From af7744ab6955721fa4afe81d1ca4bfeb19f202d4 Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Thu, 1 Feb 2024 17:14:20 +0200 Subject: [PATCH 1/4] Change base to base-plus for MAXO --- src/ontology/maxo.Makefile | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/src/ontology/maxo.Makefile b/src/ontology/maxo.Makefile index dad27bb1..0d7bb110 100644 --- a/src/ontology/maxo.Makefile +++ b/src/ontology/maxo.Makefile @@ -15,6 +15,17 @@ test: maxo-base.json test_fast: $(MAKE_FAST) test +$(ONT)-base.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(IMPORT_FILES) + $(ROBOT_RELEASE_IMPORT_MODE) \ + reason --reasoner ELK --equivalent-classes-allowed asserted-only --exclude-tautologies structural \ + relax \ + reduce -r ELK \ + remove --base-iri $(URIBASE)/OBA --axioms external --preserve-structure false --trim false \ + $(SHARED_ROBOT_COMMANDS) \ + annotate --link-annotation http://purl.org/dc/elements/1.1/type http://purl.obolibrary.org/obo/IAO_8000001 \ + --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \ + --output $@.tmp.owl && mv $@.tmp.owl $@ + ######################################### ### Generating all ROBOT templates ###### ######################################### From bc99ecc4a39ba7bcc34d6e2735e280c3db756cd3 Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Thu, 1 Feb 2024 17:14:24 +0200 Subject: [PATCH 2/4] Update run.sh --- src/ontology/run.sh | 0 1 file changed, 0 insertions(+), 0 deletions(-) mode change 100644 => 100755 src/ontology/run.sh diff --git a/src/ontology/run.sh b/src/ontology/run.sh old mode 100644 new mode 100755 From 7708cd90d1ffe5652bb16fbd4c0a4f25c3bf22eb Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Thu, 1 Feb 2024 17:14:37 +0200 Subject: [PATCH 3/4] Update QC to scream on equivalents --- src/ontology/Makefile | 4 ++-- src/ontology/maxo-odk.yaml | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/src/ontology/Makefile b/src/ontology/Makefile index 98b0429b..0e333cb4 100644 --- a/src/ontology/Makefile +++ b/src/ontology/Makefile @@ -85,7 +85,7 @@ release_diff: $(REPORTDIR)/release-diff.md .PHONY: reason_test reason_test: $(EDIT_PREPROCESSED) - $(ROBOT) reason --input $< --reasoner ELK --equivalent-classes-allowed all \ + $(ROBOT) reason --input $< --reasoner ELK --equivalent-classes-allowed asserted-only \ --exclude-tautologies structural --output test.owl && rm test.owl .PHONY: odkversion @@ -762,7 +762,7 @@ $(ONT)-base.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) # Full: The full artefacts with imports merged, reasoned. $(ONT)-full.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(IMPORT_FILES) $(ROBOT_RELEASE_IMPORT_MODE) \ - reason --reasoner ELK --equivalent-classes-allowed all --exclude-tautologies structural \ + reason --reasoner ELK --equivalent-classes-allowed asserted-only --exclude-tautologies structural \ relax \ reduce -r ELK \ $(SHARED_ROBOT_COMMANDS) annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output $@.tmp.owl && mv $@.tmp.owl $@ diff --git a/src/ontology/maxo-odk.yaml b/src/ontology/maxo-odk.yaml index c8ef6cc0..a0790f30 100644 --- a/src/ontology/maxo-odk.yaml +++ b/src/ontology/maxo-odk.yaml @@ -88,7 +88,7 @@ components: use_template: TRUE templates: - maxo-in-progress.tsv -allow_equivalents: all +allow_equivalents: asserted-only robot_report: use_base_iris: True fail_on : ERROR From 946efbc59370d689466798f06eeb2050568cb184 Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Thu, 1 Feb 2024 18:21:21 +0200 Subject: [PATCH 4/4] Update maxo.Makefile --- src/ontology/maxo.Makefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ontology/maxo.Makefile b/src/ontology/maxo.Makefile index 0d7bb110..22bf4c48 100644 --- a/src/ontology/maxo.Makefile +++ b/src/ontology/maxo.Makefile @@ -20,7 +20,7 @@ $(ONT)-base.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(IMPORT_FILES) reason --reasoner ELK --equivalent-classes-allowed asserted-only --exclude-tautologies structural \ relax \ reduce -r ELK \ - remove --base-iri $(URIBASE)/OBA --axioms external --preserve-structure false --trim false \ + remove --base-iri $(URIBASE)/MAXO_ --axioms external --preserve-structure false --trim false \ $(SHARED_ROBOT_COMMANDS) \ annotate --link-annotation http://purl.org/dc/elements/1.1/type http://purl.obolibrary.org/obo/IAO_8000001 \ --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \