Merge pull request #27 from Medical-Event-Data-Standard/v2_release_ca…

…ndidate MEDS v2 Release
Medical-Event-Data-Standard · May 4, 2024 · a69ec50 · a69ec50
2 parents 965b5de + 08b2562
commit a69ec50
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Showing 5 changed files with 18 additions and 36 deletions.
diff --git a/.gitignore b/.gitignore
@@ -1,4 +1,5 @@
 # Byte-compiled / optimized / DLL files
+_version.py
 __pycache__/
 *.py[cod]
 *$py.class

diff --git a/README.md b/README.md
@@ -10,16 +10,11 @@ The Python type signature for the schema is as follows:
 
 Patient = TypedDict('Patient', {
   'patient_id': int,
-  'static_measurements': List[Measurement],
   'events': List[Event],
 })
 
 Event = TypedDict('Event',{
-    'time': datetime.datetime,
-    'measurements': List[Measurement],
-})
-
-Measurement = TypedDict('Measurement', {
+    'time': NotRequired[datetime.datetime],
     'code': str,
     'text_value': NotRequired[str],
     'numeric_value': NotRequired[float],

diff --git a/src/meds/__init__.py b/src/meds/__init__.py
@@ -1,6 +1,6 @@
 from meds._version import __version__  # noqa
 
-from .schema import (patient_schema, Measurement, Event, Patient, label, Label,
+from .schema import (patient_schema, Event, Patient, label, Label,
                      code_metadata_entry, code_metadata, dataset_metadata,
                      CodeMetadataEntry, CodeMetadata, DatasetMetadata, birth_code,
                      death_code)
@@ -9,7 +9,6 @@
 # List all objects that we want to export
 _exported_objects = {
     'patient_schema': patient_schema,
-    'Measurement': Measurement,
     'Event': Event,
     'Patient': Patient,
     'label': label,

diff --git a/src/meds/schema.py b/src/meds/schema.py
@@ -21,26 +21,23 @@
 birth_code = "SNOMED/184099003"
 death_code = "SNOMED/419620001"
 
-
-def patient_schema(per_event_metadata_schema=pa.null()):
+def patient_schema(per_event_properties_schema=pa.null()):
     # Return a patient schema with a particular per event metadata subschema
-    measurement = pa.struct(
+    event = pa.struct(
         [
+            ("time", pa.timestamp("us")), # Static events will have a null timestamp
             ("code", pa.string()),
             ("text_value", pa.string()),
             ("numeric_value", pa.float32()),
             ("datetime_value", pa.timestamp("us")),
-            ("metadata", per_event_metadata_schema),
+            ("properties", per_event_properties_schema),
         ]
     )
 
-    event = pa.struct([("time", pa.timestamp("us")), ("measurements", pa.list_(measurement))])
-
     patient = pa.schema(
         [
             ("patient_id", pa.int64()),
-            ("static_measurements", pa.list_(measurement)),
-            ("events", pa.list_(event)),  # Require ordered by time
+            ("events", pa.list_(event)),  # Require ordered by time, nulls must be first
         ]
     )
 
@@ -49,20 +46,19 @@ def patient_schema(per_event_metadata_schema=pa.null()):
 
 # Python types for the above schema
 
-Measurement = TypedDict(
-    "Measurement",
+Event = TypedDict(
+    "Event",
     {
+        "time": NotRequired[datetime.datetime],
         "code": str,
         "text_value": NotRequired[str],
         "numeric_value": NotRequired[float],
         "datetime_value": NotRequired[datetime.datetime],
-        "metadata": NotRequired[Any],
+        "properties": NotRequired[Any],
     },
 )
 
-Event = TypedDict("Event", {"time": datetime.datetime, "measurements": List[Measurement]})
-
-Patient = TypedDict("Patient", {"patient_id": int, "static_measurements": List[Measurement], "events": List[Event]})
+Patient = TypedDict("Patient", {"patient_id": int, "events": List[Event]})
 
 ############################################################
 

diff --git a/tests/test_schema.py b/tests/test_schema.py
@@ -15,22 +15,13 @@ def test_patient_schema():
     patient_data = [
         {
             "patient_id": 123,
-            "static_measurements": [{
-                "code": "some_static_code",
-                "text_value": "example",
-                "numeric_value": 1.0,
-                "datetime_value": datetime.datetime(2019, 1, 1, 0, 0, 0),
-                "metadata": None,
-            }],
             "events": [{  # Nested list for events
                 "time": datetime.datetime(2020, 1, 1, 12, 0, 0),
-                "measurements": [{  # Nested list for measurements
-                    "code": "some_code",
-                    "text_value": "Example",
-                    "numeric_value": 10.0,
-                    "datetime_value": datetime.datetime(2020, 1, 1, 12, 0, 0),
-                    "metadata": None
-                }]
+                "code": "some_code",
+                "text_value": "Example",
+                "numeric_value": 10.0,
+                "datetime_value": datetime.datetime(2020, 1, 1, 12, 0, 0),
+                "properties": None
             }]
         }
     ]