Merge branch 'feat/ehrshot' of https://github.com/som-shahlab/femr in…

…to feat/ehrshot

src/femr/labelers/ehrshot.py

@@ -95,10 +95,7 @@ def get_outpatient_visit_measurements(
     measurements: List[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

@@ -12,12 +12,12 @@
 
 from femr.transforms import delta_encode, remove_nones
 from femr.transforms.stanford import (
+    join_consecutive_day_visits,
     move_billing_codes,
     move_pre_birth,
     move_to_day_end,
     move_visit_start_to_first_event_start,
     switch_to_icd10cm,
-    join_consecutive_day_visits,
 )
 
 

src/femr/transforms/stanford.py

@@ -181,10 +181,14 @@ def join_consecutive_day_visits(patient: meds.Patient) -> meds.Patient:
         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']) if isinstance(m['metadata']['end'], str) else m['metadata']['end']
+                m_end = (
+                    datetime.datetime.fromisoformat(m["metadata"]["end"])
+                    if isinstance(m["metadata"]["end"], str)
+                    else m["metadata"]["end"]
+                )
                 if current_visit_id is None:
                     # Start a new visit
-                    current_visit_id = m['metadata']['visit_id']
+                    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:
@@ -196,13 +200,13 @@ def join_consecutive_day_visits(patient: meds.Patient) -> meds.Patient:
                     current_visit_end = max(m_end, current_visit_end)
                     current_visit_code = select_code(current_visit_code, m['code'])
                 else:
-                    if (event['time'] - current_visit_end).days <= 1:
+                    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'])
                     else:
                         # Start a new visit
-                        current_visit_id = m['metadata']['visit_id']
+                        current_visit_id = m["metadata"]["visit_id"]
                         current_visit_end = m_end
                         current_visit_code = m['code']
                 # NOTE: Need to update both this visit_id and the current_visit_id
@@ -238,6 +242,7 @@ def join_consecutive_day_visits(patient: meds.Patient) -> meds.Patient:
     patient['events'] = events
     return patient
 
+
 def move_billing_codes(patient: meds.Patient) -> meds.Patient:
     """Move billing codes to the end of each visit.
 

tests/labelers/test_CodeLabelers.py

@@ -6,12 +6,8 @@
 from femr_test_tools import EventsWithLabels, run_test_for_labeler
 
 from femr.labelers import TimeHorizon
-from femr.labelers.omop import (
-    CodeLabeler,
-    LupusCodeLabeler,
-    MortalityCodeLabeler,
-    OMOPConceptCodeLabeler,
-)
+from femr.labelers.omop import CodeLabeler, LupusCodeLabeler, MortalityCodeLabeler, OMOPConceptCodeLabeler
+
 # from femr.labelers.ehrshot import (
 #     AnemiaCodeLabeler,
 #     HyperkalemiaCodeLabeler,