Commit 00e3c7f0 authored by Venkat Malladi's avatar Venkat Malladi
Browse files

Add in tumor registry diagnosis date.

parent 6667d2e7
Pipeline #7802 failed with stage
in 1 minute and 37 seconds
......@@ -42,17 +42,14 @@ def filter_table(demographics, tumor_registry):
# Column filters
demo_filter_col = ["MRN", "GENDER", "ETHNICITY", "RACE", "BIRTH_DATE",
"DEATH_DATE", "DEATH_SOURCE"]
tumor_filter_col = ["Medical Record Number", "Date of Last Contact-Date", "Vital Status"]
tumor_filter_col = ["Medical Record Number", "Date of Last Contact-Date", "Vital Status", 'Date of Diagnosis-Date']
# Filter
demo_filter = demographics.loc[:, demo_filter_col]
tumor_filter = tumor_registry.loc[:, tumor_filter_col]
# Filter for dead status
tumor_dead = tumor_filter[tumor_filter["Vital Status"] == 0]
# merge
df_merged = demo_filter.merge(tumor_dead, left_on='MRN',
df_merged = demo_filter.merge(tumor_filter, left_on='MRN',
right_on='Medical Record Number', how='left')
return df_merged
......@@ -95,6 +92,8 @@ def calculate_shift(merged):
merged['BIRTH_DATE'] = pd.to_datetime(merged['BIRTH_DATE'])
merged['DEATH_DATE'] = pd.to_datetime(merged['DEATH_DATE'])
merged['Date of Last Contact-Date'] = pd.to_datetime(merged['Date of Last Contact-Date'])
merged['Date of Diagnosis-Date'] = pd.to_datetime(merged['Date of Diagnosis-Date'])
# Calculate date shift relative to 1800/01/01
shift_date = datetime.datetime(1800, 1, 1)
......@@ -109,6 +108,7 @@ def calculate_shift(merged):
# Calculate date Shift for death date
merged['DEATH_DATE'] = merged['DEATH_DATE'] + merged['Shift']
merged['DIAGNOSIS_DATE'] = merged['Date of Diagnosis-Date'] + merged['Shift']
# Shift to total seconds
time_delta_series = merged['Shift']
......@@ -149,8 +149,8 @@ def main():
# Write out patients table
shifted_filtered = shifted_df[["MRN", "GENDER", "ETHNICITY", "RACE",
'DEATH_DATE', 'DEATH_SOURCE']]
shifted_filtered.columns = ['mrn', 'sex', 'ethnicity', 'race', 'death_date', 'death_source']
'DEATH_DATE', 'DEATH_SOURCE', 'DIAGNOSIS_DATE']]
shifted_filtered.columns = ['mrn', 'sex', 'ethnicity', 'race', 'death_date', 'death_source', 'diagnosis_date']
shifted_filtered.to_csv(patients, index=False)
# Write out shift table
......
This diff is collapsed.
......@@ -2,20 +2,28 @@ MRN,Shift
934,-4969728000.0
313,-4865961600.0
398,-4432060800.0
398,-4432060800.0
215,-5721235200.0
904,-5552841600.0
411,-4322073600.0
266,-4628880000.0
266,-4628880000.0
707,-4058726400.0
350,-5616604800.0
350,-5616604800.0
399,-4056393600.0
399,-4056393600.0
903,-6081350400.0
903,-6081350400.0
628,-5599238400.0
558,-5419612800.0
590,-5277312000.0
590,-5277312000.0
822,-3583958400.0
532,-5058979200.0
687,-5002819200.0
687,-5002819200.0
423,-4573411200.0
423,-4573411200.0
33,-4528396800.0
88,-4755628800.0
mrn,sex,ethnicity,race,death_date,death_source
934,Female,Hispanic,White,,
313,Female,Non-hispanic,Black,1858-01-14,UTSouthwestern Hospital
398,Female,Non-hispanic,Black,,
215,Female,Non-hispanic,White,,
904,Male,Non-hispanic,White,,
411,Female,Unknown,Unknown,,
266,Male,Hispanic,White,,
707,Male,Non-hispanic,American Indian,,
350,Female,Unknown,Unknown,,
399,Male,Non-hispanic,Asian,,
903,Female,Non-hispanic,White,1824-09-11,UTSouthwestern Hospital
628,Male,Non-hispanic,White,,
558,Male,Hispanic,White,,
590,Female,Hispanic,Other,,
822,Female,Unknown,Unknown,,
532,Male,Declined,Declined,,
687,Male,Non-hispanic,White,,
423,Female,Declined,White,,
33,Male,Non-hispanic,Asian,,
88,Female,Non-hispanic,Hawaiian Pacific Islander,1860-09-18,UTSouthwestern Hospital
mrn,sex,ethnicity,race,death_date,death_source,diagnosis_date
934,Female,Hispanic,White,,,
313,Female,Non-hispanic,Black,1858-01-14 00:00:00.000000000,UTSouthwestern Hospital,1815-10-22 00:00:00.020090219
398,Female,Non-hispanic,Black,,,1829-07-22 00:00:00.020120816
398,Female,Non-hispanic,Black,,,1829-07-22 00:00:00.020140208
215,Female,Non-hispanic,White,,,1788-09-13 00:00:00.020150511
904,Male,Non-hispanic,White,,,1794-01-14 00:00:00.020090701
411,Female,Unknown,Other,,,1833-01-15 00:00:00.020150525
266,Male,Hispanic,White,,,1823-04-27 00:00:00.020080930
266,Male,Hispanic,White,,,1823-04-27 00:00:00.020080910
707,Male,Non-hispanic,American Indian,,,1841-05-21 00:00:00.020100615
350,Female,Unknown,Other,,,1792-01-07 00:00:00.020050724
350,Female,Unknown,Other,,,1792-01-07 00:00:00.020050703
399,Male,Non-hispanic,Asian,,,1841-06-17 00:00:00.020060621
399,Male,Non-hispanic,Asian,,,1841-06-17 00:00:00.020060608
903,Female,Non-hispanic,White,1824-09-11 00:00:00.000000000,UTSouthwestern Hospital,1777-04-16 00:00:00.020150122
903,Female,Non-hispanic,White,1824-09-11 00:00:00.000000000,UTSouthwestern Hospital,1777-04-16 00:00:00.020150203
628,Male,Non-hispanic,White,,,1792-07-26 00:00:00.019980115
558,Male,Hispanic,White,,,1798-04-05 00:00:00.020150307
590,Female,Hispanic,Other,,,1802-10-09 00:00:00.020050716
590,Female,Hispanic,Other,,,1802-10-09 00:00:00.020050721
822,Female,Unknown,Other,,,1856-06-06 00:00:00.020150216
532,Male,Declined,Declined,,,1809-09-09 00:00:00.020070715
687,Male,Non-hispanic,White,,,1811-06-21 00:00:00.020120429
687,Male,Non-hispanic,White,,,1811-06-21 00:00:00.020120503
423,Female,Declined,White,,,1825-01-28 00:00:00.020150505
423,Female,Declined,White,,,1825-01-28 00:00:00.020160627
33,Male,Non-hispanic,Asian,,,1826-07-03 00:00:00.020100807
88,Female,Non-hispanic,Hawaiian Pacific Islander,1860-09-18 00:00:00.000000000,UTSouthwestern Hospital,1819-04-21 00:00:00.020100401
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