Clinical Genomic APIs for Oracle Healthcare Foundation

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

Response

Supported Media Types

application/json
application/xml

200 Response

successful operation

Model for paginated collections of data.

Root Schema : PageableCollectionClinicalSpecimenMetadata

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/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.",
            "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 ClinicalSpecimenMetadata

Model for a Clinical Specimen Metadata object in CDM.

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

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 : ClinicalSpecimenMetadata

Type: object

Model for a Clinical Specimen Metadata object in CDM.

Show Source

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

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 : Metadata

Type: object

Model for a Metadata Attribute object in CDM.

Show Source

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

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"
    }
  ]
}