[WidgetsMCP]: First look at the open targets widgets-mcp

.gitignore

@@ -1,5 +1,7 @@
 # See https://help.github.com/articles/ignoring-files/ for more about ignoring files.
 
+apps/mcp-widgets-server/.env
+.claude/
 # dependencies
 node_modules
 .pnp

apps/mcp-widgets-server/.dockerignore

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+# Build context is the monorepo root.
+# Paths here are relative to the repo root.
+
+# Dependencies (reinstalled inside the image)
+node_modules
+**/node_modules
+
+# Other apps — only mcp-widgets-server is needed
+apps/platform/
+apps/platform-test/
+
+# Package sources not needed at server runtime
+packages/ui/src
+packages/ot-config/src
+packages/ot-constants/src
+packages/ot-utils/src
+packages/tsconfig/
+
+# Widget build artifacts that are not the pre-built bundles
+apps/mcp-widgets-server/widget-src/
+apps/mcp-widgets-server/vite/
+apps/mcp-widgets-server/scripts/
+apps/mcp-widgets-server/certs/
+
+# Misc
+**/.DS_Store
+**/*.swp
+**/.env
+**/.env.local
+**/npm-debug.log*
+**/yarn-debug.log*
+**/yarn-error.log*
+.git/

apps/mcp-widgets-server/.env.example

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+# GraphQL endpoint for data prefetch (server-side) and widget runtime (browser-side)
+OT_API_URL=https://dev.opentargets.xyz/api/v4/graphql

apps/mcp-widgets-server/.gitignore

@@ -0,0 +1,2 @@
+.env
+dist/

apps/mcp-widgets-server/Dockerfile

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+# ── Stage 1: Install dependencies ─────────────────────────────────────────────
+# Yarn v1 workspaces require all workspace package.json files to be present
+# so the lockfile resolves correctly. We copy only manifests here so that
+# dependency installation is cached independently of source changes.
+FROM node:22-alpine AS deps
+
+WORKDIR /app
+
+COPY package.json yarn.lock ./
+
+# Workspace package manifests (source not needed — server doesn't import them at runtime)
+COPY apps/mcp-widgets-server/package.json   apps/mcp-widgets-server/
+COPY packages/ui/package.json               packages/ui/
+COPY packages/sections/package.json         packages/sections/
+COPY packages/ot-config/package.json        packages/ot-config/
+COPY packages/ot-constants/package.json     packages/ot-constants/
+COPY packages/ot-utils/package.json         packages/ot-utils/
+COPY packages/tsconfig/package.json         packages/tsconfig/
+COPY packages/platform-test/package.json    packages/platform-test/
+
+# Install all deps (including devDeps — tsx is needed at runtime)
+RUN yarn install --frozen-lockfile --ignore-scripts
+
+# ── Stage 2: Runtime ──────────────────────────────────────────────────────────
+FROM node:22-alpine
+
+WORKDIR /app
+
+# Bring in installed node_modules from the deps stage
+COPY --from=deps /app/node_modules ./node_modules
+
+# Server TypeScript source
+COPY apps/mcp-widgets-server/src   apps/mcp-widgets-server/src
+
+# Pre-built widget IIFE bundles (built locally, committed to the repo)
+COPY apps/mcp-widgets-server/dist  apps/mcp-widgets-server/dist
+
+# GQL query files — read at startup by loadSectionQuery to auto-detect operation names.
+# Only .gql files are needed; .tsx source is not used at server runtime.
+COPY packages/sections/src         packages/sections/src
+
+# Profile config scripts — read per-request by makeWidgetShell (OT_PROFILE env var
+# picks "platform" or "ppp") and inlined into every widget's HTML shell.
+COPY apps/platform/public/profiles apps/platform/public/profiles
+
+# Cloud Run injects PORT (default 8080). OT_API_URL can be overridden at deploy time.
+ENV PORT=8080
+ENV NODE_ENV=production
+
+EXPOSE 8080
+
+CMD ["node_modules/.bin/tsx", "apps/mcp-widgets-server/src/index.ts"]

