Merge pull request galaxyproject#19305 from jmchilton/sample_sheets

Implement Sample Sheets

Author: mvdbeek

client/src/api/datasetCollections.ts

@@ -8,12 +8,21 @@ import {
     type HDCASummary,
     isHDCA,
 } from "@/api";
+import type { components } from "@/api/schema";
 import { rethrowSimple } from "@/utils/simple-error";
 
 const DEFAULT_LIMIT = 50;
 
 export type CollectionType = string;
 
+export type SampleSheetCollectionType =
+    | "sample_sheet"
+    | "sample_sheet:paired"
+    | "sample_sheet:paired_or_unpaired"
+    | "sample_sheet:record";
+// mirror the python definition here
+export type SampleSheetColumnValueT = string | number | boolean;
+
 /**
  * Fetches the details of a collection.
  * @param params.id The ID of the collection (HDCA) to fetch.
@@ -126,3 +135,34 @@ export async function createHistoryDatasetCollectionInstanceFull(payload: Create
     }
     return data;
 }
+
+export type CreateWorkbookForCollectionPayload = components["schemas"]["CreateWorkbookForCollectionApi"];
+export type CreateWorkbookPayload = components["schemas"]["CreateWorkbookRequest"];
+
+export async function createWorkbook(payload: CreateWorkbookPayload): Promise<Blob> {
+    const { data, error } = await GalaxyApi().POST("/api/sample_sheet_workbook", {
+        body: payload,
+        parseAs: "blob",
+    });
+
+    if (error) {
+        rethrowSimple(error);
+    }
+    return data;
+}
+
+export async function createWorkbookForCollection(
+    hdca_id: string,
+    payload: CreateWorkbookForCollectionPayload
+): Promise<Blob> {
+    const { data, error } = await GalaxyApi().POST("/api/dataset_collections/{hdca_id}/sample_sheet_workbook", {
+        params: { path: { hdca_id: hdca_id } },
+        body: payload,
+        parseAs: "blob",
+    });
+
+    if (error) {
+        rethrowSimple(error);
+    }
+    return data;
+}

client/src/api/index.ts

@@ -327,6 +327,10 @@ export type ObjectExportTaskResponse = components["schemas"]["ObjectExportTaskRe
 export type ExportObjectRequestMetadata = components["schemas"]["ExportObjectRequestMetadata"];
 export type ExportObjectResultMetadata = components["schemas"]["ExportObjectResultMetadata"];
 
+export type SampleSheetColumnDefinition = components["schemas"]["SampleSheetColumnDefinitionModel"];
+export type SampleSheetColumnDefinitionType = SampleSheetColumnDefinition["type"];
+export type SampleSheetColumnDefinitions = SampleSheetColumnDefinition[] | null;
+
 export type AsyncTaskResultSummary = components["schemas"]["AsyncTaskResultSummary"];
 
 export type CollectionElementIdentifiers = components["schemas"]["CollectionElementIdentifier"][];

client/src/api/jobs.ts

@@ -8,6 +8,10 @@ export type JobInputSummary = components["schemas"]["JobInputSummary"];
 export type JobDisplayParametersSummary = components["schemas"]["JobDisplayParametersSummary"];
 export type JobMetric = components["schemas"]["JobMetric"];
 
+export const NON_TERMINAL_STATES = ["new", "queued", "running", "waiting", "paused", "resubmitted", "stop"];
+export const ERROR_STATES = ["error", "deleted", "deleting"];
+export const TERMINAL_STATES = ["ok", "skipped", "stop", "stopping", "skipped"].concat(ERROR_STATES);
+
 interface JobDef {
     tool_id: string;
 }