Clinical Genomic APIs for Oracle Healthcare Foundation

Retrieve Export Definitions for Export Identifiers

get

/ohfapi/cg/v3.3/exports

This endpoint supports the retrieval of Export Definitions for an Export Identifier, Start Date or End Date.

Request

Supported Media Types

application/json
application/xml

Query Parameters

endDate(optional): string

File Export End Date

id: array

Collection Format: multi

Minimum Number of Items: 0

Maximum Number of Items: 2147483647

List of File Export Row IDs

[0]: integer(int64)

{
    "name":"id",
    "in":"query",
    "description":"List of File Export Row IDs",
    "required":true,
    "type":"array",
    "items":{
        "type":"integer",
        "format":"int64"
    },
    "collectionFormat":"multi",
    "maxItems":2147483647,
    "minItems":0
}

startDate(optional): string

File Export Start Date

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 OmicsExportDefinition

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

Nested Schema : OmicsExportDefinition

Type: object

Show Source

alignmentId: integer(int64)

Alignment id.

Example: "alignmentId": 1
allDataOption(optional): boolean

Export definition must have either allDataOption or genomicPosition/bedFileNameUploadService or set of genes (geneHugoNames, pathwayNames, geneSetIds).

Example: false
anatomicalSiteCodes(optional): object CodeCodeSysContainerDS

Provide a list of code and of system code combinations.
bedFileNameUploadService(optional): string

BED file contains genomic positions. Can be specified as {bucket name}/{object name} or {file name}. Export definition must have either allDataOption or genomicPosition/bedFileNameUploadService or set of genes (geneHugoNames, pathwayNames, geneSetIds).

Example: BedFileBucket/BedFileObjectName or BedFileName.txt
context: string

Sets the context as Patient or Subject.

Example: PATIENT or SUBJECT
fileWids(optional): array fileWids

List of file load record ids.
geneHugoNames(optional): array geneHugoNames

List of gene hugo names. Export definition must have either allDataOption or genomicPosition/bedFileNameUploadService or set of genes (geneHugoNames, pathwayNames, geneSetIds).
geneSetIds(optional): array geneSetIds

List of gene set ids. Export definition must have either allDataOption or genomicPosition/bedFileNameUploadService or set of genes (geneHugoNames, pathwayNames, geneSetIds).
genomicPosition(optional): array genomicPosition

Genomic positions. CHROMOSOME ID, START POSITION, END POSITION. START POSITION, END POSITION are optional. Can be sourced from Gene reference APIs or Genomic position APIs. Export definition must have either allDataOption or genomicPosition/bedFileNameUploadService or set of genes (geneHugoNames, pathwayNames, geneSetIds).
id(optional): object OdbIdentifier

Identifier assigned by a given system
link(optional): string

A link containing href to submit the file export job

Example: {rel: 'submit',href: '/exports/{exportId}/jobs'}
pathwayNames(optional): array pathwayNames

List of pathway names. Export definition must have either allDataOption or genomicPosition/bedFileNameUploadService or set of genes (geneHugoNames, pathwayNames, geneSetIds).
patientSubjectCohortListId(optional): integer(int64)

Record id of a saved list of patients or subjects. The export definition must have either a source of patients/subjects or a source of specimens(specified in specimenIdsCdm and specimenIdsODB). If both are provided the specimen source takes precedence

Example: "patientSubjectCohortListId": 10000000635009
patientSubjectId(optional): array patientSubjectId

List of patient or subject record ids. The export definition must have either a source of patients/subjects or a source of specimens(specified in specimenIdsCdm and specimenIdsODB). If both are provided the specimen source takes precedence
queryCriteria(optional): object AllCriteriaList

Contains all the Query Criteria
queryCriteriaJson(optional): string

Used to transfer query criteria JSON representation from web layer to ejb layer so the JSON can be persisted to support the Retrieve Export Definition API's the @GET export definition API's will return the JSON bound to this property as well as queryCriteria
queryName(optional): string

Cohort Explorer Query Name. The export definition must have either a source of patients/subjects or a source of specimens(specified in specimenIdsCdm and specimenIdsODB). If both are provided the specimen source takes precedence

Example: "queryName" : "Variant_multipleRegions"
serviceProviderIdentifier(optional): string

The service provider identifier (a.k.a. namespace) to be used to find alias values.

