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Merge pull request #378 from INCATools/fix-376
Update Makefile.jinja2
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@@ -364,23 +364,23 @@ $(SIMPLESEED): $(SRCMERGED) $(ONTOLOGYTERMS) | |
| {% if project.use_dosdps %} | ||
| # Ugly hack which should be replaced by the dynamic import revision pipeline | ||
| $(IMPORTSEED): $(PRESEED) prepare_patterns $(PATTERNDIR)/all_pattern_terms.txt | ||
| @if [ $(IMP) = true ]; then cat $(PRESEED) $(PATTERNDIR)/all_pattern_terms.txt | sort | uniq > $@; fi | ||
| if [ $(IMP) = true ]; then cat $(PRESEED) $(PATTERNDIR)/all_pattern_terms.txt | sort | uniq > $@; fi | ||
| {% else %} | ||
| $(IMPORTSEED): $(PRESEED) | ||
| @if [ $(IMP) = true ]; then cat $(PRESEED) | sort | uniq > $@; fi | ||
| if [ $(IMP) = true ]; then cat $(PRESEED) | sort | uniq > $@; fi | ||
| {% endif %} | ||
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| # Generate terms.txt for each import. (Assume OBO-style Possibly hacky step?) | ||
| # Should be able to drop this if robot can just take a big messy list of terms as input. | ||
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| imports/%_terms_combined.txt: $(IMPORTSEED) imports/%_terms.txt | ||
| @if [ $(IMP) = true ]; then cat $^ | grep -v ^# | sort | uniq > $@; fi | ||
| if [ $(IMP) = true ]; then cat $^ | grep -v ^# | sort | uniq > $@; fi | ||
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| # -- Generate Import Modules -- | ||
| # | ||
| # This pattern uses ROBOT to generate an import module | ||
| imports/%_import.owl: mirror/%.owl imports/%_terms_combined.txt | ||
| @if [ $(IMP) = true ]; then $(ROBOT) extract -i $< -T imports/$*_terms_combined.txt --force true --method BOT \ | ||
| if [ $(IMP) = true ]; then $(ROBOT) extract -i $< -T imports/$*_terms_combined.txt --force true --method BOT \ | ||
| query --update ../sparql/inject-subset-declaration.ru \ | ||
| annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output [email protected] && mv [email protected] $@; fi | ||
| .PRECIOUS: imports/%_import.owl | ||
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@@ -390,15 +390,15 @@ imports/%_import.owl: mirror/%.owl imports/%_terms_combined.txt | |
| # this can be useful for spot-checks and diffs. | ||
| # we set strict mode to false by default. For discussion see https://github.com/owlcs/owlapi/issues/752 | ||
| imports/%_import.obo: imports/%_import.owl | ||
| @if [ $(IMP) = true ]; then $(ROBOT) convert --check false -i $< -f obo -o [email protected] && mv [email protected] $@; fi | ||
| if [ $(IMP) = true ]; then $(ROBOT) convert --check false -i $< -f obo -o [email protected] && mv [email protected] $@; fi | ||
| {% endif -%} | ||
| {% if 'ttl' in project.export_formats -%} | ||
| imports/%_import.ttl: imports/%_import.owl | ||
| @if [ $(IMP) = true ]; then $(ROBOT) convert --check false -i $< -f ttl -o [email protected] && mv [email protected] $@; fi | ||
| if [ $(IMP) = true ]; then $(ROBOT) convert --check false -i $< -f ttl -o [email protected] && mv [email protected] $@; fi | ||
| {% endif -%} | ||
| {% if 'json' in project.export_formats -%} | ||
| imports/%_import.json: imports/%_import.owl | ||
| @if [ $(IMP) = true ]; then $(ROBOT) convert --check false -i $< -f json -o [email protected] && mv [email protected] $@; fi | ||
| if [ $(IMP) = true ]; then $(ROBOT) convert --check false -i $< -f json -o [email protected] && mv [email protected] $@; fi | ||
| {% endif -%} | ||
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@@ -416,7 +416,7 @@ imports/%_import.json: imports/%_import.owl | |
