diff --git a/client/src/api/schema/schema.ts b/client/src/api/schema/schema.ts index 44f5457df6bf..2f41a56da3b0 100644 --- a/client/src/api/schema/schema.ts +++ b/client/src/api/schema/schema.ts @@ -6852,10 +6852,11 @@ export interface components { tool_version?: string | null; /** * Type - * @description The type of workflow module. - * @default data_collection_input + * @constant */ - type?: components["schemas"]["WorkflowModuleType"]; + type: "data_collection_input"; + /** When */ + when: string | null; }; /** InputDataStep */ InputDataStep: { @@ -6893,10 +6894,11 @@ export interface components { tool_version?: string | null; /** * Type - * @description The type of workflow module. - * @default data_input + * @constant */ - type?: components["schemas"]["WorkflowModuleType"]; + type: "data_input"; + /** When */ + when: string | null; }; /** InputParameterStep */ InputParameterStep: { @@ -6934,10 +6936,11 @@ export interface components { tool_version?: string | null; /** * Type - * @description The type of workflow module. - * @default parameter_input + * @constant */ - type?: components["schemas"]["WorkflowModuleType"]; + type: "parameter"; + /** When */ + when: string | null; }; /** InputReferenceByLabel */ InputReferenceByLabel: { @@ -9703,12 +9706,28 @@ export interface components { input_steps: { [key: string]: components["schemas"]["InputStep"] | undefined; }; + /** + * Tool ID + * @description The unique name of the tool associated with this step. + */ + tool_id?: string | null; + /** + * Tool Inputs + * @description TODO + */ + tool_inputs?: Record; + /** + * Tool Version + * @description The version of the tool associated with this step. + */ + tool_version?: string | null; /** * Type - * @description The type of workflow module. - * @default pause + * @constant */ - type?: components["schemas"]["WorkflowModuleType"]; + type: "pause"; + /** When */ + when: string | null; }; /** Person */ Person: { @@ -11109,12 +11128,28 @@ export interface components { input_steps: { [key: string]: components["schemas"]["InputStep"] | undefined; }; + /** + * Tool ID + * @description The unique name of the tool associated with this step. + */ + tool_id?: string | null; + /** + * Tool Inputs + * @description TODO + */ + tool_inputs?: Record; + /** + * Tool Version + * @description The version of the tool associated with this step. + */ + tool_version?: string | null; /** * Type - * @description The type of workflow module. - * @default subworkflow + * @constant */ - type?: components["schemas"]["WorkflowModuleType"]; + type: "subworkflow"; + /** When */ + when: string | null; /** * Workflow ID * @description The encoded ID of the workflow that will be run on this step. @@ -11301,10 +11336,11 @@ export interface components { tool_version?: string | null; /** * Type - * @description The type of workflow module. - * @default tool + * @constant */ - type?: components["schemas"]["WorkflowModuleType"]; + type: "tool"; + /** When */ + when: string | null; }; /** Tour */ Tour: { @@ -12303,18 +12339,6 @@ export interface components { [key: string]: number | undefined; }; }; - /** - * WorkflowModuleType - * @description Available types of modules that represent a step in a Workflow. - * @enum {string} - */ - WorkflowModuleType: - | "data_input" - | "data_collection_input" - | "parameter_input" - | "subworkflow" - | "tool" - | "pause"; /** WriteInvocationStoreToPayload */ WriteInvocationStoreToPayload: { /** diff --git a/client/src/components/Grid/GridHistory.vue b/client/src/components/Grid/GridHistory.vue index a54e2437d3be..76229f380ea8 100644 --- a/client/src/components/Grid/GridHistory.vue +++ b/client/src/components/Grid/GridHistory.vue @@ -24,6 +24,7 @@ interface Props { const props = withDefaults(defineProps(), { activeList: "my", + username: undefined, }); @@ -65,8 +66,16 @@ const props = withDefaults(defineProps(), { Public Histories - + Archived Histories + diff --git a/client/src/components/Grid/GridList.vue b/client/src/components/Grid/GridList.vue index da08de2739c5..39cc6985aeec 100644 --- a/client/src/components/Grid/GridList.vue +++ b/client/src/components/Grid/GridList.vue @@ -363,7 +363,7 @@ watch(operationMessage, () => {
