Job

Overview

Job data model hosts information about any job.

Summary

Field	Create	Update	Unique	Required
id
uuid
description
tool
userId
commandLine
params
creationDate
modificationDate
priority
release
outDir
input
output
tags
dependsOn
execution
stdout
stderr
visited
release
study
attributes

Data Model

Job

You can find the Java code here.

Field	Description
id String	Object ID is a mandatory parameter when creating a new one, this ID cannot be changed at the moment.
uuid String	Unique 32-character identifier assigned automatically by OpenCGA.
description String	Users may provide a description for the entry.
tool ToolInfo	Job tool info.
userId String	Job user id.
commandLine String	Job command line.
params Map<String,Object>	Job params.
creationDate String	Autogenerated date following the format YYYYMMDDhhmmss containing the date when the entry was first registered.
modificationDate String since: 1.0	Autogenerated date following the format YYYYMMDDhhmmss containing the date when the entry was last modified.
priority Priority	Job priority.
release JobInternal	An integer describing the current data release.
outDir File	Output dir for the job.
input List<File>	List of input files.
output List<File>	List of output files.
tags List<String>	List of tags for the job.
dependsOn List<Job>	List of jobs the current job depends on.
execution ExecutionResult	Result of the execution.
stdout File	Standard out file.
stderr File	Standard error file.
visited boolean	Boolean that represents if the job has been visited or not.
release int	An integer describing the current data release.
study JobStudyParam	Job study.
attributes Map<String,Object>	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	Object ID is a mandatory parameter when creating a new one, this ID cannot be changed at the moment.
executor ExecutorInfo	Object describes execution information.
start Date	Date the execution started.
end Date	Date the execution was completed.
status Status	Executor status can have the values PENDING, RUNNING, DONE and ERROR.
externalFiles List<URI>	List of uris to the external files.
steps List<ToolStep>	List of ToolStep.
events List<Event>	List of Event.
attributes ObjectMap	You can use this field to store any other information, keep in mind this is not indexed so you cannot search by attributes.

JobStudyParam

You can find the Java code here.

Field	Description
id String	Object ID is a mandatory parameter when creating a new one, this ID cannot be changed at the moment.
others List<String>	List of strings.

ToolInfo

You can find the Java code here.

Field	Description
id String	Object ID is a mandatory parameter when creating a new one, this ID cannot be changed at the moment.
description String	Users may provide a description for the entry.
scope Scope	Tool info scope can have the values GLOBAL, PROJECT and STUDY.
type Type	Tool info type can have the values OPERATION and ANALYSIS.
resource Resource	Tool info resource can have the values AUDIT, USER, PROJECT, STUDY, FILE, SAMPLE, JOB, INDIVIDUAL, COHORT, DISEASE_PANEL, FAMILY, CLINICAL_ANALYSIS, INTERPRETATION, VARIANT, ALIGNMENT, CLINICAL, EXPRESSION, RGA and FUNCTIONAL.

JobInternal

You can find the Java code here.

Field	Description
status ExecutionStatus	Job internal status can have the values PENDING, QUEUED, RUNNING, DONE, ERROR, UNKNOWN, REGISTERING, UNREGISTERED, ABORTED, DELETED.
webhook JobInternalWebhook	Job internal Webhook.
events List<Event>	Events of the internal job.
status InternalStatus	Status of the internal object.
registrationDate String	Registration date of the internal object.
lastModified String	Date of the last modification of the internal object.

Status

You can find the Java code here.

InternalStatus

You can find the Java code here.

JobInternalWebhook

You can find the Java code here.

Field	Description
webhook URL	Webhook URL.
status Map<String,Status>	Webhook status map can have the values SUCCESS or ERROR.

ToolStep

You can find the Java code here.

Field	Description
id String	Object ID is a mandatory parameter when creating a new one, this ID cannot be changed at the moment.
start Date	Date the execution started.
end Date	Date the execution was completed.
status Type	Executor status can have the values PENDING, RUNNING, DONE and ERROR.
attributes ObjectMap	You can use this field to store any other information, keep in mind this is not indexed so you cannot search by attributes.

URI

You can find the Java code here.

Date

You can find the Java code here.

ExecutionStatus

You can find the Java code here.

ExecutorInfo

You can find the Java code here.

Field	Description
id String	Object ID is a mandatory parameter when creating a new one, this ID cannot be changed at the moment.
clazz String	ExecutorInfo class.
params ObjectMap	ExecutorInfo params.
source Source	Executor info source can have the values FILE, PARQUET_FILE, MONGODB, HBASE, STORAGE.
framework Framework	Executor info framework can have the values LOCAL, MAP_REDUCE, SPARK.

URL

You can find the Java code here.