The RCSB PDB GraphQL service for amino/nucleic acid and identifier mapping among multiple sequence resources. The service integrates pairwise sequence alignments including NCBI (genome and proteins), UniProt and PDB. In addition, sequence annotations can be mapped among the different sequence references. The service exposes blocking and reactive operations.
The project is divided in 3 modules:
org.rcsb.graphqlschema: Contains the interface and type definitions for the service endpoints queries and responses. At project build time GrapQL schema is built from these definitions (org.rcsb.graphqlschema.schema.SchemaGenerator).org.rcsb.rcsbsequencecoordinates: Defines the Spring Boot application based on GraphQL, reactive streams and RSocket.configuration: The GraphQL service uses a custom wiring factorGraphqlWiringFactory. Data objects are defined as documents (org.bson.Document). The wiring factory defines the right way of accessing the GraphQL schema fields in data objects.controller: Defines the different GraphQL entry points for alignments and annotations requests. Some of the GrapQL schema fields are mapped to specific entry points using the@SchemaMappingannotation.
org.rcsb.collector: Contains the methods to fetch alignments and annotations from a MongoDB. Data is always dispatched as streams.
Configuration happens through the usual rcsb config method (from the
rcsb-util package). Pass the configuration directory
with -DrcsbConfigProfile=<URL>. The rcsb-sequence-coordinates config file must be called
borrego.app.properties.
The properties are:
| Property | Action |
|---|---|
aw.mongodb.db.name |
Set the DB name for the annotations warehouse DB. |
aw.mongodb.uri |
Set the MongoDB connection URI (including host, username and password) for the AWH. |
The GraphQL schema builder is based on the libray:
- graphql-spqr: creation of GraphQL schema from POJOs
without annotations. graphql-spqr also provides annotations to implement wiring for the data.
See class
GraphQLService. The POJOs used are those inorg.rcsb.mojave.autoandorg.rcsb.graphqlschema.responsepackages. The json annotations in those POJOs are ignored by graphql-spqr, for instance camel to snake case is done via a specific transformation implemented by us.
All contributions are welcome. Please, make a pull request or open an issue.
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