-
+
{
-
- -
@@ -402,6 +399,7 @@ watch(operationMessage, () => { top: 0; } .grid-sticky { + left: 0; z-index: 2; background: $white; opacity: 0.95; diff --git a/client/src/components/Grid/configs/histories.ts b/client/src/components/Grid/configs/histories.ts index 678c55eaa993..8216cda71560 100644 --- a/client/src/components/Grid/configs/histories.ts +++ b/client/src/components/Grid/configs/histories.ts @@ -241,7 +241,7 @@ const fields: FieldArray = [ ], }, { - key: "hid_counter", + key: "count", title: "Items", type: "text", }, diff --git a/client/src/components/Grid/configs/historiesPublished.ts b/client/src/components/Grid/configs/historiesPublished.ts index 23dc4bcccaff..9a1fd770391f 100644 --- a/client/src/components/Grid/configs/historiesPublished.ts +++ b/client/src/components/Grid/configs/historiesPublished.ts @@ -20,6 +20,7 @@ type SortKeyLiteral = "name" | "update_time" | undefined; */ async function getData(offset: number, limit: number, search: string, sort_by: string, sort_desc: boolean) { const { data, headers } = await historiesFetcher({ + view: "summary", limit, offset, search, diff --git a/client/src/components/History/CurrentCollection/CollectionPanel.vue b/client/src/components/History/CurrentCollection/CollectionPanel.vue index 2f58d1356e2a..10c830ca4601 100644 --- a/client/src/components/History/CurrentCollection/CollectionPanel.vue +++ b/client/src/components/History/CurrentCollection/CollectionPanel.vue @@ -43,7 +43,16 @@ const dsc = computed(() => { } return currentCollection; }); -const collectionElements = computed(() => collectionElementsStore.getCollectionElements(dsc.value, offset.value)); + +watch( + () => [dsc.value, offset.value], + () => { + collectionElementsStore.fetchMissingElements(dsc.value, offset.value); + }, + { immediate: true } +); + +const collectionElements = computed(() => collectionElementsStore.getCollectionElements(dsc.value) ?? []); const loading = computed(() => collectionElementsStore.isLoadingCollectionElements(dsc.value)); const jobState = computed(() => ("job_state_summary" in dsc.value ? dsc.value.job_state_summary : undefined)); const populatedStateMsg = computed(() => @@ -99,7 +108,8 @@ watch( watch( jobState, () => { - collectionElementsStore.loadCollectionElements(dsc.value); + collectionElementsStore.invalidateCollectionElements(dsc.value); + collectionElementsStore.fetchMissingElements(dsc.value, offset.value); }, { deep: true } ); diff --git a/client/src/components/History/CurrentHistory/PreferredStorePopover.vue b/client/src/components/History/CurrentHistory/PreferredStorePopover.vue index 9ea39503c6bc..ff28f962fba7 100644 --- a/client/src/components/History/CurrentHistory/PreferredStorePopover.vue +++ b/client/src/components/History/CurrentHistory/PreferredStorePopover.vue @@ -22,24 +22,30 @@ const preferredObjectStoreId = computed(() => { + diff --git a/client/src/components/History/Modals/SelectorModal.vue b/client/src/components/History/Modals/SelectorModal.vue index a15aedf55295..4c7be641955d 100644 --- a/client/src/components/History/Modals/SelectorModal.vue +++ b/client/src/components/History/Modals/SelectorModal.vue @@ -100,6 +100,17 @@ function selectHistories() { function setFilterValue(newFilter: string, newValue: string) { filter.value = HistoriesFilters.setFilterValue(filter.value, newFilter, newValue); } + +// hacky