New method for semsim ingestion #215
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Very, very nice looking code. I would prefer if you could get a @yaseminbridges review as well!
I have no concerns, just a few questions for my own learnings
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What is the purpose of this file?
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These .bkp files are used during the test execution. After ingesting data into the H2 database, we need to copy this backup and restore the database's state after the tests are over.
testdata/phenotype/2302_phenotype/2302_phenotype_test.trace.db.bkp
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| data (_type_): row data | ||
| """ | ||
| # TODO:Improve string escaping. Replace this code with parametrised query | ||
| return f"""({mapping_id}, '{data['subject_id']}', '{data['subject_label'].replace("'", "")}', '{data['object_id']}', '{data['object_label'].replace("'", "")}', {data['jaccard_similarity']}, {data['ancestor_information_content']}, {data['phenodigm_score']}, '{data['ancestor_id'].split(",")[0]}', '{data['ancestor_label'].replace("'", "")}')""" # noqa |
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Could this be changed so that the code looks a bit neater, this is a bit confusing to read
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Could this be changed so that the code looks a bit neater, this is a bit confusing to read
Yes, I'd like to use an ORM for escaping SQL, but it will be implemented in a future PR…
Fixes #214