Merge branch 'dev' into 'main' (bd6d9cf7) · Commits · NDIP / Galaxy

.gitlab-ci.yml

+12 −12

Original line number	Diff line number	Diff line
		@@ -6,16 +6,16 @@ stages:

		variables:
		GIT_STRATEGY: clone
		CONTAINER_GALAXY_URL: "${CI_REGISTRY_IMAGE}"
		CONTAINER_GALAXY_URL: "${NDIP_DOCKER_REPOSITORY}/${CI_PROJECT_PATH}"
		CONTAINER_GALAXY_BASE_URL: "${CONTAINER_GALAXY_URL}/base"
		CONTAINER_GALAXY_COMMIT_URL: "${CONTAINER_GALAXY_URL}/commit"
		GALAXY_VERSION_PYTHON: 24.1.dev3+ornl
		GALAXY_VERSION_DOCKER: 24.1.dev3.ornl
		GALAXY_VERSION_PYTHON: 24.1.dev4+ornl
		GALAXY_VERSION_DOCKER: 24.1.dev4.ornl

		# This import is for the func_rse_docker_* functions
		before_script:
		- curl https://code.ornl.gov/rse-deployment/rse-sharables/raw/master/rse-bash-modules.sh -O
		- docker login -u $CI_REGISTRY_USER -p $CI_REGISTRY_PASSWORD $CI_REGISTRY
		- docker login -u $NDIP_DOCKER_USER -p $NDIP_DOCKER_PASSWORD $NDIP_DOCKER_REPOSITORY
		- source rse-bash-modules.sh
		- func_rse_docker_cleanup

		@@ -33,8 +33,8 @@ service-build:
		docker build
		-f dockerfiles/Dockerfile
		-t galaxy .
		- docker tag galaxy $CONTAINER_GALAXY_COMMIT_URL:$CI_COMMIT_SHORT_SHA
		- docker push $CONTAINER_GALAXY_COMMIT_URL:$CI_COMMIT_SHORT_SHA
		- docker tag galaxy $CONTAINER_GALAXY_COMMIT_URL:build-$CI_COMMIT_SHORT_SHA
		- docker push $CONTAINER_GALAXY_COMMIT_URL:build-$CI_COMMIT_SHORT_SHA
		tags:
		- rse-multi-builder
		except:
		@@ -46,7 +46,7 @@ client-tests:
		- >
		docker run
		--entrypoint=""
		$CONTAINER_GALAXY_COMMIT_URL:$CI_COMMIT_SHORT_SHA
		$CONTAINER_GALAXY_COMMIT_URL:build-$CI_COMMIT_SHORT_SHA
		bash -c ". .venv/bin/activate && cd client && yarn run jest"
		tags:
		- rse-multi-builder
		@@ -63,7 +63,7 @@ client-tests:
		# docker run
		# --entrypoint=""
		# --network=host
		# $CONTAINER_GALAXY_COMMIT_URL:$CI_COMMIT_SHORT_SHA
		# $CONTAINER_GALAXY_COMMIT_URL:build-$CI_COMMIT_SHORT_SHA
		# bash -c "GALAXY_TEST_DBURI=postgresql://postgres:psql@127.0.0.1:5432/galaxy_test ./run_tests.sh -api"
		# - docker rm -f postgres
		# tags:
		@@ -78,7 +78,7 @@ unit-tests:
		- >
		docker run
		--entrypoint=""
		$CONTAINER_GALAXY_COMMIT_URL:$CI_COMMIT_SHORT_SHA
		$CONTAINER_GALAXY_COMMIT_URL:build-$CI_COMMIT_SHORT_SHA
		bash -c "GALAXY_SKIP_EXTERNAL_DEPENDENCY_MANAGEMENT=1 ./run_tests.sh -unit"
		tags:
		- rse-multi-builder
		@@ -108,7 +108,7 @@ package:
		script:
		- >
		docker run
		$CONTAINER_GALAXY_COMMIT_URL:$CI_COMMIT_SHORT_SHA
		$CONTAINER_GALAXY_COMMIT_URL:build-$CI_COMMIT_SHORT_SHA
		bash -c ". .venv/bin/activate . && pip install build twine && cd packages/objectstore &&
		sed -i -e '/version =/ s/= .*/= '$GALAXY_VERSION_PYTHON'/' setup.cfg &&
		make dist &&
		@@ -123,8 +123,8 @@ package:
		tag-docker:
		stage: deploy
		script:
		- docker pull $CONTAINER_GALAXY_COMMIT_URL:$CI_COMMIT_SHORT_SHA
		- docker tag $CONTAINER_GALAXY_COMMIT_URL:$CI_COMMIT_SHORT_SHA $CONTAINER_GALAXY_URL:$GALAXY_VERSION_DOCKER
		- docker pull $CONTAINER_GALAXY_COMMIT_URL:build-$CI_COMMIT_SHORT_SHA
		- docker tag $CONTAINER_GALAXY_COMMIT_URL:build-$CI_COMMIT_SHORT_SHA $CONTAINER_GALAXY_URL:$GALAXY_VERSION_DOCKER
		- docker push $CONTAINER_GALAXY_URL:$GALAXY_VERSION_DOCKER
		when: manual
		except:

