Merge remote-tracking branch 'origin/dev' into masthead_update

.github/workflows/build_client.yaml

@@ -32,5 +32,7 @@ jobs:
           path: 'galaxy root/static'
       - name: Build client
         if: steps.cache.outputs.cache-hit != 'true'
+        env:
+          GALAXY_PLUGIN_BUILD_FAIL_ON_ERROR: 1
         run: make client
         working-directory: 'galaxy root'

.gitignore

@@ -167,14 +167,14 @@ packages/*/*.egg-info
 config/plugins/**/static/dist
 config/plugins/**/static/script.js
 config/plugins/**/static/main.css
+config/plugins/**/static/script.css
 config/plugins/**/static/plugin_build_hash.txt
 config/plugins/**/static/*.map
 
 # Viz-specific build artifacts to ignore (until these are removed from codebase)
 config/plugins/visualizations/annotate_image/static/jquery.contextMenu.css
 config/plugins/visualizations/nvd3/nvd3_bar/static/nvd3.js
-config/plugins/visualizations/h5web/static/script.css
-config/plugins/visualizations/tiffviewer/static/script.css
+config/plugins/visualizations/scatterplot/static/scatterplot.js
 
 # CWL conformance tests
 lib/galaxy_test/api/cwl/test_cwl_conformance_v1_?.py

Makefile

@@ -13,10 +13,12 @@ OPEN_RESOURCE=bash -c 'open $$0 || xdg-open $$0'
 SLIDESHOW_TO_PDF?=bash -c 'docker run --rm -v `pwd`:/cwd astefanutti/decktape /cwd/$$0 /cwd/`dirname $$0`/`basename -s .html $$0`.pdf'
 YARN := $(shell $(IN_VENV) command -v yarn 2> /dev/null)
 YARN_INSTALL_OPTS=--network-timeout 300000 --check-files
+# Default to not fail on error, set to 1 to fail client builds on a plugin error.
+GALAXY_PLUGIN_BUILD_FAIL_ON_ERROR?=0
 # Respect predefined NODE_OPTIONS, otherwise set maximum heap size low for
 # compatibility with smaller machines.
 NODE_OPTIONS ?= --max-old-space-size=3072
-NODE_ENV = env NODE_OPTIONS=$(NODE_OPTIONS)
+NODE_ENV = env NODE_OPTIONS=$(NODE_OPTIONS) GALAXY_PLUGIN_BUILD_FAIL_ON_ERROR=$(GALAXY_PLUGIN_BUILD_FAIL_ON_ERROR)	
 CWL_TARGETS := test/functional/tools/cwl_tools/v1.0/conformance_tests.yaml \
 	test/functional/tools/cwl_tools/v1.1/conformance_tests.yaml \
 	test/functional/tools/cwl_tools/v1.2/conformance_tests.yaml \

client/gulpfile.js

@@ -27,16 +27,17 @@ const STATIC_PLUGIN_BUILD_IDS = [
     "msa",
     "mvpapp",
     "ngl",
+    "nora",
     "nvd3/nvd3_bar",
     "openlayers",
     "openseadragon",
     "PCA_3Dplot",
     "phylocanvas",
     "pv",
-    "nora",
-    "venn",
+    "scatterplot",
     "tiffviewer",
     "ts_visjs",
+    "venn",
 ];
 const DIST_PLUGIN_BUILD_IDS = ["new_user"];
 const PLUGIN_BUILD_IDS = Array.prototype.concat(DIST_PLUGIN_BUILD_IDS, STATIC_PLUGIN_BUILD_IDS);
@@ -56,6 +57,11 @@ const PATHS = {
     },
 };
 
+const failOnError =
+    process.env.GALAXY_PLUGIN_BUILD_FAIL_ON_ERROR && process.env.GALAXY_PLUGIN_BUILD_FAIL_ON_ERROR !== "0"
+        ? true
+        : false;
+
 PATHS.pluginBaseDir =
     (process.env.GALAXY_PLUGIN_PATH && process.env.GALAXY_PLUGIN_PATH !== "None"
         ? process.env.GALAXY_PLUGIN_PATH
@@ -186,6 +192,13 @@ function buildPlugins(callback, forceRebuild) {
                 console.error(
                     `Error building ${pluginName}, not saving build state.  Please report this issue to the Galaxy Team.`
                 );
+                if (failOnError) {
+                    // Fail on error.
+                    console.error(
+                        "Failing build due to GALAXY_PLUGIN_BUILD_FAIL_ON_ERROR being set, see error(s) above."
+                    );
+                    process.exit(1);
+                }
             }
         }
     });

client/src/api/index.ts

@@ -211,6 +211,10 @@ export function isHistorySummaryExtended(history: AnyHistory): history is Histor
     return "contents_active" in history && "user_id" in history;
 }
 
+export function isHistoryItem(item: object): item is HistoryItemSummary {
+    return item && "history_content_type" in item;
+}
+
 type QuotaUsageResponse = components["schemas"]["UserQuotaUsage"];
 