| {% for component in project.components.products %} | ||
| {% if component.source is not none %} | ||
| {{ project.components.directory }}/{{ component.filename }}: .FORCE | ||
| @if [ $(IMP) = true ]; then $(ROBOT) merge -I {{ component.source }} \ | ||
| if [ $(IMP) = true ]; then $(ROBOT) merge -I {{ component.source }} \ | ||
| annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) -o $@; fi | ||
| .PRECIOUS: {{ project.components.directory }}/{{ component.filename }} | ||
| {% endif %} | ||
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@@ -449,10 +449,10 @@ mirror/{{ ont.id }}.trigger: | |
| {% endif -%} | ||
| {% if ont.mirror_from %} | ||
| mirror/{{ ont.id }}.owl: mirror/{{ ont.id }}.trigger | ||
| @if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(ROBOT) convert -I {{ ont.mirror_from }} -o [email protected] && mv [email protected] $@; fi | ||
| if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(ROBOT) convert -I {{ ont.mirror_from }} -o [email protected] && mv [email protected] $@; fi | ||
| {% else %} | ||
| mirror/{{ ont.id }}.owl: mirror/{{ ont.id }}.trigger | ||
| @if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(ROBOT) convert -I $(URIBASE)/{{ ont.id }}.owl -o [email protected] && mv [email protected] $@; fi | ||
| if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(ROBOT) convert -I $(URIBASE)/{{ ont.id }}.owl -o [email protected] && mv [email protected] $@; fi | ||
| {% endif %} | ||
| .PRECIOUS: mirror/%.owl | ||
| {% endfor -%} | ||
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@@ -526,17 +526,17 @@ pattern_clean: | |
| echo "Not implemented" | ||
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| pattern_schema_checks: update_patterns | ||
| @if [ $(PAT) = true ]; then $(PATTERN_TESTER) $(PATTERNDIR)/dosdp-patterns/; fi | ||
| if [ $(PAT) = true ]; then $(PATTERN_TESTER) $(PATTERNDIR)/dosdp-patterns/; fi | ||
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| #This command is a workaround for the absence of -N and -i in wget of alpine (the one ODK depend on now). It downloads all patterns specified in external.txt | ||
| update_patterns: .FORCE | ||
| @if [ $(PAT) = true ]; then rm -f $(PATTERNDIR)/dosdp-patterns/*.yaml.1 || true; fi | ||
| @if [ $(PAT) = true ]; then wget -i $(PATTERNDIR)/dosdp-patterns/external.txt --backups=1 -P $(PATTERNDIR)/dosdp-patterns; fi | ||
| @if [ $(PAT) = true ]; then rm -f $(PATTERNDIR)/dosdp-patterns/*.yaml.1 || true; fi | ||
| if [ $(PAT) = true ]; then rm -f $(PATTERNDIR)/dosdp-patterns/*.yaml.1 || true; fi | ||
| if [ $(PAT) = true ]; then wget -i $(PATTERNDIR)/dosdp-patterns/external.txt --backups=1 -P $(PATTERNDIR)/dosdp-patterns; fi | ||
| if [ $(PAT) = true ]; then rm -f $(PATTERNDIR)/dosdp-patterns/*.yaml.1 || true; fi | ||
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| $(PATTERNDIR)/pattern.owl: pattern_schema_checks update_patterns | ||
| @if [ $(PAT) = true ]; then $(DOSDPT) prototype --obo-prefixes --template=$(PATTERNDIR)/dosdp-patterns --outfile=$@; fi | ||
| if [ $(PAT) = true ]; then $(DOSDPT) prototype --obo-prefixes --template=$(PATTERNDIR)/dosdp-patterns --outfile=$@; fi | ||
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| individual_patterns_default := $(patsubst %.tsv, $(PATTERNDIR)/data/default/%.ofn, $(notdir $(wildcard $(PATTERNDIR)/data/default/*.tsv))) | ||
| pattern_term_lists_default := $(patsubst %.tsv, $(PATTERNDIR)/data/default/%.txt, $(notdir $(wildcard $(PATTERNDIR)/data/default/*.tsv))) | ||
