistoryContentItemBase[]) {
+ const collectionsInHistory = historyContentsPayload.filter(
+ (entry) => entry.history_content_type === "dataset_collection"
+ ) as HDCASummary[];
+ for (const collection of collectionsInHistory) {
+ set(storedCollections.value, collection.id, collection);
+ }
+ }
+
+ async function getCollection(collectionId: string) {
+ const collection = storedCollections.value[collectionId];
+ if (!collection) {
+ return await fetchCollection({ id: collectionId });
+ }
+ return collection;
+ }
+
+ async function fetchCollection(params: { id: string }) {
+ set(loadingCollectionElements.value, params.id, true);
+ try {
+ const collection = await fetchCollectionDetails({ hdcaId: params.id });
+ set(storedCollections.value, collection.id, collection);
+ return collection;
+ } finally {
+ del(loadingCollectionElements.value, params.id);
+ }
+ }
+
+ function isPlaceholder(element: DCEEntry): element is ContentPlaceholder {
+ return "id" in element === false;
+ }
+
+ function initWithPlaceholderElements(collection: CollectionEntry): ContentPlaceholder[] {
+ const totalElements = collection.element_count ?? 0;
+ const placeholderElements = new Array(totalElements);
+ for (let i = 0; i < totalElements; i++) {
+ placeholderElements[i] = { element_index: i };
+ }
+ return placeholderElements;
+ }
+
+ return {
+ storedCollections,
+ storedCollectionElements,
+ getCollectionElements,
+ isLoadingCollectionElements,
+ getCollection,
+ fetchCollection,
+ loadCollectionElements,
+ saveCollections,
+ getCollectionKey,
+ };
+});
diff --git a/client/src/stores/configurationStore.ts b/client/src/stores/configurationStore.ts
new file mode 100644
index 000000000000..41edab531320
--- /dev/null
+++ b/client/src/stores/configurationStore.ts
@@ -0,0 +1,43 @@
+import { defineStore } from "pinia";
+import { computed, ref } from "vue";
+
+import { fetcher } from "@/schema";
+
+// Temporary set to any until schema model is defined
+type GalaxyConfiguration = any;
+
+const fetchConfiguration = fetcher.path("/api/configuration").method("get").create();
+
+export const useConfigStore = defineStore("configurationStore", () => {
+ const config = ref(null);
+ const isLoading = ref(false);
+ const isLoaded = computed(() => !!config.value);
+
+ async function loadConfig() {
+ if (!isLoaded.value && !isLoading.value) {
+ isLoading.value = true;
+ try {
+ const { data } = await fetchConfiguration({});
+ config.value = data;
+ console.debug("Galaxy configuration loaded", config.value);
+ } catch (err) {
+ console.error("Error loading Galaxy configuration", err);
+ } finally {
+ isLoading.value = false;
+ }
+ }
+ }
+
+ function setConfiguration(configuration: GalaxyConfiguration) {
+ config.value = configuration;
+ }
+
+ loadConfig();
+
+ return {
+ config,
+ isLoaded,
+ loadConfig,
+ setConfiguration,
+ };
+});
diff --git a/client/src/stores/datasetStore.ts b/client/src/stores/datasetStore.ts
new file mode 100644
index 000000000000..9f2a66e37828
--- /dev/null
+++ b/client/src/stores/datasetStore.ts
@@ -0,0 +1,62 @@
+import { defineStore } from "pinia";
+import Vue, { computed, ref } from "vue";
+
+import { DatasetDetails, DatasetEntry, HistoryContentItemBase } from "./services";
+import { fetchDatasetDetails } from "./services/dataset.service";
+
+export const useDatasetStore = defineStore("datasetStore", () => {
+ const storedDatasets = ref<{ [key: string]: DatasetDetails }>({});
+ const loadingDatasets = ref<{ [key: string]: boolean }>({});
+
+ const getDataset = computed(() => {
+ return (datasetId: string) => {
+ const dataset = storedDatasets.value[datasetId];
+ if (needsUpdate(dataset)) {
+ fetchDataset({ id: datasetId });
+ }
+ return dataset ?? null;
+ };
+ });
+
+ const isLoadingDataset = computed(() => {
+ return (datasetId: string) => {
+ return loadingDatasets.value[datasetId] ?? false;
+ };
+ });
+
+ async function fetchDataset(params: { id: string }) {
+ Vue.set(loadingDatasets.value, params.id, true);
+ try {
+ const dataset = await fetchDatasetDetails(params);
+ Vue.set(storedDatasets.value, dataset.id, dataset);
+ return dataset;
+ } finally {
+ Vue.delete(loadingDatasets.value, params.id);
+ }
+ }
+
+ function saveDatasets(historyContentsPayload: HistoryContentItemBase[]) {
+ const datasetList = historyContentsPayload.filter(
+ (entry) => entry.history_content_type === "dataset"
+ ) as DatasetEntry[];
+ for (const dataset of datasetList) {
+ Vue.set(storedDatasets.value, dataset.id, dataset);
+ }
+ }
+
+ function needsUpdate(dataset?: DatasetEntry) {
+ if (!dataset) {
+ return true;
+ }
+ const isNotDetailed = !("peek" in dataset);
+ return isNotDetailed;
+ }
+
+ return {
+ storedDatasets,
+ getDataset,
+ isLoadingDataset,
+ fetchDataset,
+ saveDatasets,
+ };
+});
diff --git a/client/src/stores/historyStore.ts b/client/src/stores/historyStore.ts
index 112f0ebee168..a0cc1a47e8e2 100644
--- a/client/src/stores/historyStore.ts
+++ b/client/src/stores/historyStore.ts
@@ -151,7 +151,7 @@ export const useHistoryStore = defineStore("historyStore", () => {
if (currentHistoryId.value !== historyId) {
await setCurrentHistory(historyId);
}
- const filterText = HistoryFilters.getFilterText(HistoryFilters.getValidFilterSettings(filters));
+ const filterText = HistoryFilters.getFilterText(filters);
setFilterText(historyId, filterText);
}
diff --git a/client/src/stores/notificationsStore.ts b/client/src/stores/notificationsStore.ts
index 88f2131239ce..2784c4deebe6 100644
--- a/client/src/stores/notificationsStore.ts
+++ b/client/src/stores/notificationsStore.ts
@@ -30,9 +30,8 @@ export const useNotificationsStore = defineStore("notificationsStore", () => {
const unreadNotifications = computed(() => notifications.value.filter((n) => !n.seen_time));
async function loadNotifications() {
- await loadNotificationsFromServer().then((data) => {
- notifications.value = mergeObjectListsById(data, [], "create_time", "desc");
- });
+ const data = await loadNotificationsFromServer();
+ notifications.value = mergeObjectListsById(data, [], "create_time", "desc");
}
async function getNotificationStatus() {
@@ -43,16 +42,15 @@ export const useNotificationsStore = defineStore("notificationsStore", () => {
await broadcastsStore.loadBroadcasts();
await loadNotifications();
} else {
- await loadNotificationsStatus(lastNotificationUpdate.value).then((data) => {
- totalUnreadCount.value = data.total_unread_count;
- notifications.value = mergeObjectListsById(
- notifications.value,
- data.notifications,
- "create_time",
- "desc"
- );
- broadcastsStore.updateBroadcasts(data.broadcasts);
- });
+ const data = await loadNotificationsStatus(lastNotificationUpdate.value);
+ totalUnreadCount.value = data.total_unread_count;
+ notifications.value = mergeObjectListsById(
+ notifications.value,
+ data.notifications as UserNotification[],
+ "create_time",
+ "desc"
+ );
+ broadcastsStore.updateBroadcasts(data.broadcasts);
}
lastNotificationUpdate.value = new Date();
} catch (e) {
diff --git a/client/src/stores/services/dataset.service.ts b/client/src/stores/services/dataset.service.ts
new file mode 100644
index 000000000000..bef7f0899914
--- /dev/null
+++ b/client/src/stores/services/dataset.service.ts
@@ -0,0 +1,12 @@
+import { fetcher } from "@/schema";
+
+import { DatasetDetails } from ".";
+
+const getDataset = fetcher.path("/api/datasets/{dataset_id}").method("get").create();
+
+export async function fetchDatasetDetails(params: { id: string }): Promise {
+ const { data } = await getDataset({ dataset_id: params.id, view: "detailed" });
+ // We know that the server will return a DatasetDetails object because of the view parameter
+ // but the type system doesn't, so we have to cast it.
+ return data as unknown as DatasetDetails;
+}
diff --git a/client/src/stores/services/datasetCollection.service.ts b/client/src/stores/services/datasetCollection.service.ts
new file mode 100644
index 000000000000..c52aabfc3350
--- /dev/null
+++ b/client/src/stores/services/datasetCollection.service.ts
@@ -0,0 +1,62 @@
+import { fetcher } from "@/schema";
+
+import { CollectionEntry, DatasetCollectionAttributes, DCESummary, HDCADetailed, isHDCA } from ".";
+
+const DEFAULT_LIMIT = 50;
+
+const getCollectionDetails = fetcher.path("/api/dataset_collections/{id}").method("get").create();
+
+export async function fetchCollectionDetails(params: { hdcaId: string }): Promise {
+ const { data } = await getCollectionDetails({ id: params.hdcaId });
+ return data;
+}
+
+const getCollectionContents = fetcher
+ .path("/api/dataset_collections/{hdca_id}/contents/{parent_id}")
+ .method("get")
+ .create();
+
+export async function fetchCollectionElements(params: {
+ /** The ID of the top level HDCA that associates this collection with the History it belongs to. */
+ hdcaId: string;
+ /** The ID of the collection itself. */
+ collectionId: string;
+ /** The offset to start fetching elements from. */
+ offset?: number;
+ /** The maximum number of elements to fetch. */
+ limit?: number;
+}): Promise {
+ const { data } = await getCollectionContents({
+ instance_type: "history",
+ hdca_id: params.hdcaId,
+ parent_id: params.collectionId,
+ offset: params.offset,
+ limit: params.limit,
+ });
+ return data;
+}
+
+export async function fetchElementsFromCollection(params: {
+ /** The HDCA or sub-collection to fetch elements from. */
+ entry: CollectionEntry;
+ /** The offset to start fetching elements from. */
+ offset?: number;
+ /** The maximum number of elements to fetch. */
+ limit?: number;
+}): Promise {
+ const hdcaId = isHDCA(params.entry) ? params.entry.id : params.entry.hdca_id;
+ const collectionId = isHDCA(params.entry) ? params.entry.collection_id : params.entry.id;
+ return fetchCollectionElements({
+ hdcaId: hdcaId,
+ collectionId: collectionId,
+ offset: params.offset ?? 0,
+ limit: params.limit ?? DEFAULT_LIMIT,
+ });
+}
+
+const getCollectionAttributes = fetcher.path("/api/dataset_collections/{id}/attributes").method("get").create();
+
+export async function fetchCollectionAttributes(params: { hdcaId: string }): Promise {
+ const { data } = await getCollectionAttributes({ id: params.hdcaId, instance_type: "history" });
+ return data;
+}
diff --git a/client/src/stores/services/index.ts b/client/src/stores/services/index.ts
new file mode 100644
index 000000000000..5cea4cd8e8da
--- /dev/null
+++ b/client/src/stores/services/index.ts
@@ -0,0 +1,96 @@
+import { components } from "@/schema";
+
+/**
+ * Contains minimal information about a HistoryContentItem.
+ */
+export type HistoryContentItemBase = components["schemas"]["EncodedHistoryContentItem"];
+
+/**
+ * Contains summary information about a HistoryDatasetAssociation.
+ */
+export type DatasetSummary = components["schemas"]["HDASummary"];
+
+/**
+ * Contains additional details about a HistoryDatasetAssociation.
+ */
+export type DatasetDetails = components["schemas"]["HDADetailed"];
+
+/**
+ * Represents a HistoryDatasetAssociation with either summary or detailed information.
+ */
+export type DatasetEntry = DatasetSummary | DatasetDetails;
+
+/**
+ * Contains summary information about a DCE (DatasetCollectionElement).
+ *
+ * DCEs associate a parent collection to its elements. Those elements can be either
+ * HDAs or other DCs (DatasetCollections).
+ * The type of the element is indicated by the `element_type` field and the element
+ * itself is contained in the `object` field.
+ */
+export type DCESummary = components["schemas"]["DCESummary"];
+
+/**
+ * DatasetCollectionElement specific type for collections.
+ */
+export interface DCECollection extends DCESummary {
+ element_type: "dataset_collection";
+ object: DCObject;
+}
+
+/**
+ * Contains summary information about a HDCA (HistoryDatasetCollectionAssociation).
+ *
+ * HDCAs are (top level only) history items that contains information about the association
+ * between a History and a DatasetCollection.
+ */
+export type HDCASummary = components["schemas"]["HDCASummary"];
+
+/**
+ * Contains additional details about a HistoryDatasetCollectionAssociation.
+ */
+export type HDCADetailed = components["schemas"]["HDCADetailed"];
+
+/**
+ * Contains information about a DatasetCollection.
+ *
+ * DatasetCollections are immutable and contain one or more DCEs.
+ */
+export type DCObject = components["schemas"]["DCObject"];
+
+export type DatasetCollectionAttributes = components["schemas"]["DatasetCollectionAttributesResult"];
+
+/**
+ * A SubCollection is a DatasetCollectionElement of type `dataset_collection`
+ * with additional information to simplify its handling.
+ *
+ * This is used to be able to distinguish between top level HDCAs and sub-collections.
+ * It helps simplify both, the representation of sub-collections in the UI, and fetching of elements.
+ */
+export interface SubCollection extends DCObject {
+ /** The name of the collection. Usually corresponds to the DCE identifier. */
+ name: string;
+ /** The ID of the top level HDCA that associates this collection with the History it belongs to. */
+ hdca_id: string;
+}
+
+/**
+ * Represents either a top level HDCASummary or a sub-collection.
+ */
+export type CollectionEntry = HDCASummary | SubCollection;
+
+/**
+ * Returns true if the given entry is a top level HDCA and false for sub-collections.
+ */
+export function isHDCA(entry?: CollectionEntry): entry is HDCASummary {
+ return (
+ entry !== undefined && "history_content_type" in entry && entry.history_content_type === "dataset_collection"
+ );
+}
+
+/**
+ * Returns true if the given element of a collection is a DatasetCollection.
+ */
+export function isCollectionElement(element: DCESummary): element is DCECollection {
+ return element.element_type === "dataset_collection";
+}
diff --git a/client/src/stores/services/notifications.service.ts b/client/src/stores/services/notifications.service.ts
index 6bfca112825e..8ca375f303a7 100644
--- a/client/src/stores/services/notifications.service.ts
+++ b/client/src/stores/services/notifications.service.ts
@@ -1,10 +1,11 @@
+import type { UserNotification } from "@/components/Notifications";
import { type components, fetcher } from "@/schema";
const getNotifications = fetcher.path("/api/notifications").method("get").create();
export async function loadNotificationsFromServer() {
const { data } = await getNotifications({});
- return data;
+ return data as UserNotification[];
}
type UserNotificationsBatchUpdateRequest = components["schemas"]["UserNotificationsBatchUpdateRequest"];
diff --git a/client/src/stores/toolStore.ts b/client/src/stores/toolStore.ts
new file mode 100644
index 000000000000..f6c969cc46c7
--- /dev/null
+++ b/client/src/stores/toolStore.ts
@@ -0,0 +1,250 @@
+/**
+ * Requests tools, and various panel views
+ */
+
+import axios from "axios";
+import { defineStore } from "pinia";
+import Vue, { computed, Ref, ref } from "vue";
+
+import { createWhooshQuery, filterTools } from "@/components/Panels/utilities";
+import { useUserLocalStorage } from "@/composables/userLocalStorage";
+import { getAppRoot } from "@/onload/loadConfig";
+
+export interface Tool {
+ model_class: string;
+ id: string;
+ name: string;
+ version: string;
+ description: string;
+ labels: string[];
+ edam_operations: string[];
+ edam_topics: string[];
+ hidden: "" | boolean;
+ is_workflow_compatible: boolean;
+ xrefs: string[];
+ config_file: string;
+ link: string;
+ min_width: number;
+ target: string;
+ panel_section_id: string | null;
+ panel_section_name: string | null;
+ form_style: string;
+ disabled?: boolean;
+}
+
+export interface ToolSection {
+ model_class: string;
+ id: string;
+ name: string;
+ version?: string;
+ description?: string;
+ links?: Record;
+ tools?: (string | ToolSectionLabel)[];
+ elems?: (Tool | ToolSection)[];
+}
+
+export interface ToolSectionLabel {
+ model_class: string;
+ id: string;
+ text: string;
+ version?: string;
+ description?: string | null;
+ links?: Record | null;
+}
+
+export interface FilterSettings {
+ [key: string]: string | undefined;
+ name?: string;
+ section?: string;
+ ontology?: string;
+ id?: string;
+ owner?: string;
+ help?: string;
+}
+
+export const useToolStore = defineStore("toolStore", () => {
+ const currentPanelView: Ref = useUserLocalStorage("tool-store-view", "");
+ const toolsById = ref>({});
+ const toolResults = ref>({});
+ const panel = ref>>({});
+ const loading = ref(false);
+
+ const getToolForId = computed(() => {
+ return (toolId: string) => toolsById.value[toolId];
+ });
+
+ const getToolNameById = computed(() => {
+ return (toolId: string) => {
+ const details = toolsById.value[toolId];
+ if (details && details.name) {
+ return details.name;
+ } else {
+ return "...";
+ }
+ };
+ });
+
+ const getToolsById = computed(() => {
+ return (filterSettings: FilterSettings) => {
+ if (Object.keys(filterSettings).length === 0) {
+ return toolsById.value;
+ } else {
+ const q = createWhooshQuery(filterSettings);
+ return filterTools(toolsById.value, toolResults.value[q] || []);
+ }
+ };
+ });
+
+ const currentPanel = computed(() => {
+ const effectiveView = currentPanelView.value;
+ const val = panel.value[effectiveView] || {};
+ return val;
+ });
+
+ const isPanelPopulated = computed(() => {
+ return allToolsByIdFetched.value && Object.keys(currentPanel.value).length > 0;
+ });
+
+ const allToolsByIdFetched = computed(() => {
+ return Object.keys(toolsById.value).length > 0;
+ });
+
+ /** These are filtered tool sections (`ToolSection[]`) for the `currentPanel`;
+ * Only sections that are typically referenced by `Tool.panel_section_id`
+ * are included for the `default` view, while for ontologies, only ontologies are
+ * included and `Uncategorized` section is skipped.
+ */
+ const panelSections = computed(() => {
+ return (panelView: string) => {
+ return Object.values(panel.value[panelView] || {}).filter((section) => {
+ const sec = section as ToolSection;
+ return (
+ sec.tools &&
+ sec.tools.length > 0 &&
+ sec.id !== "uncategorized" &&
+ sec.id !== "builtin_converters" &&
+ sec.name !== undefined
+ );
+ });
+ };
+ });
+ const sectionDatalist = computed(() => {
+ return (panelView: string) => {
+ return panelSections.value(panelView).map((section) => {
+ return { value: section.id, text: section.name };
+ });
+ };
+ });
+
+ async function fetchToolForId(toolId: string) {
+ console.log("fetching tool");
+ const { data } = await axios.get(`${getAppRoot()}api/tools/${toolId}`);
+ saveToolForId(toolId, data);
+ }
+
+ async function fetchTools(filterSettings?: FilterSettings) {
+ if (filterSettings && Object.keys(filterSettings).length !== 0) {
+ // Parsing filterSettings to Whoosh query
+ const q = createWhooshQuery(filterSettings);
+ // already have results for this query
+ if (toolResults.value[q]) {
+ return;
+ }
+ const { data } = await axios.get(`${getAppRoot()}api/tools`, { params: { q } });
+ saveToolResults(q, data);
+ }
+ if (!loading.value && !allToolsByIdFetched.value) {
+ loading.value = true;
+ await axios
+ .get(`${getAppRoot()}api/tool_panel?in_panel=False`)
+ .then(({ data }) => {
+ saveAllTools(data.tools);
+ loading.value = false;
+ })
+ .catch((error) => {
+ console.error(error);
+ loading.value = false;
+ });
+ }
+ }
+
+ // Directly related to the ToolPanel
+ async function initCurrentPanelView(siteDefaultPanelView: string) {
+ if (!loading.value && !isPanelPopulated.value) {
+ loading.value = true;
+ const panelView = currentPanelView.value || siteDefaultPanelView;
+ if (currentPanelView.value == "") {
+ currentPanelView.value = panelView;
+ }
+ await axios
+ .get(`${getAppRoot()}api/tool_panel?in_panel=true&view=${panelView}`)
+ .then(({ data }) => {
+ loading.value = false;
+ savePanelView(panelView, data[panelView]);
+ })
+ .catch(async (error) => {
+ loading.value = false;
+ if (error.response && error.response.status == 400) {
+ // Assume the stored panelView disappeared, revert to the panel default for this site.
+ await setCurrentPanelView(siteDefaultPanelView);
+ }
+ });
+ }
+ }
+
+ async function setCurrentPanelView(panelView: string) {
+ if (!loading.value) {
+ currentPanelView.value = panelView;
+ if (panel.value[panelView]) {
+ return;
+ }
+ loading.value = true;
+ const { data } = await axios.get(`${getAppRoot()}api/tool_panel?in_panel=true&view=${panelView}`);
+ savePanelView(panelView, data[panelView]);
+ loading.value = false;
+ }
+ }
+
+ async function fetchPanel(panelView: string) {
+ const { data } = await axios.get(`${getAppRoot()}api/tool_panel?in_panel=true&view=${panelView}`);
+ savePanelView(panelView, data[panelView]);
+ }
+
+ function saveToolForId(toolId: string, toolData: Tool) {
+ Vue.set(toolsById.value, toolId, toolData);
+ }
+
+ function saveToolResults(whooshQuery: string, toolsData: Array) {
+ Vue.set(toolResults.value, whooshQuery, toolsData);
+ }
+
+ function saveAllTools(toolsData: Record) {
+ toolsById.value = toolsData;
+ }
+
+ function savePanelView(panelView: string, newPanel: { [id: string]: ToolSection | Tool }) {
+ Vue.set(panel.value, panelView, newPanel);
+ }
+
+ return {
+ toolsById,
+ panel,
+ currentPanelView,
+ loading,
+ getToolForId,
+ getToolNameById,
+ getToolsById,
+ currentPanel,
+ isPanelPopulated,
+ sectionDatalist,
+ fetchToolForId,
+ fetchTools,
+ initCurrentPanelView,
+ setCurrentPanelView,
+ fetchPanel,
+ saveToolForId,
+ saveToolResults,
+ saveAllTools,
+ savePanelView,
+ };
+});
diff --git a/client/src/stores/userStore.ts b/client/src/stores/userStore.ts
index 5cb89f483c41..13093688433c 100644
--- a/client/src/stores/userStore.ts
+++ b/client/src/stores/userStore.ts
@@ -2,6 +2,7 @@ import { defineStore } from "pinia";
import { computed, ref } from "vue";
import { useUserLocalStorage } from "@/composables/userLocalStorage";
+import { components } from "@/schema";
import { useHistoryStore } from "@/stores/historyStore";
import {
addFavoriteToolQuery,
@@ -10,7 +11,9 @@ import {
setCurrentThemeQuery,
} from "@/stores/users/queries";
-interface User {
+type QuotaUsageResponse = components["schemas"]["UserQuotaUsage"];
+
+interface User extends QuotaUsageResponse {
id: string;
email: string;
tags_used: string[];
@@ -54,20 +57,22 @@ export const useUserStore = defineStore("userStore", () => {
currentUser.value = user;
}
- function loadUser() {
+ function loadUser(includeHistories = true) {
if (!loadPromise) {
loadPromise = getCurrentUser()
.then(async (user) => {
- const historyStore = useHistoryStore();
currentUser.value = { ...user, isAnonymous: !user.email };
currentPreferences.value = user?.preferences ?? null;
// TODO: This is a hack to get around the fact that the API returns a string
if (currentPreferences.value?.favorites) {
currentPreferences.value.favorites = JSON.parse(user?.preferences?.favorites ?? { tools: [] });
}
- await historyStore.loadCurrentHistory();
- // load first few histories for user to start pagination
- await historyStore.loadHistories();
+ if (includeHistories) {
+ const historyStore = useHistoryStore();
+ await historyStore.loadCurrentHistory();
+ // load first few histories for user to start pagination
+ await historyStore.loadHistories();
+ }
})
.catch((e) => {
console.error("Failed to load user", e);
diff --git a/client/src/stores/workflowConnectionStore.test.ts b/client/src/stores/workflowConnectionStore.test.ts
index 156fa0e9555a..e1d14da96148 100644
--- a/client/src/stores/workflowConnectionStore.test.ts
+++ b/client/src/stores/workflowConnectionStore.test.ts
@@ -38,25 +38,25 @@ const connection: Connection = {
describe("Connection Store", () => {
beforeEach(() => {
setActivePinia(createPinia());
- const workflowStepStore = useWorkflowStepStore();
+ const workflowStepStore = useWorkflowStepStore("mock-workflow");
workflowStepStore.addStep(workflowStepZero);
workflowStepStore.addStep(workflowStepOne);
});
it("adds connection", () => {
- const connectionStore = useConnectionStore();
+ const connectionStore = useConnectionStore("mock-workflow");
expect(connectionStore.connections.length).toBe(0);
connectionStore.addConnection(connection);
expect(connectionStore.connections.length).toBe(1);
});
it("removes connection", () => {
- const connectionStore = useConnectionStore();
+ const connectionStore = useConnectionStore("mock-workflow");
connectionStore.addConnection(connection);
connectionStore.removeConnection(inputTerminal);
expect(connectionStore.connections.length).toBe(0);
});
it("finds connections for steps", () => {
- const connectionStore = useConnectionStore();
+ const connectionStore = useConnectionStore("mock-workflow");
expect(connectionStore.getConnectionsForStep(0)).toStrictEqual([]);
expect(connectionStore.getConnectionsForStep(1)).toStrictEqual([]);
connectionStore.addConnection(connection);
@@ -67,7 +67,7 @@ describe("Connection Store", () => {
expect(connectionStore.getConnectionsForStep(1)).toStrictEqual([]);
});
it("finds output terminals for input terminal", () => {
- const connectionStore = useConnectionStore();
+ const connectionStore = useConnectionStore("mock-workflow");
expect(connectionStore.getOutputTerminalsForInputTerminal(getTerminalId(connection.input))).toStrictEqual([]);
connectionStore.addConnection(connection);
expect(connectionStore.getOutputTerminalsForInputTerminal(getTerminalId(connection.input))).toStrictEqual([
diff --git a/client/src/stores/workflowConnectionStore.ts b/client/src/stores/workflowConnectionStore.ts
index 522a86bb2b23..686cc9b4a287 100644
--- a/client/src/stores/workflowConnectionStore.ts
+++ b/client/src/stores/workflowConnectionStore.ts
@@ -42,82 +42,88 @@ interface TerminalToOutputTerminals {
[index: string]: OutputTerminal[];
}
-export const useConnectionStore = defineStore("workflowConnectionStore", {
- state: (): State => ({
- connections: [] as Array>,
- invalidConnections: {} as InvalidConnections,
- inputTerminalToOutputTerminals: {} as TerminalToOutputTerminals,
- terminalToConnection: {} as { [index: string]: Connection[] },
- stepToConnections: {} as { [index: number]: Connection[] },
- }),
- getters: {
- getOutputTerminalsForInputTerminal(state: State) {
- return (terminalId: string): OutputTerminal[] => {
- return state.inputTerminalToOutputTerminals[terminalId] || [];
- };
+export const useConnectionStore = (workflowId: string) => {
+ if (!workflowId) {
+ throw new Error("WorkflowId is undefined");
+ }
+
+ return defineStore(`workflowConnectionStore${workflowId}`, {
+ state: (): State => ({
+ connections: [] as Array>,
+ invalidConnections: {} as InvalidConnections,
+ inputTerminalToOutputTerminals: {} as TerminalToOutputTerminals,
+ terminalToConnection: {} as { [index: string]: Connection[] },
+ stepToConnections: {} as { [index: number]: Connection[] },
+ }),
+ getters: {
+ getOutputTerminalsForInputTerminal(state: State) {
+ return (terminalId: string): OutputTerminal[] => {
+ return state.inputTerminalToOutputTerminals[terminalId] || [];
+ };
+ },
+ getConnectionsForTerminal(state: State) {
+ return (terminalId: string): Connection[] => {
+ return state.terminalToConnection[terminalId] || [];
+ };
+ },
+ getConnectionsForStep(state: State) {
+ return (stepId: number): Connection[] => state.stepToConnections[stepId] || [];
+ },
},
- getConnectionsForTerminal(state: State) {
- return (terminalId: string): Connection[] => {
- return state.terminalToConnection[terminalId] || [];
- };
- },
- getConnectionsForStep(state: State) {
- return (stepId: number): Connection[] => state.stepToConnections[stepId] || [];
- },
- },
- actions: {
- addConnection(this, _connection: Connection) {
- const connection = Object.freeze(_connection);
- this.connections.push(connection);
- const stepStore = useWorkflowStepStore();
- stepStore.addConnection(connection);
- this.terminalToConnection = updateTerminalToConnection(this.connections);
- this.inputTerminalToOutputTerminals = updateTerminalToTerminal(this.connections);
- this.stepToConnections = updateStepToConnections(this.connections);
- },
- markInvalidConnection(this: State, connectionId: string, reason: string) {
- Vue.set(this.invalidConnections, connectionId, reason);
- },
- dropFromInvalidConnections(this: State, connectionId: string) {
- Vue.delete(this.invalidConnections, connectionId);
- },
- removeConnection(this, terminal: InputTerminal | OutputTerminal | ConnectionId) {
- const stepStore = useWorkflowStepStore();
- this.connections = this.connections.filter((connection) => {
- const id = getConnectionId(connection);
-
- if (typeof terminal === "string") {
- if (id === terminal) {
- stepStore.removeConnection(connection);
- Vue.delete(this.invalidConnections, id);
- return false;
- } else {
- return true;
- }
- } else if (terminal.connectorType === "input") {
- if (connection.input.stepId == terminal.stepId && connection.input.name == terminal.name) {
- stepStore.removeConnection(connection);
- Vue.delete(this.invalidConnections, id);
- return false;
- } else {
- return true;
- }
- } else {
- if (connection.output.stepId == terminal.stepId && connection.output.name == terminal.name) {
- stepStore.removeConnection(connection);
- Vue.delete(this.invalidConnections, id);
- return false;
+ actions: {
+ addConnection(this, _connection: Connection) {
+ const connection = Object.freeze(_connection);
+ this.connections.push(connection);
+ const stepStore = useWorkflowStepStore(workflowId);
+ stepStore.addConnection(connection);
+ this.terminalToConnection = updateTerminalToConnection(this.connections);
+ this.inputTerminalToOutputTerminals = updateTerminalToTerminal(this.connections);
+ this.stepToConnections = updateStepToConnections(this.connections);
+ },
+ markInvalidConnection(this: State, connectionId: string, reason: string) {
+ Vue.set(this.invalidConnections, connectionId, reason);
+ },
+ dropFromInvalidConnections(this: State, connectionId: string) {
+ Vue.delete(this.invalidConnections, connectionId);
+ },
+ removeConnection(this, terminal: InputTerminal | OutputTerminal | ConnectionId) {
+ const stepStore = useWorkflowStepStore(workflowId);
+ this.connections = this.connections.filter((connection) => {
+ const id = getConnectionId(connection);
+
+ if (typeof terminal === "string") {
+ if (id === terminal) {
+ stepStore.removeConnection(connection);
+ Vue.delete(this.invalidConnections, id);
+ return false;
+ } else {
+ return true;
+ }
+ } else if (terminal.connectorType === "input") {
+ if (connection.input.stepId == terminal.stepId && connection.input.name == terminal.name) {
+ stepStore.removeConnection(connection);
+ Vue.delete(this.invalidConnections, id);
+ return false;
+ } else {
+ return true;
+ }
} else {
- return true;
+ if (connection.output.stepId == terminal.stepId && connection.output.name == terminal.name) {
+ stepStore.removeConnection(connection);
+ Vue.delete(this.invalidConnections, id);
+ return false;
+ } else {
+ return true;
+ }
}
- }
- });
- this.terminalToConnection = updateTerminalToConnection(this.connections);
- this.inputTerminalToOutputTerminals = updateTerminalToTerminal(this.connections);
- this.stepToConnections = updateStepToConnections(this.connections);
+ });
+ this.terminalToConnection = updateTerminalToConnection(this.connections);
+ this.inputTerminalToOutputTerminals = updateTerminalToTerminal(this.connections);
+ this.stepToConnections = updateStepToConnections(this.connections);
+ },
},
- },
-});
+ })();
+};
function updateTerminalToTerminal(connections: Connection[]) {
