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(analysisId: str = None, study: str = None, analysisState: str = 'UNPUBLISHED', sample: List[overture_song.entities.CompositeEntity] = None, file: List[overture_song.entities.File] = None)[source]¶ Bases: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= 'UNPUBLISHED'¶
-
file
= None¶
-
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
-
donor
= None¶
-
specimen
= None¶
-
-
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
-
donorGender
= None¶
-
donorId
= None¶
-
donorSubmitterId
= None¶
-
studyId
= None¶
-
-
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¶
-
-
class
overture_song.entities.
Metadata
(info: dict = None)[source]¶ Bases:
overture_song.entities.Entity
-
info
= None¶
-
-
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
-
sampleId
= None¶
-
sampleSubmitterId
= None¶
-
sampleType
= None¶
-
specimenId
= None¶
-
-
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
create
(aligned, alignmentTool, insertSize, libraryStrategy, pairedEnd, referenceGenome, analysisId=None)[source]¶
-
insertSize
= None¶
-
libraryStrategy
= None¶
-
pairedEnd
= None¶
-
referenceGenome
= None¶
-
-
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¶
-
-
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¶
-
classmethod
-
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
-
description
= None¶
-
name
= None¶
-
organization
= None¶
-
studyId
= None¶
-
-
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¶
-
matchedNormalSampleSubmitterId
= None¶
-
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¶
-