usdm3 0.3.2__py3-none-any.whl

usdm3/__init__.py

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+import pathlib
+from usdm3.rules.rules_validation import RulesValidation3
+from usdm3.rules.rules_validation_results import RulesValidationResults
+from usdm3.minimum.minimum import Minimum
+from usdm3.api.wrapper import Wrapper
+
+
+class USDM3:
+    def __init__(self):
+        self.root = self._root_path()
+        self.validator = RulesValidation3(self.root, "usdm3.rules.library")
+
+    def validate(self, file_path: str) -> RulesValidationResults:
+        return self.validator.validate(file_path)
+
+    def minimum(self, study_name: str, sponsor_id: str, version: str) -> Wrapper:
+        return Minimum.minimum(study_name, sponsor_id, version)
+
+    def _root_path(self) -> str:
+        return pathlib.Path(__file__).parent.resolve()

usdm3/__version__.py

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+__package_version__ = "0.3.2"
+__model_version__ = "3.0.0"

usdm3/api/__init__.py

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+from .activity import Activity
+from .address import Address
+from .administration_duration import AdministrationDuration
+from .agent_administration import AgentAdministration
+from .alias_code import AliasCode
+from .analysis_population import AnalysisPopulation
+from .biomedical_concept_category import BiomedicalConceptCategory
+from .biomedical_concept_property import BiomedicalConceptProperty
+from .biomedical_concept_surrogate import BiomedicalConceptSurrogate
+from .biomedical_concept import BiomedicalConcept
+from .code import Code
+from .condition import Condition
+from .eligibility_criterion import EligibilityCriterion
+from .encounter import Encounter
+from .endpoint import Endpoint
+from .estimand import Estimand
+from .geographic_scope import GeographicScope
+from .governance_date import GovernanceDate
+from .indication import Indication
+from .intercurrent_event import IntercurrentEvent
+from .masking import Masking
+from .narrative_content import NarrativeContent
+from .objective import Objective
+from .organization import Organization
+from .population_definition import PopulationDefinition
+from .procedure import Procedure
+from .quantity import Quantity
+from .range import Range
+from .response_code import ResponseCode
+from .schedule_timeline_exit import ScheduleTimelineExit
+from .schedule_timeline import ScheduleTimeline
+from .scheduled_instance import ScheduledInstance
+from .study_amendment import StudyAmendment
+from .study_amendment_reason import StudyAmendmentReason
+from .study_arm import StudyArm
+from .study_cell import StudyCell
+from .study_design import StudyDesign
+from .study_element import StudyElement
+from .study_epoch import StudyEpoch
+from .study_identifier import StudyIdentifier
+from .study_intervention import StudyIntervention
+from .study_protocol_document_version import StudyProtocolDocumentVersion
+from .study_protocol_document import StudyProtocolDocument
+from .study_site import StudySite
+from .study_title import StudyTitle
+from .study_version import StudyVersion
+from .study import Study
+from .syntax_template import SyntaxTemplate
+from .syntax_template_dictionary import SyntaxTemplateDictionary
+from .timing import Timing
+from .transition_rule import TransitionRule
+from .wrapper import Wrapper
+
+__all__ = [
+    "Activity",
+    "Address",
+    "AdministrationDuration",
+    "AgentAdministration",
+    "AliasCode",
+    "AnalysisPopulation",
+    "BiomedicalConceptCategory",
+    "BiomedicalConceptProperty",
+    "BiomedicalConceptSurrogate",
+    "BiomedicalConcept",
+    "Code",
+    "Condition",
+    "EligibilityCriterion",
+    "Encounter",
+    "Endpoint",
+    "Enrollment",
+    "Estimand",
+    "GeographicScope",
+    "GovernanceDate",
+    "Indication",
+    "IntercurrentEvent",
+    "InvestigationalIntervention",
+    "Masking",
+    "NarrativeContent",
+    "Objective",
+    "Organization",
+    "PopulationDefinition",
+    "Procedure",
+    "Quality",
+    "Range",
+    "ResponseCode",
+    "ResearchOrganization",
+    "ScheduleTimelineExit",
+    "ScheduleTimeline",
+    "ScheduledInstance",
+    "ScheduledActivityInstance",
+    "ScheduledDecisionInstance",
+    "StudyAmendment",
+    "StudyAmendmentReason",
+    "StudyArm",
+    "StudyCell",
+    "StudyCohort",
+    "StudyDesignPopulation",
+    "StudyDesign",
+    "StudyElement",
+    "StudyEpoch",
+    "StudyIdentifier",
+    "StudyProtocolDocumentVersion",
+    "StudyProtocolDocument",
+    "StudySite",
+    "StudyTitle",
+    "StudyVersion",
+    "Study",
+    "SubjectEnrollment",
+    "SyntaxTemplate",
+    "SyntaxTemplateDictionary",
+    "Timing",
+    "TransitionRule",
+    "StudyIntervention",
+    "Quantity",
+    "Wrapper",
+]