const inputTerminalToOutputTerminals: TerminalToOutputTerminals = {};
diff --git a/client/src/stores/workflowEditorStateStore.ts b/client/src/stores/workflowEditorStateStore.ts
index 4dcbecd3167f..b7e5f1bdfbfb 100644
--- a/client/src/stores/workflowEditorStateStore.ts
+++ b/client/src/stores/workflowEditorStateStore.ts
@@ -33,67 +33,69 @@ interface State {
stepLoadingState: { [index: number]: { loading?: boolean; error?: string } };
}
-export const useWorkflowStateStore = defineStore("workflowStateStore", {
- state: (): State => ({
- inputTerminals: {},
- outputTerminals: {},
- draggingPosition: null,
- draggingTerminal: null,
- activeNodeId: null,
- scale: 1,
- stepPosition: {},
- stepLoadingState: {},
- }),
- getters: {
- getInputTerminalPosition(state: State) {
- return (stepId: number, inputName: string) => {
- return state.inputTerminals[stepId]?.[inputName] as InputTerminalPosition | undefined;
- };
+export const useWorkflowStateStore = (workflowId: string) => {
+ return defineStore(`workflowStateStore${workflowId}`, {
+ state: (): State => ({
+ inputTerminals: {},
+ outputTerminals: {},
+ draggingPosition: null,
+ draggingTerminal: null,
+ activeNodeId: null,
+ scale: 1,
+ stepPosition: {},
+ stepLoadingState: {},
+ }),
+ getters: {
+ getInputTerminalPosition(state: State) {
+ return (stepId: number, inputName: string) => {
+ return state.inputTerminals[stepId]?.[inputName] as InputTerminalPosition | undefined;
+ };
+ },
+ getOutputTerminalPosition(state: State) {
+ return (stepId: number, outputName: string) => {
+ return state.outputTerminals[stepId]?.[outputName] as OutputTerminalPosition | undefined;
+ };
+ },
+ getStepLoadingState(state: State) {
+ return (stepId: number) => state.stepLoadingState[stepId];
+ },
},
- getOutputTerminalPosition(state: State) {
- return (stepId: number, outputName: string) => {
- return state.outputTerminals[stepId]?.[outputName] as OutputTerminalPosition | undefined;
- };
- },
- getStepLoadingState(state: State) {
- return (stepId: number) => state.stepLoadingState[stepId];
- },
- },
- actions: {
- setInputTerminalPosition(stepId: number, inputName: string, position: InputTerminalPosition) {
- if (!this.inputTerminals[stepId]) {
- Vue.set(this.inputTerminals, stepId, {});
- }
+ actions: {
+ setInputTerminalPosition(stepId: number, inputName: string, position: InputTerminalPosition) {
+ if (!this.inputTerminals[stepId]) {
+ Vue.set(this.inputTerminals, stepId, {});
+ }
- Vue.set(this.inputTerminals[stepId]!, inputName, position);
- },
- setOutputTerminalPosition(stepId: number, outputName: string, position: OutputTerminalPosition) {
- if (!this.outputTerminals[stepId]) {
- Vue.set(this.outputTerminals, stepId, reactive({}));
- }
+ Vue.set(this.inputTerminals[stepId]!, inputName, position);
+ },
+ setOutputTerminalPosition(stepId: number, outputName: string, position: OutputTerminalPosition) {
+ if (!this.outputTerminals[stepId]) {
+ Vue.set(this.outputTerminals, stepId, reactive({}));
+ }
- Vue.set(this.outputTerminals[stepId]!, outputName, position);
- },
- deleteInputTerminalPosition(stepId: number, inputName: string) {
- delete this.inputTerminals[stepId]?.[inputName];
- },
- deleteOutputTerminalPosition(stepId: number, outputName: string) {
- delete this.outputTerminals[stepId]?.[outputName];
- },
- setActiveNode(nodeId: number | null) {
- this.activeNodeId = nodeId;
- },
- setScale(scale: number) {
- this.scale = scale;
- },
- setStepPosition(stepId: number, position: UnwrapRef) {
- Vue.set(this.stepPosition, stepId, position);
- },
- deleteStepPosition(stepId: number) {
- delete this.stepPosition[stepId];
- },
- setLoadingState(stepId: number, loading: boolean, error: string | undefined) {
- Vue.set(this.stepLoadingState, stepId, { loading, error });
+ Vue.set(this.outputTerminals[stepId]!, outputName, position);
+ },
+ deleteInputTerminalPosition(stepId: number, inputName: string) {
+ delete this.inputTerminals[stepId]?.[inputName];
+ },
+ deleteOutputTerminalPosition(stepId: number, outputName: string) {
+ delete this.outputTerminals[stepId]?.[outputName];
+ },
+ setActiveNode(nodeId: number | null) {
+ this.activeNodeId = nodeId;
+ },
+ setScale(scale: number) {
+ this.scale = scale;
+ },
+ setStepPosition(stepId: number, position: UnwrapRef) {
+ Vue.set(this.stepPosition, stepId, position);
+ },
+ deleteStepPosition(stepId: number) {
+ delete this.stepPosition[stepId];
+ },
+ setLoadingState(stepId: number, loading: boolean, error: string | undefined) {
+ Vue.set(this.stepLoadingState, stepId, { loading, error });
+ },
},
- },
-});
+ })();
+};
diff --git a/client/src/stores/workflowStepStore.test.ts b/client/src/stores/workflowStepStore.test.ts
index a3fbe8f1559f..9d9258b96550 100644
--- a/client/src/stores/workflowStepStore.test.ts
+++ b/client/src/stores/workflowStepStore.test.ts
@@ -32,29 +32,29 @@ describe("Connection Store", () => {
});
it("adds step", () => {
- const stepStore = useWorkflowStepStore();
+ const stepStore = useWorkflowStepStore("mock-workflow");
expect(stepStore.steps).toStrictEqual({});
stepStore.addStep(workflowStepZero);
expect(stepStore.getStep(0)).toStrictEqual(workflowStepZero);
expect(workflowStepZero.id).toBe(0);
});
it("removes step", () => {
- const stepStore = useWorkflowStepStore();
+ const stepStore = useWorkflowStepStore("mock-workflow");
const addedStep = stepStore.addStep(workflowStepZero);
expect(addedStep.id).toBe(0);
stepStore.removeStep(addedStep.id);
expect(stepStore.getStep(0)).toBe(undefined);
});
it("creates connection if step has connection", () => {
- const stepStore = useWorkflowStepStore();
- const connectionStore = useConnectionStore();
+ const stepStore = useWorkflowStepStore("mock-workflow");
+ const connectionStore = useConnectionStore("mock-workflow");
stepStore.addStep(workflowStepZero);
stepStore.addStep(workflowStepOne);
expect(connectionStore.connections.length).toBe(1);
});
it("removes connection if step has connection", () => {
- const stepStore = useWorkflowStepStore();
- const connectionStore = useConnectionStore();
+ const stepStore = useWorkflowStepStore("mock-workflow");
+ const connectionStore = useConnectionStore("mock-workflow");
stepStore.addStep(workflowStepZero);
const stepOne = stepStore.addStep(workflowStepOne);
expect(connectionStore.connections.length).toBe(1);
diff --git a/client/src/stores/workflowStepStore.ts b/client/src/stores/workflowStepStore.ts
index 8457cf5c98b3..81d4b15674cb 100644
--- a/client/src/stores/workflowStepStore.ts
+++ b/client/src/stores/workflowStepStore.ts
@@ -59,6 +59,7 @@ export interface ParameterOutput extends Omit
}
interface BaseStepInput {
+ valid?: boolean;
name: string;
label: string;
multiple: boolean;
@@ -106,6 +107,7 @@ export interface NewStep {
position?: StepPosition;
post_job_actions?: PostJobActions;
tool_state: Record;
+ tool_version?: string;
tooltip?: string;
type: "tool" | "data_input" | "data_collection_input" | "subworkflow" | "parameter_input" | "pause";
uuid?: string;
@@ -142,165 +144,187 @@ interface StepInputMapOver {
[index: number]: { [index: string]: CollectionTypeDescriptor };
}
-export const useWorkflowStepStore = defineStore("workflowStepStore", {
- state: (): State => ({
- steps: {} as Steps,
- stepMapOver: {} as { [index: number]: CollectionTypeDescriptor },
- stepInputMapOver: {} as StepInputMapOver,
- stepIndex: -1,
- stepExtraInputs: {} as { [index: number]: InputTerminalSource[] },
- }),
- getters: {
- getStep(state: State) {
- return (stepId: number): Step | undefined => {
- return state.steps[stepId.toString()];
- };
- },
- getStepExtraInputs(state: State) {
- return (stepId: number) => this.stepExtraInputs[stepId] || [];
- },
- getStepIndex(state: State) {
- return Math.max(...Object.values(state.steps).map((step) => step.id), state.stepIndex);
- },
- hasActiveOutputs(state: State) {
- return Boolean(Object.values(state.steps).find((step) => step.workflow_outputs?.length));
+export const useWorkflowStepStore = (workflowId: string) => {
+ return defineStore(`workflowStepStore${workflowId}`, {
+ state: (): State => ({
+ steps: {} as Steps,
+ stepMapOver: {} as { [index: number]: CollectionTypeDescriptor },
+ stepInputMapOver: {} as StepInputMapOver,
+ stepIndex: -1,
+ stepExtraInputs: {} as { [index: number]: InputTerminalSource[] },
+ }),
+ getters: {
+ getStep(state: State) {
+ return (stepId: number): Step | undefined => {
+ return state.steps[stepId.toString()];
+ };
+ },
+ getStepExtraInputs(state: State) {
+ return (stepId: number) => this.stepExtraInputs[stepId] || [];
+ },
+ getStepIndex(state: State) {
+ return Math.max(...Object.values(state.steps).map((step) => step.id), state.stepIndex);
+ },
+ hasActiveOutputs(state: State) {
+ return Boolean(Object.values(state.steps).find((step) => step.workflow_outputs?.length));
+ },
+ workflowOutputs(state: State) {
+ const workflowOutputs: WorkflowOutputs = {};
+ Object.values(state.steps).forEach((step) => {
+ if (step.workflow_outputs?.length) {
+ step.workflow_outputs.forEach((workflowOutput) => {
+ if (workflowOutput.label) {
+ workflowOutputs[workflowOutput.label] = {
+ outputName: workflowOutput.output_name,
+ stepId: step.id,
+ };
+ }
+ });
+ }
+ });
+ return workflowOutputs;
+ },
+ duplicateLabels(state: State) {
+ const duplicateLabels: Set = new Set();
+ const labels: Set = new Set();
+ Object.values(state.steps).forEach((step) => {
+ if (step.workflow_outputs?.length) {
+ step.workflow_outputs.forEach((workflowOutput) => {
+ if (workflowOutput.label) {
+ if (labels.has(workflowOutput.label)) {
+ duplicateLabels.add(workflowOutput.label);
+ }
+ labels.add(workflowOutput.label);
+ }
+ });
+ }
+ });
+ return duplicateLabels;
+ },
},
- workflowOutputs(state: State) {
- const workflowOutputs: WorkflowOutputs = {};
- Object.values(state.steps).forEach((step) => {
- if (step.workflow_outputs?.length) {
- step.workflow_outputs.forEach((workflowOutput) => {
- if (workflowOutput.label) {
- workflowOutputs[workflowOutput.label] = {
- outputName: workflowOutput.output_name,
- stepId: step.id,
- };
- }
- });
+ actions: {
+ addStep(newStep: NewStep): Step {
+ const stepId = newStep.id ? newStep.id : this.getStepIndex + 1;
+ const step = Object.freeze({ ...newStep, id: stepId } as Step);
+ Vue.set(this.steps, stepId.toString(), step);
+ const connectionStore = useConnectionStore(workflowId);
+ stepToConnections(step).map((connection) => connectionStore.addConnection(connection));
+ this.stepExtraInputs[step.id] = getStepExtraInputs(step);
+ return step;
+ },
+ insertNewStep(
+ contentId: NewStep["content_id"],
+ name: NewStep["name"],
+ type: NewStep["type"],
+ position: NewStep["position"]
+ ) {
+ const stepData: NewStep = {
+ name: name,
+ content_id: contentId,
+ input_connections: {},
+ type: type,
+ inputs: [],
+ outputs: [],
+ position: position,
+ post_job_actions: {},
+ tool_state: {},
+ };
+ return this.addStep(stepData);
+ },
+ updateStep(this: State, step: Step) {
+ const workflow_outputs = step.workflow_outputs?.filter((workflowOutput) =>
+ step.outputs.find((output) => workflowOutput.output_name == output.name)
+ );
+ this.steps[step.id.toString()] = Object.freeze({ ...step, workflow_outputs });
+ this.stepExtraInputs[step.id] = getStepExtraInputs(step);
+ },
+ changeStepMapOver(stepId: number, mapOver: CollectionTypeDescriptor) {
+ Vue.set(this.stepMapOver, stepId, mapOver);
+ },
+ resetStepInputMapOver(stepId: number) {
+ Vue.set(this.stepInputMapOver, stepId, {});
+ },
+ changeStepInputMapOver(stepId: number, inputName: string, mapOver: CollectionTypeDescriptor) {
+ if (this.stepInputMapOver[stepId]) {
+ Vue.set(this.stepInputMapOver[stepId]!, inputName, mapOver);
+ } else {
+ Vue.set(this.stepInputMapOver, stepId, { [inputName]: mapOver });
}
- });
- return workflowOutputs;
- },
- },
- actions: {
- addStep(newStep: NewStep): Step {
- const stepId = newStep.id ? newStep.id : this.getStepIndex + 1;
- const step = Object.freeze({ ...newStep, id: stepId } as Step);
- Vue.set(this.steps, stepId.toString(), step);
- const connectionStore = useConnectionStore();
- stepToConnections(step).map((connection) => connectionStore.addConnection(connection));
- this.stepExtraInputs[step.id] = getStepExtraInputs(step);
- return step;
- },
- insertNewStep(
- contentId: NewStep["content_id"],
- name: NewStep["name"],
- type: NewStep["type"],
- position: NewStep["position"]
- ) {
- const stepData: NewStep = {
- name: name,
- content_id: contentId,
- input_connections: {},
- type: type,
- inputs: [],
- outputs: [],
- position: position,
- post_job_actions: {},
- tool_state: {},
- };
- return this.addStep(stepData);
- },
- updateStep(this: State, step: Step) {
- const workflow_outputs = step.workflow_outputs?.filter((workflowOutput) =>
- step.outputs.find((output) => workflowOutput.output_name == output.name)
- );
- this.steps[step.id.toString()] = Object.freeze({ ...step, workflow_outputs });
- this.stepExtraInputs[step.id] = getStepExtraInputs(step);
- },
- changeStepMapOver(stepId: number, mapOver: CollectionTypeDescriptor) {
- Vue.set(this.stepMapOver, stepId, mapOver);
- },
- resetStepInputMapOver(stepId: number) {
- Vue.set(this.stepInputMapOver, stepId, {});
- },
- changeStepInputMapOver(stepId: number, inputName: string, mapOver: CollectionTypeDescriptor) {
- if (this.stepInputMapOver[stepId]) {
- Vue.set(this.stepInputMapOver[stepId]!, inputName, mapOver);
- } else {
- Vue.set(this.stepInputMapOver, stepId, { [inputName]: mapOver });
- }
- },
- addConnection(connection: Connection) {
- const inputStep = this.getStep(connection.input.stepId);
- assertDefined(
- inputStep,
- `Failed to add connection, because step with id ${connection.input.stepId} is undefined`
- );
- const input = inputStep.inputs.find((input) => input.name === connection.input.name);
- const connectionLink: ConnectionOutputLink = {
- output_name: connection.output.name,
- id: connection.output.stepId,
- };
- if (input && "input_subworkflow_step_id" in input && input.input_subworkflow_step_id !== undefined) {
- connectionLink["input_subworkflow_step_id"] = input.input_subworkflow_step_id;
- }
- let connectionLinks: ConnectionOutputLink[] = [connectionLink];
- let inputConnection = inputStep.input_connections[connection.input.name];
- if (inputConnection) {
- if (!Array.isArray(inputConnection)) {
- inputConnection = [inputConnection];
+ },
+ addConnection(connection: Connection) {
+ const inputStep = this.getStep(connection.input.stepId);
+ assertDefined(
+ inputStep,
+ `Failed to add connection, because step with id ${connection.input.stepId} is undefined`
+ );
+ const input = inputStep.inputs.find((input) => input.name === connection.input.name);
+ const connectionLink: ConnectionOutputLink = {
+ output_name: connection.output.name,
+ id: connection.output.stepId,
+ };
+ if (input && "input_subworkflow_step_id" in input && input.input_subworkflow_step_id !== undefined) {
+ connectionLink["input_subworkflow_step_id"] = input.input_subworkflow_step_id;
+ }
+ let connectionLinks: ConnectionOutputLink[] = [connectionLink];
+ let inputConnection = inputStep.input_connections[connection.input.name];
+ if (inputConnection) {
+ if (!Array.isArray(inputConnection)) {
+ inputConnection = [inputConnection];
+ }
+ inputConnection = inputConnection.filter(
+ (connection) =>
+ !(
+ connection.id === connectionLink.id &&
+ connection.output_name === connectionLink.output_name
+ )
+ );
+ connectionLinks = [...connectionLinks, ...inputConnection];
}
- inputConnection = inputConnection.filter(
- (connection) =>
- !(connection.id === connectionLink.id && connection.output_name === connectionLink.output_name)
+ const updatedStep = {
+ ...inputStep,
+ input_connections: {
+ ...inputStep.input_connections,
+ [connection.input.name]: connectionLinks.sort((a, b) =>
+ a.id === b.id ? a.output_name.localeCompare(b.output_name) : a.id - b.id
+ ),
+ },
+ };
+ this.updateStep(updatedStep);
+ },
+ removeConnection(connection: Connection) {
+ const inputStep = this.getStep(connection.input.stepId);
+ assertDefined(
+ inputStep,
+ `Failed to remove connection, because step with id ${connection.input.stepId} is undefined`
);
- connectionLinks = [...connectionLinks, ...inputConnection];
- }
- const updatedStep = {
- ...inputStep,
- input_connections: {
- ...inputStep.input_connections,
- [connection.input.name]: connectionLinks.sort((a, b) =>
- a.id === b.id ? a.output_name.localeCompare(b.output_name) : a.id - b.id
- ),
- },
- };
- this.updateStep(updatedStep);
- },
- removeConnection(connection: Connection) {
- const inputStep = this.getStep(connection.input.stepId);
- assertDefined(
- inputStep,
- `Failed to remove connection, because step with id ${connection.input.stepId} is undefined`
- );
- const inputConnections = inputStep.input_connections[connection.input.name];
- if (this.getStepExtraInputs(inputStep.id).find((input) => connection.input.name === input.name)) {
- inputStep.input_connections[connection.input.name] = undefined;
- } else {
- if (Array.isArray(inputConnections)) {
- inputStep.input_connections[connection.input.name] = inputConnections.filter(
- (outputLink) =>
- !(outputLink.id === connection.output.stepId,
- outputLink.output_name === connection.output.name)
- );
+ const inputConnections = inputStep.input_connections[connection.input.name];
+ if (this.getStepExtraInputs(inputStep.id).find((input) => connection.input.name === input.name)) {
+ inputStep.input_connections[connection.input.name] = undefined;
} else {
- Vue.delete(inputStep.input_connections, connection.input.name);
+ if (Array.isArray(inputConnections)) {
+ inputStep.input_connections[connection.input.name] = inputConnections.filter(
+ (outputLink) =>
+ !(outputLink.id === connection.output.stepId,
+ outputLink.output_name === connection.output.name)
+ );
+ } else {
+ Vue.delete(inputStep.input_connections, connection.input.name);
+ }
}
- }
- this.updateStep(inputStep);
- },
- removeStep(this: State, stepId: number) {
- const connectionStore = useConnectionStore();
- connectionStore
- .getConnectionsForStep(stepId)
- .forEach((connection) => connectionStore.removeConnection(getConnectionId(connection)));
- Vue.delete(this.steps, stepId.toString());
- Vue.delete(this.stepExtraInputs, stepId);
+ this.updateStep(inputStep);
+ },
+ removeStep(this: State, stepId: number) {
+ const connectionStore = useConnectionStore(workflowId);
+ connectionStore
+ .getConnectionsForStep(stepId)
+ .forEach((connection) => connectionStore.removeConnection(getConnectionId(connection)));
+ Vue.delete(this.steps, stepId.toString());
+ Vue.delete(this.stepExtraInputs, stepId);
+ },
},
- },
-});
+ })();
+};
export function stepToConnections(step: Step): Connection[] {
const connections: Connection[] = [];
diff --git a/client/src/stores/workflowStore.ts b/client/src/stores/workflowStore.ts
index a890b44749a1..aca2e887f5e7 100644
--- a/client/src/stores/workflowStore.ts
+++ b/client/src/stores/workflowStore.ts
@@ -5,9 +5,12 @@ import { computed, ref, set } from "vue";
import { getAppRoot } from "@/onload/loadConfig";
import type { Steps } from "@/stores/workflowStepStore";
-interface Workflow {
- [index: string]: any;
+export interface Workflow {
+ name: string;
+ id: string;
steps: Steps;
+ step_count?: number;
+ latest_id?: string;
}
export const useWorkflowStore = defineStore("workflowStore", () => {
diff --git a/client/src/style/scss/base.scss b/client/src/style/scss/base.scss
index 2a3cb110d1cc..0b08c0aa0af1 100644
--- a/client/src/style/scss/base.scss
+++ b/client/src/style/scss/base.scss
@@ -37,8 +37,6 @@ $fa-font-path: "../../../node_modules/@fortawesome/fontawesome-free/webfonts/";
@import "charts.scss";
@import "message.scss";
@import "markdown.scss";
-@import "toolshed.scss";
-@import "workflow.scss";
@import "multiselect.scss";
@import "icon-btn.scss";
@import "peek-columns.scss";
diff --git a/client/src/style/scss/multiselect.scss b/client/src/style/scss/multiselect.scss
index f0c4dd61fa01..cafc6647eb9f 100644
--- a/client/src/style/scss/multiselect.scss
+++ b/client/src/style/scss/multiselect.scss
@@ -1,24 +1,40 @@
.multiselect {
font-weight: normal;
+ .multiselect__content-wrapper {
+ background: darken($white, 2%);
+ overflow-x: hidden;
+ }
+ .multiselect__input {
+ background: transparent;
+ }
.multiselect__option {
white-space: normal;
font-size: $font-size-base;
}
.multiselect__option--highlight {
- background: $brand-light;
- color: $brand-dark;
+ background-color: $brand-info;
+ color: $white;
}
.multiselect__option--selected {
background: $brand-primary;
color: $brand-light;
}
- .multiselect__single {
- font-size: $font-size-base;
- }
.multiselect__tag {
min-height: 0;
+ white-space: normal;
+ word-break: break-all;
}
.multiselect__tags {
+ background: transparent;
border: $border-default;
+ min-height: unset;
+ .multiselect__single {
+ background: transparent;
+ color: $text-color;
+ font-size: $font-size-base;
+ overflow: hidden;
+ white-space: normal;
+ word-break: break-all;
+ }
}
}
diff --git a/client/src/style/scss/overrides.scss b/client/src/style/scss/overrides.scss
index dde16959fd41..8c647d74517f 100644
--- a/client/src/style/scss/overrides.scss
+++ b/client/src/style/scss/overrides.scss
@@ -193,6 +193,10 @@ table.info_data_table th:nth-child(1) {
border: none;
}
+.btn.disabled {
+ pointer-events: unset !important;
+}
+
// enable titles on disabled dropdown items
.dropdown-menu {
.dropdown-item.disabled {
@@ -214,3 +218,8 @@ table.info_data_table th:nth-child(1) {
.sticky-top {
z-index: 800;
}
+
+// remove margin for labels with for attribute
+label[for] {
+ margin-bottom: 0;
+}
diff --git a/client/src/style/scss/theme/blue.scss b/client/src/style/scss/theme/blue.scss
index 42f522dde449..724e5695192f 100644
--- a/client/src/style/scss/theme/blue.scss
+++ b/client/src/style/scss/theme/blue.scss
@@ -125,6 +125,7 @@ $panel_footer_height: 25px;
// Portlets
$portlet-bg-color: $gray-200;
+$portlet-focus-color: $brand-info;
// Borders
$border-radius-base: 0.1875rem;
diff --git a/client/src/style/scss/toolshed.scss b/client/src/style/scss/toolshed.scss
deleted file mode 100644
index 72a4c8b68852..000000000000
--- a/client/src/style/scss/toolshed.scss
+++ /dev/null
@@ -1,40 +0,0 @@
-@import "theme/blue.scss";
-.shed-style-container {
- width: 95%;
- margin: auto;
- margin-top: 1em;
- overflow: auto !important;
- .header {
- h2 {
- float: left;
- }
- span {
- float: right;
- }
- }
-}
-.ui-autocomplete {
- background-color: #fff;
- li.ui-menu-item {
- list-style-type: none;
- }
-}
-
-.masthead-simple {
- background-color: $brand-dark;
- height: $masthead-height;
- .navbar-brand {
- position: absolute;
- left: 0.5rem;
- .navbar-brand-image {
- max-height: 2rem;
- }
- }
- .navbar-brand-title {
- color: $brand-light;
- font-size: 1.1rem;
- }
- .nav-link {
- color: $brand-light !important;
- }
-}
diff --git a/client/src/style/scss/ui.scss b/client/src/style/scss/ui.scss
index a9761d8072af..30f090bd5ac2 100644
--- a/client/src/style/scss/ui.scss
+++ b/client/src/style/scss/ui.scss
@@ -138,8 +138,9 @@ $ui-margin-horizontal-large: $margin-v * 2;
}
.portlet-operations {
button {
- @extend .ml-1;
- @extend .py-0;
+ margin-left: 0.25rem;
+ padding-top: 0;
+ padding-bottom: 0;
}
}
}
@@ -171,7 +172,11 @@ $ui-margin-horizontal-large: $margin-v * 2;
@extend .mb-2;
border: none;
border-left: solid 3px $portlet-bg-color;
- border-radius: $border-radius-large;
+ border-radius: $border-radius-large $border-radius-large $border-radius-large 0;
+ &:focus-within {
+ border-left: solid 3px $portlet-focus-color;
+ }
+
.portlet-header:first-child {
@extend .rounded-0;
@extend .p-2;
@@ -213,10 +218,6 @@ $ui-margin-horizontal-large: $margin-v * 2;
}
}
-.ui-input-error {
- border-color: $brand-danger;
-}
-
.ui-textarea {
@extend .ui-input;
height: 100px !important;
@@ -348,23 +349,25 @@ $ui-margin-horizontal-large: $margin-v * 2;
}
}
-.ui-dragover {
+.ui-dragover-warning {
+ @extend .rounded;
@extend .p-1;
- border-radius: $border-radius-base;
- border: 2px solid $state-warning-bg;
background: lighten($state-warning-bg, 10%);
+ border: 2px solid $state-warning-bg;
}
.ui-dragover-danger {
- @extend .ui-dragover;
- border: 2px solid $state-danger-bg;
+ @extend .rounded;
+ @extend .p-1;
background: lighten($state-danger-bg, 10%);
+ border: 2px solid $state-danger-bg;
}
.ui-dragover-success {
- @extend .ui-dragover;
- border: 2px solid $state-success-bg;
+ @extend .rounded;
+ @extend .p-1;
background: lighten($state-success-bg, 10%);
+ border: 2px solid $state-success-bg;
}
/* Used for tree in tool recommendations */
@@ -440,3 +443,18 @@ $ui-margin-horizontal-large: $margin-v * 2;
.overflow-x-hidden {
overflow-x: hidden !important;
}
+
+// TODO: move this to component library, once that exists
+.inline-icon-button {
+ border: none;
+ background-color: transparent;
+ color: $brand-primary;
+ display: inline;
+
+ padding: 0 0.1rem;
+
+ &:hover {
+ background-color: $brand-primary;
+ color: $brand-light;
+ }
+}
diff --git a/client/src/style/scss/unsorted.scss b/client/src/style/scss/unsorted.scss
index adbf5f8679e4..4c3799859c8f 100644
--- a/client/src/style/scss/unsorted.scss
+++ b/client/src/style/scss/unsorted.scss
@@ -932,7 +932,6 @@ div.toolSectionTitle {
}
/* Toolshed, reports custom styles from mako templates */
-body.toolshed,
body.reports {
margin: 0;
padding: 0;
diff --git a/client/src/style/scss/upload.scss b/client/src/style/scss/upload.scss
index cac5c6804481..d6bffbe9dc0b 100644
--- a/client/src/style/scss/upload.scss
+++ b/client/src/style/scss/upload.scss
@@ -1,12 +1,3 @@
-.upload-dialog {
- width: 900px;
-}
-
-.upload-dialog-body {
- height: 500px;
- overflow: hidden;
-}
-
.upload-button {
@extend .w-100;
@extend .mb-2;
@@ -39,35 +30,7 @@
}
}
-.upload-input {
- font-size: $font-size-base;
- color: $text-color;
- height: 20px;
- line-height: 18px;
-}
-
-.upload-select2 {
- .select2-arrow b {
- position: absolute;
- top: -3px;
- }
- .select2-choice {
- @extend .upload-input;
- background: transparent;
- }
- .select2-container-disabled {
- .select2-arrow {
- background: transparent;
- }
- }
- .select2-choice {
- background: transparent;
- text-align: center;
- font-weight: normal;
- }
-}
-
-.upload-view-default {
+.upload-wrapper {
.upload-box.highlight {
border-color: $border-color;
border-width: 2px;
@@ -76,22 +39,11 @@
color: $border-color;
}
}
- .upload-icon {
- position: relative;
- cursor: default;
- font-size: $font-size-base;
- width: $font-size-base;
- }
- .upload-icon-button {
- @extend .upload-icon;
- cursor: pointer;
- }
.upload-box {
@extend .mt-2;
@extend .p-2;
width: 100%;
height: 300px;
- text-align: center;
overflow: scroll;
font-size: $font-size-base;
-moz-border-radius: $border-radius-large;
@@ -99,71 +51,53 @@
border: 1px dashed $border-color;
overflow-x: hidden;
-ms-overflow-style: none;
+ input[type="file"] {
+ display: none;
+ }
+ .upload-error {
+ background: $state-danger-bg;
+ }
+ .upload-success {
+ background: $state-success-bg;
+ }
+ .upload-running {
+ background: $state-running-bg;
+ }
.upload-helper {
@extend h3;
padding: 120px;
color: $border-color;
+ text-align: center;
i {
@extend .mr-2;
font-size: inherit;
}
}
+ .upload-text-message {
+ @extend .my-1;
+ @extend .text-primary;
+ text-align: center;
+ }
.upload-row {
- @extend .upload-select2;
- .upload-title {
- width: 130px;
- word-wrap: break-word;
- background: inherit;
- }
- input.upload-title {
- @extend .upload-input;
- }
- .upload-title-extended {
- width: 580px;
- word-wrap: break-word;
- }
- .upload-size {
- width: 60px;
- white-space: nowrap;
- }
- .upload-extension {
- width: 100px;
- }
- .upload-genome {
- width: 150px;
+ button.dropdown-toggle {
+ @extend .px-2;
+ @extend .py-0;
}
- .upload-mode {
- @extend .upload-icon;
- @extend .m-1;
- float: left;
+ input {
+ font-size: $font-size-base;
+ color: $text-color;
+ height: 22px;
}
- .upload-text-column {
- position: relative;
- .upload-text {
- position: absolute;
- display: none;
- .upload-text-content {
- width: 100%;
- height: 80px;
- resize: none;
- background: inherit;
- color: $text-color;
- white-space: pre;
- overflow: auto;
- }
- .upload-text-info {
- @extend .text-primary;
- }
- }
- }
- .upload-info {
+ .upload-progress {
width: 130px;
line-height: $font-size-base;
.progress {
- @extend .upload-input;
+ height: 22px;
+ font-size: $font-size-base;
+ background-color: $gray-400;
width: 100%;
position: relative;
- line-height: 1.6em;
+ line-height: 22px;
.progress-bar {
border-radius: inherit;
-moz-border-radius: inherit;
@@ -176,146 +110,41 @@
}
}
}
+ .upload-size {
+ width: 60px;
+ white-space: nowrap;
+ }
+ .upload-title {
+ width: 130px;
+ word-wrap: break-word;
+ background: inherit;
+ }
+ .upload-text-content {
+ background: inherit;
+ color: $text-color;
+ height: 80px;
+ overflow: auto;
+ white-space: pre;
+ width: 100%;
+ }
}
}
- .upload-rule-option {
- padding-top: 20px;
- .upload-rule-option-title {
- font-weight: bold;
- padding-bottom: 5px;
- }
- }
- .upload-box-solid {
- border: 1px solid $btn-default-border;
- }
.upload-buttons {
padding-top: 30px;
button {
@extend .ml-1;
}
}
-}
-
-.upload-view-composite {
- @extend .upload-view-default;
- .upload-box {
- .upload-row {
- .upload-title {
- width: 175px;
- }
- .upload-source {
- width: 80px;
- .btn {
- padding: 0px 10px;
- }
- }
- }
- }
-}
-
-.upload-ftp {
- height: 250px;
- width: 550px;
- position: relative;
- overflow-y: auto;
- overflow-x: hidden;
- .upload-ftp-row {
- cursor: pointer;
- .ftp-name {
- width: 290px;
- }
- .ftp-size {
- width: 60px;
- }
- .ftp-time {
- width: 165px;
- }
- }
- .upload-ftp-wait {
- font-size: $font-size-base;
- position: absolute;
- bottom: 10px;
- right: 10px;
- }
- .upload-ftp-help {
- margin-bottom: 10px;
- }
- .upload-ftp-warning {
+ .upload-footer {
+ @extend .mt-2;
+ height: 20px;
text-align: center;
- margin-top: 50px;
- }
- .upload-ftp-row {
- cursor: pointer;
- .ftp-name {
- position: relative;
- word-wrap: break-word;
- }
- .ftp-size {
- white-space: nowrap;
- }
- .ftp-time {
- white-space: nowrap;
+ .upload-footer-title {
+ @extend .ml-2;
+ font-weight: bold;
}
}
- .upload-ftp-row:hover {
- @extend .current;
- }
- th {
- padding: 5px !important;
- }
- td {
- padding: 8px 5px !important;
- }
-}
-
-.upload-table {
- @extend .table;
- @extend .table-striped;
- td {
- padding: 0.5rem;
- }
- .alert-success {
- background: $brand-success !important;
- }
-}
-
-.upload-settings {
- position: relative;
- .upload-settings-cover {
- position: absolute;
- width: 100%;
- height: 100%;
- top: 0px;
- left: 0px;
- background: $white;
- opacity: 0.4;
- cursor: no-drop;
- }
- tr {
- cursor: pointer;
- }
- tr:hover {
- @extend .current;
- }
-}
-
-.upload-footer {
- @extend .mt-2;
- height: 20px;
- text-align: center;
- .upload-footer-title {
- @extend .ml-2;
- font-weight: bold;
- }
- @extend .upload-select2;
- .select2-choice {
- width: 150px;
- }
-}
-
-.upload-top {
- text-align: center;
- .upload-top-info {
+ .upload-header {
font-weight: $font-size-base;
text-align: center;
}
diff --git a/client/src/style/scss/workflow.scss b/client/src/style/scss/workflow.scss
deleted file mode 100644
index d78e1b4b4002..000000000000
--- a/client/src/style/scss/workflow.scss
+++ /dev/null
@@ -1,250 +0,0 @@
-.canvas-svg {
- // not sure if hack or not ...
