Merge pull request #81 from pennsignals/flowsheet_kind

Allow multiple flowsheet kinds from one predictions table and one flowsheet publisher

local/configuration.yaml

@@ -2,8 +2,10 @@
 flowsheets: !flowsheets
   client_id: ${EPIC_CLIENT_ID}
   cookie: ${EPIC_COOKIE}
-  flowsheet_id: ${EPIC_FLOWSHEET_ID}
-  flowsheet_template_id: ${EPIC_FLOWSHEET_TEMPLATE_ID}
+  kinds:
+    score:
+      flowsheet_id: ${EPIC_FLOWSHEET_ID}
+      flowsheet_template_id: ${EPIC_FLOWSHEET_TEMPLATE_ID}
   password: ${EPIC_PASSWORD}
   url: ${EPIC_URL}api/epic/2011/clinical/patient/addflowsheetvalue/flowsheetvalue
   username: ${EPIC_USERNAME}

local/test.yaml

@@ -4,8 +4,10 @@ gold: ./predict/gold/gold.pkl
 flowsheets: !flowsheets
   client_id: ${EPIC_CLIENT_ID}
   cookie: ${EPIC_COOKIE}
-  flowsheet_id: ${EPIC_FLOWSHEET_ID}
-  flowsheet_template_id: ${EPIC_FLOWSHEET_TEMPLATE_ID}
+  kinds:
+    score:
+      flowsheet_id: ${EPIC_FLOWSHEET_ID}
+      flowsheet_template_id: ${EPIC_FLOWSHEET_TEMPLATE_ID}
   password: ${EPIC_PASSWORD}
   url: ${EPIC_URL}api/epic/2011/clinical/patient/addflowsheetvalue/flowsheetvalue
   username: ${EPIC_USERNAME}

postgres/sql/patchdb.d/005.public.sql

@@ -86,6 +86,7 @@ begin
         id int primary key generated always as identity,
         run_id int not null,
         subject_id int not null,
+	kind varchar not null default "score",
         score double precision not null,
         constraint predictions_require_a_run
             foreign key (run_id) references runs (id)
@@ -94,8 +95,8 @@ begin
         -- document your assumptions about how many predictions are made per subject
         -- per visit?
         -- per run?
-        constraint only_one_prediction_per_subject_and_run
-            unique (run_id, subject_id),
+        constraint only_one_prediction_per_subject_kind_and_run
+            unique (run_id, subject_id, kind),
         -- pick one of the following two constaints
         constraint prediction_score_must_be_a_normal
             check (0.0 <= score and score <= 1.0),

src/dsdk/flowsheet.py

@@ -8,7 +8,7 @@
 from datetime import datetime
 from json import JSONDecodeError, dumps
 from time import sleep as default_sleep
-from typing import TYPE_CHECKING, Any, Generator
+from typing import TYPE_CHECKING, Any, Generator, Mapping
 from urllib.parse import urlencode
 
 from cfgenvy import YamlMapping
@@ -56,6 +56,33 @@ def __str__(self):
         return str(self.__dict__)
 
 
+class Kind(YamlMapping):
+    """Kind."""
+
+    def __init__(
+        self,
+        *,
+        flowsheet_id: str,
+        flowsheet_template_id: str,
+        flowsheet_id_type: str = "external",
+        flowsheet_template_id_type: str = "external",
+    ):
+        """__init__."""
+        self.flowsheet_id = flowsheet_id
+        self.flowsheet_id_type = flowsheet_id_type
+        self.flowsheet_template_id = flowsheet_template_id
+        self.flowsheet_template_id_type = flowsheet_template_id_type
+
+    def as_yaml(self) -> dict[str, Any]:
+        """As yaml."""
+        return {
+            "flowsheet_id": self.flowsheet_id,
+            "flowsheet_id_type": self.flowsheet_id_type,
+            "flowsheet_template_id": self.flowsheet_template_id,
+            "flowsheet_template_id_type": self.flowsheet_template_id_type,
+        }
+
+
 class Flowsheet(YamlMapping):  # pylint: disable=too-many-instance-attributes
     """Flowsheet."""
 