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@@ -550,40 +550,40 @@ pattern_term_lists_{{ pipeline.id }} := $(patsubst %.tsv, $(PATTERNDIR)/data/{{ | |
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| # Generating the individual pattern modules and merging them into definitions.owl | ||
| $(PATTERNDIR)/definitions.owl: prepare_patterns update_patterns dosdp_patterns_default {% if project.pattern_pipelines_group is defined %} {% for pipeline in project.pattern_pipelines_group.products %} dosdp_patterns_{{ pipeline.id }}{% endfor %}{% endif %} | ||
| @if [ $(PAT) = true ]; then $(ROBOT) merge $(addprefix -i , $(individual_patterns_default)) {% if project.pattern_pipelines_group is defined %} {% for pipeline in project.pattern_pipelines_group.products %} $(addprefix -i , $(individual_patterns_{{ pipeline.id }})){% endfor %}{% endif %} annotate --ontology-iri $(ONTBASE)/patterns/definitions.owl --version-iri $(ONTBASE)/releases/$(TODAY)/patterns/definitions.owl --annotation owl:versionInfo $(VERSION) -o definitions.ofn && mv definitions.ofn $@; fi | ||
| if [ $(PAT) = true ]; then $(ROBOT) merge $(addprefix -i , $(individual_patterns_default)) {% if project.pattern_pipelines_group is defined %} {% for pipeline in project.pattern_pipelines_group.products %} $(addprefix -i , $(individual_patterns_{{ pipeline.id }})){% endfor %}{% endif %} annotate --ontology-iri $(ONTBASE)/patterns/definitions.owl --version-iri $(ONTBASE)/releases/$(TODAY)/patterns/definitions.owl --annotation owl:versionInfo $(VERSION) -o definitions.ofn && mv definitions.ofn $@; fi | ||
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| individual_patterns_names_default := $(strip $(patsubst %.tsv,%, $(notdir $(wildcard $(PATTERNDIR)/data/default/*.tsv)))) | ||
| dosdp_patterns_default: $(SRC) all_imports .FORCE | ||
| @if [ $(PAT) = true ] && [ "${individual_patterns_names_default}" ]; then $(DOSDPT) generate --catalog=catalog-v001.xml --infile=$(PATTERNDIR)/data/default/ --template=$(PATTERNDIR)/dosdp-patterns --batch-patterns="$(individual_patterns_names_default)" --ontology=$< {{ project.dosdp_tools_options }} --outfile=$(PATTERNDIR)/data/default; fi | ||
| if [ $(PAT) = true ] && [ "${individual_patterns_names_default}" ]; then $(DOSDPT) generate --catalog=catalog-v001.xml --infile=$(PATTERNDIR)/data/default/ --template=$(PATTERNDIR)/dosdp-patterns --batch-patterns="$(individual_patterns_names_default)" --ontology=$< {{ project.dosdp_tools_options }} --outfile=$(PATTERNDIR)/data/default; fi | ||
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| {% if project.pattern_pipelines_group is defined %} | ||
| {% for pipeline in project.pattern_pipelines_group.products %} | ||
| individual_patterns_names_{{ pipeline.id }} := $(strip $(patsubst %.tsv,%, $(notdir $(wildcard $(PATTERNDIR)/data/{{ pipeline.id }}/*.tsv)))) | ||
| dosdp_patterns_{{ pipeline.id }}: $(SRC) all_imports .FORCE | ||
| @if [ $(PAT) = true ] && [ "${individual_patterns_names_{{ pipeline.id }}}" ]; then $(DOSDPT) generate --catalog=catalog-v001.xml --infile=$(PATTERNDIR)/data/{{ pipeline.id }} --template=$(PATTERNDIR)/dosdp-patterns/ --batch-patterns="$(individual_patterns_names_{{ pipeline.id }})" --ontology=$< {{ pipeline.dosdp_tools_options }} --outfile=$(PATTERNDIR)/data/{{ pipeline.id }}; fi | ||
| if [ $(PAT) = true ] && [ "${individual_patterns_names_{{ pipeline.id }}}" ]; then $(DOSDPT) generate --catalog=catalog-v001.xml --infile=$(PATTERNDIR)/data/{{ pipeline.id }} --template=$(PATTERNDIR)/dosdp-patterns/ --batch-patterns="$(individual_patterns_names_{{ pipeline.id }})" --ontology=$< {{ pipeline.dosdp_tools_options }} --outfile=$(PATTERNDIR)/data/{{ pipeline.id }}; fi | ||
