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Remove builds from all ontologies' metadata (#2892)
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Makefile

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# Remove and/or revert all targets to their repository versions:
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clean:
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rm -Rf registry/ontologies.nt registry/ontologies.ttl registry/ontologies.yml sparql-consistency-report.txt jenkins-output.txt valid-purl-report.txt valid-purl-report.txt.tmp _site/ tmp/ reports/
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rm -Rf registry/ontologies.nt registry/ontologies.ttl registry/ontologies.yml sparql-consistency-report.txt valid-purl-report.txt valid-purl-report.txt.tmp _site/ tmp/ reports/
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git checkout _config.yml registry/ontologies.jsonld registry/ontologies.ttl registry/ontologies.yml
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sparql-consistency-report.txt: registry/ontologies.yml
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./util/processor.py -i $< sparql-compare > $@.tmp && mv $@.tmp $@
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# output of central OBO build
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# See FAQ for more details, and also README.md
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jenkins-output.txt:
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wget http://build.berkeleybop.org/job/simple-build-obo-all/lastBuild/consoleFull -O $@
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reports/%.csv: registry/ontologies.ttl sparql/%.sparql
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arq --data $< --query sparql/$*.sparql --results csv > $@.tmp && mv $@.tmp $@

README.md

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TODO: add a quick guide to yaml, and the tags we use.
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## Central OBO library build
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(see also the FAQ entry on this)
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The central OBO build runs here:
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* http://build.berkeleybop.org/job/simple-build-obo-all/
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It takes as metadata input the yml file from this repository. It makes
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use of the `build` object.
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The output of this job is a set of obo and owl files deposited in
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* http://berkeleybop.org/ontologies/
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Depending on the build configuration, this may also make additional files. See for example:
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* http://berkeleybop.org/ontologies/uberon/
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A http://berkeleybop.org/ontologies/ URL should never be handed out directly. This service exists so that:
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* Un PURL-registered ontologies will have a fall-through
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* Registered PURL ontologies that do not want to take charge of either OBO or OWL generation will have a place to 302-redirect to
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This job will fail if ontologies marked as `infallible` fail. To debug, the full log of the last build can be examined:
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* https://build.berkeleybop.org/job/simple-build-obo-all/lastBuild/consoleFull
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(Look for the text "should not fail")
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## Instructions for Website Development
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See [README-sitedev.md](README-sitedev.md)

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