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Retrieve Variants for Reference Identifiers and Database with POST Request

post

/ohfapi/cg/v3.3/variants/byReferenceId

This endpoint supports the retrieval of Variant Identifiers for multiple Reference Identifiers, multiple Database and single Assembly/Alignment ID.It also returns if any Invalid Reference Identifiers are passed in the Request.

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

Body ()

Root Schema : VariantReferenceIdDatabaseDef

Type: object

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• alignmentId: integer(int64)
  Minimum Value: 0

  Minimum Value: > false

  Assembly/Alignment ID
• databases(optional): array databases
  List of Database Names. For ex.,dbSNP_142
• referenceIds: array referenceIds
  Minimum Number of Items: 1

  Maximum Number of Items: 2147483647

  List of Reference IDs to External Database. For ex.,rs13079411

{
    "type":"object",
    "required":[
        "alignmentId",
        "referenceIds"
    ],
    "properties":{
        "alignmentId":{
            "type":"integer",
            "format":"int64",
            "description":"Assembly/Alignment ID",
            "minimum":0,
            "exclusiveMinimum":false
        },
        "referenceIds":{
            "type":"array",
            "description":"List of Reference IDs to External Database. For ex.,rs13079411",
            "items":{
                "type":"string"
            },
            "maxItems":2147483647,
            "minItems":1
        },
        "databases":{
            "type":"array",
            "description":"List of Database Names. For ex.,dbSNP_142",
            "items":{
                "type":"string"
            }
        }
    }
}

Nested Schema : databases

Type: array

List of Database Names. For ex.,dbSNP_142

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• Array of: string

{
    "type":"array",
    "description":"List of Database Names. For ex.,dbSNP_142",
    "items":{
        "type":"string"
    }
}

Nested Schema : referenceIds

Type: array

Minimum Number of Items: 1

Maximum Number of Items: 2147483647

List of Reference IDs to External Database. For ex.,rs13079411

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• Array of: string

{
    "type":"array",
    "description":"List of Reference IDs to External Database. For ex.,rs13079411",
    "items":{
        "type":"string"
    },
    "maxItems":2147483647,
    "minItems":1
}

Security

• basicAuth: basic
  Type: basic

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Response

Supported Media Types

• application/json
• application/xml

200 Response

successful operation

Body ()

Root Schema : PageableDetailedCollection

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.
• invalidAssemblies(optional): array invalidAssemblies
  List of Invalid Assemblies in request.
• invalidGeneNames(optional): array invalidGeneNames
  List of Invalid Genenames in request.
• invalidHugoNames(optional): array invalidHugoNames
  List of Invalid Hugonames in request.
• invalidReferenceIds(optional): array invalidReferenceIds
  List of Invalid Reference IDs in request.
• 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/Serializable"
            }
        },
        "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"
            }
        },
        "invalidReferenceIds":{
            "type":"array",
            "description":"List of Invalid Reference IDs in request.",
            "items":{
                "type":"string"
            }
        },
        "invalidHugoNames":{
            "type":"array",
            "description":"List of Invalid Hugonames in request.",
            "items":{
                "type":"string"
            }
        },
        "invalidGeneNames":{
            "type":"array",
            "description":"List of Invalid Genenames in request.",
            "items":{
                "type":"string"
            }
        },
        "invalidAssemblies":{
            "type":"array",
            "description":"List of Invalid Assemblies in request.",
            "items":{
                "type":"string"
            }
        }
    },
    "description":"Model for paginated collections of data."
}

Nested Schema : invalidAssemblies

Type: array

List of Invalid Assemblies in request.

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• Array of: string

{
    "type":"array",
    "description":"List of Invalid Assemblies in request.",
    "items":{
        "type":"string"
    }
}

Nested Schema : invalidGeneNames

Type: array

List of Invalid Genenames in request.

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• Array of: string

{
    "type":"array",
    "description":"List of Invalid Genenames in request.",
    "items":{
        "type":"string"
    }
}

Nested Schema : invalidHugoNames

Type: array

List of Invalid Hugonames in request.

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• Array of: string

{
    "type":"array",
    "description":"List of Invalid Hugonames in request.",
    "items":{
        "type":"string"
    }
}

Nested Schema : invalidReferenceIds

Type: array

List of Invalid Reference IDs in request.

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• Array of: string

{
    "type":"array",
    "description":"List of Invalid Reference IDs in request.",
    "items":{
        "type":"string"
    }
}

Nested Schema : items

Type: array

A collection of paged items.

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• Array of: object Serializable

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

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 : Serializable

Type: object

400 Response

Assembly/Alignment Id is not supplied

404 Response

Variants not found for the Reference Ids and Reference Databases supplied

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Examples

The following example submits a POST request.

API URL

http://localhost:7010/ohfapi/cg/v3.3/variants/byReferenceId?limit=2&offset=0

Example of Request Body

The following example shows the response returned in JSON format.

{
    "alignmentId": 1,
    "referenceIds": [
        "rs142950474",
        "rs142950477",
        "COSM297314",
        "COSM",
        "rs"
    ],
    "databases": [
        "dbSNP_138",
        "COSMIC_COSMIC.V67"
    ]
}

Example of Response Body

The following example shows the response returned in JSON format.

{
  "resourceType" : "Variants",
  "items" : [ {
    "identifier" : {
      "system" : "ODB",
      "value" : "4754980"
    }
  }, {
    "identifier" : {
      "system" : "ODB",
      "value" : "38063682"
    }
  } ],
  "count" : 2,
  "hasMore" : true,
  "links" : [ {
    "rel" : "self",
    "href" : "http://localhost:7010/ohfapi/cg/v3.3/variants/byReferenceId?limit=2&offset=0"
  }, {
    "rel" : "next",
    "href" : "http://localhost:7010/ohfapi/cg/v3.3/variants/byReferenceId?offset=2&limit=2"
  } ],
  "invalidReferenceIds" : [ "COSM", "rs" ]
}

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