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Use OFN as the intermediate format more widely. #8

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Merged
gouttegd merged 3 commits into from
Apr 20, 2026
Merged

Use OFN as the intermediate format more widely. #8

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83b48b0
Use OFN as the intermediate format more widely.
gouttegd Mar 15, 2026
9a7eaa0
Merge branch 'main' into use-ofn-as-intermediate-format
gouttegd Mar 17, 2026
fcb784e
Write OWL translation files in OFN format.
gouttegd Apr 20, 2026
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14 changes: 7 additions & 7 deletions src/incatools/odk/templates/src/ontology/Makefile.jinja2
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Original file line number Diff line number Diff line change
Expand Up @@ -504,7 +504,7 @@ $(PRESEED): $(SRCMERGED)
$(SRCMERGED): $(EDIT_PREPROCESSED) $(OTHER_SRC)
$(ROBOT) remove --input $< --select imports --trim false \
merge $(foreach src, $(OTHER_SRC), --input $(src)) \
--output $@
convert --format ofn --output $@

$(EDIT_PREPROCESSED): $(SRC)
$(ROBOT) convert --input $< --format ofn --output $@
Expand Down Expand Up @@ -839,8 +839,7 @@ $(COMPONENTSDIR)/{{ component.filename }}: download-component-{{ component.filen
$(ROBOT) merge -i $(TMPDIR)/download-component-{{ component.filename }} \{% if component.make_base %}
remove {% for iri in component.base_iris %}--base-iri {{ iri }} \
{% endfor %}--axioms external --preserve-structure false --trim false \{% endif %}
annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \
--output $@ ; \
$(ANNOTATE_CONVERT_FILE) ; \
fi

.PRECIOUS: $(COMPONENTSDIR)/{{ component.filename }}
Expand Down Expand Up @@ -905,7 +904,7 @@ $(MIRRORDIR)/{{ ont.id }}.owl: download-mirror-{{ ont.id }}
--base-iri {{ iri }} \{% endfor %}{% else %}
--base-iri $(OBOBASE)/{{ ont.id.upper() }} \{% endif %}
--axioms external --preserve-structure false --trim false \
convert {% else %}convert -i $(TMPDIR)/download-mirror-{{ ont.id }}.owl {% endif %}-o $@ ; \
convert {% else %}convert -i $(TMPDIR)/download-mirror-{{ ont.id }}.owl {% endif %}--format ofn -o $@ ; \
fi

{% if ont.is_large -%}
Expand All @@ -924,7 +923,8 @@ MERGE_MIRRORS = true

ifeq ($(MERGE_MIRRORS),true)
$(MIRRORDIR)/merged.owl: $(ALL_MIRRORS)
$(ROBOT) merge $(patsubst %, -i %, $^) {% if project.import_group.annotate_defined_by %}--annotate-defined-by true{% endif %} {% if project.import_group.base_merge_drop_equivalent_class_axioms %}remove --axioms equivalent --preserve-structure false {% endif %}-o $@
$(ROBOT) merge $(foreach mirror,$^,-i $(mirror)) {% if project.import_group.annotate_defined_by %}--annotate-defined-by true{% endif %} {% if project.import_group.base_merge_drop_equivalent_class_axioms %}remove --axioms equivalent --preserve-structure false {% endif %}\
convert --format ofn -o $@
.PRECIOUS: $(MIRRORDIR)/merged.owl
endif
{% endif -%}
Expand Down Expand Up @@ -1278,7 +1278,7 @@ $(TRANSLATIONSDIR)/%.synonyms.owl: $(TRANSLATIONSDIR)/%.synonyms.tsv
--ontology-iri $(ONTBASE)/translations/$*.synonyms.owl \
-V $(ONTBASE)/releases/$(VERSION)/translations/$*.synonyms.owl \
--annotation owl:versionInfo $(VERSION) \
convert -f owl --output $@
convert --format ofn --output $@
.PRECIOUS: $(TRANSLATIONSDIR)/%.synonyms.owl

$(TRANSLATIONSDIR)/%.babelon.owl: $(TRANSLATIONSDIR)/%-preprocessed.babelon.tsv
Expand All @@ -1288,7 +1288,7 @@ $(TRANSLATIONSDIR)/%.babelon.owl: $(TRANSLATIONSDIR)/%-preprocessed.babelon.tsv
--ontology-iri $(ONTBASE)/translations/$*.babelon.owl \
-V $(ONTBASE)/releases/$(VERSION)/translations/$*.babelon.owl \
--annotation owl:versionInfo $(VERSION) \
convert -f owl --output $@
convert --format ofn --output $@
@rm $@.tmp
.PRECIOUS: $(TRANSLATIONSDIR)/%.babelon.owl

Expand Down
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