Example: "serviceProviderIdentifier": "vcf"
specimenIdsCdm(optional): array specimenIdsCdm

List of specimen ids from CDM schema. The export definition must have either a source of patients/subjects or a source of specimens(specified in specimenIdsCdm and specimenIdsODB). If both are provided the specimen source takes precedence
specimenIdsOdb(optional): array specimenIdsOdb

List of specimen ids from ODB schema. The export definition must have either a source of patients/subjects or a source of specimens(specified in specimenIdsCdm and specimenIdsODB). If both are provided the specimen source takes precedence
specimenTypeCodes(optional): object CodeCodeSysContainerDS

Provide a list of code and of system code combinations.
studyNames(optional): array studyNames

List of study names.

{
    "type":"object",
    "required":[
        "alignmentId",
        "context"
    ],
    "properties":{
        "id":{
            "description":"Contains the export definition id. Used in response, not needed for the Create Export Definition API.",
            "$ref":"#/definitions/OdbIdentifier"
        },
        "context":{
            "type":"string",
            "example":"PATIENT or SUBJECT",
            "description":"Sets the context as Patient or Subject."
        },
        "allDataOption":{
            "type":"boolean",
            "example":false,
            "description":"Export definition must have either allDataOption or \ngenomicPosition/bedFileNameUploadService or set of genes (geneHugoNames, pathwayNames, geneSetIds)."
        },
        "queryCriteria":{
            "example":"\"queryCriteria\": {\n        \"allCriteriaList\": [{\n            \"type\": \"DemographicsCriteria\",\n            \"patientIdList\": [\"1\", \"2\"],\n            \"ageRange\": {\n                \"value\": 60,\n                \"secondValue\": 80,\n                \"op\": {\n                    \"code\": \"COMP_OP_BETWEEN\"\n                }\n            }\n        }, {\n            \"type\": \"DiagnosisCriteria\",\n            \"diagnosisNameList\": [\"D1\", \"D2\"],\n            \"onsetDateRange\": {\n                \"value\": \"01/30/2016\",\n                \"secondValue\": \"01/30/2017\",\n                \"op\": {\n                    \"code\": \"COMP_OP_BETWEEN\"\n                }\n            }\n        }]\n    }",
            "description":"Query criteria.\nThe export definition must have either a source of patients/subjects or a source of specimens(specified in specimenIdsCdm and specimenIdsODB).\nIf both are provided the specimen source takes precedence",
            "$ref":"#/definitions/OracleDBQueryDS"
        },
        "queryCriteriaJson":{
            "type":"string",
            "description":"Used to transfer query criteria JSON representation from web layer to ejb layer\nso the JSON can be persisted to support the Retrieve Export Definition API's \nthe @GET export definition API's will return the JSON bound to this property as well as queryCriteria"
        },
        "queryName":{
            "type":"string",
            "example":"\"queryName\" : \"Variant_multipleRegions\"",
            "description":"Cohort Explorer Query Name.\nThe export definition must have either a source of patients/subjects or a source of specimens(specified in specimenIdsCdm and specimenIdsODB).\nIf both are provided the specimen source takes precedence"
        },
        "genomicPosition":{
            "type":"array",
            "example":"\"genomicPosition\": [{\n        \"chromosomeId\": 10,\n        \"startPosition\": 89682891,\n        \"endPosition\": 100682893\n    }, {\n        \"chromosomeId\": 7,\n        \"startPosition\": 89682891\n    }, {\n        \"chromosomeId\": 5\n    }]",
            "description":"Genomic positions. CHROMOSOME ID, START POSITION, END POSITION. \nSTART POSITION, END POSITION are optional. Can be sourced from Gene reference APIs \nor Genomic position APIs. Export definition must have either allDataOption or \ngenomicPosition/bedFileNameUploadService or set of genes (geneHugoNames, pathwayNames, geneSetIds).",
            "items":{
                "$ref":"#/definitions/GenomicPositionFileExport"
            }
        },
        "geneHugoNames":{
            "type":"array",
            "example":"\"geneHugoNames\": [\"CASZ1\",\"CAMTA1-IT1\",\"RP3-453P22.2\"]",
            "description":"List of gene hugo names.\nExport definition must have either allDataOption or genomicPosition/bedFileNameUploadService \nor set of genes (geneHugoNames, pathwayNames, geneSetIds).",
            "items":{
                "type":"string"
            }
        },
        "geneSetIds":{
            "type":"array",
            "example":"\"geneSetIds\" : [1,2]",
            "description":"List of gene set ids.\nExport definition must have either allDataOption or genomicPosition/bedFileNameUploadService \nor set of genes (geneHugoNames, pathwayNames, geneSetIds).",
            "items":{
                "type":"integer",
                "format":"int64"
            }
        },
        "pathwayNames":{