workaround for popovers in date pickers being cutoff +// https://github.com/galaxyproject/galaxy/issues/17711 +const modalBodyClasses = computed(() => { + return [ + "history-selector-modal-body", + showAdvanced.value + ? "history-selector-modal-body-allow-overflow" + : "history-selector-modal-body-prevent-overflow", + ]; +}); @@ -33,3 +35,8 @@ export default { }, }; + diff --git a/client/src/components/Workflow/Run/WorkflowTargetPreferredObjectStorePopover.vue b/client/src/components/Workflow/Run/WorkflowTargetPreferredObjectStorePopover.vue index 197e2968a0ab..b78eb8db9255 100644 --- a/client/src/components/Workflow/Run/WorkflowTargetPreferredObjectStorePopover.vue +++ b/client/src/components/Workflow/Run/WorkflowTargetPreferredObjectStorePopover.vue @@ -1,18 +1,22 @@ @@ -34,3 +38,9 @@ export default { }, }; + + diff --git a/client/src/components/Workflow/WorkflowActions.vue b/client/src/components/Workflow/WorkflowActions.vue index 122f0571aeec..52d6037ff89b 100644 --- a/client/src/components/Workflow/WorkflowActions.vue +++ b/client/src/components/Workflow/WorkflowActions.vue @@ -242,7 +242,7 @@ const menuActions: ComputedRef = computed(() => { :data-workflow-actions-dropdown="workflow.id" right no-caret - class="workflow-actions-dropdown show-in-card" + class="workflow-actions-dropdown" toggle-class="inline-icon-button" title="Workflow actions" variant="link"> diff --git a/client/src/components/Workflow/WorkflowCard.vue b/client/src/components/Workflow/WorkflowCard.vue index f82a13870038..5734a6ae9ac6 100644 --- a/client/src/components/Workflow/WorkflowCard.vue +++ b/client/src/components/Workflow/WorkflowCard.vue @@ -123,38 +123,34 @@ async function onTagClick(tag: string) { :class="{ 'workflow-shared': workflow.published, }"> -
-
-
- - - - {{ workflow.name }} - - - - -
+
+ -
- +
+ - -
+
+ + {{ workflow.name }} + + + + + diff --git a/client/src/entry/analysis/router.js b/client/src/entry/analysis/router.js index 5bf39d07f2fa..2c0dddc768d4 100644 --- a/client/src/entry/analysis/router.js +++ b/client/src/entry/analysis/router.js @@ -291,6 +291,7 @@ export function getRouter(Galaxy) { props: { activeList: "archived", }, + redirect: redirectAnon(), }, { path: "histories/list", diff --git a/client/src/store/historyStore/model/utilities.js b/client/src/store/historyStore/model/utilities.js index 86b5ac13bc61..6a7ccb2d3f0c 100644 --- a/client/src/store/historyStore/model/utilities.js +++ b/client/src/store/historyStore/model/utilities.js @@ -1,9 +1,9 @@ -import Vue from "vue"; +import { set } from "vue"; /* This function merges the existing data with new incoming data. */ export function mergeArray(id, payload, items, itemKey) { if (!items[id]) { - Vue.set(items, id, []); + set(items, id, []); } const itemArray = items[id]; for (const item of payload) { @@ -16,7 +16,7 @@ export function mergeArray(id, payload, items, itemKey) { }); } } else { - Vue.set(itemArray, itemIndex, item); + set(itemArray, itemIndex, item); } } } diff --git a/client/src/stores/collectionElementsStore.test.ts b/client/src/stores/collectionElementsStore.test.ts index b34435288554..4a2c7be2e2ce 100644 --- a/client/src/stores/collectionElementsStore.test.ts +++ b/client/src/stores/collectionElementsStore.test.ts @@ -38,13 +38,15 @@ describe("useCollectionElementsStore", () => { expect(store.storedCollectionElements).toEqual({}); expect(store.isLoadingCollectionElements(collection)).toEqual(false); - const offset = 0; + // Getting collection elements should be side effect free + store.getCollectionElements(collection); + expect(store.isLoadingCollectionElements(collection)).toEqual(false); + await flushPromises(); + expect(fetchCollectionElements).not.toHaveBeenCalled(); + const limit = 5; - // Getting collection elements