Merge pull request #19377 from jmchilton/fixed_length_collections (c212434d) · Commits · NDIP / Galaxy

client/src/api/datasetCollections.ts

+10 −7

Original line number	Diff line number	Diff line
		import {
		type CollectionElementIdentifiers,
		type CollectionEntry,
		type components,
		type CreateNewCollectionPayload,
		type DCESummary,
		GalaxyApi,
		type HDCADetailed,
		@@ -87,10 +88,7 @@ export async function fetchElementsFromCollection(params: {
		});
		}

		type CollectionElementIdentifiers = components["schemas"]["CollectionElementIdentifier"][];
		type CreateNewCollectionPayload = components["schemas"]["CreateNewCollectionPayload"];

		type NewCollectionOptions = {
		export type NewCollectionOptions = {
		name: string;
		element_identifiers: CollectionElementIdentifiers;
		collection_type: string;
		@@ -107,13 +105,18 @@ export function createCollectionPayload(options: NewCollectionOptions): CreateNe
		element_identifiers: options.element_identifiers,
		collection_type: options.collection_type,
		instance_type: "history",
		fields: "auto",
		copy_elements: options.copy_elements \|\| true,
		hide_source_items: hideSourceItems,
		};
		} as CreateNewCollectionPayload;
		}

		export async function createHistoryDatasetCollectionInstance(options: NewCollectionOptions) {
		export async function createHistoryDatasetCollectionInstanceSimple(options: NewCollectionOptions) {
		const payload = createCollectionPayload(options);
		return createHistoryDatasetCollectionInstanceFull(payload);
		}

		export async function createHistoryDatasetCollectionInstanceFull(payload: CreateNewCollectionPayload) {
		const { data, error } = await GalaxyApi().POST("/api/dataset_collections", {
		body: payload,
		});

client/src/api/datasets.ts

+1 −0

Original line number	Diff line number	Diff line
		@@ -88,6 +88,7 @@ export async function copyDataset(
		type,
		copy_elements: true,
		// TODO: Investigate. These should be optional, but the API requires explicit null values?
		fields: null,
		hide_source_items: null,
		instance_type: null,
		},

client/src/api/index.ts

+6 −0

Original line number	Diff line number	Diff line
		@@ -317,6 +317,9 @@ export type DatasetTransform = components["schemas"]["DatasetSourceTransform"];
		*/
		export type MessageException = components["schemas"]["MessageExceptionModel"];

		export type FieldDict = components["schemas"]["FieldDict"];
		export type FieldType = FieldDict["type"];

		export type StoreExportPayload = components["schemas"]["StoreExportPayload"];
		export type ModelStoreFormat = components["schemas"]["ModelStoreFormat"];
		export type ObjectExportTaskResponse = components["schemas"]["ObjectExportTaskResponse"];
		@@ -324,3 +327,6 @@ export type ExportObjectRequestMetadata = components["schemas"]["ExportObjectReq
		export type ExportObjectResultMetadata = components["schemas"]["ExportObjectResultMetadata"];

		export type AsyncTaskResultSummary = components["schemas"]["AsyncTaskResultSummary"];

		export type CollectionElementIdentifiers = components["schemas"]["CollectionElementIdentifier"][];
		export type CreateNewCollectionPayload = components["schemas"]["CreateNewCollectionPayload"];

client/src/api/schema/schema.ts

+23 −0

Original line number	Diff line number	Diff line
		@@ -7067,6 +7067,12 @@ export interface components {
		* @description List of elements that should be in the new collection.
		*/
		element_identifiers?: components["schemas"]["CollectionElementIdentifier"][] \| null;
		/**
		* Fields
		* @description List of fields to create for this collection. Set to 'auto' to guess fields from identifiers.
		* @default []
		*/
		fields: string \| components["schemas"]["FieldDict"][] \| null;
		/**
		* Folder Id
		* @description The ID of the library folder that will contain the collection. Required if `instance_type=library`.
		@@ -7265,6 +7271,12 @@ export interface components {
		* @description List of elements that should be in the new collection.
		*/
		element_identifiers?: components["schemas"]["CollectionElementIdentifier"][] \| null;
		/**
		* Fields
		* @description List of fields to create for this collection. Set to 'auto' to guess fields from identifiers.
		* @default []
		*/
		fields: string \| components["schemas"]["FieldDict"][] \| null;
		/**
		* Folder Id
		* @description The ID of the library folder that will contain the collection. Required if `instance_type=library`.
		@@ -9249,6 +9261,17 @@ export interface components {
		/** Hash Value */
		hash_value: string;
		};
		/** FieldDict */
		FieldDict: {
		/** Format */
		format?: string \| null;
		/** Name */
		name: string;
		/** Type */
		type:
		\| ("File" \| "null" \| "boolean" \| "int" \| "float" \| "string")
		\| ("File" \| "null" \| "boolean" \| "int" \| "float" \| "string")[];
		};
		/** FileDataElement */
		FileDataElement: {
		/** Md5 */

