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biolink / biolinkml

DEPRECATED: replaced by linkml
https://github.com/linkml/linkml
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change owlgen to use default_prefix for namespace #180

Closed cmungall closed 4 years ago

cmungall commented 4 years ago

Fixes bug where owlgen placed all classes, properties into meta namespace. The fix incvolves changing how definition_uri is populated while schema loading. Fixes #163 

hsolbrig commented 4 years ago

A couple of questions / problems with this fix:

1) The separator between the base URI and item has been changed from '/' to '#'. This breaks some existing code -- we need to discuss why and whether there might be a gentler way to do it. 2) There is a problem with aliases in the owl generator. See: [tests/test_issues/input/issue_163c.yaml]() for details. We need to discuss approaches

cmungall commented 4 years ago

hmm I don't recall intending to change anything from / to #...

hsolbrig commented 4 years ago

@cmungall - see https://github.com/biolink/biolinkml/blob/issue-163-redux/biolinkml/utils/mergeutils.py#L70

cmungall commented 4 years ago

OK, changed '#' to '/' (this is only the case where a prefix is not declared)

Looks like I now have conflicts, most of these seem to be generated test files, maybe I shouldn't have included in the PR

hsolbrig commented 4 years ago

We'll catch the conflicts -- @jiaola is going to create a merge action that automatically rewrites them. Thanks!