fix stuff to make it start (1ae13009) · Commits · NDIP / Galaxy

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

deleted100644 → 0

+0 −134

Original line number	Diff line number	Diff line
		/**
		* Simple ajax queries that run against the api.
		*
		* A few history queries still hit routes that don't begin with /api. I have noted them
		* in the comments.
		*/

		import axios from "axios";
		import { prependPath } from "utils/redirect";

		/**
		* Generic json getter
		* @param {*} response
		*/

		const doResponse = (response) => {
		if (response.status != 200) {
		throw new Error(response);
		}
		return response.data;
		};

		/**
		* Legacy query string rendering. (generates q/qv syntax queries).
		* TODO: remove these converters when the api is modernized.
		*/
		function buildQueryStringFrom(filters) {
		const queryString = Object.entries(filters)
		.map(([f, v]) => `q=${f}&qv=${v}`)
		.join("&");
		return queryString;
		}

		// #endregion

		/**
		* Content Queries
		*/

		/**
		* Deletes item from history
		*
		* @param {Object} content Content object
		* @param {Boolean} purge Permanent delete
		* @param {Boolean} recursive Scorch the earth?
		*/
		export async function deleteContent(content, deleteParams = {}) {
		const defaults = { purge: false, recursive: false, stop_job: true };
		const params = Object.assign({}, defaults, deleteParams);
		const { history_id, history_content_type, id } = content;
		const url = `api/histories/${history_id}/contents/${history_content_type}s/${id}`;
		const response = await axios.delete(prependPath(url), { params });
		return doResponse(response);
		}

		/**
		* Stops job and marks it as complete.
		*/
		export async function stopJob(job_id) {
		const url = `api/jobs/${job_id}/finish`;
		const response = await axios.put(prependPath(url));
		return doResponse(response);
		}

		/**
		* Update specific fields on datasets or collections.
		* @param {Object} content content object
		* @param {Object} newFields key/value object of properties to update
		*/
		export async function updateContentFields(content, newFields = {}) {
		const { history_id, id, history_content_type: type } = content;
		const url = `api/histories/${history_id}/contents/${type}s/${id}`;
		const response = await axios.put(prependPath(url), newFields);
		return doResponse(response);
		}

		/** Get all objects that match filters in a history
		*
		* @param {string} historyId
		* @param {Object} filters
		* @param {string} type
		*
		*/
		export async function getHistoryContent(historyId, filters = {}, type = "dataset") {
		const filterQuery = buildQueryStringFrom(filters);
		const url = `api/histories/${historyId}/contents/${type}s?v=dev&${filterQuery}`;
		const response = await axios.get(prependPath(url));
		return doResponse(response);
		}

		/**
		* Performs an operation on a specific set of items or all the items
		* matching the filters.
		* If a specific set of items is provided, the filters are ignored, otherwise
		* the filters will determine which items are processed.
		*
		* @param {Object} history The history that contains the items
		* @param {String} operation The operation to perform on all items
		* @param {Object} filters The filter query parameters
		* @param {Object[]} items The set of items to process as `{ id, history_content_type }`
		* @param {Object} params Optional extra parameters passed to the operation
		*/
		export async function bulkUpdate(history, operation, filters, items = [], params = null) {
		const { id } = history;
		const filterQuery = buildQueryStringFrom(filters);
		const url = `api/histories/${id}/contents/bulk?${filterQuery}`;
		const payload = {
		operation,
		items,
		params,
		};
		const response = await axios.put(prependPath(url), payload);
		return doResponse(response);
		}

		/**
		* Collections
		*/

		export async function createDatasetCollection(history, inputs = {}) {
		const defaults = {
		collection_type: "list",
		copy_elements: true,
		name: "list",
		element_identifiers: [],
		hide_source_items: true,
		type: "dataset_collection",
		};

		const payload = Object.assign({}, defaults, inputs);
		const url = `api/histories/${history.id}/contents`;
		const response = await axios.post(prependPath(url), payload);
		return doResponse(response);
		}