usdm3/api/activity.py

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+from typing import List, Literal, Union
+from .api_base_model import ApiBaseModelNameLabelDesc
+from .procedure import Procedure
+
+
+class Activity(ApiBaseModelNameLabelDesc):
+    previousId: Union[str, None] = None
+    nextId: Union[str, None] = None
+    definedProcedures: List[Procedure] = []
+    biomedicalConceptIds: List[str] = []
+    bcCategoryIds: List[str] = []
+    bcSurrogateIds: List[str] = []
+    timelineId: Union[str, None] = None
+    instanceType: Literal["Activity"]

usdm3/api/address.py

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+from typing import Literal, Union
+from .api_base_model import ApiBaseModel
+from .code import Code
+
+
+class Address(ApiBaseModel):
+    text: Union[str, None] = None
+    line: Union[str, None] = None
+    city: Union[str, None] = None
+    district: Union[str, None] = None
+    state: Union[str, None] = None
+    postalCode: Union[str, None] = None
+    country: Union[Code, None] = None
+    instanceType: Literal["Address"]

usdm3/api/administration_duration.py

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+from typing import Literal, Union
+from .api_base_model import ApiBaseModel
+from .quantity import Quantity
+
+
+class AdministrationDuration(ApiBaseModel):
+    quantity: Union[Quantity, None] = None
+    description: str
+    durationWillVary: bool
+    reasonDurationWillVary: str
+    instanceType: Literal["AdministrationDuration"]

usdm3/api/agent_administration.py

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+from typing import Literal
+from .api_base_model import ApiBaseModelNameLabelDesc
+from .quantity import Quantity
+from .administration_duration import AdministrationDuration
+from .alias_code import AliasCode
+
+
+class AgentAdministration(ApiBaseModelNameLabelDesc):
+    duration: AdministrationDuration
+    dose: Quantity
+    route: AliasCode
+    frequency: AliasCode
+    instanceType: Literal["AgentAdministration"]

usdm3/api/alias_code.py

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+from typing import List, Literal
+from .api_base_model import ApiBaseModel
+from .code import Code
+
+
+class AliasCode(ApiBaseModel):
+    standardCode: Code
+    standardCodeAliases: List[Code] = []
+    instanceType: Literal["AliasCode"]

usdm3/api/analysis_population.py

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+from .api_base_model import ApiBaseModelNameLabelDesc
+from typing import Literal
+
+
+class AnalysisPopulation(ApiBaseModelNameLabelDesc):
+    text: str
+    instanceType: Literal["AnalysisPopulation"]

usdm3/api/api_base_model.py

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+import json
+import enum
+import datetime
+from typing import Union
+from pydantic import BaseModel, Field
+from uuid import UUID
+
+
+def _serialize_as_json(obj):
+    if isinstance(obj, enum.Enum):
+        return obj.value
+    elif isinstance(obj, datetime.date):
+        return obj.isoformat()
+    elif isinstance(obj, UUID):
+        return str(obj)
+    else:
+        return obj.__dict__
+
+
+class ApiBaseModel(BaseModel):
+    id: str = Field(min_length=1)
+
+    def to_json(self):
+        return json.dumps(self, default=_serialize_as_json)
+
+
+class ApiBaseModelAndDesc(ApiBaseModel):
+    description: Union[str, None] = None
+
+
+class ApiBaseModelName(ApiBaseModel):
+    name: str = Field(min_length=1)
+
+
+class ApiBaseModelNameLabelDesc(ApiBaseModelName):
+    label: Union[str, None] = None
+    description: Union[str, None] = None
+
+
+class ApiBaseModelNameLabel(ApiBaseModelName):
+    label: Union[str, None] = None
+
+
+class ApiBaseModelNameDesc(ApiBaseModelName):
+    description: Union[str, None] = None

usdm3/api/biomedical_concept.py

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+from typing import List, Literal
+from .alias_code import AliasCode
+from .api_base_model import ApiBaseModelNameLabel
+from .biomedical_concept_property import BiomedicalConceptProperty
+
+
+class BiomedicalConcept(ApiBaseModelNameLabel):
+    synonyms: List[str] = []
+    reference: str
+    properties: List[BiomedicalConceptProperty] = []
+    code: AliasCode
+    instanceType: Literal["BiomedicalConcept"]

