entities¶

class overture_song.entities.Analysis(analysisId: str = None, study: str = None, analysisState: str = 'UNPUBLISHED', sample: List[overture_song.entities.CompositeEntity] = None, file: List[overture_song.entities.File] = None)[source]¶

Bases: overture_song.entities.Entity

analysisId = None¶

analysisState = 'UNPUBLISHED'¶

classmethod builder()[source]¶

file = None¶

classmethod from_json(json_string)[source]¶

sample = None¶

study = None¶

class overture_song.entities.CompositeEntity(info: dict = None, sampleId: str = None, specimenId: str = None, sampleSubmitterId: str = None, sampleType: str = None, specimen: Type[overture_song.entities.Specimen] = None, donor: Type[overture_song.entities.Donor] = None)[source]¶

Bases: overture_song.entities.Sample

classmethod base_on_sample(sample)[source]¶

classmethod create(donor, specimen, sample)[source]¶

donor = None¶

specimen = None¶

validate()[source]¶

class overture_song.entities.Donor(info: dict = None, donorId: str = None, donorSubmitterId: str = None, studyId: str = None, donorGender: str = None)[source]¶

Bases: overture_song.entities.Metadata, overture_song.validation.Validatable

classmethod create(donorSubmitterId, studyId, donorGender, donorId=None, info=None)[source]¶

donorGender = None¶

donorId = None¶

donorSubmitterId = None¶

studyId = None¶

validate()[source]¶

class overture_song.entities.Entity[source]¶

Bases: object

to_dict()[source]¶

to_json()[source]¶

class overture_song.entities.Experiment(info: dict = None)[source]¶: Bases: overture_song.entities.Metadata

class overture_song.entities.File(info: dict = None, objectId: str = None, analysisId: str = None, fileName: str = None, studyId: str = None, fileSize: int = -1, fileType: str = None, fileMd5sum: str = None, fileAccess: str = None)[source]¶

Bases: overture_song.entities.Metadata, overture_song.validation.Validatable

analysisId = None¶

classmethod create(fileName, fileSize, fileType, fileMd5sum, fileAccess, studyId=None, analysisId=None, objectId=None, info=None)[source]¶

fileAccess = None¶

fileMd5sum = None¶

fileName = None¶

fileSize = -1¶

fileType = None¶

objectId = None¶

studyId = None¶

validate()[source]¶

class overture_song.entities.Metadata(info: dict = None)[source]¶

Bases: overture_song.entities.Entity

add_info(data: dict)[source]¶

info = None¶

set_info(key: str, value: Any)[source]¶

class overture_song.entities.Sample(info: dict = None, sampleId: str = None, specimenId: str = None, sampleSubmitterId: str = None, sampleType: str = None)[source]¶

Bases: overture_song.entities.Metadata, overture_song.validation.Validatable

classmethod create(specimenId, sampleSubmitterId, sampleType, sampleId=None, info=None)[source]¶

sampleId = None¶

sampleSubmitterId = None¶

sampleType = None¶

specimenId = None¶

validate()[source]¶

class overture_song.entities.SequencingRead(info: dict = None, analysisId: str = None, aligned: bool = None, alignmentTool: str = None, insertSize: int = None, libraryStrategy: str = None, pairedEnd: bool = None, referenceGenome: str = None)[source]¶

Bases: overture_song.entities.Experiment, overture_song.validation.Validatable

aligned = None¶

alignmentTool = None¶

analysisId = None¶

classmethod builder()[source]¶

classmethod create(aligned, alignmentTool, insertSize, libraryStrategy, pairedEnd, referenceGenome, analysisId=None)[source]¶

insertSize = None¶

libraryStrategy = None¶

pairedEnd = None¶

referenceGenome = None¶

validate()[source]¶

class overture_song.entities.SequencingReadAnalysis(analysisId: str = None, study: str = None, analysisState: str = 'UNPUBLISHED', sample: List[overture_song.entities.CompositeEntity] = None, file: List[overture_song.entities.File] = None, analysisType: str = 'sequencingRead', experiment: Type[overture_song.entities.SequencingRead] = None)[source]¶

Bases: overture_song.entities.Analysis, overture_song.validation.Validatable

analysisType = 'sequencingRead'¶

classmethod create(experiment, sample, file, analysisId=None, study=None, analysisState='UNPUBLISHED', info=None)[source]¶

experiment = None¶

validate()[source]¶

class overture_song.entities.Specimen(info: dict = None, specimenId: str = None, donorId: str = None, specimenSubmitterId: str = None, specimenClass: str = None, specimenType: str = None)[source]¶

Bases: overture_song.entities.Metadata, overture_song.validation.Validatable

classmethod create(donorId, specimenSubmitterId, specimenClass, specimenType, specimenId=None, info=None)[source]¶

donorId = None¶

specimenClass = None¶

specimenId = None¶

specimenSubmitterId = None¶

specimenType = None¶

validate()[source]¶

class overture_song.entities.Study(info: dict = None, studyId: str = None, name: str = None, organization: str = None, description: str = None)[source]¶

Bases: overture_song.entities.Metadata, overture_song.validation.Validatable

classmethod create(studyId, name=None, description=None, organization=None)[source]¶

classmethod create_from_raw(study_obj)[source]¶

description = None¶

name = None¶

organization = None¶

studyId = None¶

validate()[source]¶

class overture_song.entities.VariantCall(info: dict = None, analysisId: str = None, variantCallingTool: str = None, matchedNormalSampleSubmitterId: str = None)[source]¶

Bases: overture_song.entities.Experiment, overture_song.validation.Validatable

analysisId = None¶

classmethod create(variantCallingTool, matchedNormalSampleSubmitterId, analysisId=None)[source]¶

matchedNormalSampleSubmitterId = None¶

validate()[source]¶

variantCallingTool = None¶

class overture_song.entities.VariantCallAnalysis(analysisId: str = None, study: str = None, analysisState: str = 'UNPUBLISHED', sample: List[overture_song.entities.CompositeEntity] = None, file: List[overture_song.entities.File] = None, analysisType: str = 'variantCall', experiment: Type[overture_song.entities.VariantCall] = None)[source]¶

Bases: overture_song.entities.Analysis, overture_song.validation.Validatable

analysisType = 'variantCall'¶

classmethod create(experiment, sample, file, analysisId=None, study=None, analysisState='UNPUBLISHED', info=None)[source]¶

experiment = None¶

validate()[source]¶