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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
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Pull Request Overview
This PR adds a GraphQL API layer to the MARRVEL server, providing unified access to various genomic databases including Clinvar, genes, DIOPT, phenotype ontology, Pharos, and STRING protein-protein interactions.
Key changes:
- Added GraphQL dependencies (
graphql,graphql-http,ruru) and upgraded Express to v4.21.2 - Implemented GraphQL schemas and resolvers for Clinvar, genes, DIOPT, phenotype ontology, Pharos, and STRING databases
- Configured GraphQL endpoint at
/graphqlwith GraphiQL interface at/graphiqlfor development
Reviewed Changes
Copilot reviewed 18 out of 19 changed files in this pull request and generated 1 comment.
Show a summary per file
| File | Description |
|---|---|
| server/package.json | Added GraphQL dependencies and upgraded Express |
| server/package-lock.json | Updated lock file with new dependencies |
| server/models/string-interactions.model.js | Added Mongoose model for STRING protein-protein interactions |
| server/graphql/schemas/*.graphql | Defined GraphQL type definitions for all data sources |
| server/graphql/resolvers/*.resolvers.js | Implemented resolver functions for GraphQL queries |
| server/graphql/graphqlHandler.js | Main GraphQL handler that combines schemas and resolvers |
| server/graphql/index.js | Module entry point and documentation |
| server/graphql/README.md | Comprehensive API documentation with examples |
| server/app.js | Integrated GraphQL endpoints into Express application |
Files not reviewed (1)
- server/package-lock.json: Language not supported
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Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
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