Merge branch 'main' into feature/backend-infrastructure

Author: dannon

.linkmllint.yaml

@@ -1,4 +1,4 @@
 extends: recommended
 rules:
   standard_naming:
-    permissible_values_upper_case: true
+    level: disabled

@types/theme.d.ts

@@ -4,11 +4,21 @@ import { PaletteColorOptions } from "@mui/material/styles";
  * Palette definitions.
  */
 declare module "@mui/material/styles" {
+  interface BrandColors {
+    accent: string;
+    burntSienna: string;
+    darkSienna: string;
+    rawSienna: string;
+    surface: string;
+  }
+
   interface Palette {
+    brand: BrandColors;
     caution: PaletteColor;
   }
 
   interface PaletteOptions {
+    brand?: Partial<BrandColors>;
     caution?: PaletteColorOptions;
   }
 }

app/apis/catalog/brc-analytics-catalog/common/entities.ts

@@ -1,11 +1,11 @@
 import { MDXRemoteSerializeResult } from "next-mdx-remote";
-import { WorkflowUrlParameter } from "../../../../utils/galaxy-api/entities";
 import {
   ORGANISM_PLOIDY,
   OUTBREAK_PRIORITY,
   OUTBREAK_RESOURCE_TYPE,
   WORKFLOW_PARAMETER_VARIABLE,
   WORKFLOW_PLOIDY,
+  WorkflowUrlSpec,
 } from "./schema-entities";
 
 export type BRCCatalog =
@@ -123,8 +123,16 @@ export interface Workflow {
   workflowName: string;
 }
 
+export interface WorkflowDataRequirements {
+  description?: string;
+  library_layout?: string;
+  library_source?: string[];
+  library_strategy?: string[];
+}
+
 export interface WorkflowParameter {
+  data_requirements?: WorkflowDataRequirements;
   key: string;
-  url_spec?: WorkflowUrlParameter;
+  url_spec?: WorkflowUrlSpec;
   variable?: WORKFLOW_PARAMETER_VARIABLE;
 }

app/apis/catalog/brc-analytics-catalog/common/schema-entities.ts

@@ -4,4 +4,5 @@ export {
   OutbreakResourceType as OUTBREAK_RESOURCE_TYPE,
   WorkflowParameterVariable as WORKFLOW_PARAMETER_VARIABLE,
   WorkflowPloidy as WORKFLOW_PLOIDY,
+  type WorkflowUrlSpec,
 } from "../../../../../catalog/schema/generated/schema";

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

@@ -0,0 +1,21 @@
+import {
+  WORKFLOW_PLOIDY,
+  WORKFLOW_PARAMETER_VARIABLE,
+} from "../../../../../../apis/catalog/brc-analytics-catalog/common/schema-entities";
+import { Workflow } from "../../../../../../apis/catalog/brc-analytics-catalog/common/entities";
+
+export const CUSTOM_WORKFLOW: Workflow = {
+  iwcId: "",
+  parameters: [
+    {
+      key: "Reference annotation",
+      variable: WORKFLOW_PARAMETER_VARIABLE.GENE_MODEL_URL,
+    },
+  ],
+  ploidy: WORKFLOW_PLOIDY.ANY,
+  taxonomyId: null,
+  trsId: "custom-workflow",
+  workflowDescription:
+    "Analyze selected data in the context of this assembly in your own Galaxy workflow.",
+  workflowName: "Custom / No Workflow",
+};

app/components/Entity/components/AnalysisMethod/components/CustomWorkflow/customWorkflow.tsx

