feat: add differential expression workflow under feature flag (#1054)

app/components/Entity/components/AnalysisMethod/components/DifferentialExpressionAnalysis/constants.ts

@@ -0,0 +1,13 @@
+import { WORKFLOW_PLOIDY } from "../../../../../../apis/catalog/brc-analytics-catalog/common/schema-entities";
+import { Workflow } from "../../../../../../apis/catalog/brc-analytics-catalog/common/entities";
+
+export const DIFFERENTIAL_EXPRESSION_ANALYSIS: Workflow = {
+  iwcId: "",
+  parameters: [],
+  ploidy: WORKFLOW_PLOIDY.ANY,
+  taxonomyId: null,
+  trsId: "differential-expression-analysis",
+  workflowDescription:
+    "Analyze differential gene expression from raw reads to DE results.",
+  workflowName: "Differential Expression Analysis",
+};

app/components/Entity/components/AnalysisMethod/components/WorkflowAccordion/types.ts

@@ -0,0 +1,7 @@
+import { Workflow } from "../../../../../../apis/catalog/brc-analytics-catalog/common/entities";
+
+export interface Props {
+  buttonText?: string;
+  entityId: string;
+  workflow: Workflow;
+}

app/components/Entity/components/AnalysisMethod/components/CustomWorkflow/customWorkflow.tsx → app/components/Entity/components/AnalysisMethod/components/WorkflowAccordion/workflowAccordion.tsx

@@ -17,12 +17,15 @@ import { ROUTES } from "../../../../../../../routes/constants";
 import { replaceParameters } from "@databiosphere/findable-ui/lib/utils/replaceParameters";
 import { TYPOGRAPHY_PROPS } from "@databiosphere/findable-ui/lib/styles/common/mui/typography";
 import { FluidPaper } from "@databiosphere/findable-ui/lib/components/common/Paper/components/FluidPaper/fluidPaper";
-import { CUSTOM_WORKFLOW } from "./constants";
-import { StyledAccordion } from "./customWorkflow.styles";
+import { StyledAccordion } from "./workflowAccordion.styles";
 import { ChevronRightRounded } from "@mui/icons-material";
 
-export const CustomWorkflow = ({ entityId }: Props): JSX.Element => {
-  const { trsId, workflowDescription, workflowName } = CUSTOM_WORKFLOW;
+export const WorkflowAccordion = ({
+  buttonText = "Select Data",
+  entityId,
+  workflow,
+}: Props): JSX.Element => {
+  const { trsId, workflowDescription, workflowName } = workflow;
   return (
     <StyledAccordion component={FluidPaper}>
       <AccordionSummary
@@ -50,7 +53,7 @@ export const CustomWorkflow = ({ entityId }: Props): JSX.Element => {
           })}
           rel={REL_ATTRIBUTE.NO_OPENER}
         >
-          Select Data
+          {buttonText}
         </Button>
       </AccordionDetails>
     </StyledAccordion>

app/components/Entity/components/AnalysisMethodsCatalog/analysisMethodsCatalog.tsx

@@ -2,11 +2,14 @@ import { AnalysisMethod } from "../AnalysisMethod/analysisMethod";
 import { Props } from "./types";
 import { useRouter } from "next/router";
 import { Fragment } from "react";
-import { CustomWorkflow } from "../AnalysisMethod/components/CustomWorkflow/customWorkflow";
+import { WorkflowAccordion } from "../AnalysisMethod/components/WorkflowAccordion/workflowAccordion";
+import { CUSTOM_WORKFLOW } from "../AnalysisMethod/components/CustomWorkflow/constants";
+import { DIFFERENTIAL_EXPRESSION_ANALYSIS } from "../AnalysisMethod/components/DifferentialExpressionAnalysis/constants";
 import { AnalysisTypeHeader } from "./components/AnalysisTypeHeader/analysisTypeHeader";
 import { Stack } from "@mui/material";
 import { buildAssemblyWorkflows } from "./utils";
 import WORKFLOW_CATEGORIES from "../../../../../catalog/output/workflows.json";
+import { useFeatureFlag } from "@databiosphere/findable-ui/lib/hooks/useFeatureFlag/useFeatureFlag";
 
 export const AnalysisMethodsCatalog = ({ assembly }: Props): JSX.Element => {
   const workflowCategories = buildAssemblyWorkflows(
@@ -18,6 +21,8 @@ export const AnalysisMethodsCatalog = ({ assembly }: Props): JSX.Element => {
     query: { entityId },
   } = useRouter();
 
