Retrieve Genomic Specimen File Metadata for Specimen Identifier
get
/ohfapi/cg/v3.3/{apiContext}/genomicspecimens/{id}/fileMetadata
This endpoints supports the retrieval of Genomic Specimen File Metadata for Specimen Identifier. It returns Genomic Specimen File Metadata information like File Identifier, File Name, Category Name, Tag, String Value, Number Value, Date Value and other Genomic Specimen File Metadata associated information.
Request
Supported Media Types
- application/json
- application/xml
Path Parameters
-
id: integer(int64)
Minimum Value:
0
Query Parameters
-
limit(optional): integer(int32)
Number of rows to return
-
offset(optional): integer(int32)
Row number to start from
Security
-
basicAuth: basic
Type:
basic
Response
Supported Media Types
- application/json
- application/xml
200 Response
successful operation
Root Schema : GenomicSpecimen
Type:
Show Source
object-
genomicFileMetadata(optional):
object LinkedReference
-
genomicSpecimenMetadata(optional):
object LinkedReference
-
identifier(optional):
object Identifier
Identifier assigned by a given system
-
patient(optional):
object LinkedReference
-
resourceType(optional):
string
-
specimenNumber(optional):
string
Specimen identifier in linked Specimen Datasource Database
-
specimenVendorNumber(optional):
string
Vendor Identifier in linked Specimen Datasource Database
-
subject(optional):
object LinkedReference
Nested Schema : Identifier
Type:
objectIdentifier assigned by a given system
Show Source
-
system(optional):
string
System which assigned this identifier
-
value(optional):
string
Identifier value
400 Response
Invalid request parameters
404 Response
file metadata not found
Examples
The following example submits a GET request.
API URL
http://localhost:7010/ohfapi/cg/v3.3/patientapi/genomicspecimens/362/fileMetadata
Example of Response Body
The following example shows the contents of the response body in JSON format:
{
"resourceType": "GenomicFileMetadata",
"items": [
{
"fileId": 9,
"fileName": "chr1_split_500_samples.vcf",
"category": [
{
"categoryName": "ANALYSIS",
"metadata": [
{
"tag": "ANALYSISDATE",
"strValue": "01/13/2015 01:18",
"dateValue": "01/13/2015"
},
{
"tag": "ANALYSISID",
"strValue": "GENOME_GPS"
},
{
"tag": "ANALYSISSYS",
"strValue": "NGS"
},
{
"tag": "ANALYSISVERSION",
"strValue": "2.0.2"
},
{
"tag": "DATAFILE",
"strValue": "dataFiles/gvcf/14-001385_1409700144.gvcf.gz"
},
{
"tag": "DATATYPE",
"strValue": "variant"
},
{
"tag": "DELETEEXISTINGRESULT",
"strValue": "Y"
},
{
"tag": "GENOMEBUILD",
"strValue": "GRCh37"
}
]
},
{
"categoryName": "RUN",