- overflow: visible;
- display: block;
-}
-
-.node-area {
- position: absolute;
- top: 0;
- left: 0;
- width: 100%;
- height: 100%;
- transform-origin: 0 0;
-}
-.workflow-client {
- .workflow-panel {
- background: $white;
- }
- .workflow-center {
- z-index: 0;
- display: flex;
- flex-direction: column;
- flex-grow: 1;
- .workflow-recommendations {
- height: 30rem;
- }
- .workflow-node {
- @extend .card;
- @extend .position-absolute;
- z-index: 100;
- width: $workflow-node-width;
- border: solid $brand-primary 1px;
- &.node-highlight {
- z-index: 1001;
- border: solid $white 1px;
- box-shadow: 0 0 0 2px $brand-primary;
- }
- &.node-on-scroll-to {
- z-index: 1001;
- border: solid $white 1px;
- box-shadow: 0 0 0 4px $brand-primary;
- transition: box-shadow 0.5s ease-in-out;
- }
- &.node-active {
- z-index: 1001;
- border: solid $white 1px;
- box-shadow: 0 0 0 3px $brand-primary;
- }
- .node-header {
- @extend .card-header;
- @extend .py-1;
- @extend .px-2;
- cursor: move;
- background: $brand-primary;
- color: $white;
- }
- .node-error {
- @extend .m-0;
- @extend .rounded-0;
- @extend .rounded-bottom;
- }
- .node-body {
- @extend .card-body;
- @extend .p-0;
- @extend .mx-2;
- .rule {
- height: 0;
- border: none;
- border-bottom: dotted $brand-primary 1px;
- margin: 0 5px;
- }
- }
- }
- .workflow-canvas {
- // Set the position to relative, so that absolute position coordinates are relative to the canvas (and not the top of the iframe)
- position: relative;
-
- .canvas-content {
- width: 100%;
- height: 100%;
- position: absolute;
- left: 0px;
- top: 0px;
- overflow: hidden;
- }
- .base-terminal {
- @extend .fa;
- @extend .fa-circle;
- @extend .mt-1;
- color: $brand-light;
- position: absolute;
- .icon {
- @extend .fa;
- @extend .fa-chevron-circle-right;
- color: $brand-primary;
- position: absolute;
- left: 0px;
- top: 0px;
- }
- }
- .input-terminal {
- @extend .base-terminal;
- left: -0.65rem;
- }
- .output-terminal {
- @extend .base-terminal;
- right: -0.65rem;
- &:hover > .icon {
- color: $brand-success;
- }
- }
- .input-terminal.multiple {
- font-size: 1.2rem;
- left: -0.8rem;
- top: 3px;
- }
- .output-terminal.multiple {
- font-size: 1.2rem;
- right: -0.8rem;
- bottom: 6px;
- }
- .input-terminal-active.can-accept > .icon {
- color: $brand-success;
- }
- .input-terminal-active.cannot-accept > .icon {
- color: $brand-warning;
- }
- .drag-terminal {
- @extend .fa;
- @extend .fa-circle;
- color: $brand-success;
- position: absolute;
- }
- .mark-terminal {
- @extend .far;
- @extend .fa-square;
- color: $brand-primary;
- cursor: pointer;
- &.mark-terminal-active {
- @extend .fa;
- @extend .fa-check-square;
- }
- &.mark-terminal-visible {
- @extend .fa;
- @extend .fa-eye;
- }
- &.mark-terminal-hidden {
- @extend .fa;
- @extend .fa-eye-slash;
- }
- }
- .delete-terminal {
- @extend .btn;
- @extend .btn-sm;
- @extend .btn-danger;
- @extend .fa;
- @extend .fa-minus-circle;
- @extend .p-1;
- @extend .mt-1;
- cursor: pointer;
- position: absolute;
- z-index: 2500;
- top: 2px;
- left: -0.8rem;
- }
- .callout-terminal {
- @extend .float-left;
- @extend .mr-1;
- }
- .workflow-overview {
- --workflow-overview-size: 150px;
- --workflow-overview-min-size: 50px;
- --workflow-overview-max-size: 300px;
- --workflow-overview-padding: 7px;
- --workflow-overview-border: 1px;
-
- border-top-left-radius: 0.3rem;
- cursor: nwse-resize;
- position: absolute;
- width: var(--workflow-overview-size);
- height: var(--workflow-overview-size);
- right: 0px;
- bottom: 0px;
- border-top: solid $border-color var(--workflow-overview-border);
- border-left: solid $border-color var(--workflow-overview-border);
- background: $workflow-overview-bg no-repeat url("../../assets/images/resizable.png");
- z-index: 20000;
- overflow: hidden;
- padding: var(--workflow-overview-padding) 0 0 var(--workflow-overview-padding);
-
- // account for padding and border
- max-width: calc(
- var(--workflow-overview-max-size) + var(--workflow-overview-padding) +
- var(--workflow-overview-border)
- );
- max-height: calc(
- var(--workflow-overview-max-size) + var(--workflow-overview-padding) +
- var(--workflow-overview-border)
- );
- min-width: calc(
- var(--workflow-overview-min-size) + var(--workflow-overview-padding) +
- var(--workflow-overview-border)
- );
- min-height: calc(
- var(--workflow-overview-min-size) + var(--workflow-overview-padding) +
- var(--workflow-overview-border)
- );
-
- .workflow-overview-body {
- cursor: pointer;
- position: relative;
- overflow: hidden;
- width: 100%;
- height: 100%;
- }
- }
- #input-choices-menu {
- color: black;
- }
- }
- .workflow-report-body {
- display: flex;
- }
- #overview-container {
- position: absolute;
- }
- #overview-canvas {
- width: 100%;
- height: 100%;
- }
- #overview-viewport {
- @extend .rounded;
- position: absolute;
- width: 0px;
- height: 0px;
- border: solid $brand-info 3px;
- background: $white;
- opacity: 0.8;
- z-index: 10;
- }
- }
-}
-
-.workflow-recommendations {
- display: block;
- .header-background {
- border-bottom: solid 1px $brand-primary;
- margin-bottom: 0.5rem;
- }
-}
diff --git a/client/src/toolshed/groups/group-detail-view.js b/client/src/toolshed/groups/group-detail-view.js
deleted file mode 100644
index bb4836c95056..000000000000
--- a/client/src/toolshed/groups/group-detail-view.js
+++ /dev/null
@@ -1,141 +0,0 @@
-import Backbone from "backbone";
-import $ from "jquery";
-import mod_group_model from "toolshed/groups/group-model";
-import { Toast } from "ui/toast";
-import _ from "underscore";
-
-// toolshed group detail view
-const GroupDetailView = Backbone.View.extend({
- el: "#groups_element",
- options: {},
- app: null,
-
- initialize: function (options) {
- this.options = _.extend(this.options, options);
- this.app = window.globalTS.groups;
-
- if (this.app.collection !== null) {
- this.model = this.app.collection.get(this.options.group_id);
- this.render();
- } else {
- this.fetchGroup();
- }
- },
-
- fetchGroup: function (options) {
- const that = this;
- this.options = _.extend(this.options, options);
- this.model = new mod_group_model.Group({ id: this.options.group_id });
- this.model.fetch({
- success: function (model) {
- console.log("received data: ");
- console.log(model);
- that.render();
- },
- error: function (model, response) {
- if (typeof response.responseJSON !== "undefined") {
- Toast.error(response.responseJSON.err_msg);
- } else {
- Toast.error("An error occurred.");
- }
- },
- });
- },
-
- render: function () {
- const template = this.templateRow();
- this.$el.html(template({ group: this.model }));
- $('#center [data-toggle="tooltip"]').tooltip({ trigger: "hover" });
- $("#center").css("overflow", "auto");
- },
-
- templateRow: function () {
- return _.template(
- [
- "">',
- '"><%= _.escape(group.get("name")) %> ',
- // 'description ',
- '<%= group.get("total_members") %> ',
- '<%= group.get("total_repos") %> ',
- " ",
- ].join("")
- );
- },
-});
-
-export default {
- GroupListRowView: GroupListRowView,
-};
diff --git a/client/src/toolshed/groups/group-model.js b/client/src/toolshed/groups/group-model.js
deleted file mode 100644
index e001830830d6..000000000000
--- a/client/src/toolshed/groups/group-model.js
+++ /dev/null
@@ -1,20 +0,0 @@
-import Backbone from "backbone";
-import { getAppRoot } from "onload/loadConfig";
-
-// ============================================================================
-// TS GROUP RELATED MODELS
-
-const Group = Backbone.Model.extend({
- urlRoot: `${getAppRoot()}api/groups`,
-});
-
-const Groups = Backbone.Collection.extend({
- url: `${getAppRoot()}api/groups`,
-
- model: Group,
-});
-
-export default {
- Group: Group,
- Groups: Groups,
-};
diff --git a/client/src/toolshed/toolshed.groups.js b/client/src/toolshed/toolshed.groups.js
deleted file mode 100644
index 89fb79623d45..000000000000
--- a/client/src/toolshed/toolshed.groups.js
+++ /dev/null
@@ -1,43 +0,0 @@
-// MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM
-// === MAIN TOOLSHED GROUP MODULE ====
-// MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM
-
-import Backbone from "backbone";
-import mod_group_detail from "toolshed/groups/group-detail-view";
-import mod_group_list from "toolshed/groups/group-list-view";
-
-// ============================================================================
-// ROUTER
-const ToolshedRouter = Backbone.Router.extend({
- routes: {
- "": "groups",
- ":group_id": "group_page",
- },
-});
-
-const ToolshedGroups = Backbone.View.extend({
- groupListView: null,
- groupDetailView: null,
- collection: null,
-
- initialize: function () {
- window.globalTS.groups = this;
-
- this.ts_router = new ToolshedRouter();
- this.ts_router.on("route:groups", () => {
- window.globalTS.groups.groupListView = new mod_group_list.GroupListView();
- });
-
- this.ts_router.on("route:group_page", (group_id) => {
- window.globalTS.groups.groupDetailView = new mod_group_detail.GroupDetailView({
- group_id: group_id,
- });
- });
-
- Backbone.history.start({ pushState: false });
- },
-});
-
-export default {
- ToolshedGroups: ToolshedGroups,
-};
diff --git a/client/src/utils/data.js b/client/src/utils/data.js
index 7c53c745a7ac..e43e2bcd8e86 100644
--- a/client/src/utils/data.js
+++ b/client/src/utils/data.js
@@ -1,14 +1,15 @@
import { getGalaxyInstance } from "app";
import axios from "axios";
import { FilesDialog } from "components/FilesDialog";
-import { uploadModelsToPayload } from "components/Upload/helpers";
import { useGlobalUploadModal } from "composables/globalUploadModal";
import $ from "jquery";
import { getAppRoot } from "onload/loadConfig";
import { rewatchHistory } from "store/historyStore/model/watchHistory";
-import { submitUpload } from "utils/uploadbox";
import Vue from "vue";
+import { uploadPayload } from "@/utils/upload-payload.js";
+import { uploadSubmit } from "@/utils/upload-submit.js";
+
import DataDialog from "components/DataDialog/DataDialog.vue";
import DatasetCollectionDialog from "components/SelectionDialog/DatasetCollectionDialog.vue";
@@ -95,8 +96,7 @@ export function create(options) {
return options.history_id;
}
getHistory().then((history_id) => {
- submitUpload({
- url: `${getAppRoot()}api/tools/fetch`,
+ uploadSubmit({
success: (response) => {
refreshContentsWrapper();
if (options.success) {
@@ -105,7 +105,7 @@ export function create(options) {
},
error: options.error,
data: {
- payload: uploadModelsToPayload([options], history_id),
+ payload: uploadPayload([options], history_id),
},
});
});
diff --git a/client/src/utils/filterConversion.test.js b/client/src/utils/filterConversion.test.js
index 164e5e7db576..6437d64802ac 100644
--- a/client/src/utils/filterConversion.test.js
+++ b/client/src/utils/filterConversion.test.js
@@ -1,40 +1,120 @@
import { HistoryFilters } from "components/History/HistoryFilters";
+import { PublishedWorkflowFilters } from "components/Workflow/WorkflowFilters";
-describe("test filtering helpers to convert settings to filter text", () => {
- it("conversion from settings to new filter text", async () => {
- const normalized = HistoryFilters.getDefaults();
+describe("test filtering helpers to convert filters to filter text", () => {
+ it("conversion from filters to new filter text", async () => {
+ const normalized = HistoryFilters.defaultFilters;
expect(Object.keys(normalized).length).toBe(2);
- expect(normalized["deleted:"]).toBe(false);
- expect(normalized["visible:"]).toBe(true);
+ expect(normalized["deleted"]).toBe(false);
+ expect(normalized["visible"]).toBe(true);
});
it("verify the existence of defaults", async () => {
- const settings = {};
+ let filters = {};
Object.entries(HistoryFilters.defaultFilters).forEach(([key, value]) => {
- settings[`${key}:`] = value;
+ filters[key] = value;
});
- expect(HistoryFilters.containsDefaults(settings)).toBe(true);
- settings["deleted:"] = !HistoryFilters.defaultFilters.deleted;
- expect(HistoryFilters.containsDefaults(settings)).toBe(false);
- settings["deleted:"] = HistoryFilters.defaultFilters.deleted;
- settings["visible:"] = !HistoryFilters.defaultFilters.visible;
- expect(HistoryFilters.containsDefaults(settings)).toBe(false);
- settings["visible:"] = String(HistoryFilters.defaultFilters.visible).toUpperCase();
- expect(HistoryFilters.containsDefaults(settings)).toBe(true);
+ expect(HistoryFilters.containsDefaults(filters)).toBe(true);
+ filters["deleted"] = !HistoryFilters.defaultFilters.deleted;
+ expect(HistoryFilters.containsDefaults(filters)).toBe(false);
+ filters["deleted"] = HistoryFilters.defaultFilters.deleted;
+ filters["visible"] = !HistoryFilters.defaultFilters.visible;
+ expect(HistoryFilters.containsDefaults(filters)).toBe(false);
+ filters["visible"] = String(HistoryFilters.defaultFilters.visible).toUpperCase();
+ expect(HistoryFilters.containsDefaults(filters)).toBe(true);
+ filters = {};
+ Object.entries(PublishedWorkflowFilters.defaultFilters).forEach(([key, value]) => {
+ filters[key] = value;
+ });
+ expect(PublishedWorkflowFilters.containsDefaults(filters)).toBe(true);
+ filters["published"] = !PublishedWorkflowFilters.defaultFilters.published;
+ expect(PublishedWorkflowFilters.containsDefaults(filters)).toBe(false);
+ });
+
+ it("verify correct conversion of filters", async () => {
+ const filters = {
+ deleted: HistoryFilters.defaultFilters.deleted,
+ visible: HistoryFilters.defaultFilters.visible,
+ name: "name",
+ other: "other",
+ tag: ["tag1", "tag2"],
+ genome_build: "",
+ published: PublishedWorkflowFilters.defaultFilters.published,
+ };
+ const validHistFilters = HistoryFilters.getValidFilters(filters);
+ expect(Object.keys(validHistFilters)).toEqual(["deleted", "visible", "name"]);
+ const validWfFilters = PublishedWorkflowFilters.getValidFilters(filters);
+ expect(Object.keys(validWfFilters)).toEqual(["deleted", "name", "tag", "published"]);
+
+ expect(HistoryFilters.getFilterText(filters)).toBe("name:name");
+ filters["visible"] = !HistoryFilters.defaultFilters.visible;
+ expect(HistoryFilters.getFilterText(filters)).toBe("deleted:false visible:false name:name");
+ filters["visible"] = HistoryFilters.defaultFilters.visible;
+ expect(HistoryFilters.getFilterText(filters)).toBe("name:name");
+
+ expect(PublishedWorkflowFilters.getFilterText(filters, true)).toBe("name:name tag:tag1 tag:tag2 is:published");
+ delete filters["published"];
+ expect(PublishedWorkflowFilters.getFilterText(filters, true)).toBe("name:name tag:tag1 tag:tag2");
+ });
+});
+
+describe("test filtering helpers to convert filter text to filters", () => {
+ function getFilters(filteringClass, filterText) {
+ return filteringClass.getValidFilters(Object.fromEntries(filteringClass.getFiltersForText(filterText)));
+ }
+
+ it("verify the existence of defaults", async () => {
+ let filterText = "";
+ expect(HistoryFilters.containsDefaults(getFilters(HistoryFilters, filterText))).toBe(true);
+ filterText = "deleted:true";
+ expect(HistoryFilters.containsDefaults(getFilters(HistoryFilters, filterText))).toBe(false);
+ filterText = "visible:false";
+ expect(HistoryFilters.containsDefaults(getFilters(HistoryFilters, filterText))).toBe(false);
+ filterText = "deleted:any";
+ expect(HistoryFilters.containsDefaults(getFilters(HistoryFilters, filterText))).toBe(false);
+ filterText = "deleted:false visible:true";
+ expect(HistoryFilters.containsDefaults(getFilters(HistoryFilters, filterText))).toBe(true);
+
+ filterText = "";
+ expect(PublishedWorkflowFilters.containsDefaults(getFilters(PublishedWorkflowFilters, filterText))).toBe(true);
+ filterText = "is:published is:deleted";
+ expect(PublishedWorkflowFilters.containsDefaults(getFilters(PublishedWorkflowFilters, filterText))).toBe(true);
+ });
+
+ it("verify correct conversion of filterText (HistoryFilters)", async () => {
+ const filters = {
+ deleted: HistoryFilters.defaultFilters.deleted,
+ visible: HistoryFilters.defaultFilters.visible,
+ name: "name",
+ };
+ let filterText = "name:name";
+ expect(getFilters(HistoryFilters, filterText)).toEqual(filters);
+ filterText = "visible:false name:name";
+ filters["visible"] = !HistoryFilters.defaultFilters.visible;
+ delete filters["deleted"];
+ expect(getFilters(HistoryFilters, filterText)).toEqual(filters);
+ filterText = "visible:false deleted:any name:name";
+ expect(getFilters(HistoryFilters, filterText)).toEqual(filters);
+ filterText = "visible:false deleted:true name:name";
+ filters["deleted"] = true;
+ expect(getFilters(HistoryFilters, filterText)).toEqual(filters);
+ filterText = "visible:false deleted:true name:name invalid:invalid";
+ expect(getFilters(HistoryFilters, filterText)).toEqual(filters);
});
- it("verify correct conversion of settings", async () => {
- const settings = {
- "deleted:": HistoryFilters.defaultFilters.deleted,
- "visible:": HistoryFilters.defaultFilters.visible,
- "other:": "other",
- "anything:": undefined,
- "value:": "",
+ it("verify correct conversion of filterText (PublishedWorkflowFilters)", async () => {
+ const filters = {
+ published: PublishedWorkflowFilters.defaultFilters.published,
+ name: "name",
};
- expect(HistoryFilters.getFilterText(settings)).toBe("other:other");
- settings["visible:"] = !HistoryFilters.defaultFilters.visible;
- expect(HistoryFilters.getFilterText(settings)).toBe("deleted:false visible:false other:other");
- settings["visible:"] = HistoryFilters.defaultFilters.visible;
- expect(HistoryFilters.getFilterText(settings)).toBe("other:other");
+ let filterText = "name:name";
+ expect(getFilters(PublishedWorkflowFilters, filterText)).toEqual(filters);
+ filterText = "published:false name:name";
+ // filters["visible"] = !PublishedWorkflowFilters.defaultFilters.visible;
+ // delete filters["deleted"];
+ expect(getFilters(PublishedWorkflowFilters, filterText)).toEqual(filters);
+ filterText = "name:name invalid:invalid is:deleted";
+ filters["deleted"] = true;
+ expect(getFilters(PublishedWorkflowFilters, filterText)).toEqual(filters);
});
});
diff --git a/client/src/utils/filtering.test.js b/client/src/utils/filtering.test.js
index 7313a782f681..16afb6f2cda7 100644
--- a/client/src/utils/filtering.test.js
+++ b/client/src/utils/filtering.test.js
@@ -14,9 +14,7 @@ const sampleFilters = [
validFilters: {
deleted: true,
},
- validSettings: {
- "deleted:": true,
- },
+ validText: "deleted:true visible:any",
},
{
filters: {
@@ -30,11 +28,7 @@ const sampleFilters = [
related: 10,
hid_gt: 5,
},
- validSettings: {
- "deleted:": "any",
- "related:": 10,
- "hid>": 5,
- },
+ validText: "deleted:any related:10 hid>5 visible:any",
},
];
@@ -95,7 +89,7 @@ describe("filtering", () => {
test("parse get valid filters and settings", () => {
sampleFilters.forEach((sample) => {
expect(HistoryFilters.getValidFilters(sample.filters)).toEqual(sample.validFilters);
- expect(HistoryFilters.getValidFilterSettings(sample.filters)).toEqual(sample.validSettings);
+ expect(HistoryFilters.getFilterText(sample.filters)).toEqual(sample.validText);
});
});
test("parse filter text as entries", () => {
@@ -160,7 +154,7 @@ describe("filtering", () => {
"deleted:any visible:true"
);
expect(HistoryFilters.applyFiltersToText({ deleted: "any" }, "deleted:any visible:true", true)).toEqual(
- "visible:true"
+ "visible:true deleted:any"
);
});
test("set a single valid filter to existing filterText", () => {
@@ -204,23 +198,23 @@ describe("filtering", () => {
expect(HistoryFilters.testFilters(filters, { ...item, deleted: "nottrue" })).toBe(true);
});
});
- test("Parsing & sync of filter settings", () => {
- // Expected parsed settings
- const parsedFilterSettings = {
- "name:": "name of item",
- "hid>": "10",
- "hid<": "100",
- "create_time>": "2021-01-01",
- "update_time<": "2022-01-01",
- "state:": "success",
- "extension:": "ext",
- "tag:": "first",
- "deleted:": "false",
- "visible:": "true",
+ test("Parsing & sync of filters", () => {
+ // Expected parsed filters
+ const parsedFilters = {
+ name: "name of item",
+ hid_gt: "10",
+ hid_lt: "100",
+ create_time_gt: "2021-01-01",
+ update_time_lt: "2022-01-01",
+ state: "success",
+ extension: "ext",
+ tag: "first",
+ deleted: "false",
+ visible: "true",
};
- // iterate through filterTexts and compare with parsedFilterSettings
+ // iterate through filterTexts and compare with parsedFilters
filterTexts.forEach((filterText) => {
- expect(HistoryFilters.toAlias(HistoryFilters.getFiltersForText(filterText))).toEqual(parsedFilterSettings);
+ expect(Object.fromEntries(HistoryFilters.getFiltersForText(filterText))).toEqual(parsedFilters);
});
});
test("named tag (hash) conversion", () => {
diff --git a/client/src/utils/filtering.ts b/client/src/utils/filtering.ts
index 85e266038d47..905b41a4fd41 100644
--- a/client/src/utils/filtering.ts
+++ b/client/src/utils/filtering.ts
@@ -7,13 +7,12 @@
* for values that contain spaces.
* Each query key has a default suffix defined e.g. name:foo will be converted to name-eq:foo.
* Comparison aliases are allowed converting e.g. '>' to '-gt' and '<' to '-lt'.
- *
- * TODO: Reduce usage of `filterText` as a param in several functions
*/
-import { omit } from "lodash";
+import { isEqual, omit } from "lodash";
+import type { DefineComponent } from "vue";
-type Converter = (value: T) => T;
+export type Converter = (value: T) => T;
type Handler = (v: T, q: T) => boolean;
/** Add comparison aliases i.e. '*>value' is converted to '*_gt=value' */
@@ -31,9 +30,46 @@ const operatorForAlias = {
} as const satisfies Record;
type OperatorForAlias = typeof operatorForAlias;
-type Alias = keyof OperatorForAlias;
+export type Alias = keyof OperatorForAlias;
type Operator = OperatorForAlias[Alias];
+/** A ValidFilter with a `handler` for the `Filtering` class,
+ * and remaining properties for the `FilterMenu` component
+ * */
+export type ValidFilter = {
+ /** The `FilterMenu` input field/tooltip/label placeholder */
+ placeholder?: string;
+ /** The data type of the `FilterMenu` input field */
+ type?: typeof String | typeof Number | typeof Boolean | typeof Date | "MultiTags";
+ /** If type: Boolean:
+ * - booleanType: 'default' creates: `filter:true|false|any`
+ * - booleanType: 'is' creates: `is:filter`
+ */
+ boolType?: "default" | "is";
+ /** The handler function for this filter */
+ handler: HandlerReturn;
+ /** Is this a filter to include as a field in `FilterMenu`?
+ * (if `false` the filter is still valid for the search bar `filterText`)
+ */
+ menuItem: boolean;
+ /** Is there a datalist of values for this field */
+ datalist?:
+ | string[]
+ | {
+ value: string;
+ text: string;
+ }[];
+ /** Is this a `FilterMenu` range filter?
+ * (if yes, the `filter` key is taken and aliased into 2 input
+ * fields: `filter-gt` & `filter-lt`)
+ */
+ isRangeInput?: boolean;
+ /** The help info component to append to the `FilterMenu` input field */
+ helpInfo?: DefineComponent | string;
+ /** A default value (will make this a default filter for an empty `filterText`) */
+ default?: T;
+};
+
/** Converts user input to backend compatible date
* @param value
* @returns seconds since epoch
@@ -77,6 +113,22 @@ export function expandNameTag(value: T): string {
return toLower(value);
}
+/** Converts name tags starting with "#" to "'name:...'"; forces quotation marks
+ * and **is also case-sensitive**
+ * @param value
+ * @returns Lowercase value with 'name:' replaced with '#'
+ */
+export function expandNameTagWithQuotes(value: T): string {
+ if (value && typeof value === "string") {
+ if (value.startsWith("'#") && value.endsWith("'")) {
+ value = value.replace(/^'#/g, "'name:") as T;
+ } else if (value.startsWith("#")) {
+ value = `'name:${value.slice(1)}'` as T;
+ }
+ }
+ return value as string;
+}
+
/** Converts string alias to string operator, e.g.: 'gt' to '>'
* @param alias
* @returns Arithmetic operator, e.g.: '>'
@@ -166,46 +218,96 @@ export function compare(attribute: string, variant: string, converter?: Conve
};
}
+/**
+ * Class for filtering (menus). Handles user input as one string filterText
+ * or multiple filters (e.g. 'name:foo type:bar'), with appropriate functions.
+ * @param validFilters: Record of valid filters with their handlers,
+ * and FilterMenu properties (if menuItem = true)
+ * @param validAliases: Array of valid aliases for filters
+ * @param quoteStrings: Whether to auto quote filter strings in the query
+ * @param nameMatching: Whether to apply name filter for unspecified filterText
+ * (e.g. filterText = 'foo' -> 'name:foo')
+ * @returns Filtering object
+ * */
export default class Filtering {
- validFilters: Record>;
+ validFilters: Record>;
validAliases: Array<[string, string]>;
- useDefaultFilters: boolean;
- defaultFilters: Record = {
- deleted: false as T,
- visible: true as T,
- };
+ defaultFilters: Record;
+ quoteStrings: boolean;
+ nameMatching: boolean;
constructor(
- validFilters: Record>,
- useDefaultFilters = true,
- validAliases?: Array<[string, string]>
+ validFilters: Record>,
+ validAliases?: Array<[string, string]>,
+ quoteStrings = true,
+ nameMatching = true
) {
this.validFilters = validFilters;
- this.useDefaultFilters = useDefaultFilters;
this.validAliases = validAliases || defaultValidAliases;
+ this.quoteStrings = quoteStrings;
+ this.nameMatching = nameMatching;
+ // If (default) we are nameMatching, add `name` filter if not present
+ if (this.nameMatching && this.validFilters["name"] === undefined) {
+ this.validFilters["name"] = {
+ handler: contains("name"),
+ menuItem: false,
+ };
+ }
+ this.defaultFilters = this.createDefaultFiltersIfPresent();
+ this.addRangedFiltersIfNotPresent();
+ }
+
+ /** For `FilterMenu` validFilters, if `isRangeInput`, then adds handlers
+ * for the `lt` & `gt` filters if not included in `validFilters` already
+ */
+ addRangedFiltersIfNotPresent() {
+ Object.entries(this.validFilters).forEach(([key, filter]) => {
+ if (filter.isRangeInput) {
+ const { converter } = filter.handler as HandlerReturn;
+ if (this.validFilters[`${key}_gt`] === undefined) {
+ this.validFilters[`${key}_gt`] = {
+ ...filter,
+ handler: compare(key, "gt", converter),
+ menuItem: false,
+ };
+ }
+ if (this.validFilters[`${key}_lt`] === undefined) {
+ this.validFilters[`${key}_lt`] = {
+ ...filter,
+ handler: compare(key, "lt", converter),
+ menuItem: false,
+ };
+ }
+ }
+ });
}
- /** Returns normalize defaults by adding the operator to the key identifier
- * @returns Dictionary with query key and values for default filters
+ /** If any `validFilters` are given the `default` key, a `defaultFilters`
+ * object is created with provided values, that an empty `filterText`
+ * corresponds to.
