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Allow refreshing the mirrors under IMP=false. #973

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merged 2 commits into from
Jan 8, 2024
Merged

Allow refreshing the mirrors under IMP=false. #973

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ac63e56
Allow refreshing the mirrors under IMP=false.
gouttegd Dec 20, 2023
7a93b15
Merge branch 'master' into fix-mirroring-pipeline
matentzn Jan 7, 2024
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48 changes: 29 additions & 19 deletions template/src/ontology/Makefile.jinja2
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Original file line number Diff line number Diff line change
Expand Up @@ -586,6 +586,7 @@ IMP=true # Global parameter to bypass import generation
MIR=true # Global parameter to bypass mirror generation
IMP_LARGE=true # Global parameter to bypass handling of large imports

ifeq ($(strip $(MIR)),true)
{% for ont in project.import_group.products %}

## ONTOLOGY: {{ ont.id }}
Expand All @@ -598,55 +599,64 @@ IMP_LARGE=true # Global parameter to bypass handling of large imports
.PRECIOUS: $(MIRRORDIR)/{{ ont.id }}.owl
{%- endif -%}

{%- if ont.is_large %}
ifeq ($(strip $(IMP_LARGE)),true)
{%- endif %}
{%- if ont.mirror_from %}
mirror-{{ ont.id }}: | $(TMPDIR)
if [ $(MIR) = true ] && [ $(IMP) = true ]{% if ont.is_large %} && [ $(IMP_LARGE) = true ]{% endif %}; then $(ROBOT) convert -I {{ ont.mirror_from }} -o $@.tmp.owl{%- if ont.make_base or 'base' == ont.mirror_type %} && \
$(ROBOT) remove -i $@.tmp.owl {% if ont.base_iris is not none %}{% for iri in ont.base_iris %}--base-iri {{iri}} {% endfor %}{% else %}--base-iri $(OBOBASE)/{{ ont.id.upper() }} {% endif %}--axioms external --preserve-structure false --trim false -o $@.tmp.owl{% endif %} &&\
mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
$(ROBOT) {% if ont.make_base or 'base' == ont.mirror_type %}remove -I {{ ont.mirror_from }} {% if ont.base_iris is not none %}{% for iri in ont.base_iris %}--base-iri {{iri}} {% endfor %}{% else %}--base-iri $(OBOBASE)/{{ ont.id.upper() }} {% endif %} --axioms external --preserve-structure false --trim false{% else %}convert -I {{ ont.mirror_from }}{% endif %} -o $(TMPDIR)/$@.owl
{%- elif ont.use_base %}
{%- if ont.use_gzipped %}
mirror-{{ ont.id }}: | $(TMPDIR)
if [ $(MIR) = true ] && [ $(IMP) = true ]{% if ont.is_large %} && [ $(IMP_LARGE) = true ]{% endif %}; then curl -L $(OBOBASE)/{{ ont.id }}/{{ ont.id }}-base.owl.gz --create-dirs -o $(MIRRORDIR)/{{ ont.id }}-base.owl.gz --retry {{ project.import_group.mirror_retry_download }} --max-time {{ project.import_group.mirror_max_time_download }} &&\
$(ROBOT) convert -i $(MIRRORDIR)/{{ ont.id }}-base.owl.gz -o $@.tmp.owl{%- if ont.make_base or 'base' == ont.mirror_type %} &&\
$(ROBOT) remove -i $@.tmp.owl {% if ont.base_iris is not none %}{% for iri in ont.base_iris %}--base-iri {{iri}} {% endfor %}{% else %}--base-iri $(OBOBASE)/{{ ont.id.upper() }} {% endif %}--axioms external --preserve-structure false --trim false -o $@.tmp.owl{% endif %} &&\
mv $@.tmp.owl $(TMPDIR)/$@.owl; fi{%- else %}
curl -L $(OBOBASE)/{{ ont.id }}/{{ ont.id }}-base.owl.gz --create-dirs -o $(MIRRORDIR)/{{ ont.id }}-base.owl.gz --retry {{project.import_group.mirror_retry_download}} --max-time {{ project.import_group.mirror_max_time_download }} && \
$(ROBOT) {% if ont.make_base or 'base' == ont.mirror_type %}remove -i $(MIRROR_DIR)/{{ ont.id }}-base.owl.gz {% if ont.base_iris is not none %}{% for iri in ont.base_iris %}--base-iri {{iri}} {% endfor %}{ else %}--base-iri $(OBOBASE)/{{ ont.id.upper() }} {% endif %} --axioms external --preserve-structure false --trim false{% else %}convert -i $(MIRRORDIR)/{{ ont.id }}-base.owl.gz{% endif %} -o $(TMPDIR)/$@.owl
{%- else %}
mirror-{{ ont.id }}: | $(TMPDIR)
if [ $(MIR) = true ] && [ $(IMP) = true ]{% if ont.is_large %} && [ $(IMP_LARGE) = true ]{% endif %}; then curl -L $(OBOBASE)/{{ ont.id }}/{{ ont.id }}-base.owl --create-dirs -o $(TMPDIR)/{{ ont.id }}-download.owl --retry {{ project.import_group.mirror_retry_download }} --max-time {{ project.import_group.mirror_max_time_download }} &&\
