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b/pyproject.toml @@ -19,7 +19,7 @@ python = "^3.10" biolink-model = "^4.2.0" bmt = "^1.0.15" cat-merge = "0.2.1" -closurizer = "0.5.1" +closurizer = "0.7.0" kghub-downloader = "^0.3.10" kgx = "^2.4.2" koza = "^0.6.1" diff --git a/scripts/load_solr.sh b/scripts/load_solr.sh index 5c490680..93f24ea6 100755 --- a/scripts/load_solr.sh +++ b/scripts/load_solr.sh @@ -19,8 +19,8 @@ echo "Download the schema from monarch-py" # retrieve the schema from the main branch on monarch-app -curl -O https://raw.githubusercontent.com/monarch-initiative/monarch-app/add-disease-context-qualifier/backend/src/monarch_py/datamodels/model.yaml -curl -O https://raw.githubusercontent.com/monarch-initiative/monarch-app/add-disease-context-qualifier/backend/src/monarch_py/datamodels/similarity.yaml +curl -O https://raw.githubusercontent.com/monarch-initiative/monarch-app/add-species-context-qualifier/backend/src/monarch_py/datamodels/model.yaml +curl -O https://raw.githubusercontent.com/monarch-initiative/monarch-app/add-species-context-qualifier/backend/src/monarch_py/datamodels/similarity.yaml echo "Starting the server" poetry run lsolr start-server diff --git a/src/monarch_ingest/cli_utils.py b/src/monarch_ingest/cli_utils.py index 3f776a51..67f4fa31 100644 --- a/src/monarch_ingest/cli_utils.py +++ b/src/monarch_ingest/cli_utils.py @@ -390,15 +390,20 @@ def apply_closure( closure_file=closure_file, edges_output_file=edges_output_file, nodes_output_file=nodes_output_file, + # full closure expansion for these fields edge_fields=[ "subject", "object", + "disease_context_qualifier", + ], + # just populate _label, _category, _namespace properties for these fields + edge_fields_to_label=[ "qualifiers", - "frequency_qualifier", - "onset_qualifier", - "sex_qualifier", + "species_context_qualifier", "stage_qualifier", - "disease_context_qualifier" + "sex_qualifier", + "onset_qualifier", + "frequency_qualifier", ], node_fields=["has_phenotype"], evidence_fields=["has_evidence", "publications"],