usdm3/api/biomedical_concept_category.py

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+from typing import List, Literal, Union
+from .api_base_model import ApiBaseModelNameLabelDesc
+from .alias_code import AliasCode
+
+
+class BiomedicalConceptCategory(ApiBaseModelNameLabelDesc):
+    childIds: List[str] = []
+    memberIds: List[str] = []
+    code: Union[AliasCode, None] = None
+    instanceType: Literal["BiomedicalConceptCategory"]

usdm3/api/biomedical_concept_property.py

@@ -0,0 +1,13 @@
+from typing import List, Literal
+from .alias_code import AliasCode
+from .api_base_model import ApiBaseModelNameLabel
+from .response_code import ResponseCode
+
+
+class BiomedicalConceptProperty(ApiBaseModelNameLabel):
+    isRequired: bool
+    isEnabled: bool
+    datatype: str
+    responseCodes: List[ResponseCode] = []
+    code: AliasCode
+    instanceType: Literal["BiomedicalConceptProperty"]

usdm3/api/biomedical_concept_surrogate.py

@@ -0,0 +1,7 @@
+from typing import Literal, Union
+from .api_base_model import ApiBaseModelNameLabelDesc
+
+
+class BiomedicalConceptSurrogate(ApiBaseModelNameLabelDesc):
+    reference: Union[str, None] = None
+    instanceType: Literal["BiomedicalConceptSurrogate"]

usdm3/api/characteristic.py

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+from typing import Literal
+from .syntax_template import SyntaxTemplate
+
+
+class Characteristic(SyntaxTemplate):
+    instanceType: Literal["Characteristic"]

usdm3/api/code.py

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+from typing import Literal
+from .api_base_model import ApiBaseModel
+
+
+class Code(ApiBaseModel):
+    code: str
+    codeSystem: str
+    codeSystemVersion: str
+    decode: str
+    instanceType: Literal["Code"]

usdm3/api/condition.py

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+from typing import List, Literal, Union
+from .api_base_model import ApiBaseModelNameLabelDesc
+
+
+class Condition(ApiBaseModelNameLabelDesc):
+    text: str
+    dictionaryId: Union[str, None] = None
+    contextIds: List[str] = []
+    appliesToIds: List[str] = []
+    instanceType: Literal["Condition"]

usdm3/api/eligibility_criterion.py

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+from typing import Literal, Union
+from .syntax_template import SyntaxTemplate
+from .code import Code
+
+
+class EligibilityCriterion(SyntaxTemplate):
+    category: Code
+    identifier: str
+    nextId: Union[str, None] = None
+    previousId: Union[str, None] = None
+    contextId: Union[str, None] = None
+    instanceType: Literal["EligibilityCriterion"]

usdm3/api/encounter.py

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+from typing import List, Literal, Union
+from .api_base_model import ApiBaseModelNameLabelDesc
+from .code import Code
+from .transition_rule import TransitionRule
+
+
+class Encounter(ApiBaseModelNameLabelDesc):
+    type: Code
+    previousId: Union[str, None] = None
+    nextId: Union[str, None] = None
+    scheduledAtId: Union[str, None] = None
+    environmentalSetting: List[Code] = []
+    contactModes: List[Code] = []
+    transitionStartRule: Union[TransitionRule, None] = None
+    transitionEndRule: Union[TransitionRule, None] = None
+    instanceType: Literal["Encounter"]

usdm3/api/endpoint.py

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+from .syntax_template import SyntaxTemplate
+from .code import Code
+from typing import Literal
+
+
+class Endpoint(SyntaxTemplate):
+    purpose: str
+    level: Code
+    instanceType: Literal["Endpoint"]

usdm3/api/estimand.py

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+from typing import List, Literal
+from .api_base_model import ApiBaseModel
+from .analysis_population import AnalysisPopulation
+from .intercurrent_event import IntercurrentEvent
+
+
+class Estimand(ApiBaseModel):
+    summaryMeasure: str
+    analysisPopulation: AnalysisPopulation
+    interventionId: str
+    variableOfInterestId: str
+    intercurrentEvents: List[IntercurrentEvent]
+    instanceType: Literal["Estimand"]