$(ROBOT) convert -i $(TMPDIR)/{{ ont.id }}-download.owl -o $@.tmp.owl && mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
curl -L $(OBOBASE)/{{ ont.id }}/{{ ont.id }}-base.owl --create-dirs -o $(TMPDIR)/{{ ont.id }}-download.owl --retry {{ project.import_group.mirror_retry_download }} --max-time {{ project.import_group.mirror_max_time_download }} && \
$(ROBOT) convert -i $(TMPDIR)/{{ ont.id }}-download.owl -o $(TMPDIR)/$@.owl
{%- endif %}
{%- else %}
{%- if ont.use_gzipped %}
mirror-{{ ont.id }}: | $(TMPDIR)
if [ $(MIR) = true ] && [ $(IMP) = true ]{% if ont.is_large %} && [ $(IMP_LARGE) = true ]{% endif %}; then curl -L $(OBOBASE)/{{ ont.id }}.owl.gz --create-dirs -o $(MIRRORDIR)/{{ ont.id }}.owl.gz --retry {{ project.import_group.mirror_retry_download }} --max-time {{ project.import_group.mirror_max_time_download }} &&\
$(ROBOT) convert -i $(MIRRORDIR)/{{ ont.id }}.owl.gz -o $@.tmp.owl{%- if ont.make_base or 'base' == ont.mirror_type %} && \
$(ROBOT) remove -i $@.tmp.owl {% if ont.base_iris is not none %}{% for iri in ont.base_iris %}--base-iri {{iri}} {% endfor %}{% else %}--base-iri $(OBOBASE)/{{ ont.id.upper() }} {% endif %}--axioms external --preserve-structure false --trim false -o $@.tmp.owl{% endif %} &&\
mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
curl -L $(OBOBASE)/{{ ont.id }}.owl.gz --create-dirs -o $(MIRRORDIR)/{{ ont.id }}.owl.gz --retry {{ project.import_group.mirror_retry_download }} --max-time {{ project.import_group.mirror_max_time_download }} && \
$(ROBOT) {% if ont.make_base or 'base' == ont.mirror_type %}remove -i $(MIRRORDIR)/{{ ont.id }}.owl.gz {% if ont.base_iris is not none %}{% for iri in ont.base_iris %}--base-iri {{iri}} {% endfor %}{% else %}--base-iri $(OBOBASE)/{{ ont.id.upper() }} {% endif %}--axioms external --preserve-structure false --trim false{% else %}convert -i $(MIRRORDIR)/{{ ont.id }}.owl.gz{% endif %} -o $(TMPDIR)/$@.owl
{%- elif 'custom' == ont.mirror_type %}
$(MIRRORDIR)/{{ ont.id }}.owl:
echo "ERROR: You have configured your default mirror type to be custom; this behavior needs to be overwritten in {{ project.id }}.Makefile!" && false
{%- elif 'no_mirror' == ont.mirror_type -%}
## You have configured your default mirror type to no_mirror.
{%- else %}
mirror-{{ ont.id }}: | $(TMPDIR)
if [ $(MIR) = true ] && [ $(IMP) = true ]{% if ont.is_large %} && [ $(IMP_LARGE) = true ]{% endif %}; then curl -L $(OBOBASE)/{{ ont.id }}.owl --create-dirs -o $(TMPDIR)/{{ ont.id }}-download.owl --retry {{ project.import_group.mirror_retry_download }} --max-time {{ project.import_group.mirror_max_time_download }} &&\
$(ROBOT) convert -i $(TMPDIR)/{{ ont.id }}-download.owl -o $@.tmp.owl{%- if ont.make_base or 'base' == ont.mirror_type %} && \
$(ROBOT) remove -i $@.tmp.owl {% if ont.base_iris is not none %}{% for iri in ont.base_iris %}--base-iri {{iri}} {% endfor %}{% else %}--base-iri $(OBOBASE)/{{ ont.id.upper() }} {% endif %}--axioms external --preserve-structure false --trim false -o $@.tmp.owl{% endif %} &&\
mv $@.tmp.owl $(TMPDIR)/$@.owl; fi{%- endif %}
curl -L $(OBOBASE)/{{ ont.id }}.owl --create-dirs -o $(TMPDIR)/{{ ont.id }}-download.owl --retry {{ project.import_group.mirror_retry_download }} --max-time {{ project.import_group.mirror_max_time_download }} && \
$(ROBOT) {% if ont.make_base or 'base' == ont.mirror_type %}remove -i $(TMPDIR)/{{ ont.id }}-download.owl {% if ont.base_iris is not none %}{% for iri in ont.base_iris %}--base-iri {{iri}} {% endfor %}{% else %}--base-iri $(OBOBASE)/{{ ont.id.upper() }} {% endif %}--axioms external --preserve-structure false --trim false{% else %}convert -i $(TMPDIR)/{{ ont.id }}-download.owl{% endif %} -o $(TMPDIR)/$@.owl
{%- endif %}
{%- endif %}
{%- if ont.is_large %}
else
mirror-{{ ont.id }}:
@echo "Not refreshing {{ ont.id }} because refreshing large imports is disabled (IMP_LARGE=$(IMP_LARGE))."
endif
{%- endif %}
{% endfor -%}
{% if project.import_group.use_base_merging %}
ALL_MIRRORS = $(patsubst %, $(MIRRORDIR)/%.owl, $(IMPORTS))
MERGE_MIRRORS = true