            "type":"array",
            "example":"\"pathwayNames\": [\"PATHWAY1\",\"PATHWAY2\"]",
            "description":"List of pathway names.\nExport definition must have either allDataOption or genomicPosition/bedFileNameUploadService \nor set of genes (geneHugoNames, pathwayNames, geneSetIds).",
            "items":{
                "type":"string"
            }
        },
        "alignmentId":{
            "type":"integer",
            "format":"int64",
            "example":"\"alignmentId\": 1",
            "description":"Alignment id."
        },
        "specimenIdsOdb":{
            "type":"array",
            "example":"\"specimenIdsOdb\" : [1,2]",
            "description":"List of specimen ids from ODB schema.\nThe export definition must have either a source of patients/subjects or a source of specimens(specified in specimenIdsCdm and specimenIdsODB).\nIf both are provided the specimen source takes precedence",
            "items":{
                "type":"integer",
                "format":"int64"
            }
        },
        "specimenIdsCdm":{
            "type":"array",
            "example":"\"specimenIdsCdm\" : [1,2]",
            "description":"List of specimen ids from CDM schema.\nThe export definition must have either a source of patients/subjects or a source of specimens(specified in specimenIdsCdm and specimenIdsODB).\nIf both are provided the specimen source takes precedence",
            "items":{
                "type":"integer",
                "format":"int64"
            }
        },
        "specimenTypeCodes":{
            "example":"\"specimenTypeCodes\": {\n        \"codeCodeSysList\" : [ {\n          \"codeSys\" : [ \"CODE_SYS_ID_4\" ],\n          \"code\" : [ \"COD_4\" ]\n        }, {\n          \"codeSys\" : [ \"CODE_SYS_ID_5\", \"CODE_SYS_ID_6\", \"CODE_SYS_ID_7\" ],\n          \"code\" : [ \"COD_5\", \"COD_10\", \"COD_11\" ]\n        } ]\n      }",
            "description":"List of specimen type codes and system code combinations.",
            "$ref":"#/definitions/CodeCodeSysContainerDS"
        },
        "anatomicalSiteCodes":{
            "example":"\"anatomicalSiteCodes\": {\n        \"codeCodeSysList\" : [ {\n          \"codeSys\" : [ \"CODE_SYS_ID_4\" ],\n          \"code\" : [ \"COD_4\" ]\n        }, {\n          \"codeSys\" : [ \"CODE_SYS_ID_5\", \"CODE_SYS_ID_6\", \"CODE_SYS_ID_7\" ],\n          \"code\" : [ \"COD_5\", \"COD_10\", \"COD_11\" ]\n        } ]\n      }",
            "description":"List of anatomical site codes and system code combinations.",
            "$ref":"#/definitions/CodeCodeSysContainerDS"
        },
        "fileWids":{
            "type":"array",
            "example":"\"fileWids\" : [1,2]",
            "description":"List of file load record ids.",
            "items":{
                "type":"integer",
                "format":"int64"
            }
        },
        "studyNames":{
            "type":"array",
            "example":"\"studyNames\": [\"STUDY1\",\"STUDY2\"]",
            "description":"List of study names.",
            "items":{
                "type":"string"
            }
        },
        "patientSubjectCohortListId":{
            "type":"integer",
            "format":"int64",
            "example":"\"patientSubjectCohortListId\": 10000000635009",
            "description":"Record id of a saved list of patients or subjects.\nThe export definition must have either a source of patients/subjects or a source of specimens(specified in specimenIdsCdm and specimenIdsODB).\nIf both are provided the specimen source takes precedence"
        },
        "patientSubjectId":{
            "type":"array",
            "example":"\"patientSubjectId\" : [1,2]",
            "description":"List of patient or subject record ids.\nThe export definition must have either a source of patients/subjects or a source of specimens(specified in specimenIdsCdm and specimenIdsODB).\nIf both are provided the specimen source takes precedence",
            "items":{
                "type":"integer",
                "format":"int64"
            }
        },
        "serviceProviderIdentifier":{
            "type":"string",
            "example":"\"serviceProviderIdentifier\": \"vcf\"",
            "description":"The service provider identifier (a.k.a. namespace) to be used to find alias values."
        },
        "bedFileNameUploadService":{
            "type":"string",
            "example":"BedFileBucket/BedFileObjectName or BedFileName.txt",
            "description":"BED file contains genomic positions.\nCan be specified as {bucket name}/{object name} or {file name}.\nExport definition must have either allDataOption or genomicPosition/bedFileNameUploadService \nor set of genes (geneHugoNames, pathwayNames, geneSetIds)."
        },
        "link":{
            "type":"string",
            "example":"{rel: 'submit',href: '/exports/{exportId}/jobs'}",
            "xml":{
                "wrapped":true
            },
            "description":"A link containing href to submit the file export job"
        }
    }
}

