diff --git a/template/src/ontology/Makefile.jinja2 b/template/src/ontology/Makefile.jinja2 index 1ee7c6ea..eddfa0f9 100644 --- a/template/src/ontology/Makefile.jinja2 +++ b/template/src/ontology/Makefile.jinja2 @@ -36,6 +36,7 @@ SRC = $(ONT)-edit.$(EDIT_FORMAT) MAKE_FAST= $(MAKE) IMP=false PAT=false COMP=false MIR=false CATALOG= {{ project.catalog_file }} ROBOT= robot --catalog $(CATALOG) +REASONER= {{ project.reasoner }} {% if project.owltools_memory|length %}OWLTOOLS_MEMORY= {{ project.owltools_memory }}{% endif %} OWLTOOLS= {% if project.owltools_memory|length %}OWLTOOLS_MEMORY=$(OWLTOOLS_MEMORY) {% endif %}owltools --use-catalog RELEASEDIR= ../.. @@ -131,7 +132,7 @@ release_diff: $(REPORTDIR)/release-diff.md .PHONY: reason_test reason_test: $(EDIT_PREPROCESSED) - $(ROBOT) reason --input $< --reasoner {{ project.reasoner }} --equivalent-classes-allowed {{ project.allow_equivalents }} \ + $(ROBOT) reason --input $< --reasoner $(REASONER) --equivalent-classes-allowed {{ project.allow_equivalents }} \ --exclude-tautologies {{ project.exclude_tautologies }} --output test.owl && rm test.owl .PHONY: odkversion @@ -1118,10 +1119,10 @@ merge $(patsubst %, -i %, $(OTHER_SRC)) {% endif %} # base: A version of the ontology that does not include any externally imported axioms. $(ONT)-base.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(IMPORT_FILES) $(ROBOT_RELEASE_IMPORT_MODE) \{% if project.release_use_reasoner %} - reason --reasoner {{ project.reasoner }} --equivalent-classes-allowed {{ project.allow_equivalents }} --exclude-tautologies {{ project.exclude_tautologies }} --annotate-inferred-axioms {{ project.release_annotate_inferred_axioms|default('false')|lower }} \{% if project.release_materialize_object_properties is defined and project.release_materialize_object_properties %} + reason --reasoner $(REASONER) --equivalent-classes-allowed {{ project.allow_equivalents }} --exclude-tautologies {{ project.exclude_tautologies }} --annotate-inferred-axioms {{ project.release_annotate_inferred_axioms|default('false')|lower }} \{% if project.release_materialize_object_properties is defined and project.release_materialize_object_properties %} materialize {% for iri in project.release_materialize_object_properties %}--term {{iri}} {% endfor %} \{% endif %}{% endif %} relax $(RELAX_OPTIONS) \{% if project.release_use_reasoner %} - reduce -r {{ project.reasoner }} \{% endif %} + reduce -r $(REASONER) \{% endif %} remove {% if project.namespaces is not none %}{% for iri in project.namespaces %}--base-iri {{iri}} {% endfor %}{% else %}--base-iri $(URIBASE)/{{ project.id.upper() }} {% endif %}--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 \ @@ -1141,10 +1142,10 @@ $(ONT)-baselite.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 {{ project.reasoner }} --equivalent-classes-allowed {{ project.allow_equivalents }} --exclude-tautologies {{ project.exclude_tautologies }} \{% if project.release_materialize_object_properties is defined and project.release_materialize_object_properties %} + reason --reasoner $(REASONER) --equivalent-classes-allowed {{ project.allow_equivalents }} --exclude-tautologies {{ project.exclude_tautologies }} \{% if project.release_materialize_object_properties is defined and project.release_materialize_object_properties %} materialize {% for iri in project.release_materialize_object_properties %}--term {{iri}} {% endfor %} \{% endif %} relax $(RELAX_OPTIONS) \ - reduce -r {{ project.reasoner }} \ + reduce -r $(REASONER) \ $(SHARED_ROBOT_COMMANDS) annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) {% if project.release_date -%}--annotation oboInOwl:date "$(OBODATE)" {% endif -%}--output $@.tmp.owl && mv $@.tmp.owl $@ {% endif -%} @@ -1161,11 +1162,11 @@ $(ONT)-non-classified.