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Fix SSSOM Schema not having bijective prefix map #302

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merged 3 commits into from
Jul 25, 2023
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@cthoyt cthoyt commented Jul 25, 2023

There are issues in mapping-commons/sssom-py#397 because the base schema does not have a valid prefix map - dc and dcterms are both used as prefixes for the same URI prefix. This happens because LinkML makes some inference about what needs to be there - there are some assorted uses throughout the schema definition with both DC and DCTERMS. This PR updates the schema to only use DCTERMS and puts explicit entries for DCTERMS in the prefix map to address this. It then regenerates the whole project.

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@hrshdhgd When you tink this is good to go, can you merge it and make a new release?

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Thanks a lot @cthoyt !!

@matentzn , I ran make all.

@hrshdhgd hrshdhgd requested a review from matentzn July 25, 2023 13:28
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hrshdhgd commented Jul 25, 2023

Actually hold on ... there still seems more removing to be done.

@hrshdhgd hrshdhgd marked this pull request as draft July 25, 2023 13:39
cthoyt added a commit that referenced this pull request Jul 25, 2023
This PR does not change the underlying schema, it just runs `make all`

This also motivates some kind of CI check that when the schema is updated, then this gets run.

I want to do this to reduce spurious diff in #302
@cthoyt cthoyt mentioned this pull request Jul 25, 2023
cthoyt added a commit that referenced this pull request Jul 25, 2023
This PR does not change the underlying schema, it just runs `make all`

This also motivates some kind of CI check that when the schema is
updated, then this gets run.

I want to do this to reduce spurious diff in #302
Note that the shex project seems to not be getting the prefix map properly, this seems to be an upstream bug
@cthoyt cthoyt marked this pull request as ready for review July 25, 2023 14:12
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cthoyt commented Jul 25, 2023

everything in this is looking good now

@cthoyt cthoyt requested a review from hrshdhgd July 25, 2023 14:15
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lgtm

@cthoyt cthoyt merged commit 0ff31e4 into master Jul 25, 2023
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@cthoyt cthoyt deleted the cthoyt-patch-1 branch July 25, 2023 14:50
cthoyt added a commit to mapping-commons/sssom-py that referenced this pull request Jul 25, 2023
This was possible thanks to mapping-commons/sssom#302
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3 participants