Merge pull request #609 from monarch-initiative/add-maxo-and-go-quali…

…fiers Add species context qualifier, update closurizer
monarch-initiative · Nov 19, 2024 · a4894f4 · a4894f4
2 parents 4d2eb7a + 3fd0aa5
commit a4894f4
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Showing 4 changed files with 72 additions and 54 deletions.
diff --git a/poetry.lock b/poetry.lock
diff --git a/pyproject.toml 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
@@ -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
@@ -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"],