feat: stub add flu workflow

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

@@ -8,21 +8,67 @@ import { UcscTrack } from "../../../../../../../../../../../../utils/ucsc-tracks
 import { COLUMN_TYPE } from "../../SampleSheetClassificationStep/types";
 import { Strandedness } from "../../StrandednessStep/types";
 
-export interface ConfiguredValue {
+// Base configured values shared across all scopes
+export interface BaseConfiguredValue {
+  readRunsPaired: EnaSequencingReads[] | null;
+  readRunsSingle: EnaSequencingReads[] | null;
+  tracks: UcscTrack[] | null;
+}
+
+// ASSEMBLY scope: workflows that operate on a specific genome assembly
+export interface AssemblyConfiguredValue extends BaseConfiguredValue {
+  _scope: "ASSEMBLY";
   designFormula: string | null;
   geneModelUrl: string | null;
-  numberOfHits?: number;
   primaryContrasts: PrimaryContrasts | null;
-  readRunsPaired: EnaSequencingReads[] | null;
-  readRunsSingle: EnaSequencingReads[] | null;
   referenceAssembly: string;
   sampleSheet: Record<string, string>[] | null;
   sampleSheetClassification: Record<string, COLUMN_TYPE | null> | null;
-  sequence?: string;
   strandedness: Strandedness | undefined;
-  tracks: UcscTrack[] | null;
 }
 
+// ORGANISM scope: workflows that operate at organism level (may not require specific assembly)
+// Organism scope workflows may have collection_spec (defined in workflow YAML) and variables.
+// fastaCollection can be either:
+// - User-selected assembly accessions (string[]) for user-defined FASTA collections
+// - Auto-configured via collection_spec in workflow YAML (handled by Galaxy API)
+export interface OrganismConfiguredValue extends BaseConfiguredValue {
+  _scope: "ORGANISM";
+  fastaCollection: string[] | null;
+}
+
+// SEQUENCE scope: workflows that operate on user-provided sequences
+export interface SequenceConfiguredValue extends BaseConfiguredValue {
+  _scope: "SEQUENCE";
+  numberOfHits?: number;
+  sequence?: string;
+}
+
+// Type guards for ConfiguredValue discrimination
+export function isAssemblyConfiguredValue(
+  value: ConfiguredValue
+): value is AssemblyConfiguredValue {
+  return value._scope === "ASSEMBLY";
+}
+
+export function isOrganismConfiguredValue(
+  value: ConfiguredValue
+): value is OrganismConfiguredValue {
+  return value._scope === "ORGANISM";
+}
+
+export function isSequenceConfiguredValue(
+  value: ConfiguredValue
+): value is SequenceConfiguredValue {
+  return value._scope === "SEQUENCE";
+}
+
+// Union type for all configured values
+export type ConfiguredValue =
+  | AssemblyConfiguredValue
+  | OrganismConfiguredValue
+  | SequenceConfiguredValue;
+
 export interface Status {
   disabled: boolean;
   error: string | null;

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

@@ -11,9 +11,115 @@ import { CUSTOM_WORKFLOW } from "../../../../../../../../../../../../views/Analy
 import { DIFFERENTIAL_EXPRESSION_ANALYSIS } from "../../../../../../../../../../../../views/AnalyzeWorkflowsView/differentialExpressionAnalysis/constants";
 import { LEXICMAP } from "../../../../../../../../../../../../views/AnalyzeWorkflowsView/lexicmap/constants";
 import { LOGAN_SEARCH } from "../../../../../../../../../../../../views/AnalyzeWorkflowsView/loganSearch/constants";
-import { Props, UseLaunchGalaxy } from "./types";
+import { Workflow } from "../../../../../../../../../../../../apis/catalog/brc-analytics-catalog/common/entities";
+import {
+  ConfiguredValue,
+  isAssemblyConfiguredValue,
+  isSequenceConfiguredValue,
+  Props,
+  UseLaunchGalaxy,
+} from "./types";
 import { getConfiguredValues, launchGalaxy } from "./utils";
 