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(IMPORT_FILES) # remove --select imports --trim false $(ONT)-simple.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(SIMPLESEED) $(IMPORT_FILES) $(ROBOT_RELEASE_IMPORT_MODE) \{% if project.release_use_reasoner %} - reason --reasoner {{ project.reasoner }} --equivalent-classes-allowed {{ project.allow_equivalents }} --exclude-tautologies {{ project.exclude_tautologies }} --annotate-inferred-axioms {{ project.release_annotate_inferred_axioms|default('false')|lower }} \{% endif %} + reason --reasoner $(REASONER) --equivalent-classes-allowed {{ project.allow_equivalents }} --exclude-tautologies {{ project.exclude_tautologies }} --annotate-inferred-axioms {{ project.release_annotate_inferred_axioms|default('false')|lower }} \{% endif %} relax $(RELAX_OPTIONS) \ remove --axioms equivalent \ filter --term-file $(SIMPLESEED) --select "annotations ontology anonymous self" --trim true --signature true \{% if project.release_use_reasoner %} - reduce -r {{ project.reasoner }} \{% endif %} + reduce -r $(REASONER) \{% endif %} query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru \ $(SHARED_ROBOT_COMMANDS) annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) {% if project.release_date -%}--annotation oboInOwl:date "$(OBODATE)" {% endif -%}--output $@.tmp.owl && mv $@.tmp.owl $@ {% endif -%} @@ -1177,7 +1178,7 @@ $(ONT)-simple.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(SIMPLESEED) $(IMPORT_FILE $(ONT)-simple-non-classified.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(SIMPLESEED) $(IMPORT_FILES) $(ROBOT_RELEASE_IMPORT_MODE_BASE) \ remove --axioms equivalent \{% if project.release_use_reasoner %} - reduce -r {{ project.reasoner }} \{% endif %} + reduce -r $(REASONER) \{% endif %} filter --select ontology --term-file $(SIMPLESEED) --trim false \ $(SHARED_ROBOT_COMMANDS) annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) {% if project.release_date -%}--annotation oboInOwl:date "$(OBODATE)" {% endif -%}--output $@.tmp.owl && mv $@.tmp.owl $@ {% endif -%} @@ -1196,13 +1197,13 @@ $(ONT)-international.owl: $(ONT).owl $(TRANSLATIONS_OWL) # removes any axioms that contains one of the ops that not in the whitelist file $(ONT)-basic.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(SIMPLESEED) $(KEEPRELATIONS) $(IMPORT_FILES) $(ROBOT_RELEASE_IMPORT_MODE) \{% if project.release_use_reasoner %} - reason --reasoner {{ project.reasoner }} --equivalent-classes-allowed {{ project.allow_equivalents }} --exclude-tautologies {{ project.exclude_tautologies }} --annotate-inferred-axioms {{ project.release_annotate_inferred_axioms|default('false')|lower }} \{% endif %} + reason --reasoner $(REASONER) --equivalent-classes-allowed {{ project.allow_equivalents }} --exclude-tautologies {{ project.exclude_tautologies }} --annotate-inferred-axioms {{ project.release_annotate_inferred_axioms|default('false')|lower }} \{% endif %} relax $(RELAX_OPTIONS) \ remove --axioms equivalent \ remove --axioms disjoint \ remove --term-file $(KEEPRELATIONS) --select complement --select object-properties --trim true \ filter --term-file $(SIMPLESEED) --select "annotations ontology anonymous self" --trim true --signature true \ - reduce -r {{ project.reasoner }} \ + reduce -r $(REASONER) \ $(SHARED_ROBOT_COMMANDS) annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) {% if project.release_date -%}--annotation oboInOwl:date "$(OBODATE)" {% endif -%}--output $@.tmp.owl && mv $@.tmp.owl $@ {% endif -%} {% for r in project.release_artefacts %}