apps/mcp-widgets-server/WIDGETS.md

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+# MCP Widgets Server — Architecture & Widget Registry
+
+## Directory Structure
+
+```
+apps/mcp-widgets-server/
+├── src/                        # Server-side Node.js code (runs in Claude Desktop / MCP host)
+│   ├── sections/
+│   │   └── registry.ts         # Single source of truth: all section widget definitions
+│   ├── widgets/
+│   │   ├── index.ts            # Widget registry builder + sectionPathToId utility
+│   │   ├── molecular-structure.ts  # Manual widget def (AlphaFold 3D viewer)
+│   │   └── types.ts            # WidgetDef type
+│   ├── mcp-server.ts           # MCP tool + resource registration, widget HTML shell, CSP
+│   ├── index.ts                # Server entrypoint
+│   └── stdio.ts                # stdio MCP transport
+│
+├── widget-src/                 # Browser-side React code (compiled to IIFE bundles)
+│   ├── molecular-structure/    # Custom 3D viewer React app (only custom widget entry)
+│   └── shared/
+│       ├── createWidgetEntry.tsx  # mountWidget() — React root bootstrapper for all widgets
+│       └── stubs/
+│           ├── ui-index.tsx    # Stub replacements for @ot/ui barrel (used by all section widgets)
+│           └── ui-ms-index.tsx # Stub/real mix for molecular-structure widget (includes real Viewer providers)
+│
+└── vite/                       # Build tooling
+    ├── widget.config.base.ts   # Shared Vite config factory + Vite plugins
+    ├── section-widget.plugin.ts # Auto-generates entry code + Vite config for section widgets
+    └── widget.config.ms.ts     # Custom Vite config for molecular-structure widget
+```
+
+### `src/` vs `widget-src/` — the key distinction
+
+| | `src/` | `widget-src/` |
+|---|---|---|
+| **Runs in** | Node.js (server / MCP host) | Browser (iframe inside Claude Desktop) |
+| **Purpose** | Registers MCP tools, serves the widget HTML shell + CSP allowlist | React components compiled into self-contained IIFE bundles |
+| **Output** | Running MCP server process | `dist/widgets/*.js` IIFE bundle files |
+| **Build tool** | `tsx` (TypeScript execution) | Vite (browser bundle) |
+
+When Claude calls an MCP tool, `src/mcp-server.ts` serves the widget HTML shell (bundle inlined)
+as an MCP App resource, with `_meta.ui.csp.connectDomains` allowlisting the GraphQL API origin
+(and any extra origins the widget needs, via `WidgetDef.extraConnectDomains`). The widget's own
+Apollo client then fetches data directly from the iframe — there is no server-side prefetch.
+
+---
+
+## How to add a new section widget
+
+1. Add an entry to `src/sections/registry.ts`
+2. Run `yarn build:widgets:<entity>` (or `yarn build:widgets` for all)
+3. Restart Claude Desktop
+
+If the section fetches anything beyond the OT GraphQL API (e.g. a third-party CDN), set
+`extraConnectDomains` on the `SectionDef` entry itself (see `target/Bibliography`,
+`evidence/EuropePmc`, `target/SubcellularLocation`, or `target/MolecularStructure` for examples).
+
+If the section imports a package directly rather than through a shared `ui` wrapper (e.g. `3dmol`),
