KPMP-6538: added code to return the ontology id to cell type mapping#205
KPMP-6538: added code to return the ontology id to cell type mapping#205
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WalkthroughIntroduces Hubmap cell type mapping feature with new JPA entity, repository, and service for building ID-to-cell-type maps. Extends QueryController to expose GraphQL query endpoint. Updates build configuration and removes unused imports. Changes
Sequence DiagramsequenceDiagram
actor Client
participant GraphQL as GraphQL API
participant QueryController
participant HubmapCellTypeMappingService
participant HubmapOnotologyCellTypeRepository
participant Database
Client->>GraphQL: getHubmapTermMap()
GraphQL->>QueryController: getHubmapTermMap()
QueryController->>HubmapCellTypeMappingService: buildHubmapIdToCellTypeMap()
HubmapCellTypeMappingService->>HubmapOnotologyCellTypeRepository: findAll()
HubmapOnotologyCellTypeRepository->>Database: SELECT * FROM humbapOntology_celltype_v
Database-->>HubmapOnotologyCellTypeRepository: HubmapOntologyCellType list
HubmapOnotologyCellTypeRepository-->>HubmapCellTypeMappingService: cached result
HubmapCellTypeMappingService->>HubmapCellTypeMappingService: build Map<hubmapOntologyId, cell_type>
HubmapCellTypeMappingService-->>QueryController: Map<String, String>
QueryController-->>GraphQL: Map<String, String>
GraphQL-->>Client: JSON response
✨ Finishing Touches
🧪 Generate unit tests (beta)
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Actionable comments posted: 3
🧹 Nitpick comments (1)
src/main/java/org/kpmp/cellType/HubmapOnotologyCellTypeRepository.java (1)
11-11: Rename repository type to fix spelling (Onotology→Ontology).The current type name is misspelled and will propagate across service/tests. Please rename to
HubmapOntologyCellTypeRepositoryfor maintainability.
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📒 Files selected for processing (13)
.classpath.java-versionsrc/main/java/org/kpmp/QueryController.javasrc/main/java/org/kpmp/cellType/HubmapCellTypeMappingService.javasrc/main/java/org/kpmp/cellType/HubmapOnotologyCellTypeRepository.javasrc/main/java/org/kpmp/cellType/HubmapOntologyCellType.javasrc/main/java/org/kpmp/cellTypeSummary/ClusterHiearchyRepository.javasrc/main/java/org/kpmp/cellTypeSummary/ClusterHierarchy.javasrc/main/java/org/kpmp/umap/SNMetadataRepository2025.javasrc/main/resources/graphql/knowledge_environment.graphqlssrc/test/java/org/kpmp/QueryControllerTest.javasrc/test/java/org/kpmp/cellType/HubmapCellTypeMappingServiceTest.javasrc/test/java/org/kpmp/cellType/HubmapOntologyCellTypeTest.java
💤 Files with no reviewable changes (3)
- src/main/java/org/kpmp/cellTypeSummary/ClusterHierarchy.java
- src/main/java/org/kpmp/umap/SNMetadataRepository2025.java
- src/main/java/org/kpmp/cellTypeSummary/ClusterHiearchyRepository.java
| import jakarta.persistence.Table; | ||
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| @Entity | ||
| @Table(name = "humbapOntology_celltype_v") |
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Fix @Table name annotation: typo "humbap" should be "hubmap".
The table name humbapOntology_celltype_v contains a typo. The class name, field names, methods, service names, and cache key all consistently use hubmap, not humbap. This mismatch will cause JPA to fail mapping the entity to the database table at runtime.
| @@ -1,3 +1,5 @@ | |||
| scalar JSON | |||
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Add JSON scalar wiring to resolve schema at runtime.
The scalar JSON declaration requires explicit wiring to function. GraphQL Java does not auto-register custom scalars, and no scalar configuration was found in the codebase (no ExtendedScalars, GraphQLScalarType, or RuntimeWiringConfigurer). Without wiring, query execution will fail with scalar serialization errors.
Register the JSON scalar in your GraphQL schema provider or configuration bean using ExtendedScalars.Json or a custom GraphQLScalarType.
| getAtlasMessages: [AtlasMessages] | ||
| getExperimentalStrategyCountsByParticipant(redcapId: String!): [ParticipantRepoDataTypeInformation] | ||
| getParticipantClinicalDataset(redcapId: String!): ParticipantClinicalDataset | ||
| getHubmapTermMap(): JSON |
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🌐 Web query:
GraphQL SDL field definition empty argument list () syntax specification
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In GraphQL SDL, a field’s argument definitions cannot use an empty parentheses list ().
Per the spec grammar:
FieldDefinition : ... Name ArgumentsDefinition? : Type ...(spec.graphql.org)ArgumentsDefinition : ( InputValueDefinition list )(spec.graphql.org)Symbol listmeans one or more occurrences (not zero). (spec.graphql.org)
So field(): String is invalid SDL; omit the parentheses instead: field: String.
Citations:
- 1: https://spec.graphql.org/June2018/
- 2: https://spec.graphql.org/June2018/
- 3: https://spec.graphql.org/June2018/
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Remove empty argument list from GraphQL field definition.
getHubmapTermMap(): JSON violates GraphQL SDL specification. Per the spec, ArgumentsDefinition requires one or more arguments when parentheses are present; no-argument fields must omit the parentheses entirely.
Fix
- getHubmapTermMap(): JSON
+ getHubmapTermMap: JSON📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| getHubmapTermMap(): JSON | |
| getHubmapTermMap: JSON |
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