File

Overview

Created by jacobo on 11/09/14.

Summary

Field	create	update	unique	required
id
name
type
format
bioformat
checksum
uri
path
description
external
size
software
experiment
sampleIds
jobId
tags
relatedFiles
qualityControl
stats
status
attributes
uuid
release
creationDate
modificationDate
internal

Data Model

File

You can find the Java code here.

Field	Description
id String	File ID is a mandatory parameter when creating a new File, this ID cannot be changed at the moment.Tags: required, immutable, unique
uuid String	Global unique ID at the whole OpenCGA installation. This is automatically created during the File creation and cannot be changed.Tags: internal, unique, immutable
name String
type File.Type	Formats: file, folder, index.
format File.Format	Formats: txt, executable, image, ...
bioformat File.Bioformat	BAM, VCF, ...
checksum String
uri URI
path String
release int	An integer describing the current data release.Tags: internal
creationDate String	String representing when the File was created, this is automatically set by OpenCGA.Tags: internal
modificationDate String	String representing when was the last time the File was modified, this is automatically set by OpenCGA.Tags: internal
description String	An string to describe the properties of the File.
external boolean
size long
software Software
experiment FileExperiment
sampleIds List<String>
jobId String
tags List<String>
relatedFiles List<FileRelatedFile>
qualityControl FileQualityControl
stats Map<Object,String>
status CustomStatus	An object describing the status of the File.
internal FileInternal	An object describing the internal information of the File. This is managed by OpenCGA.Tags: internal
attributes Map<Object,String>	You can use this field to store any other information, keep in mind this is not indexed so you cannot search by attributes.

FileRelatedFile

You can find the Java code here.

Field	Description
file File
relation FileRelatedFile.Relation

SampleInternal

You can find the Java code here.

Field	Description
status Status
rga RgaIndex

IndividualInternal

You can find the Java code here.

Field	Description
status Status

FamilyInternal

You can find the Java code here.

Field	Description
status FamilyStatus

FileInternal

You can find the Java code here.

Field	Description
status FileStatus
index FileIndex
sampleMap Map<String>
missingSamples MissingSamples

JobInternal

You can find the Java code here.

Field	Description
status ExecutionStatus
webhook JobInternalWebhook
events List<Event>

InterpretationInternal

You can find the Java code here.

Field	Description
status InterpretationStatus

ProjectInternal

You can find the Java code here.

Field	Description
datastores Datastores
cellbase CellBaseConfiguration
status Status

CohortInternal

You can find the Java code here.

Field	Description
status CohortStatus

ClinicalAnalysisInternal

You can find the Java code here.

Field	Description
status ClinicalAnalysisStatus

StudyInternal

You can find the Java code here.

Field	Description
status Status
configuration StudyConfiguration