+set `extraDedupe` too — see `target/MolecularStructure`. Before adding a new section, check it for
+components that import platform modules (`Link`, `useConfigContext`, etc.) via a **relative path**
+rather than the `"ui"` barrel — those bypass the widget stubs in `widget-src/shared/stubs/` and need
+handling at the Vite-plugin level (`createPlatformStubsPlugin` in `vite/widget.config.base.ts`), not
+just a barrel re-export. This bit `PublicationWrapper`/`ConfigurationProvider`/`Link` and
+`OtAsyncTooltip`/`OtGenomicLocation` during the initial migration — grep the section's files for
+`^import` and check anything not going through `"ui"`.
+
+---
+
+## Included section widgets (69 total)
+
+### Target (18 sections)
+
+| Tool name | Section | Input | Notes |
+|-----------|---------|-------|-------|
+| `get_target_cancer_hallmarks_widget` | `target/CancerHallmarks` | `ensemblId` | |
+| `get_target_chemical_probes_widget` | `target/ChemicalProbes` | `ensemblId` | |
+| `get_target_comparative_genomics_widget` | `target/ComparativeGenomics` | `ensemblId` | |
+| `get_target_depmap_widget` | `target/DepMap` | `ensemblId` | |
+| `get_target_drugs_widget` | `target/Drugs` | `ensemblId` | |
+| `get_target_baseline_expression_widget` | `target/BaselineExpression` | `ensemblId` | |
+| `get_target_bibliography_widget` | `target/Bibliography` | `ensemblId` | |
+| `get_target_gene_ontology_widget` | `target/GeneOntology` | `ensemblId` | |
+| `get_target_genetic_constraint_widget` | `target/GeneticConstraint` | `ensemblId` | |
+| `get_target_molecular_interactions_widget` | `target/MolecularInteractions` | `ensemblId` | |
+| `get_target_molecular_structure_widget` | `target/MolecularStructure` | `ensemblId` | Experimental PDB + AlphaFold viewer; raw `3dmol` usage (`extraDedupe`) and 3 extra CSP domains (UniProt, AlphaFold, PDBe) — distinct from the manual `variant/MolecularStructure` widget |
+| `get_target_mouse_phenotypes_widget` | `target/MousePhenotypes` | `ensemblId` | |
+| `get_target_pathways_widget` | `target/Pathways` | `ensemblId` | |
+| `get_target_pharmacogenomics_widget` | `target/Pharmacogenomics` | `ensemblId` | |
+| `get_target_qtl_credible_sets_widget` | `target/QTLCredibleSets` | `ensemblId` | |
+| `get_target_safety_widget` | `target/Safety` | `ensemblId` | |
+| `get_target_subcellular_location_widget` | `target/SubcellularLocation` | `ensemblId` | |
+| `get_target_tractability_widget` | `target/Tractability` | `ensemblId` | |
+
+### Disease (6 sections)
+
+| Tool name | Section | Input |
+|-----------|---------|-------|
+| `get_disease_drugs_widget` | `disease/Drugs` | `efoId` |
+| `get_disease_bibliography_widget` | `disease/Bibliography` | `efoId` |
+| `get_disease_gwas_studies_widget` | `disease/GWASStudies` | `efoId` |
+| `get_disease_ot_projects_widget` | `disease/OTProjects` | `efoId` |
+| `get_disease_ontology_widget` | `disease/Ontology` | `efoId` |
+| `get_disease_phenotypes_widget` | `disease/Phenotypes` | `efoId` |
+
+### Drug (6 sections)
+
+| Tool name | Section | Input | Notes |
+|-----------|---------|-------|-------|
+| `get_drug_adverse_events_widget` | `drug/AdverseEvents` | `chemblId` | |
+| `get_drug_bibliography_widget` | `drug/Bibliography` | `chemblId` | |
