Codegen queries.py

entities/Makefile

@@ -52,15 +52,20 @@ local-tests: ## Run entities tests
 	$(docker_compose_run) entities bash -c "poetry run pytest -s"
 	$(MAKE) cerbos-tests
 
-CODEGEN_TO_LINT = database/models/ api/types/ cli/gql_schema.py
+DIR_LINT_CODEGEN = database/models/ api/types/
+DIR_LINT_GRAPHQL = cli/gql_schema.py
 .PHONY: codegen
 codegen:  ## Update the GQL types used by the CLI
 	$(docker_compose) exec entities python3 codegen/generator.py api generate --schemafile schema/platformics.yaml --output-prefix .
+	$(docker_compose_run) $(FOLDER) black $(DIR_LINT_CODEGEN)
+	$(docker_compose_run) $(FOLDER) ruff check --fix $(DIR_LINT_CODEGEN)
+
 	$(docker_compose_run) entities strawberry export-schema api.main:schema > api/schema.graphql
 	$(docker_compose) exec entities python3 -m sgqlc.introspection --exclude-deprecated --exclude-description http://localhost:8008/graphql api/schema.json
 	$(docker_compose) exec entities sgqlc-codegen schema api/schema.json cli/gql_schema.py
-	$(docker_compose_run) $(FOLDER) black $(CODEGEN_TO_LINT)
-	$(docker_compose_run) $(FOLDER) ruff check --fix $(CODEGEN_TO_LINT)
+	$(docker_compose_run) $(FOLDER) black $(DIR_LINT_GRAPHQL)
+	$(docker_compose_run) $(FOLDER) ruff check --fix $(DIR_LINT_GRAPHQL)
+
 	$(docker_compose) exec entities gen-erdiagram schema/platformics.yaml > schema/README.md
 
 ### CERBOS #############################################

entities/api/queries.py

@@ -1,19 +1,46 @@
-import typing
+# Auto-generated by running 'make codegen'. Do not edit.
+# Make changes to the template codegen/templates/api/queries.py.j2 instead.
+
 import strawberry
 from strawberry import relay
+from typing import Sequence
+from api.files import File, resolve_files
 from api.types.sample import Sample, resolve_sample
 from api.types.sequencing_read import SequencingRead, resolve_sequencing_read
+from api.types.genomic_range import GenomicRange, resolve_genomic_range
+from api.types.reference_genome import ReferenceGenome, resolve_reference_genome
+from api.types.sequence_alignment_index import SequenceAlignmentIndex, resolve_sequence_alignment_index
+from api.types.metadatum import Metadatum, resolve_metadatum
+from api.types.metadata_field import MetadataField, resolve_metadata_field
+from api.types.metadata_field_project import MetadataFieldProject, resolve_metadata_field_project
+from api.types.consensus_genome import ConsensusGenome, resolve_consensus_genome
+from api.types.metric_consensus_genome import MetricConsensusGenome, resolve_metric_consensus_genome
+from api.types.coverage_viz import CoverageViz, resolve_coverage_viz
+from api.types.taxon import Taxon, resolve_taxon
+from api.types.upstream_database import UpstreamDatabase, resolve_upstream_database
 from api.types.contig import Contig, resolve_contig
-from api.files import File, resolve_files
 
 
 @strawberry.type
 class Query:
     # Allow queries by node ID
     node: relay.Node = relay.node()
 
-    # Queries for each entity
-    samples: typing.Sequence[Sample] = resolve_sample
-    sequencing_reads: typing.Sequence[SequencingRead] = resolve_sequencing_read
-    contigs: typing.Sequence[Contig] = resolve_contig
-    files: typing.Sequence[File] = resolve_files
+    # Query files
+    files: Sequence[File] = resolve_files
+
+    # Query entities
+    sample: Sequence[Sample] = resolve_sample
+    sequencing_read: Sequence[SequencingRead] = resolve_sequencing_read
+    genomic_range: Sequence[GenomicRange] = resolve_genomic_range
+    reference_genome: Sequence[ReferenceGenome] = resolve_reference_genome
+    sequence_alignment_index: Sequence[SequenceAlignmentIndex] = resolve_sequence_alignment_index
+    metadatum: Sequence[Metadatum] = resolve_metadatum
+    metadata_field: Sequence[MetadataField] = resolve_metadata_field
+    metadata_field_project: Sequence[MetadataFieldProject] = resolve_metadata_field_project
+    consensus_genome: Sequence[ConsensusGenome] = resolve_consensus_genome
+    metric_consensus_genome: Sequence[MetricConsensusGenome] = resolve_metric_consensus_genome
+    coverage_viz: Sequence[CoverageViz] = resolve_coverage_viz
+    taxon: Sequence[Taxon] = resolve_taxon
+    upstream_database: Sequence[UpstreamDatabase] = resolve_upstream_database
+    contig: Sequence[Contig] = resolve_contig