File
Last updated
Last updated
File data model hosts information about any file.
Field | Create | Update | Unique | Required |
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You can find the Java code here.
You can find the Java code here.
You can find the Java code here.
You can find the Java code here.
You can find the Java code here.
You can find the Java code here.
You can find the Java code here.
You can find the Java code here.
You can find the Java code here.
You can find the Java code here.
You can find the Java code here.
You can find the Java code here.
You can find the Java code here.
Field | Description |
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Field | Description |
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Field | Description |
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Field | Description |
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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.
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 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.
existing List<String>
List of existing samples.
nonExisting List<String>
List of non existing samples.
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