Merge branch 'release_23.0' into dev

client/package.json

@@ -187,7 +187,7 @@
     "vue-template-compiler": "^2.7.14",
     "webpack": "^5.75.0",
     "webpack-cli": "^5.0.1",
-    "webpack-dev-server": "^4.11.1",
+    "webpack-dev-server": "^4.12.0",
     "webpack-merge": "^5.8.0",
     "yaml-jest": "^1.2.0",
     "yaml-loader": "^0.8.0"

client/src/components/Common/ExportRecordDetails.vue

@@ -4,10 +4,16 @@ import { BAlert, BCard, BCardTitle } from "bootstrap-vue";
 import LoadingSpan from "components/LoadingSpan";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { library } from "@fortawesome/fontawesome-svg-core";
-import { faExclamationCircle, faExclamationTriangle, faCheckCircle, faClock } from "@fortawesome/free-solid-svg-icons";
+import {
+    faExclamationCircle,
+    faExclamationTriangle,
+    faCheckCircle,
+    faClock,
+    faLink,
+} from "@fortawesome/free-solid-svg-icons";
 import { ExportRecordModel } from "./models/exportRecordModel";
 
-library.add(faExclamationCircle, faExclamationTriangle, faCheckCircle, faClock);
+library.add(faExclamationCircle, faExclamationTriangle, faCheckCircle, faClock, faLink);
 
 const props = defineProps({
     record: {
@@ -28,7 +34,7 @@ const props = defineProps({
     },
 });
 
-const emit = defineEmits(["onReimport", "onDownload", "onActionMessageDismissed"]);
+const emit = defineEmits(["onReimport", "onDownload", "onCopyDownloadLink", "onActionMessageDismissed"]);
 
 const title = computed(() => (props.record.isReady ? `Exported` : `Export started`));
 const preparingMessage = computed(
@@ -43,6 +49,10 @@ function downloadObject() {
     emit("onDownload", props.record);
 }
 
+function copyDownloadLink() {
+    emit("onCopyDownloadLink", props.record);
+}
+
 function onMessageDismissed() {
     emit("onActionMessageDismissed");
 }
@@ -113,6 +123,14 @@ function onMessageDismissed() {
                         @click="downloadObject">
                         Download
                     </b-button>
+                    <b-button
+                        v-if="props.record.canDownload"
+                        title="Copy Download Link"
+                        size="sm"
+                        variant="link"
+                        @click.stop="copyDownloadLink">
+                        <font-awesome-icon icon="link" />
+                    </b-button>
                     <b-button
                         v-if="props.record.canReimport"
                         class="record-reimport-btn"

client/src/components/Common/ExportRecordTable.vue

@@ -9,9 +9,10 @@ import {
     faDownload,
     faFileImport,
     faSpinner,
+    faLink,
 } from "@fortawesome/free-solid-svg-icons";
 
-library.add(faExclamationCircle, faCheckCircle, faDownload, faFileImport, faSpinner);
+library.add(faExclamationCircle, faCheckCircle, faDownload, faFileImport, faSpinner, faLink);
 
 const props = defineProps({
     records: {
@@ -32,7 +33,7 @@ const fields = [
 ];
 
 const isExpanded = ref(false);
-const title = computed(() => (isExpanded.value ? `Hide export records` : `Show export records`));
+const title = computed(() => (isExpanded.value ? `Hide old export records` : `Show old export records`));
 
 async function reimportObject(record) {
     emit("onReimport", record);
@@ -41,6 +42,10 @@ async function reimportObject(record) {
 function downloadObject(record) {
     emit("onDownload", record);
 }
+
+function copyDownloadLink(record) {
+    emit("onCopyDownloadLink", record);
+}
 </script>
 
 <template>
@@ -113,6 +118,12 @@ function downloadObject(record) {
                                     @click="downloadObject(row.item)">
                                     <font-awesome-icon icon="download" />
                                 </b-button>
+                                <b-button
+                                    v-if="row.item.canDownload"
+                                    title="Copy Download Link"
+                                    @click.stop="copyDownloadLink(row.item)">
+                                    <font-awesome-icon icon="link" />
+                                </b-button>
                                 <b-button
                                     v-b-tooltip.hover.bottom
                                     :disabled="!row.item.canReimport"

client/src/components/History/Export/HistoryExport.vue

@@ -11,15 +11,25 @@ import { useTaskMonitor } from "composables/taskMonitor";
 import { useFileSources } from "composables/fileSources";
 import { useShortTermStorage, DEFAULT_EXPORT_PARAMS } from "composables/shortTermStorage";
 import { useConfirmDialog } from "composables/confirmDialog";
+import { copy as sendToClipboard } from "utils/clipboard";
+import { absPath } from "@/utils/redirect";
 
 const {
     isRunning: isExportTaskRunning,
     waitForTask,
     requestHasFailed: taskMonitorRequestFailed,
     hasFailed: taskHasFailed,
 } = useTaskMonitor();
+
 const { hasWritable: hasWritableFileSources } = useFileSources();
-const { isPreparing: isPreparingDownload, downloadHistory, downloadObjectByRequestId } = useShortTermStorage();
+
+const {
+    isPreparing: isPreparingDownload,
+    downloadHistory,
+    downloadObjectByRequestId,
+    getDownloadObjectUrl,
+} = useShortTermStorage();
+
 const { confirm } = useConfirmDialog();
 
 const props = defineProps({
@@ -104,6 +114,13 @@ function downloadFromRecord(record) {
     }
 }
 
