Merge branch 'galaxyproject:dev' into port-history-panel-to-compositi…

…on-api-and-typescript
galaxyproject · Jan 18, 2024 · 8d2ad5c · 8d2ad5c
2 parents a94add7 + f12984b
commit 8d2ad5c
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diff --git a/.github/workflows/test_galaxy_packages.yaml b/.github/workflows/test_galaxy_packages.yaml
@@ -23,6 +23,11 @@ jobs:
       - uses: actions/checkout@v3
         with:
           path: 'galaxy root'
+      - uses: actions/setup-node@v3
+        with:
+          node-version: '18.12.1'
+          cache: 'yarn'
+          cache-dependency-path: 'galaxy root/client/yarn.lock'
       - uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}

diff --git a/client/src/api/histories.ts b/client/src/api/histories.ts
@@ -2,5 +2,6 @@ import { fetcher } from "@/api/schema";
 
 export const historiesFetcher = fetcher.path("/api/histories").method("get").create();
 export const archivedHistoriesFetcher = fetcher.path("/api/histories/archived").method("get").create();
+export const deleteHistory = fetcher.path("/api/histories/{history_id}").method("delete").create();
 export const undeleteHistory = fetcher.path("/api/histories/deleted/{history_id}/undelete").method("post").create();
-export const purgeHistory = fetcher.path("/api/histories/{history_id}").method("delete").create();
+export const historiesQuery = fetcher.path("/api/histories/query").method("get").create();
diff --git a/client/src/api/schema/schema.ts b/client/src/api/schema/schema.ts
diff --git a/client/src/components/Collections/ListCollectionCreatorModal.js b/client/src/components/Collections/ListCollectionCreatorModal.js
@@ -29,7 +29,6 @@ function listCollectionCreatorModal(elements, options) {
  */
 function createListCollection(contents, defaultHideSourceItems = true) {
     const elements = contents.toJSON();
-    let copyElements;
     const promise = listCollectionCreatorModal(elements, {
         defaultHideSourceItems: defaultHideSourceItems,
         creationFn: function (elements, name, hideSourceItems) {
@@ -39,8 +38,7 @@ function createListCollection(contents, defaultHideSourceItems = true) {
                 //TODO: this allows for list:list even if the filter above does not - reconcile
                 src: element.src || (element.history_content_type == "dataset" ? "hda" : "hdca"),
             }));
-            copyElements = !hideSourceItems;
-            return contents.createHDCA(elements, "list", name, hideSourceItems, copyElements);
+            return contents.createHDCA(elements, "list", name, hideSourceItems);
         },
     });
     return promise;

diff --git a/client/src/components/Collections/PairCollectionCreatorModal.js b/client/src/components/Collections/PairCollectionCreatorModal.js
@@ -25,16 +25,14 @@ function pairCollectionCreatorModal(elements, options) {
 }
 function createPairCollection(contents, defaultHideSourceItems = true) {
     var elements = contents.toJSON();
-    var copyElements;
     var promise = pairCollectionCreatorModal(elements, {
         defaultHideSourceItems: defaultHideSourceItems,
         creationFn: function (elements, name, hideSourceItems) {
             elements = [
                 { name: "forward", src: elements[0].src || "hda", id: elements[0].id },
                 { name: "reverse", src: elements[1].src || "hda", id: elements[1].id },
             ];
-            copyElements = !hideSourceItems;
-            return contents.createHDCA(elements, "paired", name, hideSourceItems, copyElements);
+            return contents.createHDCA(elements, "paired", name, hideSourceItems);
         },
     });
     return promise;

diff --git a/client/src/components/Collections/PairedListCollectionCreatorModal.js b/client/src/components/Collections/PairedListCollectionCreatorModal.js
@@ -29,7 +29,6 @@ function pairedListCollectionCreatorModal(elements, options) {
  */
 function createPairedListCollection(contents, defaultHideSourceItems) {
     const elements = contents.toJSON();
-    var copyElements;
     const promise = pairedListCollectionCreatorModal(elements, {
         defaultHideSourceItems: defaultHideSourceItems,
         creationFn: function (elements, name, hideSourceItems) {
@@ -50,8 +49,7 @@ function createPairedListCollection(contents, defaultHideSourceItems) {
                     },
                 ],
             }));
-            copyElements = !hideSourceItems;
-            return contents.createHDCA(elements, "list:paired", name, hideSourceItems, copyElements);
+            return contents.createHDCA(elements, "list:paired", name, hideSourceItems);
         },
     });
     return promise;

