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Commits on Aug 25, 2024

• Add ability to set `maxGenesWithoutNotes` (default value = 100) on the command line

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Commits on Aug 16, 2024

• Correctly delete temporary files after validation

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Commits on Aug 15, 2024

• Delete temporary files after validation

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Commits on Nov 22, 2023

• Just a little minor rearrangement.

  

  Sam Hokin

  committed
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• Some package updates.

  

  Sam Hokin

  committed
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• Check that obo and trait file trait names are present in result file.

  

  Sam Hokin

  committed
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• Warn, not error, on genes without notes up to 100 records.

  

  Sam Hokin

  committed
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• Just a handy-dandy routine to get XML for a path query.

  

  Sam Hokin

  committed
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Commits on Oct 9, 2023

• Improved gene record Note and GO term logic. Yanked pathways.

  

  Sam Hokin

  committed
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Commits on Sep 7, 2023

• Empty so remove.

  

  Sam Hokin

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Commits on Sep 6, 2023

• Switch to individual vector upserts to catch errors.

  

  Sam Hokin

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• Tweakage.

  

  Sam Hokin

  committed
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Commits on Jul 31, 2023

• Added accession_group.

  

  Sam Hokin

  committed
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Commits on Jul 19, 2023

• Merge branch 'main' of https://github.com/ncgr/java

  

  Sam Hokin

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• Show parsed attributes in error message.

  

  Sam Hokin

  committed
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Commits on Jul 17, 2023

• More diagnostic messages.

  

  Sam Hokin

  committed
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Commits on Jul 11, 2023

• Hand-rolled pinecone package because of change at Pinecone.

  

  Sam Hokin

  committed
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Commits on Jun 16, 2023

• Merge branch 'main' of https://github.com/ncgr/java

  

  Sam Hokin

  committed
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• Switch to gpt-3.5-turbo-0613. (gpt-3.5-turbo overloaded a lot.)

  

  Sam Hokin

  committed
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Commits on Jun 6, 2023

• Switch to gpt-3.5-turbo (not 0301)

  

  Sam Hokin

  committed
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• Update mode for PubMed/PubAg search upserts. Plus tweaks.

  

  Sam Hokin

  committed
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Commits on May 23, 2023

• Merge branch 'main' of https://github.com/ncgr/java

  

  Sam Hokin

  committed
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• Vector to abstract dumper/loader; other weaks.

  

  Sam Hokin

  committed
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Commits on May 22, 2023

• GFF must have gene records; they must have Note attribute; it must have

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  Sam Hokin

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• Added getters.

  

  Sam Hokin

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Commits on May 18, 2023

• Ignore web.xml.

  

  Sam Hokin

  committed
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• Remove web.xml from github.

  

  Sam Hokin

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Commits on May 17, 2023

• Added needed libs, fixed a package name.

  

  Sam Hokin

  committed
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• All new pubmed package. Need to update mine loaders.

  

  Sam Hokin

  committed
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• Added pubag.

  

  Sam Hokin

  committed
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• Added chatbot.

  

  Sam Hokin

  committed
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Commits on May 11, 2023

• Pangene set collections.

  

  Sam Hokin

  committed
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• Added genus description class plus pangene set support.

  

  Sam Hokin

  committed
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Commits on Feb 13, 2023

• More dupe checks, I think.

  

  Sam Hokin

  committed
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Commits on Jan 25, 2023

• Validate against duplicate IDs in GFF. Also bumped biojava.

  

  Sam Hokin

  committed
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