Feat/graphql #58
Merged
Feat/graphql #58
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
* 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
Contributor
There was a problem hiding this comment.
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
💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
No description provided.