+  const isDEEnabled = useFeatureFlag("de");
+
   return (
     <Stack gap={8} useFlexGap>
       {/* Custom Analysis */}
@@ -26,7 +31,10 @@ export const AnalysisMethodsCatalog = ({ assembly }: Props): JSX.Element => {
           description="Prefer to explore the data without a predefined workflow?"
           title="Custom Analysis"
         />
-        <CustomWorkflow entityId={entityId as string} />
+        <WorkflowAccordion
+          entityId={entityId as string}
+          workflow={CUSTOM_WORKFLOW}
+        />
       </Stack>
       <Stack gap={4} useFlexGap>
         {/* Workflow Analysis */}
@@ -49,6 +57,13 @@ export const AnalysisMethodsCatalog = ({ assembly }: Props): JSX.Element => {
           }
           title="Select a Workflow"
         />
+        {isDEEnabled && (
+          <WorkflowAccordion
+            buttonText="Configure Inputs"
+            entityId={entityId as string}
+            workflow={DIFFERENTIAL_EXPRESSION_ANALYSIS}
+          />
+        )}
         {workflowCategories.map((workflowCategory) => {
           return (
             <AnalysisMethod

app/components/Entity/components/ConfigureWorkflowInputs/components/Main/components/Stepper/steps/utils.ts

@@ -4,6 +4,7 @@ import { StepConfig } from "../components/Step/types";
 import { STEP } from "./constants";
 import { CUSTOM_WORKFLOW } from "../../../../../../../../../components/Entity/components/AnalysisMethod/components/CustomWorkflow/constants";
 import { ConfiguredInput } from "../../../../../../../../../views/WorkflowInputsView/hooks/UseConfigureInputs/types";
+import { DIFFERENTIAL_EXPRESSION_ANALYSIS } from "../../../../../../AnalysisMethod/components/DifferentialExpressionAnalysis/constants";
 
 /**
  * Augment the configured steps with two additional sequencing steps "READ_RUNS_PAIRED" and "READ_RUNS_SINGLE".
@@ -42,6 +43,11 @@ export function buildSteps(workflow: Workflow): StepConfig[] {
     );
   }
 
+  // Return steps for differential expression analysis
+  if (workflow.trsId === DIFFERENTIAL_EXPRESSION_ANALYSIS.trsId) {
+    return [STEP.ASSEMBLY_ID, STEP.GENE_MODEL_URL].filter(isStepConfigured);
+  }
+
   // Get workflow variables from the workflow.
   const variables = workflow.parameters
     .map((param) => param.variable)

app/services/workflows/loader.ts

@@ -8,6 +8,7 @@ import {
 } from "../../apis/catalog/brc-analytics-catalog/common/entities";
 import { formatTrsId } from "../../components/Entity/components/AnalysisMethodsCatalog/utils";
 import { CUSTOM_WORKFLOW } from "../../components/Entity/components/AnalysisMethod/components/CustomWorkflow/constants";
+import { DIFFERENTIAL_EXPRESSION_ANALYSIS } from "../../components/Entity/components/AnalysisMethod/components/DifferentialExpressionAnalysis/constants";
 
 /**
  * Fetches entities from the API.
@@ -81,6 +82,12 @@ export async function loadWorkflows(): Promise<void> {
   // Add custom workflow.
   workflowById.set(CUSTOM_WORKFLOW.trsId, CUSTOM_WORKFLOW);
 