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

+18 −0

Original line number	Diff line number	Diff line
		@@ -32,6 +32,24 @@ export async function deleteContent(
		return data;
		}

		/**
		* 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 } },
		// });


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


		/**
		* Update specific fields on datasets or collections.
		*/

client/src/components/JobInformation/JobInformation.vue

+0 −12

Original line number	Diff line number	Diff line
		@@ -87,18 +87,6 @@ function updateConsoleOutputs(output) {
		}
		}

		function updateConsoleOutputs(output) {
		// Keep stdout in memory and only fetch new text via JobProvider
		if (output) {
		if (output.stdout != null) {
		stdout_text.value += output.stdout;
		}
		if (output.stderr != null) {
		stderr_text.value += output.stderr;
		}
		}
		}

		function filterMetadata(jobMessages) {
		return jobMessages.map((item) => {
		return Object.entries(item).reduce((acc, [key, value]) => {

client/src/components/Upload/UploadModal.test.js

+10 −4

Original line number	Diff line number	Diff line
		@@ -6,7 +6,10 @@ import { useServerMock } from "@/api/client/__mocks__";
		import { useHistoryStore } from "@/stores/historyStore";
		import { useUserStore } from "@/stores/userStore";

		import UploadContainerORNL from "./UploadContainerORNL.vue";
		// todo: gcage
		#import UploadContainerORNL from "./UploadContainerORNL.vue";
		import UploadContainer from "./UploadContainer.vue";

		import UploadModal from "./UploadModal.vue";

		jest.mock("@/composables/config", () => ({
		@@ -84,13 +87,15 @@ describe("UploadModal.vue", () => {
		});

		it("should load with correct defaults", async () => {
		const contentWrapper = wrapper.findComponent(UploadContainerORNL);
		//const contentWrapper = wrapper.findComponent(UploadContainerORNL);
		const contentWrapper = wrapper.findComponent(UploadContainer);
		expect(contentWrapper.vm.auto.id).toBe("auto");
		expect(contentWrapper.vm.datatypesDisableAuto).toBe(false);
		});

		it("should fetch datatypes and parse them", async () => {
		const contentWrapper = wrapper.findComponent(UploadContainerORNL);
		//const contentWrapper = wrapper.findComponent(UploadContainerORNL);
		const contentWrapper = wrapper.findComponent(UploadContainer);
		expect(contentWrapper.exists()).toBe(true);
		expect(contentWrapper.vm.listExtensions.length).toBe(2);
		expect(contentWrapper.vm.listExtensions[0].id).toBe("auto");
		@@ -98,7 +103,8 @@ describe("UploadModal.vue", () => {
		});

		it("should fetch genomes and parse them", async () => {
		const contentWrapper = wrapper.findComponent(UploadContainerORNL);
		//const contentWrapper = wrapper.findComponent(UploadContainerORNL);
		const contentWrapper = wrapper.findComponent(UploadContainer);
		expect(contentWrapper.vm.listDbKeys.length).toBe(3);
		});
		});

client/src/components/Upload/UploadModal.vue

+4 −2

Original line number	Diff line number	Diff line
		@@ -9,7 +9,9 @@ import { useUserHistories } from "@/composables/userHistories";
		import { useUserStore } from "@/stores/userStore";
		import { wait } from "@/utils/utils";

		import UploadContainerORNL from "./UploadContainerORNL.vue";
		// todo: gcage
		//import UploadContainerORNL from "./UploadContainerORNL.vue";
		import UploadContainer from "./UploadContainer.vue";
		import ExternalLink from "../ExternalLink.vue";
		import HelpText from "../Help/HelpText.vue";

		@@ -127,7 +129,7 @@ defineExpose({
		</BCarousel>
		</div>
		</template>
		<UploadContainerORNL
		<UploadContainer
		v-if="currentHistoryId"
		ref="content"
		:current-user-id="currentUser?.id"