client/src/components/Collections/BuildFileSetWizard.vue

0 → 100644

+220 −0

Original line number	Diff line number	Diff line
		<script setup lang="ts">
		import { BCardGroup } from "bootstrap-vue";
		import { computed, ref } from "vue";

		import { getGalaxyInstance } from "@/app";
		import { attemptCreate, type CollectionCreatorComponent } from "@/components/Collections/common/useCollectionCreator";
		import { rawToTable } from "@/components/Collections/tables";
		import { useWizard } from "@/components/Common/Wizard/useWizard";
		import { useToolRouting } from "@/composables/route";

		import { type RemoteFile, type RulesCreatingWhat, type RulesSourceFrom } from "./wizard/types";
		import { useFileSetSources } from "./wizard/useFileSetSources";

		import CreatingWhat from "./wizard/CreatingWhat.vue";
		import PasteData from "./wizard/PasteData.vue";
		import SelectDataset from "./wizard/SelectDataset.vue";
		import SelectFolder from "./wizard/SelectFolder.vue";
		import SourceFromCollection from "./wizard/SourceFromCollection.vue";
		import SourceFromDatasetAsTable from "./wizard/SourceFromDatasetAsTable.vue";
		import SourceFromPastedData from "./wizard/SourceFromPastedData.vue";
		import SourceFromRemoteFiles from "./wizard/SourceFromRemoteFiles.vue";
		import GenericWizard from "@/components/Common/Wizard/GenericWizard.vue";
		import RuleCollectionBuilder from "@/components/RuleCollectionBuilder.vue";

		const isBusy = ref<boolean>(false);
		const { pasteData, tabularDatasetContents, uris, setRemoteFilesFolder, onFtp, setDatasetContents, setPasteTable } =
		useFileSetSources(isBusy);

		interface Props {
		fileSourcesConfigured: boolean;
		ftpUploadSite?: string;
		mode: "uploadModal" \| "standalone";
		}

		const props = defineProps<Props>();

		const ruleState = ref(false);
		const creatingWhat = ref<RulesCreatingWhat>("datasets");
		const creatingWhatTitle = computed(() => {
		return creatingWhat.value == "datasets" ? "Datasets" : "Collections";
		});
		const sourceInstructions = computed(() => {
		return `${creatingWhatTitle.value} can be created from a set or files, URIs, or existing datasets.`;
		});
		const collectionCreator = ref<CollectionCreatorComponent \| undefined>();

		const sourceFrom = ref<RulesSourceFrom>("remote_files");

		const { routeToTool } = useToolRouting();

		const wizard = useWizard({
		"select-what": {
		label: "What is being created?",
		instructions: computed(() => {
		return `Are you creating datasets or collections?`;
		}),
		isValid: () => true,
		isSkippable: () => false,
		},
		"select-source": {
		label: "Select source",
		instructions: sourceInstructions,
		isValid: () => true,
		isSkippable: () => false,
		},
		"select-remote-files-folder": {
		label: "Select folder",
		instructions: "Select folder of files to import.",
		isValid: () => sourceFrom.value === "remote_files" && Boolean(uris.value.length > 0),
		isSkippable: () => sourceFrom.value !== "remote_files",
		},
		"paste-data": {
		label: "Paste data",
		instructions: "Paste data (or drop file) containing URIs and optional extra metadata.",
		isValid: () => sourceFrom.value === "pasted_table" && pasteData.value.length > 0,
		isSkippable: () => sourceFrom.value !== "pasted_table",
		},
		"select-dataset": {
		label: "Select dataset",
		instructions: "Select tabular dataset to load URIs and metadata from.",
		isValid: () => sourceFrom.value === "dataset_as_table" && tabularDatasetContents.value.length > 0,
		isSkippable: () => sourceFrom.value !== "dataset_as_table",
		},
		"rule-builder": {
		label: "Specify Rules",
		instructions: "Use this form to describe rules for importing",
		isValid: () => ruleState.value,
		isSkippable: () => props.mode == "uploadModal",
		width: "100%",
		},
		});

		const importButtonLabel = computed(() => {
		if (sourceFrom.value == "collection") {
		return "Transform";
		} else {
		return "Import";
		}
		});

		const emit = defineEmits(["dismiss", "created"]);
		type SelectionType = "raw" \| "remote_files";
		type ElementsType = RemoteFile[] \| string[][];

