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Retrieve Genomic Files for a Specimen Number and Specimen Vendor Number

get

/ohfapi/cg/v3.3/genomicspecimens/genomicFiles

This endpoint supports the retrieval of Genomic Files for a Specimen Number and Specimen Vendor Number. It returns Genomic File information like File Name, File Uri, Loader Name, Ensembl Version and other Genomic File associated information.

Request

Supported Media Types

• application/json
• application/xml

Query Parameters

• limit(optional): integer(int32)
  Number of rows to return
• offset(optional): integer(int32)
  Row number to start from
• specimenNumber: string
  Specimen Number
• specimenVendorNumber: string
  Specimen Vendor Number

Security

• basicAuth: basic
  Type: basic

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Response

Supported Media Types

• application/json
• application/xml

200 Response

successful operation

Body ()

Root Schema : PageableCollection

Type: object

Model for paginated collections of data.

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• count(optional): integer(int64)
  Number of objects in the 'items' collection.
• hasMore(optional): boolean
  A boolean indicating if more pages are available.
• items(optional): array items
  A collection of paged items.
• links(optional): array links
  A collection of links containing hrefs to the current, next, and previous pages as applicable.
• resourceType(optional): string
  Identify the resource type

{
    "type":"object",
    "properties":{
        "resourceType":{
            "type":"string",
            "description":"Identify the resource type"
        },
        "items":{
            "type":"array",
            "xml":{
                "wrapped":true
            },
            "description":"A collection of paged items.",
            "items":{
                "$ref":"#/definitions/Serializable"
            }
        },
        "count":{
            "type":"integer",
            "format":"int64",
            "description":"Number of objects in the 'items' collection."
        },
        "hasMore":{
            "type":"boolean",
            "description":"A boolean indicating if more pages are available."
        },
        "links":{
            "type":"array",
            "example":"{rel: 'next',href: '/patientapi/patients?limit=100&offset=300'}",
            "xml":{
                "wrapped":true
            },
            "description":"A collection of links containing hrefs to the current, next, and previous pages as applicable.",
            "items":{
                "type":"string"
            }
        }
    },
    "description":"Model for paginated collections of data."
}

Nested Schema : items

Type: array

A collection of paged items.

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• Array of: object Serializable

{
    "type":"array",
    "xml":{
        "wrapped":true
    },
    "description":"A collection of paged items.",
    "items":{
        "$ref":"#/definitions/Serializable"
    }
}

Nested Schema : links

Type: array

A collection of links containing hrefs to the current, next, and previous pages as applicable.

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• Array of: string

{
    "type":"array",
    "example":"{rel: 'next',href: '/patientapi/patients?limit=100&offset=300'}",
    "xml":{
        "wrapped":true
    },
    "description":"A collection of links containing hrefs to the current, next, and previous pages as applicable.",
    "items":{
        "type":"string"
    }
}

Example:

{rel: 'next',href: '/patientapi/patients?limit=100&offset=300'}

Nested Schema : Serializable

Type: object

400 Response

Invalid request parameters

404 Response

Genomic specimen files not found

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Examples

The following example submits a GET request.

API URL

http://localhost:7010/ohfapi/cg/v3.3/genomicspecimens/genomicFiles?specimenNumber=HG00099&specimenVendorNumber=vcf

Example of Response Body

The following example shows the response returned in JSON format.

{
 "resourceType" : "GenomicSpecimen",
 "items" : [ {
 "rsltSpecimenWid" : {
 "system" : "ODB",
 "value" : "64"
 },
 "fileUri" : "file://trc/149/summary_SNP-INDEL-LargeSV_16-Jan-2015.vcf",
 "fileName" : "summary_SNP-INDEL-LargeSV_16-Jan-2015.vcf",
 "fileSize" : 1899127,
 "fileTypecode" : "VCF",
 "loaderName" : "ODB_RSLT_GVCF_UTIL",
 "loadContext" : "Patient Specimen",
 "loadSequence" : 1,
 "loadStartDate" : "02/02/2016",
 "ensemblVersion" : "GRCH37.75",
 "specimenNumber" : "HG00099",
 "specimenVendorNumber" : "vcf"
 }, {
 "rsltSpecimenWid" : {
 "system" : "ODB",
 "value" : "64"
 },
 "fileUri" : "file://trc/155/summary_SNP-INDEL-LargeSV_16-Jan-2015.vcf",
 "fileName" : "summary_SNP-INDEL-LargeSV_16-Jan-2015.vcf",
 "fileSize" : 1899127,
 "fileTypecode" : "VCF",
 "loaderName" : "ODB_RSLT_GVCF_UTIL",
 "loadContext" : "Patient Specimen",
 "loadSequence" : 1,
 "loadStartDate" : "02/03/2016",
 "ensemblVersion" : "GRCH37.75",
 "specimenNumber" : "HG00099",
 "specimenVendorNumber" : "vcf"
 }, {
 "rsltSpecimenWid" : {
 "system" : "ODB",
 "value" : "66"
 },
 "fileUri" : "file://trc/155/summary_SNP-INDEL-LargeSV_16-Jan-2015.vcf",
 "fileName" : "summary_SNP-INDEL-LargeSV_16-Jan-2015.vcf",
 "fileSize" : 1899127,
 "fileTypecode" : "VCF",
 "loaderName" : "ODB_RSLT_GVCF_UTIL",
 "loadContext" : "Patient Specimen",
 "loadSequence" : 1,
 "loadStartDate" : "02/03/2016",
 "ensemblVersion" : "GRCH37.75",
 "specimenNumber" : "HG00097",
 "specimenVendorNumber" : "vcf"
 } ],
 "count" : 3,
 "hasMore" : false,
 "links" : [ {
 "rel" : "self",
 "href" : "http://localhost:62701/genomicspecimens/genomicFiles?specimenNumber=HG00099&specimenVendorNumber=vcf&limit=10&offset=0"
 } ]
}

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