Clinical Genomic APIs for Oracle Healthcare Foundation

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

Response

Supported Media Types

application/json
application/xml

200 Response

successful operation

Model for paginated collections of data.

Root Schema : PageableCollectionGenomicFile

Type: object

Model for paginated collections of data.

Show Source

count(optional): integer(int64)

Number of objects in the 'items' collection.
hasMore(optional): boolean

Default Value: false

A boolean indicating if more pages are available.
items(optional): array items

A collection of paged items.
links(optional): array link

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":{
                "name":"items",
                "wrapped":true
            },
            "description":"A collection of paged items.",
            "items":{
                "$ref":"#/definitions/GenomicFile"
            }
        },
        "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.",
            "default":false
        },
        "links":{
            "type":"array",
            "example":"{rel: 'next',href: '/patientapi/patients?limit=100&offset=300'}",
            "xml":{
                "name":"link",
                "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.

Show Source

Array of: object GenomicFile

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

Nested Schema : link

Type: array

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

Show Source

Array of: string

{
    "type":"array",
    "example":"{rel: 'next',href: '/patientapi/patients?limit=100&offset=300'}",
    "xml":{
        "name":"link",
        "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 : GenomicFile

Type: object

Show Source

ensemblVersion(optional): string

Ensembl Version. For ex.,GRCH37.75
fileLoadWid(optional): integer(int64)

File Load Wid - fileWids (FILE_WID) property in create file export definition API
fileName(optional): string

File Name
fileSize(optional): integer(int64)

File size in bytes
fileTypecode(optional): string

Code for File Type
fileUri(optional): string

Vendor Identifier in linked Specimen Datasource Database
loadCompleteDate(optional): string(date-time)

File Load Complete Date
loadContext(optional): string

Patient/Subject Context
loaderName(optional): string

Name of Loader Package
loadSequence(optional): integer(int64)

Sequence of each file that is Loaded Consecutive times
loadStartDate(optional): string(date-time)

File Load Start Date
patientIdentifier(optional): string

Patient Identifier
rsltSpecimenWid(optional): object Identifier

Identifier assigned by a given system
specimenNumber(optional): string

Specimen identifier in linked Specimen Datasource Database
specimenVendorNumber(optional): string

Vendor Identifier in linked Specimen Datasource Database
subjectIdentifier(optional): string

Subject Identifier

{
    "type":"object",
    "properties":{
        "rsltSpecimenWid":{
            "description":"Genomic Specimen Identifier",
            "$ref":"#/definitions/Identifier"
        },
        "patientIdentifier":{
            "type":"string",
            "description":"Patient Identifier"
        },
        "subjectIdentifier":{
            "type":"string",
            "description":"Subject Identifier"
        },
        "specimenNumber":{
            "type":"string",
            "description":"Specimen identifier in linked Specimen Datasource Database"
        },
        "specimenVendorNumber":{
            "type":"string",
            "description":"Vendor Identifier in linked Specimen Datasource Database"
        },
        "fileUri":{
            "type":"string",
            "description":"Vendor Identifier in linked Specimen Datasource Database"
        },
        "fileName":{
            "type":"string",
            "description":"File Name"
        },
        "fileLoadWid":{
            "type":"integer",
            "format":"int64",
            "description":"File Load Wid - fileWids (FILE_WID) property in create file export definition API"
        },
        "fileSize":{
            "type":"integer",
            "format":"int64",
            "description":"File size in bytes"
        },
        "fileTypecode":{
            "type":"string",
            "description":"Code for File Type"
        },
        "loaderName":{
            "type":"string",
            "description":"Name of Loader Package"
        },
        "loadContext":{
            "type":"string",
            "description":"Patient/Subject Context"
        },
        "loadSequence":{
            "type":"integer",
            "format":"int64",
            "description":"Sequence of each file that is Loaded Consecutive times"
        },
        "loadStartDate":{
            "type":"string",
            "format":"date-time",
            "description":"File Load Start Date"
        },
        "loadCompleteDate":{
            "type":"string",
            "format":"date-time",
            "description":"File Load Complete Date"
        },
        "ensemblVersion":{
            "type":"string",
            "description":"Ensembl Version. For ex.,GRCH37.75"
        }
    }
}

Nested Schema : Identifier

Type: object

Identifier assigned by a given system

Show Source

system(optional): string

System which assigned this identifier
value(optional): string

Identifier value

{
    "type":"object",
    "properties":{
        "system":{
            "type":"string",
            "description":"System which assigned this identifier"
        },
        "value":{
            "type":"string",
            "description":"Identifier value"
        }
    },
    "description":"Identifier assigned by a given system"
}

400 Response

Invalid request parameters

404 Response

Genomic specimen files not found

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"
 } ]
}