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Change to SQLAlchemy >= 2 #24

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cebel opened this issue Sep 2, 2023 · 1 comment · May be fixed by #25
Open

Change to SQLAlchemy >= 2 #24

cebel opened this issue Sep 2, 2023 · 1 comment · May be fixed by #25
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@brucetony

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@cebel
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cebel commented Sep 2, 2023

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@brucetony
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brucetony commented Sep 15, 2023 •
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Work to do:

  • Update dep versions

Update Models to use mapped_column() and test insert/update:

  • biogrid
  • chebi
  • clinical trials
  • clinvar
  • disgenet
  • drugbank
  • ensembl
  • expression atlas
  • gwas catalog
  • hgnc
  • human ortholog
  • intact
  • iuphar
  • kegg
  • mirtarbase
  • ncbi
  • nsides
  • pathway commons
  • protein atlas
  • reactome
  • stringdb
  • uniprot

Nice to have but not crucial for operation:

  • Update queries to use select() instead of the temporary text() (unlisted biodbs were done before)
    • biogrid
    • clinvar
    • disgenet
    • expression atlas
    • kegg
    • nsides
    • uniprot

@brucetony brucetony self-assigned this Sep 15, 2023
@brucetony brucetony linked a pull request Sep 15, 2023 that will close this issue
Sqlalchemy 2.0 update #25
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Sqlalchemy 2.0 update e-bel/ebel
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@brucetony @cebel