Merge remote-tracking branch 'upstream/release_25.0' into merge_25.0_into_dev_sept (f823afcc) · Commits · NDIP / Galaxy

.github/workflows/integration.yaml

+1 −1

Original line number	Diff line number	Diff line
		@@ -64,7 +64,7 @@ jobs:
		uses: medyagh/setup-minikube@latest
		with:
		driver: none
		kubernetes-version: '1.23.0'
		kubernetes-version: '1.28.0'
		- name: Check pods
		run: kubectl get pods -A
		- uses: actions/checkout@v4

client/src/components/History/Content/GenericItem.vue

+15 −2

Original line number	Diff line number	Diff line
		<template>
		<component :is="providerComponent" :id="itemId" v-slot="{ result: item, loading }" auto-refresh>
		<component
		:is="providerComponent"
		:id="itemId"
		:key="view"
		v-slot="{ result: item, loading }"
		:view="view"
		auto-refresh>
		<LoadingSpan v-if="loading" message="Loading dataset" />
		<div v-else>
		<ContentItem
		@@ -11,7 +17,7 @@
		:expand-dataset="expandDataset"
		:is-dataset="item.history_content_type == 'dataset' \|\| item.element_type == 'hda'"
		@update:expand-dataset="expandDataset = $event"
		@view-collection="viewCollection = !viewCollection"
		@view-collection="onViewCollection"
		@delete="onDelete"
		@toggleHighlights="onHighlight(item)"
		@undelete="onUndelete(item)"
		@@ -60,6 +66,7 @@ export default {
		return {
		viewCollection: false,
		expandDataset: false,
		view: this.itemSrc === "hdca" ? "collection" : "element",
		};
		},
		computed: {
		@@ -124,6 +131,12 @@ export default {
		this.onError(error, "Failed to highlight related items");
		}
		},
		onViewCollection(collection) {
		if (this.view === "collection" && collection.model_class === "HistoryDatasetCollectionAssociation") {
		this.view = "element";
		}
		this.viewCollection = !this.viewCollection;
		},
		},
		};
		</script>

client/src/components/Tool/ToolForm.vue

+23 −4

Original line number	Diff line number	Diff line
		@@ -87,7 +87,7 @@
		id="execute"
		class="text-nowrap"
		title="Run Tool"
		:disabled="!canMutateHistory"
		:disabled="runButtonDisabled"
		size="small"
		:wait="showExecuting"
		:tooltip="tooltip"
		@@ -97,7 +97,7 @@
		<ButtonSpinner
		title="Run Tool"
		class="mt-3 mb-3"
		:disabled="!canMutateHistory"
		:disabled="runButtonDisabled"
		:wait="showExecuting"
		:tooltip="tooltip"
		@onClick="onExecute(config, currentHistoryId)" />
		@@ -205,6 +205,7 @@ export default {
		],
		immutableHistoryMessage:
		"This history is immutable and you cannot run tools in it. Please switch to a different history.",
		formConfigInitialized: false,
		};
		},
		computed: {
		@@ -227,6 +228,12 @@ export default {
		if (!this.canMutateHistory) {
		return this.immutableHistoryMessage;
		}
		if (this.hasConfigOrValErrors) {
		return "Please resolve highlighted issues before running the tool.";
		}
		if (this.showExecuting) {
		return "Tool is being executed...";
		}
		return `Run tool: ${this.formConfig.name} (${this.formConfig.version})`;
		},
		errorContentPretty() {
		@@ -252,8 +259,15 @@ export default {
		canMutateHistory() {
		return this.currentHistory && canMutateHistory(this.currentHistory);
		},
		runButtonTitle() {
		return "Run Tool";
		runButtonDisabled() {
		return this.disabled \|\| !this.canMutateHistory \|\| this.hasConfigOrValErrors;
		},
		/** If there are any backend returned `formConfig.errors` or internal/client checked validation errors. */
		hasConfigOrValErrors() {
		return (
		(this.formConfig.errors && Object.values(this.formConfig.errors).length > 0) \|\|
		this.validationInternal?.length
		);
		},
		},
		watch: {
		@@ -286,7 +300,12 @@ export default {
		this.formData = newData;
		if (refreshRequest) {
		this.onUpdate();
		} else if (this.formConfigInitialized && this.hasConfigOrValErrors) {
		// After the first manual change to a form input, for every change, if there isn't a request to refresh,
		// we reset the errors since we haven't received a tool form update via the backend.
		this.formConfig.errors = null;
		}
		this.formConfigInitialized = true;
		},
		onUpdate() {
		this.disabled = true;

client/src/components/providers/DatasetCollectionProvider.js

+7 −2

Original line number	Diff line number	Diff line
		import { SingleQueryProvider } from "components/providers/SingleQueryProvider";

		import { fetchCollectionDetails } from "@/api/datasetCollections";
		import { fetchCollectionDetails, fetchCollectionSummary } from "@/api/datasetCollections";

		// There isn't really a good way to know when to stop polling for HDCA updates,
		// but we know the populated_state should at least be ok.
		export default SingleQueryProvider(
		(params) => fetchCollectionDetails({ hdca_id: params.id }),
		(params) => {
		if (params.view && params.view === "collection") {
		return fetchCollectionSummary({ hdca_id: params.id });
		}
		return fetchCollectionDetails({ hdca_id: params.id });
		},
		(result) => result.populated_state === "ok",
		);

client/src/composables/useInvocationGraph.ts

+2 −2

Original line number	Diff line number	Diff line
		@@ -10,7 +10,7 @@ import {
		} from "@fortawesome/free-solid-svg-icons";
		import { computed, type Ref, ref, set } from "vue";

		import { fetchCollectionDetails } from "@/api/datasetCollections";
		import { fetchCollectionSummary } from "@/api/datasetCollections";
		import { fetchDatasetDetails } from "@/api/datasets";
		import type { InvocationStep, StepJobSummary, WorkflowInvocationElementView } from "@/api/invocations";
		import type { StoredWorkflowDetailed } from "@/api/workflows";
		@@ -323,7 +323,7 @@ export function useInvocationGraph(
		set(graphStep, "state", getContentItemState(hda));
		set(graphStep, "nodeText", `${hda.hid}: <b>${hda.name}</b>`);
		} else {
		const hdca = await fetchCollectionDetails({ hdca_id: inputItem.id });
		const hdca = await fetchCollectionSummary({ hdca_id: inputItem.id });
		// TODO: Same type mismatch as above
		set(graphStep, "state", getContentItemState(hdca));
		set(graphStep, "nodeText", `${hdca.hid}: <b>${hdca.name}</b>`);