ifeq ($(strip $(MERGE_MIRRORS)),true)
$(MIRRORDIR)/merged.owl: $(ALL_MIRRORS)
if [ $(IMP) = true ] && [ $(MERGE_MIRRORS) = true ]; then $(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 $@; fi
$(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 $@
.PRECIOUS: $(MIRRORDIR)/merged.owl
endif
{% endif %}

$(MIRRORDIR)/%.owl: mirror-% | $(MIRRORDIR)
if [ $(IMP) = true ] && [ $(MIR) = true ] && [ -f $(TMPDIR)/mirror-$*.owl ]; then if cmp -s $(TMPDIR)/mirror-$*.owl $@ ; then echo "Mirror identical, ignoring."; else echo "Mirrors different, updating." &&\
if [ -f $(TMPDIR)/mirror-$*.owl ]; then if cmp -s $(TMPDIR)/mirror-$*.owl $@ ; then echo "Mirror identical, ignoring."; else echo "Mirrors different, updating." &&\
cp $(TMPDIR)/mirror-$*.owl $@; fi; fi

else # MIR=false
$(MIRRORDIR)/%.owl:
@echo "Not refreshing $@ because the mirrorring pipeline is disabled (MIR=$(MIR))."
endif
{% endif %}

{% if project.subset_group is defined %}
Expand Down