canvas 0.1.15__py3-none-any.whl → 0.2.10__py3-none-any.whl

canvas_sdk/v1/data/allergy_intolerance.py

@@ -0,0 +1,63 @@
+from django.contrib.postgres.fields import ArrayField
+from django.db import models
+
+from canvas_sdk.v1.data.base import CommittableModelManager
+from canvas_sdk.v1.data.patient import Patient
+from canvas_sdk.v1.data.user import CanvasUser
+
+
+class AllergyIntolerance(models.Model):
+    """AllergyIntolerance."""
+
+    class Meta:
+        managed = False
+        app_label = "canvas_sdk"
+        db_table = "canvas_sdk_data_api_allergyintolerance_001"
+
+    objects = CommittableModelManager()
+
+    id = models.UUIDField()
+    dbid = models.BigIntegerField(primary_key=True)
+    created = models.DateTimeField()
+    modified = models.DateTimeField()
+    editors = ArrayField(models.IntegerField())
+    deleted = models.BooleanField()
+    committer = models.ForeignKey(CanvasUser, on_delete=models.DO_NOTHING)
+    entered_in_error = models.ForeignKey(CanvasUser, on_delete=models.DO_NOTHING)
+    patient = models.ForeignKey(
+        Patient,
+        on_delete=models.DO_NOTHING,
+        related_name="allergy_intolerances",
+    )
+    note_id = models.BigIntegerField()
+    allergy_intolerance_type = models.CharField()
+    category = models.IntegerField()
+    status = models.CharField()
+    severity = models.CharField()
+    onset_date = models.DateField()
+    onset_date_original_input = models.CharField()
+    last_occurrence = models.DateField()
+    last_occurrence_original_input = models.CharField()
+    recorded_date = models.DateTimeField()
+    narrative = models.CharField()
+
+
+class AllergyIntoleranceCoding(models.Model):
+    """AllergyIntoleranceCoding."""
+
+    class Meta:
+        managed = False
+        app_label = "canvas_sdk"
+        db_table = "canvas_sdk_data_api_allergyintolerancecoding_001"
+
+    dbid = models.BigIntegerField(primary_key=True)
+    system = models.CharField()
+    version = models.CharField()
+    code = models.CharField()
+    display = models.CharField()
+    user_selected = models.BooleanField()
+    allergy_intolerance = models.ForeignKey(
+        AllergyIntolerance,
+        on_delete=models.DO_NOTHING,
+        related_name="codings",
+    )

canvas_sdk/v1/data/base.py

@@ -0,0 +1,47 @@
+from typing import TYPE_CHECKING, Type
+
+from django.db import models
+from django.db.models import Q
+
+if TYPE_CHECKING:
+    from canvas_sdk.value_set.value_set import ValueSet
+
+
+class CommittableModelManager(models.Manager):
+    def get_queryset(self) -> "models.QuerySet":
+        # TODO: Should we just filter these out at the view level?
+        return super().get_queryset().filter(deleted=False)
+
+    def committed(self) -> "models.QuerySet":
+        # The committer_id IS set, and the entered_in_error_id IS NOT set
+        return self.filter(committer_id__isnull=False, entered_in_error_id__isnull=True)
+
+    def for_patient(self, patient_id: str) -> "models.QuerySet":
+        return self.filter(patient__id=patient_id)
+
+
+class ValueSetLookupQuerySet(models.QuerySet):
+    def find(self, value_set: Type["ValueSet"]) -> models.QuerySet:
+        """
+        Filters conditions, medications, etc. to those found in the inherited ValueSet class that is passed.
+
+        For example:
+
+        from canvas_sdk.v1.data.condition import Condition
+        from canvas_sdk.value_set.v2022.condition import MorbidObesity
+        morbid_obesity_conditions = Condition.objects.find(MorbidObesity)
+
+        This method can also be chained like so:
+
+        Condition.objects.find(MorbidObesity).find(AnaphylacticReactionToCommonBakersYeast)
+        """
+        values_dict = value_set.values
+        uri_codes = [
+            (i[1], values_dict[i[0]])
+            for i in value_set.CODE_SYSTEM_MAPPING.items()
+            if i[0] in values_dict
+        ]
+        q_filter = Q()
+        for system, codes in uri_codes:
+            q_filter |= Q(codings__system=system, codings__code__in=codes)
+        return self.filter(q_filter).distinct()

