REST API for Oracle Healthcare Translational Research

Retrieve Genomic Files for a Specimen Number and Specimen Vendor Number

get

/HSDataService-web/api/3.2.0/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: Type: integer (int32)

Number of rows to return
offset: Type: integer (int32)

Row number to start from
specimenNumber: Type: string

Required: true

Specimen Number
specimenVendorNumber: Type: string

Required: true

Specimen Vendor Number

Response

Supported Media Types

application/json
application/xml

200 Response

successful operation

Body

Model for paginated collections of data.

Root Schema : PageableCollection

Type: object

Model for paginated collections of data.

Properties

count: Type: integer (int64)

Number of objects in the 'items' collection.
hasMore: Type: boolean

Default Value: false

A boolean indicating if more pages are available.
items: Type: array items

A collection of paged items.
links: Type: array links

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

Identify the resource type

Nested Schema : items

Type: array

A collection of paged items.

Items

Type: object Serializable

Nested Schema : links

Type: array

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

Example

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

Items

Type: string

Nested Schema : Serializable

Type: object

400 Response

Invalid request parameters

404 Response

Genomic specimen files not found

Examples

The following example submits a GET request.

API URL

http://localhost:7001/HSDataService-web/api/3.2.0/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"
 } ]
}