should trigger a fetch and change the loading state - store.getCollectionElements(collection, offset, limit); - expect(store.isLoadingCollectionElements(collection)).toEqual(true); + store.fetchMissingElements(collection, 0, limit); await flushPromises(); - expect(store.isLoadingCollectionElements(collection)).toEqual(false); expect(fetchCollectionElements).toHaveBeenCalled(); const collectionKey = store.getCollectionKey(collection); @@ -70,18 +72,20 @@ describe("useCollectionElementsStore", () => { const offset = 0; const limit = storedCount; // Getting the same collection elements range should not trigger a fetch - store.getCollectionElements(collection, offset, limit); + store.fetchMissingElements(collection, offset, limit); expect(store.isLoadingCollectionElements(collection)).toEqual(false); expect(fetchCollectionElements).not.toHaveBeenCalled(); }); it("should fetch only missing elements if the requested range is not already stored", async () => { + jest.useFakeTimers(); + const totalElements = 10; const collection: HDCASummary = mockCollection("1", totalElements); const store = useCollectionElementsStore(); const initialElements = 3; - store.getCollectionElements(collection, 0, initialElements); + store.fetchMissingElements(collection, 0, initialElements); await flushPromises(); expect(fetchCollectionElements).toHaveBeenCalled(); const collectionKey = store.getCollectionKey(collection); @@ -92,11 +96,10 @@ describe("useCollectionElementsStore", () => { const offset = 2; const limit = 5; - // Getting collection elements should trigger a fetch in this case - store.getCollectionElements(collection, offset, limit); - expect(store.isLoadingCollectionElements(collection)).toEqual(true); + // Fetching collection elements should trigger a fetch in this case + store.fetchMissingElements(collection, offset, limit); + jest.runAllTimers(); await flushPromises(); - expect(store.isLoadingCollectionElements(collection)).toEqual(false); expect(fetchCollectionElements).toHaveBeenCalled(); elements = store.storedCollectionElements[collectionKey]; diff --git a/client/src/stores/collectionElementsStore.ts b/client/src/stores/collectionElementsStore.ts index ddeb60102012..73c63ade28a2 100644 --- a/client/src/stores/collectionElementsStore.ts +++ b/client/src/stores/collectionElementsStore.ts @@ -4,6 +4,8 @@ import { computed, del, ref, set } from "vue"; import type { CollectionEntry, DCESummary, HDCASummary, HistoryContentItemBase } from "@/api"; import { isHDCA } from "@/api"; import { fetchCollectionDetails, fetchElementsFromCollection } from "@/api/datasetCollections"; +import { ensureDefined } from "@/utils/assertions"; +import { ActionSkippedError, LastQueue } from "@/utils/lastQueue"; /** * Represents an element in a collection that has not been fetched yet. @@ -24,7 +26,11 @@ export interface ContentPlaceholder { fetching?: boolean; } -export type DCEEntry = ContentPlaceholder | DCESummary; +export type InvalidDCEEntry = (ContentPlaceholder | DCESummary) & { + valid: false; +}; + +export type DCEEntry = ContentPlaceholder | DCESummary | InvalidDCEEntry; const FETCH_LIMIT = 50; @@ -46,11 +52,8 @@ export const useCollectionElementsStore = defineStore("collectionElementsStore", } const getCollectionElements = computed(() => { - return (collection: CollectionEntry, offset = 0, limit = FETCH_LIMIT) => { - const storedElements = - storedCollectionElements.value[getCollectionKey(collection)] ?? initWithPlaceholderElements(collection); - fetchMissingElements({ collection, storedElements, offset, limit }); - return storedElements; + return (collection: CollectionEntry) => { + return storedCollectionElements.value[getCollectionKey(collection)]; }; }); @@ -60,47 +63,91 @@ export const useCollectionElementsStore = defineStore("collectionElementsStore", }; }); - async function fetchMissingElements(params: { - collection: CollectionEntry; + type FetchParams = { storedElements: DCEEntry[]; + collection: CollectionEntry; offset: number; limit: number; - }) { - const collectionKey = getCollectionKey(params.collection); + }; + + async function fetchMissing({ storedElements, collection, offset, limit = FETCH_LIMIT }: FetchParams) { + const collectionKey = getCollectionKey(collection); + try { - // We should fetch only missing (placeholder) elements from the range - const firstMissingIndexInRange = params.storedElements - .slice(params.offset, params.offset + params.limit) - .findIndex((element) => isPlaceholder(element) && !element.fetching); - - if (firstMissingIndexInRange === -1) { - // All elements in the range are already stored or being fetched - return; + if (collection.element_count !== null) { + // We should fetch only missing (placeholder) elements from the range + const firstMissingIndexInRange = storedElements + .slice(offset, offset + limit) + .findIndex((element) => (isPlaceholder(element) && !element.fetching) || isInvalid(element)); + + if (firstMissingIndexInRange === -1) { + // All elements in the range are already stored or being fetched + return; + } + + // Adjust the offset to the first missing element + offset += firstMissingIndexInRange; + } else { + // Edge case where element_count is incorrect + // TODO: remove me once element_count is reported reliably + offset = 0; } - // Adjust the offset to the first missing element - params.offset += firstMissingIndexInRange; set(loadingCollectionElements.value, collectionKey, true); // Mark all elements in the range as fetching - params.storedElements - .slice(params.offset, params.offset + params.limit) + storedElements + .slice(offset, offset + limit) .forEach((element) => isPlaceholder(element) && (element.fetching = true)); + const fetchedElements = await fetchElementsFromCollection({ - entry: params.collection, - offset: params.offset, - limit: params.limit, + entry: collection, + offset: offset, + limit: limit, }); - // Update only the elements that were fetched - params.storedElements.splice(params.offset, fetchedElements.length, ...fetchedElements); - set(storedCollectionElements.value, collectionKey, params.storedElements); + + return { fetchedElements, elementOffset: offset }; } finally { del(loadingCollectionElements.value, collectionKey); } } - async function loadCollectionElements(collection: CollectionEntry) { - const elements = await fetchElementsFromCollection({ entry: collection }); - set(storedCollectionElements.value, getCollectionKey(collection), elements); + const lastQueue = new LastQueue(1000, true); + + async function fetchMissingElements(collection: CollectionEntry, offset: number, limit = FETCH_LIMIT) { + const key = getCollectionKey(collection); + let storedElements = storedCollectionElements.value[key]; + + if (!storedElements) { + storedElements = initWithPlaceholderElements(collection); + set(storedCollectionElements.value, key, storedElements); + } + + try { + const data = await lastQueue.enqueue(fetchMissing, { storedElements, collection, offset, limit }, key); + + if (data) { + const from = data.elementOffset; + const to = from + data.fetchedElements.length; + + for (let index = from; index < to; index++) { + const element = ensureDefined(data.fetchedElements[index - from]); + set(storedElements, index, element); + } + + set(storedCollectionElements.value, key, storedElements); + } + } catch (e) { + if (!