feat!: support PostgreSQL as optional storage backend #116
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korikuzma
requested changes
May 8, 2023
| if not click.confirm("Are you sure you want to overwrite existing data?"): | ||
| click.get_current_context().exit() | ||
| if not data_url: | ||
| data_url = os.environ.get("DISEASE_NORM_REMOTE_DB_URL") |
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Are you working on a similar docs issue as you did in gene-normalizer? If so, it would be good to add DISEASE_NORM_REMOTE_DB_URL to that issue
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Yeah, I want to do one more iteration on the gene docs and then I'll start building out comparable stuff with disease and therapy
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@jsstevenson It also looks like there's some conflicts that need resolved before merging |
korikuzma
requested changes
May 8, 2023
.github/workflows/github-actions.yml
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| - name: Build local DynamoDB server | ||
| - name: Build local DynamoDB | ||
| if: ${{ env.GENE_NORM_DB_URL == 'http://localhost:8000' }} |
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Suggested change
| if: ${{ env.GENE_NORM_DB_URL == 'http://localhost:8000' }} | |
| if: ${{ env.DISEASE_NORM_DB_URL == 'http://localhost:8000' }} |
.github/workflows/github-actions.yml
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| ./tests/unit/dynamodb_build.bash | ||
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| - name: Install DynamoDB dependencies | ||
| if: ${{ env.GENE_NORM_DB_URL == 'http://localhost:8000' }} |
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Suggested change
| if: ${{ env.GENE_NORM_DB_URL == 'http://localhost:8000' }} | |
| if: ${{ env.DISEASE_NORM_DB_URL == 'http://localhost:8000' }} |
.github/workflows/github-actions.yml
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| run: python3 -m pip install ".[etl,test]" | ||
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| - name: Install PG dependencies | ||
| if: ${{ env.GENE_NORM_DB_URL != 'http://localhost:8000' }} |
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Suggested change
| if: ${{ env.GENE_NORM_DB_URL != 'http://localhost:8000' }} | |
| if: ${{ env.DISEASE_NORM_DB_URL != 'http://localhost:8000' }} |
korikuzma
previously approved these changes
May 8, 2023
korikuzma
approved these changes
May 12, 2023
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Finalizes a dev release implementing an optional Postgres DB backend to use in TheraPy CI. Once tests are passing for everything, there will be another full release.
Otherwise, everything is basically the same as the gene PR. I've noticed that all three normalizers have slightly different query method structure, which would be good to fix up at some point, but not pressing rn.