canvas_sdk/v1/data/condition.py

@@ -0,0 +1,48 @@
+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 ConditionQuerySet(ValueSetLookupQuerySet):
+    """ConditionQuerySet."""
+
+    pass
+
+
+class Condition(models.Model):
+    """Condition."""
+
+    class Meta:
+        managed = False
+        app_label = "canvas_sdk"
+        db_table = "canvas_sdk_data_api_condition_001"
+
+    objects = CommittableModelManager.from_queryset(ConditionQuerySet)()
+
+    id = models.UUIDField()
+    dbid = models.BigIntegerField(primary_key=True)
+    onset_date = models.DateField()
+    resolution_date = models.DateField()
+    deleted = models.BooleanField()
+    entered_in_error = models.ForeignKey(CanvasUser, on_delete=models.DO_NOTHING)
+    committer = models.ForeignKey(CanvasUser, on_delete=models.DO_NOTHING)
+    patient = models.ForeignKey(Patient, on_delete=models.DO_NOTHING, related_name="conditions")
+
+
+class ConditionCoding(models.Model):
+    """ConditionCoding."""
+
+    class Meta:
+        managed = False
+        app_label = "canvas_sdk"
+        db_table = "canvas_sdk_data_api_conditioncoding_001"
+
+    dbid = models.BigIntegerField(primary_key=True)
+    system = models.CharField()
+    version = models.CharField()
+    code = models.CharField()
+    display = models.CharField()
+    user_selected = models.BooleanField()
+    condition = models.ForeignKey(Condition, on_delete=models.DO_NOTHING, related_name="codings")

canvas_sdk/v1/data/lab.py

@@ -0,0 +1,96 @@
+from django.db import models
+
+from canvas_sdk.v1.data.base import CommittableModelManager
+from canvas_sdk.v1.data.patient import Patient
+from canvas_sdk.v1.data.user import CanvasUser
+
+
+class LabReport(models.Model):
+    class Meta:
+        managed = False
+        app_label = "canvas_sdk"
+        db_table = "canvas_sdk_data_api_labreport_001"
+
+    objects = CommittableModelManager()
+
+    id = models.UUIDField()
+    dbid = models.BigIntegerField(primary_key=True)
+    created = models.DateTimeField()
+    modified = models.DateTimeField()
+    review_mode = models.CharField()
+    junked = models.BooleanField()
+    requires_signature = models.BooleanField()
+    assigned_date = models.DateTimeField()
+    patient = models.ForeignKey(Patient, on_delete=models.DO_NOTHING, related_name="lab_reports")
+    transmission_type = models.CharField()
+    for_test_only = models.BooleanField()
+    external_id = models.CharField()
+    version = models.IntegerField()
+    requisition_number = models.CharField()
+    review = models.ForeignKey("LabReview", related_name="reports", on_delete=models.DO_NOTHING)
+    original_date = models.DateTimeField()
+    date_performed = models.DateTimeField()
+    custom_document_name = models.CharField()
+    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()
+
+
+class LabReview(models.Model):
+    class Meta:
+        managed = False
+        app_label = "canvas_sdk"
+        db_table = "canvas_sdk_data_api_labreview_001"
+
+    objects = CommittableModelManager()
+
+    id = models.UUIDField()
+    dbid = models.BigIntegerField(primary_key=True)
+    created = models.DateTimeField()
+    modified = models.DateTimeField()
+    originator = models.ForeignKey(CanvasUser, on_delete=models.DO_NOTHING)
+    deleted = models.BooleanField()
+    committer = models.ForeignKey(CanvasUser, on_delete=models.DO_NOTHING)
+    entered_in_error = models.ForeignKey(CanvasUser, on_delete=models.DO_NOTHING)
+    internal_comment = models.TextField()
+    message_to_patient = models.CharField()
+    status = models.CharField()
+    patient = models.ForeignKey(Patient, on_delete=models.DO_NOTHING)
+    patient_communication_method = models.CharField()
+
+
+class LabValue(models.Model):
+    class Meta:
+        managed = False
+        app_label = "canvas_sdk"
+        db_table = "canvas_sdk_data_api_labvalue_001"
+
+    id = models.UUIDField()
+    dbid = models.BigIntegerField(primary_key=True)
+    created = models.DateTimeField()
+    modified = models.DateTimeField()
+    report = models.ForeignKey("LabReport", related_name="values", on_delete=models.DO_NOTHING)
+    value = models.TextField()
+    units = models.CharField()
+    abnormal_flag = models.CharField()
+    reference_range = models.CharField()
+    low_threshold = models.CharField()
+    high_threshold = models.CharField()
+    comment = models.TextField()
+    observation_status = models.CharField()
+
+
+class LabValueCoding(models.Model):
+    class Meta:
+        managed = False
+        app_label = "canvas_sdk"
+        db_table = "canvas_sdk_data_api_labvaluecoding_001"
+
+    dbid = models.BigIntegerField(primary_key=True)
+    created = models.DateTimeField()
+    modified = models.DateTimeField()
+    value = models.ForeignKey(LabValue, on_delete=models.DO_NOTHING, related_name="codings")
+    code = models.CharField()
+    name = models.CharField()
+    system = models.CharField()