"metadata": [
{
"tag": "APPLICATIONTYPE",
"strValue": "exome"
},
{
"tag": "CAPTUREKIT",
"strValue": "Agilent SS Custom Capture"
},
{
"tag": "CUSTOMINDEX",
"strValue": "IGCCAAT"
},
{
"tag": "CYCLE",
"strValue": "1011"
},
{
"tag": "FLOWCELLID",
"strValue": "UNKNOWN"
},
{
"tag": "ISVENDORINDEX",
"strValue": "UNKNOWN"
},
{
"tag": "LANENUMBER",
"strValue": "8",
"numValue": 8
},
{
"tag": "READTYPE",
"strValue": "Paired End Reads"
},
{
"tag": "RUNID",
"strValue": "485544"
}
]
},
{
"categoryName": "SPECIMEN",
"metadata": [
{
"tag": "ADDSAMPLEMETAFILE",
"strValue": "Y"
},
{
"tag": "IRB",
"strValue": "14-001385"
},
{
"tag": "ISCLINICAL",
"strValue": "N"
},
{
"tag": "PROJECTID",
"strValue": "NGSLBP-1407602"
},
{
"tag": "REQUESTTU",
"strValue": "tu0"
},
{
"tag": "SAMPLEIDSOURCE",
"strValue": "MAYO_RLIMS"
},
{
"tag": "SPECIESNAME",
"strValue": "Homo sapiens"
}
]
}
]
},
{
"fileId": 14,
"fileName": "chr1_split_500_samples.vcf",
"category": [
{
"categoryName": "ANALYSIS",
"metadata": [
{
"tag": "ANALYSISDATE",
"strValue": "01/23/2015 01:18",
"dateValue": "01/23/2015"
},
{
"tag": "ANALYSISID",
"strValue": "GENOME_GPS"
},
{
"tag": "ANALYSISSYS",
"strValue": "NGS"
},
{
"tag": "ANALYSISVERSION",
"strValue": "2.0.2"
},
{
"tag": "DATAFILE",
"strValue": "dataFiles/gvcf/14-001385_1409700144.gvcf.gz"
},
{
"tag": "DATATYPE",
"strValue": "variant"
},
{
"tag": "DELETEEXISTINGRESULT",
"strValue": "Y"
},
{
"tag": "GENOMEBUILD",
"strValue": "GRCh37"
}
]
},
{
"categoryName": "RUN",
"metadata": [
{
"tag": "APPLICATIONTYPE",
"strValue": "exome"
},
{
"tag": "CAPTUREKIT",
"strValue": "Agilent SS Custom Capture"
},
{
"tag": "CUSTOMINDEX",
"strValue": "IGCCAAT"
},
{
"tag": "CYCLE",
"strValue": "1010"
},
{
"tag": "FLOWCELLID",
"strValue": "UNKNOWN"
},
{
"tag": "ISVENDORINDEX",
"strValue": "UNKNOWN"
},
{
"tag": "LANENUMBER",
"strValue": "7",
"numValue": 7
},
{
"tag": "READTYPE",
"strValue": "Paired End Reads"
},
{
"tag": "RUNID",
"strValue": "485543"
}
]
},
{
"categoryName": "SPECIMEN",
"metadata": [
{
"tag": "ADDSAMPLEMETAFILE",
"strValue": "Y"
},
{
"tag": "IRB",
"strValue": "14-001385"
},
{
"tag": "ISCLINICAL",
"strValue": "N"
},
{
"tag": "PROJECTID",
"strValue": "NGSLBP-1407602"
},
{
"tag": "REQUESTTU",
"strValue": "tu9"
},
{
"tag": "SAMPLEIDSOURCE",
"strValue": "MAYO_RLIMS"
},
{
"tag": "SPECIESNAME",
"strValue": "Homo sapiens"
}
]
}
]
},
{
"fileId": 17,
"fileName": "chr3_split_1-900_samples.vcf",
"category": [
{
"categoryName": "ANALYSIS",
"metadata": [
{
"tag": "ANALYSISDATE",
"strValue": "02/02/2015 01:18",
"dateValue": "02/02/2015"
},
{
"tag": "ANALYSISID",
