canvas 0.3.0__py3-none-any.whl → 0.4.0__py3-none-any.whl

canvas_sdk/v1/data/observation.py

@@ -0,0 +1,117 @@
+from django.db import models
+
+from canvas_sdk.v1.data.base import CommittableModelManager, ValueSetLookupQuerySet
+from canvas_sdk.v1.data.patient import Patient
+from canvas_sdk.v1.data.user import CanvasUser
+
+
+class ObservationQuerySet(ValueSetLookupQuerySet):
+    """ObservationQuerySet."""
+
+    pass
+
+
+class Observation(models.Model):
+    """Observation."""
+
+    class Meta:
+        managed = False
+        app_label = "canvas_sdk"
+        db_table = "canvas_sdk_data_api_observation_001"
+
+    objects = CommittableModelManager.from_queryset(ObservationQuerySet)()
+
+    id = models.UUIDField()
+    dbid = models.BigIntegerField(primary_key=True)
+    created = models.DateTimeField()
+    modified = models.DateTimeField()
+    originator = models.ForeignKey(CanvasUser, on_delete=models.DO_NOTHING)
+    committer = models.ForeignKey(CanvasUser, on_delete=models.DO_NOTHING)
+    entered_in_error = models.ForeignKey(CanvasUser, on_delete=models.DO_NOTHING)
+    deleted = models.BooleanField()
+    patient = models.ForeignKey(Patient, on_delete=models.DO_NOTHING, related_name="observations")
+    is_member_of = models.ForeignKey(
+        "self", on_delete=models.DO_NOTHING, null=True, related_name="members"
+    )
+    category = models.CharField()
+    units = models.TextField()
+    value = models.TextField()
+    note_id = models.BigIntegerField()
+    name = models.TextField()
+    effective_datetime = models.DateTimeField()
+
+
+class ObservationCoding(models.Model):
+    """ObservationCoding."""
+
+    class Meta:
+        managed = False
+        app_label = "canvas_sdk"
+        db_table = "canvas_sdk_data_api_observationcoding_001"
+
+    dbid = models.BigIntegerField(primary_key=True)
+    system = models.CharField()
+    version = models.CharField()
+    code = models.CharField()
+    display = models.CharField()
+    user_selected = models.BooleanField()
+    observation = models.ForeignKey(
+        Observation, on_delete=models.DO_NOTHING, related_name="codings"
+    )
+
+
+class ObservationComponent(models.Model):
+    """ObservationComponent."""
+
+    class Meta:
+        managed = False
+        app_label = "canvas_sdk"
+        db_table = "canvas_sdk_data_api_observationcomponent_001"
+
+    dbid = models.BigIntegerField(primary_key=True)
+    created = models.DateTimeField()
+    modified = models.DateTimeField()
+    observation = models.ForeignKey(
+        Observation, on_delete=models.DO_NOTHING, related_name="components"
+    )
+    value_quantity = models.TextField()
+    value_quantity_unit = models.TextField()
+    name = models.TextField()
+
+
+class ObservationComponentCoding(models.Model):
+    """ObservationComponentCoding."""
+
+    class Meta:
+        managed = False
+        app_label = "canvas_sdk"
+        db_table = "canvas_sdk_data_api_observationcomponentcoding_001"
+
+    dbid = models.BigIntegerField(primary_key=True)
+    system = models.CharField()
+    version = models.CharField()
+    code = models.CharField()
+    display = models.CharField()
+    user_selected = models.BooleanField()
+    observation_component = models.ForeignKey(
+        ObservationComponent, on_delete=models.DO_NOTHING, related_name="codings"
+    )
+
+
+class ObservationValueCoding(models.Model):
+    """ObservationValueCoding."""
+
+    class Meta:
+        managed = False
+        app_label = "canvas_sdk"
+        db_table = "canvas_sdk_data_api_observationvaluecoding_001"
+
+    dbid = models.BigIntegerField(primary_key=True)
+    system = models.CharField()
+    version = models.CharField()
+    code = models.CharField()
+    display = models.CharField()
+    user_selected = models.BooleanField()
+    observation = models.ForeignKey(
+        Observation, on_delete=models.DO_NOTHING, related_name="value_codings"
+    )

canvas_sdk/v1/data/patient.py

@@ -49,4 +49,7 @@ class Patient(models.Model):
     @classmethod
     def find(cls, id: str) -> Self:
         """Find a patient by id."""
-        return cls.objects.get(id=id)
+        return cls._default_manager.get(id=id)
+
+    def __str__(self) -> str:
+        return f"{self.first_name} {self.last_name}"

canvas_sdk/v1/data/questionnaire.py

@@ -109,7 +109,7 @@ class Questionnaire(models.Model):
     code_system = models.CharField()
     code = models.CharField()
     search_tags = models.CharField()
-    questions = models.ManyToManyField(Question, through="QuestionnaireQuestionMap")
+    questions = models.ManyToManyField(Question, through="canvas_sdk.QuestionnaireQuestionMap")  # type: ignore[misc, var-annotated]
     use_in_shx = models.BooleanField()
     carry_forward = models.TextField()
 
