File

Overview

File data model hosts information about any file.

Summary

Field	Create	Update	Unique	Required
id
uuid
name
type
format
bioformat
checksum
uri
path
release
creationDate
modificationDate
description
external
size
software
experiment
sampleIds
jobId
tags
relatedFiles
qualityControl
stats
status
internal
attributes

Data Model

File

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.
name String	The name of the file.
type Type	The type can have the values FILE or DIRECTORY.
format Format	The format can have the values VCF, BCF, GVCF, TBI, BIGWIG, SAM, BAM, BAI, CRAM, CRAI, FASTQ, FASTA, PED, TAB_SEPARATED_VALUES, COMMA_SEPARATED_VALUES, XML, PROTOCOL_BUFFER, JSON, AVRO, PARQUET, IMAGE, PLAIN, BINARY, NONE and UNKNOWN.
bioformat Bioformat	The bioformat can have the values MICROARRAY_EXPRESSION_ONECHANNEL_AGILENT, MICROARRAY_EXPRESSION_ONECHANNEL_AFFYMETRIX, MICROARRAY_EXPRESSION_ONECHANNEL_GENEPIX, MICROARRAY_EXPRESSION_TWOCHANNELS_AGILENT, MICROARRAY_EXPRESSION_TWOCHANNELS_GENEPIX, DATAMATRIX_EXPRESSION, IDLIST, IDLIST_RANKED, ANNOTATION_GENEVSANNOTATION, OTHER_NEWICK, OTHER_BLAST, OTHER_INTERACTION, OTHER_GENOTYPE, OTHER_PLINK, OTHER_VCF, OTHER_PED, @Deprecated VCF4, VARIANT, ALIGNMENT, COVERAGE, SEQUENCE, PEDIGREE, REFERENCE_GENOME, NONE and UNKNOWN.
checksum String	The checksum of the file.
uri URI	The uri of the file.
path String	The path of the file.
release int	An integer describing the current data release.
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.
description String	Users may provide a description for the entry.
external boolean	Indicates the file is external or not.
size long	The size of the file.
software Software	Software related with file.
experiment FileExperiment	File experiment.
sampleIds List<String>	List of sample ids of the file.
jobId String	File job id.
tags List<String>	File tags.
relatedFiles List<FileRelatedFile>	List of objects FileRelatedFiles describing related files.
qualityControl FileQualityControl	Contains different metrics to evaluate the quality of the individual.
stats Map<String,Object> Deprecated	Stats of the object.
status Status	Object to set a custom status.
internal FileInternal	Internal field for manage the object.
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.

FileExperiment

You can find the Java code here.

FileRelatedFile

You can find the Java code here.

Software

You can find the Java code here.

Field	Description
name String	Software name
version String	Software version
repository String	Software repository
commit String	Software commit
website String	Software website
params Map<String,String>	Software params

Status

You can find the Java code here.

URI

You can find the Java code here.

FileInternal

You can find the Java code here.

Field	Description
status FileStatus	File status can have the values READY, DELETED, TRASHED, STAGE, MISSING, PENDING_DELETE, DELETING, REMOVED and MISSING_SAMPLES.
variant FileInternalVariant	File internal variant.
alignment FileInternalAlignment	File internal alignment.
sampleMap Map<String,String>	Map of samples.
missingSamples MissingSamples	Object describes missing samples.
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.

FileQualityControl

You can find the Java code here.

MissingSamples

You can find the Java code here.

Field	Description
existing List<String>	List of existing samples.
nonExisting List<String>	List of non existing samples.

FileStatus

You can find the Java code here.

FileInternalAlignment

You can find the Java code here.

InternalStatus

You can find the Java code here.

FileInternalVariant

You can find the Java code here.