Models¶

Phenopackets service¶

class chord_metadata_service.phenopackets.models.Biosample(*args, **kwargs)¶

Class to describe a unit of biological material

FHIR: Specimen

exception DoesNotExist¶

exception MultipleObjectsReturned¶

get_project_id()¶: Returns the Project.identifier of the project that owns this object. Template method design pattern, implementation left to inheritors.

property schema_type¶: Returns the SchemaType of the model. Template method design pattern, implementation left to inheritors.

class chord_metadata_service.phenopackets.models.Diagnosis(*args, **kwargs)¶

Class to refer to disease that is present in the individual analyzed

FHIR: Condition

exception DoesNotExist¶

exception MultipleObjectsReturned¶

class chord_metadata_service.phenopackets.models.Disease(*args, **kwargs)¶

Class to represent a diagnosis and inference or hypothesis about the cause underlying the observed phenotypic abnormalities

FHIR: Condition

exception DoesNotExist¶

exception MultipleObjectsReturned¶

class chord_metadata_service.phenopackets.models.Gene(*args, **kwargs)¶

Class to represent an identifier for a gene

FHIR: ? Draft extension for Gene is in development where Gene defined via class CodeableConcept

exception DoesNotExist¶

exception MultipleObjectsReturned¶

class chord_metadata_service.phenopackets.models.GenomicInterpretation(*args, **kwargs)¶

Class to represent a statement about the contribution of a genomic element towards the observed phenotype

FHIR: Observation

exception DoesNotExist¶

exception MultipleObjectsReturned¶

clean()¶: Hook for doing any extra model-wide validation after clean() has been called on every field by self.clean_fields. Any ValidationError raised by this method will not be associated with a particular field; it will have a special-case association with the field defined by NON_FIELD_ERRORS.

class chord_metadata_service.phenopackets.models.HtsFile(*args, **kwargs)¶

Class to link HTC files with data

FHIR: DocumentReference

exception DoesNotExist¶

exception MultipleObjectsReturned¶

class chord_metadata_service.phenopackets.models.Interpretation(*args, **kwargs)¶

Class to represent the interpretation of a genomic analysis

FHIR: DiagnosticReport

exception DoesNotExist¶

exception MultipleObjectsReturned¶

class chord_metadata_service.phenopackets.models.MetaData(*args, **kwargs)¶

Class to store structured definitions of the resources and ontologies used within the phenopacket

FHIR: Metadata

exception DoesNotExist¶

exception MultipleObjectsReturned¶

class chord_metadata_service.phenopackets.models.Phenopacket(*args, **kwargs)¶

Class to aggregate Individual’s experiments data

FHIR: Composition

exception DoesNotExist¶

exception MultipleObjectsReturned¶

get_project_id()¶: Returns the Project.identifier of the project that owns this object. Template method design pattern, implementation left to inheritors.

property schema_type¶: Returns the SchemaType of the model. Template method design pattern, implementation left to inheritors.

class chord_metadata_service.phenopackets.models.PhenotypicFeature(*args, **kwargs)¶

Class to describe a phenotype of an Individual

FHIR: Condition or Observation

exception DoesNotExist¶

exception MultipleObjectsReturned¶

class chord_metadata_service.phenopackets.models.Procedure(*args, **kwargs)¶

Class to represent a clinical procedure performed on an individual (subject) in order to extract a biosample

FHIR: Procedure

exception DoesNotExist¶

exception MultipleObjectsReturned¶

class chord_metadata_service.phenopackets.models.Variant(*args, **kwargs)¶

Class to describe Individual variants or diagnosed causative variants

FHIR: Observation ? Draft extension for Variant is in development

exception DoesNotExist¶

exception MultipleObjectsReturned¶

Patients service¶

class chord_metadata_service.patients.models.Individual(*args, **kwargs)¶

Class to store demographic information about an Individual (Patient)

exception DoesNotExist¶

exception MultipleObjectsReturned¶

get_project_id()¶: Returns the Project.identifier of the project that owns this object. Template method design pattern, implementation left to inheritors.

property schema_type¶: Returns the SchemaType of the model. Template method design pattern, implementation left to inheritors.

Mcode service¶

Experiments service¶

class chord_metadata_service.experiments.models.Experiment(*args, **kwargs)¶

Class to store Experiment information. This model is primarily designed for genomic experiments; it is thus linked to a specific bisample.

Experiments can be linked via a many-to-many relationship to ExperimentResults; many-to-many because a result may be derived from multiple experiments. Consider, for example, the results of a pairwise analysis derived from two Experiments, each of which was performed on a different Biosample.

exception DoesNotExist¶

exception MultipleObjectsReturned¶

class chord_metadata_service.experiments.models.ExperimentResult(*args, **kwargs)¶

Class to represent information about analysis of sequencing data in a file format.

exception DoesNotExist¶

exception MultipleObjectsReturned¶

class chord_metadata_service.experiments.models.Instrument(*args, **kwargs)¶

Class to represent information about instrument used to perform a sequencing experiment.

exception DoesNotExist¶

exception MultipleObjectsReturned¶

Resources service¶

class chord_metadata_service.resources.models.Resource(*args, **kwargs)¶

Class to represent a description of an external resource used for referencing an object

FHIR: CodeSystem

exception DoesNotExist¶

exception MultipleObjectsReturned¶

clean()¶: Hook for doing any extra model-wide validation after clean() has been called on every field by self.clean_fields. Any ValidationError raised by this method will not be associated with a particular field; it will have a special-case association with the field defined by NON_FIELD_ERRORS.

save(*args, **kwargs)¶

Save the current instance. Override this in a subclass if you want to control the saving process.

The ‘force_insert’ and ‘force_update’ parameters can be used to insist that the “save” must be an SQL insert or update (or equivalent for non-SQL backends), respectively. Normally, they should not be set.

CHORD service¶

class chord_metadata_service.chord.models.Project(*args, **kwargs)¶

Class to represent a Project, which contains multiple Datasets which are each a group of Phenopackets.

exception DoesNotExist¶

exception MultipleObjectsReturned¶

class chord_metadata_service.chord.models.Dataset(*args, **kwargs)¶

Class to represent a Dataset, which contains multiple Phenopackets.

exception DoesNotExist¶

exception MultipleObjectsReturned¶

clean()¶: Hook for doing any extra model-wide validation after clean() has been called on every field by self.clean_fields. Any ValidationError raised by this method will not be associated with a particular field; it will have a special-case association with the field defined by NON_FIELD_ERRORS.

save(*args, **kwargs)¶

Save the current instance. Override this in a subclass if you want to control the saving process.

The ‘force_insert’ and ‘force_update’ parameters can be used to insist that the “save” must be an SQL insert or update (or equivalent for non-SQL backends), respectively. Normally, they should not be set.

class chord_metadata_service.chord.models.ProjectJsonSchema(id, project, required, json_schema, schema_type)¶

exception DoesNotExist¶

exception MultipleObjectsReturned¶

clean()¶: Creation of ProjectJsonSchema is prohibited if the target project already contains data matching the schema_type

save(*args, **kwargs)¶

Save the current instance. Override this in a subclass if you want to control the saving process.

The ‘force_insert’ and ‘force_update’ parameters can be used to insist that the “save” must be an SQL insert or update (or equivalent for non-SQL backends), respectively. Normally, they should not be set.