(e instanceof ActionSkippedError)) { + throw e; + } + } + } + + async function invalidateCollectionElements(collection: CollectionEntry) { + const storedElements = storedCollectionElements.value[getCollectionKey(collection)] ?? []; + storedElements.forEach((element) => { + (element as InvalidDCEEntry).valid = false; + }); } function saveCollections(historyContentsPayload: HistoryContentItemBase[]) { @@ -135,6 +182,10 @@ export const useCollectionElementsStore = defineStore("collectionElementsStore", return "id" in element === false; } + function isInvalid(element: DCEEntry): element is InvalidDCEEntry { + return (element as InvalidDCEEntry)["valid"] === false; + } + function initWithPlaceholderElements(collection: CollectionEntry): ContentPlaceholder[] { const totalElements = collection.element_count ?? 0; const placeholderElements = new Array(totalElements); @@ -151,8 +202,9 @@ export const useCollectionElementsStore = defineStore("collectionElementsStore", isLoadingCollectionElements, getCollection, fetchCollection, - loadCollectionElements, + invalidateCollectionElements, saveCollections, getCollectionKey, + fetchMissingElements, }; }); diff --git a/client/src/utils/lastQueue.ts b/client/src/utils/lastQueue.ts index 317d7dfa3a3c..ff27690f0b5f 100644 --- a/client/src/utils/lastQueue.ts +++ b/client/src/utils/lastQueue.ts @@ -1,4 +1,4 @@ -type QueuedAction R, R = unknown> = { +type QueuedAction R, R = ReturnType> = { action: T; arg: Parameters[0]; resolve: (value: R) => void; @@ -13,7 +13,7 @@ export class ActionSkippedError extends Error {} * This is useful when promises earlier enqueued become obsolete. * See also: https://stackoverflow.com/questions/53540348/js-async-await-tasks-queue */ -export class LastQueue R, R = unknown> { +export class LastQueue R, R = ReturnType> { throttlePeriod: number; /** Throw an error if a queued action is skipped. This avoids dangling promises */ rejectSkipped: boolean; @@ -34,7 +34,7 @@ export class LastQueue R, R = unknown> { promise?.reject(new ActionSkippedError()); } - async enqueue(action: T, arg: Parameters[0], key: string | number = 0) { + async enqueue(action: T, arg: Parameters[0], key: string | number = 0): Promise { return new Promise((resolve, reject) => { this.skipPromise(key); this.queuedPromises[key] = { action, arg, resolve, reject }; diff --git a/lib/galaxy/managers/workflows.py b/lib/galaxy/managers/workflows.py index 43b65e6b0615..18a61ffba6c5 100644 --- a/lib/galaxy/managers/workflows.py +++ b/lib/galaxy/managers/workflows.py @@ -1615,9 +1615,9 @@ def callback(input, prefixed_name, **kwargs): def _workflow_to_dict_instance(self, trans, stored, workflow, legacy=True): encode = self.app.security.encode_id sa_session = self.app.model.context - item = stored.to_dict(view="element", value_mapper={"id": encode}) + item = stored.to_dict(view="element") item["name"] = workflow.name - item["url"] = trans.url_builder("workflow", id=item["id"]) + item["url"] = trans.url_builder("workflow", id=encode(stored.id)) item["owner"] = stored.user.username item["email_hash"] = md5_hash_str(stored.user.email) item["slug"] = stored.slug @@ -1668,7 +1668,7 @@ def _workflow_to_dict_instance(self, trans, stored, workflow, legacy=True): del step_dict["tool_id"] del step_dict["tool_version"] del step_dict["tool_inputs"] - step_dict["workflow_id"] = encode(step.subworkflow.id) + step_dict["workflow_id"] = step.subworkflow.id for conn in step.input_connections: step_id = step.id if legacy else step.order_index diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py index c9e6cd6ac7d5..ca3aeb7ace59 100644 --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -7730,7 +7730,7 @@ class WorkflowStep(Base, RepresentById): uuid = Column(UUIDType) label = Column(Unicode(255)) temp_input_connections: Optional[InputConnDictType] - parent_comment_id = Column(Integer, ForeignKey("workflow_comment.id"), nullable=True) + parent_comment_id = Column(Integer, ForeignKey("workflow_comment.id"), index=True, nullable=True) parent_comment = relationship( "WorkflowComment", @@ -8177,7 +8177,7 @@ class WorkflowComment(Base, RepresentById): type = Column(String(16)) color = Column(String(16)) data = Column(JSONType) - parent_comment_id = Column(Integer, ForeignKey("workflow_comment.id"), nullable=True) + parent_comment_id = Column(Integer, ForeignKey("workflow_comment.id"), index=True, nullable=True) workflow = relationship( "Workflow", diff --git a/lib/galaxy/model/migrations/alembic/versions_gxy/2dc3386d091f_add_indexes_for_workflow_comment_.py b/lib/galaxy/model/migrations/alembic/versions_gxy/2dc3386d091f_add_indexes_for_workflow_comment_.py new file mode 100644 index 000000000000..14c990e3086a --- /dev/null +++ b/lib/galaxy/model/migrations/alembic/versions_gxy/2dc3386d091f_add_indexes_for_workflow_comment_.py @@ -0,0 +1,44 @@ +"""add_indexes_for_workflow_comment_foreign_keys + +Revision ID: 2dc3386d091f +Revises: 8a19186a6ee7 +Create Date: 2024-03-13 15:25:52.587488 + +""" + +from galaxy.model.database_object_names import build_index_name +from galaxy.model.migrations.util import ( + create_index, + drop_index, +) + +# revision identifiers, used by Alembic. +revision = "2dc3386d091f" +down_revision = "8a19186a6ee7" +branch_labels = None +depends_on = None + +workflow_comment_table_name = "workflow_comment" +workflow_step_table_name = "workflow_step" +workflow_id_column_name = "workflow_id" +parent_comment_id_column_name = "parent_comment_id" + +workflow_step_parent_comment_index_name = build_index_name(workflow_step_table_name, parent_comment_id_column_name) +workflow_comment_workflow_id_index_name = build_index_name(workflow_comment_table_name, workflow_id_column_name) +workflow_comment_parent_comment_index_name = build_index_name( + workflow_comment_table_name, parent_comment_id_column_name +) + + +def upgrade(): + create_index(workflow_step_parent_comment_index_name, workflow_step_table_name, [parent_comment_id_column_name]) + create_index(workflow_comment_workflow_id_index_name, workflow_comment_table_name, [workflow_id_column_name]) + create_index( + workflow_comment_parent_comment_index_name, workflow_comment_table_name, [parent_comment_id_column_name] + ) + + +def downgrade(): + drop_index(workflow_step_parent_comment_index_name, workflow_step_table_name) + drop_index(workflow_comment_workflow_id_index_name, workflow_comment_table_name) + drop_index(workflow_comment_parent_comment_index_name, workflow_comment_table_name) diff --git a/lib/galaxy/schema/schema.py b/lib/galaxy/schema/schema.py index ec96b40fede0..ab2e22909ca6 100644 --- a/lib/galaxy/schema/schema.py +++ b/lib/galaxy/schema/schema.py @@ -2099,7 +2099,7 @@ class JobFullDetails(JobDetails): class StoredWorkflowSummary(Model, WithModelClass): - id: DecodedDatabaseIdField + id: EncodedDatabaseIdField model_class: STORED_WORKFLOW_MODEL_CLASS = ModelClassField(STORED_WORKFLOW_MODEL_CLASS) create_time: datetime = CreateTimeField update_time: datetime = UpdateTimeField @@ -2203,33 +2203,21 @@ class InputStep(Model): ) -class WorkflowModuleType(str, Enum): - """Available types of modules that represent a step in a Workflow.""" - - data_input = "data_input" - data_collection_input = "data_collection_input" - parameter_input = "parameter_input" - subworkflow = "subworkflow" - tool = "tool" - pause = "pause" # Experimental - - class WorkflowStepBase(Model): id: int = Field( ..., title="ID", description="The identifier of the step. It matches the index order of the step inside the workflow.", ) - type: WorkflowModuleType = Field(..., title="Type", description="The type of workflow module.") annotation: Optional[str] = AnnotationField input_steps: Dict[str, InputStep] = Field( ..., title="Input Steps", description="A dictionary containing information about the