+/**
+ * Gets the appropriate landing URL based on workflow type.
+ * @param workflow - Workflow to launch.
+ * @param configuredValue - Configured values for the workflow.
+ * @param origin - Origin URL for the Galaxy instance.
+ * @param run - Async runner function from useAsync hook.
+ * @returns Promise resolving to the Galaxy workflow landing URL.
+ */
+async function getLandingUrlForWorkflow(
+  workflow: Workflow,
+  configuredValue: ConfiguredValue,
+  origin: string,
+  run: (promise: Promise<string>) => Promise<string>
+): Promise<string> {
+  if (workflow.trsId === CUSTOM_WORKFLOW.trsId) {
+    if (!isAssemblyConfiguredValue(configuredValue)) {
+      throw new Error("Invalid configured value for CUSTOM workflow");
+    }
+    return run(
+      getDataLandingUrl(
+        configuredValue.referenceAssembly,
+        configuredValue.geneModelUrl,
+        configuredValue.readRunsSingle,
+        configuredValue.readRunsPaired,
+        null,
+        configuredValue.tracks,
+        origin
+      )
+    );
+  }
+
+  if (
+    workflow.trsId === LOGAN_SEARCH.trsId ||
+    workflow.trsId === LEXICMAP.trsId
+  ) {
+    if (!workflow.workflowId) {
+      throw new Error("Missing workflow ID for LMLS workflow");
+    }
+    if (
+      !isSequenceConfiguredValue(configuredValue) ||
+      !configuredValue.numberOfHits ||
+      !configuredValue.sequence
+    ) {
+      throw new Error("Missing required values for LMLS workflow");
+    }
+    return run(
+      getLMLSLandingUrl(
+        workflow.workflowId,
+        configuredValue.numberOfHits,
+        configuredValue.sequence,
+        origin
+      )
+    );
+  }
+
+  if (workflow.trsId === DIFFERENTIAL_EXPRESSION_ANALYSIS.trsId) {
+    if (
+      !workflow.workflowId ||
+      !isAssemblyConfiguredValue(configuredValue) ||
+      !configuredValue.geneModelUrl ||
+      !configuredValue.sampleSheet ||
+      !configuredValue.sampleSheetClassification ||
+      !configuredValue.designFormula
+    ) {
+      throw new Error("Missing required values for DE workflow");
+    }
+    return run(
+      getDeSeq2LandingUrl(
+        workflow.workflowId,
+        configuredValue.referenceAssembly,
+        configuredValue.geneModelUrl,
+        configuredValue.sampleSheet,
+        configuredValue.sampleSheetClassification,
+        configuredValue.designFormula,
+        configuredValue.primaryContrasts,
+        configuredValue.strandedness,
+        origin
+      )
+    );
+  }
+
+  return run(
+    getWorkflowLandingUrl(
+      workflow.trsId,
+      isAssemblyConfiguredValue(configuredValue)
+        ? configuredValue.referenceAssembly
+        : "",
+      isAssemblyConfiguredValue(configuredValue)
+        ? configuredValue.geneModelUrl
+        : null,
+      configuredValue.readRunsSingle,
+      configuredValue.readRunsPaired,
+      null,
+      workflow.parameters,
+      origin
+    )
+  );
+}
+
 export const useLaunchGalaxy = ({
   configuredInput,
   workflow,
@@ -27,79 +133,17 @@ export const useLaunchGalaxy = ({
     if (!configuredValue) return;
     const origin = config.browserURL || window.location.origin;
 
-    let landingUrl = "";
-
-    if (workflow.trsId === CUSTOM_WORKFLOW.trsId) {
-      landingUrl = await run(
-        getDataLandingUrl(
-          configuredValue.referenceAssembly,
-          configuredValue.geneModelUrl,
-          configuredValue.readRunsSingle,
-          configuredValue.readRunsPaired,
-          null, // fastaCollection - not yet supported in UI
-          configuredValue.tracks,
-          origin
-        )
-      );
-    } else if (
-      workflow.trsId === LOGAN_SEARCH.trsId ||
-      workflow.trsId === LEXICMAP.trsId
-    ) {
-      // LMLS workflows use stored workflow IDs with sequence and numberOfHits parameters
-      if (!workflow.workflowId) {
-        throw new Error("Missing workflow ID for LMLS workflow");
-      }
-      landingUrl = await run(
-        getLMLSLandingUrl(
-          workflow.workflowId,
-          configuredValue.numberOfHits!,
-          configuredValue.sequence!,
-          origin
-        )
-      );
-    } else if (workflow.trsId === DIFFERENTIAL_EXPRESSION_ANALYSIS.trsId) {
-      if (
-        !workflow.workflowId ||
-        !configuredValue.geneModelUrl ||
-        !configuredValue.sampleSheet ||
-        !configuredValue.sampleSheetClassification ||
-        !configuredValue.designFormula
-      ) {
-        throw new Error("Missing required values for DE workflow");
-      }
-      landingUrl = await run(
-        getDeSeq2LandingUrl(
-          workflow.workflowId,
-          configuredValue.referenceAssembly,
-          configuredValue.geneModelUrl,
-          configuredValue.sampleSheet,
-          configuredValue.sampleSheetClassification,
-          configuredValue.designFormula,
-          configuredValue.primaryContrasts,
-          configuredValue.strandedness,
-          origin
-        )
-      );
-    } else {
-      landingUrl = await run(
-        getWorkflowLandingUrl(
-          workflow.trsId,
-          configuredValue.referenceAssembly,
-          configuredValue.geneModelUrl,
-          configuredValue.readRunsSingle,
-          configuredValue.readRunsPaired,
-          null, // fastaCollection - not yet supported in UI
-          workflow.parameters,
-          origin
-        )
-      );
-    }
+    const landingUrl = await getLandingUrlForWorkflow(
+      workflow,
+      configuredValue,
+      origin,
+      run
+    );
 
     if (!landingUrl) {
       throw new Error("Failed to retrieve Galaxy workflow launch URL.");
     }
 
-    // Launch the Galaxy workflow.
     launchGalaxy(landingUrl);
   }, [config, configuredValue, run, workflow]);