usdm3/api/geographic_scope.py

@@ -0,0 +1,16 @@
+from typing import Literal, Union
+from .api_base_model import ApiBaseModel
+from .code import Code
+from .alias_code import AliasCode
+from .quantity import Quantity
+
+
+class GeographicScope(ApiBaseModel):
+    type: Code
+    code: Union[AliasCode, None] = None
+    instanceType: Literal["GeographicScope"]
+
+
+class SubjectEnrollment(GeographicScope):
+    quantity: Quantity
+    instanceType: Literal["SubjectEnrollment"]

usdm3/api/governance_date.py

@@ -0,0 +1,12 @@
+from typing import List, Literal
+from .api_base_model import ApiBaseModelNameLabelDesc
+from datetime import date
+from .code import Code
+from .geographic_scope import GeographicScope
+
+
+class GovernanceDate(ApiBaseModelNameLabelDesc):
+    type: Code
+    dateValue: date
+    geographicScopes: List[GeographicScope]
+    instanceType: Literal["GovernanceDate"]

usdm3/api/indication.py

@@ -0,0 +1,9 @@
+from typing import List, Literal
+from .api_base_model import ApiBaseModelNameLabelDesc
+from .code import Code
+
+
+class Indication(ApiBaseModelNameLabelDesc):
+    codes: List[Code] = []
+    isRareDisease: bool
+    instanceType: Literal["Indication"]

usdm3/api/intercurrent_event.py

@@ -0,0 +1,7 @@
+from typing import Literal
+from .api_base_model import ApiBaseModelNameLabelDesc
+
+
+class IntercurrentEvent(ApiBaseModelNameLabelDesc):
+    strategy: str
+    instanceType: Literal["IntercurrentEvent"]

usdm3/api/masking.py

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+from .api_base_model import ApiBaseModelAndDesc
+from .code import Code
+from typing import Literal
+
+
+class Masking(ApiBaseModelAndDesc):
+    role: Code
+    instanceType: Literal["Masking"]

usdm3/api/narrative_content.py

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+from typing import List, Literal, Union
+from .api_base_model import ApiBaseModelName
+
+
+class NarrativeContent(ApiBaseModelName):
+    sectionNumber: str
+    sectionTitle: str
+    text: Union[str, None] = None
+    childIds: List[str] = []
+    previousId: Union[str, None] = None
+    nextId: Union[str, None] = None
+    instanceType: Literal["NarrativeContent"]

usdm3/api/objective.py

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+from typing import List, Literal
+from .syntax_template import SyntaxTemplate
+from .code import Code
+from .endpoint import Endpoint
+
+
+class Objective(SyntaxTemplate):
+    level: Code
+    endpoints: List[Endpoint] = []
+    instanceType: Literal["Objective"]

usdm3/api/organization.py

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+from typing import List, Literal, Union
+from .api_base_model import ApiBaseModelNameLabel
+from .code import Code
+from .address import Address
+from .study_site import StudySite
+
+
+class Organization(ApiBaseModelNameLabel):
+    organizationType: Code
+    identifierScheme: str
+    identifier: str
+    legalAddress: Union[Address, None] = None
+    instanceType: Literal["Organization"]
+
+
+class ResearchOrganization(Organization):
+    manages: List[StudySite]
+    instanceType: Literal["ResearchOrganization"]

usdm3/api/population_definition.py

@@ -0,0 +1,26 @@
+from typing import Union, List, Literal
+from .api_base_model import ApiBaseModelNameLabelDesc
+from .code import Code
+from .range import Range
+from .eligibility_criterion import EligibilityCriterion
+from .characteristic import Characteristic
+
+
+class PopulationDefinition(ApiBaseModelNameLabelDesc):
+    includesHealthySubjects: bool
+    plannedEnrollmentNumber: Union[Range, None] = None
+    plannedCompletionNumber: Union[Range, None] = None
+    plannedSex: List[Code] = []
+    criteria: List[EligibilityCriterion]
+    plannedAge: Union[Range, None] = None
+    instanceType: Literal["PopulationDefinition"]
+
+
+class StudyCohort(PopulationDefinition):
+    characteristics: List[Characteristic] = []
+    instanceType: Literal["StudyCohort"]
+
+
+class StudyDesignPopulation(PopulationDefinition):
+    cohorts: List[StudyCohort] = []
+    instanceType: Literal["StudyDesignPopulation"]

usdm3/api/procedure.py

@@ -0,0 +1,10 @@
+from typing import Literal, Union
+from .api_base_model import ApiBaseModelNameLabelDesc
+from .code import Code
+
+
+class Procedure(ApiBaseModelNameLabelDesc):
+    procedureType: str
+    code: Code
+    studyInterventionId: Union[str, None] = None
+    instanceType: Literal["Procedure"]

