Merge pull request #16534 from mvdbeek/dev

Merge 23.1 into dev
galaxyproject · Aug 9, 2023 · e28069d · e28069d
2 parents 085132d + 130d2b0
commit e28069d
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diff --git a/client/src/components/Common/DelayedInput.vue b/client/src/components/Common/DelayedInput.vue
@@ -13,7 +13,7 @@
         <b-input-group-append>
             <b-button
                 v-if="enableAdvanced"
-                v-b-tooltip.hover
+                v-b-tooltip.hover.noninteractive
                 aria-haspopup="true"
                 size="sm"
                 :pressed="showAdvanced"
@@ -25,7 +25,7 @@
                 <icon v-else fixed-width icon="angle-double-down" />
             </b-button>
             <b-button
-                v-b-tooltip.hover
+                v-b-tooltip.hover.noninteractive
                 aria-haspopup="true"
                 class="search-clear"
                 size="sm"

diff --git a/client/src/components/History/Content/model/StatesInfo.vue b/client/src/components/History/Content/model/StatesInfo.vue
@@ -46,15 +46,15 @@ function onFilter(value: string) {
         <p>Here are all available item states in Galaxy:</p>
         <p><i>(Note that the colors for each state correspond to content item state colors in the history)</i></p>
         <dl v-for="(state, key, index) in states" :key="index">
-            <b-alert :variant="state.status || 'success'" show>
+            <div :class="['alert', 'content-item', 'alert-' + state.status]" :data-state="key">
                 <dt>
                     <a class="text-decoration-none" href="javascript:void(0)" @click="onFilter(key)"
                         ><code>{{ key }}</code></a
                     >
                     <icon v-if="state.icon" :icon="state.icon" />
                 </dt>
                 <dd>{{ helpText[key] || state.text }}</dd>
-            </b-alert>
+            </div>
         </dl>
     </b-modal>
 </template>
diff --git a/client/src/components/Panels/Buttons/FavoritesButton.vue b/client/src/components/Panels/Buttons/FavoritesButton.vue
@@ -1,6 +1,6 @@
 <template>
     <b-button
-        v-b-tooltip.hover
+        v-b-tooltip.hover.noninteractive
         class="panel-header-button-toolbox"
         size="sm"
         variant="link"

diff --git a/client/src/components/Panels/Buttons/PanelViewButton.vue b/client/src/components/Panels/Buttons/PanelViewButton.vue
@@ -1,6 +1,6 @@
 <template>
     <b-dropdown
-        v-b-tooltip.hover
+        v-b-tooltip.hover.noninteractive
         right
         title="Show panel options"
         variant="link"

diff --git a/client/src/components/Panels/Common/ToolPanelLabel.vue b/client/src/components/Panels/Common/ToolPanelLabel.vue
@@ -1,5 +1,5 @@
 <template>
-    <div v-b-tooltip.topright.hover class="tool-panel-label" tabindex="0" :title="description">
+    <div v-b-tooltip.topright.hover.noninteractive class="tool-panel-label" tabindex="0" :title="description">
         {{ definition.text }}
         <ToolPanelLinks :links="definition.links" />
     </div>

diff --git a/client/src/components/Panels/Common/ToolSection.vue b/client/src/components/Panels/Common/ToolSection.vue
@@ -1,7 +1,7 @@
 <template>
     <div v-if="isSection && hasElements" class="tool-panel-section">
         <div
-            v-b-tooltip.topright.hover
+            v-b-tooltip.topright.hover.noninteractive
             :class="['toolSectionTitle', `tool-menu-section-${sectionName}`]"
             :title="title">
             <a class="title-link" href="javascript:void(0)" @click="toggleMenu()">