| {% endfor %} | ||
| {% endif %} | ||
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| # Generating the seed file from all the TSVs. If Pattern generation is deactivated, we still extract a seed from definitions.owl | ||
| $(PATTERNDIR)/all_pattern_terms.txt: $(pattern_term_lists_default) {% if project.pattern_pipelines_group is defined %} {% for pipeline in project.pattern_pipelines_group.products %} $(pattern_term_lists_{{ pipeline.id }}){% endfor %}{% endif %} $(PATTERNDIR)/pattern_owl_seed.txt | ||
| @if [ $(PAT) = true ]; then cat $^ | sort | uniq > $@; else $(ROBOT) query --use-graphs true -f csv -i ../patterns/definitions.owl --query ../sparql/terms.sparql $@; fi | ||
| if [ $(PAT) = true ]; then cat $^ | sort | uniq > $@; else $(ROBOT) query --use-graphs true -f csv -i ../patterns/definitions.owl --query ../sparql/terms.sparql $@; fi | ||
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| $(PATTERNDIR)/pattern_owl_seed.txt: $(PATTERNDIR)/pattern.owl | ||
| @if [ $(PAT) = true ]; then $(ROBOT) query --use-graphs true -f csv -i $< --query ../sparql/terms.sparql $@; fi | ||
| if [ $(PAT) = true ]; then $(ROBOT) query --use-graphs true -f csv -i $< --query ../sparql/terms.sparql $@; fi | ||
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| $(PATTERNDIR)/data/default/%.txt: $(PATTERNDIR)/dosdp-patterns/%.yaml $(PATTERNDIR)/data/default/%.tsv .FORCE | ||
| @if [ $(PAT) = true ]; then $(DOSDPT) terms --infile=$(word 2, $^) --template=$< --obo-prefixes=true --outfile=$@; fi | ||
| if [ $(PAT) = true ]; then $(DOSDPT) terms --infile=$(word 2, $^) --template=$< --obo-prefixes=true --outfile=$@; fi | ||
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| .PHONY: prepare_patterns | ||
| prepare_patterns: | ||
| @if [ $(PAT) = true ]; then touch $(PATTERNDIR)/data $(pattern_term_lists_default) {% if project.pattern_pipelines_group is defined %} {% for pipeline in project.pattern_pipelines_group.products %} $(pattern_term_lists_{{ pipeline.id }}){% endfor %}{% endif %}; fi | ||
| @if [ $(PAT) = true ]; then touch $(PATTERNDIR)/data $(individual_patterns_default) {% if project.pattern_pipelines_group is defined %} {% for pipeline in project.pattern_pipelines_group.products %} $(individual_patterns_{{ pipeline.id }}){% endfor %}{% endif %}; fi | ||
| if [ $(PAT) = true ]; then touch $(PATTERNDIR)/data $(pattern_term_lists_default) {% if project.pattern_pipelines_group is defined %} {% for pipeline in project.pattern_pipelines_group.products %} $(pattern_term_lists_{{ pipeline.id }}){% endfor %}{% endif %}; fi | ||
| if [ $(PAT) = true ]; then touch $(PATTERNDIR)/data $(individual_patterns_default) {% if project.pattern_pipelines_group is defined %} {% for pipeline in project.pattern_pipelines_group.products %} $(individual_patterns_{{ pipeline.id }}){% endfor %}{% endif %}; fi | ||
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| {% if project.pattern_pipelines_group is defined -%} | ||
| {% for pipeline in project.pattern_pipelines_group.products %} | ||
| $(PATTERNDIR)/data/{{ pipeline.id }}/%.txt: $(PATTERNDIR)/dosdp-patterns/%.yaml $(PATTERNDIR)/data/{{ pipeline.id }}/%.tsv .FORCE | ||
| @if [ $(PAT) = true ]; then $(DOSDPT) terms --infile=$(word 2, $^) --template=$< --obo-prefixes=true --outfile=$@; fi | ||
| if [ $(PAT) = true ]; then $(DOSDPT) terms --infile=$(word 2, $^) --template=$< --obo-prefixes=true --outfile=$@; fi | ||
| {% endfor %} | ||
| {% endif -%} | ||
| {% endif %} | ||
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