Have pandas upsert to db and clean up archive code #391
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krivard
suggested changes
Jan 21, 2021
integrations/acquisition/covidcast_nowcast/test_csv_uploading.py
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| except Exception: | ||
| move(filepath, filepath.replace("receiving", "archive/failed")) | ||
| _move_after_processing(filepath, success=False) | ||
| raise |
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Do you need a finally block to do any connection cleanup with the database? I know the mysql.connect library requires something like
but not sure if sqlalchemy needs something similar
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i wondered that too when i first implemented it, since ive had to cloes sqlalchemy connections before, but the to_sql method can take an engine and not a connection. Based on this answer, looks like it isn't needed. The connection used for the connection metadata is in a context manager so i think thats ok as well
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Pandas to_sql only inserts and doesnt update if there's a duplicate unique key, so this change makes it upsert. Full disclosure, i just copy pasted most of this off a stackoverflow answer since im not very familiar with how sqlalchemy and pandas sql insertion methods work. Wrote a test that failed before, and this code made it pass 🤷
Also cleaned up some file moving code to reduce duplication and handle generating directories if they don't exist.