Synchronization: SubClassOf

src/ontology/mondo-ingest.Makefile

@@ -321,7 +321,7 @@ documentation: j2 $(ALL_DOCS) unmapped-terms-docs mapped-deprecated-terms-docs s
 build-mondo-ingest:
 	$(MAKE) refresh-imports exclusions-all mondo-ingest.db slurp-all mappings matches \
 		mapped-deprecated-terms mapping-progress-report \
-		recreate-unmapped-components documentation
+		recreate-unmapped-components sync documentation
 	$(MAKE) prepare_release
 
 .PHONY: build-mondo-ingest-no-imports
@@ -502,6 +502,19 @@ slurp-all-no-updates: $(foreach n,$(ALL_COMPONENT_IDS), slurp-no-updates-$(n))
 .PHONY: slurp-all
 slurp-all: $(foreach n,$(ALL_COMPONENT_IDS), slurp-$(n))
 
+
+#############################
+###### Synchronization ######
+#############################
+.PHONY: sync
+sync: sync-subclassof
+
+.PHONY: sync-subclassof
+sync-subclassof: reports/sync-subclassof.robot.template.tsv
+
+reports/sync-subclassof.robot.template.tsv: tmp/merged.db
+	python3 $(SCRIPTSDIR)/sync_subclassof.py --ontology-db tmp/merged.db --outpath $@
+
 #############################
 ######### Analysis ##########
 #############################

src/scripts/sync_subclassof.py

@@ -0,0 +1,38 @@
+"""Create a robot template for purpose of syncing subclassof relations.
+
+Resources
+- GitHub issue: https://github.com/monarch-initiative/mondo-ingest/issues/92
+- GitHub PR: https://github.com/monarch-initiative/mondo-ingest/pull/363
+"""
+from argparse import ArgumentParser
+
+# import curies
+import pandas as pd
+from oaklib import get_implementation_from_shorthand
+# from oaklib.types import CURIE, URI
+# from sssom.util import is_curie
+
+# from utils import remove_angle_brackets
+
+
+def sync_subclassof():
+    """Run"""
+    pass
+
+
+# TODO: --ontology-db tmp/merged.db --outpath reports/sync-subclassof.robot.template.tsv
+def cli():
+    """Command line interface."""
+    parser = ArgumentParser('Create a robot template for purpose of syncing subclassof relations.')
+    parser.add_argument('-d', '--db-path', required=True, help='')
+    parser.add_argument(
+        '-o', '--outpath', required=True,
+        help='')
+    parser.add_argument(
+        '-d', '--ontology-db', required=True,
+        help='Path to SemanticSQL sqlite ONTO_NAME.db.')
+    sync_subclassof(**vars(parser.parse_args()))
+
+
+if __name__ == '__main__':
+    cli()