canvas 0.8.1__tar.gz → 0.9.0__tar.gz

{canvas-0.8.1 → canvas-0.9.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: canvas
-Version: 0.8.1
+Version: 0.9.0
 Summary: SDK to customize event-driven actions in your Canvas instance
 License: MIT
 Author: Canvas Team

{canvas-0.8.1 → canvas-0.9.0}/canvas_cli/apps/plugin/plugin.py

@@ -54,7 +54,7 @@ def _build_package(package: Path) -> Path:
 def _get_name_from_metadata(host: str, token: str, package: Path) -> str | None:
     """Extract metadata from a provided package and return the package name if it exists in the metadata."""
     try:
-        with open(package) as package_file:
+        with open(package, "rb") as package_file:
             metadata_response = requests.post(
                 plugin_url(host, "extract-metadata"),
                 headers={"Authorization": f"Bearer {token}"},

{canvas-0.8.1 → canvas-0.9.0}/canvas_sdk/protocols/clinical_quality_measure.py

@@ -1,13 +1,18 @@
-from typing import Any, cast
+from typing import TYPE_CHECKING, Any, cast
 
 import arrow
-from django.db.models import Model
 
 from canvas_sdk.events import EventType
 from canvas_sdk.protocols.base import BaseProtocol
 from canvas_sdk.protocols.timeframe import Timeframe
+from canvas_sdk.v1.data import Patient
 from canvas_sdk.v1.data.condition import Condition
+from canvas_sdk.v1.data.lab import LabOrder, LabReport
 from canvas_sdk.v1.data.medication import Medication
+from canvas_sdk.v1.data.protocol_override import ProtocolOverride
+
+if TYPE_CHECKING:
+    from django.db.models import Model
 
 
 class ClinicalQualityMeasure(BaseProtocol):
@@ -54,6 +59,19 @@ class ClinicalQualityMeasure(BaseProtocol):
         """
         return cls.__name__
 
+    @staticmethod
+    def relative_float(value: str) -> float:
+        """Relative float method (better explanation needed here)."""
+        try:
+            sigma = 0.0
+            if value[0] == "<" and value[1] != "=":
+                sigma = -1e-6
+            elif value[0] == ">" and value[1] != "=":
+                sigma = +1e-6
+            return float(value.strip("<≤=≥>")) + sigma
+        except (ValueError, IndexError):
+            return 0
+
     @property
     def timeframe(self) -> Timeframe:
         """The default Timeframe (self.timeframe) for all protocols.
@@ -74,27 +92,41 @@ class ClinicalQualityMeasure(BaseProtocol):
         incurring more SQL queries.
         """
 
-        def patient_id(model: type[Model]) -> str:
-            return cast(
-                str,
-                model._default_manager.select_related("patient")
-                .values_list("patient__id")
-                .get(id=self.event.target)[0],
-            )
+        def patient_id(model: "type[Model]") -> str:
+            if model == Patient:
+                return self.target
+            else:
+                return cast(
+                    str,
+                    model._default_manager.select_related("patient")
+                    .values_list("patient__id")
+                    .get(id=self.event.target)[0],
+                )
+
+        models = {
+            EventType.CONDITION_ASSESSED: Condition,
+            EventType.CONDITION_CREATED: Condition,
+            EventType.CONDITION_RESOLVED: Condition,
+            EventType.CONDITION_UPDATED: Condition,
+            EventType.LAB_ORDER_CREATED: LabOrder,
+            EventType.LAB_ORDER_UPDATED: LabOrder,
+            EventType.LAB_REPORT_CREATED: LabReport,
+            EventType.LAB_REPORT_UPDATED: LabReport,
+            EventType.MEDICATION_LIST_ITEM_CREATED: Medication,
+            EventType.MEDICATION_LIST_ITEM_UPDATED: Medication,
+            EventType.PATIENT_CREATED: Patient,
+            EventType.PATIENT_UPDATED: Patient,
+            EventType.PROTOCOL_OVERRIDE_CREATED: ProtocolOverride,
+            EventType.PROTOCOL_OVERRIDE_DELETED: ProtocolOverride,
+            EventType.PROTOCOL_OVERRIDE_UPDATED: ProtocolOverride,
+        }
 
         if not self._patient_id:
-            # TODO: Add cases for ProtocolOverride
-            match self.event.type:
-                case EventType.CONDITION_CREATED | EventType.CONDITION_UPDATED:
-                    self._patient_id = patient_id(Condition)
-                case (
-                    EventType.MEDICATION_LIST_ITEM_CREATED
-                    | EventType.MEDICATION_LIST_ITEM_UPDATED
-                ):
-                    self._patient_id = patient_id(Medication)
-                case _:
-                    raise AssertionError(
-                        f"Event type {self.event.type} not supported by 'patient_id_from_event'"
-                    )
+            try:
+                self._patient_id = patient_id(models[self.event.type])
+            except KeyError as error:
+                raise ValueError(
+                    f"Event type {self.event.type} not supported by 'patient_id_from_event'"
+                ) from error
 
         return self._patient_id

{canvas-0.8.1 → canvas-0.9.0}/canvas_sdk/v1/data/lab.py

@@ -1,6 +1,10 @@
 from django.db import models
 
-from canvas_sdk.v1.data.base import CommittableModelManager
+from canvas_sdk.v1.data.base import (
+    CommittableModelManager,
+    TimeframeLookupQuerySetMixin,
+    ValueSetLookupQuerySet,
+)
 from canvas_sdk.v1.data.condition import Condition
 from canvas_sdk.v1.data.patient import Patient
 