@@ -152,7 +152,9 @@ class Interview(models.Model):
     patient = models.ForeignKey(Patient, on_delete=models.DO_NOTHING, related_name="interviews")
     note_id = models.BigIntegerField()
     appointment_id = models.BigIntegerField()
-    questionnaires = models.ManyToManyField(Questionnaire, through="InterviewQuestionnaireMap")
+    questionnaires = models.ManyToManyField(  # type: ignore[var-annotated]
+        Questionnaire, through="canvas_sdk.InterviewQuestionnaireMap"  # type: ignore[misc]
+    )
     progress_status = models.CharField()
     created = models.DateTimeField()
     modified = models.DateTimeField()

canvas_sdk/value_set/tests/test_value_sets.py

@@ -1,11 +1,10 @@
-import pytest
-
 from canvas_sdk.value_set.v2022.condition import (
     DisordersOfTheImmuneSystem,
     EncephalopathyDueToChildhoodVaccination,
     Rhabdomyolysis,
     StableAndUnstableAngina,
 )
+from canvas_sdk.value_set.value_set import CombinedValueSet
 
 
 def test_value_set_class_values_property() -> None:
@@ -15,7 +14,9 @@ def test_value_set_class_values_property() -> None:
 
 
 def test_value_set_class_pipe_operator_with_two_value_sets() -> None:
-    combined_value_set = DisordersOfTheImmuneSystem | EncephalopathyDueToChildhoodVaccination
+    combined_value_set: CombinedValueSet = (
+        DisordersOfTheImmuneSystem | EncephalopathyDueToChildhoodVaccination
+    )
 
     both_classes_icd_10_codes = DisordersOfTheImmuneSystem.ICD10CM.union(
         EncephalopathyDueToChildhoodVaccination.ICD10CM
@@ -29,7 +30,7 @@ def test_value_set_class_pipe_operator_with_two_value_sets() -> None:
 
 
 def test_value_set_class_pipe_operator_with_three_value_sets() -> None:
-    combined_value_set = (
+    combined_value_set: CombinedValueSet = (
         DisordersOfTheImmuneSystem | EncephalopathyDueToChildhoodVaccination | Rhabdomyolysis
     )
 
@@ -45,8 +46,10 @@ def test_value_set_class_pipe_operator_with_three_value_sets() -> None:
 
 
 def test_value_set_class_pipe_operator_with_two_combined_value_sets() -> None:
-    combined_value_set_1 = DisordersOfTheImmuneSystem | EncephalopathyDueToChildhoodVaccination
-    combined_value_set_2 = Rhabdomyolysis | StableAndUnstableAngina
+    combined_value_set_1: CombinedValueSet = (
+        DisordersOfTheImmuneSystem | EncephalopathyDueToChildhoodVaccination
+    )
+    combined_value_set_2: CombinedValueSet = Rhabdomyolysis | StableAndUnstableAngina
 
     combined_value_set = combined_value_set_1 | combined_value_set_2
 

canvas_sdk/value_set/v2022/intervention.py

@@ -1,30 +1,6 @@
 from ..value_set import ValueSet
 
 
-class HospiceCareAmbulatory(ValueSet):
-    """
-    **Clinical Focus:** The purpose of this value set is to represent concepts of interventions to identify patients receiving hospice care outside of a hospital or long term care facility.
-
-    **Data Element Scope:** This value set may use a model element related to Procedure or Intervention.
-
-    **Inclusion Criteria:** Includes concepts that represent a procedure or intervention for hospice care.
-
-    **Exclusion Criteria:** Excludes concepts that represent palliative care or comfort measures.
-
-    ** Used in:** CMS90v11, CMS134v10, CMS165v10, CMS146v10, CMS124v10, CMS139v10, CMS154v10, CMS56v10, CMS74v11, CMS75v10, CMS137v10, CMS136v11, CMS128v10, CMS122v10, CMS153v10, CMS66v10, CMS130v10, CMS155v10, CMS127v10, CMS117v10, CMS131v10, CMS156v10, CMS125v10
-    """
-
-    VALUE_SET_NAME = "Hospice care ambulatory"
-    OID = "2.16.840.1.113762.1.4.1108.15"
-    DEFINITION_VERSION = "20170504"
-    EXPANSION_VERSION = "eCQM Update 2021-05-06"
-
-    SNOMEDCT = {
-        "385763009",  # Hospice care (regime/therapy)
-        "385765002",  # Hospice care management (procedure)
-    }
-
-
 class PalliativeCareIntervention(ValueSet):
     """
     **Clinical Focus:** The purpose of this value set is to represent concepts for palliative care interventions.

canvas_sdk/value_set/value_set.py

@@ -1,5 +1,7 @@
 from collections import defaultdict
-from typing import Dict, Union, cast
+from typing import Union, cast
+
+from django.utils.functional import classproperty
 
 
 class CodeConstants:
@@ -33,7 +35,7 @@ class CodeConstants:
     URL_NDC = "http://hl7.org/fhir/sid/ndc"
 
 
-class CodeConstantsURLMapping:
+class CodeConstantsURLMappingMixin:
     """A class that maps code systems to their URLs."""
 