* */
- getDefaults(): Record {
- const normalized: Record = {};
- Object.entries(this.defaultFilters).forEach(([key, value]) => {
- normalized[`${key}:`] = value;
+ createDefaultFiltersIfPresent(): Record {
+ const defaultFilters: Record = {};
+ Object.entries(this.validFilters).forEach(([key, filter]) => {
+ if (filter.default !== undefined) {
+ defaultFilters[key] = filter.default;
+ }
});
- return normalized;
+ return defaultFilters;
}
/** Returns true if default filter values are not changed
- * @param filterSettings Object containing filter settings
+ * @param filters Object containing filters
* @returns true if default filter values are not changed
* **/
- containsDefaults(filterSettings: Record): boolean {
- const normalized = this.getDefaults();
+ containsDefaults(filters: Record): boolean {
+ if (this.defaultFilters === undefined) {
+ return false;
+ }
let hasDefaults = true;
- for (const key in normalized) {
- const value = String(filterSettings[key]).toLowerCase();
- const normalizedValue = String(normalized[key]).toLowerCase();
+ for (const key in this.defaultFilters) {
+ const value = String(filters[key]).toLowerCase();
+ const normalizedValue = String(this.defaultFilters[key]).toLowerCase();
if (value !== normalizedValue) {
hasDefaults = false;
break;
@@ -220,30 +322,57 @@ export default class Filtering {
* @returns true if all default __keys__ are found in `filters`
*/
hasAllDefaultKeys(filters: Record): boolean {
- return Object.keys(this.defaultFilters).every((def) => Object.keys(filters).includes(def));
+ return (
+ this.defaultFilters !== undefined &&
+ Object.keys(this.defaultFilters).every((def) => Object.keys(filters).includes(def))
+ );
}
- /** Build a text filter from filter settings (with aliases: `{"filter:": "value", ...}`)
- * @param filterSettings Object containing filter settings
+ /** Build a text filter from filters {filter: "value", ...} => "filter:value"
+ * @param filters Object containing filters
+ * @param backendFormatted If true, returns a string formatted for the backend
* @returns Parsed filter text string
* */
- getFilterText(filterSettings: Record): string {
- const normalized = this.getDefaults();
- const hasDefaults = this.containsDefaults(filterSettings);
+ getFilterText(filters: Record, backendFormatted = false): string {
+ filters = this.getValidFilters(filters, backendFormatted);
+ const hasDefaults = this.containsDefaults(filters);
let newFilterText = "";
- Object.entries(filterSettings).forEach(([key, value]) => {
- const skipDefault = hasDefaults && normalized[key] !== undefined;
- if (!skipDefault && value !== null && value !== undefined && value !== "") {
+ Object.entries(filters).forEach(([key, value]) => {
+ // this is a default filter, skip it if ALL default filters have default values
+ const skipDefault = !backendFormatted && hasDefaults && this.defaultFilters[key] !== undefined;
+ if (!skipDefault) {
if (newFilterText) {
newFilterText += " ";
}
- if (String(value).includes(" ")) {
- value = `'${value}'` as T;
+ if (this.validFilters[key]?.type === Boolean && this.validFilters[key]?.boolType === "is") {
+ if (value === true) {
+ newFilterText += `is:${key}`;
+ }
+ } else if (this.validFilters[key]?.type == "MultiTags" && Array.isArray(value) && value.length > 0) {
+ newFilterText += `${value.map((v) => `${this.toAliasKey(key)}${v}`).join(" ")}`;
+ } else if (this.quoteStrings && String(value).includes(" ")) {
+ newFilterText += `${this.toAliasKey(key)}'${value}'`;
+ } else {
+ newFilterText += `${this.toAliasKey(key)}${value}`;
}
- newFilterText += `${key}${value}`;
}
});
+ // enforce `filter:any` for any default *boolean* filters missing in filters object
+ if (!hasDefaults && this.defaultFilters !== undefined) {
+ Object.entries(this.defaultFilters).forEach(([key, value]) => {
+ if (
+ filters[key] == undefined &&
+ typeof value === "boolean" &&
+ this.validFilters[key]?.boolType !== "is"
+ ) {
+ if (newFilterText) {
+ newFilterText += " ";
+ }
+ newFilterText += `${this.toAliasKey(key)}any`;
+ }
+ });
+ }
return newFilterText;
}
@@ -253,7 +382,9 @@ export default class Filtering {
* @returns Filters as 2D array of of [field, value] pairs
* */
getFiltersForText(filterText: string, removeAny = true): [string, T][] {
- const pairSplitRE = /[^\s'"]+(?:['"][^'"]*['"][^\s'"]*)*|(?:['"][^'"]*['"][^\s'"]*)+/g;
+ const pairSplitRE = this.quoteStrings
+ ? /[^\s'"]+(?:['"][^'"]*['"][^\s'"]*)*|(?:['"][^'"]*['"][^\s'"]*)+/g
+ : /(\S+):(.*?)(?=\s+\S+:|$)/g;
const matches = filterText.match(pairSplitRE);
let result: Record = {};
let hasMatches = false;
@@ -262,9 +393,9 @@ export default class Filtering {
const elgRE = /(\S+)([:><])(.+)/g;
const elgMatch = elgRE.exec(pair);
if (elgMatch) {
- let field = elgMatch[1]!;
- const elg = elgMatch[2]!;
- const value = elgMatch[3]!;
+ let field = elgMatch[1];
+ const elg = elgMatch[2];
+ const value = elgMatch[3];
// replace alias for less and greater symbol
for (const [alias, substitute] of this.validAliases) {
if (elg === alias) {
@@ -273,33 +404,53 @@ export default class Filtering {
}
}
// replaces dashes with underscores in query field names
- const normalizedField = field.split("-").join("_");
- if (this.validFilters[normalizedField]) {
+ const normalizedField = field?.split("-").join("_");
+ if (
+ normalizedField &&
+ this.validFilters[normalizedField] &&
+ this.validFilters[normalizedField]?.boolType !== "is"
+ ) {
// removes quotation and applies lower-case to filter value
- result[normalizedField] = toLowerNoQuotes(value) as T;
+ const newVal = this.quoteStrings ? (toLowerNoQuotes(value) as T) : (value as T);
+ // if the field is a MultiTags field, we need to push each value to an array
+ if (this.validFilters[normalizedField]?.type === "MultiTags") {
+ if (result[normalizedField] === undefined) {
+ result[normalizedField] = [newVal] as T;
+ } else {
+ (result[normalizedField] as T[]).push(newVal);
+ }
+ } else {
+ result[normalizedField] = newVal;
+ }
+ hasMatches = true;
+ } else if (value && field === "is" && elg === ":" && this.validFilters[value]?.boolType === "is") {
+ // handle `is:filter` syntax
+ result[value] = true as T;
hasMatches = true;
}
}
});
}
// assume name matching if no filter key has been matched
- if (!hasMatches && filterText.length > 0) {
+ if (this.nameMatching && !hasMatches && filterText.length > 0) {
result["name"] = filterText as T;
}
- // check if any default filter keys have been used
- let hasDefaults = false;
- Object.keys(this.defaultFilters).forEach((defaultKey) => {
- const value = result[defaultKey];
- if (value !== undefined) {
- if (value == "any" && removeAny) {
- delete result[defaultKey];
+ // check if any default filter keys have been used in the filter text
+ if (this.defaultFilters !== undefined) {
+ let hasDefaults = false;
+ Object.keys(this.defaultFilters).forEach((defaultKey) => {
+ const value = result[defaultKey];
+ if (value !== undefined) {
+ if (value == "any" && removeAny) {
+ delete result[defaultKey];
+ }
+ hasDefaults = true;
}
- hasDefaults = true;
+ });
+ // use default filters if none of the default filters has been explicitly specified
+ if (!hasDefaults) {
+ result = { ...result, ...this.defaultFilters };
}
- });
- // use default filters if none of the default filters has been explicitly specified
- if (!hasDefaults && this.useDefaultFilters) {
- result = { ...result, ...this.defaultFilters };
}
return Object.entries(result);
@@ -313,60 +464,57 @@ export default class Filtering {
* @returns Parsed `filterText` string with added/removed filter(s)
*/
applyFiltersToText(filters: Record, existingText: string, remove = false) {
- let validSettings = this.getValidFilterSettings(filters);
- const existingSettings = this.toAlias(this.getFiltersForText(existingText, false));
+ let validFilters = this.getValidFilters(filters);
+ const existingFilters = Object.fromEntries(this.getFiltersForText(existingText, false));
if (remove) {
- validSettings = omit(existingSettings, Object.keys(validSettings));
+ validFilters = omit(existingFilters, Object.keys(validFilters));
} else {
- validSettings = Object.assign(existingSettings, validSettings);
+ validFilters = Object.assign(existingFilters, validFilters);
}
- return this.getFilterText(validSettings);
+ return this.getFilterText(validFilters);
}
- getValidFilters(filters: Record) {
+ /** Takes a filters object and returns a new object with only valid filters
+ *
+ * @param filters A filters object (e.g.: {hid: "3", name: "test", invalid: "x"}})
+ * @param backendFormatted default: `false` Whether to convert the values to backend format
+ * @returns valid filters object (e.g.: {hid: "3", name: "test"}})
+ */
+ getValidFilters(filters: Record, backendFormatted = false) {
const validFilters: Record = {};
Object.entries(filters).forEach(([key, value]) => {
- const validValue = this.getConvertedValue(key, value);
- if (validValue !== undefined) {
- validFilters[key] = validValue;
+ if (this.validFilters[key]?.type === "MultiTags" && Array.isArray(value)) {
+ const validValues = value
+ .map((v) => this.getConvertedValue(key, v, backendFormatted))
+ .filter((v) => v !== undefined);
+ if (validValues.length > 0) {
+ validFilters[key] = validValues as T;
+ }
+ } else {
+ const validValue = this.getConvertedValue(key, value, backendFormatted);
+ if (validValue !== undefined) {
+ validFilters[key] = validValue;
+ }
}
});
return validFilters;
}
- /** Returns a dictionary resembling filterSettings (for HistoryFilters):
- * e.g.: Unlike getFiltersForText or getQueryDict, this maintains "hid>":"3" instead
- * of changing it to "hid-gt":"3"
- * (Used to sync filterSettings in HistoryFilters)
- * @param filters Parsed filters object from getFiltersForText()
- * @returns `filterSettings` as dict of {"field:": "value"} pairs
+ /** Convert a valid filter key (`filter`/`filter-gt`) to alias filter key (`filter:`/`filter>`)
+ * to use in creating `filterText` string.
+ *
+ * e.g.: filter = "hid-gt" becomes "hid>", filter = "hid" becomes "hid:"
+ * @param filter Parsed filters object from getFiltersForText()
+ * @returns filter key
*/
- toAlias(filters: [string, T][]) {
- const result: Record = {};
- for (const [key, value] of filters) {
- let hasAlias = false;
- for (const [alias, substitute] of this.validAliases) {
- if (key.endsWith(substitute)) {
- const keyPrefix = key.slice(0, -substitute.length);
- result[`${keyPrefix}${alias}`] = value;
- hasAlias = true;
- break;
- }
- }
- if (!hasAlias) {
- result[`${key}:`] = value;
+ toAliasKey(filter: string) {
+ for (const [alias, substitute] of this.validAliases) {
+ if (filter.endsWith(substitute)) {
+ const keyPrefix = filter.slice(0, -substitute.length);
+ return `${keyPrefix}${alias}`;
}
}
- return result;
- }
-
- /** Returns valid filters with valid keys and values.
- * @param filters Raw dictionary with **(potentially invalid)** filters and keys
- * @returns **Valid** `filterSettings` as dict of {"field:": "value"} pairs
- */
- getValidFilterSettings(filters: Record) {
- const validFilters = this.getValidFilters(filters);
- return this.toAlias(Object.entries(validFilters));
+ return `${filter}:`;
}
/** Returns a dictionary with query key and values.
@@ -377,9 +525,11 @@ export default class Filtering {
const queryDict: Record = {};
const filters = this.getFiltersForText(filterText);
for (const [key, value] of filters) {
- const query = this.validFilters[key]!.query;
- const converter = this.validFilters[key]!.converter;
- queryDict[query] = converter ? converter(value) : value;
+ const query = this.validFilters[key]?.handler.query;
+ const converter = this.validFilters[key]?.handler.converter;
+ if (query) {
+ queryDict[query] = converter ? converter(value) : value;
+ }
}
return queryDict;
}
@@ -406,13 +556,21 @@ export default class Filtering {
* @returns converted value if there is a converter, else `filterValue`
*/
getConvertedValue(filterName: string, filterValue: T, backendFormatted = false): T | undefined {
- if (this.validFilters[filterName]) {
- const { converter } = this.validFilters[filterName] as HandlerReturn;
+ if (
+ this.validFilters[filterName] &&
+ !Array.isArray(filterValue) &&
+ filterValue !== null &&
+ filterValue !== undefined &&
+ filterValue !== ""
+ ) {
+ const { converter } = this.validFilters[filterName]?.handler as HandlerReturn;
if (converter) {
if (converter == toBool && filterValue == "any") {
return filterValue;
- } else if (!backendFormatted && (converter == expandNameTag || converter == toDate)) {
+ } else if (!backendFormatted && ([expandNameTag, toDate] as Converter[]).includes(converter)) {
return toLower(filterValue) as T;
+ } else if (!backendFormatted && converter == expandNameTagWithQuotes) {
+ return (filterValue as string).startsWith("#") ? (`'${filterValue}'` as T) : filterValue;
}
return converter(filterValue);
} else {
@@ -443,10 +601,17 @@ export default class Filtering {
getFilterValue(filterText: string, filterName: string, backendFormatted = false): T | undefined {
const filters = Object.fromEntries(this.getFiltersForText(filterText));
let filterVal = filters[filterName];
- if (filterVal !== undefined) {
+ const defaultFilterValue = this.defaultFilters[filterName];
+ // if filterVal is an array, convert each value
+ if (Array.isArray(filterVal)) {
+ filterVal = filterVal
+ .map((v) => this.getConvertedValue(filterName, v, backendFormatted))
+ .filter((v) => v !== undefined) as T;
+ return filterVal;
+ } else if (filterVal !== undefined) {
filterVal = this.getConvertedValue(filterName, filterVal, backendFormatted);
return filterVal;
- } else if (Object.keys(this.defaultFilters).includes(filterName)) {
+ } else if (defaultFilterValue !== undefined && typeof defaultFilterValue == "boolean") {
filterVal = this.getConvertedValue(filterName, "any" as T, backendFormatted);
return filterVal;
}
@@ -455,7 +620,7 @@ export default class Filtering {
return filters[filterName];
}
- return this.defaultFilters[filterName];
+ return defaultFilterValue;
}
/**
@@ -468,12 +633,32 @@ export default class Filtering {
setFilterValue(filterText: string, newFilter: string, newVal: T) {
let updatedText = "";
const oldVal = this.getFilterValue(filterText, newFilter);
- const convVal = this.getConvertedValue(newFilter, newVal);
- if (convVal == undefined) {
+ let convVal = this.getConvertedValue(newFilter, newVal) as T;
+ if (convVal == undefined && !Array.isArray(newVal)) {
return filterText;
}
+ // for MultiTags filter
+ if (this.validFilters[newFilter]?.type === "MultiTags" || Array.isArray(oldVal)) {
+ // if newVal is an array, convert each value, else put already converted val in array
+ let valuesToAdd = Array.isArray(newVal)
+ ? newVal.map((v) => this.getConvertedValue(newFilter, v)).filter((v) => v !== undefined)
+ : [convVal];
+ // if oldVal is an array, convert new value(s), and only add ones that aren't already in oldVal
+ if (Array.isArray(oldVal)) {
+ const updatedArr = [...oldVal] as T[];
+ (valuesToAdd as T[]).forEach((value) => {
+ if (!oldVal.includes(value)) {
+ updatedArr.push(value);
+ } else {
+ updatedArr.splice(updatedArr.indexOf(value), 1);
+ }
+ });
+ valuesToAdd = updatedArr.length !== 0 ? updatedArr : oldVal;
+ }
+ convVal = valuesToAdd as T;
+ }
const settings = { [newFilter]: convVal };
- if (oldVal == convVal) {
+ if (isEqual(oldVal, convVal) || oldVal == convVal) {
updatedText = this.applyFiltersToText(settings, filterText, true);
} else {
updatedText = this.applyFiltersToText(settings, filterText);
@@ -491,11 +676,14 @@ export default class Filtering {
if (!(key in this.validFilters)) {
console.error(`Invalid filter ${key}`);
} else {
- const filterAttribute = this.validFilters[key]!.attribute;
- const filterHandler = this.validFilters[key]!.handler;
- const itemValue = item[filterAttribute];
- if (itemValue === undefined || !filterHandler(itemValue, filterValue)) {
- return false;
+ const validFilter = this.validFilters[key];
+ if (validFilter) {
+ const filterAttribute = validFilter.handler.attribute;
+ const filterHandler = validFilter.handler.handler;
+ const itemValue = item[filterAttribute];
+ if (itemValue === undefined || !filterHandler(itemValue, filterValue)) {
+ return false;
+ }
}
}
}
diff --git a/client/src/utils/navigation/navigation.yml b/client/src/utils/navigation/navigation.yml
index 7fa348039a9e..ce285d29982b 100644
--- a/client/src/utils/navigation/navigation.yml
+++ b/client/src/utils/navigation/navigation.yml
@@ -122,8 +122,8 @@ change_user_address:
sign_out:
selectors:
- cancel_button: '.modal-footer .buttons #button-0'
- sign_out_button: '.modal-footer .buttons #button-1'
+ cancel_button: '.modal-footer .btn-secondary'
+ sign_out_button: '.modal-footer .btn-primary'
dataset_details:
selectors:
@@ -357,7 +357,7 @@ edit_collection_attributes:
data_value:
type: xpath
selector: '//span[contains(text(), "${data_change}")]'
- genome_select_search: ".database-dropdown input.multiselect__input"
+ genome_select_search: '.database-dropdown input.multiselect__input'
datatype_select_search: '.datatype-dropdown input.multiselect__input'
save_dbkey_btn: '.save-dbkey-edit'
save_datatype_btn: '.save-datatype-edit'
@@ -398,8 +398,8 @@ multi_history_panel:
published_histories:
selectors:
histories: '#published-histories-table tbody tr'
- search_input: '#published-histories-filter'
- advanced_search_toggle: '#published-histories-advanced-filter-toggle'
+ search_input: '#published-histories input.search-query[data-description="filter text input"]'
+ advanced_search_toggle: '#published-histories [data-description="toggle advanced search"]'
advanced_search_name_input: '#published-histories-advanced-filter-name'
advanced_search_tag_input: '#published-histories-advanced-filter-tag'
advanced_search_submit: '#published-histories-advanced-filter-submit'
@@ -555,15 +555,14 @@ tool_form:
parameter_checkbox: 'div.ui-form-element[id="form-element-${parameter}"] .ui-switch'
parameter_input: 'div.ui-form-element[id="form-element-${parameter}"] .ui-input'
parameter_textarea: 'div.ui-form-element[id="form-element-${parameter}"] textarea'
- parameter_data_input_single:
- type: xpath
- selector: //div[@id='form-element-${parameter}']//i[contains(@class, 'fa-file-o')]/parent::label
- parameter_batch_dataset_collection:
- type: xpath
- selector: //div[@id='form-element-${parameter}']//i[contains(@class, 'fa-folder-o')]/parent::label
- data_option_value: option[value="${item_id}"]
+ parameter_data_input_single: 'div.ui-form-element[id="form-element-${parameter}"] button[title="Single dataset"]'
+ parameter_data_input_collection: 'div.ui-form-element[id="form-element-${parameter}"] button[title="Dataset collection"]'
+ parameter_data_label: 'div.ui-form-element[id="form-element-${parameter}"] [data-description="form data label"]'
+ parameter_data_select: 'div.ui-form-element[id="form-element-${parameter}"] .multiselect'
repeat_insert: '[data-description="repeat insert"]'
+ repeat_move_up: '#${parameter}_up'
+ repeat_move_down: '#${parameter}_down'
reference: '.formatted-reference'
about: '.tool-footer'
storage_options: '.tool-storage'
@@ -571,7 +570,6 @@ tool_form:
drilldown_option: '.drilldown-option'
drilldown_expand: '.fa-plus-square'
-
labels:
generate_tour: 'Generate Tour'
@@ -580,7 +578,12 @@ workflows:
new_button: '#workflow-create'
import_button: '#workflow-import'
save_button: '#workflow-save-button'
- search_box: "#workflow-search"
+ search_box: '.workflows-list input.search-query[data-description="filter text input"]'
+ clear_filter: '.workflows-list [data-description="reset query"]'
+ advanced_search_toggle: '.workflows-list [data-description="toggle advanced search"]'
+ advanced_search_name_input: '#workflows-advanced-filter-name'
+ advanced_search_tag_input: '#workflows-advanced-filter-tag .stateless-tags'
+ advanced_search_submit: '#workflows-advanced-filter-submit'
workflow_table: "#workflow-table"
workflow_rows: "#workflow-table > tbody > tr:not(.b-table-empty-row, [style*='display: none'])"
external_link: '.workflow-external-link'
@@ -647,7 +650,7 @@ workflow_run:
selectors:
warning: ".ui-form-composite .alert-warning"
input_div: "[step-label='${label}']"
- input_data_div: "[step-label='${label}'] .select2-container"
+ input_data_div: "[step-label='${label}'] .multiselect"
# TODO: put step labels in the DOM ideally
subworkflow_step_icon: ".portlet-title-icon.fa-sitemap"
run_workflow: "#run-workflow"
@@ -672,10 +675,11 @@ workflow_editor:
clone: '${_} .node-clone'
output_data_row:
type: xpath
- selector: '//div[contains(@class, "output-data-row") and contains(string(), "${output_name} (${extension})")]'
+ selector: '//div[@data-output-name="${output_name}"]//span[contains(text(), "(${extension})")]'
output_terminal: "${_} [output-name='${name}']"
input_terminal: "${_} [input-name='${name}']"
- input_mapping_icon: "${_} [input-name='${name}'].multiple"
+ input_mapping_icon: "${_} [input-name='${name}'].mapped-over"
+ connector_destroy_callout: "${_} [input-name='${name}'] + .delete-terminal-button"
workflow_output_toggle: "${_} [data-output-name='${name}'] .callout-terminal "
workflow_output_toggle_active: "${_} [data-output-name='${name}'] .mark-terminal-active"
selectors:
@@ -770,7 +774,6 @@ workflow_editor:
tool_version_button: ".tool-versions"
connector_for: "#connection-${sink_id}-${source_id}"
connector_invalid_for: "#connection-${sink_id}-${source_id} .connection.invalid"
- connector_destroy_callout: '.delete-terminal'
save_button: '.editor-button-save'
save_workflow_confirmation_button: '#save-workflow-confirmation .btn-primary'
state_modal_body: '.state-upgrade-modal'
@@ -778,7 +781,7 @@ workflow_editor:
workflow_show:
selectors:
- _: '.workflow-display'
+ _: '.published-workflow'
title: '[data-description="workflow name"]'
import_link: '[data-description="workflow import"]'
@@ -811,7 +814,7 @@ invocations:
step_output_collection_toggle: '[data-step="${order_index}"] .invocation-step-output-collection-details .name'
step_output_collection_element_identifier:
type: xpath
- selector: '//span[@class="content-title name"][text()="${element_identifier}"]'
+ selector: '//span[contains(@class, "content-title name")][text()="${element_identifier}"]'
step_output_collection_element_datatype: '[data-step="${order_index}"] .invocation-step-output-collection-details .not-loading .datatype .value'
step_job_details: '[data-step="${order_index}"] .invocation-step-job-details'
step_job_table: '[data-step="${order_index}"] .invocation-step-job-details table'
@@ -1026,38 +1029,35 @@ gies:
iframe: 'body iframe[seamless="seamless"]'
upload:
- composite:
- selectors:
- table: 'div#composite table.upload-table'
- close: 'div#composite div.upload-buttons button'
-
selectors:
- tab: '#tab-title-link-${tab}'
- ftp_add: '#btn-ftp'
- ftp_popup: '.upload-ftp-body'
- ftp_items: '.upload-ftp-row'
- ftp_close: '.popover-header .popover-close'
- row: '#upload-row-${n}'
- settings_button: '#upload-row-${n} .upload-settings'
+ build_button: '#rule-based #btn-build'
+ close_button: '#regular #btn-close'
+ composite_close_button: '#composite #btn-close'
+ create_button: '#btn-new'
+ file_dialog: '#btn-remote-files'
+ file_dialog_ok: '.file-dialog-modal-ok'
+ file_source_selector:
+ type: xpath
+ selector: '//span[contains(@title, "${path}")]'
+ paste_option: '#upload-row-${n} .upload-source .dropdown-menu .dropdown-item .fa-edit'
paste_content: '#upload-row-${n} .upload-text-content'
- settings: '.upload-settings-table'
- setting_deferred: '.upload-deferred'
- start: '#activity-upload'
- start_uploading: '.upload-start'
- close: '.upload-close'
- rule_source_content: 'textarea.upload-rule-source-content'
- rule_select_data_type: '.rule-data-type'
- rule_select_input_type: '.rule-select-type'
+ row: '#upload-row-${n}'
+ rule_dataset_dialog: '[data-description="rules dataset dialog"]'
rule_dataset_selector:
selector: '.selection-dialog-modal'
rule_dataset_selector_row:
selector: '.selection-dialog-modal [aria-rowindex="${rowindex}"]'
- build_btn: '#rule-based #btn-build'
- file_source_selector:
- type: xpath
- selector: '//span[contains(@title, "${path}")]'
- file_dialog_ok: '.file-dialog-modal-ok'
- paste_new: .upload-paste
+ rule_select_data_type: '.rule-data-type'
+ rule_source_content: 'textarea.upload-rule-source-content'
+ tab: '#tab-title-link-${tab}'
+ title: '#upload-row-${n} .upload-title'
+ settings: '.upload-settings-table'
+ settings_button: '#upload-row-${n} .upload-settings span'
+ setting_deferred: '.upload-deferred'
+ setting_space_to_tab: '.upload-space-to-tab'
+ source_button: '#upload-row-${n} .upload-source'
+ start: '#activity-upload'
+ start_button: '#btn-start'
new_user_welcome:
selectors:
diff --git a/client/src/utils/upload-payload.js b/client/src/utils/upload-payload.js
new file mode 100644
index 000000000000..31a0306180e3
--- /dev/null
+++ b/client/src/utils/upload-payload.js
@@ -0,0 +1,120 @@
+export const DEFAULT_FILE_NAME = "New File";
+export const URI_PREFIXES = [
+ "http://",
+ "https://",
+ "ftp://",
+ "file://",
+ "gxfiles://",
+ "gximport://",
+ "gxuserimport://",
+ "gxftp://",
+ "drs://",
+];
+
+export function isUrl(content) {
+ return URI_PREFIXES.some((prefix) => content.startsWith(prefix));
+}
+
+export function uploadPayload(items, historyId, composite = false) {
+ const files = [];
+ const elements = items
+ .map((item) => {
+ if (!item.optional || item.fileSize > 0) {
+ // avoid submitting default file name, server will set file name
+ let fileName = item.fileName;
+ if (fileName === DEFAULT_FILE_NAME) {
+ fileName = null;
+ }
+ // consolidate exclusive file content attributes
+ const urlContent = (item.fileUri || item.filePath || item.fileContent || "").trim();
+ const hasFileData = item.fileData && item.fileData.size > 0;
+ if (urlContent.length === 0 && !hasFileData) {
+ throw new Error("Content not available.");
+ }
+ // collect common element attributes
+ const elem = {
+ dbkey: item.dbKey ?? "?",
+ ext: item.extension ?? "auto",
+ name: fileName,
+ space_to_tab: item.spaceToTab,
+ to_posix_lines: item.toPosixLines,
+ deferred: item.deferred,
+ };
+ // match file mode
+ switch (item.fileMode) {
+ case "new":
+ if (isUrl(urlContent)) {
+ /* Could be multiple URLs pasted in.
+ TODO: suggesting to split multiple URLs
+ across multiple uploads directly in upload modal,
+ instead of this intransparent magic. */
+ return urlContent.split("\n").map((urlSplit) => {
+ const urlTrim = urlSplit.trim();
+ if (isUrl(urlTrim)) {
+ return {
+ src: "url",
+ url: urlTrim,
+ ...elem,
+ };
+ } else {
+ throw new Error(`Invalid url: ${urlTrim}`);
+ }
+ });
+ } else {
+ return {
+ src: "pasted",
+ paste_content: item.fileContent,
+ ...elem,
+ };
+ }
+ case "url":
+ if (isUrl(urlContent)) {
+ return {
+ src: "url",
+ url: urlContent,
+ ...elem,
+ };
+ } else {
+ throw new Error(`Invalid url: ${urlContent}.`);
+ }
+ case "local":
+ files.push(item.fileData);
+ return {
+ src: "files",
+ ...elem,
+ };
+ default:
+ throw new Error(`Unknown file mode: ${item.fileMode}.`);
+ }
+ }
+ })
+ .filter((item) => item)
+ .flat();
+ if (elements.length === 0) {
+ throw new Error("No valid items provided.");
+ }
+ const target = {
+ destination: { type: "hdas" },
+ elements: elements,
+ };
+ if (composite) {
+ const compositeItems = [
+ {
+ src: "composite",
+ dbkey: elements[0].dbkey,
+ ext: elements[0].ext,
+ composite: {
+ items: target.elements,
+ },
+ },
+ ];
+ delete target["elements"];
+ target["items"] = compositeItems;
+ }
+ return {
+ history_id: historyId,
+ targets: [target],
+ auto_decompress: true,
+ files: files,
+ };
+}
diff --git a/client/src/utils/upload-payload.test.js b/client/src/utils/upload-payload.test.js
new file mode 100644
index 000000000000..9a3bc946391e
--- /dev/null
+++ b/client/src/utils/upload-payload.test.js
@@ -0,0 +1,195 @@
+import { isUrl, uploadPayload } from "./upload-payload.js";
+
+describe("uploadPayload", () => {
+ test("basic validation", () => {
+ expect(() => uploadPayload([], "historyId")).toThrow("No valid items provided.");
+ expect(() => uploadPayload([{}], "historyId")).toThrow("Content not available.");
+ expect(() => uploadPayload([{ fileContent: "fileContent" }], "historyId")).toThrow(
+ "Unknown file mode: undefined."
+ );
+ expect(() =>
+ uploadPayload(
+ [
+ {
+ dbKey: "dbKey",
+ deferred: false,
+ extension: "extension",
+ fileName: "3",
+ fileContent: " http://test.me.0 \n xyz://test.me.1",
+ fileMode: "new",
+ spaceToTab: false,
+ toPosixLines: false,
+ },
+ ],
+ "historyId"
+ )
+ ).toThrow("Invalid url: xyz://test.me.1");
+ });
+
+ test("url detection", () => {
+ expect(isUrl("xyz://")).toBeFalsy();
+ expect(isUrl("ftp://")).toBeTruthy();
+ expect(isUrl("http://")).toBeTruthy();
+ });
+
+ test("regular payload", () => {
+ const p = uploadPayload(
+ [
+ { fileContent: " fileContent ", fileMode: "new", fileName: "1" },
+ {
+ dbKey: "dbKey2",
+ deferred: true,
+ extension: "extension2",
+ fileData: { size: 1 },
+ fileMode: "local",
+ fileName: "2",
+ spaceToTab: true,
+ toPosixLines: true,
+ },
+ {
+ dbKey: "dbKey3",
+ deferred: false,
+ extension: "extension3",
+ fileName: "3",
+ fileContent: " http://test.me.0\nhttp://test.me.1 ",
+ fileMode: "new",
+ spaceToTab: false,
+ toPosixLines: false,
+ },
+ {
+ dbKey: "dbKey4",
+ deferred: false,
+ extension: "extension4",
+ fileName: "4",
+ fileUri: "http://test.me",
+ fileMode: "url",
+ spaceToTab: false,
+ toPosixLines: false,
+ },
+ ],
+ "historyId"
+ );
+ expect(p).toEqual({
+ auto_decompress: true,
+ files: [{ size: 1 }],
+ history_id: "historyId",
+ targets: [
+ {
+ destination: { type: "hdas" },
+ elements: [
+ {
+ dbkey: "?",
+ deferred: undefined,
+ ext: "auto",
+ name: "1",
+ paste_content: " fileContent ",
+ space_to_tab: undefined,
+ src: "pasted",
+ to_posix_lines: undefined,
+ },
+ {
+ dbkey: "dbKey2",
+ deferred: true,
+ ext: "extension2",
+ name: "2",
+ space_to_tab: true,
+ src: "files",
+ to_posix_lines: true,
+ },
+ {
+ dbkey: "dbKey3",
+ deferred: false,
+ ext: "extension3",
+ name: "3",
+ space_to_tab: false,
+ src: "url",
+ to_posix_lines: false,
+ url: "http://test.me.0",
+ },
+ {
+ dbkey: "dbKey3",
+ deferred: false,
+ ext: "extension3",
+ name: "3",
+ space_to_tab: false,
+ src: "url",
+ to_posix_lines: false,
+ url: "http://test.me.1",
+ },
+ {
+ dbkey: "dbKey4",
+ deferred: false,
+ ext: "extension4",
+ name: "4",
+ space_to_tab: false,
+ src: "url",
+ to_posix_lines: false,
+ url: "http://test.me",
+ },
+ ],
+ },
+ ],
+ });
+ });
+
+ test("composite payload", () => {
+ const p = uploadPayload(
+ [
+ { fileContent: "fileContent", fileMode: "new", fileName: "1" },
+ {
+ dbKey: "dbKey",
+ deferred: true,
+ extension: "extension",
+ fileContent: "fileContent",
+ fileData: "fileData",
+ fileMode: "local",
+ fileName: "2",
+ spaceToTab: true,
+ toPosixLines: true,
+ },
+ ],
+ "historyId",
+ true
+ );
+ expect(p).toEqual({
+ auto_decompress: true,
+ files: ["fileData"],
+ history_id: "historyId",
+ targets: [
+ {
+ destination: { type: "hdas" },
+ items: [
+ {
+ composite: {
+ items: [
+ {
+ dbkey: "?",
+ deferred: undefined,
+ ext: "auto",
+ name: "1",
+ paste_content: "fileContent",
+ space_to_tab: undefined,
+ src: "pasted",
+ to_posix_lines: undefined,
+ },
+ {
+ dbkey: "dbKey",
+ deferred: true,
+ ext: "extension",
+ name: "2",
+ space_to_tab: true,
+ src: "files",
+ to_posix_lines: true,
+ },
+ ],
+ },
+ dbkey: "?",
+ ext: "auto",
+ src: "composite",
+ },
+ ],
+ },
+ ],
+ });
+ });
+});
diff --git a/client/src/utils/upload-queue.js b/client/src/utils/upload-queue.js
new file mode 100644
index 000000000000..6990965e58d4
--- /dev/null
+++ b/client/src/utils/upload-queue.js
@@ -0,0 +1,167 @@
+/*
+ galaxy upload utilities - requires FormData and XMLHttpRequest
+*/
+import { uploadPayload } from "@/utils/upload-payload.js";
+import { sendPayload, uploadSubmit } from "@/utils/upload-submit.js";
+
+export class UploadQueue {
+ constructor(options) {
+ this.opts = {
+ announce: (d) => {},
+ get: (d) => {},
+ progress: (d, m) => {},
+ success: (d, m) => {},
+ warning: (d, m) => {},
+ error: (d, m) => {
+ console.error(m);
+ },
+ complete: () => {},
+ multiple: true,
+ ...options,
+ };
+ this.queue = new Map(); // items stored by key (referred to as index)
+ this.nextIndex = 0;
+ this.fileSet = new Set(); // Used for fast duplicate checking
+ this.isRunning = false;
+ this.isPaused = false;
+ }
+
+ // Add new files to upload queue
+ add(files) {
+ if (files && files.length && !this.isRunning) {
+ files.forEach((file) => {
+ const fileSetKey = file.name + file.size; // Concat name and size to create a "file signature".
+ if (file.mode === "new" || !this.fileSet.has(fileSetKey)) {
+ this.fileSet.add(fileSetKey);
+ const index = String(this.nextIndex++);
+ this.queue.set(index, file);
+ this.opts.announce(index, file);
+ }
+ });
+ }
+ }
+
+ // Set options
+ configure(options) {
+ this.opts = Object.assign(this.opts, options);
+ return this.opts;
+ }
+
+ // Remove file from queue and file set by index
+ remove(index) {
+ const file = this.queue.get(index);
+ const fileSetKey = file.name + file.size;
+ this.queue.delete(index) && this.fileSet.delete(fileSetKey);
+ }
+
+ // Remove all entries from queue
+ reset() {
+ this.queue.clear();
+ this.fileSet.clear();
+ }
+
+ // Returns queue size
+ get size() {
+ return this.queue.size;
+ }
+
+ // Initiate upload process
+ start() {
+ if (!this.isRunning) {
+ this.isRunning = true;
+ this._processUrls();
+ this._process();
+ }
+ }
+
+ // Pause upload process
+ stop() {
+ this.isPaused = true;
+ }
+
+ // Process an upload, recursive
+ _process() {
+ if (this.size === 0 || this.isPaused) {
+ this.isRunning = false;
+ this.isPaused = false;
+ this.opts.complete();
+ return;
+ } else {
+ this.isRunning = true;
+ }
+ // Return index to first item in queue (in FIFO order).