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

+14 −2

Original line number	Diff line number	Diff line
		@@ -87,6 +87,18 @@ describe("FormData", () => {
		expect(wrapper.find(SELECTED_VALUE).text()).toEqual("4: hdaName4");
		});

		it("regular data no batch input", async () => {
		const wrapper = createTarget({
		value: null,
		options: defaultOptions,
		disableBatchInput: true,
		});
		const options = wrapper.find(".btn-group").findAll("button");
		expect(options.length).toBe(2);
		expect(options.at(0).classes()).toContain("active");
		expect(options.at(0).attributes("title")).toBe("Single dataset");
		});

		it("optional dataset", async () => {
		const wrapper = createTarget({
		value: null,
		@@ -114,7 +126,7 @@ describe("FormData", () => {
		const options = wrapper.find(".btn-group").findAll("button");
		expect(options.length).toBe(3);
		expect(options.at(0).classes()).toContain("active");
		expect(options.at(0).attributes("title")).toBe("Multiple datasets");
		expect(options.at(0).attributes("title")).toBe("Dataset(s)");
		expect(wrapper.emitted().input[0][0]).toEqual({
		batch: false,
		product: false,
		@@ -451,7 +463,7 @@ describe("FormData", () => {
		const selectedValues = wrapper.findAll(SELECTED_VALUE);
		expect(selectedValues.length).toBe(1);
		expect(selectedValues.at(0).text()).toBe("5: hdcaName5");
		await wrapper.find("[title='Multiple datasets'").trigger("click");
		await wrapper.find("[title='Dataset(s)'").trigger("click");
		expect(options.at(0).classes()).toContain("active");
		expect(wrapper.emitted().input[2][0]).toEqual(null);
		});

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

+9 −1

Original line number	Diff line number	Diff line
		@@ -39,6 +39,7 @@ const props = withDefaults(
		collectionTypes?: Array<string>;
		flavor?: string;
		tag?: string;
		disableBatchInput?: boolean;
		}>(),
		{
		loading: false,
		@@ -50,12 +51,14 @@ const props = withDefaults(
		collectionTypes: undefined,
		flavor: undefined,
		tag: undefined,
		disableBatchInput: false,
		}
		);

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


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

		// Determines wether values should be processed as linked or unlinked
		@@ -222,6 +225,11 @@ const variant = computed(() => {
		const flavorKey = props.flavor ? `${props.flavor}_` : "";
		const multipleKey = props.multiple ? `_multiple` : "";
		const variantKey = `${flavorKey}${props.type}${multipleKey}`;
		if (props.disableBatchInput && VARIANTS[variantKey]) {
		return VARIANTS[variantKey]!.filter((v) => {
		return v.batch === BATCH.DISABLED;
		});
		}
		return VARIANTS[variantKey];
		});

		@@ -521,7 +529,7 @@ const noOptionsWarningMessage = computed(() => {
		@dragover.prevent
		@drop.prevent="onDrop">
		<div class="d-flex flex-column">
		<BButtonGroup v-if="variant && variant.length > 1" buttons class="align-self-start">
		<BButtonGroup v-if="variant && variant.length > 0" buttons class="align-self-start">
		<BButton
		v-for="(v, index) in variant"
		:key="index"

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

+1 −1

Original line number	Diff line number	Diff line
		@@ -44,7 +44,7 @@ export const VARIANTS: Record<string, Array<VariantInterface>> = {
		{
		src: SOURCE.DATASET,
		icon: "fa-copy",
		tooltip: "Multiple datasets",
		tooltip: "Dataset(s)",
		library: true,
		multiple: true,
		batch: BATCH.DISABLED,

client/src/components/Form/FormElement.vue

+4 −0

Original line number	Diff line number	Diff line
		@@ -7,6 +7,7 @@ import { sanitize } from "dompurify";
		import type { ComputedRef } from "vue";
		import { computed, ref, useAttrs } from "vue";

		import { getGalaxyInstance } from "@/app";
		import { linkify } from "@/utils/utils";

		import type { FormParameterAttributes, FormParameterTypes, FormParameterValue } from "./parameterTypes";
		@@ -88,6 +89,8 @@ const collapsed = ref(false);
		const collapsible = computed(() => !props.disabled && collapsibleValue.value !== undefined);
		const connectable = computed(() => collapsible.value && Boolean(attrs.value["connectable"]));

		const disableBatchInput = computed(() => getGalaxyInstance().config.disable_batch_input);

		// Determines whether to expand or collapse the input
		{
		const valueJson = JSON.stringify(props.value);
		@@ -298,6 +301,7 @@ function onAlert(value: string \| undefined) {
		:tag="attrs.tag"
		:type="props.type"
		:collection-types="attrs.collection_types"
		:disable-batch-input="disableBatchInput"
		@alert="onAlert" />
		<FormDrilldown
		v-else-if="props.type === 'drill_down'"