Jbeck/ag 1144/transform gene info testing #121
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… code to test the passing scenario
…tep were both false
…ow errors, created failure case test code
…ins transform to conform to the function definition
…ead of a dict, biodomains now drops rows with NaN biodomain names, added check for boolean values in tep_info. Updated test to work with these fixes
…ed tests for duplicate Ensembl IDs, fixed issue with null ensembl_info in the gene_info transform
jaclynbeck-sage
commented
Feb 12, 2024
| drop_columns=["ensembl_gene_id"], | ||
| nested_field_is_list=False, | ||
| ) | ||
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FYI The above chunk of code has been moved further down the file.
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…to jbeck/AG-1144/transform_gene_info_testing
Co-authored-by: Brad Macdonald <52762200+BWMac@users.noreply.github.com>
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Feb 14, 2024
…to jbeck/AG-1144/transform_gene_info_testing
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This PR adds integration testing for the
gene_infotransform. I also fixed several bugs/missing handling in the transform that I discovered while writing the tests.There are 2 'passing' cases with good data, using two sets of values for
adjusted_p_value_thresholdandprotein_level_threshold, which are specified in the config file.There are 10 'failure' cases where we expect the code to throw errors:
tep_adi_infotep_adi_infoI tried to document a description of each of the data sets and what conditions would pass/fail for each one, at the top of the test_gene_info.py file.
Unfortunately, the
gene_metadatatest files have to be in feather format, not csv, due to having lists of items inside thealiasandensembl_possible_replacementsfields. So those files are not human-readable.Changes made to the transform itself:
is_adiandis_tepfields are boolean (or missing, which is also ok)ensembl_infoends up asnullinstead of a dictionary of null values. Moving thenest_fieldscall for this field from before the merge withgene_infoto after all other data sets were merged, and ensuring that allensembl_possible_replacementsvalues were a list or empty list and notnull, solves the issue.