AG-1117: Add new ensembl info fields to gene_info transform #95
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jaclynbeck-sage
commented
Nov 3, 2023
| df=target_list, | ||
| grouping="ensembl_gene_id", | ||
| new_column="target_nominations", | ||
| drop_columns=["ensembl_gene_id"], |
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Note: changes like this are from the black formatter, I didn't change anything functional.
jaclynbeck-sage
commented
Nov 3, 2023
| @@ -97,6 +106,21 @@ def transform_gene_info( | |||
| axis=1, | |||
| ) | |||
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Real changes I made start here.
JessterB
reviewed
Nov 6, 2023
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This looks good, although I still need to think about whether this will work for us:
Currently, if no Ensembl archive is available for the Ensembl release of the gene, the URL will be for the most recent available archive that is older than the gene's Ensembl release.)
Regardless, this will unblock feature implementation while we figure out if those links are what we want.
JessterB
approved these changes
Nov 6, 2023
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Adds a nested
ensembl_infofield to thegene_infotransform per this JIRA task. The nested field contains variables:ensembl_release(number)ensembl_possible_replacements(list, may be empty)ensembl_permalink(URL. Currently, if no Ensembl archive is available for the Ensembl release of the gene, the URL will be for the most recent available archive that is older than the gene's Ensembl release.)I spot-checked the output JSON file and confirmed that it the only changes are the addition of the
ensembl_infodata, which has the structure defined in the JIRA task.We don't have tests written for the
gene_infotransform so there are none to update.