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Updating to new SSSOM model#172

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matentzn merged 60 commits intomasterfrom
update-sssom
Dec 3, 2021
Merged

Updating to new SSSOM model#172
matentzn merged 60 commits intomasterfrom
update-sssom

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@matentzn
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@matentzn matentzn commented Oct 8, 2021

Will probably break quite a few things.

@hrshdhgd I have updated SSSOM here, not tested anything, not looked at anything.. Can you fix it before #163 and then we can test that properly :P

Thanks.

Will probably break quite a few things.
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matentzn commented Oct 8, 2021

Yeah this will be seriously hard.. Its a very much newer linkml version that generated the python file.. It does not look too bad:

sssom/util.py:31: error: Module "sssom.sssom_datamodel" has no attribute "Entity"
sssom/util.py:31: error: Module "sssom.sssom_datamodel" has no attribute "slots"
sssom/__init__.py:1: error: Module "sssom.sssom_datamodel" has no attribute "slots"
sssom/writers.py:18: error: Module "sssom.sssom_datamodel" has no attribute "slots"
sssom/rdf_util.py:9: error: Module "sssom.sssom_datamodel" has no attribute "EntityId"

But its actually quite touch because the concept of "Entity" was removed from the metadamodel.

If this is too hard, let me know, I will do it then when I get to it @hrshdhgd :)

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I have updated sssom.yaml in https://github.com/mapping-commons/sssom

so you should pull changes to the repo and ditch any changes you have locally in that repo. This also adds the predicate_modifier column.

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hrshdhgd commented Dec 1, 2021

The mappings type being dict has been fixed where now it is a list. See this on linkml and this in our repo.

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@hrshdhgd looks great. I made a few refactoring suggestions.. After that, this can be merged.

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hrshdhgd commented Dec 2, 2021

I have addressed all of your refactored suggestions. Thank you Nico!

@matentzn matentzn merged commit 8db6c75 into master Dec 3, 2021
@matentzn matentzn deleted the update-sssom branch December 3, 2021 12:04
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3 participants