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 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.
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