Change to SQLAlchemy >= 2 - Githubissues

e-bel / ebel

Software package for parsing and validating Biological Expresison Language files as well as constructing and enriching knowledge graphs in the OrientDB environment.

MIT License

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Change to SQLAlchemy >= 2 #24

Open cebel opened 1 year ago

brucetony commented 1 year ago

Work to do:

[x] Update dep versions

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

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

Nice to have but not crucial for operation:

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