Commit re-generated Makefile.

obophenotype · Dec 6, 2024 · 88f5a44 · 88f5a44
1 parent 856bb6e
commit 88f5a44
Showing 1 changed file with 28 additions and 6 deletions.
diff --git a/src/ontology/Makefile b/src/ontology/Makefile
@@ -1,7 +1,7 @@
 # ----------------------------------------
 # Makefile for uberon
 # Generated using ontology-development-kit
-# ODK Version: v1.5.2
+# ODK Version: v1.5.4
 # ----------------------------------------
 # IMPORTANT: DO NOT EDIT THIS FILE. To override default make goals, use uberon.Makefile instead
 
@@ -10,7 +10,7 @@
 # More information: https://github.com/INCATools/ontology-development-kit/
 
 # Fingerprint of the configuration file when this Makefile was last generated
-CONFIG_HASH=                60e47a069bd32a71a48c480dcf88b75d116c5eef7d1f9a55073500ff79968b28
+CONFIG_HASH=                44192e006a6ee9949d79b91dd1f17315be1c22bd1c9bd1e6399ec1b96ed199e0
 
 
 # ----------------------------------------
@@ -47,7 +47,7 @@ REPORT_PROFILE_OPTS =       --profile $(ROBOT_PROFILE)
 OBO_FORMAT_OPTIONS =        
 SPARQL_VALIDATION_CHECKS =  equivalent-classes owldef-self-reference illegal-annotation-property taxon-range orcid-contributor obsolete-replaced_by xrefs-mesh-pattern label-synonym-polysemy id-format 
 SPARQL_EXPORTS =            basic-report 
-ODK_VERSION_MAKEFILE =      v1.5.2
+ODK_VERSION_MAKEFILE =      v1.5.4
 
 TODAY ?=                    $(shell date +%Y-%m-%d)
 OBODATE ?=                  $(shell date +'%d:%m:%Y %H:%M')
@@ -65,13 +65,13 @@ PATTERN_RELEASE_FILES=      $(PATTERNDIR)/definitions.owl $(PATTERNDIR)/pattern.
 MAPPINGDIR=                 ../mappings
 MAPPING_TESTER=             sssom validate
 SSSOMPY=                    sssom
-MAPPINGS=                   fbbt cl biomappings uberon-local uberon import-corrections 
+MAPPINGS=                   fbbt cl sslso biomappings uberon-local uberon import-corrections 
 MAPPING_RELEASE_FILES=      $(foreach n,$(MAPPINGS), $(MAPPINGDIR)/$(n).sssom.tsv)
 
 
 FORMATS = $(sort  owl obo json owl)
 FORMATS_INCL_TSV = $(sort $(FORMATS) tsv)
-RELEASE_ARTEFACTS = $(sort $(ONT)-base $(ONT)-full $(ONT)-simple $(ONT)-basic collected-metazoan composite-metazoan composite-metazoan-basic composite-vertebrate composite-vertebrate-basic common-anatomy )
+RELEASE_ARTEFACTS = $(sort $(ONT)-base $(ONT)-full $(ONT)-simple $(ONT)-basic collected-metazoan composite-metazoan composite-metazoan-basic composite-vertebrate composite-vertebrate-basic collected-lifestages composite-lifestages common-anatomy )
 
 ifeq ($(ODK_DEBUG),yes)
 ODK_DEBUG_FILE = debug.log
@@ -202,7 +202,7 @@ all_subsets: $(SUBSET_FILES)
 # ----------------------------------------
 
 
-MAPPINGS =  fbbt cl biomappings uberon-local uberon import-corrections
+MAPPINGS =  fbbt cl sslso biomappings uberon-local uberon import-corrections
 
 MAPPING_FILES = $(patsubst %, $(MAPPINGDIR)/%.sssom.tsv, $(MAPPINGS))
 
@@ -756,6 +756,10 @@ $(MAPPINGDIR)/fbbt.sssom.tsv:
 $(MAPPINGDIR)/cl.sssom.tsv:
 	test -f $@
 
+# This mappingset is manually curated, so we only check that the file actually exists.
+$(MAPPINGDIR)/sslso.sssom.tsv:
+	test -f $@
+
 # This mappingset is manually curated, so we only check that the file actually exists.
 $(MAPPINGDIR)/biomappings.sssom.tsv:
 	test -f $@
@@ -836,6 +840,18 @@ composite-vertebrate-basic.json: composite-vertebrate-basic.owl
 	$(ROBOT) annotate --input $< --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \
 		convert --check false -f json -o $@.tmp.json &&\
 		mv $@.tmp.json $@
+collected-lifestages.obo: collected-lifestages.owl
+	$(ROBOT) convert --input $< --check false -f obo $(OBO_FORMAT_OPTIONS) -o $@.tmp.obo && grep -v ^owl-axioms $@.tmp.obo > $@ && rm $@.tmp.obo
+collected-lifestages.json: collected-lifestages.owl
+	$(ROBOT) annotate --input $< --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \
+		convert --check false -f json -o $@.tmp.json &&\
+		mv $@.tmp.json $@
+composite-lifestages.obo: composite-lifestages.owl
+	$(ROBOT) convert --input $< --check false -f obo $(OBO_FORMAT_OPTIONS) -o $@.tmp.obo && grep -v ^owl-axioms $@.tmp.obo > $@ && rm $@.tmp.obo
+composite-lifestages.json: composite-lifestages.owl
+	$(ROBOT) annotate --input $< --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \
+		convert --check false -f json -o $@.tmp.json &&\
+		mv $@.tmp.json $@
 common-anatomy.obo: common-anatomy.owl
 	$(ROBOT) convert --input $< --check false -f obo $(OBO_FORMAT_OPTIONS) -o $@.tmp.obo && grep -v ^owl-axioms $@.tmp.obo > $@ && rm $@.tmp.obo
 common-anatomy.json: common-anatomy.owl
@@ -932,6 +948,12 @@ composite-vertebrate.owl:
 composite-vertebrate-basic.owl:
 	echo "ERROR: You have configured a custom release artefact ($@); this release artefact needs to be define in uberon.Makefile!" && false
 
+collected-lifestages.owl:
+	echo "ERROR: You have configured a custom release artefact ($@); this release artefact needs to be define in uberon.Makefile!" && false
+
+composite-lifestages.owl:
+	echo "ERROR: You have configured a custom release artefact ($@); this release artefact needs to be define in uberon.Makefile!" && false
+
 common-anatomy.owl:
 	echo "ERROR: You have configured a custom release artefact ($@); this release artefact needs to be define in uberon.Makefile!" && false
 # ----------------------------------------