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Make a PCO release

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Ramona Walls edited this page Feb 13, 2020 · 20 revisions

Make release files

All edits should happen in src/ontology/pco-edit.owl.

Make a release with ROBOT/ODK

As of the Feb. 2020 release, this repo was updated to the latest version of ODK.

Because the import files are customized, I modified the make file (/src/ontology/Makefile) to skip the regeneration of import files in /src/ontology/imports by setting IMP=false on line 242.

This means that .obo files must be created manually before a release by saving each .owl file in /src/ontology/imports as .obo.

Also in the make file, change the references to 'ELK' that are not in comments to 'hermit'.

Navigate to /src/ontology and run sh run.sh make prepare_release. This generates:

Make a release with OORT.

This protocol is not longer used, but I keep a copy for reference.

When you are ready for a release, first make a test file. Browse to src/ontology and type "make test". This will generate a file src/ontology/pco.owl.

When you are satisfied that the test file is what you want, make the release by typing "make release" from within src/ontology. This will generate a new version of src/ontology/pco.owl plus a new version of pco.owl in the root directory (which will become live automatically, because that's where the PURL points).

To make a version of PCO that has all the imports merged requires manual editing:

  • Open src/ontology/pco.owl in Protege
  • Under the Refactor menu, select Merge ontologies...
  • From the menu, select everything except pco
  • Select "Merge into existing ontology"
  • Select PCO as the target ontology
  • Delete (x out) all of the imported ontologies
  • Until RO is fixed, delete GO:0040011 and GO:0048018
  • Delete all the extra ontology annotations that got added with the merge (under Ontology Header on the Active Ontology tab) except the dc:source annotations
  • Change the ontology IRI to http://purl.obolibrary.org/obo/pco_merged_inferred.owl and change the corresponding version IRI
  • Save at src/ontology/pco_merged_inferred.owl, replacing the existing copy of that file

Push all changes to the repo

Make a release on Github

To do this, you need to created a tag.

  • Click on Releases
  • Click Draft a new release
  • Name the tag and the release by the date as YYYY-MM-DD
  • Describe the changes that are included in the release
  • Click Publish Release

Update PURLS

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