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Retrieve Clinical Specimen Alias for Specimen Identifiers

get

/ohfapi/cg/v3.3/{apiContext}/clinicalspecimens/aliases

This endpoint supports the retrieval of Patient/Subject Clinical Specimen Aliases for multiple Clinical Specimen Row IDs. It returns Paginated List of Clinical Specimen Aliases information like Specimen alias and its Row ID, Service Provider Identifier and reference to the Clinical Specimen details. Result includes only aliases to which user has read access.

Request

Supported Media Types

• application/json
• application/xml

Path Parameters

• apiContext: string
  Pattern: subjectapi|patientapi

  Patient/Subject API context

Query Parameters

• id: array
  Collection Format: multi

  Minimum Number of Items: 1

  Maximum Number of Items: 2147483647

  Patient/Subject Clinical Specimen Row IDs

  • [0]: integer(int64)

  {
      "name":"id",
      "in":"query",
      "description":"Patient/Subject Clinical Specimen Row IDs",
      "required":true,
      "type":"array",
      "items":{
          "type":"integer",
          "format":"int64"
      },
      "collectionFormat":"multi",
      "maxItems":2147483647,
      "minItems":1
  }

• limit(optional): integer(int32)
  Pagination query params: ?limit=2&offset=0
• offset(optional): integer(int32)
  Pagination query params: ?limit=2&offset=0

Security

• basicAuth: basic
  Type: basic

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Response

Supported Media Types

• application/json
• application/xml

200 Response

successful operation

Body ()

Root Schema : PageableCollectionClinicalSpecimenAlias

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/ClinicalSpecimenAlias"
            }
        },
        "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.

Show Source

• Array of: object ClinicalSpecimenAlias
  Model for a Clinical Specimen Alias object in CDM.

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

Nested Schema : links

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":{
        "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 : ClinicalSpecimenAlias

Type: object

Model for a Clinical Specimen Alias object in CDM.

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• identifier(optional): object Identifier
  Identifier assigned by a given system
• serviceProviderIdentifier(optional): string
  Identifier of the Service Provider that issued the Alias for the Clinical Specimen.
• specimenAlias(optional): string
  Clinical Specimen Alias value.
• specimenAliasUpper(optional): string
  Clinical Specimen Alias upper case value.
• specimenReference(optional): object LinkedReference

{
    "type":"object",
    "properties":{
        "identifier":{
            "description":"Clinical Specimen Alias Row ID value.",
            "$ref":"#/definitions/Identifier"
        },
        "serviceProviderIdentifier":{
            "type":"string",
            "description":"Identifier of the Service Provider that issued the Alias for the Clinical Specimen."
        },
        "specimenAlias":{
            "type":"string",
            "description":"Clinical Specimen Alias value."
        },
        "specimenAliasUpper":{
            "type":"string",
            "description":"Clinical Specimen Alias upper case value."
        },
        "specimenReference":{
            "description":"Reference link to the patient/subject Clinical Specimen.",
            "$ref":"#/definitions/LinkedReference"
        }
    },
    "description":"Model for a Clinical Specimen Alias object in CDM."
}

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"
}

Nested Schema : LinkedReference

Type: object

Show Source

• display(optional): string
• reference(optional): string

{
    "type":"object",
    "properties":{
        "reference":{
            "type":"string"
        },
        "display":{
            "type":"string"
        }
    }
}

400 Response

Invalid parameters supplied

404 Response

Clinical specimen or clinical specimen metadata not found

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Examples

The following example submits a GET request.

API URL ??? Patient Context

http://localhost:7010/ohfapi/cg/v3.3/patientapi/clinicalspecimens/aliases?id=1005&id=1010&id=1012&id=1015

Example of Response Body

The following example shows the response returned in JSON format.

{
  "resourceType": "SpecimenAlias",
  "items": [
    {
      "identifier": {
        "system": "CDM",
        "value": "159"
      },
      "serviceProviderIdentifier": "vcf",
      "specimenAlias": "ALIAS_SVCPRV1_SN 005",
      "specimenAliasUpper": "ALIAS_SVCPRV1_SN 005",
      "specimenReference": {
        "reference": "/ohfapi/cg/v3.3/patientapi/clinicalspecimens/1005"
      }
    },
    {
      "identifier": {
        "system": "CDM",
        "value": "16"
      },
      "serviceProviderIdentifier": "vcf",
      "specimenAlias": "ALIAS_SVCPRV1_CNV_dummy_01",
      "specimenAliasUpper": "ALIAS_SVCPRV1_CNV_DUMMY_01",
      "specimenReference": {
        "reference": "/ohfapi/cg/v3.3/patientapi/clinicalspecimens/1010"
      }
    },
    {
      "identifier": {
        "system": "CDM",
        "value": "17"
      },
      "serviceProviderIdentifier": "vcf",
      "specimenAlias": "ALIAS_SVCPRV1_TCGA-06-0187-01A-01W2",
      "specimenAliasUpper": "ALIAS_SVCPRV1_TCGA-06-0187-01A-01W2",
      "specimenReference": {
        "reference": "/ohfapi/cg/v3.3/patientapi/clinicalspecimens/1015"
      }
    }
  ],
  "count": 3,
  "hasMore": false,
  "links": [
    {
      "rel": "self",
      "href": "/ohfapi/cg/v3.3/patientapi/clinicalspecimens/aliases?id=1005&id=1010&id=1012&id=1015"
    }
  ]
} 

API URL ??? Subject Context

http://localhost:7010/ohfapi/cg/v3.3/subjectapi/clinicalspecimens/aliases?id=1035&id=1040&id=1041&id=1075

Example of Response Body

The following example shows the response returned in JSON format.

{
  "resourceType": "SpecimenAlias",
  "items": [
    {
      "identifier": {
        "system": "CDM",
        "value": "89"
      },
      "serviceProviderIdentifier": "SVCPRV1",
      "specimenAlias": "ALIAS_SVCPRV1_TCGA-08-0375-11A-8109",
      "specimenAliasUpper": "ALIAS_SVCPRV1_TCGA-08-0375-11A-8109",
      "specimenReference": {
        "reference": "/ohfapi/cg/v3.3/subjectapi/clinicalspecimens/1035"
      }
    },
    {
      "identifier": {
        "system": "CDM",
        "value": "4"
      },
      "serviceProviderIdentifier": "SVCPRV1",
      "specimenAlias": "ALIAS_SVCPRV1_TCGA-02-0026-10A-01W",
      "specimenAliasUpper": "ALIAS_SVCPRV1_TCGA-02-0026-10A-01W",
      "specimenReference": {
        "reference": "/ohfapi/cg/v3.3/subjectapi/clinicalspecimens/1040"
      }
    },
    {
      "identifier": {
        "system": "CDM",
        "value": "47"
      },
      "serviceProviderIdentifier": "SVCPRV1",
      "specimenAlias": "ALIAS_SVCPRV1_NEGATIVE 2",
      "specimenAliasUpper": "ALIAS_SVCPRV1_NEGATIVE 2",
      "specimenReference": {
        "reference": "/ohfapi/cg/v3.3/subjectapi/clinicalspecimens/1075"
      }
    }
  ],
  "count": 3,
  "hasMore": false,
  "links": [
    {
      "rel": "self",
      "href": "/ohfapi/cg/v3.3/subjectapi/clinicalspecimens/aliases?id=1035&id=1040&id=1041&id=1075"
    }
  ]
}

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