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…t == float for length, molecular wweights and pi
Add error handling when run main.py for network database
… protein interactions to have timestamp and for gene and protein tables and annotation type for physical interactions table
… protein_protein_interactions to include _new, and fixing the populate data scripts to add timestamp and source to the gene and protein tables, and adding annotation type for both GRN and PPI network and interactions table
… namespaces and addition of timestamp. need to test that queries work correctly
…, and rename database2 to database
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This PR should be ready to review. I'm sorry, this PR is large :(((. I didn't mean to ..... |
…ry to only have timestamp query if timestamp is 2025 or later. need to fix query though since ZAP1 gene is not showing correct self-regulating expression
…constants.js, removed trailing spaces.
…ed constants to dbConstants, and now queries don't perform correctly
…ot currently using dbConstants file
…s and protein-dals. correctly make query based on timestamp, need to check if add source to query
…y_network_with_timestamp
Updating database [Cecilia's PR]
dondi
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Mar 11, 2025
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dondi
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Phew! It’s a lot of code and documentation, but it’s actually a net 450 fewer lines 💪🏼
We should look into ways to protect against SQL injection in a future ticket, plus of course we should actually migrate our existing databases to this new approach. I’ll write up new issues for those
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| return `SELECT DISTINCT protein1, protein2${annotation} FROM | ||
| ${namespace}.physical_interactions WHERE | ||
| physical_interactions.time_stamp='${timestamp}' AND physical_interactions.source='${source}' AND | ||
| ${buildNetworkProteinsQuery(proteins)} ORDER BY protein1 DESC;`; |
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Just noting that the approach leaves us theoretically vulnerable to SQL injection attacks. For future work, we should look into safer ways to build our SQL queries
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