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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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15 changes: 11 additions & 4 deletions genie/consortium_to_public.py
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@rxu17 rxu17 May 28, 2024 •
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Just a comment. Nothing actionable here. I think it's OK we don't have unit tests for these giant functions: stagingToCbio, store_clinical_files and consortiumToPublic in the database_to_staging and consortium_to_public code just because these are better tested using integration tests and we already did that with our pipeline comparisons and our test runs on the test pipeline.

Doing this would be outside the scope of this ticket and is already part of our tech debt epic to refactor and add tests.

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Yes, I agree that we add unit tests later for these functions for our tech debt epic.

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The more we can spin out "unit functions" within these larger functions, the more they will be better served as integration tests.

If we think of these as ETL, it should tell the story of data processing.

Original file line number Diff line number Diff line change
Expand Up @@ -139,10 +139,12 @@ def consortiumToPublic(
)

# Clinical release scope filter
# If consortium -> Don't release to public
# TODO: check why this synapse id is hard coded?
clinical_tier_release_scope_synid = databaseSynIdMappingDf["Id"][
databaseSynIdMappingDf["Database"] == "clinical_tier_release_scope"
][0]
publicRelease = extract.get_syntabledf(
syn=syn, query_string="SELECT * FROM syn8545211 where releaseScope = 'public'"
syn=syn,
query_string=f"SELECT * FROM {clinical_tier_release_scope_synid} where releaseScope = 'public'",
)

allClin = clinicalDf[clinicalDf["SAMPLE_ID"].isin(publicReleaseSamples)]
Expand Down Expand Up @@ -186,7 +188,12 @@ def consortiumToPublic(
)

# Grab mapping table to fill in clinical headers
mapping = extract.get_syntabledf(syn=syn, query_string="SELECT * FROM syn9621600")
clinical_code_to_desc_map_synid = databaseSynIdMappingDf["Id"][
databaseSynIdMappingDf["Database"] == "clinical_code_to_desc_map"
][0]
mapping = extract.get_syntabledf(
syn=syn, query_string=f"SELECT * FROM {clinical_code_to_desc_map_synid}"
)
genePanelEntities = []
for entName, entId in consortiumRelease[2]:
is_deprecated_file = entName in ["data_fusions.txt"]
Expand Down
17 changes: 14 additions & 3 deletions genie/database_to_staging.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1013,6 +1013,7 @@ def store_clinical_files(
release_synid,
current_release_staging,
center_mappingdf,
databaseSynIdMappingDf,
used=None,
):
"""
Expand All @@ -1030,6 +1031,7 @@ def store_clinical_files(
release_synid: Synapse id to store release file
current_release_staging: Staging flag
center_mappingdf: Center mapping dataframe
databaseSynIdMappingDf: Database to Synapse Id mapping

Returns:
pandas.DataFrame: configured clinical dataframe
Expand Down Expand Up @@ -1154,7 +1156,12 @@ def store_clinical_files(
keep_merged_consortium_samples = clinicaldf.SAMPLE_ID
# This mapping table is the GENIE clinical code to description
# mapping to generate the headers of the clinical file
mapping = extract.get_syntabledf(syn=syn, query_string="SELECT * FROM syn9621600")
clinical_code_to_desc_map_synid = databaseSynIdMappingDf["Id"][
databaseSynIdMappingDf["Database"] == "clinical_code_to_desc_map"
][0]
mapping = extract.get_syntabledf(
syn=syn, query_string=f"SELECT * FROM {clinical_code_to_desc_map_synid}"
)
clinical_path = os.path.join(GENIE_RELEASE_DIR, "data_clinical.txt")
clinical_sample_path = os.path.join(GENIE_RELEASE_DIR, "data_clinical_sample.txt")
clinical_patient_path = os.path.join(GENIE_RELEASE_DIR, "data_clinical_patient.txt")
Expand Down Expand Up @@ -1564,6 +1571,9 @@ def stagingToCbio(
sv_synid = databaseSynIdMappingDf["Id"][databaseSynIdMappingDf["Database"] == "sv"][
0
]
clinical_tier_release_scope_synid = databaseSynIdMappingDf["Id"][
databaseSynIdMappingDf["Database"] == "clinical_tier_release_scope"
][0]
# Grab assay information
assay_info_ind = databaseSynIdMappingDf["Database"] == "assayinfo"
assay_info_synid = databaseSynIdMappingDf["Id"][assay_info_ind][0]
Expand Down Expand Up @@ -1592,7 +1602,8 @@ def stagingToCbio(
# Clinical release scope filter
# If private -> Don't release to public
clinicalReleaseScopeDf = extract.get_syntabledf(
syn, "SELECT * FROM syn8545211 where releaseScope <> 'private'"
syn,
f"SELECT * FROM {clinical_tier_release_scope_synid} where releaseScope <> 'private'",
)

patientCols = clinicalReleaseScopeDf["fieldName"][
Expand Down Expand Up @@ -1655,6 +1666,7 @@ def stagingToCbio(
consortiumReleaseSynId,
current_release_staging,
CENTER_MAPPING_DF,
databaseSynIdMappingDf,
used=[sample_used, patient_used],
)

Expand Down Expand Up @@ -1884,7 +1896,6 @@ def create_link_version(
]
if clinical_ent:
# Set private permission for the data_clinical.txt link
syn.setPermissions(clinical_ent[0], principalId=3346558, accessType=[])
syn.setPermissions(clinical_ent[0], principalId=3326313, accessType=[])

for ents in case_list_entities:
Expand Down
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
11 changes: 9 additions & 2 deletions tests/test_clinical.py
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Original file line number Diff line number Diff line change
Expand Up @@ -956,8 +956,15 @@ def test_remap_clinical_values_sampletype():
)
def test_remap_clinical_values(col):
"""Test Remapping clinical values"""
testdf = pd.DataFrame({col: [1, 2, 99]})
expecteddf = pd.DataFrame({col: ["Male", "Female", "Unknown"]})
testdf = pd.DataFrame({"SEX": [1, 2, 99], "PRIMARY_RACE": [1, 2, 99]})
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expecteddf = pd.DataFrame(
{
"SEX": ["Male", "Female", "Unknown"],
"PRIMARY_RACE": ["Male", "Female", "Unknown"],
"PRIMARY_RACE_DETAILED": ["Male", "Female", "Not coded"],
"SEX_DETAILED": ["Male", "Female", "Not coded"],
}
)
remappeddf = genie_registry.clinical.remap_clinical_values(
testdf, sexdf, sexdf, sexdf, sexdf
)
Expand Down
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