Job

Overview

Created by jacobo on 11/09/14.

Summary

Field	create	update	unique	required
id
description
tool
userId
commandLine
params
priority
outDir
input
output
tags
dependsOn
execution
stdout
stderr
visited
OPENCGA_PARENTS
study
attributes
uuid
creationDate
modificationDate
internal
release

Data Model

Job

You can find the Java code here.

Field	Description
id String	Job ID is a mandatory parameter when creating a new sample, 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 sample creation and cannot be changed.Tags: internal, unique, immutable
description String	An string to describe the properties of the Job.
tool ToolInfo
userId String
commandLine String
params Map<Object,String>
creationDate String	String representing when the sample was created, this is automatically set by OpenCGA.Tags: internal
modificationDate String	String representing when was the last time the sample was modified, this is automatically set by OpenCGA.Tags: internal
priority Priority
internal JobInternal	An object describing the internal information of the Sample. This is managed by OpenCGA.Tags: internal
outDir File
input List<File>
output List<File>
tags List<String>
dependsOn List<Job>
execution ExecutionResult
stdout File
stderr File
visited boolean
OPENCGA_PARENTS String
release int	An integer describing the current data release.Tags: internal
study JobStudyParam
attributes Map<Object,String>

JobStudyParam

You can find the Java code here.

Field	Description
id String
others List<String>

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.

ExecutionResult

You can find the Java code here.

Field	Description
id String
executor ExecutorInfo
start Date>
end Date>
status Status
externalFiles List<URI>
steps List<ToolStep>
events List<Event>
attributes ObjectMap

Enum Enums.Priority

Enumeration class. You can find the Java code here.

Field	Description
URGENT
HIGH
MEDIUM
LOW
UNKNOWN
value

ToolInfo

You can find the Java code here.

Field	Description
id String
description String
scope Scope
type Type
resource Resource

SampleInternal

You can find the Java code here.

Field	Description
status Status
rga RgaIndex

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>

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

StudyInternal

You can find the Java code here.

Field	Description
status Status
configuration StudyConfiguration