diff --git a/client/src/components/Panels/ToolBoxWorkflow.vue b/client/src/components/Panels/ToolBoxWorkflow.vue
@@ -22,9 +22,19 @@
                 placeholder="search tools"
                 :toolbox="workflowTools"
                 :query="query"
+                :query-pending="queryPending"
                 @onQuery="onQuery"
                 @onResults="onResults" />
-            <div v-if="queryTooShort" class="pb-2">
+            <div v-if="closestTerm" class="pb-2">
+                <b-badge class="alert-danger w-100">
+                    Did you mean:
+                    <i>
+                        <a href="javascript:void(0)" @click="onQuery(closestTerm)">{{ closestTerm }}</a>
+                    </i>
+                    ?
+                </b-badge>
+            </div>
+            <div v-else-if="queryTooShort" class="pb-2">
                 <b-badge class="alert-danger w-100">Search string too short!</b-badge>
             </div>
             <div v-else-if="noResults" class="pb-2">
@@ -40,21 +50,21 @@
                     :category="category"
                     tool-key="name"
                     :section-name="category.name"
-                    :query-filter="query"
+                    :query-filter="queryFilter"
                     :disable-filter="true"
                     @onClick="onInsertModule" />
                 <ToolSection
                     v-if="hasDataManagerSection"
                     :key="dataManagerSection.id"
                     :category="dataManagerSection"
-                    :query-filter="query"
+                    :query-filter="queryFilter"
                     :disable-filter="true"
                     @onClick="onInsertTool" />
                 <ToolSection
                     v-for="section in sections"
                     :key="section.id"
                     :category="section"
-                    :query-filter="query"
+                    :query-filter="queryFilter"
                     @onClick="onInsertTool" />
                 <ToolSection
                     v-if="hasWorkflowSection"
@@ -64,7 +74,7 @@
                     :sort-items="false"
                     operation-icon="fa fa-files-o"
                     operation-title="Insert individual steps."
-                    :query-filter="query"
+                    :query-filter="queryFilter"
                     :disable-filter="true"
                     @onClick="onInsertWorkflow"
                     @onOperation="onInsertWorkflowSteps" />
@@ -114,7 +124,10 @@ export default {
     },
     data() {
         return {
+            closestTerm: null,
             query: null,
+            queryPending: false,
+            queryFilter: null,
             results: null,
         };
     },
@@ -167,9 +180,13 @@ export default {
     methods: {
         onQuery(query) {
             this.query = query;
+            this.queryPending = true;
         },
-        onResults(results) {
+        onResults(results, closestTerm = null) {
             this.results = results;
+            this.closestTerm = closestTerm;
+            this.queryFilter = !this.noResults ? this.query : null;
+            this.queryPending = false;
         },
         onInsertTool(tool, evt) {
             evt.preventDefault();

diff --git a/client/src/components/Upload/UploadButton.vue b/client/src/components/Upload/UploadButton.vue
@@ -1,7 +1,7 @@
 <template>
     <b-button
         id="activity-upload"
-        v-b-tooltip.hover.bottom
+        v-b-tooltip.hover.noninteractive.bottom
         :aria-label="title | localize"
         :title="title | localize"
         class="upload-button"

diff --git a/client/src/components/Workflow/WorkflowDropdown.vue b/client/src/components/Workflow/WorkflowDropdown.vue
@@ -10,21 +10,21 @@
             @dragend="onDragEnd">
             <Icon icon="caret-down" class="fa-lg" />
             <span class="workflow-dropdown-name">{{ workflow.name }}</span>
+            <span
+                v-if="sourceType.includes('trs')"
+                v-b-tooltip.hover
+                aria-haspopup="true"
+                :title="getWorkflowTooltip(sourceType, workflow)">
+                <Icon fixed-width icon="check" class="mr-1 workflow-trs-icon" />
+            </span>
+            <span
+                v-if="sourceType == 'url'"
+                v-b-tooltip.hover
+                aria-haspopup="true"
+                :title="getWorkflowTooltip(sourceType, workflow)">
+                <Icon fixed-width icon="link" class="mr-1 workflow-external-link" />
+            </span>
         </b-link>
-        <span
-            v-if="sourceType.includes('trs')"
-            v-b-tooltip.hover
-            aria-haspopup="true"
-            :title="getWorkflowTooltip(sourceType, workflow)">
-            <Icon fixed-width icon="check" class="mr-1 workflow-trs-icon" />
-        </span>
-        <span
-            v-if="sourceType == 'url'"
-            v-b-tooltip.hover
-            aria-haspopup="true"
-            :title="getWorkflowTooltip(sourceType, workflow)">
-            <Icon fixed-width icon="link" class="mr-1 workflow-external-link" />
-        </span>
         <p v-if="workflow.description" class="workflow-dropdown-description">
             <TextSummary :description="workflow.description" :show-details.sync="showDetails" />
         </p>

diff --git a/client/src/onload/index.js b/client/src/onload/index.js
@@ -8,6 +8,7 @@ import "scss/base.scss";
 import "./publicPath";
 // Default Font
 import "@fontsource/atkinson-hyperlegible";
+import "@fontsource/atkinson-hyperlegible/700.css";
 