Nested Schema : CodeCodeSysContainerDS

Type: object

Provide a list of code and of system code combinations.

Show Source

codeCodeSysList(optional): array codeCodeSysList

List of code and system code combinations

{
    "type":"object",
    "properties":{
        "codeCodeSysList":{
            "type":"array",
            "description":"List of code and system code combinations",
            "items":{
                "$ref":"#/definitions/CodeCodeSysDS"
            }
        }
    },
    "description":"Provide a list of code and of system code combinations."
}

Nested Schema : fileWids

Type: array

List of file load record ids.

Show Source

Array of: integer(int64)

{
    "type":"array",
    "example":"\"fileWids\" : [1,2]",
    "description":"List of file load record ids.",
    "items":{
        "type":"integer",
        "format":"int64"
    }
}

Example:

"fileWids" : [1,2]

Nested Schema : geneHugoNames

Type: array

List of gene hugo names. Export definition must have either allDataOption or genomicPosition/bedFileNameUploadService or set of genes (geneHugoNames, pathwayNames, geneSetIds).

Show Source

Array of: string

{
    "type":"array",
    "example":"\"geneHugoNames\": [\"CASZ1\",\"CAMTA1-IT1\",\"RP3-453P22.2\"]",
    "description":"List of gene hugo names.\nExport definition must have either allDataOption or genomicPosition/bedFileNameUploadService \nor set of genes (geneHugoNames, pathwayNames, geneSetIds).",
    "items":{
        "type":"string"
    }
}

Example:

"geneHugoNames": ["CASZ1","CAMTA1-IT1","RP3-453P22.2"]

Nested Schema : geneSetIds

Type: array

List of gene set ids. Export definition must have either allDataOption or genomicPosition/bedFileNameUploadService or set of genes (geneHugoNames, pathwayNames, geneSetIds).

Show Source

Array of: integer(int64)

{
    "type":"array",
    "example":"\"geneSetIds\" : [1,2]",
    "description":"List of gene set ids.\nExport definition must have either allDataOption or genomicPosition/bedFileNameUploadService \nor set of genes (geneHugoNames, pathwayNames, geneSetIds).",
    "items":{
        "type":"integer",
        "format":"int64"
    }
}

Example:

"geneSetIds" : [1,2]

Nested Schema : genomicPosition

Type: array

Genomic positions. CHROMOSOME ID, START POSITION, END POSITION. START POSITION, END POSITION are optional. Can be sourced from Gene reference APIs or Genomic position APIs. Export definition must have either allDataOption or genomicPosition/bedFileNameUploadService or set of genes (geneHugoNames, pathwayNames, geneSetIds).