diff --git a/client/src/components/Collections/RuleBasedCollectionCreatorModal.js b/client/src/components/Collections/RuleBasedCollectionCreatorModal.js
@@ -48,7 +48,6 @@ function createCollectionViaRules(selection, defaultHideSourceItems = true) {
     let elementsType;
     let importType;
     const selectionType = selection.selectionType;
-    const copyElements = !defaultHideSourceItems;
     if (!selectionType) {
         // Have HDAs from the history panel.
         elements = selection.toJSON();
@@ -82,7 +81,7 @@ function createCollectionViaRules(selection, defaultHideSourceItems = true) {
         ftpUploadSite: selection.ftpUploadSite,
         defaultHideSourceItems: defaultHideSourceItems,
         creationFn: function (elements, collectionType, name, hideSourceItems) {
-            return selection.createHDCA(elements, collectionType, name, hideSourceItems, copyElements);
+            return selection.createHDCA(elements, collectionType, name, hideSourceItems);
         },
     });
     return promise;

diff --git a/client/src/components/Grid/GridElements/GridDatasets.vue b/client/src/components/Grid/GridElements/GridDatasets.vue
@@ -0,0 +1,82 @@
+<script setup lang="ts">
+import axios from "axios";
+import { onMounted, type Ref, ref } from "vue";
+
+import { withPrefix } from "@/utils/redirect";
+import { rethrowSimple } from "@/utils/simple-error";
+
+interface Props {
+    historyId?: string;
+}
+const props = defineProps<Props>();
+
+interface HistoryStats {
+    nice_size: string;
+    contents_active: {
+        deleted?: number;
+        hidden?: number;
+        active?: number;
+    };
+    contents_states: {
+        error?: number;
+        ok?: number;
+        new?: number;
+        running?: number;
+        queued?: number;
+    };
+}
+const historyStats: Ref<HistoryStats | null> = ref(null);
+
+async function getCounts() {
+    if (props.historyId) {
+        try {
+            const { data } = await axios.get(
+                withPrefix(`/api/histories/${props.historyId}?keys=nice_size,contents_active,contents_states`)
+            );
+            historyStats.value = data;
+        } catch (e) {
+            rethrowSimple(e);
+        }
+    }
+}
+
+onMounted(() => {
+    getCounts();
+});
+</script>
+
+<template>
+    <span v-if="historyStats" class="grid-datasets">
+        <span v-if="historyStats.nice_size" class="mr-2">
+            {{ historyStats.nice_size }}
+        </span>
+        <span
+            v-for="(stateCount, state) of historyStats.contents_states"
+            :key="state"
+            :class="`stats state-color-${state}`"
+            :title="`${state} datasets`">
+            {{ stateCount }}
+        </span>
+        <span v-if="historyStats.contents_active.deleted" class="stats state-color-deleted" title="Deleted datasets">
+            {{ historyStats.contents_active.deleted }}
+        </span>
+        <span v-if="historyStats.contents_active.hidden" class="stats state-color-hidden" title="Hidden datasets">
+            {{ historyStats.contents_active.hidden }}
+        </span>
+    </span>
+</template>
+
+<style lang="scss" scoped>
+@import "~bootstrap/scss/bootstrap.scss";
+.grid-datasets {
+    @extend .d-flex;
+    @extend .text-nowrap;
+    .stats {
+        @extend .rounded;
+        @extend .px-1;
+        @extend .mr-1;
+        border-width: 1px;
+        border-style: solid;
+    }
+}
+</style>
diff --git a/client/src/components/Grid/GridElements/GridOperations.vue b/client/src/components/Grid/GridElements/GridOperations.vue
@@ -38,15 +38,16 @@ function hasCondition(conditionHandler: (rowData: RowData, config: GalaxyConfigu
             data-toggle="dropdown"
             aria-haspopup="true"
             aria-expanded="false"
-            class="ui-link font-weight-bold">
+            class="ui-link font-weight-bold text-nowrap">
             <FontAwesomeIcon icon="caret-down" class="fa-lg" />
             <span class="font-weight-bold">{{ title }}</span>
         </button>
         <div class="dropdown-menu" aria-labelledby="dataset-dropdown">
             <span v-for="(operation, operationIndex) in operations" :key="operationIndex">
                 <button
-                    v-if="operation && operation.condition && hasCondition(operation.condition)"
+                    v-if="operation && (!operation.condition || hasCondition(operation.condition))"
                     class="dropdown-item"
+                    :data-description="`grid operation ${operation.title.toLowerCase()}`"
                     @click.prevent="emit('execute', operation)">
                     <icon :icon="operation.icon" />
                     <span v-localize>{{ operation.title }}</span>