+ const index = this._processIndex();
+ try {
+ // Remove item from queue
+ this.remove(index);
+ // Collect upload request data
+ const data = uploadPayload([this.opts.get(index)], this.opts.historyId);
+ // Initiate upload request
+ this._processSubmit(index, data);
+ } catch (e) {
+ // Parse error message for failed upload item
+ this.opts.error(index, String(e));
+ // Continue queue
+ this._process();
+ }
+ }
+
+ // Submit remote files as single batch request
+ _processUrls() {
+ const list = [];
+ for (const index of this.queue.keys()) {
+ const model = this.opts.get(index);
+ if (model.status === "queued" && model.fileMode === "url") {
+ list.push({ index, ...model });
+ this.remove(index);
+ }
+ }
+ if (list.length > 0) {
+ try {
+ const data = uploadPayload(list, this.opts.historyId);
+ sendPayload(data, {
+ success: (message) => {
+ list.forEach((model) => {
+ this.opts.success(model.index, message);
+ });
+ },
+ error: (message) => {
+ list.forEach((model) => {
+ this.opts.error(model.index, message);
+ });
+ },
+ });
+ } catch (e) {
+ list.forEach((model) => {
+ this.opts.error(model.index, String(e));
+ });
+ }
+ }
+ }
+
+ // Get next item to be processed
+ _processIndex() {
+ return this.queue.keys().next().value;
+ }
+
+ // Submit request data
+ _processSubmit(index, data) {
+ uploadSubmit({
+ data: data,
+ success: (message) => {
+ this.opts.success(index, message);
+ this._process();
+ },
+ warning: (message) => {
+ this.opts.warning(index, message);
+ },
+ error: (message) => {
+ this.opts.error(index, message);
+ this._process();
+ },
+ progress: (percentage) => {
+ this.opts.progress(index, percentage);
+ },
+ });
+ }
+}
diff --git a/client/src/utils/upload-queue.test.js b/client/src/utils/upload-queue.test.js
new file mode 100644
index 000000000000..473d578dd1da
--- /dev/null
+++ b/client/src/utils/upload-queue.test.js
@@ -0,0 +1,230 @@
+import { sendPayload } from "@/utils/upload-submit.js";
+
+import { UploadQueue } from "./upload-queue.js";
+
+jest.mock("@/utils/upload-submit.js");
+sendPayload.mockImplementation(() => jest.fn());
+
+function StubFile(name = null, size = 0, mode = "local") {
+ return { name, size, mode };
+}
+
+describe("UploadQueue", () => {
+ test("a queue is initialized to correct state", () => {
+ const q = new UploadQueue({ foo: 1 });
+ expect(q.size).toEqual(0);
+ expect(q.isRunning).toBe(false);
+ expect(q.opts.foo).toEqual(1); // passed as options
+ expect(q.opts.multiple).toBe(true); // default value
+ });
+
+ test("resetting the queue removes all files from it", () => {
+ const q = new UploadQueue();
+ q.add([StubFile("a"), StubFile("b")]);
+ expect(q.size).toEqual(2);
+ q.reset();
+ expect(q.size).toEqual(0);
+ });
+
+ test("calling configure updates options", () => {
+ const q = new UploadQueue({ foo: 1 });
+ expect(q.opts.foo).toEqual(1);
+ expect(q.opts.bar).toBeUndefined();
+ q.configure({ bar: 2 }); // overwrite bar
+ expect(q.opts.foo).toEqual(1); // value unchangee
+ expect(q.opts.bar).toEqual(2); // value overwritten
+ });
+
+ test("calling start sets isRunning to true", () => {
+ const q = new UploadQueue();
+ q._process = jest.fn(); // mock this, otherwise it'll reset isRunning after it's done.
+ expect(q.isRunning).toBe(false);
+ q.start();
+ expect(q.isRunning).toBe(true);
+ });
+
+ test("calling start is a noop if queue is running", () => {
+ const q = new UploadQueue();
+ const mockedProcess = jest.fn();
+ q._process = mockedProcess();
+ q.isRunning = true;
+ q.start();
+ expect(mockedProcess.mock.calls.length === 0); // function was not called
+ });
+
+ test("calling start processes all files in queue", () => {
+ const fileEntries = {};
+ const q = new UploadQueue({
+ get: (index) => fileEntries[index],
+ announce: (index, file) => {
+ fileEntries[index] = {
+ fileMode: file.mode,
+ fileName: file.name,
+ fileSize: file.size,
+ fileContent: "fileContent",
+ };
+ },
+ });
+ const spy = jest.spyOn(q, "_process");
+ const mockedSubmit = jest.fn(() => q._process());
+ q._processSubmit = mockedSubmit;
+ q.add([StubFile("a"), StubFile("b")]);
+ q.start();
+ expect(q.size).toEqual(0);
+ expect(spy.mock.calls.length).toEqual(3); // called for 2, 1, 0 files.
+ spy.mockRestore(); // not necessary, but safer, in case we later modify implementation.
+ });
+
+ test("calling stop sets isPaused to true", () => {
+ const q = new UploadQueue();
+ q.start();
+ expect(q.isPaused).toBe(false);
+ q.stop();
+ expect(q.isPaused).toBe(true);
+ });
+
+ test("adding files increases the queue size by the number of files", () => {
+ const q = new UploadQueue();
+ expect(q.size).toEqual(0);
+ q.add([StubFile("a"), StubFile("b")]);
+ expect(q.nextIndex).toEqual(2);
+ expect(q.size).toEqual(2);
+ q.add([StubFile("c")]);
+ expect(q.size).toEqual(3);
+ });
+
+ test("adding files increases the next index by the number of files", () => {
+ const q = new UploadQueue();
+ expect(q.nextIndex).toEqual(0);
+ q.add([StubFile("a"), StubFile("b")]);
+ expect(q.nextIndex).toEqual(2);
+ });
+
+ test("duplicate files are not added to the queue, unless the mode is set to 'new'", () => {
+ const q = new UploadQueue();
+ const file1 = StubFile("a", 1);
+ const file2 = StubFile("a", 1);
+ const file3 = StubFile("a", 1, "new");
+ q.add([file1, file2]); // file2 is a duplicate of file1, so only 1 file is added
+ expect(q.size).toEqual(1); // queue size incremented by 1
+ expect(q.nextIndex).toEqual(1); // next index value incremented by 1
+ q.add([file3]); // file3 is a duplicate of file1 and file2, but its mode is "new"
+ expect(q.size).toEqual(2); // queue size incremented by 1
+ expect(q.nextIndex).toEqual(2); // next index value incremented by 1
+ });
+
+ test("adding a file calls opts.announce with correct arguments", () => {
+ const mockAnnounce = jest.fn();
+ const q = new UploadQueue({ announce: mockAnnounce });
+ const file = StubFile("a");
+ expect(mockAnnounce.mock.calls.length).toBe(0);
+ q.add([file]);
+ expect(mockAnnounce.mock.calls.length).toBe(1); // called once
+ expect(mockAnnounce.mock.calls[0][0]).toBe("0"); // first arg is index=0
+ expect(mockAnnounce.mock.calls[0][1]).toBe(file); // second arg is file
+ });
+
+ test("removing a file reduces the queue size by 1", () => {
+ const fileEntries = {};
+ const q = new UploadQueue({
+ announce: (index, file) => {
+ fileEntries[index] = file;
+ },
+ });
+ q.add([StubFile("a"), StubFile("b")]);
+ expect(q.size).toEqual(2);
+ q.remove("0");
+ expect(q.size).toEqual(1);
+ });
+
+ test("removing a file by index out of sequence is allowed", () => {
+ const q = new UploadQueue();
+ const file1 = StubFile("a");
+ const file2 = StubFile("b");
+ const file3 = StubFile("c");
+ q.add([file1, file2, file3]);
+ expect(q.size).toEqual(3);
+ q.remove("1"); // remove file2 (which has index=1)
+ expect(q.size).toEqual(2);
+ expect(q.queue.get("0")).toBe(file1);
+ expect(q.queue.get("1")).toBeUndefined();
+ expect(q.queue.get("2")).toBe(file3);
+ });
+
+ test("removing a file via _processIndex, obeys FIFO protocol", () => {
+ const q = new UploadQueue();
+ q.add([StubFile("a"), StubFile("b")]);
+ let nextIndex = q._processIndex();
+ expect(nextIndex).toEqual("0");
+ q.remove(nextIndex);
+ nextIndex = q._processIndex();
+ expect(nextIndex).toEqual("1");
+ q.remove(nextIndex);
+ expect(q._processIndex()).toBeUndefined();
+ });
+
+ test("remote file batch", () => {
+ const fileEntries = {};
+ const q = new UploadQueue({
+ historyId: "historyId",
+ announce: (index, file) => {
+ fileEntries[index] = {
+ deferred: true,
+ fileContent: `http://test.me.${index}`,
+ fileMode: "url",
+ fileName: file.name,
+ fileSize: 100,
+ spaceToTab: true,
+ status: "queued",
+ toPosixLines: false,
+ };
+ },
+ get: (index) => fileEntries[index],
+ });
+ q.add([StubFile("a"), StubFile("b"), StubFile("c")]);
+ expect(q.size).toEqual(3);
+ q.start();
+ expect(sendPayload.mock.calls[0][0]).toEqual({
+ auto_decompress: true,
+ files: [],
+ history_id: "historyId",
+ targets: [
+ {
+ destination: { type: "hdas" },
+ elements: [
+ {
+ dbkey: "?",
+ deferred: true,
+ ext: "auto",
+ name: "a",
+ space_to_tab: true,
+ src: "url",
+ to_posix_lines: false,
+ url: "http://test.me.0",
+ },
+ {
+ dbkey: "?",
+ deferred: true,
+ ext: "auto",
+ name: "b",
+ space_to_tab: true,
+ src: "url",
+ to_posix_lines: false,
+ url: "http://test.me.1",
+ },
+ {
+ dbkey: "?",
+ deferred: true,
+ ext: "auto",
+ name: "c",
+ space_to_tab: true,
+ src: "url",
+ to_posix_lines: false,
+ url: "http://test.me.2",
+ },
+ ],
+ },
+ ],
+ });
+ });
+});
diff --git a/client/src/utils/upload-submit.js b/client/src/utils/upload-submit.js
new file mode 100644
index 000000000000..14625d20a62c
--- /dev/null
+++ b/client/src/utils/upload-submit.js
@@ -0,0 +1,126 @@
+/*
+ galaxy upload utilities - requires FormData and XMLHttpRequest
+*/
+
+import axios from "axios";
+import { getAppRoot } from "onload/loadConfig";
+import * as tus from "tus-js-client";
+
+function buildFingerprint(cnf) {
+ return async (file) => {
+ return ["tus-br", file.name, file.type, file.size, file.lastModified, cnf.data.history_id].join("-");
+ };
+}
+
+export function sendPayload(payload, cnf) {
+ axios
+ .post(`${getAppRoot()}api/tools/fetch`, payload)
+ .then((response) => {
+ cnf.success(response.data);
+ })
+ .catch((error) => {
+ cnf.error(error.response?.data.err_msg || "Request failed.");
+ });
+}
+
+function tusUpload(uploadables, index, data, tusEndpoint, cnf) {
+ // uploadables must be an array of files or blobs with a name property
+ const startTime = performance.now();
+ const chunkSize = cnf.chunkSize;
+ const uploadable = uploadables[index];
+ if (!uploadable) {
+ // We've uploaded all files or blobs; delete files from data and submit fetch payload
+ delete data["files"];
+ return sendPayload(data, cnf);
+ }
+ console.debug(`Starting chunked upload for ${uploadable.name} [chunkSize=${chunkSize}].`);
+ const upload = new tus.Upload(uploadable, {
+ endpoint: tusEndpoint,
+ retryDelays: [0, 3000, 10000],
+ fingerprint: buildFingerprint(cnf),
+ chunkSize: chunkSize,
+ metadata: data.payload,
+ onError: function (err) {
+ const status = err.originalResponse?.getStatus();
+ if (status == 403) {
+ console.error(`Failed because of missing authorization: ${err}`);
+ cnf.error(err);
+ } else {
+ // 🎵 Never gonna give you up 🎵
+ console.log(`Failed because: ${err}\n, will retry in 10 seconds`);
+ setTimeout(() => tusUploadStart(upload), 10000);
+ }
+ },
+ onChunkComplete: function (chunkSize, bytesAccepted, bytesTotal) {
+ const percentage = ((bytesAccepted / bytesTotal) * 100).toFixed(2);
+ console.log(bytesAccepted, bytesTotal, percentage + "%");
+ cnf.progress(Math.round(percentage));
+ },
+ onSuccess: function () {
+ console.log(
+ `Upload of ${uploadable.name} to ${upload.url} took ${(performance.now() - startTime) / 1000} seconds`
+ );
+ data[`files_${index}|file_data`] = {
+ session_id: upload.url.split("/").at(-1),
+ name: uploadable.name,
+ };
+ tusUpload(uploadables, index + 1, data, tusEndpoint, cnf);
+ },
+ });
+ tusUploadStart(upload);
+}
+
+function tusUploadStart(upload) {
+ // Check if there are any previous uploads to continue.
+ upload.findPreviousUploads().then(function (previousUploads) {
+ // Found previous uploads so we select the first one.
+ if (previousUploads.length) {
+ console.log("previous Upload", previousUploads);
+ upload.resumeFromPreviousUpload(previousUploads[0]);
+ }
+ // Start the upload
+ upload.start();
+ });
+}
+
+// Posts chunked files to the API.
+export function uploadSubmit(config) {
+ // set options
+ const cnf = {
+ data: {},
+ success: () => {},
+ error: () => {},
+ warning: () => {},
+ progress: () => {},
+ attempts: 70000,
+ timeout: 5000,
+ error_file: "File not provided.",
+ error_attempt: "Maximum number of attempts reached.",
+ error_tool: "Tool submission failed.",
+ chunkSize: 10485760,
+ isComposite: false,
+ ...config,
+ };
+ // initial validation
+ var data = cnf.data;
+ if (data.error_message) {
+ cnf.error(data.error_message);
+ return;
+ }
+ // execute upload
+ const tusEndpoint = `${getAppRoot()}api/upload/resumable_upload/`;
+ if (data.files.length || cnf.isComposite) {
+ return tusUpload(data.files, 0, data, tusEndpoint, cnf);
+ } else {
+ if (data.targets.length && data.targets[0].elements.length) {
+ const pasted = data.targets[0].elements[0];
+ if (pasted.src == "url") {
+ return sendPayload(data, cnf);
+ } else {
+ const blob = new Blob([pasted.paste_content]);
+ blob.name = data.targets[0].elements[0].name || "default";
+ return tusUpload([blob], 0, data, tusEndpoint, cnf);
+ }
+ }
+ }
+}
diff --git a/client/src/utils/uploadbox.js b/client/src/utils/uploadbox.js
deleted file mode 100644
index 7aada2d5a204..000000000000
--- a/client/src/utils/uploadbox.js
+++ /dev/null
@@ -1,348 +0,0 @@
-/*
- galaxy upload utilities - requires FormData and XMLHttpRequest
-*/
-
-import axios from "axios";
-import jQuery from "jquery";
-import { getAppRoot } from "onload/loadConfig";
-import * as tus from "tus-js-client";
-import _ from "underscore";
-
-function submitPayload(payload, cnf) {
- axios
- .post(`${getAppRoot()}api/tools/fetch`, payload)
- .then((response) => {
- cnf.success(response.data);
- })
- .catch((error) => {
- cnf.error(error.response?.data.err_msg || "Request failed.");
- });
-}
-
-function buildFingerprint(cnf) {
- async function customFingerprint(file, options) {
- return ["tus-br", file.name, file.type, file.size, file.lastModified, cnf.data.history_id].join("-");
- }
-
- return customFingerprint;
-}
-
-function tusUpload(uploadables, index, data, tusEndpoint, cnf) {
- // uploadables must be an array of files or blobs with a name property
- const startTime = performance.now();
- const chunkSize = cnf.chunkSize;
- const uploadable = uploadables[index];
- if (!uploadable) {
- // We've uploaded all files or blobs; delete files from data and submit fetch payload
- delete data["files"];
- return submitPayload(data, cnf);
- }
- console.debug(`Starting chunked upload for ${uploadable.name} [chunkSize=${chunkSize}].`);
- const upload = new tus.Upload(uploadable, {
- endpoint: tusEndpoint,
- retryDelays: [0, 3000, 10000],
- fingerprint: buildFingerprint(cnf),
- chunkSize: chunkSize,
- metadata: data.payload,
- onError: function (err) {
- const status = err.originalResponse?.getStatus();
- if (status == 403) {
- console.error(`Failed because of missing authorization: ${err}`);
- cnf.error(err);
- } else {
- // 🎵 Never gonna give you up 🎵
- console.log(`Failed because: ${err}\n, will retry in 10 seconds`);
-
- setTimeout(() => startTusUpload(upload), 10000);
- }
- },
- onChunkComplete: function (chunkSize, bytesAccepted, bytesTotal) {
- const percentage = ((bytesAccepted / bytesTotal) * 100).toFixed(2);
- console.log(bytesAccepted, bytesTotal, percentage + "%");
- cnf.progress(percentage);
- },
- onSuccess: function () {
- console.log(
- `Upload of ${uploadable.name} to ${upload.url} took ${(performance.now() - startTime) / 1000} seconds`
- );
- data[`files_${index}|file_data`] = {
- session_id: upload.url.split("/").at(-1),
- name: uploadable.name,
- };
- tusUpload(uploadables, index + 1, data, tusEndpoint, cnf);
- },
- });
- startTusUpload(upload);
-}
-
-function startTusUpload(upload) {
- // Check if there are any previous uploads to continue.
- upload.findPreviousUploads().then(function (previousUploads) {
- // Found previous uploads so we select the first one.
- if (previousUploads.length) {
- console.log("previous Upload", previousUploads);
- upload.resumeFromPreviousUpload(previousUploads[0]);
- }
- // Start the upload
- upload.start();
- });
-}
-
-// Posts chunked files to the API.
-export function submitUpload(config) {
- // set options
- const cnf = {
- data: {},
- success: () => {},
- error: () => {},
- warning: () => {},
- progress: () => {},
- attempts: 70000,
- timeout: 5000,
- url: null,
- error_file: "File not provided.",
- error_attempt: "Maximum number of attempts reached.",
- error_tool: "Tool submission failed.",
- chunkSize: 10485760,
- ...config,
- };
-
- // initial validation
- var data = cnf.data;
- if (data.error_message) {
- cnf.error(data.error_message);
- return;
- }
- const tusEndpoint = `${getAppRoot()}api/upload/resumable_upload/`;
-
- if (hasFiles(data) || isComposite(data)) {
- return tusUpload(data.files, 0, data, tusEndpoint, cnf);
- } else {
- if (data.targets.length && data.targets[0].elements.length) {
- const pasted = data.targets[0].elements[0];
- if (isUrl(pasted)) {
- return submitPayload(data, cnf);
- } else {
- const blob = new Blob([pasted.paste_content]);
- blob.name = data.targets[0].elements[0].name || "default";
- return tusUpload([blob], 0, data, tusEndpoint, cnf);
- }
- }
- }
-}
-
-function hasFiles(data) {
- return data.files.length;
-}
-
-function isComposite(data) {
- return data.targets.length && data.targets[0].items && data.targets[0].items[0].composite;
-}
-
-function isUrl(pasted_item) {
- return pasted_item.src == "url";
-}
-
-(($) => {
- // add event properties
- jQuery.event.props.push("dataTransfer");
-
- /**
- Handles the upload events drag/drop etc.
- */
- $.fn.uploadinput = function (options) {
- // initialize
- var el = this;
- var opts = $.extend(
- {},
- {
- ondragover: () => {},
- ondragleave: () => {},
- onchange: () => {},
- multiple: false,
- },
- options
- );
-
- // append hidden upload field
- var $input = $(``);
- el.append(
- $input.change((e) => {
- opts.onchange(e.target.files);
- e.target.value = null;
- })
- );
-
- // drag/drop events
- const element = el.get(0);
- element.addEventListener("drop", (e) => {
- opts.ondragleave(e);
- if (e.dataTransfer) {
- opts.onchange(e.dataTransfer.files);
- e.preventDefault();
- }
- });
- element.addEventListener("dragover", (e) => {
- e.preventDefault();
- opts.ondragover(e);
- });
- element.addEventListener("dragleave", (e) => {
- e.stopPropagation();
- opts.ondragleave(e);
- });
-
- // exports
- return {
- dialog: () => {
- $input.trigger("click");
- },
- };
- };
-})(jQuery);
-
-export class UploadQueue {
- constructor(options) {
- this.opts = {
- dragover: () => {},
- dragleave: () => {},
- announce: (d) => {},
- initialize: (d) => {},
- progress: (d, m) => {},
- success: (d, m) => {},
- warning: (d, m) => {},
- error: (d, m) => {
- alert(m);
- },
- complete: () => {},
- multiple: true,
- ...options,
- };
- this.queue = new Map(); // items stored by key (referred to as index)
- this.nextIndex = 0;
- this.fileSet = new Set(); // Used for fast duplicate checking
- this._initFlags();
-
- // Element
- this.uploadinput = options.$uploadBox.uploadinput({
- multiple: this.opts.multiple,
- onchange: (files) => {
- _.each(files, (file) => {
- file.chunk_mode = true;
- });
- this.add(files);
- },
- ondragover: options.ondragover,
- ondragleave: options.ondragleave,
- });
- }
-
- _initFlags() {
- this.isRunning = false;
- this.isPaused = false;
- }
-
- // Open file browser for selection
- select() {
- this.uploadinput.dialog();
- }
-
- // Remove all entries from queue
- reset() {
- this.queue.clear();
- this.fileSet.clear();
- }
-
- // Initiate upload process
- start() {
- if (!this.isRunning) {
- this.isRunning = true;
- this._process();
- }
- }
-
- // Pause upload process
- stop() {
- this.isPaused = true;
- }
-
- // Set options
- configure(options) {
- this.opts = Object.assign(this.opts, options);
- return this.opts;
- }
-
- // Verify browser compatibility
- compatible() {
- return window.File && window.FormData && window.XMLHttpRequest && window.FileList;
- }
-
- // Add new files to upload queue
- add(files) {
- if (files && files.length && !this.isRunning) {
- files.forEach((file) => {
- const fileSetKey = file.name + file.size; // Concat name and size to create a "file signature".
- if (file.mode === "new" || !this.fileSet.has(fileSetKey)) {
- this.fileSet.add(fileSetKey);
- const index = this.nextIndex++;
- this.queue.set(index, file);
- this.opts.announce(index, file);
- }
- });
- }
- // Returns last added file index.
- return this.nextIndex - 1;
- }
-
- // Remove file from queue and file set by index
- remove(index) {
- const file = this.queue.get(index);
- const fileSetKey = file.name + file.size;
- this.queue.delete(index) && this.fileSet.delete(fileSetKey);
- }
-
- get size() {
- return this.queue.size;
- }
-
- _firstItemIndex() {
- // Return index to first item in queue (in FIFO order).
- // If queue is empty, return undefined.
- return this.queue.keys().next().value;
- }
-
- // Process an upload, recursive
- _process() {
- if (this.size === 0 || this.isPaused) {
- this._initFlags();
- this.opts.complete();
- return;
- } else {
- this.isRunning = true;
- }
- const index = this._firstItemIndex();
- this.remove(index);
- this._submitUpload(index);
- }
-
- // create and submit data
- _submitUpload(index) {
- submitUpload({
- url: this.opts.url,
- data: this.opts.initialize(index),
- success: (message) => {
- this.opts.success(index, message);
- this._process();
- },
- warning: (message) => {
- this.opts.warning(index, message);
- },
- error: (message) => {
- this.opts.error(index, message);
- this._process();
- },
- progress: (percentage) => {
- this.opts.progress(index, percentage);
- },
- });
- }
-}
diff --git a/client/src/utils/uploadbox.test.js b/client/src/utils/uploadbox.test.js
deleted file mode 100644
index b73e941f7a0c..000000000000
--- a/client/src/utils/uploadbox.test.js
+++ /dev/null
@@ -1,210 +0,0 @@
-import { UploadQueue } from "./uploadbox";
-
-describe("UploadQueue", () => {
- const mockDialog = jest.fn();
-
- function TestUploadQueue(options) {
- // Provide a stub for the $uploadBox default value (used in constuctor);
- // and a mocked dialog function (used in select).
- const stubOptions = {
- $uploadBox: {
- uploadinput: () => ({ dialog: mockDialog }),
- },
- };
- if (options) {
- Object.assign(stubOptions, options);
- }
- return new UploadQueue(stubOptions);
- }
-
- function StubFile(name = null, size = 0, mode = null) {
- this.name = name;
- this.size = size;
- this.mode = mode;
- }
-
- test("a queue is initialized to correct state", () => {
- const q = TestUploadQueue({ foo: 1 });
- expect(q.size).toEqual(0);
- expect(q.isRunning).toBe(false);
- expect(q.opts.foo).toEqual(1); // passed as options
- expect(q.opts.multiple).toBe(true); // default value
- });
-
- test("calling select calls uploadinput.dialog", () => {
- const q = TestUploadQueue();
- expect(mockDialog.mock.calls.length).toBe(0);
- q.select();
- expect(mockDialog.mock.calls.length).toBe(1); // called once
- });
-
- test("resetting the queue removes all files from it", () => {
- const q = TestUploadQueue();
- q.add([new StubFile("a"), new StubFile("b")]);
- expect(q.size).toEqual(2);
- q.reset();
- expect(q.size).toEqual(0);
- });
-
- test("calling configure updates options", () => {
- const q = TestUploadQueue({ foo: 1 });
- expect(q.opts.foo).toEqual(1);
- expect(q.opts.bar).toBeUndefined();
- q.configure({ bar: 2 }); // overwrite bar
- expect(q.opts.foo).toEqual(1); // value unchangee
- expect(q.opts.bar).toEqual(2); // value overwritten
- });
-
- describe("checking browser compatibility", () => {
- const compatibleBrowser = {
- File: 1,
- FormData: 1,
- XMLHttpRequest: 1,
- FileList: 1,
- };
- const incompatibleBrowser = Object.assign(
- {},
- compatibleBrowser,
- { File: 0 } // set File to 0 to make it incompatible.
- );
- let spy;
-
- beforeEach(() => {
- spy = jest.spyOn(window, "window", "get");
- spy.mockImplementation(() => compatibleBrowser);
- });
-
- afterEach(() => {
- spy.mockRestore();
- });
-
- test("calling compatible checks 4 window properties", () => {
- const q = TestUploadQueue();
- expect(spy.mock.calls.length).toEqual(0);
- q.compatible();
- expect(spy.mock.calls.length).toEqual(4);
- });
-
- test("calling compatible returns truthy or falsy depending on values of 4 window properties", () => {
- const q = TestUploadQueue();
- expect(q.compatible()).toBeTruthy();
- spy.mockImplementation(() => incompatibleBrowser); // make browser incompatible
- expect(q.compatible()).toBeFalsy();
- });
- });
-
- test("calling start sets isRunning to true", () => {
- const q = TestUploadQueue();
- q._process = jest.fn(); // mock this, otherwise it'll reset isRunning after it's done.
- expect(q.isRunning).toBe(false);
- q.start();
- expect(q.isRunning).toBe(true);
- });
-
- test("calling start is a noop if queue is running", () => {
- const q = TestUploadQueue();
- const mockedProcess = jest.fn();
- q._process = mockedProcess();
- q.isRunning = true;
- q.start();
- expect(mockedProcess.mock.calls.length === 0); // function was not called
- });
-
- test("calling start processes all files in queue", () => {
- const q = TestUploadQueue();
- const mockedSubmit = jest.fn((index) => q._process());
- q._submitUpload = mockedSubmit;
- const spy = jest.spyOn(q, "_process");
-
- q.add([new StubFile("a"), new StubFile("b")]);
- q.start();
- expect(q.size).toEqual(0);
- expect(spy.mock.calls.length).toEqual(3); // called for 2,1,0 files.
- spy.mockRestore(); // not necessary, but safer, in case we later modify implementation.
- });
- test("calling stop sets isPaused to true", () => {
- const q = TestUploadQueue();
- q.start();
- expect(q.isPaused).toBe(false);
- q.stop();
- expect(q.isPaused).toBe(true);
- });
-
- describe("adding files", () => {
- test("adding files increases the queue size by the number of files", () => {
- const q = TestUploadQueue();
- expect(q.size).toEqual(0);
- q.add([new StubFile("a"), new StubFile("b")]);
- expect(q.size).toEqual(2);
- q.add([new StubFile("c")]);
- expect(q.size).toEqual(3);
- });
-
- test("adding files increases the next index by the number of files", () => {
- const q = TestUploadQueue();
- expect(q.nextIndex).toEqual(0);
- q.add([new StubFile("a"), new StubFile("b")]);
- expect(q.nextIndex).toEqual(2);
- });
-
- test("duplicate files are not added to the queue, unless the mode is set to 'new'", () => {
- const q = TestUploadQueue();
- const file1 = new StubFile("a", 1);
- const file2 = new StubFile("a", 1);
- const file3 = new StubFile("a", 1, "new");
- q.add([file1, file2]); // file2 is a duplicate of file1, so only 1 file is added
- expect(q.size).toEqual(1); // queue size incremented by 1
- expect(q.nextIndex).toEqual(1); // next index value incremented by 1
- q.add([file3]); // file3 is a duplicate of file1 and file2, but its mode is "new"
- expect(q.size).toEqual(2); // queue size incremented by 1
- expect(q.nextIndex).toEqual(2); // next index value incremented by 1
- });
-
- test("adding a file calls opts.announce with correct arguments", () => {
- const mockAnnounce = jest.fn();
- const q = TestUploadQueue({ announce: mockAnnounce });
- const file = new StubFile("a");
- expect(mockAnnounce.mock.calls.length).toBe(0);
- q.add([file]);
- expect(mockAnnounce.mock.calls.length).toBe(1); // called once
- expect(mockAnnounce.mock.calls[0][0]).toBe(0); // first arg is index=0
- expect(mockAnnounce.mock.calls[0][1]).toBe(file); // second arg is file
- });
- });
-
- describe("removing files", () => {
- test("removing a file reduces the queue size by 1", () => {
- const q = TestUploadQueue();
- q.add([new StubFile("a"), new StubFile("b")]);
- expect(q.size).toEqual(2);
- q.remove(0);
- expect(q.size).toEqual(1);
- });
-
- test("removing a file by index out of sequence is allowed", () => {
- const q = TestUploadQueue();
- const file1 = new StubFile("a");
- const file2 = new StubFile("b");
- const file3 = new StubFile("c");
- q.add([file1, file2, file3]);
- expect(q.size).toEqual(3);
- q.remove(1); // remove file2 (which has index=1)
- expect(q.size).toEqual(2);
- expect(q.queue.get(0)).toBe(file1);
- expect(q.queue.get(1)).toBeUndefined();
- expect(q.queue.get(2)).toBe(file3);
- });
-
- test("removing a file via _firstItemIndex, obeys FIFO protocol", () => {
- const q = TestUploadQueue();
- q.add([new StubFile("a"), new StubFile("b")]);
- let nextIndex = q._firstItemIndex();
- expect(nextIndex).toEqual(0);
- q.remove(nextIndex);
- nextIndex = q._firstItemIndex();
- expect(nextIndex).toEqual(1);
- q.remove(nextIndex);
- expect(q._firstItemIndex()).toBeUndefined();
- });
- });
-});
diff --git a/client/tests/jest/helpers.js b/client/tests/jest/helpers.js
index 927c2cb71b21..2396578fe7e5 100644
--- a/client/tests/jest/helpers.js
+++ b/client/tests/jest/helpers.js
@@ -15,6 +15,12 @@ import { PiniaVuePlugin } from "pinia";
const defaultComparator = (a, b) => a == b;
+export function dispatchEvent(wrapper, type, props = {}) {
+ const event = new Event(type, { bubbles: true });
+ Object.assign(event, props);
+ wrapper.element.dispatchEvent(event);
+}
+
export function findViaNavigation(wrapper, component) {
return wrapper.find(component.selector);
}
diff --git a/client/tests/jest/jest-environment.js b/client/tests/jest/jest-environment.js
index 7723277ce1f1..cb044383bc8b 100644
--- a/client/tests/jest/jest-environment.js
+++ b/client/tests/jest/jest-environment.js
@@ -1,10 +1,14 @@
-import JSDOMEnvironment from "jest-environment-jsdom";
import "jsdom-worker";
+import JSDOMEnvironment from "jest-environment-jsdom";
+
export default class CustomJSDOMEnvironment extends JSDOMEnvironment {
constructor(...args) {
super(...args);
this.global.Worker = Worker;
+
+ // FIXME https://github.com/jsdom/jsdom/issues/3363
+ this.global.structuredClone = structuredClone;
}
}
diff --git a/client/webpack.config.js b/client/webpack.config.js
index e68cd301aadf..15063f8cd3e4 100644
--- a/client/webpack.config.js
+++ b/client/webpack.config.js
@@ -50,7 +50,6 @@ module.exports = (env = {}, argv = {}) => {
entry: {
analysis: ["polyfills", "bundleEntries", "entry/analysis"],
generic: ["polyfills", "bundleEntries", "entry/generic"],
- toolshed: ["polyfills", "bundleToolshed", "entry/generic"],
},
output: {
path: path.join(__dirname, "dist"),
@@ -154,18 +153,6 @@ module.exports = (env = {}, argv = {}) => {
},
],
},
- // Attaches the bundleToolshed to the window object.