Show Source

Array of: object GenomicPositionFileExport

{
    "type":"array",
    "example":"\"genomicPosition\": [{\n        \"chromosomeId\": 10,\n        \"startPosition\": 89682891,\n        \"endPosition\": 100682893\n    }, {\n        \"chromosomeId\": 7,\n        \"startPosition\": 89682891\n    }, {\n        \"chromosomeId\": 5\n    }]",
    "description":"Genomic positions. CHROMOSOME ID, START POSITION, END POSITION. \nSTART POSITION, END POSITION are optional. Can be sourced from Gene reference APIs \nor Genomic position APIs. Export definition must have either allDataOption or \ngenomicPosition/bedFileNameUploadService or set of genes (geneHugoNames, pathwayNames, geneSetIds).",
    "items":{
        "$ref":"#/definitions/GenomicPositionFileExport"
    }
}

Example:

"genomicPosition": [{
        "chromosomeId": 10,
        "startPosition": 89682891,
        "endPosition": 100682893
    }, {
        "chromosomeId": 7,
        "startPosition": 89682891
    }, {
        "chromosomeId": 5
    }]

Nested Schema : OdbIdentifier

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 : pathwayNames

Type: array

List of pathway names. Export definition must have either allDataOption or genomicPosition/bedFileNameUploadService or set of genes (geneHugoNames, pathwayNames, geneSetIds).

Show Source

Array of: string

{
    "type":"array",
    "example":"\"pathwayNames\": [\"PATHWAY1\",\"PATHWAY2\"]",
    "description":"List of pathway names.\nExport definition must have either allDataOption or genomicPosition/bedFileNameUploadService \nor set of genes (geneHugoNames, pathwayNames, geneSetIds).",
    "items":{
        "type":"string"
    }
}

Example:

"pathwayNames": ["PATHWAY1","PATHWAY2"]

Nested Schema : patientSubjectId

Type: array

List of patient or subject record ids. The export definition must have either a source of patients/subjects or a source of specimens(specified in specimenIdsCdm and specimenIdsODB). If both are provided the specimen source takes precedence

Show Source

Array of: integer(int64)

{
    "type":"array",
    "example":"\"patientSubjectId\" : [1,2]",
    "description":"List of patient or subject record ids.\nThe export definition must have either a source of patients/subjects or a source of specimens(specified in specimenIdsCdm and specimenIdsODB).\nIf both are provided the specimen source takes precedence",
    "items":{
        "type":"integer",
        "format":"int64"
    }
}

Example:

"patientSubjectId" : [1,2]

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 : specimenIdsCdm

Type: array

List of specimen ids from CDM schema. The export definition must have either a source of patients/subjects or a source of specimens(specified in specimenIdsCdm and specimenIdsODB). If both are provided the specimen source takes precedence

Show Source

Array of: integer(int64)

{
    "type":"array",
    "example":"\"specimenIdsCdm\" : [1,2]",
    "description":"List of specimen ids from CDM schema.\nThe export definition must have either a source of patients/subjects or a source of specimens(specified in specimenIdsCdm and specimenIdsODB).\nIf both are provided the specimen source takes precedence",
    "items":{
        "type":"integer",
        "format":"int64"
    }
}

Example:

"specimenIdsCdm" : [1,2]

Nested Schema : specimenIdsOdb

Type: array

List of specimen ids from ODB schema. The export definition must have either a source of patients/subjects or a source of specimens(specified in specimenIdsCdm and specimenIdsODB). If both are provided the specimen source takes precedence

Show Source

Array of: integer(int64)

{
    "type":"array",
    "example":"\"specimenIdsOdb\" : [1,2]",
    "description":"List of specimen ids from ODB schema.\nThe export definition must have either a source of patients/subjects or a source of specimens(specified in specimenIdsCdm and specimenIdsODB).\nIf both are provided the specimen source takes precedence",
    "items":{
        "type":"integer",
        "format":"int64"
    }
}

Example:

"specimenIdsOdb" : [1,2]

Nested Schema : studyNames

Type: array

List of study names.

Show Source

Array of: string

{
    "type":"array",
    "example":"\"studyNames\": [\"STUDY1\",\"STUDY2\"]",
    "description":"List of study names.",
    "items":{
        "type":"string"
    }
}

Example:

"studyNames": ["STUDY1","STUDY2"]

Nested Schema : codeCodeSysList

Type: array

List of code and system code combinations

Show Source

Array of: object CodeCodeSysDS

Provide a list of codes and a list of system codes.

{
    "type":"array",
    "description":"List of code and system code combinations",
    "items":{
        "$ref":"#/definitions/CodeCodeSysDS"
    }
}

Nested Schema : CodeCodeSysDS

Type: object

Provide a list of codes and a list of system codes.

Show Source

code(optional): array code

List codes
codeSys(optional): array codeSys

List system codes
info(optional): object ConditionMetaInfo

Keep the meta information in here. This will be used for informational purposes.