"strValue": "GENOME_GPS"
},
{
"tag": "ANALYSISSYS",
"strValue": "NGS"
},
{
"tag": "ANALYSISVERSION",
"strValue": "2.0.2"
},
{
"tag": "DATAFILE",
"strValue": "dataFiles/gvcf/14-001385_1409700144.gvcf.gz"
},
{
"tag": "DATATYPE",
"strValue": "variant"
},
{
"tag": "DELETEEXISTINGRESULT",
"strValue": "Y"
},
{
"tag": "GENOMEBUILD",
"strValue": "GRCh37"
}
]
},
{
"categoryName": "RUN",
"metadata": [
{
"tag": "APPLICATIONTYPE",
"strValue": "exome"
},
{
"tag": "CAPTUREKIT",
"strValue": "Agilent SS Custom Capture"
},
{
"tag": "CUSTOMINDEX",
"strValue": "IGCCAAT"
},
{
"tag": "CYCLE",
"strValue": "1019"
},
{
"tag": "FLOWCELLID",
"strValue": "UNKNOWN"
},
{
"tag": "ISVENDORINDEX",
"strValue": "UNKNOWN"
},
{
"tag": "LANENUMBER",
"strValue": "6",
"numValue": 6
},
{
"tag": "READTYPE",
"strValue": "Paired End Reads"
},
{
"tag": "RUNID",
"strValue": "485542"
}
]
},
{
"categoryName": "SPECIMEN",
"metadata": [
{
"tag": "ADDSAMPLEMETAFILE",
"strValue": "Y"
},
{
"tag": "IRB",
"strValue": "14-001385"
},
{
"tag": "ISCLINICAL",
"strValue": "N"
},
{
"tag": "PROJECTID",
"strValue": "NGSLBP-1407602"
},
{
"tag": "REQUESTTU",
"strValue": "tu8"
},
{
"tag": "SAMPLEIDSOURCE",
"strValue": "MAYO_RLIMS"
},
{
"tag": "SPECIESNAME",
"strValue": "Homo sapiens"
}
]
}
]
},
{
"fileId": 20,
"fileName": "chr4_split_1-900_samples.vcf",
"category": [
{
"categoryName": "ANALYSIS",
"metadata": [
{
"tag": "ANALYSISDATE",
"strValue": "02/12/2015 01:18",
"dateValue": "02/12/2015"
},
{
"tag": "ANALYSISID",
"strValue": "GENOME_GPS"
},
{
"tag": "ANALYSISSYS",
"strValue": "NGS"
},
{
"tag": "ANALYSISVERSION",
"strValue": "2.0.2"
},
{
"tag": "DATAFILE",
"strValue": "dataFiles/gvcf/14-001385_1409700144.gvcf.gz"
},
{
"tag": "DATATYPE",
"strValue": "variant"
},
{
"tag": "DELETEEXISTINGRESULT",
"strValue": "Y"
},
{
"tag": "GENOMEBUILD",
"strValue": "GRCh37"
}
]
},
{
"categoryName": "RUN",
"metadata": [
{
"tag": "APPLICATIONTYPE",
"strValue": "exome"
},
{
"tag": "CAPTUREKIT",
"strValue": "Agilent SS Custom Capture"
},
{
"tag": "CUSTOMINDEX",
"strValue": "IGCCAAT"
},
{
"tag": "CYCLE",
"strValue": "1018"
},
{
"tag": "FLOWCELLID",
"strValue": "UNKNOWN"
},
{
"tag": "ISVENDORINDEX",
"strValue": "UNKNOWN"
},
{
"tag": "LANENUMBER",
"strValue": "5",
"numValue": 5
},
{
"tag": "READTYPE",
"strValue": "Paired End Reads"
},
{
"tag": "RUNID",
"strValue": "485541"
}
]
},
{
"categoryName": "SPECIMEN",
"metadata": [
{
"tag": "ADDSAMPLEMETAFILE",
"strValue": "Y"
},
{
"tag": "IRB",
"strValue": "14-001385"
},
{
"tag": "ISCLINICAL",
"strValue": "N"
},
{
"tag": "PROJECTID",
"strValue": "NGSLBP-1407602"
},
{
"tag": "REQUESTTU",