- {
- test: `${scriptsBase}/bundleToolshed`,
- use: [
- {
- loader: "expose-loader",
- options: {
- exposes: "bundleToolshed",
- },
- },
- ],
- },
{
test: `${scriptsBase}/onload/loadConfig.js`,
use: [
diff --git a/client/yarn.lock b/client/yarn.lock
index 79d513117ceb..c9f99dc3cf4d 100644
--- a/client/yarn.lock
+++ b/client/yarn.lock
@@ -22,6 +22,14 @@
dependencies:
"@babel/highlight" "^7.18.6"
+"@babel/code-frame@^7.22.13":
+ version "7.22.13"
+ resolved "https://registry.yarnpkg.com/@babel/code-frame/-/code-frame-7.22.13.tgz#e3c1c099402598483b7a8c46a721d1038803755e"
+ integrity sha512-XktuhWlJ5g+3TJXc5upd9Ks1HutSArik6jf2eAjYFyIOf4ej3RN+184cZbzDvbPnuTJIUhPKKJE3cIsYTiAT3w==
+ dependencies:
+ "@babel/highlight" "^7.22.13"
+ chalk "^2.4.2"
+
"@babel/compat-data@^7.17.7", "@babel/compat-data@^7.18.8":
version "7.18.8"
resolved "https://registry.npmjs.org/@babel/compat-data/-/compat-data-7.18.8.tgz"
@@ -79,7 +87,7 @@
json5 "^2.2.2"
semver "^6.3.0"
-"@babel/generator@^7.18.10", "@babel/generator@^7.19.0":
+"@babel/generator@^7.18.10":
version "7.19.0"
resolved "https://registry.yarnpkg.com/@babel/generator/-/generator-7.19.0.tgz#785596c06425e59334df2ccee63ab166b738419a"
integrity sha512-S1ahxf1gZ2dpoiFgA+ohK9DIpz50bJ0CWs7Zlzb54Z4sG8qmdIrGrVqmy1sAtTVRb+9CU6U8VqT9L0Zj7hxHVg==
@@ -88,24 +96,6 @@
"@jridgewell/gen-mapping" "^0.3.2"
jsesc "^2.5.1"
-"@babel/generator@^7.20.1":
- version "7.20.4"
- resolved "https://registry.yarnpkg.com/@babel/generator/-/generator-7.20.4.tgz#4d9f8f0c30be75fd90a0562099a26e5839602ab8"
- integrity sha512-luCf7yk/cm7yab6CAW1aiFnmEfBJplb/JojV56MYEK7ziWfGmFlTfmL9Ehwfy4gFhbjBfWO1wj7/TuSbVNEEtA==
- dependencies:
- "@babel/types" "^7.20.2"
- "@jridgewell/gen-mapping" "^0.3.2"
- jsesc "^2.5.1"
-
-"@babel/generator@^7.20.5":
- version "7.20.5"
- resolved "https://registry.yarnpkg.com/@babel/generator/-/generator-7.20.5.tgz#cb25abee3178adf58d6814b68517c62bdbfdda95"
- integrity sha512-jl7JY2Ykn9S0yj4DQP82sYvPU+T3g0HFcWTqDLqiuA9tGRNIj9VfbtXGAYTTkyNEnQk1jkMGOdYka8aG/lulCA==
- dependencies:
- "@babel/types" "^7.20.5"
- "@jridgewell/gen-mapping" "^0.3.2"
- jsesc "^2.5.1"
-
"@babel/generator@^7.20.7":
version "7.20.14"
resolved "https://registry.yarnpkg.com/@babel/generator/-/generator-7.20.14.tgz#9fa772c9f86a46c6ac9b321039400712b96f64ce"
@@ -115,6 +105,16 @@
"@jridgewell/gen-mapping" "^0.3.2"
jsesc "^2.5.1"
+"@babel/generator@^7.23.0":
+ version "7.23.0"
+ resolved "https://registry.yarnpkg.com/@babel/generator/-/generator-7.23.0.tgz#df5c386e2218be505b34837acbcb874d7a983420"
+ integrity sha512-lN85QRR+5IbYrMWM6Y4pE/noaQtg4pNiqeNGX60eqOfo6gtEj6uw/JagelB8vVztSd7R6M5n1+PQkDbHbBRU4g==
+ dependencies:
+ "@babel/types" "^7.23.0"
+ "@jridgewell/gen-mapping" "^0.3.2"
+ "@jridgewell/trace-mapping" "^0.3.17"
+ jsesc "^2.5.1"
+
"@babel/generator@^7.7.2":
version "7.18.12"
resolved "https://registry.npmjs.org/@babel/generator/-/generator-7.18.12.tgz"
@@ -229,6 +229,11 @@
resolved "https://registry.npmjs.org/@babel/helper-environment-visitor/-/helper-environment-visitor-7.18.9.tgz"
integrity sha512-3r/aACDJ3fhQ/EVgFy0hpj8oHyHpQc+LPtJoY9SzTThAsStm4Ptegq92vqKoE3vD706ZVFWITnMnxucw+S9Ipg==
+"@babel/helper-environment-visitor@^7.22.20":
+ version "7.22.20"
+ resolved "https://registry.yarnpkg.com/@babel/helper-environment-visitor/-/helper-environment-visitor-7.22.20.tgz#96159db61d34a29dba454c959f5ae4a649ba9167"
+ integrity sha512-zfedSIzFhat/gFhWfHtgWvlec0nqB9YEIVrpuwjruLlXfUSnA8cJB0miHKwqDnQ7d32aKo2xt88/xZptwxbfhA==
+
"@babel/helper-explode-assignable-expression@^7.18.6":
version "7.18.6"
resolved "https://registry.npmjs.org/@babel/helper-explode-assignable-expression/-/helper-explode-assignable-expression-7.18.6.tgz"
@@ -244,6 +249,14 @@
"@babel/template" "^7.18.10"
"@babel/types" "^7.19.0"
+"@babel/helper-function-name@^7.23.0":
+ version "7.23.0"
+ resolved "https://registry.yarnpkg.com/@babel/helper-function-name/-/helper-function-name-7.23.0.tgz#1f9a3cdbd5b2698a670c30d2735f9af95ed52759"
+ integrity sha512-OErEqsrxjZTJciZ4Oo+eoZqeW9UIiOcuYKRJA4ZAgV9myA+pOXhhmpfNCKjEH/auVfEYVFJ6y1Tc4r0eIApqiw==
+ dependencies:
+ "@babel/template" "^7.22.15"
+ "@babel/types" "^7.23.0"
+
"@babel/helper-hoist-variables@^7.18.6":
version "7.18.6"
resolved "https://registry.npmjs.org/@babel/helper-hoist-variables/-/helper-hoist-variables-7.18.6.tgz"
@@ -251,6 +264,13 @@
dependencies:
"@babel/types" "^7.18.6"
+"@babel/helper-hoist-variables@^7.22.5":
+ version "7.22.5"
+ resolved "https://registry.yarnpkg.com/@babel/helper-hoist-variables/-/helper-hoist-variables-7.22.5.tgz#c01a007dac05c085914e8fb652b339db50d823bb"
+ integrity sha512-wGjk9QZVzvknA6yKIUURb8zY3grXCcOZt+/7Wcy8O2uctxhplmUPkOdlgoNhmdVee2c92JXbf1xpMtVNbfoxRw==
+ dependencies:
+ "@babel/types" "^7.22.5"
+
"@babel/helper-member-expression-to-functions@^7.18.9":
version "7.18.9"
resolved "https://registry.npmjs.org/@babel/helper-member-expression-to-functions/-/helper-member-expression-to-functions-7.18.9.tgz"
@@ -403,6 +423,13 @@
dependencies:
"@babel/types" "^7.18.6"
+"@babel/helper-split-export-declaration@^7.22.6":
+ version "7.22.6"
+ resolved "https://registry.yarnpkg.com/@babel/helper-split-export-declaration/-/helper-split-export-declaration-7.22.6.tgz#322c61b7310c0997fe4c323955667f18fcefb91c"
+ integrity sha512-AsUnxuLhRYsisFiaJwvp1QF+I3KjD5FOxut14q/GzovUe6orHLesW2C7d754kRm53h5gqrz6sFl6sxc4BVtE/g==
+ dependencies:
+ "@babel/types" "^7.22.5"
+
"@babel/helper-string-parser@^7.18.10":
version "7.18.10"
resolved "https://registry.npmjs.org/@babel/helper-string-parser/-/helper-string-parser-7.18.10.tgz"
@@ -413,6 +440,11 @@
resolved "https://registry.yarnpkg.com/@babel/helper-string-parser/-/helper-string-parser-7.19.4.tgz#38d3acb654b4701a9b77fb0615a96f775c3a9e63"
integrity sha512-nHtDoQcuqFmwYNYPz3Rah5ph2p8PFeFCsZk9A/48dPc/rGocJ5J3hAAZ7pb76VWX3fZKu+uEr/FhH5jLx7umrw==
+"@babel/helper-string-parser@^7.22.5":
+ version "7.22.5"
+ resolved "https://registry.yarnpkg.com/@babel/helper-string-parser/-/helper-string-parser-7.22.5.tgz#533f36457a25814cf1df6488523ad547d784a99f"
+ integrity sha512-mM4COjgZox8U+JcXQwPijIZLElkgEpO5rsERVDJTc2qfCDfERyob6k5WegS14SX18IIjv+XD+GrqNumY5JRCDw==
+
"@babel/helper-validator-identifier@^7.18.6":
version "7.18.6"
resolved "https://registry.npmjs.org/@babel/helper-validator-identifier/-/helper-validator-identifier-7.18.6.tgz"
@@ -423,6 +455,11 @@
resolved "https://registry.yarnpkg.com/@babel/helper-validator-identifier/-/helper-validator-identifier-7.19.1.tgz#7eea834cf32901ffdc1a7ee555e2f9c27e249ca2"
integrity sha512-awrNfaMtnHUr653GgGEs++LlAvW6w+DcPrOliSMXWCKo597CwL5Acf/wWdNkf/tfEQE3mjkeD1YOVZOUV/od1w==
+"@babel/helper-validator-identifier@^7.22.20":
+ version "7.22.20"
+ resolved "https://registry.yarnpkg.com/@babel/helper-validator-identifier/-/helper-validator-identifier-7.22.20.tgz#c4ae002c61d2879e724581d96665583dbc1dc0e0"
+ integrity sha512-Y4OZ+ytlatR8AI+8KZfKuL5urKp7qey08ha31L8b3BwewJAoJamTzyvxPR/5D+KkdJCGPq/+8TukHBlY10FX9A==
+
"@babel/helper-validator-option@^7.18.6":
version "7.18.6"
resolved "https://registry.npmjs.org/@babel/helper-validator-option/-/helper-validator-option-7.18.6.tgz"
@@ -465,30 +502,34 @@
chalk "^2.0.0"
js-tokens "^4.0.0"
+"@babel/highlight@^7.22.13":
+ version "7.22.20"
+ resolved "https://registry.yarnpkg.com/@babel/highlight/-/highlight-7.22.20.tgz#4ca92b71d80554b01427815e06f2df965b9c1f54"
+ integrity sha512-dkdMCN3py0+ksCgYmGG8jKeGA/8Tk+gJwSYYlFGxG5lmhfKNoAy004YpLxpS1W2J8m/EK2Ew+yOs9pVRwO89mg==
+ dependencies:
+ "@babel/helper-validator-identifier" "^7.22.20"
+ chalk "^2.4.2"
+ js-tokens "^4.0.0"
+
"@babel/parser@^7.1.0", "@babel/parser@^7.10.3", "@babel/parser@^7.14.7", "@babel/parser@^7.18.4":
version "7.18.11"
resolved "https://registry.npmjs.org/@babel/parser/-/parser-7.18.11.tgz"
integrity sha512-9JKn5vN+hDt0Hdqn1PiJ2guflwP+B6Ga8qbDuoF0PzzVhrzsKIJo8yGqVk6CmMHiMei9w1C1Bp9IMJSIK+HPIQ==
-"@babel/parser@^7.18.10", "@babel/parser@^7.18.11", "@babel/parser@^7.19.1":
+"@babel/parser@^7.18.10":
version "7.19.1"
resolved "https://registry.yarnpkg.com/@babel/parser/-/parser-7.19.1.tgz#6f6d6c2e621aad19a92544cc217ed13f1aac5b4c"
integrity sha512-h7RCSorm1DdTVGJf3P2Mhj3kdnkmF/EiysUkzS2TdgAYqyjFdMQJbVuXOBej2SBJaXan/lIVtT6KkGbyyq753A==
-"@babel/parser@^7.20.1":
- version "7.20.3"
- resolved "https://registry.yarnpkg.com/@babel/parser/-/parser-7.20.3.tgz#5358cf62e380cf69efcb87a7bb922ff88bfac6e2"
- integrity sha512-OP/s5a94frIPXwjzEcv5S/tpQfc6XhxYUnmWpgdqMWGgYCuErA3SzozaRAMQgSZWKeTJxht9aWAkUY+0UzvOFg==
-
-"@babel/parser@^7.20.13", "@babel/parser@^7.20.7":
+"@babel/parser@^7.20.7":
version "7.20.15"
resolved "https://registry.yarnpkg.com/@babel/parser/-/parser-7.20.15.tgz#eec9f36d8eaf0948bb88c87a46784b5ee9fd0c89"
integrity sha512-DI4a1oZuf8wC+oAJA9RW6ga3Zbe8RZFt7kD9i4qAspz3I/yHet1VvC3DiSy/fsUvv5pvJuNPh0LPOdCcqinDPg==
-"@babel/parser@^7.20.5":
- version "7.20.5"
- resolved "https://registry.yarnpkg.com/@babel/parser/-/parser-7.20.5.tgz#7f3c7335fe417665d929f34ae5dceae4c04015e8"
- integrity sha512-r27t/cy/m9uKLXQNWWebeCUHgnAZq0CpG1OwKRxzJMP1vpSU4bSIK2hq+/cp0bQxetkXx38n09rNu8jVkcK/zA==
+"@babel/parser@^7.22.15", "@babel/parser@^7.23.0":
+ version "7.23.0"
+ resolved "https://registry.yarnpkg.com/@babel/parser/-/parser-7.23.0.tgz#da950e622420bf96ca0d0f2909cdddac3acd8719"
+ integrity sha512-vvPKKdMemU85V9WE/l5wZEmImpCtLqbnTvqDS2U1fJ96KrxoW7KrXhNsNCblQlg8Ck4b85yxdTyelsMUgFUXiw==
"@babel/plugin-bugfix-safari-id-destructuring-collision-in-function-expression@^7.18.6":
version "7.18.6"
@@ -1182,83 +1223,28 @@
"@babel/parser" "^7.20.7"
"@babel/types" "^7.20.7"
-"@babel/traverse@^7.10.3", "@babel/traverse@^7.18.10", "@babel/traverse@^7.18.11", "@babel/traverse@^7.7.2":
- version "7.18.11"
- resolved "https://registry.npmjs.org/@babel/traverse/-/traverse-7.18.11.tgz"
- integrity sha512-TG9PiM2R/cWCAy6BPJKeHzNbu4lPzOSZpeMfeNErskGpTJx6trEvFaVCbDvpcxwy49BKWmEPwiW8mrysNiDvIQ==
- dependencies:
- "@babel/code-frame" "^7.18.6"
- "@babel/generator" "^7.18.10"
- "@babel/helper-environment-visitor" "^7.18.9"
- "@babel/helper-function-name" "^7.18.9"
- "@babel/helper-hoist-variables" "^7.18.6"
- "@babel/helper-split-export-declaration" "^7.18.6"
- "@babel/parser" "^7.18.11"
- "@babel/types" "^7.18.10"
- debug "^4.1.0"
- globals "^11.1.0"
-
-"@babel/traverse@^7.18.9", "@babel/traverse@^7.19.0":
- version "7.19.1"
- resolved "https://registry.yarnpkg.com/@babel/traverse/-/traverse-7.19.1.tgz#0fafe100a8c2a603b4718b1d9bf2568d1d193347"
- integrity sha512-0j/ZfZMxKukDaag2PtOPDbwuELqIar6lLskVPPJDjXMXjfLb1Obo/1yjxIGqqAJrmfaTIY3z2wFLAQ7qSkLsuA==
- dependencies:
- "@babel/code-frame" "^7.18.6"
- "@babel/generator" "^7.19.0"
- "@babel/helper-environment-visitor" "^7.18.9"
- "@babel/helper-function-name" "^7.19.0"
- "@babel/helper-hoist-variables" "^7.18.6"
- "@babel/helper-split-export-declaration" "^7.18.6"
- "@babel/parser" "^7.19.1"
- "@babel/types" "^7.19.0"
- debug "^4.1.0"
- globals "^11.1.0"
-
-"@babel/traverse@^7.19.1":
- version "7.20.1"
- resolved "https://registry.yarnpkg.com/@babel/traverse/-/traverse-7.20.1.tgz#9b15ccbf882f6d107eeeecf263fbcdd208777ec8"
- integrity sha512-d3tN8fkVJwFLkHkBN479SOsw4DMZnz8cdbL/gvuDuzy3TS6Nfw80HuQqhw1pITbIruHyh7d1fMA47kWzmcUEGA==
- dependencies:
- "@babel/code-frame" "^7.18.6"
- "@babel/generator" "^7.20.1"
- "@babel/helper-environment-visitor" "^7.18.9"
- "@babel/helper-function-name" "^7.19.0"
- "@babel/helper-hoist-variables" "^7.18.6"
- "@babel/helper-split-export-declaration" "^7.18.6"
- "@babel/parser" "^7.20.1"
- "@babel/types" "^7.20.0"
- debug "^4.1.0"
- globals "^11.1.0"
-
-"@babel/traverse@^7.20.1":
- version "7.20.5"
- resolved "https://registry.yarnpkg.com/@babel/traverse/-/traverse-7.20.5.tgz#78eb244bea8270fdda1ef9af22a5d5e5b7e57133"
- integrity sha512-WM5ZNN3JITQIq9tFZaw1ojLU3WgWdtkxnhM1AegMS+PvHjkM5IXjmYEGY7yukz5XS4sJyEf2VzWjI8uAavhxBQ==
- dependencies:
- "@babel/code-frame" "^7.18.6"
- "@babel/generator" "^7.20.5"
- "@babel/helper-environment-visitor" "^7.18.9"
- "@babel/helper-function-name" "^7.19.0"
- "@babel/helper-hoist-variables" "^7.18.6"
- "@babel/helper-split-export-declaration" "^7.18.6"
- "@babel/parser" "^7.20.5"
- "@babel/types" "^7.20.5"
- debug "^4.1.0"
- globals "^11.1.0"
-
-"@babel/traverse@^7.20.10", "@babel/traverse@^7.20.12", "@babel/traverse@^7.20.13":
- version "7.20.13"
- resolved "https://registry.yarnpkg.com/@babel/traverse/-/traverse-7.20.13.tgz#817c1ba13d11accca89478bd5481b2d168d07473"
- integrity sha512-kMJXfF0T6DIS9E8cgdLCSAL+cuCK+YEZHWiLK0SXpTo8YRj5lpJu3CDNKiIBCne4m9hhTIqUg6SYTAI39tAiVQ==
- dependencies:
- "@babel/code-frame" "^7.18.6"
- "@babel/generator" "^7.20.7"
- "@babel/helper-environment-visitor" "^7.18.9"
- "@babel/helper-function-name" "^7.19.0"
- "@babel/helper-hoist-variables" "^7.18.6"
- "@babel/helper-split-export-declaration" "^7.18.6"
- "@babel/parser" "^7.20.13"
- "@babel/types" "^7.20.7"
+"@babel/template@^7.22.15":
+ version "7.22.15"
+ resolved "https://registry.yarnpkg.com/@babel/template/-/template-7.22.15.tgz#09576efc3830f0430f4548ef971dde1350ef2f38"
+ integrity sha512-QPErUVm4uyJa60rkI73qneDacvdvzxshT3kksGqlGWYdOTIUOwJ7RDUL8sGqslY1uXWSL6xMFKEXDS3ox2uF0w==
+ dependencies:
+ "@babel/code-frame" "^7.22.13"
+ "@babel/parser" "^7.22.15"
+ "@babel/types" "^7.22.15"
+
+"@babel/traverse@^7.10.3", "@babel/traverse@^7.18.10", "@babel/traverse@^7.18.11", "@babel/traverse@^7.18.9", "@babel/traverse@^7.19.0", "@babel/traverse@^7.19.1", "@babel/traverse@^7.20.1", "@babel/traverse@^7.20.10", "@babel/traverse@^7.20.12", "@babel/traverse@^7.20.13", "@babel/traverse@^7.7.2":
+ version "7.23.2"
+ resolved "https://registry.yarnpkg.com/@babel/traverse/-/traverse-7.23.2.tgz#329c7a06735e144a506bdb2cad0268b7f46f4ad8"
+ integrity sha512-azpe59SQ48qG6nu2CzcMLbxUudtN+dOM9kDbUqGq3HXUJRlo7i8fvPoxQUzYgLZ4cMVmuZgm8vvBpNeRhd6XSw==
+ dependencies:
+ "@babel/code-frame" "^7.22.13"
+ "@babel/generator" "^7.23.0"
+ "@babel/helper-environment-visitor" "^7.22.20"
+ "@babel/helper-function-name" "^7.23.0"
+ "@babel/helper-hoist-variables" "^7.22.5"
+ "@babel/helper-split-export-declaration" "^7.22.6"
+ "@babel/parser" "^7.23.0"
+ "@babel/types" "^7.23.0"
debug "^4.1.0"
globals "^11.1.0"
@@ -1280,7 +1266,7 @@
"@babel/helper-validator-identifier" "^7.18.6"
to-fast-properties "^2.0.0"
-"@babel/types@^7.20.0", "@babel/types@^7.20.2":
+"@babel/types@^7.20.2":
version "7.20.2"
resolved "https://registry.yarnpkg.com/@babel/types/-/types-7.20.2.tgz#67ac09266606190f496322dbaff360fdaa5e7842"
integrity sha512-FnnvsNWgZCr232sqtXggapvlkk/tuwR/qhGzcmxI0GXLCjmPYQPzio2FbdlWuY6y1sHFfQKk+rRbUZ9VStQMog==
@@ -1289,15 +1275,6 @@
"@babel/helper-validator-identifier" "^7.19.1"
to-fast-properties "^2.0.0"
-"@babel/types@^7.20.5":
- version "7.20.5"
- resolved "https://registry.yarnpkg.com/@babel/types/-/types-7.20.5.tgz#e206ae370b5393d94dfd1d04cd687cace53efa84"
- integrity sha512-c9fst/h2/dcF7H+MJKZ2T0KjEQ8hY/BNnDk/H3XY8C4Aw/eWQXWn/lWntHF9ooUBnGmEvbfGrTgLWc+um0YDUg==
- dependencies:
- "@babel/helper-string-parser" "^7.19.4"
- "@babel/helper-validator-identifier" "^7.19.1"
- to-fast-properties "^2.0.0"
-
"@babel/types@^7.20.7":
version "7.20.7"
resolved "https://registry.yarnpkg.com/@babel/types/-/types-7.20.7.tgz#54ec75e252318423fc07fb644dc6a58a64c09b7f"
@@ -1307,6 +1284,15 @@
"@babel/helper-validator-identifier" "^7.19.1"
to-fast-properties "^2.0.0"
+"@babel/types@^7.22.15", "@babel/types@^7.22.5", "@babel/types@^7.23.0":
+ version "7.23.0"
+ resolved "https://registry.yarnpkg.com/@babel/types/-/types-7.23.0.tgz#8c1f020c9df0e737e4e247c0619f58c68458aaeb"
+ integrity sha512-0oIyUfKoI3mSqMvsxBdclDwxXKXAUA8v/apZbc+iSyARYou1o8ZGDxbUYyLFoW2arqS2jDGqJuZvv1d/io1axg==
+ dependencies:
+ "@babel/helper-string-parser" "^7.22.5"
+ "@babel/helper-validator-identifier" "^7.22.20"
+ to-fast-properties "^2.0.0"
+
"@bcoe/v8-coverage@^0.2.3":
version "0.2.3"
resolved "https://registry.npmjs.org/@bcoe/v8-coverage/-/v8-coverage-0.2.3.tgz"
@@ -1773,6 +1759,11 @@
resolved "https://registry.npmjs.org/@jridgewell/resolve-uri/-/resolve-uri-3.1.0.tgz"
integrity sha512-F2msla3tad+Mfht5cJq7LSXcdudKTWCVYUgw6pLFOOHSTtZlj6SWNYAp+AhuqLmWdBO2X5hPrLcu8cVP8fy28w==
+"@jridgewell/resolve-uri@^3.1.0":
+ version "3.1.1"
+ resolved "https://registry.yarnpkg.com/@jridgewell/resolve-uri/-/resolve-uri-3.1.1.tgz#c08679063f279615a3326583ba3a90d1d82cc721"
+ integrity sha512-dSYZh7HhCDtCKm4QakX0xFpsRDqjjtZf/kjI/v3T3Nwt5r8/qz/M19F9ySyOqU94SXBmeG9ttTul+YnR4LOxFA==
+
"@jridgewell/set-array@^1.0.0", "@jridgewell/set-array@^1.0.1":
version "1.1.2"
resolved "https://registry.npmjs.org/@jridgewell/set-array/-/set-array-1.1.2.tgz"
@@ -1791,6 +1782,11 @@
resolved "https://registry.npmjs.org/@jridgewell/sourcemap-codec/-/sourcemap-codec-1.4.14.tgz"
integrity sha512-XPSJHWmi394fuUuzDnGz1wiKqWfo1yXecHQMRf2l6hztTO+nPru658AyDngaBe7isIxEkRsPR3FZh+s7iVa4Uw==
+"@jridgewell/sourcemap-codec@^1.4.14":
+ version "1.4.15"
+ resolved "https://registry.yarnpkg.com/@jridgewell/sourcemap-codec/-/sourcemap-codec-1.4.15.tgz#d7c6e6755c78567a951e04ab52ef0fd26de59f32"
+ integrity sha512-eF2rxCRulEKXHTRiDrDy6erMYWqNw4LPdQ8UQA4huuxaQsVeRPFl2oM8oDGxMFhJUWZf9McpLtJasDDZb/Bpeg==
+
"@jridgewell/trace-mapping@^0.3.12", "@jridgewell/trace-mapping@^0.3.15":
version "0.3.17"
resolved "https://registry.yarnpkg.com/@jridgewell/trace-mapping/-/trace-mapping-0.3.17.tgz#793041277af9073b0951a7fe0f0d8c4c98c36985"
@@ -1799,6 +1795,14 @@
"@jridgewell/resolve-uri" "3.1.0"
"@jridgewell/sourcemap-codec" "1.4.14"
+"@jridgewell/trace-mapping@^0.3.17":
+ version "0.3.20"
+ resolved "https://registry.yarnpkg.com/@jridgewell/trace-mapping/-/trace-mapping-0.3.20.tgz#72e45707cf240fa6b081d0366f8265b0cd10197f"
+ integrity sha512-R8LcPeWZol2zR8mmH3JeKQ6QRCFb7XgUhV9ZlGhHLGyg4wpPiPZNQOOWhFZhxKw8u//yTbNGI42Bx/3paXEQ+Q==
+ dependencies:
+ "@jridgewell/resolve-uri" "^3.1.0"
+ "@jridgewell/sourcemap-codec" "^1.4.14"
+
"@jridgewell/trace-mapping@^0.3.7":
version "0.3.14"
resolved "https://registry.npmjs.org/@jridgewell/trace-mapping/-/trace-mapping-0.3.14.tgz"
@@ -3791,9 +3795,9 @@ caseless@~0.12.0:
resolved "https://registry.npmjs.org/caseless/-/caseless-0.12.0.tgz"
integrity sha512-4tYFyifaFfGacoiObjJegolkwSU4xQNGbVgUiNYVUxbQ2x2lUsFvY4hVgVzGiIe6WLOPqycWXA40l+PWsxthUw==
-chalk@^2.0.0, chalk@^2.1.0:
+chalk@^2.0.0, chalk@^2.1.0, chalk@^2.4.2:
version "2.4.2"
- resolved "https://registry.npmjs.org/chalk/-/chalk-2.4.2.tgz"
+ resolved "https://registry.yarnpkg.com/chalk/-/chalk-2.4.2.tgz#cd42541677a54333cf541a49108c1432b44c9424"
integrity sha512-Mti+f9lpJNcwF4tWV8/OrTTtF1gZi+f8FqlyAdouralcFWFQWF2+NgCHShjkCb+IFBLq9buZwE1xckQU4peSuQ==
dependencies:
ansi-styles "^3.2.1"
diff --git a/config/plugins/tours/core.deferred.yaml b/config/plugins/tours/core.deferred.yaml
index b3d80b40660c..e615eb53be38 100644
--- a/config/plugins/tours/core.deferred.yaml
+++ b/config/plugins/tours/core.deferred.yaml
@@ -17,7 +17,7 @@ steps:
postclick: true
- title: "'Upload' Your Data"
- component: upload.paste_new
+ component: upload.create_button
intro: Copy and paste data directly into Galaxy or include URLs that lead to your data
preclick: true
@@ -38,16 +38,16 @@ steps:
postclick: true
- title: Close Settings
- element: .popover-close
+ element: .popper-close
postclick: true
- title: Start Upload
- component: upload.start_uploading
+ component: upload.start_button
intro: Click the start button to begin the process of 'uploading' your deferred dataset.
postclick: true
- title: Close Upload
- component: upload.close
+ component: upload.close_button
intro: Hit the close button to close the upload dialog.
postclick: true
diff --git a/config/plugins/tours/core.galaxy_ui.yaml b/config/plugins/tours/core.galaxy_ui.yaml
index 917054d6143b..9e1be9661831 100644
--- a/config/plugins/tours/core.galaxy_ui.yaml
+++ b/config/plugins/tours/core.galaxy_ui.yaml
@@ -39,12 +39,12 @@ steps:
https://raw.githubusercontent.com/bgruening/galaxytools/adf077b912ddebd97b07b947b855cdd2862ed8ef/tools/statistics/test-data/anderson.tabular
- title: "Start the upload"
- element: "#btn-start"
+ component: upload.start_button
intro: "Upload the data into your Galaxy history."
postclick: true
- title: "Close upload/download manager"
- element: "#btn-close"
+ component: upload.close_button
intro: "Close the upload manager with this button or with a click outside of the manager window."
postclick: true
diff --git a/config/plugins/tours/core.history.yaml b/config/plugins/tours/core.history.yaml
index a7ab5c393f1b..d0c1ecce2f54 100644
--- a/config/plugins/tours/core.history.yaml
+++ b/config/plugins/tours/core.history.yaml
@@ -71,7 +71,7 @@ steps:
intro: "You can remove a dataset from the history with the trash can symbol."
postclick: true
- - element: "#current-history-panel input[data-description='filter text input']"
+ - element: "#current-history-panel .content-operations-filters input[data-description='filter text input']"
title: "Filter your datasets"
intro: "By default your history will hide all deleted datasets from you. You can visualize them by filtering."
textinsert: "deleted:true"
@@ -83,7 +83,7 @@ steps:
Please note that datasets marked as deleted can be purged by your administrator at any time.
postclick: true
- - element: "#current-history-panel [data-description='filter text input']"
+ - element: "#current-history-panel .content-operations-filters input[data-description='filter text input']"
title: "Search your History"
intro: "You can filter your history by typing your search term in here. Galaxy supports more advanced filters that can be seen here."
textinsert: ""
diff --git a/config/plugins/tours/core.windows.yaml b/config/plugins/tours/core.windows.yaml
index dd07f4d7b882..343ebc91506d 100644
--- a/config/plugins/tours/core.windows.yaml
+++ b/config/plugins/tours/core.windows.yaml
@@ -16,15 +16,15 @@ steps:
intro: "First, we will upload some tabular data into our new history."
postclick: true
- - element: "#btn-new"
+ - component: upload.create_button
intro: "We will be using the paste feature to create a new dataset."
postclick: true
- - element: "#upload-row-0 .upload-title"
+ - component: upload.title(n=0)
intro: "Giving the dataset a name"
textinsert: First Dataset
- - element: "#upload-row-0 .upload-text-content"
+ - component: upload.paste_content(n=0)
intro: "...and paste content into the text area field."
textinsert: |
1 0.039 0.000
@@ -36,25 +36,23 @@ steps:
7 0.000 0.000
8 0.000 0.000
- - element: ".upload-settings"
+ - component: upload.settings_button(n=0)
intro: "Now, we may further configure the upload content."
postclick: true
- - element: ".upload-space_to_tab"
+ - component: upload.setting_space_to_tab
intro: "...by specifying that all spaces in our table should be converted into tabs."
- postclick:
- - ".upload-space_to_tab"
- - ".popover-close"
+ postclick: true
- - element: "#btn-new"
+ - component: upload.create_button
intro: "We will create another dataset, so that we can try the Window Manager on multiple datasets."
postclick: true
- - element: "#upload-row-1 .upload-title"
+ - component: upload.title(n=1)
intro: "Giving the second dataset a name"
textinsert: Second Dataset
- - element: "#upload-row-1 .upload-text-content"
+ - component: upload.paste_content(n=1)
intro: "...and paste content into the text area field again."
textinsert: |
1 0.069 0.000
@@ -63,11 +61,11 @@ steps:
4 0.420 0.000
5 0.190 0.000
- - element: "#btn-start"
+ - component: upload.start_button
intro: "Upload the data into your Galaxy history."
postclick: true
- - element: "#btn-close"
+ - component: upload.close_button
intro: "Hit the close button to close the upload dialog."
postclick: true
diff --git a/config/plugins/visualizations/chiraviz/src/js/rna-viz.js b/config/plugins/visualizations/chiraviz/src/js/rna-viz.js
index eefaa3a1a0f4..93bc6d57ae9b 100644
--- a/config/plugins/visualizations/chiraviz/src/js/rna-viz.js
+++ b/config/plugins/visualizations/chiraviz/src/js/rna-viz.js
@@ -1,6 +1,6 @@
/***
-Chimera interactions viewer. It reads sqlite file
+Chimera interactions viewer. It reads sqlite file
and shows up the list of interactions and a summary
in multiple plots, comic alignments
diff --git a/config/plugins/visualizations/chiraviz/templates/chiraviz.mako b/config/plugins/visualizations/chiraviz/templates/chiraviz.mako
index 5dd60ad2e75e..2bbba694758a 100644
--- a/config/plugins/visualizations/chiraviz/templates/chiraviz.mako
+++ b/config/plugins/visualizations/chiraviz/templates/chiraviz.mako
@@ -18,7 +18,7 @@
-
${h.stylesheet_link( root + 'static/plugins/visualizations/graphviz/static/css/style.css' )}
+ ${h.javascript_link( root + 'static/plugins/visualizations/graphviz/static/js/jquery.min.js' )}
${h.javascript_link( root + 'static/plugins/visualizations/graphviz/static/js/cytoscape.min.js' )}
${h.javascript_link( root + 'static/plugins/visualizations/graphviz/static/js/collapse.js' )}
${h.javascript_link( root + 'static/plugins/visualizations/graphviz/static/js/toolPanelFunctions.js' )}
diff --git a/config/plugins/visualizations/h5web/package.json b/config/plugins/visualizations/h5web/package.json
index 145aa121d70a..bf378c84849c 100644
--- a/config/plugins/visualizations/h5web/package.json
+++ b/config/plugins/visualizations/h5web/package.json
@@ -1,27 +1,23 @@
{
"name": "visualization",
- "version": "0.1.0",
+ "version": "0.2.0",
"keywords": [
"galaxy",
- "visualization"
+ "visualization",
+ "h5web"
],
"license": "AFL-3.0",
"dependencies": {
- "@galaxyproject/charts": "^0.0.6",
- "@h5web/app": "^7.1.0",
- "backbone": "^1.3.3",
+ "@h5web/app": "^8.0.0",
+ "buffer": "^6.0.3",
"normalize.css": "^8.0.1",
- "react": "17.0.2",
- "react-dom": "17.0.2"
+ "react": "18.2.0",
+ "react-dom": "18.2.0"
},
"scripts": {
"build": "parcel build src/script.js --dist-dir static"
},
"devDependencies": {
- "@types/react": "^17.0.52",
- "@types/react-dom": "^17.0.18",
- "buffer": "^5.7.1",
- "parcel": "^2.0.0",
- "typescript": "4.9.3"
+ "parcel": "^2.9.3"
}
}
diff --git a/config/plugins/visualizations/h5web/src/script.js b/config/plugins/visualizations/h5web/src/script.js
index db416ab2e35a..a1a944ec045a 100644
--- a/config/plugins/visualizations/h5web/src/script.js
+++ b/config/plugins/visualizations/h5web/src/script.js
@@ -1,47 +1,58 @@
/**
* Visualizer interface for h5web (https://github.com/silx-kit/h5web)
- *
+ *
* This relies on Galaxy being able to serve files using the
- * h5grove protocol (https://silx-kit.github.io/h5grove/).