 /** Represents a registered user.**/

client/src/api/schema/schema.ts

@@ -315,7 +315,7 @@ export interface paths {
         post: operations["file_sources__test_new_instance_configuration"];
     };
     "/api/file_source_instances/{user_file_source_id}": {
-        /** Get a list of persisted file source instances defined by the requesting user. */
+        /** Get a persisted user file source instance. */
         get: operations["file_sources__instances_get"];
         /** Update or upgrade user file source instance. */
         put: operations["file_sources__instances_update"];
@@ -1266,7 +1266,7 @@ export interface paths {
         post: operations["object_stores__test_new_instance_configuration"];
     };
     "/api/object_store_instances/{user_object_store_id}": {
-        /** Get a persisted object store instances owned by the requesting user. */
+        /** Get a persisted user object store instance. */
         get: operations["object_stores__instances_get"];
         /** Update or upgrade user object store instance. */
         put: operations["object_stores__instances_update"];
@@ -5512,6 +5512,15 @@ export interface components {
              */
             url: string;
         };
+        /** GroupUpdatePayload */
+        GroupUpdatePayload: {
+            /** name of the group */
+            name?: string | null;
+            /** role IDs */
+            role_ids?: string[] | null;
+            /** user IDs */
+            user_ids?: string[] | null;
+        };
         /** GroupUserListResponse */
         GroupUserListResponse: components["schemas"]["GroupUserResponse"][];
         /** GroupUserResponse */
@@ -6146,6 +6155,8 @@ export interface components {
              * @enum {string}
              */
             model_class: "HistoryDatasetAssociation";
+            /** Purged */
+            purged: boolean;
             /**
              * State
              * @description The current state of this dataset.
@@ -8394,6 +8405,11 @@ export interface components {
              * @default false
              */
             use_cached_job?: boolean | null;
+            /**
+             * Version
+             * @description The version of the workflow to invoke.
+             */
+            version?: number | null;
         };
         /**
          * ItemTagsCreatePayload
@@ -12651,8 +12667,6 @@ export interface components {
             device?: string | null;
             /** Hidden */
             hidden: boolean;
-            /** Id */
-            id: number | string;
             /** Name */
             name?: string | null;
             /** Object Store Id */
@@ -12730,8 +12744,6 @@ export interface components {
             description: string | null;
             /** Hidden */
             hidden: boolean;
-            /** Id */
-            id: string | number;
             /** Name */
             name: string;
             /** Purged */
@@ -14966,13 +14978,13 @@ export interface operations {
         };
     };
     file_sources__instances_get: {
-        /** Get a list of persisted file source instances defined by the requesting user. */
+        /** Get a persisted user file source instance. */
         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 | null;
             };
-            /** @description The index for a persisted UserFileSourceStore object. */
+            /** @description The UUID index for a persisted UserFileSourceStore object. */
             path: {
                 user_file_source_id: string;
             };
@@ -14999,7 +15011,7 @@ export interface operations {
             header?: {
                 "run-as"?: string | null;
             };
-            /** @description The index for a persisted UserFileSourceStore object. */
+            /** @description The UUID index for a persisted UserFileSourceStore object. */
             path: {
                 user_file_source_id: string;
             };
@@ -15034,7 +15046,7 @@ export interface operations {
             header?: {
                 "run-as"?: string | null;
             };
-            /** @description The index for a persisted UserFileSourceStore object. */
+            /** @description The UUID index for a persisted UserFileSourceStore object. */
             path: {
                 user_file_source_id: string;
             };
@@ -15743,7 +15755,7 @@ export interface operations {
         };
         requestBody: {
             content: {
-                "application/json": components["schemas"]["GroupCreatePayload"];
+                "application/json": components["schemas"]["GroupUpdatePayload"];
             };
         };
         responses: {
@@ -20890,13 +20902,13 @@ export interface operations {
         };
     };
     object_stores__instances_get: {
-        /** Get a persisted object store instances owned by the requesting user. */
+        /** Get a persisted user object store instance. */
         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 | null;
             };
-            /** @description The identifier used to index a persisted UserObjectStore object. */
+            /** @description The UUID used to identify a persisted UserObjectStore object. */
             path: {
                 user_object_store_id: string;
             };
@@ -20923,7 +20935,7 @@ export interface operations {
             header?: {
                 "run-as"?: string | null;
             };
-            /** @description The identifier used to index a persisted UserObjectStore object. */
+            /** @description The UUID used to identify a persisted UserObjectStore object. */
             path: {
                 user_object_store_id: string;
             };
@@ -20958,7 +20970,7 @@ export interface operations {
             header?: {
                 "run-as"?: string | null;
             };
-            /** @description The identifier used to index a persisted UserObjectStore object. */
+            /** @description The UUID used to identify a persisted UserObjectStore object. */
             path: {
                 user_object_store_id: string;
             };

client/src/components/Common/FilterMenu.vue

@@ -4,7 +4,7 @@ import { faAngleDoubleUp, faQuestion, faSearch } from "@fortawesome/free-solid-s
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { BButton, BModal, BPopover } from "bootstrap-vue";
 import { kebabCase } from "lodash";
-import { computed, ref } from "vue";
+import { computed, ref, set } from "vue";
 
 import type Filtering from "@/utils/filtering";
 import { type Alias, type ErrorType, getOperatorForAlias, type ValidFilter } from "@/utils/filtering";
@@ -91,6 +91,8 @@ const toggleMenuButton = computed(() => {
 // Boolean for showing the help modal for the whole filter menu (if provided)
 const showHelp = ref(false);
 