     CODE_SYSTEM_MAPPING = {
@@ -53,21 +55,21 @@ class CodeConstantsURLMapping:
     }
 
 
-class CombinedValueSet(CodeConstantsURLMapping):
+class CombinedValueSet(CodeConstantsURLMappingMixin):
     """A class representing a combination of two value sets."""
 
     def __init__(
         self,
-        value_set_1: Union["ValueSet", "CombinedValueSet"],
-        value_set_2: Union["ValueSet", "CombinedValueSet"],
+        value_set_1: Union[type["ValueSet"], "CombinedValueSet"],
+        value_set_2: Union[type["ValueSet"], "CombinedValueSet"],
     ) -> None:
         self.value_set_1 = value_set_1
         self.value_set_2 = value_set_2
 
     @property
-    def values(self) -> Dict[str, set]:
+    def values(self) -> dict[str, set]:
         """A property that returns the combined values from both value sets."""
-        values: Dict[str, set] = defaultdict(set)
+        values: dict[str, set] = defaultdict(set)
 
         for vs in [self.value_set_1, self.value_set_2]:
             sub_values = vs.values
@@ -77,7 +79,7 @@ class CombinedValueSet(CodeConstantsURLMapping):
 
         return values
 
-    def __or__(self, value_set: Union["ValueSet", "CombinedValueSet"]) -> "CombinedValueSet":
+    def __or__(self, value_set: Union[type["ValueSet"], "CombinedValueSet"]) -> "CombinedValueSet":
         """Implements the `|` (or) operator to combine value sets."""
         return CombinedValueSet(self, value_set)
 
@@ -85,22 +87,23 @@ class CombinedValueSet(CodeConstantsURLMapping):
 class ValueSystems(type):
     """A metaclass for defining a ValueSet."""
 
-    @property
-    def values(cls) -> dict[str, set]:
-        """A property that returns a dictionary of code systems and their associated values."""
-        return {
-            system: getattr(cls, system)
-            for system in cast(ValueSet, cls).CODE_SYSTEM_MAPPING.keys()
-            if hasattr(cls, system)
-        }
+    def __or__(self, value_set: Union[type["ValueSet"], "CombinedValueSet"]) -> "CombinedValueSet":  # type: ignore[override]
+        """Implements the `|` (or) operator."""
+        return CombinedValueSet(cast(type["ValueSet"], self), value_set)
 
-    def __or__(self, value_set: Union["ValueSet", "CombinedValueSet"]) -> CombinedValueSet:  # type: ignore[override]
+    def __ror__(self, value_set: Union[type["ValueSet"], "CombinedValueSet"]) -> "CombinedValueSet":  # type: ignore[override]
         """Implements the `|` (or) operator."""
-        return CombinedValueSet(cast(ValueSet, self), value_set)
+        return self.__or__(value_set)
 
 
-class ValueSet(CodeConstantsURLMapping, metaclass=ValueSystems):
+class ValueSet(CodeConstantsURLMappingMixin, metaclass=ValueSystems):
     """The Base class for a ValueSet."""
 
-    values: dict[str, set]
-    pass
+    @classproperty
+    def values(cls) -> dict[str, set]:
+        """A property that returns a dictionary of code systems and their associated values."""
+        return {
+            system: getattr(cls, system)
+            for system in cls.CODE_SYSTEM_MAPPING.keys()
+            if hasattr(cls, system)
+        }

plugin_runner/authentication.py

@@ -0,0 +1,48 @@
+import os
+from typing import cast
+
+import arrow
+from jwt import encode
+
+from logger import log
+
+ONE_DAY_IN_MINUTES = 60 * 24
+
+INSECURE_DEFAULT_SIGNING_KEY = "INSECURE_KEY"
+
+
+def token_for_plugin(
+    plugin_name: str,
+    audience: str,
+    issuer: str = "plugin-runner",
+    jwt_signing_key: str = cast(
+        str, os.getenv("PLUGIN_RUNNER_SIGNING_KEY", INSECURE_DEFAULT_SIGNING_KEY)
+    ),
+    expiration_minutes: int = ONE_DAY_IN_MINUTES,
+    extra_kwargs: dict | None = None,
+) -> str:
+    """
+    Generate a JWT for the given plugin and audience.
+    """
+    if not extra_kwargs:
+        extra_kwargs = {}
+
+    if jwt_signing_key == INSECURE_DEFAULT_SIGNING_KEY:
+        log.warning(
+            "Using an insecure JWT signing key for GraphQL access. Set the PLUGIN_RUNNER_SIGNING_KEY environment variable to avoid this message."
+        )
+
+    token = encode(
+        {
+            "plugin_name": plugin_name,
+            "customer_identifier": os.getenv("CUSTOMER_IDENTIFIER"),
+            "exp": arrow.utcnow().shift(minutes=expiration_minutes).datetime,
+            "aud": audience,
+            "iss": issuer,
+            **extra_kwargs,
+        },
+        jwt_signing_key,
+        algorithm="HS256",
+    )
+
+    return token