+function copyDownloadLinkFromRecord(record) {
+    if (record.canDownload) {
+        const relativeLink = getDownloadObjectUrl(record.stsDownloadId);
+        sendToClipboard(absPath(relativeLink), "Download link copied to your clipboard");
+    }
+}
+
 function findValidUpToDateDownloadRecord() {
     return exportRecords.value
         ? exportRecords.value.find(
@@ -203,6 +220,7 @@ function updateExportParams(newParams) {
             :action-message="actionMessage"
             :action-message-variant="actionMessageVariant"
             @onDownload="downloadFromRecord"
+            @onCopyDownloadLink="copyDownloadLinkFromRecord"
             @onReimport="reimportFromRecord"
             @onActionMessageDismissed="onActionMessageDismissedFromRecord" />
         <b-alert v-else id="no-export-records-alert" variant="info" class="mt-3" show>

client/src/components/Panels/Common/ToolSearch.vue

@@ -110,7 +110,7 @@ export default {
                     this.$emit("onResults", this.favoritesResults);
                 } else {
                     // keys with sorting order
-                    const keys = { exact: 3, name: 2, description: 1, combined: 0 };
+                    const keys = { exact: 4, name: 3, hyphenated: 2, description: 1, combined: 0 };
                     this.$emit("onResults", searchToolsByKeys(this.toolsList, keys, q));
                 }
             } else {

client/src/components/Panels/utilities.js

@@ -92,6 +92,8 @@ export function searchToolsByKeys(tools, keys, query) {
             let actualValue = "";
             if (key === "combined") {
                 actualValue = tool.name.toLowerCase() + " " + tool.description.toLowerCase();
+            } else if (key === "hyphenated") {
+                actualValue = tool.name.toLowerCase().replaceAll("-", " ");
             } else {
                 actualValue = tool[key] ? tool[key].toLowerCase() : "";
             }

client/src/components/Panels/utilities.test.js

@@ -44,6 +44,28 @@ describe("test helpers in tool searching utilities", () => {
         keys = { description: 1, name: 2, combined: 0 };
         results = searchToolsByKeys(normalizeTools(toolsList), keys, q);
         expect(results).toEqual(expectedResults);
+
+        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",
+                    },
+                ],
+                model_class: "ToolSection",
+                id: "fasta/fastq",
+                name: "FASTA/FASTQ",
+            },
+        ];
+        // 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, hyphenated: 0 };
+        results = searchToolsByKeys(normalizeTools(tempToolsList), keys, q);
+        expect(results).toEqual(expectedResults);
     });
 
     it("test tool filtering helpers on toolsList given list of ids", async () => {

client/src/components/Workflow/Editor/Index.vue

@@ -656,6 +656,7 @@ export default {
             getModule(stepData, id, this.stateStore.setLoadingState).then((response) => {
                 this.stepStore.updateStep({
                     ...stepData,
+                    id: id,
                     tool_state: response.tool_state,
                     inputs: response.inputs,
                     outputs: response.outputs,

client/src/components/Workflow/Editor/Node.vue

@@ -81,7 +81,6 @@
                 :root-offset="rootOffset"
                 :scroll="scroll"
                 :scale="scale"
-                v-on="$listeners"
                 @onChange="onChange" />
             <div v-if="showRule" class="rule" />
             <node-output
@@ -97,7 +96,7 @@
                 :scroll="scroll"
                 :scale="scale"
                 :datatypes-mapper="datatypesMapper"
-                v-on="$listeners"
+                @onDragConnector="onDragConnector"
                 @stopDragging="onStopDragging"
                 @onChange="onChange" />
         </div>
@@ -117,7 +116,7 @@ import NodeOutput from "@/components/Workflow/Editor/NodeOutput.vue";
 import DraggableWrapper from "@/components/Workflow/Editor/DraggablePan.vue";
 import { computed, ref } from "vue";
 import { useNodePosition } from "@/components/Workflow/Editor/composables/useNodePosition";
-import { useWorkflowStateStore, type XYPosition } from "@/stores/workflowEditorStateStore";
+import { useWorkflowStateStore, type TerminalPosition, type XYPosition } from "@/stores/workflowEditorStateStore";
 import type { Step } from "@/stores/workflowStepStore";
 import { DatatypesMapperModel } from "@/components/Datatypes/model";
 import type { UseElementBoundingReturn, UseScrollReturn } from "@vueuse/core";
@@ -126,6 +125,7 @@ import { useWorkflowStepStore } from "@/stores/workflowStepStore";
 import { faCodeBranch } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { library } from "@fortawesome/fontawesome-svg-core";
+import type { OutputTerminals } from "./modules/terminals";
 
 Vue.use(BootstrapVue);
 
@@ -158,6 +158,7 @@ const emit = defineEmits([
     "onClone",
     "onUpdateStepPosition",
     "pan-by",
+    "onDragConnector",
     "stopDragging",
 ]);
 
@@ -240,6 +241,10 @@ const outputs = computed(() => {
     return [...stepOutputs, ...invalidOutputs.value];
 });
 
+function onDragConnector(dragPosition: TerminalPosition, terminal: OutputTerminals) {
+    emit("onDragConnector", dragPosition, terminal);
+}
+
 function onMoveTo(position: XYPosition) {
     emit("onUpdateStepPosition", props.id, {
         top: position.y + props.scroll.y.value / props.scale,

client/src/components/Workflow/Editor/NodeInput.vue

@@ -196,9 +196,6 @@ export default {
         dragLeave(event) {
             this.$root.$emit("bv::hide::tooltip", this.iconId);
         },
-        onChange() {
-            this.$emit("onChange");
-        },
         onRemove() {
             const connections = this.connectionStore.getConnectionsForTerminal(this.id);
             connections.forEach((connection) => this.terminal.disconnect(connection));