Rename EnaPairedReads to EnaSequencingReads

Author: mvdbeek

app/components/Entity/components/ConfigureWorkflowInputs/components/Main/components/Stepper/components/Step/SequencingStep/components/ENASequencingData/components/CollectionSelector/collectionSelector.tsx

@@ -6,7 +6,7 @@ import { BUTTON_PROPS } from "@databiosphere/findable-ui/lib/components/common/B
 import { useState } from "react";
 import { Table } from "./components/Table/table";
 import { RowSelectionState } from "@tanstack/table-core";
-import { buildEnaPairedReads } from "../../utils";
+import { buildEnaSequencingReads } from "../../utils";
 
 export const CollectionSelector = ({
   onClose,
@@ -40,7 +40,7 @@ export const CollectionSelector = ({
           {...BUTTON_PROPS.PRIMARY_CONTAINED}
           disabled={selectedCount === 0}
           onClick={() => {
-            onConfigure(stepKey, buildEnaPairedReads(table));
+            onConfigure(stepKey, buildEnaSequencingReads(table));
             onClose();
           }}
         >

app/components/Entity/components/ConfigureWorkflowInputs/components/Main/components/Stepper/components/Step/SequencingStep/components/ENASequencingData/enaSequencingData.tsx

@@ -5,7 +5,7 @@ import { useDialog } from "@databiosphere/findable-ui/lib/components/common/Dial
 import { Props } from "./types";
 import { CollectionSummary } from "./components/CollectionSummary/collectionSummary";
 import { AccessionSelector } from "./components/AccessionSelector/accessionSelector";
-import { buildEnaPairedReads } from "./utils";
+import { buildEnaSequencingReads } from "./utils";
 
 export const ENASequencingData = ({
   clearErrors,
@@ -20,7 +20,7 @@ export const ENASequencingData = ({
   const selectedCount = Object.values(table.getState().rowSelection).length;
 
   useEffect(() => {
-    const pairedReads = buildEnaPairedReads(table);
+    const pairedReads = buildEnaSequencingReads(table);
     onConfigure(stepKey, pairedReads.length > 0 ? pairedReads : null);
     // eslint-disable-next-line react-hooks/exhaustive-deps -- Intended behavior to only run on mount.
   }, []);

app/components/Entity/components/ConfigureWorkflowInputs/components/Main/components/Stepper/components/Step/SequencingStep/components/ENASequencingData/utils.ts

@@ -1,15 +1,17 @@
 import { Table } from "@tanstack/react-table";
-import { EnaPairedReads } from "../../../../../../../../../../../../../utils/galaxy-api/entities";
+import { EnaSequencingReads } from "../../../../../../../../../../../../../utils/galaxy-api/entities";
 import { ReadRun } from "./types";
 
 /**
- * Build EnaPairedReads from table selected rows.
+ * Build EnaSequencingReads from table selected rows.
  * @param table - Table.
- * @returns Array of EnaPairedReads.
+ * @returns Array of EnaSequencingReads.
  */
-export function buildEnaPairedReads(table: Table<ReadRun>): EnaPairedReads[] {
+export function buildEnaSequencingReads(
+  table: Table<ReadRun>
+): EnaSequencingReads[] {
   return table.getSelectedRowModel().rows.map(
-    (row): EnaPairedReads => ({
+    (row): EnaSequencingReads => ({
       md5Hashes: row.original.fastq_md5,
       runAccession: row.original.run_accession,
       urls: row.original.fastq_ftp,

app/components/Entity/components/ConfigureWorkflowInputs/components/Main/components/Stepper/components/Step/hooks/UseLaunchGalaxy/types.ts

@@ -1,11 +1,11 @@
-import { EnaPairedReads } from "app/utils/galaxy-api/entities";
+import { EnaSequencingReads } from "app/utils/galaxy-api/entities";
 import { Workflow } from "../../../../../../../../../../../../apis/catalog/brc-analytics-catalog/common/entities";
 import { ConfiguredInput } from "../../../../../../../../../../../../views/WorkflowInputsView/hooks/UseConfigureInputs/types";
 
 export interface ConfiguredValue {
   geneModelUrl: string | null;
-  readRunsPaired: EnaPairedReads[] | null;
-  readRunsSingle: EnaPairedReads[] | null;
+  readRunsPaired: EnaSequencingReads[] | null;
+  readRunsSingle: EnaSequencingReads[] | null;
   referenceAssembly: string;
 }
 

app/utils/galaxy-api/entities.ts

@@ -1,4 +1,4 @@
-export interface EnaPairedReads {
+export interface EnaSequencingReads {
   md5Hashes: string;
   runAccession: string;
   urls: string;

app/utils/galaxy-api/galaxy-api.ts

@@ -4,7 +4,7 @@ import ky from "ky";
 import { GALAXY_ENVIRONMENT } from "site-config/common/galaxy";
 import {
   EnaFileInfo,
-  EnaPairedReads,
+  EnaSequencingReads,
   WorkflowLanding,
   WorkflowLandingsBody,
   WorkflowLandingsBodyRequestState,
@@ -31,8 +31,8 @@ export async function getWorkflowLandingUrl(
   workflowId: string,
   referenceGenome: string,
   geneModelUrl: string | null,
-  readRunsSingle: EnaPairedReads[] | null,
-  readRunsPaired: EnaPairedReads[] | null,
+  readRunsSingle: EnaSequencingReads[] | null,
+  readRunsPaired: EnaSequencingReads[] | null,
   parameters: WorkflowParameter[]
 ): Promise<string> {
   const body: WorkflowLandingsBody = {
@@ -70,8 +70,8 @@ function buildFastaUrl(identifier: string): string {
 function paramVariableToRequestValue(
   variable: WORKFLOW_PARAMETER_VARIABLE,
   geneModelUrl: string | null,
-  readRunsSingle: EnaPairedReads[] | null,
-  readRunsPaired: EnaPairedReads[] | null,
+  readRunsSingle: EnaSequencingReads[] | null,
+  readRunsPaired: EnaSequencingReads[] | null,
   referenceGenome: string
 ): WorkflowParameterValue | null {
   // Because this `switch` has no default case, and the function doesn't allow `undefined` as a return type,
@@ -241,8 +241,8 @@ function getRunUrlsInfo(
 function getWorkflowLandingsRequestState(
   referenceGenome: string,
   geneModelUrl: string | null,
-  readRunsSingle: EnaPairedReads[] | null,
-  readRunsPaired: EnaPairedReads[] | null,
+  readRunsSingle: EnaSequencingReads[] | null,
+  readRunsPaired: EnaSequencingReads[] | null,
   parameters: WorkflowParameter[]
 ): WorkflowLandingsBodyRequestState {
   const result: WorkflowLandingsBodyRequestState = {};

app/views/WorkflowInputsView/hooks/UseConfigureInputs/types.ts

@@ -1,4 +1,4 @@
-import { EnaPairedReads } from "app/utils/galaxy-api/entities";
+import { EnaSequencingReads } from "app/utils/galaxy-api/entities";
 
 export type OnConfigure = (...p: OnConfigureParams) => void;
 
@@ -11,8 +11,8 @@ export type OnConfigureParams = {
 
 export interface ConfiguredInput {
   geneModelUrl?: string | null;
-  readRunsPaired?: EnaPairedReads[] | null;
-  readRunsSingle?: EnaPairedReads[] | null;
+  readRunsPaired?: EnaSequencingReads[] | null;
+  readRunsSingle?: EnaSequencingReads[] | null;
   referenceAssembly?: string;
 }