Merge branch 'upstream' into 111-update-galaxy-24-1 (3e99851c) · Commits · NDIP / Galaxy

.github/workflows/lint_openapi_schema.yml

+5 −0

Original line number	Diff line number	Diff line
		@@ -28,6 +28,11 @@ jobs:
		- uses: actions/setup-python@v5
		with:
		python-version: ${{ matrix.python-version }}
		- uses: actions/setup-node@v4
		with:
		node-version: '18.12.1'
		cache: 'yarn'
		cache-dependency-path: 'galaxy root/client/yarn.lock'
		- name: Get full Python version
		id: full-python-version
		shell: bash

client/src/api/schema/schema.ts

+12 −1

Original line number	Diff line number	Diff line
		@@ -5648,6 +5648,15 @@ 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 */
		@@ -6282,6 +6291,8 @@ export interface components {
		* @enum {string}
		*/
		model_class: "HistoryDatasetAssociation";
		/** Purged */
		purged: boolean;
		/**
		* State
		* @description The current state of this dataset.
		@@ -15969,7 +15980,7 @@ export interface operations {
		};
		requestBody: {
		content: {
		"application/json": components["schemas"]["GroupCreatePayload"];
		"application/json": components["schemas"]["GroupUpdatePayload"];
		};
		};
		responses: {

client/src/components/Form/Elements/FormData/FormData.test.js

+4 −0

Original line number	Diff line number	Diff line
		@@ -3,6 +3,8 @@ import { mount } from "@vue/test-utils";
		import { PiniaVuePlugin } from "pinia";
		import { dispatchEvent, getLocalVue } from "tests/jest/helpers";

		import { testDatatypesMapper } from "@/components/Datatypes/test_fixtures";
		import { useDatatypesMapperStore } from "@/stores/datatypesMapperStore";
		import { useEventStore } from "@/stores/eventStore";

		import MountTarget from "./FormData.vue";
		@@ -15,6 +17,8 @@ let eventStore;
		function createTarget(propsData) {
		const pinia = createTestingPinia({ stubActions: false });
		eventStore = useEventStore();
		const datatypesStore = useDatatypesMapperStore();
		datatypesStore.datatypesMapper = testDatatypesMapper;
		return mount(MountTarget, {
		localVue,
		propsData,

client/src/components/Form/Elements/FormData/FormData.vue

+62 −12

Original line number	Diff line number	Diff line
		@@ -7,6 +7,7 @@ import { BAlert, BButton, BButtonGroup, BCollapse, BFormCheckbox, BTooltip } fro
		import { computed, onMounted, type Ref, ref, watch } from "vue";

		import { getGalaxyInstance } from "@/app";
		import { useDatatypesMapper } from "@/composables/datatypesMapper";
		import { useUid } from "@/composables/utils/uid";
		import { type EventData, useEventStore } from "@/stores/eventStore";
		import { orList } from "@/utils/strings";
		@@ -35,6 +36,7 @@ const props = withDefaults(
		};
		extensions?: Array<string>;
		type?: string;
		collectionTypes?: Array<string>;
		flavor?: string;
		tag?: string;
		}>(),
		@@ -45,14 +47,16 @@ const props = withDefaults(
		value: undefined,
		extensions: () => [],
		type: "data",
		collectionTypes: undefined,
		flavor: undefined,
		tag: undefined,
		}
		);

		const eventStore = useEventStore();
		const { datatypesMapper } = useDatatypesMapper();

		const $emit = defineEmits(["input"]);
		const $emit = defineEmits(["input", "alert"]);

		// Determines wether values should be processed as linked or unlinked
		const currentLinked = ref(true);
		@@ -302,6 +306,10 @@ function getSourceType(val: DataOption) {
		function handleIncoming(incoming: Record<string, unknown>, partial = true) {
		if (incoming) {
		const values = Array.isArray(incoming) ? incoming : [incoming];
		const extensions = values.map((v) => v.extension \|\| v.elements_datatypes).filter((v) => (v ? true : false));
		if (!canAcceptDatatype(extensions)) {
		return false;
		}
		if (values.length > 0) {
		const incomingValues: Array<DataOption> = [];
		values.forEach((v) => {
		@@ -311,14 +319,28 @@ function handleIncoming(incoming: Record<string, unknown>, partial = true) {
		const newName = v.name ? v.name : newId;
		const newSrc =
		v.src \|\| (v.history_content_type === "dataset_collection" ? SOURCE.COLLECTION : SOURCE.DATASET);
		const newValue = {
		const newValue: DataOption = {
		id: newId,
		src: newSrc,
		batch: false,
		map_over_type: undefined,
		hid: newHid,
		name: newName,
		keep: true,
		tags: [],
		};
		if (v.collection_type && props.collectionTypes?.length > 0) {
		if (!props.collectionTypes.includes(v.collection_type)) {
		const mapOverType = props.collectionTypes.find((collectionType) =>
		v.collection_type.endsWith(collectionType)
		);
		if (!mapOverType) {
		return false;
		}
		newValue["batch"] = true;
		newValue["map_over_type"] = mapOverType;
		}
		}
		// Verify that new value has corresponding option
		const keepKey = `${newId}_${newSrc}`;
		const existingOptions = props.options && props.options[newSrc];
		@@ -349,6 +371,7 @@ function handleIncoming(incoming: Record<string, unknown>, partial = true) {
		}
		}
		}
		return true;
		}

		/**
		@@ -372,10 +395,36 @@ function onBrowse() {
		}
		}

		function canAcceptDatatype(itemDatatypes: string \| Array<string>) {
		if (!(props.extensions?.length > 0)) {
		return true;
		}
		let datatypes: Array<string>;
		if (!Array.isArray(itemDatatypes)) {
		datatypes = [itemDatatypes];
		} else {
		datatypes = itemDatatypes;
		}
		const incompatibleItem = datatypes.find(
		(extension) => !datatypesMapper.value?.isSubTypeOfAny(extension, props.extensions)
		);
		if (incompatibleItem) {
		return false;
		}
		return true;
		}

		// Drag/Drop event handlers
		function onDragEnter(evt: MouseEvent) {
		const eventData = eventStore.getDragData();
		if (eventData) {
		const extensions = (eventData.extension as string) \|\| (eventData.elements_datatypes as Array<string>);
		if (!canAcceptDatatype(extensions)) {
		currentHighlighting.value = "warning";
		$emit("alert", `${extensions} is not an acceptable format for this parameter.`);
		} else {
		currentHighlighting.value = "success";
		}
		dragTarget.value = evt.target;
		dragData.value = eventData;
		}
		@@ -384,23 +433,24 @@ function onDragEnter(evt: MouseEvent) {
		function onDragLeave(evt: MouseEvent) {
		if (dragTarget.value === evt.target) {
		currentHighlighting.value = null;
		}
		}

		function onDragOver() {
		if (dragData.value !== null) {
		currentHighlighting.value = "warning";
		$emit("alert", undefined);
		}
		}

		function onDrop() {
		if (dragData.value) {
		let accept = false;
		if (eventStore.multipleDragData) {
		handleIncoming(Object.values(dragData.value) as any, false);
		accept = handleIncoming(Object.values(dragData.value) as any, false);
		} else {
		handleIncoming(dragData.value);
		accept = handleIncoming(dragData.value);
		}
		if (accept) {
		currentHighlighting.value = "success";
		} else {
		currentHighlighting.value = "warning";
		}
		$emit("alert", undefined);
		dragData.value = null;
		clearHighlighting();
		}
		@@ -468,7 +518,7 @@ const noOptionsWarningMessage = computed(() => {
		:class="currentHighlighting && `ui-dragover-${currentHighlighting}`"
		@dragenter.prevent="onDragEnter"
		@dragleave.prevent="onDragLeave"
		@dragover.prevent="onDragOver"
		@dragover.prevent
		@drop.prevent="onDrop">
		<div class="d-flex flex-column">
		<BButtonGroup v-if="variant && variant.length > 1" buttons class="align-self-start">

client/src/components/Form/Elements/FormData/types.ts

+1 −0

Original line number	Diff line number	Diff line
		@@ -3,6 +3,7 @@ export type DataOption = {
		hid: number;
		is_dataset?: boolean;
		keep: boolean;
		batch: boolean;
		map_over_type?: string;
		name: string;
		src: string;