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Including DisGeNET converter #7

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merged 2 commits into from
Jun 21, 2021
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AdrianBZG
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This pull requests aims at including the DisGeNET converter to the main set of converters for HumanMine. It optionally takes a gene list CSV file as input to only integrate data for a specific subset of human genes, but includes data for all genes in the DisGeNET data source if no list is given (default behaviour)

@AdrianBZG AdrianBZG requested a review from sergiocontrino May 12, 2021 15:27
@AdrianBZG AdrianBZG added the enhancement New feature or request label May 12, 2021
@AdrianBZG AdrianBZG requested a review from danielabutano May 12, 2021 15:34
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Just a few comments.

  • please run checkstyleMain (I think you haven't, because e.g. copyright should be 2002-2020)
  • I would move the contructor method up (first method)
  • not sure about the constants GENE_LIST_FILE , what is used for? It's always empty, correct? so probably the processGeneList is never called....

@AdrianBZG
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AdrianBZG commented May 18, 2021

Thanks @danielabutano ,

I just made the suggested changes and some slight clean-up. Regarding the gene list part, this was a functionality to integrate the data only for a specific set of genes given in an input file, as that was useful for the specific use case for which this data converter was made originally. However this is probably not relevant for HumanMine and we'd prefer to integrate the data for all genes.

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Thanks @AdrianBZG ! I leave the merge to @sergiocontrino

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hi @AdrianBZG, i did change a few things for the humanmine build, mainly the key (from symbol to primaryid), but also some in the parsing, using directly the ncbi identifier and not the id resolver. unless you have other ideas, i'll make a PR to your repo first. thanks!

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thank you @AdrianBZG! i'll merge the pull request and then modify the code with the adaptations for humanmine. you can disregard the PR on your repo.

@sergiocontrino sergiocontrino merged commit 8e69ccc into intermine:master Jun 21, 2021
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thanks!

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3 participants