Subclass Sync - Direct in source, indirect in Mondo

- Update: Formalized new output *confirmed-direct-source-indirect-mondo.robot.tsv

src/ontology/mondo-ingest.Makefile

@@ -553,7 +553,7 @@ sync: sync-subclassof sync-synonyms
 
 # Synchronization: SubclassOf
 .PHONY: sync-subclassof
-sync-subclassof: $(REPORTDIR)/sync-subClassOf.confirmed.tsv $(REPORTDIR)/sync-subClassOf.direct-in-mondo-only.tsv $(TMPDIR)/sync-subClassOf.added.self-parentage.tsv
+sync-subclassof: $(REPORTDIR)/sync-subClassOf.confirmed.tsv $(REPORTDIR)/sync-subClassOf.confirmed-direct-source-indirect-mondo.tsv $(REPORTDIR)/sync-subClassOf.direct-in-mondo-only.tsv $(TMPDIR)/sync-subClassOf.added.self-parentage.tsv
 
 # todo: drop this? This is really just an alias here for quality of life, but not used by anything.
 .PHONY: sync-subclassof-%
@@ -570,11 +570,16 @@ $(REPORTDIR)/sync-subClassOf.direct-in-mondo-only.tsv: $(foreach n,$(ALL_COMPONE
 $(REPORTDIR)/sync-subClassOf.confirmed.tsv: $(foreach n,$(ALL_COMPONENT_IDS), $(REPORTDIR)/$(n).subclass.confirmed.robot.tsv)
 	awk '(NR == 1) || (NR == 2) || (FNR > 2)' $(REPORTDIR)/*.subclass.confirmed.robot.tsv > $@
 
+# TODO: implement this goal && add to master goal
+$(REPORTDIR)/sync-subClassOf.confirmed-direct-source-indirect-mondo.tsv: $(foreach n,$(ALL_COMPONENT_IDS), $(REPORTDIR)/$(n).subclass.confirmed-direct-source-indirect-mondo.robot.tsv)
+	awk '(NR == 1) || (NR == 2) || (FNR > 2)' $(REPORTDIR)/*.subclass.confirmed-direct-source-indirect-mondo.robot.tsv > $@
+
 $(REPORTDIR)/%.subclass.confirmed.robot.tsv $(REPORTDIR)/%.subclass.added.robot.tsv $(REPORTDIR)/%.subclass.added-obsolete.robot.tsv $(REPORTDIR)/%.subclass.direct-in-mondo-only.tsv $(TMPDIR)/%.subclass.self-parentage.tsv: $(TMPDIR)/mondo-ingest.db $(TMPDIR)/mondo.db $(TMPDIR)/mondo.sssom.tsv
 	python3 $(SCRIPTSDIR)/sync_subclassof.py \
 	--outpath-added $(REPORTDIR)/$*.subclass.added.robot.tsv \
 	--outpath-added-obsolete $(REPORTDIR)/$*.subclass.added-obsolete.robot.tsv \
 	--outpath-confirmed $(REPORTDIR)/$*.subclass.confirmed.robot.tsv \
+	--outpath-confirmed-direct-source-indirect-mondo $(REPORTDIR)/$*.subclass.confirmed-direct-source-indirect-mondo.robot.tsv \
 	--outpath-direct-in-mondo-only $(REPORTDIR)/$*.subclass.direct-in-mondo-only.tsv \
 	--outpath-self-parentage $(TMPDIR)/$*.subclass.self-parentage.tsv \
 	--mondo-db-path $(TMPDIR)/mondo.db \

src/scripts/sync_subclassof.py

@@ -225,6 +225,7 @@ def _convert_edge_namespace(
 
 def sync_subclassof(
     outpath_added: str = EX_DEFAULTS['outpath_added'], outpath_confirmed: str = EX_DEFAULTS['outpath_confirmed'],
+    outpath_confirmed_direct_source_indirect_mondo: str = EX_DEFAULTS['outpath_confirmed_direct_source_indirect_mondo'],
     outpath_added_obsolete: str = EX_DEFAULTS['outpath_added_obsolete'],
     mondo_db_path: str = EX_DEFAULTS['mondo_db_path'], mondo_ingest_db_path: str = EX_DEFAULTS['mondo_ingest_db_path'],
     mondo_mappings_path: str = EX_DEFAULTS['mondo_mappings_path'],
@@ -402,8 +403,7 @@ def sync_subclassof(
     _confirmed_df(in_both_direct, outpath_confirmed)
 
