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TaskExtractorConfig accepts optional predicates_path to split predica… (
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#82)

* TaskExtractorConfig accepts optional predicates_path to split predicates from main config_path (#42)

* Extract trigger only (#85)

* Make windows struct optional when loading config

* Update spacing

* Added patient_demographics and parsing of static variables (#48) (#86)

* Added patient_demographics and parsing of static variables (#48)

* Added filtering based on static predicates (#48)

* Fix tests and column renames to match MEDS

* Update e2e test

* Added tests to boost coverage

* Added more tests for coverage
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@justin13601
justin13601 authored Aug 5, 2024
1 parent 3817bd4 commit 74d0abf
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4 changes: 4 additions & 0 deletions sample_configs/inhospital_mortality.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,10 @@ predicates:
discharge_or_death:
expr: or(discharge, death)

patient_demographics:
male:
code: SEX//male

trigger: admission

windows:
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107 changes: 55 additions & 52 deletions sample_data/sample_data.csv
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Original file line number Diff line number Diff line change
@@ -1,52 +1,55 @@
subject_id,timestamp,admission,death,discharge,lab,spo2,normal_spo2,abnormally_low_spo2,abnormally_high_spo2,procedure_start,procedure_end,ventilation,diagnosis_ICD9CM_41071,diagnosis_ICD10CM_I214
1,12/1/1989 12:03,1,0,0,0,0,0,0,0,0,0,0,0,0
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1,12/1/1989 16:17,0,0,0,1,1,1,0,0,0,0,0,0,0
1,12/1/1989 20:17,0,0,0,1,1,1,0,0,0,0,0,0,0
1,12/2/1989 3:00,0,0,0,1,1,1,0,0,0,0,0,0,0
1,12/2/1989 9:00,0,0,0,0,0,0,0,0,0,0,0,0,0
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1,12/2/1989 14:22,0,0,0,0,0,0,0,0,0,1,1,0,0
1,12/2/1989 15:00,0,0,1,0,0,0,0,0,0,0,0,0,0
1,1/21/1991 11:59,0,0,0,0,0,0,0,0,0,0,0,1,0
1,1/27/1991 23:32,1,0,0,0,0,0,0,0,0,0,0,0,0
1,1/27/1991 23:46,0,0,0,1,1,1,0,0,0,0,0,0,0
1,1/28/1991 3:18,0,0,0,1,0,0,0,0,0,0,0,0,0
1,1/28/1991 3:28,0,0,0,0,0,0,0,0,1,0,1,0,0
1,1/28/1991 4:36,0,0,0,1,1,1,0,0,0,0,0,0,0
1,1/29/1991 23:32,0,0,0,1,1,1,0,0,0,0,0,0,0
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2,6/7/1996 9:00,0,0,0,1,1,0,1,0,0,0,0,0,0
2,6/7/1996 12:00,0,0,0,1,1,1,0,0,0,0,0,0,0
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2,6/8/1996 3:00,0,1,0,0,0,0,0,0,0,0,0,0,0
3,3/8/1996 2:22,0,0,0,0,0,0,0,0,1,0,1,0,0
3,3/8/1996 2:24,1,0,0,0,0,0,0,0,0,0,0,0,0
3,3/8/1996 2:37,0,0,0,1,1,1,0,0,0,0,0,0,0
3,3/9/1996 8:00,0,0,0,1,0,0,0,0,0,0,0,0,0
3,3/9/1996 11:00,0,0,0,1,1,1,0,0,0,0,0,0,0
3,3/9/1996 19:00,0,0,0,1,1,1,0,0,0,0,0,0,0
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3,3/11/1996 21:00,0,0,0,0,0,0,0,0,0,1,1,0,0
3,3/12/1996 0:00,0,1,0,0,0,0,0,0,0,0,0,0,0
subject_id,timestamp,male,female,admission,death,discharge,lab,spo2,normal_spo2,abnormally_low_spo2,abnormally_high_spo2,procedure_start,procedure_end,ventilation,diagnosis_ICD9CM_41071,diagnosis_ICD10CM_I214
1,,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0
1,12/1/1989 12:03,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0
1,12/1/1989 13:14,0,0,0,0,0,1,1,1,0,0,0,0,0,0,0
1,12/1/1989 15:17,0,0,0,0,0,1,1,1,0,0,0,0,0,0,0
1,12/1/1989 16:17,0,0,0,0,0,1,1,1,0,0,0,0,0,0,0
1,12/1/1989 20:17,0,0,0,0,0,1,1,1,0,0,0,0,0,0,0
1,12/2/1989 3:00,0,0,0,0,0,1,1,1,0,0,0,0,0,0,0
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1,12/2/1989 14:22,0,0,0,0,0,0,0,0,0,0,0,1,1,0,0
1,12/2/1989 15:00,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0
1,1/21/1991 11:59,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0
1,1/27/1991 23:32,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0
1,1/27/1991 23:46,0,0,0,0,0,1,1,1,0,0,0,0,0,0,0
1,1/28/1991 3:18,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0
1,1/28/1991 3:28,0,0,0,0,0,0,0,0,0,0,1,0,1,0,0
1,1/28/1991 4:36,0,0,0,0,0,1,1,1,0,0,0,0,0,0,0
1,1/29/1991 23:32,0,0,0,0,0,1,1,1,0,0,0,0,0,0,0
1,1/30/1991 5:00,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0
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1,1/30/1991 11:00,0,0,0,0,0,1,1,1,0,0,0,0,0,0,0
1,1/30/1991 14:00,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
1,1/30/1991 14:15,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0
1,1/31/1991 1:00,0,0,0,0,0,0,0,0,0,0,0,1,1,0,0
1,1/31/1991 2:15,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0
1,2/8/1991 8:15,0,0,0,0,0,1,1,1,0,0,0,0,0,0,0
1,3/3/1991 19:33,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0
1,3/3/1991 20:33,0,0,0,0,0,1,1,0,1,0,0,0,0,0,0
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2,,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0
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2,3/8/1996 16:00,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0
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2,6/5/1996 0:48,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1
2,6/5/1996 1:59,0,0,0,0,0,0,0,0,0,0,1,0,1,0,0
2,6/7/1996 6:00,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0
2,6/7/1996 9:00,0,0,0,0,0,1,1,0,1,0,0,0,0,0,0
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2,6/8/1996 3:00,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0
3,,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0
3,3/8/1996 2:22,0,0,0,0,0,0,0,0,0,0,1,0,1,0,0
3,3/8/1996 2:24,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0
3,3/8/1996 2:37,0,0,0,0,0,1,1,1,0,0,0,0,0,0,0
3,3/9/1996 8:00,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0
3,3/9/1996 11:00,0,0,0,0,0,1,1,1,0,0,0,0,0,0,0
3,3/9/1996 19:00,0,0,0,0,0,1,1,1,0,0,0,0,0,0,0
3,3/9/1996 22:00,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
3,3/11/1996 21:00,0,0,0,0,0,0,0,0,0,0,0,1,1,0,0
3,3/12/1996 0:00,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0
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