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Merge pull request #973 from INCATools/fix-mirroring-pipeline
Allow refreshing the mirrors under IMP=false.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -630,6 +630,7 @@ 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 | ||
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| ifeq ($(strip $(MIR)),true) | ||
| {% for ont in project.import_group.products %} | ||
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| ## ONTOLOGY: {{ ont.id }} | ||
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@@ -642,55 +643,64 @@ IMP_LARGE=true # Global parameter to bypass handling of large imports | |
| .PRECIOUS: $(MIRRORDIR)/{{ ont.id }}.owl | ||
| {%- endif -%} | ||
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| {%- if ont.is_large %} | ||
| ifeq ($(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 [email protected]{%- if ont.make_base or 'base' == ont.mirror_type %} && \ | ||
| $(ROBOT) remove -i [email protected] {% 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 [email protected]{% endif %} &&\ | ||
| mv [email protected] $(TMPDIR)/[email protected]; 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)/[email protected] | ||
| {%- 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 [email protected]{%- if ont.make_base or 'base' == ont.mirror_type %} &&\ | ||
| $(ROBOT) remove -i [email protected] {% 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 [email protected]{% endif %} &&\ | ||
| mv [email protected] $(TMPDIR)/[email protected]; 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)/[email protected] | ||
| {%- 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 [email protected] $(TMPDIR)/[email protected]; 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)/[email protected] | ||
| {%- 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 [email protected]{%- if ont.make_base or 'base' == ont.mirror_type %} && \ | ||
| $(ROBOT) remove -i [email protected] {% 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 [email protected]{% endif %} &&\ | ||
| mv [email protected] $(TMPDIR)/[email protected]; 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)/[email protected] | ||
| {%- 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 [email protected]{%- if ont.make_base or 'base' == ont.mirror_type %} && \ | ||
| $(ROBOT) remove -i [email protected] {% 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 [email protected]{% endif %} &&\ | ||
| mv [email protected] $(TMPDIR)/[email protected]; 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 $(TMPDIR)/[email protected] | ||
| {%- endif %} | ||
| {%- endif %} | ||
| {%- if ont.is_large %} | ||
| else | ||
| mirror-{{ ont.id }}: | ||
| @echo "Not refreshing {{ ont.id }} because refreshing large imports is disabled (IMP_LARGE=$(IMP_LARGE))." | ||
| endif | ||
| {%- endif %} | ||
| {% endfor -%} | ||
| {% if project.import_group.use_base_merging %} | ||
| ALL_MIRRORS = $(patsubst %, $(MIRRORDIR)/%.owl, $(IMPORTS)) | ||
| MERGE_MIRRORS = true | ||
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| ifeq ($(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 %} | ||
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| $(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 | ||
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| else # MIR=false | ||
| $(MIRRORDIR)/%.owl: | ||
| @echo "Not refreshing $@ because the mirrorring pipeline is disabled (MIR=$(MIR))." | ||
| endif | ||
| {% endif %} | ||
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| {% if project.subset_group is defined %} | ||
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