{
    "type":"object",
    "properties":{
        "codeSys":{
            "type":"array",
            "description":"List system codes",
            "items":{
                "type":"string"
            }
        },
        "code":{
            "type":"array",
            "description":"List codes",
            "items":{
                "type":"string"
            }
        },
        "info":{
            "description":"To store Meta Information",
            "$ref":"#/definitions/ConditionMetaInfo"
        }
    },
    "description":"Provide a list of codes and a list of system codes."
}

Nested Schema : code

Type: array

List codes

Show Source

Array of: string

{
    "type":"array",
    "description":"List codes",
    "items":{
        "type":"string"
    }
}

Nested Schema : codeSys

Type: array

List system codes

Show Source

Array of: string

{
    "type":"array",
    "description":"List system codes",
    "items":{
        "type":"string"
    }
}

Nested Schema : ConditionMetaInfo

Type: object

Keep the meta information in here. This will be used for informational purposes.

Show Source

comment(optional): string

Comment
name(optional): string

Name

{
    "type":"object",
    "properties":{
        "name":{
            "type":"string",
            "description":"Name"
        },
        "comment":{
            "type":"string",
            "description":"Comment"
        }
    },
    "description":"Keep the meta information in here. This will be used for informational purposes."
}

Nested Schema : GenomicPositionFileExport

Type: object

Show Source

chromosomeId(optional): integer(int64)

Record identifier of the chromosome.
endPosition(optional): integer(int64)

Optional. End location of sequence
startPosition(optional): integer(int64)

Optional. Start location of sequence

{
    "type":"object",
    "properties":{
        "chromosomeId":{
            "type":"integer",
            "format":"int64",
            "description":"Record identifier of the chromosome."
        },
        "startPosition":{
            "type":"integer",
            "format":"int64",
            "description":"Optional. Start location of sequence"
        },
        "endPosition":{
            "type":"integer",
            "format":"int64",
            "description":"Optional. End location of sequence"
        }
    }
}

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

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

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

Examples

The following example submits a GET request.

Example 1

API URL

http://localhost:7010/ohfapi/cg/v3.3/exports

Example of Response Body

The following example shows the response returned in JSON format.

[
  {
    "id": {
      "system": "ODB",
      "value": "940"
    },
    "context": "PATIENT",
    "geneHugoNames": [
      "ANKRD30BL"
    ],
    "alignmentId": 1,
    "patientSubjectId": [
      841,
      838
    ],
    "link": {
      "rel": "SUBMITJOB",
      "href": "/ohfapi/cg/v3.3/exports/940/jobs"
    }
  },
  {
    "id": {
      "system": "ODB",
      "value": "942"
    },
    "context": "PATIENT",
    "geneHugoNames": [
      "CCDC3",
      "OPTN"
    ],
    "versionId": 3,
    "alignmentId": 1,
    "patientSubjectId": [
      841
    ],
    "link": {
      "rel": "SUBMITJOB",
      "href": "/ohfapi/cg/v3.3/exports/942/jobs"
    }
  }
]

Example 2

API URL ??? by Date

http://localhost:7010/ohfapi/cg/v3.3/exports?startDate=02/09/2017

Example of Response Body

The following example shows the response returned in JSON format.

[
  {
    "id": {
      "system": "ODB",
      "value": "1267"
    },
    "context": "PATIENT",
    "geneHugoNames": [
      "ANKRD30BL"
    ],
    "alignmentId": 1,
    "patientSubjectId": [
      841,
      838
    ],
    "link": {
      "rel": "SUBMITJOB",
      "href": "/ohfapi/cg/v3.3/exports/1267/jobs"
    }
  },
  {
    "id": {
      "system": "ODB",
      "value": "1268"
    },
    "context": "SUBJECT",
    "geneHugoNames": [
      "VAV2",
      "TTC34",
      "SLC9A1",
      "NSFP1",
      "EGFR"
    ],
    "alignmentId": 1,
    "specimenTypeCodes": [
      "SPCMN_TYP_CD_BLOOD"
    ],
    "anatomicalSiteCodes": [
      "SPCMN_ANA_SITE_CD_CODE_3"
    ],
    "studyNames": [
      "study1"
    ],
    "patientSubjectId": [
      1622,
      1634,
      1700,
      1682,
      1701
    ],
    "link": {
      "rel": "SUBMITJOB",
      "href": "/ohfapi/cg/v3.3/exports/1268/jobs"
    }
  },
  {
    "id": {
      "system": "ODB",
      "value": "1270"
    },
    "context": "PATIENT",
    "geneHugoNames": [
      "PIK3C2G",
      "RERGL"
    ],
    "alignmentId": 1,
    "specimenIdsOdb": [
      58
    ],
    "patientSubjectId": [
      817
    ],
    "link": {
      "rel": "SUBMITJOB",
      "href": "/ohfapi/cg/v3.3/exports/1270/jobs"
    }
  }
]