inputs connected to this workflow step.", ) - - -class ToolBasedWorkflowStep(WorkflowStepBase): + when: Optional[str] + # TODO: these should move to ToolStep, however we might be breaking scripts that iterate over steps and + # assume tool_id is a valid key for every step. tool_id: Optional[str] = Field( None, title="Tool ID", description="The unique name of the tool associated with this step." ) @@ -2239,37 +2227,29 @@ class ToolBasedWorkflowStep(WorkflowStepBase): tool_inputs: Any = Field(None, title="Tool Inputs", description="TODO") -class InputDataStep(ToolBasedWorkflowStep): - type: WorkflowModuleType = Field( - WorkflowModuleType.data_input, title="Type", description="The type of workflow module." - ) +class InputDataStep(WorkflowStepBase): + type: Literal["data_input"] -class InputDataCollectionStep(ToolBasedWorkflowStep): - type: WorkflowModuleType = Field( - WorkflowModuleType.data_collection_input, title="Type", description="The type of workflow module." - ) +class InputDataCollectionStep(WorkflowStepBase): + type: Literal["data_collection_input"] -class InputParameterStep(ToolBasedWorkflowStep): - type: WorkflowModuleType = Field( - WorkflowModuleType.parameter_input, title="Type", description="The type of workflow module." - ) +class InputParameterStep(WorkflowStepBase): + type: Literal["parameter"] class PauseStep(WorkflowStepBase): - type: WorkflowModuleType = Field(WorkflowModuleType.pause, title="Type", description="The type of workflow module.") + type: Literal["pause"] -class ToolStep(ToolBasedWorkflowStep): - type: WorkflowModuleType = Field(WorkflowModuleType.tool, title="Type", description="The type of workflow module.") +class ToolStep(WorkflowStepBase): + type: Literal["tool"] class SubworkflowStep(WorkflowStepBase): - type: WorkflowModuleType = Field( - WorkflowModuleType.subworkflow, title="Type", description="The type of workflow module." - ) - workflow_id: DecodedDatabaseIdField = Field( + type: Literal["subworkflow"] + workflow_id: EncodedDatabaseIdField = Field( ..., title="Workflow ID", description="The encoded ID of the workflow that will be run on this step." ) diff --git a/lib/galaxy/schema/workflows.py b/lib/galaxy/schema/workflows.py index 598878d749c2..cbc5379e49e6 100644 --- a/lib/galaxy/schema/workflows.py +++ b/lib/galaxy/schema/workflows.py @@ -197,7 +197,12 @@ class StoredWorkflowDetailed(StoredWorkflowSummary): ToolStep, SubworkflowStep, ], - ] = Field({}, title="Steps", description="A dictionary with information about all the steps of the workflow.") + ] = Field( + {}, + title="Steps", + description="A dictionary with information about all the steps of the workflow.", + discriminator="type", + ) importable: Optional[bool] = Field( ..., title="Importable", diff --git a/lib/galaxy_test/api/test_workflows.py b/lib/galaxy_test/api/test_workflows.py index 4f6f9a5cbe05..4919f6ca814e 100644 --- a/lib/galaxy_test/api/test_workflows.py +++ b/lib/galaxy_test/api/test_workflows.py @@ -328,6 +328,15 @@ def test_show_valid(self): # workflow was created first in this instance. assert sorted(step["id"] for step in workflow["steps"].values()) != [0, 1, 2] + def test_show_subworkflow(self): + workflow_id = self.workflow_populator.upload_yaml_workflow(WORKFLOW_NESTED_SIMPLE) + workflow = self._get(f"workflows/{workflow_id}", {"style": "instance"}).json() + assert isinstance(workflow["id"], str) + subworkflow_step = workflow["steps"]["2"] + assert subworkflow_step["type"] == "subworkflow" + assert isinstance(subworkflow_step["workflow_id"], str) + self._get(f"workflows/{subworkflow_step['workflow_id']}", {"style": "instance"}).json() + def test_show_invalid_key_is_400(self): show_response = self._get(f"workflows/{self._random_key()}") self._assert_status_code_is(show_response, 400)