[pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

src/femr/labelers/ehrshot.py

@@ -117,10 +117,7 @@ def get_inpatient_admission_measurements(
     measurements: List[Tuple[datetime.datetime, meds.Measurement]] = []
     for e in patient["events"]:
         for m in e["measurements"]:
-            if (
-                m["metadata"]["table"] == "visit"
-                and m["code"] in admission_codes
-            ):
+            if m["metadata"]["table"] == "visit" and m["code"] in admission_codes:
                 if isinstance(m["metadata"]["end"], str):
                     m["metadata"]["end"] = datetime.datetime.fromisoformat(m["metadata"]["end"])
                 # Error checking

src/femr/post_etl_pipelines/stanford.py

@@ -46,7 +46,7 @@ def _get_stanford_transformations() -> Callable[[meds.Patient], meds.Patient]:
         ),
         join_consecutive_day_visits,
     ]
-    
+
     return lambda patient: functools.reduce(lambda r, f: f(r), transforms, patient)
 
 
@@ -80,7 +80,7 @@ def femr_stanford_omop_fixer_program() -> None:
     os.mkdir(args.target_dataset)
 
     dataset = datasets.Dataset.from_parquet(os.path.join(args.source_dataset, "data", "*"))
-    
+
     fixed_patient = dataset.map(_get_stanford_transformations(), num_proc=args.num_proc, load_from_cache_file=False)
 
     os.mkdir(os.path.join(args.target_dataset, "data"))
@@ -96,5 +96,6 @@ def femr_stanford_omop_fixer_program() -> None:
     with open(os.path.join(args.target_dataset, "metadata.json"), "w") as f:
         json.dump(metadata, f)
 
-if __name__ == '__main__':
-    femr_stanford_omop_fixer_program()
+
+if __name__ == "__main__":
+    femr_stanford_omop_fixer_program()

src/femr/transforms/stanford.py

@@ -156,6 +156,7 @@ def move_pre_birth(patient: meds.Patient) -> meds.Patient:
 
     return patient
 
+
 def select_code(current_code: str, new_code: str) -> str:
     # Prefer "Visit/ERIP" > "Visit/IP" > "Visit/OP" > "Visit/" > everything else
     if current_code == "Visit/ERIP" or new_code == "Visit/ERIP":
@@ -171,15 +172,16 @@ def select_code(current_code: str, new_code: str) -> str:
     else:
         return current_code
 
+
 def join_consecutive_day_visits(patient: meds.Patient) -> meds.Patient:
     """If two visits are on consecutive days, merge them into one visit"""
     current_visit_id: int = None
     current_visit_end: datetime.datetime = None
-    current_visit_code: str = None 
+    current_visit_code: str = None
     old_visit_id_2_new_visit_id: Dict[int, int] = {}
     for e_idx, event in enumerate(patient["events"]):
-        for m_idx, m in enumerate(event['measurements']):
-            if m['metadata']['visit_id'] is not None and m['metadata']['table'] in ['visit', 'visit_detail']:
+        for m_idx, m in enumerate(event["measurements"]):
+            if m["metadata"]["visit_id"] is not None and m["metadata"]["table"] in ["visit", "visit_detail"]:
                 # Found visit measurement
                 m_end = (
                     datetime.datetime.fromisoformat(m["metadata"]["end"])
@@ -190,56 +192,58 @@ def join_consecutive_day_visits(patient: meds.Patient) -> meds.Patient:
                     # Start a new visit
                     current_visit_id = m["metadata"]["visit_id"]
                     current_visit_end = m_end
-                    current_visit_code = m['code']
-                elif m['metadata']['visit_id'] == current_visit_id:
+                    current_visit_code = m["code"]
+                elif m["metadata"]["visit_id"] == current_visit_id:
                     # Same visit, so update its end time
                     current_visit_end = max(m_end, current_visit_end)
-                    current_visit_code = select_code(current_visit_code, m['code'])
-                elif m['metadata']['visit_id'] in old_visit_id_2_new_visit_id:
+                    current_visit_code = select_code(current_visit_code, m["code"])
+                elif m["metadata"]["visit_id"] in old_visit_id_2_new_visit_id:
                     # We have already merged this visit, so update its end time
                     current_visit_end = max(m_end, current_visit_end)
-                    current_visit_code = select_code(current_visit_code, m['code'])
+                    current_visit_code = select_code(current_visit_code, m["code"])
                 else:
                     if (event["time"] - current_visit_end).days <= 1:
                         # Merge the two visits
                         current_visit_end = max(m_end, current_visit_end)
-                        current_visit_code = select_code(current_visit_code, m['code'])
+                        current_visit_code = select_code(current_visit_code, m["code"])
                     else:
                         # Start a new visit
                         current_visit_id = m["metadata"]["visit_id"]
                         current_visit_end = m_end
-                        current_visit_code = m['code']
+                        current_visit_code = m["code"]
                 # NOTE: Need to update both this visit_id and the current_visit_id
-                old_visit_id_2_new_visit_id[m['metadata']['visit_id']] = {
-                    'visit_id' : current_visit_id,
-                    'end' : current_visit_end,
-                    'code' : current_visit_code,
+                old_visit_id_2_new_visit_id[m["metadata"]["visit_id"]] = {
+                    "visit_id": current_visit_id,
+                    "end": current_visit_end,
+                    "code": current_visit_code,
                 }
                 old_visit_id_2_new_visit_id[current_visit_id] = {
-                    'visit_id' : current_visit_id,
-                    'end' : current_visit_end,
-                    'code' : current_visit_code,
+                    "visit_id": current_visit_id,
+                    "end": current_visit_end,
+                    "code": current_visit_code,
                 }
     events = []
     for e_idx, event in enumerate(patient["events"]):
         measurements = []
-        for m_idx, m in enumerate(event['measurements']):
-            if m['metadata']['visit_id']:
-                if m['metadata']['table'] == 'visit':
+        for m_idx, m in enumerate(event["measurements"]):
+            if m["metadata"]["visit_id"]:
+                if m["metadata"]["table"] == "visit":
                     # If this is a visit event, update its end time and delete (if not original visit_id)
-                    m['metadata']['end'] = old_visit_id_2_new_visit_id[m['metadata']['visit_id']]['end']
-                    m['code'] = old_visit_id_2_new_visit_id[m['metadata']['visit_id']]['code']
-                    if old_visit_id_2_new_visit_id[m['metadata']['visit_id']]['visit_id'] == m['metadata']['visit_id']:
+                    m["metadata"]["end"] = old_visit_id_2_new_visit_id[m["metadata"]["visit_id"]]["end"]
+                    m["code"] = old_visit_id_2_new_visit_id[m["metadata"]["visit_id"]]["code"]
+                    if old_visit_id_2_new_visit_id[m["metadata"]["visit_id"]]["visit_id"] == m["metadata"]["visit_id"]:
                         measurements.append(m)
                 else:
                     # Update the visit_id
-                    m['metadata']['visit_id'] = old_visit_id_2_new_visit_id[m['metadata']['visit_id']]['visit_id']
+                    m["metadata"]["visit_id"] = old_visit_id_2_new_visit_id[m["metadata"]["visit_id"]]["visit_id"]
                     measurements.append(m)
-        events.append({
-            'time' : event['time'],
-            'measurements' : measurements,
-        })
-    patient['events'] = events
+        events.append(
+            {
+                "time": event["time"],
+                "measurements": measurements,
+            }
+        )
+    patient["events"] = events
     return patient