usdm3/api/quantity.py

@@ -0,0 +1,9 @@
+from typing import Literal, Union
+from .api_base_model import ApiBaseModel
+from .alias_code import AliasCode
+
+
+class Quantity(ApiBaseModel):
+    value: float
+    unit: Union[AliasCode, None] = None
+    instanceType: Literal["Quantity"]

usdm3/api/range.py

@@ -0,0 +1,11 @@
+from typing import Literal, Union
+from .api_base_model import ApiBaseModel
+from .code import Code
+
+
+class Range(ApiBaseModel):
+    minValue: float
+    maxValue: float
+    unit: Union[Code, None] = None
+    isApproximate: bool
+    instanceType: Literal["Range"]

usdm3/api/response_code.py

@@ -0,0 +1,9 @@
+from typing import Literal
+from .api_base_model import ApiBaseModel
+from .code import Code
+
+
+class ResponseCode(ApiBaseModel):
+    isEnabled: bool
+    code: Code
+    instanceType: Literal["ResponseCode"]

usdm3/api/schedule_timeline.py

@@ -0,0 +1,15 @@
+from typing import List, Literal, Union
+from .api_base_model import ApiBaseModelNameLabelDesc
+from .schedule_timeline_exit import ScheduleTimelineExit
+from .scheduled_instance import ScheduledActivityInstance, ScheduledDecisionInstance
+from .timing import Timing
+
+
+class ScheduleTimeline(ApiBaseModelNameLabelDesc):
+    mainTimeline: bool
+    entryCondition: str
+    entryId: str
+    exits: List[ScheduleTimelineExit] = []
+    timings: List[Timing] = []
+    instances: List[Union[ScheduledActivityInstance, ScheduledDecisionInstance]] = []
+    instanceType: Literal["ScheduleTimeline"]

usdm3/api/schedule_timeline_exit.py

@@ -0,0 +1,6 @@
+from .api_base_model import ApiBaseModel
+from typing import Literal
+
+
+class ScheduleTimelineExit(ApiBaseModel):
+    instanceType: Literal["ScheduleTimelineExit"]

usdm3/api/scheduled_instance.py

@@ -0,0 +1,27 @@
+from typing import List, Literal, Union
+from .api_base_model import ApiBaseModelNameLabelDesc, ApiBaseModel
+
+
+class ConditionAssignment(ApiBaseModel):
+    condition: str
+    conditionTargetId: str
+    instanceType: Literal["ConditionAssignment"]
+
+
+class ScheduledInstance(ApiBaseModelNameLabelDesc):
+    timelineId: Union[str, None] = None
+    timelineExitId: Union[str, None] = None
+    defaultConditionId: Union[str, None] = None
+    epochId: Union[str, None] = None
+    instanceType: Literal["ScheduledInstance"]
+
+
+class ScheduledActivityInstance(ScheduledInstance):
+    activityIds: List[str] = []
+    encounterId: Union[str, None] = None
+    instanceType: Literal["ScheduledActivityInstance"]
+
+
+class ScheduledDecisionInstance(ScheduledInstance):
+    conditionAssignments: List[ConditionAssignment]
+    instanceType: Literal["ScheduledDecisionInstance"]

usdm3/api/study.py

@@ -0,0 +1,16 @@
+from typing import List, Literal, Union
+from pydantic import Field
+from .api_base_model import ApiBaseModel
+from .study_protocol_document import StudyProtocolDocument
+from .study_version import StudyVersion
+from uuid import UUID
+
+
+class Study(ApiBaseModel):
+    id: Union[UUID, None] = None
+    name: str = Field(min_length=1)
+    description: Union[str, None] = None
+    label: Union[str, None] = None
+    versions: List[StudyVersion] = []
+    documentedBy: Union[StudyProtocolDocument, None] = None
+    instanceType: Literal["Study"]

usdm3/api/study_amendment.py

@@ -0,0 +1,15 @@
+from typing import Union, List, Literal
+from .api_base_model import ApiBaseModel
+from .study_amendment_reason import StudyAmendmentReason
+from .geographic_scope import SubjectEnrollment
+
+
+class StudyAmendment(ApiBaseModel):
+    number: str
+    summary: str
+    substantialImpact: bool
+    primaryReason: StudyAmendmentReason
+    secondaryReasons: List[StudyAmendmentReason] = []
+    enrollments: List[SubjectEnrollment]
+    previousId: Union[str, None] = None
+    instanceType: Literal["StudyAmendment"]