canvas_sdk/v1/data/medication.py

@@ -0,0 +1,54 @@
+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 MedicationQuerySet(ValueSetLookupQuerySet):
+    """MedicationQuerySet."""
+
+    pass
+
+
+class Medication(models.Model):
+    """Medication."""
+
+    class Meta:
+        managed = False
+        app_label = "canvas_sdk"
+        db_table = "canvas_sdk_data_api_medication_001"
+
+    objects = CommittableModelManager.from_queryset(MedicationQuerySet)()
+
+    id = models.UUIDField()
+    dbid = models.BigIntegerField(primary_key=True)
+    patient = models.ForeignKey(Patient, on_delete=models.DO_NOTHING, related_name="medications")
+    deleted = models.BooleanField()
+    entered_in_error = models.ForeignKey(CanvasUser, on_delete=models.DO_NOTHING)
+    committer = models.ForeignKey(CanvasUser, on_delete=models.DO_NOTHING)
+    status = models.CharField()
+    start_date = models.DateField()
+    end_date = models.DateField()
+    quantity_qualifier_description = models.CharField()
+    clinical_quantity_description = models.CharField()
+    potency_unit_code = models.CharField()
+    national_drug_code = models.CharField()
+    erx_quantity = models.CharField()
+
+
+class MedicationCoding(models.Model):
+    """MedicationCoding."""
+
+    class Meta:
+        managed = False
+        app_label = "canvas_sdk"
+        db_table = "canvas_sdk_data_api_medicationcoding_001"
+
+    dbid = models.BigIntegerField(primary_key=True)
+    system = models.CharField()
+    version = models.CharField()
+    code = models.CharField()
+    display = models.CharField()
+    user_selected = models.BooleanField()
+    medication = models.ForeignKey(Medication, on_delete=models.DO_NOTHING, related_name="codings")

canvas_sdk/v1/data/patient.py

@@ -0,0 +1,49 @@
+from typing import Self
+
+from django.db import models
+
+
+class Patient(models.Model):
+    class Meta:
+        managed = False
+        app_label = "canvas_sdk"
+        db_table = "canvas_sdk_data_api_patient_001"
+
+    id = models.CharField(max_length=32, db_column="key")
+    dbid = models.BigIntegerField(db_column="dbid", primary_key=True)
+    first_name = models.CharField()
+    last_name = models.CharField()
+    birth_date = models.DateField()
+    sex_at_birth = models.CharField()
+    created = models.DateTimeField()
+    modified = models.DateTimeField()
+    prefix = models.CharField()
+    suffix = models.CharField()
+    middle_name = models.CharField()
+    maiden_name = models.CharField()
+    nickname = models.CharField()
+    sexual_orientation_term = models.CharField()
+    sexual_orientation_code = models.CharField()
+    gender_identity_term = models.CharField()
+    gender_identity_code = models.CharField()
+    preferred_pronouns = models.CharField()
+    last_known_timezone = models.CharField()
+    mrn = models.CharField()
+    active = models.BooleanField()
+    deceased = models.BooleanField()
+    deceased_datetime = models.DateTimeField()
+    deceased_cause = models.TextField()
+    deceased_comment = models.TextField()
+    other_gender_description = models.CharField()
+    social_security_number = models.CharField()
+    administrative_note = models.TextField()
+    clinical_note = models.TextField()
+    mothers_maiden_name = models.CharField()
+    multiple_birth_indicator = models.BooleanField()
+    birth_order = models.BigIntegerField()
+    default_location_id = models.BigIntegerField()
+    default_provider_id = models.BigIntegerField()
+
+    @classmethod
+    def find(cls, id: str) -> Self:
+        return cls.objects.get(id=id)

canvas_sdk/v1/data/user.py

@@ -0,0 +1,10 @@
+from django.db import models
+
+
+class CanvasUser(models.Model):
+    class Meta:
+        managed = False
+        app_label = "canvas_sdk"
+        db_table = "canvas_sdk_data_api_auth_user_001"
+
+    dbid = models.BigIntegerField(db_column="dbid", primary_key=True)

