Clinical Genomic APIs for Oracle Healthcare Foundation

Retrieve Patient Clinical Specimen Using Query Criteria

post

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

This endpoint supports the retrieval of all specimens of the patients 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 patients identified for this criteria.

Request

Supported Media Types

application/json
application/xml

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

Root Schema : APIQueryRequest

Type: object

Show Source

cohortQueryName(optional): string
createdOnDate(optional): string(date-time)
executeAsync(optional): boolean

Default Value: false
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",
            "default":false
        },
        "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
        }
    },
    "description":"Contains all the Query Criteria",
    "xml":{
        "name":"AllCriteriaList"
    }
}

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

Show Source

exclude(optional): boolean

Default Value: false

{
    "type":"object",
    "discriminator":"type",
    "properties":{
        "exclude":{
            "type":"boolean",
            "default":false
        }
    }
}

Security

basicAuth: basic

Type: basic

Response

Supported Media Types

application/json
application/xml

200 Response

successful operation

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

Examples

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

API URL

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

Example of Request Body

The following example shows the request sent in JSON format.

{
    "queryCriteria" : {
        "allCriteriaList" : [
            {
                "type" : "MedicationCriteria",
                "medicationCodeList": ["1000000"],
                "medicationOutcomeCodeList":["1"]
            },
            {
                "type":"SequenceVariantsCriteria",
                "fileTypeVCFSelected":true,
                "geneInformation":{
                   "type":"SequenceVariantsGeneDetails",
                   "geneList":[
                                 "BID"
                   ],
                   "dnaAlignmentList":[
                                  "GRCh37"
                   ],
                   "dnaVersionList":[
                                  2
                   ]
                },
                "geneRegionsList":[
                  "PROMOTER"
                ]
            }
        ]
    }
}

Example of Response Body

The following example shows the response returned in JSON format.

[
  {
    "rel": "status",
    "href": "/ohfapi/cg/v3.3/patientapi/clinicalspecimens/queries/999"
  },
  {
    "rel": "result",
    "href": "/ohfapi/cg/v3.3/patientapi/clinicalspecimens/queries/999/data"
  }
]