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Retrieve Clinical Specimen Metadata for Specimen Identifiers

get

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

This endpoint supports the retrieval of Patient/Subject Clinical Specimen Metadata for multiple Clinical Specimen Row IDs. It returns Clinical Specimen Metadata information like Specimen Number, Specimen Vendor Number and other metadata associated information.

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 List

  • [0]: integer(int64)

  {
      "name":"id",
      "in":"query",
      "description":"Patient/Subject Clinical Specimen Row IDs List",
      "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 : PageableCollectionClinicalSpecimenMetadata

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/ClinicalSpecimenMetadata"
            }
        },
        "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 ClinicalSpecimenMetadata
  Model for a Clinical Specimen Metadata object in CDM.

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

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 : ClinicalSpecimenMetadata

Type: object

Model for a Clinical Specimen Metadata object in CDM.

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• accessionIdentifier(optional): string
  The Clinical Specimen identifier.
• identifier(optional): object Identifier
  Identifier assigned by a given system
• metadata(optional): object Metadata
  Model for a Metadata Attribute object in CDM.
• specimenReference(optional): object LinkedReference
• specimenVendorNumber(optional): string
  The Clinical Specimen Vendor identifier.

{
    "type":"object",
    "properties":{
        "identifier":{
            "description":"Clinical Specimen Metadata Attribute Row ID value.",
            "$ref":"#/definitions/Identifier"
        },
        "metadata":{
            "description":"Clinical Specimen Metadata Attribute details that includes an Attribute name, description and value.",
            "$ref":"#/definitions/Metadata"
        },
        "specimenReference":{
            "description":"Reference link to the patient/subject Clinical Specimen",
            "$ref":"#/definitions/LinkedReference"
        },
        "specimenVendorNumber":{
            "type":"string",
            "description":"The Clinical Specimen Vendor identifier."
        },
        "accessionIdentifier":{
            "type":"string",
            "description":"The Clinical Specimen identifier."
        }
    },
    "description":"Model for a Clinical Specimen Metadata object in CDM."
}

Nested Schema : Identifier

Type: object

Identifier assigned by a given system

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• 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 : Metadata

Type: object

Model for a Metadata Attribute object in CDM.

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• attrDesc(optional): string
  Metadata Attribute description.
• attrName(optional): string
  Metadata Attribute name.
• strValue(optional): string
  Metadata Attribute string value.
• strValueUpper(optional): string
  Metadata Attribute upper case string value.

{
    "type":"object",
    "properties":{
        "attrName":{
            "type":"string",
            "description":"Metadata Attribute name."
        },
        "attrDesc":{
            "type":"string",
            "description":"Metadata Attribute description."
        },
        "strValue":{
            "type":"string",
            "description":"Metadata Attribute string value."
        },
        "strValueUpper":{
            "type":"string",
            "description":"Metadata Attribute upper case string value."
        }
    },
    "description":"Model for a Metadata Attribute object in CDM."
}

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

http://localhost:7010/ohfapi/cg/v3.3/subjectapi/clinicalspecimens/metadata?id=43&id=44&limit=3&offset=9

Example of Response Body

The following example shows the contents of the response body in JSON format:

{
  "resourceType": "SpecimenMetadata",
  "items": [
    {
      "identifier": {
        "system": "CDM",
        "value": "530743"
      },
      "metadata": {
        "attrName": "ATTR_8",
        "attrDesc": "ATTRIBUTE_DESC_8",
        "strValue": "ATTR_8_VAL_43",
        "strValueUpper": "ATTR_8_VAL_43"
      },
      "specimenReference": {
        "reference": "/ohfapi/cg/v3.3/subjectapi/clinicalspecimens/43",
        "display": "HG00043(vendor2)"
      },
      "specimenVendorNumber": "vendor2",
      "accessionIdentifier": "HG00043"
    },
    {
      "identifier": {
        "system": "CDM",
        "value": "53274"
      },
      "metadata": {
        "attrName": "ATTR_1",
        "attrDesc": "ATTRIBUTE_DESC_1",
        "strValue": "ATTR_1_VAL_44",
        "strValueUpper": "ATTR_1_VAL_44"
      },
      "specimenReference": {
        "reference": "/ohfapi/cg/v3.3/subjectapi/clinicalspecimens/44",
        "display": "HG00044(vendor2)"
      },
      "specimenVendorNumber": "vendor2",
      "accessionIdentifier": "HG00044"
    },
    {
      "identifier": {
        "system": "CDM",
        "value": "666491"
      },
      "metadata": {
        "attrName": "ATTR_10",
        "attrDesc": "ATTRIBUTE_DESC_10",
        "strValue": "ATTR_10_VAL_44",
        "strValueUpper": "ATTR_10_VAL_44"
      },
      "specimenReference": {
        "reference": "/ohfapi/cg/v3.3/subjectapi/clinicalspecimens/44",
        "display": "HG00044(vendor2)"
      },
      "specimenVendorNumber": "vendor2",
      "accessionIdentifier": "HG00044"
    }
  ],
  "count": 3,
  "hasMore": true,
  "links": [
    {
      "rel": "self",
      "href": "http://localhost:7010/ohfapi/cg/v3.3/subjectapi/clinicalspecimens/metadata?id=43&id=44&limit=3&offset=9"
    },
    {
      "rel": "next",
      "href": "http://localhost:7010/ohfapi/cg/v3.3/subjectapi/clinicalspecimens/metadata?offset=12&limit=3&id=43&id=44"
    },
    {
      "rel": "prev",
      "href": "http://localhost:7010/ohfapi/cg/v3.3/subjectapi/clinicalspecimens/metadata?offset=6&limit=3&id=43&id=44"
    }
  ]
}

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