Get MSDF from LinkML objects #440
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
cthoyt
changed the title
cthoyt
changed the title
cthoyt
added a commit
to cthoyt/ontology-access-kit
that referenced
this pull request
Oct 4, 2023
matentzn
reviewed
Oct 4, 2023
|
@matentzn only risks is that there are more convoluted ways people will think of on how they want to provide metadata, besides that and some of the new python idioms, this is pretty straightforward. |
|
@matentzn I added a round-trip test that demonstrates this works |
matentzn
approved these changes
Oct 5, 2023
hrshdhgd
pushed a commit
to INCATools/ontology-access-kit
that referenced
this pull request
Dec 6, 2023
* Improve SSSOM-py usage Relies on mapping-commons/sssom-py#440 * Update pyproject.toml * Update sssom_utils.py * Update sssom_utils.py * Make code independent * Fix typo * Update lexical_indexer.py * Update test_sssom_matcher.py * Update test_sssom_matcher.py * Update pyproject.toml * Update lock * Update lexical_indexer.py * Update test_sssom_matcher.py * Update pyproject.toml * Lock * Lock again * Update reqs
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Closes #439
This PR adds three methods to the
MappingSetDataFrameclass that allow instantiation from LinkML objects such asMappingSetDocument,MappingSet, or a list ofMapping.It has the benefit of pre-baking in logic for dealing with default metadata and converters, meaning that nobody has to roll this themselves downstream
This is going to help us address https://github.com/INCATools/ontology-access-kit/blob/75940bfa883001afb0e4aebb339fd62583c13844/src/oaklib/utilities/lexical/lexical_indexer.py#L313-L325, specifically in INCATools/ontology-access-kit#664