+const isDisabled = ref<Record<string, boolean>>({});
+
 const formattedSearchError = computed<ErrorType | null>(() => {
     if (props.searchError) {
         const { column, col, operation, op, value, val, err_msg, ValueError } = props.searchError;
@@ -144,6 +146,8 @@ function getValidFilter(filter: string): ValidFilter<any> {
 function onOption(filter: string, value: any) {
     filters.value[filter] = value;
 
+    setDisabled(filter, value);
+
     // for the compact view, we want to immediately search
     if (props.view === "compact") {
         onSearch();
@@ -177,6 +181,21 @@ function onToggle() {
     emit("update:show-advanced", !props.showAdvanced);
 }
 
+function setDisabled(filter: string, newVal: any) {
+    const disablesFilters = validFilters.value[filter]?.disablesFilters;
+    const type = validFilters.value[filter]?.type;
+    if (disablesFilters && type !== Boolean) {
+        for (const [disabledFilter, disablingValues] of Object.entries(disablesFilters)) {
+            if (newVal && (disablingValues === null || disablingValues.includes(newVal))) {
+                set(isDisabled.value, disabledFilter, true);
+                filters.value[disabledFilter] = undefined;
+            } else {
+                set(isDisabled.value, disabledFilter, false);
+            }
+        }
+    }
+}
+
 function updateFilterText(newFilterText: string) {
     emit("update:filter-text", newFilterText);
 }
@@ -243,6 +262,7 @@ function updateFilterText(newFilterText: string) {
                             :filters="filters"
                             :error="formattedSearchError || undefined"
                             :identifier="identifier"
+                            :disabled="isDisabled[filter] || false"
                             @change="onOption"
                             @on-enter="onSearch"
                             @on-esc="onToggle" />
@@ -269,6 +289,7 @@ function updateFilterText(newFilterText: string) {
                             :filter="getValidFilter(filter)"
                             :filters="filters"
                             :identifier="identifier"
+                            :disabled="isDisabled[filter] || false"
                             @change="onOption" />
                         <FilterMenuInput
                             v-else-if="validFilters[filter]?.type !== Boolean"
@@ -277,6 +298,7 @@ function updateFilterText(newFilterText: string) {
                             :filters="filters"
                             :error="errorForField(filter) || undefined"
                             :identifier="identifier"
+                            :disabled="isDisabled[filter] || false"
                             @change="onOption"
                             @on-enter="onSearch"
                             @on-esc="onToggle" />

client/src/components/Common/FilterMenuDropdown.vue

@@ -31,6 +31,7 @@ interface Props {
         [k: string]: FilterValue;
     };
     identifier: string;
+    disabled?: boolean;
 }
 
 const props = defineProps<Props>();
@@ -76,7 +77,9 @@ const helpToggle = ref(false);
 const modalTitle = `${capitalize(props.filter.placeholder)} Help`;
 function onHelp(_: string, value: string) {
     helpToggle.value = false;
-    localValue.value = value;
+    if (!props.disabled) {
+        localValue.value = value;
+    }
 }
 
 // Quota Source refs and operations
@@ -140,6 +143,7 @@ function setValue(val: string | QuotaUsage | undefined) {
                 menu-class="w-100"
                 size="sm"
                 boundary="window"
+                :disabled="props.disabled"
                 :toggle-class="props.error ? 'text-danger' : ''">
                 <BDropdownItem href="#" @click="setValue(undefined)"><i>(any)</i></BDropdownItem>
 

client/src/components/Common/FilterMenuInput.vue

@@ -28,6 +28,7 @@ interface Props {
     filters: {
         [k: string]: FilterType;
     };
+    disabled?: boolean;
 }
 
 const props = defineProps<Props>();
@@ -47,14 +48,18 @@ const modalTitle = `${capitalize(props.filter.placeholder)} Help`;
 
 function onHelp(_: string, value: string) {
     helpToggle.value = false;
-    localValue.value = value;
+
+    if (!props.disabled) {
+        localValue.value = value;
+    }
 }
 
 watch(
     () => localValue.value,
     (newFilter) => {
         emit("change", props.name, newFilter);
-    }
+    },
+    { immediate: true }
 );
 
 watch(
@@ -79,6 +84,7 @@ watch(
                 size="sm"
                 :state="props.error ? false : null"
                 :placeholder="`any ${props.filter.placeholder}`"
+                :disabled="props.disabled"
                 :list="props.filter.datalist ? `${identifier}-${props.name}-selectList` : null"
                 @keyup.enter="emit('on-enter')"
                 @keyup.esc="emit('on-esc')" />
@@ -99,6 +105,7 @@ watch(
                     v-model="localValue"
                     reset-button
                     button-only
+                    :disabled="props.disabled"
                     size="sm" />
             </BInputGroupAppend>
         </BInputGroup>