+| `get_drug_indications_widget` | `drug/Indications` | `chemblId` | Two-query: indications + `ClinicalRecordsQuery` (filtered on row click) |
+| `get_drug_warnings_widget` | `drug/DrugWarnings` | `chemblId` | |
+| `get_drug_mechanisms_of_action_widget` | `drug/MechanismsOfAction` | `chemblId` | |
+| `get_drug_pharmacogenomics_widget` | `drug/Pharmacogenomics` | `chemblId` | |
+
+### Evidence (23 sections)
+
+| Tool name | Section | Input | Notes |
+|-----------|---------|-------|-------|
+| `get_evidence_crispr_widget` | `evidence/CRISPR` | `ensemblId` + `efoId` | |
+| `get_evidence_crispr_screen_widget` | `evidence/CRISPRScreen` | `ensemblId` + `efoId` | |
+| `get_evidence_cancer_biomarkers_widget` | `evidence/CancerBiomarkers` | `ensemblId` + `efoId` | |
+| `get_evidence_cancer_gene_census_widget` | `evidence/CancerGeneCensus` | `ensemblId` + `efoId` | |
+| `get_evidence_chembl_widget` | `evidence/Chembl` | `ensemblId` + `efoId` | |
+| `get_evidence_clingen_widget` | `evidence/ClinGen` | `ensemblId` + `efoId` | |
+| `get_evidence_eva_widget` | `evidence/EVA` | `ensemblId` + `efoId` | |
+| `get_evidence_eva_somatic_widget` | `evidence/EVASomatic` | `ensemblId` + `efoId` | |
+| `get_evidence_europe_pmc_widget` | `evidence/EuropePmc` | `ensemblId` + `efoId` | Fetches publication details directly from EuropePMC (extra CSP `connectDomains`) |
+| `get_evidence_expression_atlas_widget` | `evidence/ExpressionAtlas` | `ensemblId` + `efoId` | |
+| `get_evidence_gwas_credible_sets_widget` | `evidence/GWASCredibleSets` | `ensemblId` + `efoId` | |
+| `get_evidence_gene2phenotype_widget` | `evidence/Gene2Phenotype` | `ensemblId` + `efoId` | |
+| `get_evidence_gene_burden_widget` | `evidence/GeneBurden` | `ensemblId` + `efoId` | |
+| `get_evidence_genomics_england_widget` | `evidence/GenomicsEngland` | `ensemblId` + `efoId` | |
+| `get_evidence_impc_widget` | `evidence/Impc` | `ensemblId` + `efoId` | |
+| `get_evidence_intogen_widget` | `evidence/IntOgen` | `ensemblId` + `efoId` | |
+| `get_evidence_ot_crispr_widget` | `evidence/OTCRISPR` | `ensemblId` + `efoId` | |
+| `get_evidence_ot_encore_widget` | `evidence/OTEncore` | `ensemblId` + `efoId` | |
+| `get_evidence_ot_validation_widget` | `evidence/OTValidation` | `ensemblId` + `efoId` | |
+| `get_evidence_orphanet_widget` | `evidence/Orphanet` | `ensemblId` + `efoId` | |
+| `get_evidence_reactome_widget` | `evidence/Reactome` | `ensemblId` + `efoId` | |
+| `get_evidence_uniprot_literature_widget` | `evidence/UniProtLiterature` | `ensemblId` + `efoId` | |
+| `get_evidence_uniprot_variants_widget` | `evidence/UniProtVariants` | `ensemblId` + `efoId` | |
+
+### Credible Set (5 sections)
+
+| Tool name | Section | Input |
+|-----------|---------|-------|
+| `get_l2g_widget` | `credibleSet/Locus2Gene` | `studyLocusId` |
+| `get_credible_set_gwas_coloc_widget` | `credibleSet/GWASColoc` | `studyLocusId` |
+| `get_credible_set_mol_qtl_coloc_widget` | `credibleSet/MolQTLColoc` | `studyLocusId` |
+| `get_credible_set_variants_widget` | `credibleSet/Variants` | `studyLocusId` |
+| `get_credible_set_e2g_widget` | `credibleSet/EnhancerToGenePredictions` | `studyLocusId` |
+