diff --git a/client/src/components/Grid/GridHistory.vue b/client/src/components/Grid/GridHistory.vue
diff --git a/client/src/components/Grid/GridList.test.js b/client/src/components/Grid/GridList.test.js
@@ -129,15 +129,15 @@ describe("GridList", () => {
         expect(wrapper.find("[data-description='grid cell 0-1'] > button").text()).toBe("link-1");
         expect(wrapper.find("[data-description='grid cell 1-1'] > button").text()).toBe("link-2");
         const firstHeader = wrapper.find("[data-description='grid header 0']");
-        expect(firstHeader.find("a").text()).toBe("id");
-        await firstHeader.find("[data-description='grid sort asc']").trigger("click");
+        expect(firstHeader.find("button").text()).toBe("id");
+        await firstHeader.find("[data-description='grid sort desc']").trigger("click");
         expect(testGrid.getData).toHaveBeenCalledTimes(2);
         expect(testGrid.getData.mock.calls[1]).toEqual([0, 25, "", "id", false]);
-        expect(firstHeader.find("[data-description='grid sort asc']").exists()).toBeFalsy();
-        expect(firstHeader.find("[data-description='grid sort desc']").exists()).toBeTruthy();
+        expect(firstHeader.find("[data-description='grid sort desc']").exists()).toBeFalsy();
+        expect(firstHeader.find("[data-description='grid sort asc']").exists()).toBeTruthy();
         const secondHeader = wrapper.find("[data-description='grid header 1']");
-        expect(secondHeader.find("[data-description='grid sort asc']").exists()).toBeFalsy();
         expect(secondHeader.find("[data-description='grid sort desc']").exists()).toBeFalsy();
+        expect(secondHeader.find("[data-description='grid sort asc']").exists()).toBeFalsy();
     });
 
     it("header rendering", async () => {

diff --git a/client/src/components/Grid/GridList.vue b/client/src/components/Grid/GridList.vue
@@ -3,13 +3,14 @@ import { library } from "@fortawesome/fontawesome-svg-core";
 import { faCaretDown, faCaretUp, faShieldAlt } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { useDebounceFn, useEventBus } from "@vueuse/core";
-import { BAlert, BButton, BLink, BPagination } from "bootstrap-vue";
+import { BAlert, BButton, BPagination } from "bootstrap-vue";
 import { computed, onMounted, onUnmounted, ref, watch } from "vue";
 import { useRouter } from "vue-router/composables";
 
 import { FieldHandler, GridConfig, Operation, RowData } from "./configs/types";
 
 import GridBoolean from "./GridElements/GridBoolean.vue";
+import GridDatasets from "./GridElements/GridDatasets.vue";
 import GridLink from "./GridElements/GridLink.vue";
 import GridOperations from "./GridElements/GridOperations.vue";
 import GridText from "./GridElements/GridText.vue";
@@ -150,6 +151,7 @@ function onSearch(query: string) {
 function onSort(sortKey: string) {
     if (sortBy.value !== sortKey) {
         sortBy.value = sortKey;
+        sortDesc.value = false;
     } else {
         sortDesc.value = !sortDesc.value;
     }
@@ -246,13 +248,17 @@ watch(operationMessage, () => {
                     class="text-nowrap px-2"
                     :data-description="`grid header ${fieldIndex}`">
                     <span v-if="gridConfig.sortKeys.includes(fieldEntry.key)">
-                        <BLink @click="onSort(fieldEntry.key)">
+                        <BButton
+                            variant="link"
+                            class="text-nowrap font-weight-bold"
+                            :data-description="`grid sort key ${fieldEntry.key}`"
+                            @click="onSort(fieldEntry.key)">
                             <span>{{ fieldEntry.title || fieldEntry.key }}</span>
                             <span v-if="sortBy === fieldEntry.key">
-                                <FontAwesomeIcon v-if="sortDesc" icon="caret-up" data-description="grid sort asc" />
-                                <FontAwesomeIcon v-else icon="caret-down" data-description="grid sort desc" />
+                                <FontAwesomeIcon v-if="sortDesc" icon="caret-down" data-description="grid sort desc" />
+                                <FontAwesomeIcon v-else icon="caret-up" data-description="grid sort asc" />
                             </span>
-                        </BLink>
+                        </BButton>
                     </span>
                     <span v-else>{{ fieldEntry.title || fieldEntry.key }}</span>
                 </th>
@@ -273,6 +279,7 @@ watch(operationMessage, () => {
                             :title="rowData[fieldEntry.key]"
                             @execute="onOperation($event, rowData)" />
                         <GridBoolean v-else-if="fieldEntry.type == 'boolean'" :value="rowData[fieldEntry.key]" />
+                        <GridDatasets v-else-if="fieldEntry.type == 'datasets'" :historyId="rowData[fieldEntry.key]" />
                         <GridText v-else-if="fieldEntry.type == 'text'" :text="rowData[fieldEntry.key]" />
                         <GridLink
                             v-else-if="fieldEntry.type == 'link'"
@@ -298,13 +305,7 @@ watch(operationMessage, () => {
         </table>
         <div class="flex-grow-1 h-100" />
         <div v-if="isAvailable" class="grid-footer d-flex justify-content-center pt-3">
-            <BPagination
-                v-model="currentPage"
-                :total-rows="totalRows"
-                :per-page="limit"
-                class="m-0"
-                size="sm"
-                aria-controls="grid-table" />
+            <BPagination v-model="currentPage" :total-rows="totalRows" :per-page="limit" class="m-0" size="sm" />
         </div>
     </div>
 </template>