transmart_loader.transmart module¶

class transmart_loader.transmart.CategoricalValue(value: str)¶

Bases: transmart_loader.transmart.Value

A categorical value

value()¶

value_type()¶

class transmart_loader.transmart.Concept(concept_code: str, name: str, concept_path: str, value_type: transmart_loader.transmart.ValueType)¶

Bases: object

Concepts to classify observations

class transmart_loader.transmart.ConceptNode(concept: transmart_loader.transmart.Concept)¶

Bases: transmart_loader.transmart.TreeNode

Concept node

class transmart_loader.transmart.DataCollection(concepts: Iterable[transmart_loader.transmart.Concept], studies: Iterable[transmart_loader.transmart.Study], trial_visits: Iterable[transmart_loader.transmart.TrialVisit], visits: Iterable[transmart_loader.transmart.Visit], ontology: Iterable[transmart_loader.transmart.TreeNode], patients: Iterable[transmart_loader.transmart.Patient], observations: Iterable[transmart_loader.transmart.Observation])¶

Bases: object

A data collection that can be loaded into TranSMART

class transmart_loader.transmart.DateValue(value: datetime.date)¶

Bases: transmart_loader.transmart.Value

A date value

value()¶

value_type()¶

class transmart_loader.transmart.Dimension(name: str, modifier_code: Optional[str] = None, value_type: Optional[transmart_loader.transmart.ValueType] = None)¶

Bases: object

Dimension metadata

class transmart_loader.transmart.NumericalValue(value: float)¶

Bases: transmart_loader.transmart.Value

A numerical value

value()¶

value_type()¶

class transmart_loader.transmart.Observation(patient: transmart_loader.transmart.Patient, concept: transmart_loader.transmart.Concept, visit: Optional[transmart_loader.transmart.Visit], trial_visit: transmart_loader.transmart.TrialVisit, start_date: Optional[datetime.date], end_date: Optional[datetime.date], value: transmart_loader.transmart.Value)¶

Bases: object

Data about an observed event or an attribute of a patient

class transmart_loader.transmart.ObservationMetadata¶

Bases: object

Metadata about an observation

class transmart_loader.transmart.Patient(identifier: str, sex: str, mappings: Sequence[transmart_loader.transmart.PatientMapping])¶

Bases: object

Patient properties

class transmart_loader.transmart.PatientMapping(source: str, identifier: str)¶

Bases: object

Patient identifiers

class transmart_loader.transmart.Study(study_id: str, name: str)¶: Bases: object

class transmart_loader.transmart.StudyNode(study: transmart_loader.transmart.Study)¶

Bases: transmart_loader.transmart.TreeNode

Study node

class transmart_loader.transmart.TextValue(value: str)¶

Bases: transmart_loader.transmart.Value

A text value

value()¶

value_type()¶

class transmart_loader.transmart.TreeNode(name: str)¶

Bases: object

Ontology node

add_child(child: transmart_loader.transmart.TreeNode)¶

class transmart_loader.transmart.TrialVisit(study: transmart_loader.transmart.Study, rel_time_label: str, rel_time_unit: Optional[str] = None, rel_time: Optional[int] = None)¶

Bases: object

Trial visit

class transmart_loader.transmart.Value¶

Bases: object

An observed value

value¶

value_type¶

class transmart_loader.transmart.ValueType¶

Bases: enum.Enum

Type of an observed value

Categorical = 2¶

Date = 4¶

Numeric = 1¶

Text = 3¶

class transmart_loader.transmart.Visit(patient: transmart_loader.transmart.Patient, identifier: str, active_status: Optional[str], start_date: Optional[datetime.date], end_date: Optional[datetime.date], inout: Optional[str], location: Optional[str], length_of_stay: Optional[int])¶

Bases: object

Patient visit