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Retrieve Subject Clinical Specimen Using Query Criteria

post

/ohfapi/cg/v3.3/subjectapi/clinicalspecimens/queries

This endpoint supports the retrieval of all specimens of the subjects identified for this query criteria. It returns Status information like Reference Links to Execution Status for checking Progress and to Access Results when the execution is done. Note: In future release this API would retrieve only the specimen which fall under the query criteria and not just all specimen of subjects identified for this criteria.

Request

Supported Media Types

• application/json
• application/xml

Body ()

Cohort Query Name,Creation Date,Retention Date Details for Subject

Root Schema : APIQueryRequest

Type: object

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• cohortQueryName(optional): string
• createdOnDate(optional): string(date-time)
• executeAsync(optional): boolean
• minRetentionPeriodDays(optional): integer(int64)
  Minimum Value: 0
• queryCriteria(optional): object AllCriteriaList
  Contains all the Query Criteria
• retentionDate(optional): string(date-time)

{
    "type":"object",
    "properties":{
        "executeAsync":{
            "type":"boolean"
        },
        "cohortQueryName":{
            "type":"string"
        },
        "minRetentionPeriodDays":{
            "type":"integer",
            "format":"int64",
            "minimum":0
        },
        "queryCriteria":{
            "$ref":"#/definitions/OracleDBQueryDS"
        },
        "createdOnDate":{
            "type":"string",
            "format":"date-time"
        },
        "retentionDate":{
            "type":"string",
            "format":"date-time"
        }
    }
}

Nested Schema : AllCriteriaList

Type: object

Contains all the Query Criteria

Show Source

• allCriteriaList: array allCriteriaList
  Minimum Number of Items: 1

  Maximum Number of Items: 2147483647

  List of Criteria Eg.DemographicsCriteria,MedicationCriteria,DiagnosisCriteria,SequenceVariantsCriteria,ConsentCriteria,DiagnosisCriteria,EncounterCriteria,ObservationCriteria,HistoryCriteria,ProceduresCriteria,SpecimenCriteria,StudyCriteria,MicroarrayExpressionCriteria,RNASeqExpressionCriteria,CopyNumberVariationCriteria,RelativeTimeEventsCriteria

{
    "type":"object",
    "required":[
        "allCriteriaList"
    ],
    "properties":{
        "allCriteriaList":{
            "type":"array",
            "description":"List of Criteria Eg.DemographicsCriteria,MedicationCriteria,DiagnosisCriteria,SequenceVariantsCriteria,ConsentCriteria,DiagnosisCriteria,EncounterCriteria,ObservationCriteria,HistoryCriteria,ProceduresCriteria,SpecimenCriteria,StudyCriteria,MicroarrayExpressionCriteria,RNASeqExpressionCriteria,CopyNumberVariationCriteria,RelativeTimeEventsCriteria",
            "items":{
                "$ref":"#/definitions/criteria"
            },
            "maxItems":2147483647,
            "minItems":1
        }
    },
    "xml":{
        "name":"AllCriteriaList"
    },
    "description":"Contains all the Query Criteria"
}

Nested Schema : allCriteriaList

Type: array

Minimum Number of Items: 1

Maximum Number of Items: 2147483647

List of Criteria Eg.DemographicsCriteria,MedicationCriteria,DiagnosisCriteria,SequenceVariantsCriteria,ConsentCriteria,DiagnosisCriteria,EncounterCriteria,ObservationCriteria,HistoryCriteria,ProceduresCriteria,SpecimenCriteria,StudyCriteria,MicroarrayExpressionCriteria,RNASeqExpressionCriteria,CopyNumberVariationCriteria,RelativeTimeEventsCriteria

Show Source

• Array of: object criteria
  Discriminator: type

{
    "type":"array",
    "description":"List of Criteria Eg.DemographicsCriteria,MedicationCriteria,DiagnosisCriteria,SequenceVariantsCriteria,ConsentCriteria,DiagnosisCriteria,EncounterCriteria,ObservationCriteria,HistoryCriteria,ProceduresCriteria,SpecimenCriteria,StudyCriteria,MicroarrayExpressionCriteria,RNASeqExpressionCriteria,CopyNumberVariationCriteria,RelativeTimeEventsCriteria",
    "items":{
        "$ref":"#/definitions/criteria"
    },
    "maxItems":2147483647,
    "minItems":1
}

Nested Schema : criteria

Type: object

Discriminator: type

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• disabled(optional): boolean
• exclude(optional): boolean

{
    "type":"object",
    "discriminator":"type",
    "properties":{
        "exclude":{
            "type":"boolean"
        },
        "disabled":{
            "type":"boolean"
        }
    }
}

Security

• basicAuth: basic
  Type: basic

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Response

Supported Media Types

• application/json
• application/xml

200 Response

successful operation

Body ()

Root Schema : schema

Type: array

Show Source

• Array of: object Link

{
    "type":"array",
    "items":{
        "$ref":"#/definitions/Link"
    }
}

Nested Schema : Link

Type: object

Show Source

• params(optional): object params
  Additional Properties Allowed: additionalProperties
• rel(optional): string
• rels(optional): array rels
• title(optional): string
• type(optional): string
• uri(optional): string(uri)
• uriBuilder(optional): object UriBuilder

{
    "type":"object",
    "properties":{
        "uriBuilder":{
            "$ref":"#/definitions/UriBuilder"
        },
        "rel":{
            "type":"string"
        },
        "rels":{
            "type":"array",
            "items":{
                "type":"string"
            }
        },
        "uri":{
            "type":"string",
            "format":"uri"
        },
        "title":{
            "type":"string"
        },
        "params":{
            "type":"object",
            "additionalProperties":{
                "type":"string"
            }
        },
        "type":{
            "type":"string"
        }
    }
}

Nested Schema : params

Type: object

Additional Properties Allowed

Show Source

• string

{
    "type":"object",
    "additionalProperties":{
        "type":"string"
    }
}

Nested Schema : rels

Type: array

Show Source

• Array of: string

{
    "type":"array",
    "items":{
        "type":"string"
    }
}

Nested Schema : UriBuilder

Type: object

202 Response

Query accepted

400 Response

Invalid Parameters

406 Response

Failed to accept query

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Examples

The following example submits a POST request. See the Criteria Classes for this endpoint.

API URL

http://localhost:7010/ohfapi/cg/v3.3/subjectapi/clinicalspecimens/queries

Example of Request Body

The following example shows the request sent in JSON format.

{
    "queryCriteria" : {
        "allCriteriaList" : [
       {
            "type" : "DiagnosisCriteria",
            "diagnosisCodeList": ["S280","M518","C9000","C9001","C900"]
       },
       {
    "type":"SequenceVariantsCriteria",
    "exclude":false,
    "radioOptionMode":"VARS_IN_GEN_REGION",
    "genomicPosition" : "CHR1:1,200,000-1,900,000",
    "genomicPositionAlignment" : "GRCh37",
    "variantTypesList":[
       {
          "variantType":"deletion"
       }
    ]
    }   ,
       {
            "type" : "HistoryCriteria",
            "historyCodeList": ["9822","1937","1"]
       }
        ]
    }
}

Example of Request Body

The following example shows the response returned in JSON format.

[
  {
    "rel": "status",
    "href": "/ohfapi/cg/v3.3/subjectapi/clinicalspecimens/queries/1002"
  },
  {
    "rel": "result",
    "href": "/ohfapi/cg/v3.3/subjectapi/clinicalspecimens/queries/1002/data"
  }
]

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