"strValue": "tu7"
},
{
"tag": "SAMPLEIDSOURCE",
"strValue": "MAYO_RLIMS"
},
{
"tag": "SPECIESNAME",
"strValue": "Homo sapiens"
}
]
}
]
},
{
"fileId": 23,
"fileName": "chr2_split_1-900_samples.vcf",
"category": [
{
"categoryName": "ANALYSIS",
"metadata": [
{
"tag": "ANALYSISDATE",
"strValue": "02/22/2015 01:18",
"dateValue": "02/22/2015"
},
{
"tag": "ANALYSISID",
"strValue": "GENOME_GPS"
},
{
"tag": "ANALYSISSYS",
"strValue": "NGS"
},
{
"tag": "ANALYSISVERSION",
"strValue": "2.0.2"
},
{
"tag": "DATAFILE",
"strValue": "dataFiles/gvcf/14-001385_1409700144.gvcf.gz"
},
{
"tag": "DATATYPE",
"strValue": "variant"
},
{
"tag": "DELETEEXISTINGRESULT",
"strValue": "Y"
},
{
"tag": "GENOMEBUILD",
"strValue": "GRCh37"
}
]
},
{
"categoryName": "RUN",
"metadata": [
{
"tag": "APPLICATIONTYPE",
"strValue": "exome"
},
{
"tag": "CAPTUREKIT",
"strValue": "Agilent SS Custom Capture"
},
{
"tag": "CUSTOMINDEX",
"strValue": "IGCCAAT"
},
{
"tag": "CYCLE",
"strValue": "1017"
},
{
"tag": "FLOWCELLID",
"strValue": "UNKNOWN"
},
{
"tag": "ISVENDORINDEX",
"strValue": "UNKNOWN"
},
{
"tag": "LANENUMBER",
"strValue": "4",
"numValue": 4
},
{
"tag": "READTYPE",
"strValue": "Paired End Reads"
},
{
"tag": "RUNID",
"strValue": "485540"
}
]
},
{
"categoryName": "SPECIMEN",
"metadata": [
{
"tag": "ADDSAMPLEMETAFILE",
"strValue": "Y"
},
{
"tag": "IRB",
"strValue": "14-001385"
},
{
"tag": "ISCLINICAL",
"strValue": "N"
},
{
"tag": "PROJECTID",
"strValue": "NGSLBP-1407602"
},
{
"tag": "REQUESTTU",
"strValue": "tu6"
},
{
"tag": "SAMPLEIDSOURCE",
"strValue": "MAYO_RLIMS"
},
{
"tag": "SPECIESNAME",
"strValue": "Homo sapiens"
}
]
}
]
},
{
"fileId": 24,
"fileName": "chr5_split_1-900_samples.vcf",
"category": [
{
"categoryName": "ANALYSIS",
"metadata": [
{
"tag": "ANALYSISDATE",
"strValue": "03/04/2015 01:18",
"dateValue": "03/04/2015"
},
{
"tag": "ANALYSISID",
"strValue": "GENOME_GPS"
},
{
"tag": "ANALYSISSYS",
"strValue": "NGS"
},
{
"tag": "ANALYSISVERSION",
"strValue": "2.0.2"
},
{
"tag": "DATAFILE",
"strValue": "dataFiles/gvcf/14-001385_1409700144.gvcf.gz"
},
{
"tag": "DATATYPE",
"strValue": "variant"
},
{
"tag": "DELETEEXISTINGRESULT",
"strValue": "Y"
},
{
"tag": "GENOMEBUILD",
"strValue": "GRCh37"
}
]
},
{
"categoryName": "RUN",
"metadata": [
{
"tag": "APPLICATIONTYPE",
"strValue": "exome"
},
{
"tag": "CAPTUREKIT",
"strValue": "Agilent SS Custom Capture"
},
{
"tag": "CUSTOMINDEX",
"strValue": "IGCCAAT"
},
{
"tag": "CYCLE",
"strValue": "1016"
},
{
"tag": "FLOWCELLID",
"strValue": "UNKNOWN"
},
{
"tag": "ISVENDORINDEX",
"strValue": "UNKNOWN"
},
{
"tag": "LANENUMBER",
