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Adds a test case to document the behavior for #156. #185

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merged 3 commits into from
Aug 28, 2024
Merged

Adds a test case to document the behavior for #156. #185

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9e3d782
Added more complex metadata extraction test that replicates part of #156
mmcdermott Aug 28, 2024
838fbea
Correct config for the test case and add a comment.
mmcdermott Aug 28, 2024
3cba71d
Manually added valueuom to MIMIC config.
mmcdermott Aug 28, 2024
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2 changes: 2 additions & 0 deletions MIMIC-IV_Example/configs/event_configs.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -100,6 +100,7 @@ hosp/labevents:
description: ["omop_concept_name", "label"] # List of strings are columns to be collated
itemid: "itemid (omop_source_code)"
parent_codes: "{omop_vocabulary_id}/{omop_concept_code}"
valueuom: "valueuom"

hosp/omr:
omr:
Expand Down Expand Up @@ -218,6 +219,7 @@ icu/chartevents:
description: ["omop_concept_name", "label"] # List of strings are columns to be collated
itemid: "itemid (omop_source_code)"
parent_codes: "{omop_vocabulary_id}/{omop_concept_code}"
valueuom: "valueuom"

icu/procedureevents:
start:
Expand Down
47 changes: 26 additions & 21 deletions tests/MEDS_Extract/test_extract_code_metadata.py
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Original file line number Diff line number Diff line change
Expand Up @@ -18,30 +18,30 @@
239684,,HEIGHT,175.271115221764
239684,"12/28/1980, 00:00:00",DOB,
239684,"05/11/2010, 17:41:51",ADMISSION//CARDIAC,
239684,"05/11/2010, 17:41:51",HR,102.6
239684,"05/11/2010, 17:41:51",HR//bpm,102.6
239684,"05/11/2010, 17:41:51",TEMP,96.0
239684,"05/11/2010, 17:48:48",HR,105.1
239684,"05/11/2010, 17:48:48",HR//bpm,105.1
239684,"05/11/2010, 17:48:48",TEMP,96.2
239684,"05/11/2010, 18:25:35",HR,113.4
239684,"05/11/2010, 18:25:35",HR//bpm,113.4
239684,"05/11/2010, 18:25:35",TEMP,95.8
239684,"05/11/2010, 18:57:18",HR,112.6
239684,"05/11/2010, 18:57:18",HR//bpm,112.6
239684,"05/11/2010, 18:57:18",TEMP,95.5
239684,"05/11/2010, 19:27:19",DISCHARGE,
1195293,,EYE_COLOR//BLUE,
1195293,,HEIGHT,164.6868838269085
1195293,"06/20/1978, 00:00:00",DOB,
1195293,"06/20/2010, 19:23:52",ADMISSION//CARDIAC,
1195293,"06/20/2010, 19:23:52",HR,109.0
1195293,"06/20/2010, 19:23:52",HR//bpm,109.0
1195293,"06/20/2010, 19:23:52",TEMP,100.0
1195293,"06/20/2010, 19:25:32",HR,114.1
1195293,"06/20/2010, 19:25:32",HR//bpm,114.1
1195293,"06/20/2010, 19:25:32",TEMP,100.0
1195293,"06/20/2010, 19:45:19",HR,119.8
1195293,"06/20/2010, 19:45:19",HR//bpm,119.8
1195293,"06/20/2010, 19:45:19",TEMP,99.9
1195293,"06/20/2010, 20:12:31",HR,112.5
1195293,"06/20/2010, 20:12:31",HR//bpm,112.5
1195293,"06/20/2010, 20:12:31",TEMP,99.8
1195293,"06/20/2010, 20:24:44",HR,107.7
1195293,"06/20/2010, 20:24:44",HR//bpm,107.7
1195293,"06/20/2010, 20:24:44",TEMP,100.0
1195293,"06/20/2010, 20:41:33",HR,107.5
1195293,"06/20/2010, 20:41:33",HR//bpm,107.5
1195293,"06/20/2010, 20:41:33",TEMP,100.4
1195293,"06/20/2010, 20:50:04",DISCHARGE,

