Avoid unnecessary dependency on sqlalchemy #1455
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To import MIMIC-IV into SQLite, import.py uses Pandas both to parse each data file (read_csv) and then to push the data into an SQL database (to_sql). The latter step can use an SQLAlchemy database connection for full generality (which might be useful sometimes), but it can also simply use an sqlite3.Connection created by the Python standard library. Since this script is solely aimed at providing an easy way to get the data into SQLite format, it's nice to avoid unnecessary dependencies.
alistairewj
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Dec 24, 2022
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alistairewj
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Looks good - I added a GitHub action to test the build too.
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sqlite/import.pyprovides a quick and easy way to import MIMIC-IV into SQLite format. As far as I can see, there's no reason for this script to be dependent on sqlalchemy.(I'd remove the pandas dependency too, but pandas is actually serving a purpose here by auto-detecting some of the column types.)
Granted, I haven't actually used sqlalchemy and I don't know if it provides any special benefits here. I also only tested this on the demo (https://physionet.org/content/mimic-iv-demo/1.0/). Let me know if you want me to do more extensive testing.
It's a minor thing, but it's nice to have one fewer dependency to worry about.