     # Case 2: SCR is direct in source, but indirect Mondo
-    _confirmed_df(in_source_direct_mondo_indirect,
-        outpath_confirmed.replace('confirmed', 'confirmed-direct-source-indirect-mondo'))
+    _confirmed_df(in_source_direct_mondo_indirect, outpath_confirmed_direct_source_indirect_mondo)
 
     # Case 3: SCR is direct in the source, but not at all in Mondo
     subheader = deepcopy(ROBOT_SUBHEADER)
@@ -486,8 +486,13 @@ def cli():  # todo: #remove-temp-defaults
              'into Mondo, except for that these terms are obsolete in Mondo.')
     parser.add_argument(
         '-c', '--outpath-confirmed', required=False, default=EX_DEFAULTS['outpath_confirmed'],
-        help='Path to output robot template containing subclass relations for given ontology that exist in Mondo and '
-             'are confirmed to also exist in the source.')
+        help='Path to output robot template containing direct subclass relations for given ontology that exist in '
+             'Mondo and are confirmed to also exist in the source.')
+    parser.add_argument(
+        '-C', '--confirmed-direct-source-indirect-mondo', required=False,
+        default=EX_DEFAULTS['outpath_confirmed_direct_source_indirect_mondo'],
+        help='Path to output robot template containing subclass relations for given ontology that exist in Mondo as '
+             'indirect relations and are confirmed to also exist in the source as direct relations.')
     parser.add_argument(
         '-M', '--outpath-direct-in-mondo-only', required=False,
         default=EX_DEFAULTS['outpath_direct_in_mondo_only'],
@@ -526,6 +531,8 @@ def run_defaults(use_cache=True):  # todo: #remove-temp-defaults
         sync_subclassof(**{
             'outpath_added': str(REPORTS_DIR / f'{name}.subclass.added.robot.tsv'),
             'outpath_confirmed': str(REPORTS_DIR / f'{name}.subclass.confirmed.robot.tsv'),
+            'outpath_confirmed_direct_source_indirect_mondo': \
+                str(REPORTS_DIR / f'{name}.subclass.confirmed-direct-source-indirect-mondo.robot.tsv'),
             'onto_config_path': str(METADATA_DIR / f'{name}.yml'),
             'mondo_db_path': str(TMP_DIR / 'mondo.db'),
             'mondo_ingest_db_path': str(TMP_DIR / 'mondo-ingest.db'),

src/scripts/sync_subclassof_config.py

@@ -30,6 +30,8 @@
     'outpath_added': str(REPORTS_DIR / f'{EX_ONTO_NAME}.subclass.added.robot.tsv'),
     'outpath_added_obsolete': str(REPORTS_DIR / f'{EX_ONTO_NAME}.subclass.added-obsolete.robot.tsv'),
     'outpath_confirmed': str(REPORTS_DIR / f'{EX_ONTO_NAME}.subclass.confirmed.robot.tsv'),
+    'outpath_confirmed_direct_source_indirect_mondo': \
+        str(REPORTS_DIR / f'{EX_ONTO_NAME}.subclass.confirmed-direct-source-indirect-mondo.robot.tsv'),
     'onto_config_path': str(METADATA_DIR / f'{EX_ONTO_NAME}.yml'),
     'mondo_db_path': str(TMP_DIR / 'mondo.db'),
     'mondo_ingest_db_path': str(TMP_DIR / 'mondo-ingest.db'),