feat/graphql: add dbNSFP #59
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* Introduced a new GraphQL API endpoint for flexible data querying * Enabled the GraphiQL playground interface in non-production environments
Added ClinVar schema and corresponding resolver to the GraphQL API, enabling ClinVar data querying through the GraphQL endpoint.
Added Gene schema and resolver to the GraphQL API, enabling gene-level queries.
* Added DIOPT-related GraphQL support: * DioptOrtholog * DioptDomain * DioptAlignment * Implemented resolvers to enable querying these DIOPT data structures.
Add comprehensive Pharos target, drug, and ligand GraphQL schemas and resolver
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
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Pull Request Overview
This PR adds comprehensive GraphQL API support to the MARRVEL server, providing a modern query interface for genomic data alongside the existing REST API. The changes include GraphQL schemas, resolvers, and dependencies for multiple data sources including Clinvar, genes, DIOPT, phenotype ontology, Pharos, STRING, and dbNSFP.
Key changes:
- Added GraphQL dependencies:
graphql,graphql-http, andrurufor GraphiQL interface - Implemented GraphQL schemas and resolvers for 7 data sources
- Configured GraphQL endpoint at
/graphqland development GraphiQL interface at/graphiql
Reviewed Changes
Copilot reviewed 20 out of 21 changed files in this pull request and generated 1 comment.
Show a summary per file
| File | Description |
|---|---|
| server/package.json | Added graphql, graphql-http, ruru dependencies; upgraded express to ^4.21.2 |
| server/package-lock.json | Lockfile updates for new dependencies and transitive packages |
| server/graphql/index.js | Entry point and module documentation for GraphQL API |
| server/graphql/graphqlHandler.js | Main GraphQL handler combining schemas and resolvers |
| server/graphql/schemas/*.graphql | Type definitions for 7 data sources |
| server/graphql/resolvers/*.js | Resolver implementations for all queries |
| server/models/string-interactions.model.js | Mongoose model for STRING protein interactions |
| server/graphql/README.md | Comprehensive API documentation with examples |
| server/app.js | Registered GraphQL routes and GraphiQL interface |
Files not reviewed (1)
- server/package-lock.json: Language not supported
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