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[GEN-1313] Export detailed columns for NAACCR codes #567

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merged 10 commits into from
May 28, 2024
Merged

[GEN-1313] Export detailed columns for NAACCR codes #567

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f1f8f92
export detailed columns for NAACCR codes
danlu1 May 17, 2024
f6eb440
replace hard code dataframe synid with genie_config
danlu1 May 17, 2024
3cac57e
replace hard code table synid
danlu1 May 20, 2024
91ef469
update unit test
danlu1 May 20, 2024
c93116e
remove Project GENIE data analysis group since it no longer exists
danlu1 May 23, 2024
39fcdbd
replace hard code in public release code
danlu1 May 24, 2024
a4578ee
reformat genie/consortium_to_public.py
danlu1 May 24, 2024
d1b472d
add clinical_tier_release_scope table synid to genie_config
danlu1 May 28, 2024
bc6b684
add more tests to the unit test
danlu1 May 28, 2024
6de52e5
Merge branch 'develop' into GEN-1313-create-naaccr-codes
danlu1 May 28, 2024
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23 changes: 18 additions & 5 deletions genie_registry/clinical.py
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Original file line number Diff line number Diff line change
Expand Up @@ -306,8 +306,16 @@ def remap_clinical_values(
sampletype_mapping.index = sampletype_mapping["CODE"]
sampletype_dict = sampletype_mapping.to_dict()

if clinicaldf.get("SAMPLE_TYPE") is not None:
clinicaldf["SAMPLE_TYPE_DETAILED"] = clinicaldf["SAMPLE_TYPE"]
for column in [
"PRIMARY_RACE",
"SECONDARY_RACE",
"TERTIARY_RACE",
"SEX",
"ETHNICITY",
"SAMPLE_TYPE",
]:
if column in clinicaldf.columns:
clinicaldf[f"{column}_DETAILED"] = clinicaldf[column]

# Use pandas mapping feature
clinicaldf = clinicaldf.replace(
Expand All @@ -316,9 +324,14 @@ def remap_clinical_values(
"SECONDARY_RACE": race_dict["CBIO_LABEL"],
"TERTIARY_RACE": race_dict["CBIO_LABEL"],
"SAMPLE_TYPE": sampletype_dict["CBIO_LABEL"],
"SAMPLE_TYPE_DETAILED": sampletype_dict["DESCRIPTION"],
"SEX": sex_dict["CBIO_LABEL"],
"ETHNICITY": ethnicity_dict["CBIO_LABEL"],
"PRIMARY_RACE_DETAILED": race_dict["DESCRIPTION"],
"SECONDARY_RACE_DETAILED": race_dict["DESCRIPTION"],
"TERTIARY_RACE_DETAILED": race_dict["DESCRIPTION"],
"SAMPLE_TYPE_DETAILED": sampletype_dict["DESCRIPTION"],
"SEX_DETAILED": sex_dict["DESCRIPTION"],
"ETHNICITY_DETAILED": ethnicity_dict["DESCRIPTION"],
}
)

Expand Down Expand Up @@ -481,12 +494,12 @@ def preprocess(self, newpath):
# hardcoded because it never changes
# TODO: Add clinical tier release scope to GENIE config
patient_cols_table = self.syn.tableQuery(
"select fieldName from syn8545211 where "
f"select fieldName from {self.genie_config['clinical_tier_release_scope']} where "
"patient is True and inClinicalDb is True"
)
patient_cols = patient_cols_table.asDataFrame()["fieldName"].tolist()
sample_cols_table = self.syn.tableQuery(
"select fieldName from syn8545211 where "
f"select fieldName from {self.genie_config['clinical_tier_release_scope']} where "
"sample is True and inClinicalDb is True"
)
sample_cols = sample_cols_table.asDataFrame()["fieldName"].tolist()
Expand Down
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