@@ -79,6 +83,21 @@ class LabReview(models.Model):
     patient_communication_method = models.CharField()
 
 
+class LabValueTimeframeLookupQuerySetMixin(TimeframeLookupQuerySetMixin):
+    """A class that adds queryset functionality to filter using timeframes."""
+
+    @property
+    def timeframe_filter_field(self) -> str:
+        """Returns the field that should be filtered on. Can be overridden for different models."""
+        return "report__original_date"
+
+
+class LabValueQuerySet(ValueSetLookupQuerySet, LabValueTimeframeLookupQuerySetMixin):
+    """LabValueQuerySet."""
+
+    pass
+
+
 class LabValue(models.Model):
     """A class representing a lab value."""
 
@@ -87,6 +106,8 @@ class LabValue(models.Model):
         app_label = "canvas_sdk"
         db_table = "canvas_sdk_data_api_labvalue_001"
 
+    objects = LabValueQuerySet.as_manager()
+
     id = models.UUIDField()
     dbid = models.BigIntegerField(primary_key=True)
     created = models.DateTimeField()

{canvas-0.8.1 → canvas-0.9.0}/canvas_sdk/v1/data/patient.py

@@ -1,7 +1,19 @@
 from typing import Self
 
 import arrow
+from django.contrib.postgres.fields import ArrayField
 from django.db import models
+from django.db.models import TextChoices
+
+
+class SexAtBirth(TextChoices):
+    """SexAtBirth."""
+
+    FEMALE = "F", "female"
+    MALE = "M", "male"
+    OTHER = "O", "other"
+    UNKNOWN = "UNK", "unknown"
+    BLANK = "", ""
 
 
 class Patient(models.Model):
@@ -17,7 +29,7 @@ class Patient(models.Model):
     first_name = models.CharField()
     last_name = models.CharField()
     birth_date = models.DateField()
-    sex_at_birth = models.CharField()
+    sex_at_birth = models.CharField(choices=SexAtBirth.choices)
     created = models.DateTimeField()
     modified = models.DateTimeField()
     prefix = models.CharField()
@@ -30,6 +42,7 @@ class Patient(models.Model):
     gender_identity_term = models.CharField()
     gender_identity_code = models.CharField()
     preferred_pronouns = models.CharField()
+    biological_race_codes = ArrayField(models.CharField())
     last_known_timezone = models.CharField()
     mrn = models.CharField()
     active = models.BooleanField()

{canvas-0.8.1 → canvas-0.9.0}/canvas_sdk/value_set/custom.py

@@ -181,6 +181,89 @@ class Antiarrhythmics(ValueSet):
     }
 
 
+class LabReportCreatinine(ValueSet):
+    """LabReportCreatinine."""
+
+    VALUE_SET_NAME = "Lab Report Creatinine"
+    EXPANSION_VERSION = "CanvasHCC Update 2018-10-04"
+
+    LOINC = {
+        "2160-0",
+    }
+
+
+class HypertensiveChronicKidneyDisease(ValueSet):
+    """
+    **Clinical Focus:** This value set contains concepts that represent hypertensive kidney disease.
+
+    **Data Element Scope:** This value set may use the Quality Data Model (QDM) category related to Diagnosis.
+
+    **Inclusion Criteria:** Includes only relevant concepts associated with hypertensive kidney disease.
+
+    **Exclusion Criteria:** No exclusions.
+    """
+
+    OID = "2.16.840.1.113883.3.464.1003.109.12.1017"
+    VALUE_SET_NAME = "Hypertensive Chronic Kidney Disease"
+    EXPANSION_VERSION = "eCQM Update 2020-05-07"
+
+    ICD10CM = {"I120", "I129", "I130", "I1310", "I1311", "I132", "I150", "I151"}
+
+    ICD9CM = {
+        "40301",
+        "40310",
+        "40311",
+        "40390",
+        "40391",
+        "40400",
+        "40401",
+        "40402",
+        "40403",
+        "40410",
+        "40411",
+        "40412",
+        "40413",
+        "40490",
+        "40491",
+        "40492",
+        "40493",
+    }
+
+    SNOMEDCT = {
+        "111438007",
+        "123799005",
+        "123800009",
+        "14973001",
+        "193003",
+        "194774006",
+        "194783001",
+        "19769006",
+        "23130000",
+        "28119000",
+        "285831000119108",
+        "285841000119104",
+        "286371000119107",
+        "32916005",
+        "38481006",
+        "39018007",
+        "397748008",
+        "427889009",
+        "428575007",
+        "473392002",
+        "49220004",
+        "57684003",
+        "62240004",
+        "65443008",
+        "66052004",
+        "66610008",
+        "73410007",
+        "78544004",
+        "81363003",
+        "86234004",
+        "90493000",
+    }
+
+
 class DiabetesWithoutComplication(ValueSet):
     """Diabetes Without Complication."""
 

{canvas-0.8.1 → canvas-0.9.0}/pyproject.toml

@@ -47,7 +47,7 @@ packages = [
   {include = "settings.py"}
 ]
 readme = "README.md"
-version = "0.8.1"
+version = "0.9.0"
 
 [tool.poetry.dependencies]
 cookiecutter = "*"