 // Client-side configuration variables (based on environment)
 import { library } from "@fortawesome/fontawesome-svg-core";

diff --git a/client/src/schema/schema.ts b/client/src/schema/schema.ts
@@ -4282,8 +4282,7 @@ export interface components {
              * @description The current state of this dataset.
              */
             state: components["schemas"]["DatasetState"];
-            /** Tags */
-            tags: string;
+            tags: components["schemas"]["TagCollection"];
             /**
              * Type
              * @enum {string}
@@ -8494,14 +8493,11 @@ export interface components {
         TaggableItemClass:
             | "History"
             | "HistoryDatasetAssociation"
+            | "HistoryDatasetCollectionAssociation"
             | "LibraryDatasetDatasetAssociation"
             | "Page"
-            | "WorkflowStep"
             | "StoredWorkflow"
-            | "Visualization"
-            | "HistoryDatasetCollection"
-            | "LibraryDatasetCollection"
-            | "Tool";
+            | "Visualization";
         /** ToolDataDetails */
         ToolDataDetails: {
             /**

diff --git 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
@@ -8,46 +8,51 @@
  * 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, "/");
+  return `${root}/${path}`.replace(slashCleanup, "/");
 }
 
 function MyApp(props) {
-    return (
-          <H5GroveProvider
-            url={props.url}
-            filepath={props.name}
-            axiosConfig={{ params: { file: props.name } }}
-          >
-            <App explorerOpen={props.explorer} />
-          </H5GroveProvider>
-      );
+  return (
+    <H5GroveProvider
+      url={props.url}
+      filepath={props.name}
+      axiosConfig={{ params: { file: props.name } }}
+    >
+      <App explorerOpen={props.explorer} />
+    </H5GroveProvider>
+  );
 }
 
 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 + prefixedDownloadUrl(options.root, "/api/datasets/" + dataset.id + "/content");
-    reactRender(
-      <MyApp
-        url={url}
-        name={dataset.name}
-        filepath={dataset.file_name}
-        explorer={explorer}
-      />,
-      document.getElementById(options.target)
-    )
-    options.chart.state('ok', 'Chart drawn.');
-    options.process.resolve();
+  const dataset = options.dataset;
+  const settings = options.chart.settings;
+  const explorer = settings.get("explorer");
+  const url =
+    window.location.origin +
+    prefixedDownloadUrl(
+      options.root,
+      "/api/datasets/" + dataset.id + "/content"
+    );
+  const root = createRoot(document.getElementById(options.target));
+  root.render(
+    <MyApp
+      url={url}
+      name={dataset.name}
+      filepath={dataset.file_name}
+      explorer={explorer}
+    />
+  );
+  options.chart.state("ok", "Chart drawn.");
+  options.process.resolve();
 };
 
 export default MyApp;
diff --git a/lib/galaxy/app_unittest_utils/galaxy_mock.py b/lib/galaxy/app_unittest_utils/galaxy_mock.py
@@ -293,9 +293,13 @@ def __init__(self, app=None, user=None, history=None, **kwargs):
         self.security = self.app.security
         self.history = history
 
-        self.request: Any = Bunch(headers={}, body=None)
+        self.request: Any = Bunch(headers={}, body=None, host="request.host")
         self.response: Any = Bunch(headers={}, set_content_type=lambda i: None)
 
+    @property
+    def tag_handler(self):
+        return self.app.tag_handler
+
     def check_csrf_token(self, payload):
         pass
 

diff --git a/lib/galaxy/datatypes/sequence.py b/lib/galaxy/datatypes/sequence.py
@@ -175,7 +175,7 @@ def do_slow_split(cls, input_datasets, subdir_generator_function, split_params):
     def do_fast_split(cls, input_datasets, toc_file_datasets, subdir_generator_function, split_params):
         data = json.load(open(toc_file_datasets[0].file_name))
         sections = data["sections"]
-        total_sequences = int(0)
+        total_sequences = 0
         for section in sections:
             total_sequences += int(section["sequences"])
         sequences_per_file = cls.get_sequences_per_file(total_sequences, split_params)
@@ -247,7 +247,7 @@ def get_split_commands_with_toc(
         sections = toc_file["sections"]
         result = []
 
-        current_sequence = int(0)
+        current_sequence = 0
         i = 0
         # skip to the section that contains my starting sequence
         while i < len(sections) and start_sequence >= current_sequence + int(sections[i]["sequences"]):

diff --git a/lib/galaxy/dependencies/pinned-lint-requirements.txt b/lib/galaxy/dependencies/pinned-lint-requirements.txt
@@ -5,6 +5,6 @@ importlib-metadata==4.2.0
 mccabe==0.7.0
 pycodestyle==2.9.1
 pyflakes==2.5.0
-ruff==0.0.280
+ruff==0.0.283
 typing_extensions==4.7.1
 zipp==3.15.0