Merge pull request #3028 from obophenotype/cleaning-up-makefile

Cleaning up makefile
obophenotype · Aug 23, 2023 · 1709721 · 1709721
2 parents fa629f5 + a719af2
commit 1709721
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Showing 4 changed files with 910 additions and 1,468 deletions.
diff --git a/src/ontology/Makefile b/src/ontology/Makefile
@@ -62,7 +62,7 @@ PATTERN_RELEASE_FILES=      $(PATTERNDIR)/definitions.owl $(PATTERNDIR)/pattern.
 
 FORMATS = $(sort  owl obo json owl)
 FORMATS_INCL_TSV = $(sort $(FORMATS) tsv)
-RELEASE_ARTEFACTS = $(sort $(ONT)-base $(ONT)-full $(ONT)-simple $(ONT)-basic ext basic composite-metazoan composite-metazoan-basic composite-vertebrate composite-vertebrate-basic common-anatomy )
+RELEASE_ARTEFACTS = $(sort $(ONT)-base $(ONT)-full $(ONT)-simple $(ONT)-basic basic composite-metazoan composite-metazoan-basic composite-vertebrate composite-vertebrate-basic common-anatomy )
 
 # ----------------------------------------
 # Top-level targets
@@ -668,12 +668,6 @@ $(ONT)-basic.json: $(ONT)-basic.owl
 	$(ROBOT) annotate --input $< --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \
 		convert --check false -f json -o $@.tmp.json &&\
 		mv $@.tmp.json $@
-ext.obo: ext.owl
-	$(ROBOT) convert --input $< --check false -f obo $(OBO_FORMAT_OPTIONS) -o $@.tmp.obo && grep -v ^owl-axioms $@.tmp.obo > $@ && rm $@.tmp.obo
-ext.json: ext.owl
-	$(ROBOT) annotate --input $< --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \
-		convert --check false -f json -o $@.tmp.json &&\
-		mv $@.tmp.json $@
 basic.obo: basic.owl
 	$(ROBOT) convert --input $< --check false -f obo $(OBO_FORMAT_OPTIONS) -o $@.tmp.obo && grep -v ^owl-axioms $@.tmp.obo > $@ && rm $@.tmp.obo
 basic.json: basic.owl
@@ -781,9 +775,6 @@ $(ONT)-basic.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(SIMPLESEED) $(KEEPRELATION
 		reduce -r ELK \
 		$(SHARED_ROBOT_COMMANDS) annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output $@.tmp.owl && mv $@.tmp.owl $@
 
-ext.owl:
-	echo "ERROR: You have configured a custom release artefact ($@); this release artefact needs to be define in uberon.Makefile!" && false
-
 basic.owl:
 	echo "ERROR: You have configured a custom release artefact ($@); this release artefact needs to be define in uberon.Makefile!" && false
 

diff --git a/src/ontology/bridge/collected-drosophila.owl b/src/ontology/bridge/collected-drosophila.owl
@@ -32,6 +32,6 @@
     </rdfs:comment>
     <owl:imports rdf:resource="http://purl.obolibrary.org/obo/uberon.owl"/>
     <owl:imports rdf:resource="http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-fbbt.owl"/>
-    <owl:imports rdf:resource="http://purl.obolibrary.org/obo/uberon/fbbt-nd.owl"/>
+    <owl:imports rdf:resource="http://purl.obolibrary.org/obo/fbbt.owl"/>
   </owl:Ontology>
 </rdf:RDF>
diff --git a/src/ontology/uberon-odk.yaml b/src/ontology/uberon-odk.yaml
@@ -20,7 +20,6 @@ release_artefacts:
   - full
   - simple
   - basic
-  - custom-ext
   - custom-basic
   - custom-composite-metazoan
   - custom-composite-metazoan-basic