+### Study (3 sections)
+
+| Tool name | Section | Input | Notes |
+|-----------|---------|-------|-------|
+| `get_gwas_credible_sets_widget` | `study/GWASCredibleSets` | `studyId` | |
+| `get_study_qtl_credible_sets_widget` | `study/QTLCredibleSets` | `studyId` | |
+| `get_shared_trait_studies_widget` | `study/SharedTraitStudies` | `studyId` | Two-query: fetches disease IDs first, then queries studies by `diseaseIds` |
+
+### Variant (8 sections)
+
+| Tool name | Section | Input |
+|-----------|---------|-------|
+| `get_variant_effect_widget` | `variant/VariantEffect` | `variantId` |
+| `get_variant_eva_widget` | `variant/EVA` | `variantId` |
+| `get_variant_e2g_widget` | `variant/EnhancerToGenePredictions` | `variantId` |
+| `get_variant_gwas_credible_sets_widget` | `variant/GWASCredibleSets` | `variantId` |
+| `get_variant_pharmacogenomics_widget` | `variant/Pharmacogenomics` | `variantId` |
+| `get_variant_qtl_credible_sets_widget` | `variant/QTLCredibleSets` | `variantId` |
+| `get_variant_uniprot_widget` | `variant/UniProtVariants` | `variantId` |
+| `get_variant_vep_widget` | `variant/VariantEffectPredictor` | `variantId` |
+
+### Manual widgets (custom entry points)
+
+| Tool name | Section | Notes |
+|-----------|---------|-------|
+| `get_molecular_structure_widget` | `variant/MolecularStructure` | Custom 3D AlphaFold viewer; fetches CIF/pathogenicity/domain data directly from AlphaFold + UniProt (extra CSP `connectDomains`) |
+
+---
+
+## Excluded sections
+
+These sections exist in `packages/sections/src` but are not in the registry.
+
+| Section | Entity | Reason excluded |
+|---------|--------|-----------------|
+| `variant/MolecularStructure` | Variant | Covered by `get_molecular_structure_widget` (manual) |
+
+Note: `target/Bibliography`, `disease/Bibliography`, `drug/Bibliography`, `disease/GWASStudies`, `target/MolecularInteractions`, `target/SubcellularLocation`, `evidence/EuropePmc`, and `target/MolecularStructure` were previously listed here but turned out not to be real blockers. The first four were mostly documentation drift — the widget entry codegen just renders `Body` directly and lets it fetch its own data, so cursor pagination and array-shaped GraphQL variables inside `Body` don't matter. `MolecularInteractions` needed a one-line `usePlatformApi()` stub fix; `SubcellularLocation` and `EuropePmc` needed one `extraConnectDomains` entry each. `target/MolecularStructure` was a genuine miscategorization — it was claimed to be "covered by the manual widget," but it's a distinct component (its own experimental-PDB + AlphaFold viewer, own CIF parser) live on the platform (unlike `target/OverlappingVariants` below); it needed new per-section `extraDedupe` support (for its direct `3dmol` usage) plus 3 CSP domains. All eight are now in the registry above — every excluded section that's actually live on the platform has been migrated.
+
+Note: `target/OverlappingVariants` was previously listed here but is out of scope entirely — it's not rendered on the real Open Targets Platform (disabled/commented out in `apps/platform/src/pages/TargetPage/Profile.tsx`), so there's no live platform widget to migrate.