@@ -90,14 +117,11 @@ def __init__(  # pylint: disable=too-many-locals
         *,
         client_id: str,
         cookie: str,
-        flowsheet_id: str,
-        flowsheet_template_id: str,
+        kinds: Mapping[str, Mapping[str, str]],
         password: str,
         url: str,
         username: str,
         contact_id_type: str = "CSN",
-        flowsheet_id_type: str = "external",
-        flowsheet_template_id_type: str = "external",
         operation_timeout: int = 5,
         patient_id_type: str = "UID",
         user_id: str = "PENNSIGNALS",
@@ -110,10 +134,7 @@ def __init__(  # pylint: disable=too-many-locals
         self.client_id = client_id
         self.contact_id_type = contact_id_type
         self.cookie = cookie
-        self.flowsheet_id = flowsheet_id
-        self.flowsheet_id_type = flowsheet_id_type
-        self.flowsheet_template_id = flowsheet_template_id
-        self.flowsheet_template_id_type = flowsheet_template_id_type
+        self.kinds = {key: Kind(**values) for key, values in kinds.items()}
         self.operation_timeout = operation_timeout
         self.password = password
         self.patient_id_type = patient_id_type
@@ -128,11 +149,9 @@ def as_yaml(self) -> dict[str, Any]:
             "client_id": self.client_id,
             "contact_id_type": self.contact_id_type,
             "cookie": self.cookie,
-            "flowsheet_id": self.flowsheet_id,
-            "flowsheet_id_type": self.flowsheet_id_type,
-            "flowsheet_template_id": self.flowsheet_template_id,
-            "flowsheet_template_id_type": self.flowsheet_template_id_type,
-            "operation_timeout": self.operation_timeout,
+            "kinds": {
+                key: value.as_yaml() for key, value in self.kinds.items()
+            },
             "password": self.password,
             "patient_id_type": self.patient_id_type,
             "url": self.url,
@@ -203,14 +222,15 @@ def rest(
         session: Session,
     ) -> Result:
         """Rest."""
+        kind = self.kinds[missing["kind"]]
         query = {
             "Comment": missing["id"],
             "ContactID": missing["csn"],
             "ContactIDType": self.contact_id_type,
-            "FlowsheetID": self.flowsheet_id,
-            "FlowsheetIDType": self.flowsheet_id_type,
-            "FlowsheetTemplateID": self.flowsheet_template_id,
-            "FlowsheetTemplateIDType": self.flowsheet_template_id_type,
+            "FlowsheetID": kind.flowsheet_id,
+            "FlowsheetIDType": kind.flowsheet_id_type,
+            "FlowsheetTemplateID": kind.flowsheet_template_id,
+            "FlowsheetTemplateIDType": kind.flowsheet_template_id_type,
             "InstantValueTaken": missing["as_of"].strftime(DATETIME_FORMAT),
             "PatientID": missing["empi"],
             "PatientIDType": self.patient_id_type,
@@ -299,14 +319,15 @@ def on_rest(
             "Should not get here with raise_for_status and a status of 400."
         )
 
-    def test(
+    def test(  # pylint: disable=too-many-arguments
         self,
         # csn=278820881,
         csn=218202909,  # inpatient admission date is 2019-02-06 at PAH
         # csn="BAD202909",
         empi="8330651951",
         # empi="BAD2345678",
         id=0,  # pylint: disable=redefined-builtin
+        kind="score",
         score="0.5",
     ):
         """Test epic API."""
@@ -315,6 +336,7 @@ def test(
             "csn": csn,
             "empi": empi,
             "id": id,
+            "kind": kind,
             "score": score,
         }
         with self.session() as session:

test/test_dsdk.py

@@ -13,6 +13,8 @@
 from dsdk import (
     Asset,
     Batch,
+    Flowsheet,
+    FlowsheetMixin,
     Model,
     ModelMixin,
     Mssql,
@@ -58,7 +60,9 @@ def __call__(self, batch: Batch, service: Service) -> None:
     assert batch.evidence["test"] is df
 
 
-class MockService(ModelMixin, MssqlMixin, PostgresMixin, Service):
+class MockService(  # pylint: disable=too-many-ancestors
+    FlowsheetMixin, ModelMixin, MssqlMixin, PostgresMixin, Service
+):
     """MockService."""
 
