2 External System Configurations

This chapter details configuration APIs for external systems used in OHPM. These are REST based services and are authenticated using BASIC authentication. Admin user (having pm_admin_group role) can use these services for configuration.

It includes the following topics:

Common Request Header

All API invocations with base path as /ohpm/opmconfigapi/ should have header value X-Requested-By set with the value OPM. For more information on configuring a sample REST client to access the OHPM API REST based services, see Article ID 2148026.1 on My Oracle Support.

2.1 Dalliance

REST API's to manage genome version details required by the Dalliance genome browser. DAS server details are required for configuring Dalliance.

2.1.1 Dalliance Configuration

PATH <server url>//ohpm/opmconfigapi/v1.0/config/dalliance
ACCEPTS application/json
RETURNS application/json

2.1.1.1 Retrieving a List of Genome Configurations

Method

GET - Genome configurations

Request

PARAMETER DESCRIPTION PARAMETER TYPE DATA TYPE/ REPRESENTATION
       

Response

HTTP Status: 200 (success)

Body: Example

{
    "name":"HG19",
    "authority":"GRCh",
    "version":"38",
    "sequenceTrackUrl":"<URL>",
    "genesTrackUrl":"<URL>",
                            "dnaVersion": "V68"
},
{
    "name":"HG18",
    "authority":"NCBI",
    "version":"37",
    "sequenceTrackUrl":"<URL>",
    "genesTrackUrl":"<URL>",
    "dnaVersion": "V68"
}

2.1.1.2 Adding a Genome Configuration

Method

POST - Add a genome configuration. You will have to provide DAS server URLs that are used in Dalliance to plot variant details.

Request

PARAMETER DESCRIPTION PARAMETER TYPE DATA TYPE/ REPRESENTATION
body   body 
{
    "name":"<UCSC_NAME>",
    "authority":"<authority_name>",
    "version":"<version_number>",
    "sequenceTrackUrl":"<DAS server sequence track URL>",
    "genesTrackUrl":"<DAS server sequence track URL>"
    "dnaVersion": "<DNA Reference Build Version>"
}

Response

Code Reason Representation
200 success 
{
  "success": "true"
}

2.1.2 Dalliance Configuration by Genome Version

PATH <server url>/ohpm/opmconfigapi/v1.0/config/dalliance/{genomeVersion}
ACCEPTS application/json
RETURNS application/json

2.1.2.1 Retrieving Configuration for a Genome Version

Method

GET - Configuration for a genome version

Request

PARAMETER DESCRIPTION PARAMETER TYPE DATA TYPE/ REPRESENTATION
genomeVersion Genome version path String

Response

Code Reason Representation (Example)
200 success 
{
    "name":"HG19",
    "authority":"GRCh",
    "version":"38",
    "sequenceTrackUrl":"<URL>",
    "genesTrackUrl":"<URL>"
    "dnaVersion": "V68"
}

2.1.2.2 Updating an Existing Genome Configuration

Method

PUT - Update an existing genome configuration

Request

PARAMETER DESCRIPTION PARAMETER TYPE DATA TYPE/ REPRESENTATION
genomeVersion Genome version path string
body   body 
{
    "name":"<UCSC_NAME>",
    "authority":"<authority_name>",
    "version":"<version_number>",
    "sequenceTrackUrl":"<URL>",
    "genesTrackUrl":"<URL>"
    "dnaVersion": "<DNA Reference Build Version>"
}

Response

Code Reason Representation
200 success 
{
    "success": "true"
}

2.1.2.3 Deleting a Genome Version Configuration

Method

DELETE - Configuration for a genome version

Request

PARAMETER DESCRIPTION PARAMETER TYPE DATA TYPE/ REPRESENTATION
genomeVersion Genome version path string

Response

Code Reason Representation (Example)
200 success  

2.2 N-Of-One

The following REST APIs have been provided to manage configurations for invoking N-of-One genomic interpretation APIs. Enable N-of-One related features after configuring N-of-One details. For details, see Section 2.3, "Enabling or Disabling Features Related to External Systems".

2.2.1 N-of-One Credential Configuration

PATH <server url>/ohpm/opmconfigapi/v1.0/config/credential/nof1
ACCEPTS application/json
RETURNS application/json

2.2.1.1 Getting Credentials Configured for N-of-One

Method

GET - User credential for N-of-One

Request

PARAMETER DESCRIPTION PARAMETER TYPE DATA TYPE/ REPRESENTATION
       

Response

Code Reason Representation
200 success 
{
    "id":"1002",
    "credentialType":"ORG",
    "authorizationToken": null
    "productKey":"<productKey>",
    "customerId":"<customerId>"
}

authorizationToken is not loaded in GET.

2.2.1.2 Adding a Credential for Invoking N-of-One

Method

POST - Add credential details for invoking N-of-One

Request

PARAMETER DESCRIPTION PARAMETER TYPE DATA TYPE/ REPRESENTATION
body   body 
{
    "authorizationToken": "<AUTH TOKEN>",
    "productKey":"<productKey>",
    "customerId":"<customerId>"
}

Response

Code Reason Representation
200 success 
{
    "id":"1231",
    "credentialType":"ORG",
    "authorizationToken": "<AUTH TOKEN>"
    "productKey":"<productKey>",
    "customerId":"<customerId>"
}

2.2.1.3 Updating Credentials for Invoking N-of-One

Method

PUT - Update credential details for N-of-One

Request

PARAMETER DESCRIPTION PARAMETER TYPE DATA TYPE/ REPRESENTATION
body   body 
{
    "authorizationToken": "<AUTH TOKEN>",
    "productKey":"<productKey>",
    "customerId":"<customerId>"
}

Response

Code Reason Representation
200 success 
{       
    "authorizationToken": "<AUTH TOKEN>"
    "productKey":"<productKey>",
    "customerId":"<customerId>"
}

2.2.1.4 Deleting Credential Used for Invoking N-of-One

Method

DELETE - Delete credential used for invoking N-of-One

Request

PARAMETER DESCRIPTION PARAMETER TYPE DATA TYPE/ REPRESENTATION
       

Response

Code Reason Representation
200 success 
{
    "success": "true"
}

2.3 Enabling or Disabling Features Related to External Systems

PATH <server url>/ohpm/opmconfigapi/v1.0/config/externalFeaturesState
ACCEPTS application/json
RETURNS application/json

2.3.1 Returning State of Current Features

Method

GET - Returns current features state

Request

PARAMETER DESCRIPTION PARAMETER TYPE DATA TYPE/ REPRESENTATION
       

Response

Code Reason Representation
200 success 
{
    "dalliance":false,
    "clinvar":true,
    "nof1":false,
    "emr":false
}

2.3.2 Enabling or Disabling Features in Oracle Healthcare Precision Medicine

Method

PUT - Enable or disable features in OHPM

Request

PARAMETER DESCRIPTION PARAMETER TYPE DATA TYPE/ REPRESENTATION
body   body 
 {
    "dalliance":false,
    "clinvar":true,
    "nof1":false,
    "emr":true
}

Response

Code Reason Representation
200 success 
{
    "success": "true"
}