Merge branch 'fix-galaxy-update-errors' into '132-update-galaxy-version' (a39cb509) · Commits · NDIP / Galaxy

client/src/api/schema/schema.ts

+62 −3

Original line number	Diff line number	Diff line
		@@ -2934,6 +2934,23 @@ export interface paths {
		patch?: never;
		trace?: never;
		};
		"/api/jobs/{job_id}/finish": {
		parameters: {
		query?: never;
		header?: never;
		path?: never;
		cookie?: never;
		};
		get?: never;
		/** Finished a job regardless of execution status (ie early job finish) */
		put: operations["finish_job_api_jobs__job_id__finish_put"];
		post?: never;
		delete?: never;
		options?: never;
		head?: never;
		patch?: never;
		trace?: never;
		};
		"/api/jobs/{job_id}/inputs": {
		parameters: {
		query?: never;
		@@ -8123,9 +8140,8 @@ export interface components {
		\| "setting_metadata"
		\| "failed_metadata"
		\| "deferred"
		/** ndip_todo: is this a right place? */
		\| "stopped"
		\| "discarded";
		\| "discarded"
		\| "stopped";
		/** DatasetStorageDetails */
		DatasetStorageDetails: {
		/**
		@@ -28239,6 +28255,49 @@ export interface operations {
		};
		};
		};
		finish_job_api_jobs__job_id__finish_put: {
		parameters: {
		query?: never;
		header?: {
		/** @description The user ID that will be used to effectively make this API call. Only admins and designated users can make API calls on behalf of other users. */
		"run-as"?: string \| null;
		};
		path: {
		job_id: string;
		};
		cookie?: never;
		};
		requestBody?: never;
		responses: {
		/** @description Successful Response */
		200: {
		headers: {
		[name: string]: unknown;
		};
		content: {
		"application/json": boolean;
		};
		};
		/** @description Request Error */
		"4XX": {
		headers: {
		[name: string]: unknown;
		};
		content: {
		"application/json": components["schemas"]["MessageExceptionModel"];
		};
		};
		/** @description Server Error */
		"5XX": {
		headers: {
		[name: string]: unknown;
		};
		content: {
		"application/json": components["schemas"]["MessageExceptionModel"];
		};
		};
		};
		};
		get_inputs_api_jobs__job_id__inputs_get: {
		parameters: {
		query?: never;

client/src/components/History/Content/model/states.ts

+1 −1

Original line number	Diff line number	Diff line
		@@ -107,8 +107,8 @@ export const STATES: StateMap = {
		},
		/** the job has been manually stopped */
		stopped: {
		text: "This job was stopped manually.",
		status: "stopped",
		text: "This job was stopped manually.",
		icon: "stop-circle",
		},
		/** the dataset is not yet loaded in the UI. This state is only visual and transitional, it does not exist in the database. */

client/src/components/History/model/queries.ts

+7 −9

Original line number	Diff line number	Diff line
		@@ -36,17 +36,15 @@ export async function deleteContent(
		* Stops job and marks it as complete.
		*/
		export async function stopJob(jobId: string) {
		// todo: gcage
		// const { data, error } = await GalaxyApi().PUT("api/jobs/${job_id}/finish", {
		// params: { path: { job_id: jobId, theme } },
		// });
		const { data, error } = await GalaxyApi().PUT("/api/jobs/{job_id}/finish", {
		params: { path: { job_id: jobId } },
		});


		// if (error) {
		// rethrowSimple(error);
		// }
		// return data;
		return {}
		if (error) {
		rethrowSimple(error);
		}
		return data;
		}

client/src/components/JobInformation/JobInformation.vue

+0 −8

Original line number	Diff line number	Diff line
		@@ -77,14 +77,6 @@ function updateConsoleOutputs(output) {
		stderr_text.value += output.stderr;
		}
		}
		if (jobIsTerminal.value) {
		if (newJob.tool_stdout) {
		stdout_text.value = newJob.tool_stdout;
		}
		if (newJob.tool_stderr) {
		stderr_text.value = newJob.tool_stderr;
		}
		}
		}

		function filterMetadata(jobMessages) {

client/src/components/Upload/DefaultBoxORNL.vue

+47 −35

Original line number	Diff line number	Diff line
		@@ -10,7 +10,6 @@ import { createDatasetCollection } from "components/History/model/queries";

		import { UploadQueue } from "@/utils/upload-queue.js";

		import { collectionBuilder } from "./builders.js";
		import { defaultModel } from "./model.js";
		import { COLLECTION_TYPES, DEFAULT_FILE_NAME, hasBrowserSupport } from "./utils";

		@@ -60,7 +59,7 @@ const props = defineProps({
		},
		lazyLoad: {
		type: Number,
		default: 50,
		default: 150,
		},
		listDbKeys: {
		type: Array,
		@@ -74,10 +73,18 @@ const props = defineProps({
		type: String,
		default: "",
		required: false,
		}
		},
		disableFooter: {
		type: Boolean,
		default: false,
		},
		emitUploaded: {
		type: Boolean,
		default: false,
		},
		});

		const emit = defineEmits(["dismiss", "progress", "updateCollectionName"]);
		const emit = defineEmits(["dismiss", "progress", "uploaded", "updateCollectionName"]);

		const collectionType = ref("list");
		const counterAnnounce = ref(0);
		@@ -164,6 +171,7 @@ function eventAnnounce(index, file) {

		/** Populates collection builder with uploaded files */
		function eventBuild() {
		try {
		const Galaxy = getGalaxyInstance();
		const models = {};
		uploadValues.value.forEach((model) => {
		@@ -192,6 +200,9 @@ function eventBuild() {
		options: {}
		};
		createDatasetCollection({ id: Galaxy.currHistoryPanel.model.id }, queryBody);
		} catch (err) {
		console.error(err)
		}
		counterRunning.value = 0;
		eventReset();
		emit("dismiss");
		@@ -435,8 +446,8 @@ defineExpose({
		:file-name="uploadItem.fileName"
		:file-size="uploadItem.fileSize"
		:info="uploadItem.info"
		:list-extensions="isCollection ? null : listExtensions"
		:list-db-keys="isCollection ? null : listDbKeys"
		:list-extensions="!isCollection && listExtensions.length > 1 ? listExtensions : null"
		:list-db-keys="!isCollection && listDbKeys.length > 1 ? listDbKeys : null"
		:percentage="uploadItem.percentage"
		:space-to-tab="uploadItem.spaceToTab"
		:status="uploadItem.status"
		@@ -453,7 +464,7 @@ defineExpose({
		</div>
		<input ref="uploadFile" type="file" :multiple="multiple" @change="addFiles($event.target.files)" />
		</UploadBox>
		<div class="upload-footer text-center">
		<div v-if="!disableFooter" class="upload-footer text-center">
		<span v-if="isCollection" class="upload-footer-title">Collection:</span>
		<UploadSelect
		v-if="isCollection"
		@@ -482,6 +493,7 @@ defineExpose({
		placeholder="Select Reference"
		@input="updateDbKey" />
		</div>
		<slot name="footer" />
		<div class="upload-buttons d-flex justify-content-end">
		<BButton id="btn-local" :disabled="!enableSources" @click="singleFileUpload()">
		<FontAwesomeIcon icon="fa-laptop" />