"strValue": "3",
"numValue": 3
},
{
"tag": "READTYPE",
"strValue": "Paired End Reads"
},
{
"tag": "RUNID",
"strValue": "485539"
}
]
},
{
"categoryName": "SPECIMEN",
"metadata": [
{
"tag": "ADDSAMPLEMETAFILE",
"strValue": "Y"
},
{
"tag": "IRB",
"strValue": "14-001385"
},
{
"tag": "ISCLINICAL",
"strValue": "N"
},
{
"tag": "PROJECTID",
"strValue": "NGSLBP-1407602"
},
{
"tag": "REQUESTTU",
"strValue": "tu5"
},
{
"tag": "SAMPLEIDSOURCE",
"strValue": "MAYO_RLIMS"
},
{
"tag": "SPECIESNAME",
"strValue": "Homo sapiens"
}
]
}
]
},
{
"fileId": 29,
"fileName": "chr6_split_1-900_samples.vcf",
"category": [
{
"categoryName": "ANALYSIS",
"metadata": [
{
"tag": "ANALYSISDATE",
"strValue": "12/04/2014 01:18",
"dateValue": "12/04/2014"
},
{
"tag": "ANALYSISID",
"strValue": "GENOME_GPS"
},
{
"tag": "ANALYSISSYS",
"strValue": "NGS"
},
{
"tag": "ANALYSISVERSION",
"strValue": "2.0.2"
},
{
"tag": "DATAFILE",
"strValue": "dataFiles/gvcf/14-001385_1409700144.gvcf.gz"
},
{
"tag": "DATATYPE",
"strValue": "variant"
},
{
"tag": "DELETEEXISTINGRESULT",
"strValue": "Y"
},
{
"tag": "GENOMEBUILD",
"strValue": "GRCh37"
}
]
},
{
"categoryName": "RUN",
"metadata": [
{
"tag": "APPLICATIONTYPE",
"strValue": "exome"
},
{
"tag": "CAPTUREKIT",
"strValue": "Agilent SS Custom Capture"
},
{
"tag": "CUSTOMINDEX",
"strValue": "IGCCAAT"
},
{
"tag": "CYCLE",
"strValue": "1015"
},
{
"tag": "FLOWCELLID",
"strValue": "UNKNOWN"
},
{
"tag": "ISVENDORINDEX",
"strValue": "UNKNOWN"
},
{
"tag": "LANENUMBER",
"strValue": "2",
"numValue": 2
},
{
"tag": "READTYPE",
"strValue": "Paired End Reads"
},
{
"tag": "RUNID",
"strValue": "485538"
}
]
},
{
"categoryName": "SPECIMEN",
"metadata": [
{
"tag": "ADDSAMPLEMETAFILE",
"strValue": "Y"
},
{
"tag": "IRB",
"strValue": "14-001385"
},
{
"tag": "ISCLINICAL",
"strValue": "N"
},
{
"tag": "PROJECTID",
"strValue": "NGSLBP-1407602"
},
{
"tag": "REQUESTTU",
"strValue": "tu4"
},
{
"tag": "SAMPLEIDSOURCE",
"strValue": "MAYO_RLIMS"
},
{
"tag": "SPECIESNAME",
"strValue": "Homo sapiens"
}
]
}
]
},
{
"fileId": 32,
"fileName": "chr7_split_1-900_samples.vcf",
"category": [
{
"categoryName": "ANALYSIS",
"metadata": [
{
"tag": "ANALYSISDATE",
"strValue": "12/14/2014 01:18",
"dateValue": "12/14/2014"
},
{
"tag": "ANALYSISID",
"strValue": "GENOME_GPS"
},
{
"tag": "ANALYSISSYS",
"strValue": "NGS"
},
{
"tag": "ANALYSISVERSION",
"strValue": "2.0.2"
},
{
"tag": "DATAFILE",
"strValue": "dataFiles/gvcf/14-001385_1409700144.gvcf.gz"
},
{
"tag": "DATATYPE",
"strValue": "variant"
},
{
"tag": "DELETEEXISTINGRESULT",
"strValue": "Y"
},
{
"tag": "GENOMEBUILD",
"strValue": "GRCh37"
}
]