+ * h5grove protocol (https://silx-kit.github.io/h5grove/).
* This provides efficient access to the contents of the
* HDF5 file and avoids having to read the whole file at any
* point.
*/
-import './styles.css';
-import React, { StrictMode } from 'react'
-import {render as reactRender} from 'react-dom'
-import {App, H5GroveProvider} from '@h5web/app'
+import "./styles.css";
+import React from "react";
+import { createRoot } from "react-dom/client";
+import { App, H5GroveProvider } from "@h5web/app";
+
+/* This will be part of the charts/viz standard lib in 23.1 */
+const slashCleanup = /(\/)+/g;
+function prefixedDownloadUrl(root, path) {
+ return `${root}/${path}`.replace(slashCleanup, "/");
+}
function MyApp(props) {
- return (
-
-
- );
+ return (
+
+
+ );
}
window.bundleEntries = window.bundleEntries || {};
window.bundleEntries.load = function (options) {
- var dataset = options.dataset;
- var settings = options.chart.settings;
- var explorer = settings.get('explorer');
- var url = window.location.origin + "/api/datasets/" + dataset.id + "/content";
- reactRender(
-
-
+
${options.name}
-
`;
- },
-});
-
-export default {
- View: View,
-};
diff --git a/client/src/mvc/ui/ui-misc.js b/client/src/mvc/ui/ui-misc.js
index 451c7f785973..af8d4a236540 100644
--- a/client/src/mvc/ui/ui-misc.js
+++ b/client/src/mvc/ui/ui-misc.js
@@ -5,9 +5,6 @@ import Backbone from "backbone";
import $ from "jquery";
import Buttons from "mvc/ui/ui-buttons";
import Modal from "mvc/ui/ui-modal";
-import Options from "mvc/ui/ui-options";
-import Select from "mvc/ui/ui-select-default";
-import Switch from "mvc/ui/ui-switch";
import _ from "underscore";
/** Displays messages used e.g. in the tool form */
@@ -124,130 +121,19 @@ export var Input = Backbone.View.extend({
},
});
-export var NullableText = Backbone.View.extend({
- initialize: function (options) {
- this.model = (options && options.model) || new Backbone.Model().set(options);
-
- // Add text field
- this.text_input = new Input(options);
-
- // Add button that determines whether an optional value should be defined
- this.optional_button = new Switch({
- id: `optional-switch-${this.model.id}`,
- });
-
- // Create element
- this.setElement("");
- this.$el.append("Set value for this optional select field?
");
- this.$el.append(this.optional_button.$el);
- this.$el.append(this.text_input.$el);
-
- // Determine true/false value of button based on initial value
- this.optional_button.model.set("value", this.text_input.model.get("value") === null ? "false" : "true");
- this.toggleButton();
- this.listenTo(this.optional_button.model, "change", this.toggleButton, this);
- },
- toggleButton: function () {
- const setOptional = this.optional_button.model.get("value");
- if (setOptional == "true") {
- // Enable text field, set value to `""` if the value is falsy and trigger change
- this.text_input.model.set("disabled", false);
- if (!this.text_input.model.get("value")) {
- this.text_input.model.set("value", "");
- this.model.get("onchange") && this.model.get("onchange")("");
- }
- } else {
- // Set text field to disabled, set model value to null and trigger change
- this.text_input.model.set("disabled", true);
- this.text_input.model.set("value", null);
- this.model.get("onchange") && this.model.get("onchange")(null);
- }
- },
- value: function (new_val) {
- const setOptional = this.optional_button.model.get("value");
- if (setOptional == "true") {
- new_val !== undefined && this.model.set("value", typeof new_val == "string" ? new_val : "");
- }
- return this.text_input.model.get("value");
- },
-});
-
-/** Creates an input element which switches between select and text field */
-export var TextSelect = Backbone.View.extend({
- initialize: function (options) {
- this.select = new options.SelectClass.View(options);
- this.model = this.select.model;
- const textInputClass = options.optional ? NullableText : Input;
- this.text = new textInputClass({
- onchange: this.model.get("onchange"),
- });
- this.on("change", () => {
- if (this.model.get("onchange")) {
- this.model.get("onchange")(this.value());
- }
- });
- this.setElement($("").append(this.select.$el).append(this.text.$el));
- this.update(options);
- },
- remove: function () {
- this.select.remove();
- this.text.remove();
- Backbone.View.prototype.remove.call(this);
- },
- wait: function () {
- this.select.wait();
- },
- unwait: function () {
- this.select.unwait();
- },
- value: function (new_val) {
- var element = this.textmode ? this.text : this.select;
- return element.value(new_val);
- },
- update: function (input_def) {
- var data = input_def.data;
- if (!data) {
- data = [];
- _.each(input_def.options, (option) => {
- data.push({ label: option[0], value: option[1] });
- });
- }
- var v = this.value();
- this.textmode = input_def.textable && (!Array.isArray(data) || data.length === 0);
- this.text.$el[this.textmode ? "show" : "hide"]();
- this.select.$el[this.textmode ? "hide" : "show"]();
- this.select.update({ data: data });
- this.value(v);
- },
-});
-
/* Make more Ui stuff directly available at this namespace (for backwards
* compatibility). We should eliminate this practice, though, and just require
* what we need where we need it, allowing for better package optimization.
*/
export const Button = Buttons.Button;
-export const ButtonCheck = Buttons.ButtonCheck;
export const ButtonMenu = Buttons.ButtonMenu;
-export const ButtonLink = Buttons.ButtonLink;
-export const Checkbox = Options.Checkbox;
-export const RadioButton = Options.RadioButton;
-export const Radio = Options.Radio;
-export { Select };
export default {
Button: Buttons.Button,
- ButtonCheck: Buttons.ButtonCheck,
ButtonMenu: Buttons.ButtonMenu,
- ButtonLink: Buttons.ButtonLink,
Input: Input,
Message: Message,
UnescapedMessage: UnescapedMessage,
Modal: Modal,
- RadioButton: Options.RadioButton,
- Checkbox: Options.Checkbox,
- Radio: Options.Radio,
- Select: Select,
- NullableText: NullableText,
- TextSelect: TextSelect,
};
diff --git a/client/src/mvc/ui/ui-options.js b/client/src/mvc/ui/ui-options.js
deleted file mode 100644
index c3d4bf7a97cf..000000000000
--- a/client/src/mvc/ui/ui-options.js
+++ /dev/null
@@ -1,297 +0,0 @@
-/** Base class for options based ui elements **/
-import Backbone from "backbone";
-import $ from "jquery";
-import Buttons from "mvc/ui/ui-buttons";
-import _ from "underscore";
-import Utils from "utils/utils";
-
-var Base = Backbone.View.extend({
- initialize: function (options) {
- this.model =
- (options && options.model) ||
- new Backbone.Model({
- visible: true,
- cls: null,
- data: [],
- id: Utils.uid(),
- error_text: "No options available.",
- wait_text: "Please wait...",
- multiple: false,
- optional: false,
- onchange: () => {},
- }).set(options);
- this.listenTo(this.model, "change:value", this._changeValue, this);
- this.listenTo(this.model, "change:wait", this._changeWait, this);
- this.listenTo(this.model, "change:data", this._changeData, this);
- this.listenTo(this.model, "change:visible", this._changeVisible, this);
- this.listenTo(this, "change", () => {
- this.model.get("onchange")(this.value());
- });
- this.render();
- },
-
- render: function () {
- var self = this;
- this.$el
- .empty()
- .removeClass()
- .addClass("ui-options")
- .addClass(this.model.get("cls"))
- .append((this.$message = $("").addClass("mt-2")))
- .append((this.$menu = $("").addClass("ui-options-menu")))
- .append((this.$options = $(this._template())));
-
- // add select/unselect all button
- this.all_button = null;
- if (this.model.get("multiple")) {
- this.all_button = new Buttons.ButtonCheck({
- onclick: function () {
- self.$("input").prop("checked", self.all_button.value() !== 0);
- self.value(self._getValue());
- self.trigger("change");
- },
- });
- this.$menu.append(this.all_button.$el);
- }
-
- // finalize dom
- this._changeData();
- this._changeWait();
- this._changeVisible();
- },
-
- /** Update available options */
- update: function (input_def) {
- if (input_def.data) {
- this.model.set("data", input_def.data);
- }
- },
-
- _changeData: function () {
- var self = this;
- this.$options.empty();
- if (this._templateOptions) {
- this.$options.append(this._templateOptions(this.model.get("data")));
- } else {
- _.each(this.model.get("data"), (option) => {
- self.$options.append(
- $(self._templateOption(option))
- .addClass("ui-option")
- .tooltip({
- title: option.tooltip || "",
- placement: "bottom",
- })
- );
- });
- }
- this.$("input").on("change", () => {
- self.value(self._getValue());
- self.trigger("change");
- });
- this._changeValue();
- this._changeWait();
- },
-
- _changeVisible: function () {
- this.$el[this.model.get("visible") ? "show" : "hide"]();
- },
-
- _changeWait: function () {
- if (this.model.get("wait")) {
- if (this.length() === 0) {
- this._messageShow(this.model.get("wait_text"), "info");
- this.$options.hide();
- this.$menu.hide();
- }
- } else {
- if (this.length() === 0) {
- this._messageShow(this.model.get("error_text"), "danger");
- this.$options.hide();
- this.$menu.hide();
- } else {
- this.$message.hide();
- this.$options.css("display", "inline-block");
- this.$menu.show();
- }
- }
- },
-
- _changeValue: function () {
- this._setValue(this.model.get("value"));
- if (this._getValue() === null && !this.model.get("multiple") && !this.model.get("optional")) {
- this._setValue(this.first());
- }
- if (this.all_button) {
- this.all_button.value(Array.isArray(this._getValue()) ? this._getValue().length : 0, this.length());
- }
- },
-
- /** Return/Set current selection */
- value: function (new_value) {
- if (new_value !== undefined) {
- this.model.set("value", new_value);
- }
- return this._getValue();
- },
-
- /** Return first available option */
- first: function () {
- var options = this.$("input").first();
- return options.length > 0 ? options.val() : null;
- },
-
- /** Show a spinner indicating that the select options are currently loaded */
- wait: function () {
- this.model.set("wait", true);
- },
-
- /** Hide spinner indicating that the request has been completed */
- unwait: function () {
- this.model.set("wait", false);
- },
-
- /** Returns the number of options */
- length: function () {
- return this.$(".ui-option").length;
- },
-
- /** Shows the options */
- show: function () {
- this.model.set("visible", true);
- },
-
- /** Hides the options */
- hide: function () {
- this.model.set("visible", false);
- },
-
- /** Set value to dom */
- _setValue: function (new_value) {
- var self = this;
- if (new_value !== undefined) {
- this.$("input").prop("checked", false);
- if (new_value !== null) {
- var values = Array.isArray(new_value) ? new_value : [new_value];
- _.each(values, (v) => {
- self.$(`input[value="${v}"]`).first().prop("checked", true);
- });
- }
- }
- },
-
- /** Return current selection */
- _getValue: function () {
- var selected = [];
- this.$(":checked").each(function () {
- selected.push($(this).val());
- });
- if (Utils.isEmpty(selected)) {
- return null;
- }
- return this.model.get("multiple") ? selected : selected[0];
- },
-
- /** Show message instead if options */
- _messageShow: function (text, status) {
- this.$message.show().removeClass().addClass(`alert alert-${status}`).html(text);
- },
-
- /** Main template function */
- _template: function () {
- return $("").addClass("ui-options-list");
- },
-});
-
-/** Iconized **/
-var BaseIcons = Base.extend({
- _templateOption: function (pair) {
- var id = Utils.uid();
- return $("")
- .addClass("ui-option")
- .addClass(this.model.get("cls_option"))
- .append(
- $("").attr({
- id: id,
- type: this.model.get("type"),
- name: this.model.id,
- value: pair.value,
- })
- )
- .append($("").addClass("ui-options-label").attr("for", id).html(pair.label));
- },
-});
-
-/** Radio button field **/
-var Radio = {};
-Radio.View = BaseIcons.extend({
- initialize: function (options) {
- options.type = "radio";
- BaseIcons.prototype.initialize.call(this, options);
- },
-});
-
-/** Checkbox options field **/
-var Checkbox = {};
-Checkbox.View = BaseIcons.extend({
- initialize: function (options) {
- options.type = "checkbox";
- options.multiple = true;
- BaseIcons.prototype.initialize.call(this, options);
- },
-});
-
-/** Radio button options field styled as classic buttons **/
-var RadioButton = {};
-RadioButton.View = Base.extend({
- initialize: function (options) {
- Base.prototype.initialize.call(this, options);
- },
-
- /** Set current value */
- _setValue: function (new_value) {
- if (new_value !== undefined) {
- this.$("input").prop("checked", false);
- this.$("label").removeClass("active");
- this.$(`[value="${new_value}"]`).prop("checked", true).closest("label").addClass("active");
- }
- },
-
- /** Template for a single option */
- _templateOption: function (pair) {
- var $el = $("").attr("role", "button");
- if (pair.icon) {
- $el.append(
- $("")
- .addClass("fa")
- .addClass(pair.icon)
- .addClass(!pair.label && "no-padding")
- );
- }
- $el.append(
- $("")
- .attr({
- type: "radio",
- name: this.model.id,
- value: pair.value,
- })
- .hide()
- );
- if (pair.label) {
- $el.append(pair.label);
- }
- return $el;
- },
-
- /** Main template function */
- _template: function () {
- return $("").addClass("ui-radiobutton");
- },
-});
-
-export default {
- Base: Base,
- BaseIcons: BaseIcons,
- Radio: Radio,
- RadioButton: RadioButton,
- Checkbox: Checkbox,
-};
diff --git a/client/src/mvc/ui/ui-popover.js b/client/src/mvc/ui/ui-popover.js
deleted file mode 100644
index 1b31bfb0df69..000000000000
--- a/client/src/mvc/ui/ui-popover.js
+++ /dev/null
@@ -1,55 +0,0 @@
-/**
- * Popover wrapper
- */
-import Backbone from "backbone";
-import $ from "jquery";
-import _ from "underscore";
-import Utils from "utils/utils";
-
-export default Backbone.View.extend({
- initialize: function (options) {
- this.options = _.defaults(options || {}, {
- title: null,
- placement: "top",
- container: "body",
- });
- this.uid = Utils.uid();
- this.$target = this.options.container;
- },
-
- /**
- * Show popover
- */
- show: function ($content) {
- const btn = "";
- $(this.$target).popover({
- title: `${this.options.title} ${btn}`,
- placement: this.options.placement,
- content: $content,
- html: true,
- trigger: "manual",
- });
- if (this.options.class) {
- $(this.$target).addClass(this.options.class);
- }
- $(this.$target).popover("show");
-
- // add event to hide if click is outside of popup and not on container
- var self = this;
- const $popover = $(this.$target.data("bs.popover").tip);
- $popover.find(".popover-header > i").on("click", () => this.hide());
- $("body").on(`mousedown.${this.uid}`, (e) => {
- if (!$($popover).is(e.target) && $($popover).has(e.target).length === 0) {
- self.hide();
- }
- });
- },
-
- /**
- * Hide popover
- */
- hide: function () {
- $(this.$target).popover("dispose");
- $("body").off(`mousedown.${this.uid}`);
- },
-});
diff --git a/client/src/mvc/ui/ui-select-content.js b/client/src/mvc/ui/ui-select-content.js
deleted file mode 100644
index 3162bf6eaa56..000000000000
--- a/client/src/mvc/ui/ui-select-content.js
+++ /dev/null
@@ -1,626 +0,0 @@
-import { getGalaxyInstance } from "app";
-import Backbone from "backbone";
-import $ from "jquery";
-import Ui from "mvc/ui/ui-misc";
-import Select from "mvc/ui/ui-select-default";
-import _ from "underscore";
-import _l from "utils/localization";
-import Utils from "utils/utils";
-
-/** Batch mode variations */
-const Batch = { DISABLED: "disabled", ENABLED: "enabled", LINKED: "linked" };
-
-/** List of available content selectors options */
-const Configurations = {
- data: [
- {
- src: "hda",
- icon: "fa-file-o",
- tooltip: _l("Single dataset"),
- library: true,
- multiple: false,
- batch: Batch.DISABLED,
- },
- {
- src: "hda",
- icon: "fa-files-o",
- tooltip: _l("Multiple datasets"),
- multiple: true,
- batch: Batch.LINKED,
- },
- {
- src: "hdca",
- icon: "fa-folder-o",
- tooltip: _l("Dataset collection"),
- multiple: false,
- batch: Batch.LINKED,
- },
- ],
- data_multiple: [
- {
- src: "hda",
- icon: "fa-files-o",
- tooltip: _l("Multiple datasets"),
- multiple: true,
- batch: Batch.DISABLED,
- },
- {
- src: "hdca",
- icon: "fa-folder-o",
- tooltip: _l("Dataset collections"),
- multiple: true,
- batch: Batch.DISABLED,
- },
- ],
- data_collection: [
- {
- src: "hdca",
- icon: "fa-folder-o",
- tooltip: _l("Dataset collection"),
- multiple: false,
- batch: Batch.DISABLED,
- },
- ],
- workflow_data: [
- {
- src: "hda",
- icon: "fa-file-o",
- tooltip: _l("Single dataset"),
- multiple: false,
- batch: Batch.DISABLED,
- },
- ],
- workflow_data_multiple: [
- {
- src: "hda",
- icon: "fa-files-o",
- tooltip: _l("Multiple datasets"),
- multiple: true,
- batch: Batch.DISABLED,
- },
- ],
- workflow_data_collection: [
- {
- src: "hdca",
- icon: "fa-folder-o",
- tooltip: _l("Dataset collection"),
- multiple: false,
- batch: Batch.DISABLED,
- },
- ],
- module_data: [
- {
- src: "hda",
- icon: "fa-file-o",
- tooltip: _l("Single dataset"),
- multiple: false,
- batch: Batch.DISABLED,
- },
- {
- src: "hda",
- icon: "fa-files-o",
- tooltip: _l("Multiple datasets"),
- multiple: true,
- batch: Batch.ENABLED,
- },
- ],
- module_data_collection: [
- {
- src: "hdca",
- icon: "fa-folder-o",
- tooltip: _l("Dataset collection"),
- multiple: false,
- batch: Batch.DISABLED,
- },
- {
- src: "hdca",
- icon: "fa-folder",
- tooltip: _l("Multiple collections"),
- multiple: true,
- batch: Batch.ENABLED,
- },
- ],
-};
-
-/** View for hda and dce content selector ui elements */
-const View = Backbone.View.extend({
- initialize: function (options) {
- const self = this;
- this.model =
- (options && options.model) ||
- new Backbone.Model({
- src_labels: { hda: "dataset", hdca: "dataset collection" },
- pagelimit: 100,
- statustimer: 1000,
- }).set(options);
- this.setElement($("").addClass("ui-select-content"));
- this.button_product = new Ui.RadioButton.View({
- value: "false",
- data: [
- {
- icon: "fa fa-chain",
- value: "false",
- tooltip:
- "Linked inputs will be run in matched order with other datasets e.g. use this for matching forward and reverse reads.",
- },
- {
- icon: "fa fa-chain-broken",
- value: "true",
- tooltip: "Unlinked dataset inputs will be run against *all* other inputs.",
- },
- ],
- });
- this.$batch = {
- linked: $(this._templateBatch()).clone(),
- enabled: $(this._templateBatch()).clone().append(this.button_product.$el),
- };
-
- // add drag-drop event handlers
- const element = this.$el.get(0);
- element.addEventListener("dragenter", (e) => {
- this.lastenter = e.target;
- self.$el.addClass("ui-dragover");
- });
- element.addEventListener("dragover", (e) => {
- e.preventDefault();
- });
- element.addEventListener("dragleave", (e) => {
- this.lastenter === e.target && self.$el.removeClass("ui-dragover");
- });
- element.addEventListener("drop", (e) => {
- e.preventDefault();
- try {
- const drop_data = JSON.parse(e.dataTransfer.getData("text"))[0];
- this._handleDropValues(drop_data);
- } catch (e) {
- this._handleDropStatus("danger");
- }
- });
-
- // track current cache elements
- this.cache = {};
-
- // add listeners
- this.listenTo(this.model, "change:data", this._changeData, this);
- this.listenTo(this.model, "change:wait", this._changeWait, this);
- this.listenTo(this.model, "change:current", this._changeCurrent, this);
- this.listenTo(this.model, "change:value", this._changeValue, this);
- this.listenTo(
- this.model,
- "change:type change:optional change:multiple change:extensions",
- this._changeType,
- this
- );
- this.render();
-
- // add change event
- this.on("change", () => {
- options.onchange && options.onchange(self.value());
- });
- },
-
- render: function () {
- this._changeType();
- this._changeValue();
- this._changeWait();
- },
-
- /** Indicate that select fields are being updated */
- wait: function () {
- this.model.set("wait", true);
- },
-
- /** Indicate that the options update has been completed */
- unwait: function () {
- this.model.set("wait", false);
- },
-
- /** Update data representing selectable options */
- update: function (input_def) {
- this.model.set("data", input_def.options);
- },
-
- /** Return the currently selected dataset values */
- value: function (new_value) {
- if (new_value) {
- this._patchValue(new_value);
- const result = this._batch(this._pickValue(new_value));
- this.model.set("value", result);
- }
- const current = this.model.get("current");
- if (this.config[current]) {
- let id_list = this.fields[current].value();
- if (id_list !== null) {
- id_list = Array.isArray(id_list) ? id_list : [id_list];
- if (id_list.length > 0) {
- const result = this._batch({ values: [] });
- for (const i in id_list) {
- const details = this.cache[`${id_list[i]}_${this.config[current].src}`];
- if (details) {
- const unpatchedValue = this._unpatchValue(details);
- result.values.push(unpatchedValue);
- } else {
- console.debug(
- "ui-select-content::value()",
- `Requested details not found for '${id_list[i]}'.`
- );
- return null;
- }
- }
- result.values.sort((a, b) => a.hid - b.hid);
- return this._pickValue(result);
- }
- }
- } else {
- console.debug("ui-select-content::value()", `Invalid value/source '${new_value}'.`);
- }
- return null;
- },
-
- /** Change of current select field */
- _changeCurrent: function () {
- _.each(this.fields, (field, i) => {
- const cnf = this.config[i];
- if (this.model.get("current") == i) {
- field.$el.show();
- _.each(this.$batch, ($batchfield, batchmode) => {
- if (cnf.batch == batchmode) {
- $batchfield.show();
- } else {
- $batchfield.hide();
- }
- });
- if (cnf.src == "hda") {
- this.button_dialog.show();
- this.upload_dialog.show();
- } else {
- this.button_dialog.hide();
- this.upload_dialog.hide();
- }
- this.button_type.value(i);
- } else {
- field.$el.hide();
- }
- });
- if (this.fields.length > 1) {
- this.button_type.show();
- } else {
- this.button_type.hide();
- }
- },
-
- /** Change of type */
- _changeType: function () {
- const self = this;
- const galaxy = getGalaxyInstance();
-
- // identify selector type identifier i.e. [ flavor ]_[ type ]_[ multiple ]
- const config_id =
- (this.model.get("flavor") ? `${this.model.get("flavor")}_` : "") +
- String(this.model.get("type")) +
- (this.model.get("multiple") ? "_multiple" : "");
- if (Configurations[config_id]) {
- this.config = Configurations[config_id];
- } else {
- this.config = Configurations["data"];
- console.debug("ui-select-content::_changeType()", `Invalid configuration/type id '${config_id}'.`);
- }
-
- // prepare extension component of error message
- const data = self.model.get("data");
- const formats = this.model.get("extensions");
- const extensions = Array.isArray(formats) ? Utils.textify(formats) : "";
- const src_labels = this.model.get("src_labels");
-
- // build radio button for data selectors
- this.fields = [];
- this.button_data = [];
- _.each(this.config, (c, i) => {
- self.button_data.push({
- value: i,
- icon: c.icon,
- tooltip: c.tooltip,
- });
- self.fields.push(
- new Select.View({
- optional: self.model.get("optional"),
- multiple: c.multiple,
- searchable:
- !c.multiple || (data && data[c.src] && data[c.src].length > self.model.get("pagelimit")),
- individual: true,
- error_text: `No ${extensions ? `${extensions} ` : ""}${src_labels[c.src] || "content"} available.`,
- onchange: function () {
- self.trigger("change");
- },
- })
- );
- });
- this.button_type = new Ui.RadioButton.View({
- value: this.model.get("current"),
- data: this.button_data,
- cls: "pr-lg-2",
- onchange: function (value) {
- self.model.set("current", value);
- self.trigger("change");
- },
- });
-
- // build data dialog button
- this.button_dialog = new Ui.Button({
- icon: "fa-folder-open-o",
- tooltip: "Browse Datasets",
- onclick: () => {
- const current = this.model.get("current");
- const cnf = this.config[current];
- galaxy.data.dialog(
- (response) => {
- this._handleDropValues(response, false);
- },
- {
- multiple: cnf.multiple,
- library: !!cnf.library,
- format: null,
- allowUpload: true,
- }
- );
- },
- });
-
- // build data dialog button
- this.upload_dialog = new Ui.Button({
- icon: "fa-upload",
- tooltip: "Upload Dataset",
- onclick: () => {
- const current = this.model.get("current");
- const cnf = this.config[current];
- // model doesn't have format yet unfortunately, need to get through to here.
- galaxy.data.dialog(
- (response) => {
- this._handleDropValues(response, false);
- },
- {
- multiple: cnf.multiple,
- formats: formats,
- new: true,
- }
- );
- },
- });
-
- // append views
- const $fields = $("").addClass("overflow-auto w-100 py-2 py-lg-0 pr-lg-2 ");
- this.$el
- .empty()
- .addClass("d-flex flex-row flex-wrap flex-lg-nowrap")
- .append($("").append(this.button_type.$el))
- .append($fields);
- if (galaxy.config.upload_from_form_button == "always-on") {
- this.$el.append($("").append(this.upload_dialog.$el));
- }
- this.$el.append($("").append(this.button_dialog.$el));
- _.each(this.fields, (field) => {
- $fields.append(field.$el);
- });
- _.each(this.$batch, ($batchfield, batchmode) => {
- $fields.append($batchfield);
- });
- this.model.set("current", 0);
- this._changeCurrent();
- this._changeData();
- },
-
- /** Change of wait flag */
- _changeWait: function () {
- const self = this;
- _.each(this.fields, (field) => {
- field[self.model.get("wait") ? "wait" : "unwait"]();
- });
- },
-
- /** Change of available options */
- _changeData: function () {
- const options = this.model.get("data");
- const self = this;
- const select_options = { hda: [], hdca: [] };
- _.each(options, (items, src) => {
- _.each(items, (item) => {
- self._patchValue(item, src);
- const current_src = item.src || src;
- const addOption = !this.model.attributes.tag || item.tags.includes(this.model.attributes.tag);
- if (addOption) {
- select_options[current_src].push({
- hid: item.hid || Infinity, // if we got no hid we have a "Selected" item
- keep: item.keep,
- label: `${item.hid || "Selected"}: ${item.name}`,
- value: item.id,
- origin: item.origin,
- tags: item.tags,
- });
- }
- self.cache[`${item.id}_${current_src}`] = item;
- });
- });
- _.each(this.config, (c, i) => {
- select_options[c.src] && self.fields[i].add(select_options[c.src], (a, b) => b.hid - a.hid);
- });
- },
-
- /** Change of incoming value */
- _changeValue: function () {
- const new_value = this.model.get("value");
- if (new_value && new_value.values && new_value.values.length > 0) {
- // sniff first suitable field type from config list
- let src = new_value.values[0].src;
- if (src === "dce") {
- src =
- this.cache[`dce${new_value.values[0].id}_hda`]?.src ||
- this.cache[`dce${new_value.values[0].id}_hdca`]?.src;
- }
- this._patchValue(new_value, src);
- // create list with content ids
- const list = [];
- _.each(new_value.values, (value) => {
- list.push(value.id);
- });
- const multiple = new_value.values.length > 1;
- for (let i = 0; i < this.config.length; i++) {
- const field = this.fields[i];
- const c = this.config[i];
- if (c.src == src && [multiple, true].indexOf(c.multiple) !== -1) {
- this.model.set("current", i);
- field.value(list);
- break;
- }
- }
- } else {
- _.each(this.fields, (field) => {
- field.value(null);
- });
- }
- },
-
- /** Source helper matches history_content_types to source types */
- _getSource: function (v) {
- return v.history_content_type == "dataset_collection" ? "hdca" : "hda";
- },
-
- /** Only utilize id, source and map_over_type when specifiying input value **/
- _pickValue: function (v) {
- if (v && v.values) {
- v.values = v.values.map((entry) => ({
- id: entry.id,
- src: entry.src,
- map_over_type: entry.map_over_type,
- }));
- }
- return v;
- },
-
- /** Library datasets are displayed and selected together with history datasets,
- Dataset collection elements are displayed together with history dataset collections **/
- _patchValue: function (v, src) {
- const patchTo = { ldda: "hda", dce: src };
- if (v.values) {
- _.each(v.values, (v) => {
- this._patchValue(v, src);
- });
- } else if (patchTo[v.src]) {
- v.origin = v.src;
- v.src = patchTo[v.src];
- v.id = `${v.origin}${v.id}`;
- }
- },
-
- /** Restores original value e.g. after patching library datasets **/
- _unpatchValue: function (v) {
- if (v.origin) {
- const d = Object.assign({}, v);
- d.id = d.id.substr(d.origin.length);
- d.src = d.origin;
- return d;
- }
- return v;
- },
-
- /** Add values from drag/drop */
- _handleDropValues: function (drop_data, drop_partial = true) {
- const self = this;
- const data = this.model.get("data");
- const current = this.model.get("current");
- const config = this.config[current];
- const field = this.fields[current];
- if (data) {
- const values = Array.isArray(drop_data) ? drop_data : [drop_data];
- if (values.length > 0) {
- let data_changed = false;
- _.each(values, (v) => {
- // element_id deals with override in old backbone code,
- // can remove when old history is deprecated
- v.id = v.element_id || v.id;
- self._patchValue(v);
- const new_id = v.id;
- const new_src = (v.src = this._getSource(v));
- const new_value = { id: new_id, src: new_src };
- if (!_.findWhere(data[new_src], new_value)) {
- data_changed = true;
- data[new_src].push({
- id: new_id,
- src: new_src,
- hid: v.hid || "Selected",
- name: v.name ? v.name : new_id,
- origin: v.origin,
- keep: true,
- tags: [],
- });
- }
- });
- if (data_changed) {
- this._changeData();
- }
- const first_id = values[0].id;
- const first_src = values[0].src;
- if (config.src == first_src && drop_partial) {
- let current_value = field.value();
- if (current_value && config.multiple) {
- _.each(values, (v) => {
- if (current_value.indexOf(v.id) == -1) {
- current_value.push(v.id);
- }
- });
- } else {
- current_value = first_id;
- }
- field.value(current_value);
- } else {
- this.model.set("value", { values: values });
- this.model.trigger("change:value");
- }
- this.trigger("change");
- }
- }
- this._handleDropStatus("success");
- },
-
- /** Highlight drag result */
- _handleDropStatus: function (status) {
- const self = this;
- this.$el.removeClass("ui-dragover").addClass(`ui-dragover-${status}`);
- setTimeout(() => {
- self.$el.removeClass(`ui-dragover-${status}`);
- }, this.model.get("statustimer"));
- },
-
- /** Assists in identifying the batch mode */
- _batch: function (result) {
- result["batch"] = false;
- const current = this.model.get("current");
- const config = this.config[current];
- if (config.src == "dce" || config.src == "hdca") {
- const element = this.cache[`${this.fields[current].value()}_${config.src}`];
- if (element && element.map_over_type) {
- result["batch"] = true;
- }
- }
- if (config.batch == Batch.LINKED || config.batch == Batch.ENABLED) {
- result["batch"] = true;
- if (config.batch == Batch.ENABLED && this.button_product.value() === "true") {
- result["product"] = true;
- }
- }
- return result;
- },
-
- /** Template for batch mode execution options */
- _templateBatch: function () {
- return `
-
-
- This is a batch mode input field. Separate jobs will be triggered for each dataset selection.
-
-
`;
- },
-});
-
-export default {
- View: View,
-};
diff --git a/client/src/mvc/ui/ui-select-default.js b/client/src/mvc/ui/ui-select-default.js
deleted file mode 100644
index ca72b3dfc95c..000000000000
--- a/client/src/mvc/ui/ui-select-default.js
+++ /dev/null
@@ -1,421 +0,0 @@
-/**
- * This class creates/wraps a default html select field as backbone class.