@@ -0,0 +1,41 @@
+import { Button, Stack, Typography } from "@mui/material";
+import { Props } from "./types";
+import { StyledGrid } from "../Workflow/workflow.styles";
+import { BUTTON_PROPS, GRID_PROPS } from "../Workflow/constants";
+import { TYPOGRAPHY_PROPS as COMPONENT_TYPOGRAPHY_PROPS } from "../../constants";
+import { REL_ATTRIBUTE } from "@databiosphere/findable-ui/lib/components/Links/common/entities";
+import Link from "next/link";
+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";
+
+export const CustomWorkflow = ({ entityId }: Props): JSX.Element => {
+  const { trsId, workflowDescription, workflowName } = CUSTOM_WORKFLOW;
+  return (
+    <FluidPaper>
+      <StyledGrid {...GRID_PROPS}>
+        <Stack spacing={1}>
+          <Typography variant={TYPOGRAPHY_PROPS.VARIANT.HEADING_XSMALL}>
+            {workflowName}
+          </Typography>
+          <Typography {...COMPONENT_TYPOGRAPHY_PROPS}>
+            {workflowDescription}
+          </Typography>
+        </Stack>
+        <Button
+          {...BUTTON_PROPS}
+          component={Link}
+          href={replaceParameters(ROUTES.CONFIGURE_WORKFLOW, {
+            entityId,
+            trsId,
+          })}
+          rel={REL_ATTRIBUTE.NO_OPENER}
+        >
+          Select Data
+        </Button>
+      </StyledGrid>
+    </FluidPaper>
+  );
+};

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

@@ -0,0 +1,3 @@
+export interface Props {
+  entityId: string;
+}

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

@@ -2,17 +2,21 @@ import workflows from "../../../../../catalog/output/workflows.json";
 import { AnalysisMethod } from "../AnalysisMethod/analysisMethod";
 import { Props } from "./types";
 import { workflowIsCompatibleWithAssembly } from "./utils";
-
 import { useRouter } from "next/router";
 import { Fragment } from "react";
+import { useFeatureFlag } from "@databiosphere/findable-ui/lib/hooks/useFeatureFlag/useFeatureFlag";
+import { CustomWorkflow } from "../AnalysisMethod/components/CustomWorkflow/customWorkflow";
 
 export const AnalysisMethodsCatalog = ({ assembly }: Props): JSX.Element => {
+  const isFeatureEnabled = useFeatureFlag("custom-workflow");
+
   const {
     query: { entityId },
   } = useRouter();
 
   return (
     <Fragment>
+      {isFeatureEnabled && <CustomWorkflow entityId={entityId as string} />}
       {workflows.map((workflowCategory) => {
         const compatibleWorkflows = workflowCategory.workflows.filter(
           (workflow) => workflowIsCompatibleWithAssembly(workflow, assembly)

app/components/Entity/components/ConfigureWorkflowInputs/components/Main/components/Stepper/components/Step/GTFStep/gtfStep.tsx

@@ -50,7 +50,7 @@ export const GTFStep = ({
   // Empty string represents "user will provide in Galaxy" similar to how sequencing steps use empty arrays
   useEffect(() => {
     if (error && active) {
-      onConfigure(STEP.key, ""); // Use empty string instead of null
+      onConfigure({ [STEP.key]: "" }); // Use empty string instead of null
     }
   }, [error, active, onConfigure]);
 
@@ -91,7 +91,7 @@ export const GTFStep = ({
                 <FormControlLabel
                   control={<Radio />}
                   key={i}
-                  onChange={() => onConfigure(STEP.key, value)}
+                  onChange={() => onConfigure({ [STEP.key]: value })}
                   label={label}
                   value={value}
                 />

app/components/Entity/components/ConfigureWorkflowInputs/components/Main/components/Stepper/components/Step/GTFStep/utils.ts

@@ -18,7 +18,7 @@ export const configureGTFStep = (
 
   // Gene model URLs are not available for this workflow.
   if (geneModelUrls.length === 0) {
-    onConfigure(STEP.key, null);
+    onConfigure({ [STEP.key]: null });
     return;
   }
 
@@ -32,7 +32,7 @@ export const configureGTFStep = (
   if (!value) return;
 
   // Otherwise, use the gene model to configure the step.
-  onConfigure(STEP.key, value);
+  onConfigure({ [STEP.key]: value });
 };
 
 /**