Fix IdentifyDuplicates to resolve NoneType mismatches#788
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| record.info.get('STRANDS'), | ||
| record.info.get('CPX_TYPE'), | ||
| record.info.get('CPX_INTERVALS') | ||
| record.info.get('CHR2') or "", |
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Thanks for the fix. Can you give me access to the testing workspaces?
I would use the built-in .get(key, default) syntax for consistency across our scripts
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| record.info.get('CHR2') or "", | |
| record.info.get('CHR2', ""), |
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Just shared the workspace with you, apologies for this oversight.
And thanks for the suggestion, just modified it to use this. Given the simplicity of the change, I did a quick sanity test locally, but let me know if I should re-build the docker / re-test with the .get(key, default) syntax as well.
epiercehoffman
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Mar 13, 2025
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LGTM. Thanks for the fix and for running the extra test!
MattWellie
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Apr 7, 2025
…#788) * Initial commit * Removed trailing whitespace * Used .get(x, y) to standardize with repo
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Description
The
IdentifyDuplicatestask looks for a match across several INFO fields in order to determine exact or insert matches. However, these INFO fields may not exist for certain records, and hence are represented asNonein the tuple that stores them. At a certain point, we sort these tuples.As highlighted in Python documentation, when sorting a list of tuples, if there is a match on the search index within each tuple, the subsequent elements in the tuples are compared to define the sort order. This means that Python starts by comparing the first element of each tuple; if they are equal, it moves to the second element, and so on, until it finds elements that differ or reaches the end of the tuples.
Hence, if we reach an element in our sort process for which the INFO field exists in one record but not another, we get the following error:
TypeError: '<' not supported between instances of 'str' and 'NoneType'. This PR is intended to avoid this by setting defaults for all INFO fields that may not exist in a record.Testing