},
{
"categoryName": "RUN",
"metadata": [
{
"tag": "APPLICATIONTYPE",
"strValue": "exome"
},
{
"tag": "CAPTUREKIT",
"strValue": "Agilent SS Custom Capture"
},
{
"tag": "CUSTOMINDEX",
"strValue": "IGCCAAT"
},
{
"tag": "CYCLE",
"strValue": "1014"
},
{
"tag": "FLOWCELLID",
"strValue": "UNKNOWN"
},
{
"tag": "ISVENDORINDEX",
"strValue": "UNKNOWN"
},
{
"tag": "LANENUMBER",
"strValue": "1",
"numValue": 1
},
{
"tag": "READTYPE",
"strValue": "Paired End Reads"
},
{
"tag": "RUNID",
"strValue": "485537"
}
]
},
{
"categoryName": "SPECIMEN",
"metadata": [
{
"tag": "ADDSAMPLEMETAFILE",
"strValue": "Y"
},
{
"tag": "IRB",
"strValue": "14-001385"
},
{
"tag": "ISCLINICAL",
"strValue": "N"
},
{
"tag": "PROJECTID",
"strValue": "NGSLBP-1407602"
},
{
"tag": "REQUESTTU",
"strValue": "tu3"
},
{
"tag": "SAMPLEIDSOURCE",
"strValue": "MAYO_RLIMS"
},
{
"tag": "SPECIESNAME",
"strValue": "Homo sapiens"
}
]
}
]
},
{
"fileId": 35,
"fileName": "chr8_split_1-900_samples.vcf",
"category": [
{
"categoryName": "ANALYSIS",
"metadata": [
{
"tag": "ANALYSISDATE",
"strValue": "12/24/2014 01:18",
"dateValue": "12/24/2014"
},
{
"tag": "ANALYSISID",
"strValue": "GENOME_GPS"
},
{
"tag": "ANALYSISSYS",
"strValue": "NGS"
},
{
"tag": "ANALYSISVERSION",
"strValue": "2.0.2"
},
{
"tag": "DATAFILE",
"strValue": "dataFiles/gvcf/14-001385_1409700144.gvcf.gz"
},
{
"tag": "DATATYPE",
"strValue": "variant"
},
{
"tag": "DELETEEXISTINGRESULT",
"strValue": "Y"
},
{
"tag": "GENOMEBUILD",
"strValue": "GRCh37"
}
]
},
{
"categoryName": "RUN",
"metadata": [
{
"tag": "APPLICATIONTYPE",
"strValue": "exome"
},
{
"tag": "CAPTUREKIT",
"strValue": "Agilent SS Custom Capture"
},
{
"tag": "CUSTOMINDEX",
"strValue": "IGCCAAT"
},
{
"tag": "CYCLE",
"strValue": "1013"
},
{
"tag": "FLOWCELLID",
"strValue": "UNKNOWN"
},
{
"tag": "ISVENDORINDEX",
"strValue": "UNKNOWN"
},
{
"tag": "LANENUMBER",
"strValue": "0",
"numValue": 0
},
{
"tag": "READTYPE",
"strValue": "Paired End Reads"
},
{
"tag": "RUNID",
"strValue": "485536"
}
]
},
{
"categoryName": "SPECIMEN",
"metadata": [
{
"tag": "ADDSAMPLEMETAFILE",
"strValue": "Y"
},
{
"tag": "IRB",
"strValue": "14-001385"
},
{
"tag": "ISCLINICAL",
"strValue": "N"
},
{
"tag": "PROJECTID",
"strValue": "NGSLBP-1407602"
},
{
"tag": "REQUESTTU",
"strValue": "tu2"
},
{
"tag": "SAMPLEIDSOURCE",
"strValue": "MAYO_RLIMS"
},
{
"tag": "SPECIESNAME",
"strValue": "Homo sapiens"
}
]
}
]
},
{
"fileId": 36,
"fileName": "ALL.chr9.phase3_shapeit2_mvncall_integrated_v5.20130502.genotypes_1_900.vcf",
"category": [
{
"categoryName": "ANALYSIS",
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