Expand All @@ -52,14 +52,14 @@
68729,,HEIGHT,160.3953106166676
68729,"03/09/1978, 00:00:00",DOB,
68729,"05/26/2010, 02:30:56",ADMISSION//PULMONARY,
68729,"05/26/2010, 02:30:56",HR,86.0
68729,"05/26/2010, 02:30:56",HR//bpm,86.0
68729,"05/26/2010, 02:30:56",TEMP,97.8
68729,"05/26/2010, 04:51:52",DISCHARGE,
814703,,EYE_COLOR//HAZEL,
814703,,HEIGHT,156.48559093209357
814703,"03/28/1976, 00:00:00",DOB,
814703,"02/05/2010, 05:55:39",ADMISSION//ORTHOPEDIC,
814703,"02/05/2010, 05:55:39",HR,170.2
814703,"02/05/2010, 05:55:39",HR//bpm,170.2
814703,"02/05/2010, 05:55:39",TEMP,100.1
814703,"02/05/2010, 07:02:30",DISCHARGE,

Expand All @@ -69,7 +69,7 @@
754281,,HEIGHT,166.22261567137025
754281,"12/19/1988, 00:00:00",DOB,
754281,"01/03/2010, 06:27:59",ADMISSION//PULMONARY,
754281,"01/03/2010, 06:27:59",HR,142.0
754281,"01/03/2010, 06:27:59",HR//bpm,142.0
754281,"01/03/2010, 06:27:59",TEMP,99.8
754281,"01/03/2010, 08:22:13",DISCHARGE,

Expand All @@ -79,21 +79,21 @@
1500733,,HEIGHT,158.60131573580904
1500733,"07/20/1986, 00:00:00",DOB,
1500733,"06/03/2010, 14:54:38",ADMISSION//ORTHOPEDIC,
1500733,"06/03/2010, 14:54:38",HR,91.4
1500733,"06/03/2010, 14:54:38",HR//bpm,91.4
1500733,"06/03/2010, 14:54:38",TEMP,100.0
1500733,"06/03/2010, 15:39:49",HR,84.4
1500733,"06/03/2010, 15:39:49",HR//bpm,84.4
1500733,"06/03/2010, 15:39:49",TEMP,100.3
1500733,"06/03/2010, 16:20:49",HR,90.1
1500733,"06/03/2010, 16:20:49",HR//bpm,90.1
1500733,"06/03/2010, 16:20:49",TEMP,100.1
1500733,"06/03/2010, 16:44:26",DISCHARGE,
"""
)


INPUT_METADATA_FILE = """
lab_code,title,loinc
HR,Heart Rate,8867-4
temp,Body Temperature,8310-5
lab_code,valueuom,title,loinc
HR,bpm,Heart Rate,8867-4
temp,,Body Temperature,8310-5
"""

DEMO_METADATA_FILE = """
Expand Down Expand Up @@ -135,14 +135,17 @@
time: col(disch_date)
time_format: "%m/%d/%Y, %H:%M:%S"
HR:
code: HR
code:
- HR
- col(valueuom)
time: col(vitals_date)
time_format: "%m/%d/%Y, %H:%M:%S"
numeric_value: HR
_metadata:
input_metadata:
description: {"title": {"lab_code": "HR"}}
parent_codes: {"LOINC/{loinc}": {"lab_code": "HR"}}
valueuom: {"valueuom": {"lab_code": "HR"}} # If we didn't have this valueuom would be null for HR rows
temp:
code: TEMP
time: col(vitals_date)
Expand All @@ -152,6 +155,7 @@
input_metadata:
description: {"title": {"lab_code": "temp"}}
parent_codes: {"LOINC/{loinc}": {"lab_code": "temp"}}
valueuom: {"valueuom": {"lab_code": "temp"}}
"""

SHARDS_JSON = {
Expand All @@ -164,7 +168,7 @@
WANT_OUTPUTS = {
"metadata/codes": pl.DataFrame(
{
"code": ["EYE_COLOR//BLUE", "EYE_COLOR//BROWN", "EYE_COLOR//HAZEL", "HR", "TEMP"],
"code": ["EYE_COLOR//BLUE", "EYE_COLOR//BROWN", "EYE_COLOR//HAZEL", "HR//bpm", "TEMP"],
"description": [
"Blue Eyes. Less common than brown.",
"Brown Eyes. The most common eye color.",
Expand All @@ -173,6 +177,7 @@
"Body Temperature",
],
"parent_codes": [None, None, None, ["LOINC/8867-4"], ["LOINC/8310-5"]],
"valueuom": [None, None, None, "bpm", None],
}
),
}
Expand Down
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