Feature: Exclusion tables

- Update: TODOs - Update: Utilizing `base_prefix_map` now instead of `prefix_map` from ontology metadata `.yml` files. - Update: get-terms-children.sparql.jinja2: Always using rdfs:subClassOf* instead of a + at the end. Updated Python code to reflect. - Update: Makefile target: Now explicitly passes params again. - Added: New exclusion files: ORDO, DO. Still pending NCIT after resolving Java heap space issue.
monarch-initiative · Jul 25, 2022 · 8497809 · 8497809
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commit 8497809
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diff --git a/src/ontology/config/doid_exclusion_reasons.robot.template.tsv b/src/ontology/config/doid_exclusion_reasons.robot.template.tsv
diff --git a/src/ontology/config/doid_term_exclusions.txt b/src/ontology/config/doid_term_exclusions.txt
diff --git a/src/ontology/config/ordo_exclusion_reasons.robot.template.tsv b/src/ontology/config/ordo_exclusion_reasons.robot.template.tsv
diff --git a/src/ontology/config/ordo_term_exclusions.txt b/src/ontology/config/ordo_term_exclusions.txt
diff --git a/src/ontology/mondo-ingest.Makefile b/src/ontology/mondo-ingest.Makefile
@@ -172,8 +172,14 @@ update-jinja-sparql-queries: python-install-dependencies
 	python3 $(SCRIPTSDIR)/ordo_mapping_annotations/create_sparql__ordo_replace_annotation_based_mappings.py
 	python3 $(SCRIPTSDIR)/ordo_mapping_annotations/create_sparql__ordo_mapping_annotations_violation.py
 
-config/%_term_exclusions.txt: config/%_exclusions.tsv component-download-%.owl $(TMPDIR)/%_relevant_signature.txt python-install-dependencies
-	python3 $(SCRIPTSDIR)/exclusion_term_expansion.py --onto-name $*
+config/%_term_exclusions.txt: config/%_exclusions.tsv component-download-%.owl $(REPORTDIR)/mirror_signature-%.tsv $(REPORTDIR)/component_signature-%.tsv metadata/%.yml python-install-dependencies
+	python3 $(SCRIPTSDIR)/exclusion_term_expansion.py \
+	--onto-name $* \
+	--exclusions-path $(word 1,$^) \
+	--onto-path $(TMPDIR)/$(word 2,$^).owl \
+	--mirror-signature-path $(word 3,$^) \
+	--component-signature-path $(word 4,$^) \
+	--config-path $(word 5,$^)
 
 #################
 # Documentation #

diff --git a/src/ontology/reports/component_signature-doid.tsv b/src/ontology/reports/component_signature-doid.tsv