Add missing queries

src/indra_cogex/apps/queries_web/cli.py

@@ -2,7 +2,7 @@
 from more_click import make_web_command
 
 from indra_cogex.apps.constants import INDRA_COGEX_EXTENSION
-from indra_cogex.apps.queries_web import api
+from indra_cogex.apps.rest_api import api
 from indra_cogex.client import Neo4jClient
 
 app = Flask(__name__)

src/indra_cogex/apps/rest_api.py

@@ -1,17 +1,61 @@
 from flask_restx import Api
-
 from .bioentity.api import bioentity_ns
-from .queries_web import query_ns
 
-__all__ = [
-    "api",
-]
+# Import and add namespaces after api is created
+from .queries_web import (
+    gene_expression_ns,
+    go_terms_ns,
+    clinical_trials_ns,
+    biological_pathways_ns,
+    drug_side_effects_ns,
+    ontology_ns,
+    literature_metadata_ns,
+    statements_ns,
+    drug_targets_ns,
+    cell_markers_ns,
+    disease_phenotypes_ns,
+    gene_disease_variant_ns,
+    research_project_output_ns,
+    gene_domains_ns,
+    phenotype_variant_ns,
+    drug_indications_ns,
+    gene_codependence_ns,
+    enzyme_activity_ns,
+    cell_line_properties_ns,
+    analysis_ns,
+    subnetwork_ns
+)
+
 
 api = Api(
     title="INDRA CoGEx Query API",
     description="REST API for INDRA CoGEx queries",
     doc="/apidocs",
 )
 
-api.add_namespace(query_ns)
+
+# Add all namespaces
+api.add_namespace(gene_expression_ns)
+api.add_namespace(go_terms_ns)
+api.add_namespace(clinical_trials_ns)
+api.add_namespace(biological_pathways_ns)
+api.add_namespace(drug_side_effects_ns)
+api.add_namespace(ontology_ns)
+api.add_namespace(literature_metadata_ns)
+api.add_namespace(statements_ns)
+api.add_namespace(drug_targets_ns)
+api.add_namespace(cell_markers_ns)
+api.add_namespace(disease_phenotypes_ns)
+api.add_namespace(gene_disease_variant_ns)
+api.add_namespace(research_project_output_ns)
+api.add_namespace(gene_domains_ns)
+api.add_namespace(phenotype_variant_ns)
+api.add_namespace(drug_indications_ns)
+api.add_namespace(gene_codependence_ns)
+api.add_namespace(enzyme_activity_ns)
+api.add_namespace(cell_line_properties_ns)
+api.add_namespace(analysis_ns)
+api.add_namespace(subnetwork_ns)
 api.add_namespace(bioentity_ns)
+
+__all__ = ["api"]

src/indra_cogex/client/neo4j_client.py

@@ -1151,8 +1151,6 @@ def do_cypher_tx(
 ) -> List[List]:
     # 'parameters' and '**kwparameters' of tx.run are ultimately merged at query
     # run-time
-
-    # Execute the query
     result = tx.run(query, parameters=query_params)
-    # Return the result
     return [record.values() for record in result]
+