- */
-import Backbone from "backbone";
-import $ from "jquery";
-import Buttons from "mvc/ui/ui-buttons";
-import _ from "underscore";
-import { keyedColorScheme } from "utils/color";
-import Utils from "utils/utils";
-
-var View = Backbone.View.extend({
- initialize: function (options) {
- this.data = [];
- this.data2 = [];
- this.model =
- (options && options.model) ||
- new Backbone.Model({
- id: Utils.uid(),
- cls: "ui-select",
- error_text: "No options available",
- empty_text: "Nothing selected",
- visible: true,
- wait: false,
- multiple: false,
- searchable: true,
- optional: false,
- disabled: false,
- readonly: false,
- onchange: function () {},
- value: null,
- individual: false,
- pagesize: 20,
- }).set(options);
- this.on("change", () => {
- if (this.model.get("onchange")) {
- this.model.get("onchange")(this.value());
- }
- });
- this.listenTo(this.model, "change:data", this._changeData, this);
- this.listenTo(this.model, "change:disabled", this._changeDisabled, this);
- this.listenTo(this.model, "change:wait", this._changeWait, this);
- this.listenTo(this.model, "change:visible", this._changeVisible, this);
- this.listenTo(this.model, "change:value", this._changeValue, this);
- this.listenTo(this.model, "change:multiple change:searchable change:cls change:id", this.render, this);
- this.render();
- },
-
- remove: function () {
- this.$select.select2("destroy");
- Backbone.View.prototype.remove.call(this);
- },
-
- render: function () {
- if (this.model.get("searchable")) {
- this._renderSearchable();
- } else {
- this._renderClassic();
- }
- this.$el.addClass(this.model.get("cls")).attr("id", this.model.get("id"));
- this.$select
- .empty()
- .addClass("select")
- .attr("id", `${this.model.get("id")}_select`)
- .prop("multiple", this.model.get("multiple"))
- .on("change", () => {
- this.value(this._getValue());
- this.trigger("change");
- });
- this._changeData();
- this._changeWait();
- this._changeVisible();
- this._changeDisabled();
- },
-
- /** Renders the classic selection field */
- _renderClassic: function () {
- this.$el
- .addClass(this.model.get("multiple") ? "ui-select-multiple" : "ui-select")
- .append((this.$select = $("")))
- .append((this.$dropdown = $("")))
- .append((this.$resize = $("").append((this.$resize_icon = $("")))));
- if (this.model.get("multiple")) {
- this.$dropdown.hide();
- this.$resize_icon.addClass("fa fa-angle-double-right fa-rotate-45").show();
- this.$resize
- .removeClass()
- .addClass("icon-resize")
- .show()
- .off("mousedown")
- .on("mousedown", (event) => {
- var currentY = event.pageY;
- var currentHeight = this.$select.height();
- this.minHeight = this.minHeight || currentHeight;
- $("#dd-helper")
- .show()
- .on("mousemove", (event) => {
- this.$select.height(Math.max(currentHeight + (event.pageY - currentY), this.minHeight));
- })
- .on("mouseup mouseleave", () => {
- $("#dd-helper").hide().off();
- });
- });
- } else {
- this.$dropdown.show();
- this.$resize.hide();
- this.$resize_icon.hide();
- }
- },
-
- /** Renders the default select2 field */
- _renderSearchable: function () {
- this.$el.append((this.$select = $(""))).append((this.$dropdown = $("")));
- this.$dropdown.hide();
- if (!this.model.get("multiple")) {
- this.$dropdown.show().on("click", () => {
- if (this.$select.select2) {
- this.$select.select2("open");
- }
- });
- }
- this.all_button = null;
- if (this.model.get("multiple") && !this.model.get("individual") && !this.model.get("readonly")) {
- this.all_button = new Buttons.ButtonCheck({
- onclick: () => {
- var new_value = [];
- if (this.all_button.value() !== 0) {
- _.each(this.model.get("data"), (option) => {
- new_value.push(option.value);
- });
- }
- this.value(new_value);
- this.trigger("change");
- },
- });
- this.$el.prepend(this.all_button.$el);
- }
- },
-
- /** Matches a search term with a given text */
- _match: function (term, text) {
- return !term || term === "" || String(text).toUpperCase().indexOf(term.toUpperCase()) >= 0;
- },
-
- /** Updates the selection options */
- _changeData: function () {
- this.data = [];
- if (!this.model.get("multiple") && this.model.get("optional")) {
- this.data.push({
- value: "__null__",
- label: this.model.get("empty_text"),
- });
- }
- _.each(this.model.get("data"), (option) => {
- this.data.push(option);
- });
- if (this.length() === 0) {
- this.data.push({
- value: "__null__",
- label: this.model.get("error_text"),
- });
- }
- if (this.model.get("searchable")) {
- this.data2 = [];
- this.data2index = {};
- _.each(this.data, (option, index) => {
- const d = {
- order: index,
- id: option.value,
- text: option.label,
- tags: option.tags,
- };
- this.data2.push(d);
- this.data2index[d.id] = d;
- });
- if (this.$select.data("select2")) {
- this.$select.select2("destroy");
- }
- this.matched_tags = {};
- this.$select.select2({
- data: this.data2,
- closeOnSelect: !this.model.get("multiple"),
- multiple: this.model.get("multiple"),
- query: (q) => {
- this.matched_tags = {};
- var pagesize = this.model.get("pagesize");
- var results = _.filter(this.data2, (e) => {
- var found = false;
- _.each(e.tags, (tag) => {
- if (this._match(q.term, tag)) {
- found = this.matched_tags[tag] = true;
- }
- });
- return found || this._match(q.term, e.text);
- });
- q.callback({
- results: results.slice((q.page - 1) * pagesize, q.page * pagesize),
- more: results.length >= q.page * pagesize,
- });
- },
- formatResult: (result) => {
- let extraTagWarning = "";
- const filteredTags = _.filter(result.tags, (t) =>
- Object.prototype.hasOwnProperty.call(this.matched_tags, t)
- );
- if (filteredTags.length > 5) {
- extraTagWarning = ` ${
- filteredTags.length - 5
- } more tags
`;
- }
- return `
- ${_.escape(result.text)}
-
- ${filteredTags.slice(0, 5).reduce((memo, tag) => {
- const tagColors = keyedColorScheme(tag);
- const isNametag = tag.indexOf("name:") === 0;
- const tagDisplayText = isNametag ? `#${tag.slice(5)}` : tag;
- const styleBlock = isNametag
- ? `style="background-color: ${tagColors.primary}; color: black; border: 1px solid ${tagColors.darker}"`
- : "";
- return `${memo} `;
- }, "")}
- ${extraTagWarning}
-
`;
- },
- });
- this.$(".select2-container .select2-search input").off("blur");
- } else {
- this.$select.find("option").remove();
- _.each(this.data, (option) => {
- this.$select.append($("").attr("value", option.value).html(_.escape(option.label)));
- });
- }
- this.model.set("disabled", this.model.get("readonly") || this.length() === 0);
- this._changeValue();
- },
-
- /** Handles field enabling/disabling, usually used when no options are available */
- _changeDisabled: function () {
- if (this.model.get("searchable")) {
- this.$select.select2(this.model.get("disabled") ? "disable" : "enable");
- } else {
- this.$select.prop("disabled", this.model.get("disabled"));
- }
- },
-
- /** Searchable fields may display a spinner e.g. while waiting for a server response */
- _changeWait: function () {
- this.$dropdown
- .removeClass()
- .addClass("icon-dropdown fa")
- .addClass(this.model.get("wait") ? "fa-spinner fa-spin" : "fa-caret-down");
- },
-
- /** Handles field visibility */
- _changeVisible: function () {
- this.$el[this.model.get("visible") ? "show" : "hide"]();
- this.$select[this.model.get("visible") ? "show" : "hide"]();
- },
-
- /** Synchronizes the model value with the actually selected field value */
- _changeValue: function () {
- this._setValue(this.model.get("value"));
- if (this.model.get("multiple")) {
- if (this.all_button) {
- var value = this._getValue();
- this.all_button.value(Array.isArray(value) ? value.length : 0, this.length());
- }
- } else if (this._getValue() === null && !this.model.get("optional")) {
- this._setValue(this.first());
- }
- },
-
- /** Return/Set current selection */
- value: function (new_value) {
- if (new_value !== undefined) {
- this.model.set("value", new_value);
- }
- return this._getValue();
- },
-
- /** Return the first select option */
- first: function () {
- return this.data.length > 0 ? this.data[0].value : null;
- },
-
- /** Check if a value is an existing option */
- exists: function (value) {
- return _.findWhere(this.data, { value: value });
- },
-
- /** Return the label/text of the current selection */
- text: function () {
- var v = this._getValue();
- var d = this.exists(Array.isArray(v) ? v[0] : v);
- return d ? d.label : "";
- },
-
- /** Show the select field */
- show: function () {
- this.model.set("visible", true);
- },
-
- /** Hide the select field */
- hide: function () {
- this.model.set("visible", false);
- },
-
- /** Show a spinner indicating that the select options are currently loaded */
- wait: function () {
- this.model.set("wait", true);
- },
-
- /** Hide spinner indicating that the request has been completed */
- unwait: function () {
- this.model.set("wait", false);
- },
-
- /** Returns true if the field is disabled */
- disabled: function () {
- return this.model.get("disabled");
- },
-
- /** Enable the select field */
- enable: function () {
- this.model.set("disabled", false);
- },
-
- /** Disable the select field */
- disable: function () {
- this.model.set("disabled", true);
- },
-
- /** Update all available options at once */
- add: function (options, sorter) {
- _.each(this.model.get("data"), (v) => {
- if (v.keep && !_.findWhere(options, { value: v.value })) {
- options.push(v);
- }
- });
- if (sorter && options) {
- options.sort(sorter);
- }
- this.model.set("data", options);
- },
-
- /** Update available options */
- update: function (input_def) {
- this.model.set("data", input_def.data);
- },
-
- /** Set the custom onchange callback function */
- setOnChange: function (callback) {
- this.model.set("onchange", callback);
- },
-
- /** Number of available options */
- length: function () {
- return Array.isArray(this.model.get("data")) ? this.model.get("data").length : 0;
- },
-
- /** Set value to dom */
- _setValue: function (new_value) {
- if (new_value === null || new_value === undefined) {
- new_value = "__null__";
- }
- if (this.model.get("multiple")) {
- new_value = Array.isArray(new_value) ? new_value : [new_value];
- } else if (Array.isArray(new_value)) {
- if (new_value.length > 0) {
- new_value = new_value[0];
- } else {
- new_value = "__null__";
- }
- }
- if (this.model.get("searchable")) {
- if (Array.isArray(new_value)) {
- var val = [];
- _.each(new_value, (v) => {
- var d = this.data2index[v];
- if (d) {
- val.push(d);
- }
- });
- new_value = val;
- } else {
- new_value = this.data2index[new_value];
- }
- this.$select.select2("data", new_value);
- } else {
- this.$select.val(new_value);
- }
- },
-
- /** Get value from dom */
- _getValue: function () {
- var val = null;
- if (this.model.get("searchable")) {
- var selected = this.$select.select2("data");
- if (selected) {
- if (Array.isArray(selected)) {
- val = [];
- selected.sort((a, b) => a.order - b.order);
- _.each(selected, (v) => {
- val.push(v.id);
- });
- } else {
- val = selected.id;
- }
- }
- } else {
- val = this.$select.val();
- }
- return Utils.isEmpty(val) ? null : val;
- },
-});
-
-export default {
- View: View,
-};
diff --git a/client/src/mvc/ui/ui-select-ftp.js b/client/src/mvc/ui/ui-select-ftp.js
deleted file mode 100644
index 961e13571e57..000000000000
--- a/client/src/mvc/ui/ui-select-ftp.js
+++ /dev/null
@@ -1,52 +0,0 @@
-import Backbone from "backbone";
-import List from "mvc/ui/ui-list";
-import { getAppRoot } from "onload/loadConfig";
-import Utils from "utils/utils";
-
-/**
- * FTP file selector
- */
-var View = Backbone.View.extend({
- // initialize
- initialize: function (options) {
- // link this
- var self = this;
-
- // create ui-list view to keep track of selected ftp files
- this.ftpfile_list = new List.View({
- name: "file",
- optional: options.optional,
- multiple: options.multiple,
- onchange: function () {
- options.onchange && options.onchange(self.value());
- },
- });
-
- // create elements
- this.setElement(this.ftpfile_list.$el);
-
- // initial fetch of ftps
- Utils.get({
- url: `${getAppRoot()}api/remote_files`,
- success: function (response) {
- var data = [];
- for (var i in response) {
- data.push({
- value: response[i]["path"],
- label: response[i]["path"],
- });
- }
- self.ftpfile_list.update(data);
- },
- });
- },
-
- /** Return/Set currently selected ftp datasets */
- value: function (val) {
- return this.ftpfile_list.value(val);
- },
-});
-
-export default {
- View: View,
-};
diff --git a/client/src/mvc/ui/ui-select-library.js b/client/src/mvc/ui/ui-select-library.js
deleted file mode 100644
index dff89d336255..000000000000
--- a/client/src/mvc/ui/ui-select-library.js
+++ /dev/null
@@ -1,126 +0,0 @@
-// dependencies
-import Backbone from "backbone";
-import List from "mvc/ui/ui-list";
-import Ui from "mvc/ui/ui-misc";
-import { getAppRoot } from "onload/loadConfig";
-
-// collection of libraries
-var Libraries = Backbone.Collection.extend({
- url: `${getAppRoot()}api/libraries?deleted=false`,
-});
-
-// collection of dataset
-var LibraryDatasets = Backbone.Collection.extend({
- initialize: function () {
- var self = this;
- this.config = new Backbone.Model({ library_id: null });
- this.config.on("change", () => {
- self.fetch({ reset: true });
- });
- },
- url: function () {
- return `${getAppRoot()}api/libraries/${this.config.get("library_id")}/contents`;
- },
-});
-
-// hda/hdca content selector ui element
-var View = Backbone.View.extend({
- // initialize
- initialize: function (options) {
- // link this
- var self = this;
-
- // collections
- this.libraries = new Libraries();
- this.datasets = new LibraryDatasets();
-
- // link app and options
- this.options = options;
-
- // select field for the library
- // TODO: Remove this once the library API supports searching for library datasets
- this.library_select = new Ui.Select.View({
- onchange: function (value) {
- self.datasets.config.set("library_id", value);
- },
- });
-
- // create ui-list view to keep track of selected data libraries
- this.dataset_list = new List.View({
- name: "dataset",
- optional: options.optional,
- multiple: options.multiple,
- onchange: function () {
- self.trigger("change");
- },
- });
-
- // add reset handler for fetched libraries
- this.libraries.on("reset", () => {
- var data = [];
- self.libraries.each((model) => {
- data.push({
- value: model.id,
- label: model.get("name"),
- });
- });
- self.library_select.update({ data: data });
- });
-
- // add reset handler for fetched library datasets
- this.datasets.on("reset", () => {
- var data = [];
- var library_current = self.library_select.text();
- if (library_current !== null) {
- self.datasets.each((model) => {
- if (model.get("type") === "file") {
- data.push({
- value: model.id,
- label: model.get("name"),
- });
- }
- });
- }
- self.dataset_list.update({ data: data });
- });
-
- // add change event. fires on trigger
- this.on("change", () => {
- if (options.onchange) {
- options.onchange(self.value());
- }
- });
-
- // create elements
- this.setElement(this._template());
- this.$(".library-select").append(this.library_select.$el);
- this.$el.append(this.dataset_list.$el);
-
- // initial fetch of libraries
- this.libraries.fetch({
- reset: true,
- success: function () {
- self.library_select.trigger("change");
- if (self.options.value !== undefined) {
- self.value(self.options.value);
- }
- },
- });
- },
-
- /** Return/Set currently selected library datasets */
- value: function (val) {
- return this.dataset_list.value(val);
- },
-
- /** Template */
- _template: function () {
- return `
-
-
`;
- },
-});
-
-export default {
- View: View,
-};
diff --git a/client/src/mvc/ui/ui-switch.js b/client/src/mvc/ui/ui-switch.js
deleted file mode 100644
index c7ba3dd9ad7b..000000000000
--- a/client/src/mvc/ui/ui-switch.js
+++ /dev/null
@@ -1,55 +0,0 @@
-import Backbone from "backbone";
-
-/** Renders a switch input element used e.g. in the tool form */
-export default Backbone.View.extend({
- initialize: function (options) {
- this.model =
- (options && options.model) ||
- new Backbone.Model({
- disabled: false,
- visible: true,
- onchange: () => {},
- }).set(options);
- this.setElement(this._template());
- this.$label = this.$(".label");
- this.$input = this.$(".custom-control-input");
- this.listenTo(this.model, "change", this.render, this);
- this.listenTo(this, "change", () => {
- this.model.get("onchange")(this.value());
- });
- this.render();
- },
- events: {
- input: "_onchange",
- },
- value: function (new_val) {
- new_val !== undefined && this.model.set("value", new_val);
- return this.model.get("value");
- },
- render: function () {
- if (this.model.get("value") == "true") {
- this.$label.text("Yes");
- this.$input.prop("checked", true);
- } else {
- this.$label.text("No");
- this.$input.prop("checked", false);
- }
- this.model.get("disabled") ? this.$input.attr("disabled", true) : this.$input.removeAttr("disabled");
- this.$el[this.model.get("visible") ? "show" : "hide"]();
- return this;
- },
- _onchange: function () {
- this.value(this.$input.prop("checked") ? "true" : "false");
- this.trigger("change");
- },
- _template: function () {
- const id = this.model.id;
- return `
-
`;
- },
-});
diff --git a/client/src/mvc/upload/collection/collection-row.js b/client/src/mvc/upload/collection/collection-row.js
deleted file mode 100644
index 0b0f010eab4f..000000000000
--- a/client/src/mvc/upload/collection/collection-row.js
+++ /dev/null
@@ -1,84 +0,0 @@
-/** Renders the collection uploader rows */
-import $ from "jquery";
-import UploadBoxRow from "mvc/upload/uploadbox-row";
-import _ from "underscore";
-import Utils from "utils/utils";
-
-export default UploadBoxRow.extend({
- initialize: function (app, options) {
- var self = this;
- this.app = app;
- this.model = options.model;
- this.setElement(this._template(options.model));
- this.$mode = this.$(".upload-mode");
- this.$title = this.$(".upload-title-extended");
- this.$text = this.$(".upload-text");
- this.$size = this.$(".upload-size");
- this.$info_text = this.$(".upload-info-text");
- this.$info_progress = this.$(".upload-info-progress");
- this.$text_content = this.$(".upload-text-content");
- this.$symbol = this.$(".upload-symbol");
- this.$progress_bar = this.$(".upload-progress-bar");
- this.$percentage = this.$(".upload-percentage");
-
- this._setupSettings();
-
- // handle click event
- this.$symbol.on("click", () => {
- self._removeRow();
- });
-
- // handle text editing event
- this.$text_content.on("change input", (e) => {
- self.model.set({
- url_paste: $(e.target).val(),
- file_size: $(e.target).val().length,
- });
- });
-
- // model events
- this._setupUploadBoxListeners();
- this.listenTo(this.model, "remove", () => {
- self.remove();
- });
- this.app.collection.on("reset", () => {
- self.remove();
- });
- },
-
- render: function () {
- var options = this.model.attributes;
- this.$title.html(_.escape(options.file_name));
- this.$size.html(Utils.bytesToString(options.file_size));
- this.$mode.removeClass().addClass("upload-mode").addClass("text-primary");
- if (options.file_mode == "new") {
- this.$text
- .css({
- width: `${this.$el.width() - 16}px`,
- top: `${this.$el.height() - 8}px`,
- })
- .show();
- this.$el.height(this.$el.height() - 8 + this.$text.height() + 16);
- this.$mode.addClass("fa fa-edit");
- } else if (options.file_mode == "local") {
- this.$mode.addClass("fa fa-laptop");
- } else if (options.file_mode == "ftp") {
- this.$mode.addClass("fa fa-folder-open-o");
- }
- },
-
- /** Refresh status */
- _refreshStatus: function () {
- var status = this.model.get("status");
- this.$symbol.removeClass().addClass("upload-symbol").addClass(this.status_classes[status]);
- this.model.set("enabled", status == "init");
- var enabled = this.model.get("enabled");
- this.$text_content.attr("disabled", !enabled);
- this._renderStatusType(status);
- },
-
- /** View template */
- _template: function (options) {
- return `
-
-
-
-
- Download data from the web by entering URLs (one per line) or directly paste content.
0%
-
-
-
- Download data from the web by entering a URL (one per line) or directly paste content.
-
-
-
-
-
-
-
- 0%
-
-
-
-
-
-
-
- Download data from the web by entering URLs (one per line) or directly paste content.
-
-
-
-
-
-
-
-
- 0%
- If you are signed-in to Galaxy using a third-party identity and you do not have a Galaxy password please use the reset password option in the login form with your email to create a password for your account.`, - help_text: `This Galaxy server allows you to upload files via FTP. To upload some files, log in to the FTP server at ${options.ftp_upload_site} using your Galaxy credentials. - For help visit the tutorial.`, - collection: null, - onchange: function () {}, - onadd: function () {}, - onremove: function () {}, - }).set(options); - - this.collection = this.model.get("collection"); - const Galaxy = getGalaxyInstance(); - if (Galaxy.config.enable_oidc) { - this.model.set("help_text", this.model.get("help_text") + this.model.get("oidc_text")); - } - this.setElement(this._template()); - this.$content = this.$(".upload-ftp-content"); - this.$wait = this.$(".upload-ftp-wait"); - this.$help = this.$(".upload-ftp-help"); - this.$number = this.$(".upload-ftp-number"); - this.$disk = this.$(".upload-ftp-disk"); - this.$body = this.$(".upload-ftp-body"); - this.$warning = this.$(".upload-ftp-warning"); - this.$select = this.$(".upload-ftp-select-all"); - this.render(); - }, - - render: function () { - var self = this; - this.$wait.show(); - this.$content.hide(); - this.$warning.hide(); - this.$help.hide(); - UploadUtils.getRemoteEntries( - function (ftp_files) { - self.model.set("ftp_files", ftp_files); - self._index(); - self._renderTable(); - }, - function () { - self._renderTable(); - } - ); - }, - - /** Fill table with ftp entries */ - _renderTable: function () { - var self = this; - var ftp_files = this.model.get("ftp_files"); - this.rows = []; - if (ftp_files && ftp_files.length > 0) { - this.$body.empty(); - var size = 0; - _.each(ftp_files, (ftp_file) => { - self.rows.push(self._renderRow(ftp_file)); - size += ftp_file.size; - }); - this.$number.html(`${ftp_files.length} files`); - this.$disk.html(Utils.bytesToString(size, true)); - if (this.collection) { - this.$("._has_collection").show(); - this.$select - .addClass(this.model.get("class_add")) - .off() - .on("click", () => { - self._all(); - }); - this._refresh(); - } - this.$content.show(); - } else { - this.$warning.show(); - } - this.model.get("help_enabled") && this.$help.show(); - this.$wait.hide(); - }, - - /** Add row */ - _renderRow: function (ftp_file) { - var self = this; - var options = this.model.attributes; - var $it = $(this._templateRow(ftp_file)); - var $icon = $it.find(".icon"); - this.$body.append($it); - if (this.collection) { - var model_index = this.ftp_index[ftp_file.path]; - $icon.addClass(model_index === undefined ? options.class_add : options.class_remove); - $it.on("click", () => { - self._switch($icon, ftp_file); - self._refresh(); - }); - } else { - $it.on("click", () => { - options.onchange(ftp_file); - }); - } - return $icon; - }, - - /** Create ftp index */ - _index: function () { - var self = this; - this.ftp_index = {}; - this.collection && - this.collection.each((model) => { - if (model.get("file_mode") == "ftp") { - self.ftp_index[model.get("file_path")] = model.id; - } - }); - }, - - /** Select all event handler */ - _all: function () { - var options = this.model.attributes; - var ftp_files = this.model.get("ftp_files"); - var add = this.$select.hasClass(options.class_add); - for (var index in ftp_files) { - var ftp_file = ftp_files[index]; - var model_index = this.ftp_index[ftp_file.path]; - if ((model_index === undefined && add) || (model_index !== undefined && !add)) { - this._switch(this.rows[index], ftp_file); - } - } - this._refresh(); - }, - - /** Handle collection changes */ - _switch: function ($icon, ftp_file) { - $icon.removeClass(); - var options = this.model.attributes; - var model_index = this.ftp_index[ftp_file.path]; - if (model_index === undefined) { - var new_index = options.onadd(ftp_file); - $icon.addClass(options.class_remove); - this.ftp_index[ftp_file.path] = new_index; - } else { - options.onremove(model_index); - $icon.addClass(options.class_add); - delete this.ftp_index[ftp_file.path]; - } - }, - - /** Refresh select all button state */ - _refresh: function () { - var counts = _.reduce( - this.ftp_index, - (memo, element) => { - element !== undefined && memo++; - return memo; - }, - 0 - ); - this.$select.removeClass(); - if (counts == 0) { - this.$select.addClass(this.model.get("class_add")); - } else { - this.$select.addClass( - counts == this.rows.length ? this.model.get("class_remove") : this.model.get("class_partial") - ); - } - }, - - /** Template of row */ - _templateRow: function (options) { - return `
-
-
`;
- },
-});
diff --git a/client/src/mvc/upload/upload-model.js b/client/src/mvc/upload/upload-model.js
deleted file mode 100644
index b558aebb2876..000000000000
--- a/client/src/mvc/upload/upload-model.js
+++ /dev/null
@@ -1,28 +0,0 @@
-import Backbone from "backbone";
-
-var Model = Backbone.Model.extend({
- defaults: {
- extension: "auto",
- genome: "?",
- url_paste: "",
- status: "init",
- optional: false,
- info: null,
- file_name: "",
- file_mode: "",
- file_size: 0,
- file_type: null,
- file_path: "",
- file_uri: null,
- file_data: null,
- percentage: 0,
- space_to_tab: false,
- to_posix_lines: true,
- enabled: true,
- },
- reset: function (attr) {
- this.clear().set(this.defaults).set(attr);
- },
-});
-var Collection = Backbone.Collection.extend({ model: Model });
-export default { Model: Model, Collection: Collection };
diff --git a/client/src/mvc/upload/upload-settings.js b/client/src/mvc/upload/upload-settings.js
deleted file mode 100644
index 3b0b570de433..000000000000
--- a/client/src/mvc/upload/upload-settings.js
+++ /dev/null
@@ -1,54 +0,0 @@
-/** This renders the content of the settings popup, allowing users to specify flags i.e. for space-to-tab conversion **/
-import Backbone from "backbone";
-import $ from "jquery";
-import _ from "underscore";
-
-export default Backbone.View.extend({
- options: {
- class_check: "fa-check-square-o",
- class_uncheck: "fa-square-o",
- parameters: [
- {
- id: "space_to_tab",
- title: "Convert spaces to tabs",
- },
- {
- id: "to_posix_lines",
- title: "Use POSIX standard",
- },
- {
- id: "deferred",
- title: "Defer dataset resolution",
- },
- ],
- },
-
- initialize: function (options) {
- this.model = options.model;
- this.setElement($("").addClass("upload-settings"));
- this.$el.append($("").addClass("upload-settings-cover"));
- this.$el.append($("${this.model.get("help_text")}
-
- Available files:
-
-
-
-
-
-
-
-
-
-
-
- | Name | -Size | -Created | -
|---|
",
- '',
- "",
- "
",
-
- "',
- "",
- "
",
- "
",
- ].join("")
- );
- },
-});
-export default {
- GroupDetailView: GroupDetailView,
-};
diff --git a/client/src/toolshed/groups/group-list-view.js b/client/src/toolshed/groups/group-list-view.js
deleted file mode 100644
index 6d21347f8144..000000000000
--- a/client/src/toolshed/groups/group-list-view.js
+++ /dev/null
@@ -1,130 +0,0 @@
-import Backbone from "backbone";
-import $ from "jquery";
-import mod_group_row from "toolshed/groups/group-listrow-view";
-import mod_group_model from "toolshed/groups/group-model";
-import { Toast } from "ui/toast";
-import _ from "underscore";
-
-const GroupListView = Backbone.View.extend({
- el: "#groups_element",
- defaults: {},
-
- /**
- * Initialize and fetch the groups from server.
- * Async render afterwards.
- * @param {object} options an object with options
- */
- initialize: function (options) {
- this.options = _.defaults(this.options || {}, this.defaults, options);
- const that = this;
- window.globalTS.groups.collection = new mod_group_model.Groups();
- window.globalTS.groups.collection.fetch({
- success: function (model) {
- that.render();
- },
- error: function (model, response) {
- if (typeof response.responseJSON !== "undefined") {
- Toast.error(response.responseJSON.err_msg);
- } else {
- Toast.error("An error occurred.");
- }
- },
- });
- },
-
- fetch: function () {},
-
- /**
- * Render the groups table from the object's own collection.
- */
- render: function (options) {
- this.options = _.extend(this.options, options);
- $(".tooltip").hide();
- const template = this.templateGroupsList();
- this.$el.html(template({ length: window.globalTS.groups.collection.models.length }));
- this.renderRows(window.globalTS.groups.collection.models);
- $('#center [data-toggle="tooltip"]').tooltip({ trigger: "hover" });
- $("#center").css("overflow", "auto");
- },
-
- /**
- * Render all given models as rows in the groups list
- * @param {array} groups_to_render array of group models to render
- */
- renderRows: function (groups_to_render) {
- for (let i = 0; i < groups_to_render.length; i++) {
- const group = groups_to_render[i];
- this.renderOne({ group: group });
- }
- },
-
- /**
- * Create a view for the given model and add it to the groups view.
- * @param {Group} model of the view that will be rendered
- */
- renderOne: function (options) {
- const rowView = new mod_group_row.GroupListRowView(options);
- this.$el.find("#group_list_body").append(rowView.el);
- },
-
- /**
- * Table heading was clicked, update sorting preferences and re-render.
- * @return {[type]} [description]
- */
- // sort_clicked : function(){
- // if (Galaxy.libraries.preferences.get('sort_order') === 'asc'){
- // Galaxy.libraries.preferences.set({'sort_order': 'desc'});
- // } else {
- // Galaxy.libraries.preferences.set({'sort_order': 'asc'});
- // }
- // this.render();
- // },
-
- /**
- * Sort the underlying collection according to the parameters received.
- * Currently supports only sorting by name.
- */
- // sortLibraries: function(){
- // if (Galaxy.libraries.preferences.get('sort_by') === 'name'){
- // if (Galaxy.libraries.preferences.get('sort_order') === 'asc'){
- // this.collection.sortByNameAsc();
- // } else if (Galaxy.libraries.preferences.get('sort_order') === 'desc'){
- // this.collection.sortByNameDesc();
- // }
- // }
- // },
-
- // MMMMMMMMMMMMMMMMMM
- // === TEMPLATES ====
- // MMMMMMMMMMMMMMMMMM
-
- templateGroupsList: function () {
- const tmpl_array = [];
-
- tmpl_array.push('<%= _.escape(group.get("name")) %>
', - '', - 'A group of <%= group.get("members").length %> members with <%= group.get("repositories").length %> repositories and a total of <%= group.get("total_downloads") %> combined repository clones.
', - - "Members
", - '| Name | ", - "Repositories | ", - "Registered | ", - "", - "", - '<% _.each(group.get("members"), function(member) { %>', - "
|---|---|---|
| ", - "<%= _.escape(member.username) %>", - " | ", - "", - '<%= member.user_repos_count %>', - " | ", - "", - "<%= member.time_created %>", - " | ", - "
Repositories
", - '| Name | ", - "Description | ", - "Clones | ", - "Owner | ", - "Categories | ", - "Created | ", - "Updated | ", - "Rating | ", - "Verified | ", - "", - "", - '<% _.each(group.get("repositories"), function(repo) { %>', - "
|---|---|---|---|---|---|---|---|---|
| ", - '<%= _.escape(repo.name) %>', - " | ", - "", - "<%= _.escape(repo.description) %>", - " | ", - "", - "<%= repo.times_downloaded %>", - " | ", - "", - "<%= _.escape(repo.owner) %>", - " | ", - "",
- "<% _.each((repo.categories), function(cat) { %>",
- '<%= cat.name %> ', - // '<%= repo.categories %>', - "<% }); %>", - " | ",
- '', - "<%= repo.time_created %>", - " | ", - '', - "<%= repo.time_updated %>", - " | ", - "", - "<%= repo.ratings_mean %>", - " | ", - "", - "<%= repo.approved %>", - " | ", - "
');
- tmpl_array.push("
");
- tmpl_array.push('');
- tmpl_array.push("<% if(length === 0) { %>");
- tmpl_array.push("');
- tmpl_array.push(" ");
- tmpl_array.push("
");
- tmpl_array.push("<% }%>");
- tmpl_array.push("
");
-
- return _.template(tmpl_array.join(""));
- },
-});
-
-export default {
- GroupListView: GroupListView,
-};
diff --git a/client/src/toolshed/groups/group-listrow-view.js b/client/src/toolshed/groups/group-listrow-view.js
deleted file mode 100644
index 8acfa31e7634..000000000000
--- a/client/src/toolshed/groups/group-listrow-view.js
+++ /dev/null
@@ -1,35 +0,0 @@
-import Backbone from "backbone";
-import _ from "underscore";
-
-// toolshed group row view
-const GroupListRowView = Backbone.View.extend({
- events: {},
-
- initialize: function (options) {
- this.render(options.group);
- },
-
- render: function (group) {
- const tmpl = this.templateRow();
- this.setElement(tmpl({ group: group }));
- this.$el.show();
- return this;
- },
-
- templateRow: function () {
- return _.template(
- [
- 'There are no groups yet.
");
- tmpl_array.push("<% } else{ %>");
- tmpl_array.push('| Name | "); - // tmpl_array.push('description | '); - tmpl_array.push("Members | "); - tmpl_array.push("Repositories | "); - tmpl_array.push(" "); - tmpl_array.push(' '); - // group item views will attach here - tmpl_array.push(" "); - tmpl_array.push("
|---|
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/lib/tool_shed/webapp/frontend/src/apiUtil.ts b/lib/tool_shed/webapp/frontend/src/apiUtil.ts
new file mode 100644
index 000000000000..9dfa3df9109d
--- /dev/null
+++ b/lib/tool_shed/webapp/frontend/src/apiUtil.ts
@@ -0,0 +1,19 @@
+import axios from "axios"
+import { RawAxiosRequestConfig } from "axios"
+import { components } from "@/schema"
+
+type User = components["schemas"]["UserV2"]
+
+export async function getCurrentUser(): Promise