apps/mcp-widgets-server/package.json

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+{
+  "name": "mcp-widgets-server",
+  "version": "0.1.0",
+  "private": true,
+  "type": "module",
+  "scripts": {
+    "dev": "tsx watch --env-file=.env src/index.ts",
+    "dev-ppp": "OT_API_URL=https://api.partner-platform.opentargets.org/api/v4/graphql OTP_MCP_URL=https://mcp.partner-platform.opentargets.org/mcp tsx watch --env-file=.env src/index.ts",
+    "start": "tsx src/index.ts",
+    "start:stdio": "tsx src/stdio.ts",
+    "build:widget:ms": "vite build --config vite/widget.config.ms.ts",
+    "build:widgets": "yarn build:widget:ms && yarn build:widgets:target && yarn build:widgets:disease && yarn build:widgets:drug && yarn build:widgets:evidence && yarn build:widgets:credibleset && yarn build:widgets:variant && yarn build:widgets:study",
+    "build:widgets:target": "tsx scripts/build-sections.ts target --no-clean",
+    "build:widgets:disease": "tsx scripts/build-sections.ts disease --no-clean",
+    "build:widgets:drug": "tsx scripts/build-sections.ts drug --no-clean",
+    "build:widgets:evidence": "tsx scripts/build-sections.ts evidence --no-clean",
+    "build:widgets:credibleset": "tsx scripts/build-sections.ts credibleSet --no-clean",
+    "build:widgets:variant": "tsx scripts/build-sections.ts variant --no-clean",
+    "build:widgets:study": "tsx scripts/build-sections.ts study --no-clean",
+    "build:widgets:sections": "tsx scripts/build-sections.ts all --no-clean",
+    "build": "yarn build:widgets"
+  },
+  "dependencies": {
+    "@modelcontextprotocol/ext-apps": "*",
+    "@modelcontextprotocol/sdk": "^1.26.0",
+    "cors": "^2.8.5",
+    "express": "^4.21.2",
+    "tsx": "^4.7.0",
+    "zod": "^3.22.0"
+  },
+  "devDependencies": {
+    "@apollo/client": "3.10.8",
+    "@types/cors": "^2.8.17",
+    "@types/express": "^4.17.21",
+    "@types/node": "^20.0.0",
+    "@types/react": "^18.0.0",
+    "@types/react-dom": "^18.0.0",
+    "@vitejs/plugin-react": "^4.0.0",
+    "d3": "*",
+    "graphql": "^15.0.0",
+    "polished": "^4.3.1",
+    "react": "^18.0.0",
+    "react-dom": "^18.0.0",
+    "react-router-dom": "6.28.0",
+    "typescript": "^5.2.2",
+    "vite": "^6.0.0"
+  }
+}

apps/mcp-widgets-server/scripts/build-sections.ts

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+/**
+ * Build all section-based MCP widget bundles for a given entity.
+ *
+ * Usage:
+ *   yarn build:widgets:target    # builds all target section widgets
+ *   yarn build:widgets:drug      # builds all drug section widgets
+ *   yarn build:widgets:evidence  # builds all evidence section widgets
+ *   yarn build:widgets:all       # builds everything (existing + sections)
+ *
+ * Bundles are emitted to dist/widgets/ (same directory as the manual widgets).
+ * The first section widget of each run clears the directory; subsequent ones append.
+ * Pass --no-clean to skip cleaning (useful when building multiple entities sequentially).
+ */
+import { build } from "vite";
+import { SECTION_REGISTRY } from "../src/sections/registry.js";
+import { createSectionWidgetConfig } from "../vite/section-widget.plugin.js";
+
+const entity = process.argv[2];
+const noClean = process.argv.includes("--no-clean");
+
+if (!entity || entity === "--help") {
+  console.log("Usage: tsx scripts/build-sections.ts <entity|all> [--no-clean]");
+  console.log("  entity: target | disease | drug | evidence | credibleSet | variant | study | all");
+  process.exit(entity ? 0 : 1);
+}
+
+const sections =
+  entity === "all"
+    ? SECTION_REGISTRY
+    : SECTION_REGISTRY.filter(s => s.entity === entity);
+
+if (sections.length === 0) {
+  console.error(`No sections found for entity: ${entity}`);
+  process.exit(1);
+}
+
+console.log(`Building ${sections.length} ${entity} widget${sections.length > 1 ? "s" : ""}…`);
+
+for (let i = 0; i < sections.length; i++) {
+  const def = sections[i];
+  const emptyOutDir = i === 0 && !noClean;
+  console.log(`  [${i + 1}/${sections.length}] ${def.toolName}`);
+  await build({
+    ...createSectionWidgetConfig(def, { emptyOutDir }),
+    logLevel: "warn",
+  });
+}
+
+console.log("Done.");