chore: deploy v0.16.0 to production (#914)

## Production Deployment: v0.16.0

This PR deploys release v0.16.0 to production.

### Release Highlights
- 32 new features (including GA2 enhancements, workflow improvements, UI
updates)
- 4 bug fixes
- 2 maintenance updates

### Full Release Notes
https://github.com/galaxyproject/brc-analytics/releases/tag/v0.16.0

### Deployment Impact
Once merged to `production`, this will trigger the automatic production
deployment workflow.

Author: dannon

.github/workflows/run-checks.yml

@@ -37,6 +37,12 @@ jobs:
       - name: Test LinkML Python generation
         # Generate Python code from the main LinkML schemas, discarding the output; this will catch more subtle errors such as references to nonexistent elements.
         run: npm run test-gen-python
-      - name: Validate catalog files
+      - name: Validate BRC catalog files
         # Validate the catalog source files against their corresponding LinkML schemas.
-        run: npm run validate-catalog
+        run: npm run validate-brc-catalog
+      - name: Validate GA2 catalog files
+        # Validate the GA2 catalog source files.
+        run: npm run validate-ga2-catalog
+      - name: poetry lint
+        # Validate the GA2 catalog source files.
+        run: poetry check -P catalog/py_package/

.github/workflows/update-catalog.yml

@@ -27,7 +27,7 @@ jobs:
       - name: Install npm dependencies
         run: npm ci
       - name: Run catalog script
-        run: npm run build-files-from-ncbi
+        run: npm run build-brc-from-ncbi
       - name: Get current date
         id: date
         run: echo "date=$(date +'%Y-%m-%d')" >> $GITHUB_OUTPUT

.prettierignore

@@ -19,4 +19,5 @@ venv
 
 #catalog
 /catalog/output
+/catalog/ga2/output
 /catalog/schema/generated

@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;
   }
 }

README.md

@@ -29,7 +29,7 @@ pip install -r ./catalog/build/py/requirements.txt
 Then run the script:
 
 ```shell
-npm run build-files-from-ncbi
+npm run build-brc-from-ncbi
 ```
 
 The environment can be deactivated by running `deactivate`, and re-activated by running `source ./venv/bin/activate`

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

@@ -1,3 +1,4 @@
+import { sanitizeEntityId } from "../../common/utils";
 import { BRCDataCatalogGenome, BRCDataCatalogOrganism } from "./entities";
 import { ORGANISM_PLOIDY, WORKFLOW_PLOIDY } from "./schema-entities";
 
@@ -23,11 +24,6 @@ export function getGenomeOrganismId(genome: BRCDataCatalogGenome): string {
   return sanitizeEntityId(genome.speciesTaxonomyId);
 }
 
-export function sanitizeEntityId(entityId?: string): string {
-  if (!entityId) return "";
-  return entityId.replace(/\./g, "_");
-}
-
 /**
  * Get whether a given workflow ploidy is compatible with a given organism ploidy.
  * @param workflowPloidy - Workflow ploidy.

app/apis/catalog/common/utils.ts

@@ -0,0 +1,9 @@
+/**
+ * Sanitize an entity ID by replacing all periods with underscores.
+ * @param entityId - Entity ID.
+ * @returns sanitized entity ID.
+ */
+export function sanitizeEntityId(entityId?: string): string {
+  if (!entityId) return "";
+  return entityId.replace(/\./g, "_");
+}

app/apis/catalog/ga2/entities.ts

@@ -0,0 +1,69 @@
+import { ORGANISM_PLOIDY } from "../brc-analytics-catalog/common/schema-entities";
+
+export type GA2Catalog = GA2AssemblyEntity | GA2OrganismEntity;
+
+export interface GA2AssemblyEntity {
+  accession: string;
+  annotationStatus: string | null;
+  chromosomes: number | null;
+  coverage: string | null;
+  gcPercent: number | null;
+  geneModelUrl: string | null;
+  isRef: "No" | "Yes";
+  length: number;
+  level: string;
+  lineageTaxonomyIds: string[];
+  ncbiTaxonomyId: string;
+  ploidy: ORGANISM_PLOIDY[];
+  scaffoldCount: number | null;
+  scaffoldL50: number | null;
+  scaffoldN50: number | null;
+  speciesTaxonomyId: string;
+  sra_data: SRAData[];
+  strainName: string | null;
+  taxonomicGroup: string[];
+  taxonomicLevelClass: string;
+  taxonomicLevelDomain: string;
+  taxonomicLevelFamily: string;
+  taxonomicLevelGenus: string;
+  taxonomicLevelKingdom: string;
+  taxonomicLevelOrder: string;
+  taxonomicLevelPhylum: string;
+  taxonomicLevelSpecies: string;
+  taxonomicLevelStrain: string;
+  tolId: string;
+  ucscBrowserUrl: string | null;
+}
+
+export interface GA2OrganismEntity {
+  assemblyCount: number;
+  assemblyTaxonomyIds: string[];
+  genomes: GA2AssemblyEntity[];
+  maxScaffoldN50: number | null;
+  ncbiTaxonomyId: string;
+  taxonomicGroup: string[];
+  taxonomicLevelClass: string;
+  taxonomicLevelDomain: string;
+  taxonomicLevelFamily: string;
+  taxonomicLevelGenus: string;
+  taxonomicLevelKingdom: string;
+  taxonomicLevelOrder: string;
+  taxonomicLevelPhylum: string;
+  taxonomicLevelSpecies: string;
+  tolId: string;
+}
+
+export interface SRAData {
+  accession: string;
+  biosample: string;
+  instrument: string;
+  library_layout: string;
+  library_source: string;
+  library_strategy: string;
+  platform: string;
+  run_total_bases: number | null;
+  sra_run_acc: string;
+  sra_sample_acc: string;
+  sra_study_acc: string;
+  total_bases: number | null;
+}

app/apis/catalog/ga2/utils.ts

@@ -0,0 +1,29 @@
+import { sanitizeEntityId } from "../common/utils";
+import { GA2AssemblyEntity, GA2OrganismEntity } from "./entities";
+
+/**
+ * Get the ID of the given assembly entity.
+ * @param entity - Entity.
+ * @returns entity ID.
+ */
+export function getAssemblyId(entity?: GA2AssemblyEntity): string {
+  return sanitizeEntityId(entity?.accession);
+}
+
+/**
+ * Get the title of the given assembly entity.
+ * @param entity - Entity.
+ * @returns entity title.
+ */
+export function getAssemblyTitle(entity?: GA2AssemblyEntity): string {
+  return entity?.taxonomicLevelSpecies || "";
+}
+
+/**
+ * Get the ID of the given organism entity.
+ * @param entity - Entity.
+ * @returns entity ID.
+ */
+export function getOrganismId(entity?: GA2OrganismEntity): string {
+  return entity?.ncbiTaxonomyId || "";
+}

app/components/Entity/components/AnalysisMethodsCatalog/utils.ts

@@ -3,6 +3,7 @@ import {
   BRCDataCatalogGenome,
   Workflow,
 } from "../../../../apis/catalog/brc-analytics-catalog/common/entities";
+import { GA2AssemblyEntity } from "../../../../apis/catalog/ga2/entities";
 
 /**
  * Formats a trsId for use in URLs by removing the hash character if it begins with one
@@ -22,7 +23,7 @@ export function formatTrsId(trsId: string): string {
  */
 export function workflowIsCompatibleWithAssembly(
   workflow: Workflow,
-  assembly: BRCDataCatalogGenome
+  assembly: BRCDataCatalogGenome | GA2AssemblyEntity
 ): boolean {
   if (
     workflow.taxonomyId !== null &&