Example 3

API URL ??? by Date Range

http://localhost:7010/ohfapi/cg/v3.3/exports?startDate=02/09/2017&endDate=02/10/2017

Example of Response Body

The following example shows the response returned in JSON format.

[
  {
    "id": {
      "system": "ODB",
      "value": "1267"
    },
    "context": "PATIENT",
    "geneHugoNames": [
      "ANKRD30BL"
    ],
    "alignmentId": 1,
    "patientSubjectId": [
      841,
      838
    ],
    "link": {
      "rel": "SUBMITJOB",
      "href": "/ohfapi/cg/v3.3/exports/1267/jobs"
    }
  },
  {
    "id": {
      "system": "ODB",
      "value": "1268"
    },
    "context": "SUBJECT",
    "geneHugoNames": [
      "VAV2",
      "TTC34",
      "SLC9A1",
      "NSFP1",
      "EGFR"
    ],
    "alignmentId": 1,
    "specimenTypeCodes": [
      "SPCMN_TYP_CD_BLOOD"
    ],
    "anatomicalSiteCodes": [
      "SPCMN_ANA_SITE_CD_CODE_3"
    ],
    "studyNames": [
      "study1"
    ],
    "patientSubjectId": [
      1622,
      1634,
      1700,
      1682,
      1701
    ],
    "link": {
      "rel": "SUBMITJOB",
      "href": "/ohfapi/cg/v3.3/exports/1268/jobs"
    }
  },
  {
    "id": {
      "system": "ODB",
      "value": "1270"
    },
    "context": "PATIENT",
    "geneHugoNames": [
      "PIK3C2G",
      "RERGL"
    ],
    "alignmentId": 1,
    "specimenIdsOdb": [
      58
    ],
    "patientSubjectId": [
      817
    ],
    "link": {
      "rel": "SUBMITJOB",
      "href": "/ohfapi/cg/v3.3/exports/1270/jobs"
    }
  }
]

Example 4

API URL ??? by ID List and Date Range

http://localhost:7010/ohfapi/cg/v3.3/exports?id=1235&id=1236&startDate=02/01/2017&endDate=02/10/2017

Example of Response Body

The following example shows the response returned in JSON format.