canvas_sdk/value_set/tests/test_value_sets.py

@@ -0,0 +1,65 @@
+import pytest
+
+from canvas_sdk.value_set.v2022.condition import (
+    DisordersOfTheImmuneSystem,
+    EncephalopathyDueToChildhoodVaccination,
+    Rhabdomyolysis,
+    StableAndUnstableAngina,
+)
+
+
+def test_value_set_class_values_property() -> None:
+    value_set = DisordersOfTheImmuneSystem
+    assert value_set.values["ICD10CM"] == DisordersOfTheImmuneSystem.ICD10CM
+    assert value_set.values["SNOMEDCT"] == DisordersOfTheImmuneSystem.SNOMEDCT
+
+
+def test_value_set_class_pipe_operator_with_two_value_sets() -> None:
+    combined_value_set = DisordersOfTheImmuneSystem | EncephalopathyDueToChildhoodVaccination
+
+    both_classes_icd_10_codes = DisordersOfTheImmuneSystem.ICD10CM.union(
+        EncephalopathyDueToChildhoodVaccination.ICD10CM
+    )
+    both_classes_snomed_codes = DisordersOfTheImmuneSystem.SNOMEDCT.union(
+        EncephalopathyDueToChildhoodVaccination.SNOMEDCT
+    )
+
+    assert both_classes_icd_10_codes == combined_value_set.values["ICD10CM"]
+    assert both_classes_snomed_codes == combined_value_set.values["SNOMEDCT"]
+
+
+def test_value_set_class_pipe_operator_with_three_value_sets() -> None:
+    combined_value_set = (
+        DisordersOfTheImmuneSystem | EncephalopathyDueToChildhoodVaccination | Rhabdomyolysis
+    )
+
+    all_classes_icd_10_codes = DisordersOfTheImmuneSystem.ICD10CM.union(
+        EncephalopathyDueToChildhoodVaccination.ICD10CM
+    ).union(Rhabdomyolysis.ICD10CM)
+    all_classes_snomed_codes = DisordersOfTheImmuneSystem.SNOMEDCT.union(
+        EncephalopathyDueToChildhoodVaccination.SNOMEDCT
+    ).union(Rhabdomyolysis.SNOMEDCT)
+
+    assert all_classes_icd_10_codes == combined_value_set.values["ICD10CM"]
+    assert all_classes_snomed_codes == combined_value_set.values["SNOMEDCT"]
+
+
+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 = combined_value_set_1 | combined_value_set_2
+
+    all_classes_icd_10_codes = (
+        DisordersOfTheImmuneSystem.ICD10CM.union(EncephalopathyDueToChildhoodVaccination.ICD10CM)
+        .union(Rhabdomyolysis.ICD10CM)
+        .union(StableAndUnstableAngina.ICD10CM)
+    )
+    all_classes_snomed_codes = (
+        DisordersOfTheImmuneSystem.SNOMEDCT.union(EncephalopathyDueToChildhoodVaccination.SNOMEDCT)
+        .union(Rhabdomyolysis.SNOMEDCT)
+        .union(StableAndUnstableAngina.SNOMEDCT)
+    )
+
+    assert combined_value_set.values["ICD10CM"] == all_classes_icd_10_codes
+    assert combined_value_set.values["SNOMEDCT"] == all_classes_snomed_codes

canvas_sdk/value_set/v2022/adverse_event.py

@@ -0,0 +1,33 @@
+from ..value_set import ValueSet
+
+
+class StatinAllergen(ValueSet):
+    """
+    **Clinical Focus:** The purpose of this value set is to represent concepts of an allergy to statin medications.
+
+    **Data Element Scope:** This value set may use a model element related to Allergy/Intolerance.
+
+    **Inclusion Criteria:** Includes concepts that define an allergy to statin medications.
+
+    **Exclusion Criteria:** No exclusions.
+
+    ** Used in:** CMS347v5
+    """
+
+    VALUE_SET_NAME = "Statin Allergen"
+    OID = "2.16.840.1.113762.1.4.1110.42"
+    DEFINITION_VERSION = "20210220"
+    EXPANSION_VERSION = "eCQM Update 2021-05-06"
+
+    RXNORM = {
+        "6472",  # lovastatin
+        "36567",  # simvastatin
+        "41127",  # fluvastatin
+        "42463",  # pravastatin
+        "83367",  # atorvastatin
+        "301542",  # rosuvastatin
+        "861634",  # pitavastatin
+    }
+    SNOMEDCT = {
+        "372912004",  # Substance with 3-hydroxy-3-methylglutaryl-coenzyme A reductase inhibitor mechanism of action (substance)
+    }