+  // Add differential expression analysis.
+  workflowById.set(
+    DIFFERENTIAL_EXPRESSION_ANALYSIS.trsId,
+    DIFFERENTIAL_EXPRESSION_ANALYSIS
+  );
+
   setEntitiesById("workflows", workflowById);
   setEntitiesByType("workflows", workflowCategories);
 }

app/views/WorkflowInputsView/workflowInputsView.tsx

@@ -9,6 +9,9 @@ import { augmentConfiguredSteps } from "../../components/Entity/components/Confi
 import { SEQUENCING_STEPS } from "../../components/Entity/components/ConfigureWorkflowInputs/components/Main/components/Stepper/steps/constants";
 import { getAssembly } from "../../services/workflows/entities";
 import { getWorkflow } from "../../services/workflows/entities";
+import { useFeatureFlag } from "@databiosphere/findable-ui/lib/hooks/useFeatureFlag/useFeatureFlag";
+import Error from "next/error";
+import { DIFFERENTIAL_EXPRESSION_ANALYSIS } from "../../components/Entity/components/AnalysisMethod/components/DifferentialExpressionAnalysis/constants";
 
 export const WorkflowInputsView = ({ entityId, trsId }: Props): JSX.Element => {
   const genome = getAssembly<Assembly>(entityId);
@@ -17,6 +20,11 @@ export const WorkflowInputsView = ({ entityId, trsId }: Props): JSX.Element => {
   const { configuredInput, onConfigure } = useConfigureInputs();
   const { configuredSteps } = useConfiguredSteps(workflow);
 
+  const isDEEnabled = useFeatureFlag("de");
+
+  if (!isDEEnabled && workflow.trsId === DIFFERENTIAL_EXPRESSION_ANALYSIS.trsId)
+    return <Error statusCode={404} />;
+
   return (
     <Detail
       mainColumn={

pages/_app.tsx

@@ -23,6 +23,7 @@ import { GoogleSignInAuthenticationProvider } from "@databiosphere/findable-ui/l
 import { ServicesProvider } from "@databiosphere/findable-ui/lib/providers/services/provider";
 import "../app/styles/fonts/fonts.css";
 import { useEntities } from "../app/services/workflows/hooks/UseEntities/hook";
+import { setFeatureFlags } from "@databiosphere/findable-ui/lib/hooks/useFeatureFlag/common/utils";
 
 const DEFAULT_ENTITY_LIST_TYPE = "organisms";
 
@@ -40,6 +41,8 @@ export type AppPropsWithComponent = AppProps & {
   pageProps: PageProps;
 };
 
+setFeatureFlags(["de"]);
+
 function MyApp({ Component, pageProps }: AppPropsWithComponent): JSX.Element {
   // Set up the site configuration, layout and theme.
   const appConfig = config();

pages/data/[entityListType]/[entityId]/[trsId]/index.tsx

@@ -20,6 +20,7 @@ import {
 import { WorkflowInputsView } from "../../../../../app/views/WorkflowInputsView/workflowInputsView";
 import { GA2AssemblyEntity } from "../../../../../app/apis/catalog/ga2/entities";
 import { CUSTOM_WORKFLOW } from "../../../../../app/components/Entity/components/AnalysisMethod/components/CustomWorkflow/constants";
+import { DIFFERENTIAL_EXPRESSION_ANALYSIS } from "../../../../../app/components/Entity/components/AnalysisMethod/components/DifferentialExpressionAnalysis/constants";
 
 interface StaticPath {
   params: PageUrlParams;
@@ -110,6 +111,15 @@ function processEntityPaths(
       },
     });
 
+    // Create differential expression analysis path.
+    paths.push({
+      params: {
+        entityId,
+        entityListType,
+        trsId: DIFFERENTIAL_EXPRESSION_ANALYSIS.trsId,
+      },
+    });
+
     // Create paths for each compatible workflow.
     compatibleWorkflows.forEach((workflow) => {
       // Format the trsId for URL use