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Add new Makefile variable REASONER. #1140

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Nov 27, 2024
Merged

Add new Makefile variable REASONER. #1140

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21 changes: 11 additions & 10 deletions template/src/ontology/Makefile.jinja2
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Original file line number Diff line number Diff line change
Expand Up @@ -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= ../..
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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 \
Expand All @@ -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 [email protected] && mv [email protected] $@
{% endif -%}

Expand All @@ -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 [email protected] && mv [email protected] $@
{% endif -%}
Expand All @@ -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 [email protected] && mv [email protected] $@
{% endif -%}
Expand All @@ -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 [email protected] && mv [email protected] $@
{% endif -%}
{% for r in project.release_artefacts %}
Expand Down