		// it would be nice to have a real type from the rule builder but
		// it is older code. This is really outlining what this component can
		// produce and not what the rule builder can consume which is a wide
		// superset of this.
		interface Entry {
		dataType: RulesCreatingWhat;
		ftpUploadSite?: string;
		elements?: ElementsType \| undefined;
		content?: string;
		selectionType: SelectionType;
		}

		const ruleBuilderModalEntryProps = computed(() => {
		let elements: ElementsType \| undefined = undefined;
		let selectionType: SelectionType = "raw";
		if (sourceFrom.value == "remote_files") {
		elements = uris.value;
		selectionType = "remote_files";
		} else if (sourceFrom.value == "pasted_table") {
		elements = pasteData.value;
		} else if (sourceFrom.value == "dataset_as_table") {
		elements = tabularDatasetContents.value;
		}
		const entry: Entry = {
		dataType: creatingWhat.value,
		ftpUploadSite: props.ftpUploadSite,
		selectionType: selectionType,
		elements: elements,
		};
		return entry;
		});

		const ruleBuilderElements = computed(() => {
		const builderProps = ruleBuilderModalEntryProps.value;
		let elements;
		if (builderProps.elements) {
		elements = builderProps.elements;
		} else {
		elements = rawToTable(builderProps.content \|\| "");
		}
		return elements;
		});

		function launchRuleBuilder() {
		const Galaxy = getGalaxyInstance();
		const entry = ruleBuilderModalEntryProps.value;
		Galaxy.currHistoryPanel.buildCollectionFromRules(entry, null, true);
		}

		function submit() {
		if (sourceFrom.value == "collection") {
		routeToTool("__APPLY_RULES__");
		} else if (props.mode == "standalone") {
		attemptCreate(collectionCreator);
		} else {
		launchRuleBuilder();
		}
		emit("dismiss");
		}

		function setCreatingWhat(what: RulesCreatingWhat) {
		creatingWhat.value = what;
		}

		function setSourceForm(newValue: RulesSourceFrom) {
		sourceFrom.value = newValue;
		}

		function onRuleState(newRuleState: boolean) {
		ruleState.value = newRuleState;
		}

		function onRuleCreate() {
		// axios response data for job currently sent, not really used but wanted to document what is available.
		emit("created");
		}
		</script>

		<template>
		<GenericWizard :use="wizard" :submit-button-label="importButtonLabel" @submit="submit">
		<div v-if="wizard.isCurrent('select-what')">
		<CreatingWhat :creating-what="creatingWhat" @onChange="setCreatingWhat" />
		</div>
		<div v-else-if="wizard.isCurrent('select-source')">
		<BCardGroup deck>
		<SourceFromRemoteFiles :selected="sourceFrom === 'remote_files'" @select="setSourceForm" />
		<SourceFromPastedData :selected="sourceFrom === 'pasted_table'" @select="setSourceForm" />
		<SourceFromDatasetAsTable :selected="sourceFrom === 'dataset_as_table'" @select="setSourceForm" />
		<SourceFromCollection
		v-if="creatingWhat == 'collections'"
		:selected="sourceFrom === 'collection'"
		@select="setSourceForm" />
		</BCardGroup>
		</div>
		<div v-else-if="wizard.isCurrent('paste-data')">
		<PasteData @onChange="setPasteTable" />
		</div>
		<div v-else-if="wizard.isCurrent('select-remote-files-folder')">
		<SelectFolder :ftp-upload-site="ftpUploadSite" @onChange="setRemoteFilesFolder" @onFtp="onFtp" />
		</div>
		<div v-else-if="wizard.isCurrent('select-dataset')">
		<SelectDataset @onChange="setDatasetContents" />
		</div>
		<div v-else-if="wizard.isCurrent('rule-builder')" style="width: 100%">
		<RuleCollectionBuilder
		ref="collectionCreator"
		grid-implementation="ag"
		:import-type="creatingWhat"
		:elements-type="ruleBuilderModalEntryProps.selectionType"
		:initial-elements="ruleBuilderElements"
		mode="wizard"
		@onCreate="onRuleCreate"
		@validInput="onRuleState" />
		</div>
		</GenericWizard>
		</template>

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