[
  {
    "id": {
      "system": "ODB",
      "value": "1235"
    },
    "context": "SUBJECT",
    "genomicPosition": [
      {
        "chromosomeId": 12,
        "startPosition": 109578044,
        "endPosition": 109629995
      },
      {
        "chromosomeId": 12,
        "startPosition": 32866557,
        "endPosition": 32890685
      },
      {
        "chromosomeId": 12,
        "startPosition": 93210312,
        "endPosition": 93214560
      },
      {
        "chromosomeId": 12,
        "startPosition": 123327143,
        "endPosition": 123333065
      },
      {
        "chromosomeId": 12,
        "startPosition": 68646871,
        "endPosition": 68646914
      },
      {
        "chromosomeId": 12,
        "startPosition": 4935808,
        "endPosition": 4943097
      }
    ],
    "alignmentId": 1,
    "studyNames": [
      "study1"
    ],
    "patientSubjectCohortListId": 10000000630009,
    "bedFileNameUploadService": "julian-test/julian-chrMT-test.txt",
    "link": {
      "rel": "SUBMITJOB",
      "href": "/ohfapi/cg/v3.3/exports/1235/jobs"
    }
  },
  {
    "id": {
      "system": "ODB",
      "value": "1236"
    },
    "context": "SUBJECT",
    "genomicPosition": [
      {
        "chromosomeId": 25,
        "startPosition": 30,
        "endPosition": 30
      },
      {
        "chromosomeId": 1,
        "startPosition": 149029121,
        "endPosition": 149029121
      },
      {
        "chromosomeId": 1,
        "startPosition": 148805730,
        "endPosition": 148805730
      },
      {
        "chromosomeId": 1,
        "startPosition": 148794984,
        "endPosition": 148794984
      },
      {
        "chromosomeId": 1,
        "startPosition": 145700000,
        "endPosition": 145700000
      },
      {
        "chromosomeId": 1,
        "startPosition": 121485435,
        "endPosition": 121485435
      },
      {
        "chromosomeId": 1,
        "startPosition": 55199420,
        "endPosition": 55199420
      },
      {
        "chromosomeId": 1,
        "startPosition": 42104031,
        "endPosition": 42104031
      },
      {
        "chromosomeId": 1,
        "startPosition": 18514685,
        "endPosition": 18514685
      },
      {
        "chromosomeId": 1,
        "startPosition": 17097664,
        "endPosition": 17097664
      },
      {
        "chromosomeId": 1,
        "startPosition": 7289606,
        "endPosition": 7289606
      },
      {
        "chromosomeId": 1,
        "startPosition": 6955905,
        "endPosition": 6955905
      },
      {
        "chromosomeId": 1,
        "startPosition": 5644647,
        "endPosition": 5644647
      },
      {
        "chromosomeId": 1,
        "startPosition": 4882351,
        "endPosition": 4882351
      },
      {
        "chromosomeId": 1,
        "startPosition": 4249151,
        "endPosition": 4249151
      },
      {
        "chromosomeId": 1,
        "startPosition": 4248463,
        "endPosition": 4248463
      },
      {
        "chromosomeId": 1,
        "startPosition": 4000001,
        "endPosition": 4000001
      },
      {
        "chromosomeId": 1,
        "startPosition": 3418614,
        "endPosition": 3418614
      },
      {
        "chromosomeId": 1,
        "startPosition": 3000001,
        "endPosition": 3000001
      },
      {
        "chromosomeId": 1,
        "startPosition": 2827695,
        "endPosition": 2827695
      },
      {
        "chromosomeId": 1,
        "startPosition": 2241376,
        "endPosition": 2241376
      },
      {
        "chromosomeId": 1,
        "startPosition": 2000000,
        "endPosition": 2000000
      },
      {
        "chromosomeId": 1,
        "startPosition": 1654038,
        "endPosition": 1654038
      },
      {
        "chromosomeId": 1,
        "startPosition": 1273278,
        "endPosition": 1273278
      },
      {
        "chromosomeId": 1,
        "startPosition": 1142720,
        "endPosition": 1142720
      },
      {
        "chromosomeId": 1,
        "startPosition": 1000101,
        "endPosition": 1000101
      },
      {
        "chromosomeId": 1,
        "startPosition": 1000001,
        "endPosition": 1000001
      },
      {
        "chromosomeId": 1,
        "startPosition": 847250,
        "endPosition": 847250
      },
      {
        "chromosomeId": 1,
        "startPosition": 807302,
        "endPosition": 807302
      },
      {
        "chromosomeId": 1,
        "startPosition": 805474,
        "endPosition": 805474
      },
      {
        "chromosomeId": 1,
        "startPosition": 738636,
        "endPosition": 738636
      },
      {
        "chromosomeId": 1,
        "startPosition": 723819,
        "endPosition": 723819
      },
      {
        "chromosomeId": 1,
        "startPosition": 714040,
        "endPosition": 714040
      },
      {
        "chromosomeId": 1,
        "startPosition": 714019,
        "endPosition": 714019
      },
      {
        "chromosomeId": 1,
        "startPosition": 87190,
        "endPosition": 87190
      },
      {
        "chromosomeId": 1,
        "startPosition": 13502,
        "endPosition": 13502
      },
      {
        "chromosomeId": 1,
        "startPosition": 13302,
        "endPosition": 13302
      }
    ],
    "alignmentId": 1,
    "studyNames": [
      "study1"
    ],
    "patientSubjectId": [
      1622,
      1682
    ],
    "bedFileNameUploadService": "thulasi/subject_chr1.txt",
    "link": {
      "rel": "SUBMITJOB",
      "href": "/ohfapi/cg/v3.3/exports/1236/jobs"
    }
  }
]