     YAML = "!test"
@@ -78,6 +82,16 @@ def __init__(self, **kwargs) -> None:
 
 CONFIGS = """
 !test
+flowsheets: !flowsheets
+  client_id: 00000000-0000-0000-0000-000000000000
+  cookie: ASP.NET_SessionId=000000000000000000000000
+  kinds:
+    score:
+      flowsheet_id: '0000000000'
+      flowsheet_template_id: '0000000000'
+  password: ${EPIC_PASSWORD}
+  url: https://interconnectbgprod.uphs.upenn.edu/interconnect-prd-web/
+  username: epic
 model: !model ./test/0.0.1.pkl
 mssql: !mssql
   database: test
@@ -99,6 +113,7 @@ def __init__(self, **kwargs) -> None:
 """.strip()
 
 ENVS = """
+EPIC_PASSWORD=password
 MSSQL_PASSWORD=password
 POSTGRES_PASSWORD=password
 """.strip()
@@ -107,6 +122,22 @@ def __init__(self, **kwargs) -> None:
 !test
 as_of: null
 duration: null
+flowsheets: !flowsheets
+  client_id: 00000000-0000-0000-0000-000000000000
+  contact_id_type: CSN
+  cookie: ASP.NET_SessionId=000000000000000000000000
+  kinds:
+    score:
+      flowsheet_id: '0000000000'
+      flowsheet_id_type: external
+      flowsheet_template_id: '0000000000'
+      flowsheet_template_id_type: external
+  password: password
+  patient_id_type: UID
+  url: https://interconnectbgprod.uphs.upenn.edu/interconnect-prd-web/
+  user_id: PENNSIGNALS
+  user_id_type: external
+  username: epic
 gold: null
 model: !model ./test/0.0.1.pkl
 mssql: !mssql
@@ -119,6 +150,7 @@ def __init__(self, **kwargs) -> None:
     ext: .sql
     path: ./assets/mssql
   username: mssql
+poll_interval: 60
 postgres: !postgres
   database: test
   host: 0.0.0.0
@@ -139,6 +171,19 @@ def build(
 ) -> tuple[Callable, dict[str, Any], str]:
     """Build from parameters."""
     cls.yaml_types()
+    flowsheets = Flowsheet(
+        client_id="00000000-0000-0000-0000-000000000000",
+        cookie="ASP.NET_SessionId=000000000000000000000000",
+        kinds={
+            "score": {
+                "flowsheet_id": "0000000000",
+                "flowsheet_template_id": "0000000000",
+            },
+        },
+        password="password",
+        url="https://interconnectbgprod.uphs.upenn.edu/interconnect-prd-web/",
+        username="epic",
+    )
     model = Model(name="test", path="./test/0.0.1.pkl", version="0.0.1")
     mssql = Mssql(
         database="test",
@@ -158,6 +203,7 @@ def build(
     return (
         cls,
         {
+            "flowsheets": flowsheets,
             "model": model,
             "mssql": mssql,
             "postgres": postgres,
@@ -176,7 +222,11 @@ def deserialize(
     pickle_file = "./test/0.0.1.pkl"
     dump_pickle_file({"name": "test", "version": "0.0.1"}, pickle_file)
 
-    env = {"POSTGRES_PASSWORD": "oops!", "MSSQL_PASSWORD": "oops!"}
+    env = {
+        "EPIC_PASSWORD": "oops!",
+        "MSSQL_PASSWORD": "oops!",
+        "POSTGRES_PASSWORD": "oops!",
+    }
     return (
         cls.loads,
         {

test/test_flowsheets.py

@@ -28,6 +28,7 @@ def test_valid(mock_flowsheets_service):
                 "csn": 218202909,
                 "empi": "8330651951",
                 "id": 0,
+                "kind": "score",
                 "run_id": 0,
                 "score": 0.5,
             }
@@ -51,6 +52,7 @@ def test_invalid_csn(mock_flowsheets_service):
                 "csn": 999999999,
                 "empi": "8330651951",
                 "id": 0,
+                "kind": "score",
                 "run_id": 0,
                 "score": 0.5,
             }
@@ -81,6 +83,7 @@ def test_invalid_empi(mock_flowsheets_service):
                 "csn": 218202909,
                 "empi": "9999999999",
                 "id": 0,
+                "kind": "score",
                 "run_id": 0,
                 "score": 0.5,
             }
@@ -120,6 +123,7 @@ def outer(*args, **kwargs):
                 "csn": 133713371,
                 "empi": "1337133713",
                 "id": 0,
+                "kind": "score",
                 "run_id": 0,
                 "score": 0.5,
             }