| Oracle® Healthcare Precision Medicine Administrator's Guide Release 1.0 E76044-01 |
|
|
PDF · Mobi · ePub |
| Oracle® Healthcare Precision Medicine Administrator's Guide Release 1.0 E76044-01 |
|
|
PDF · Mobi · ePub |
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:
All API invocations with base path as /trc/opmconfigapi/ should have header value X-Requested-By set with the value OPM.
REST API's to manage genome version details required by the Dalliance genome browser. DAS server details are required for configuring Dalliance.
| PATH | <server url>//trc/opmconfigapi/v1.0/config/dalliance |
| ACCEPTS | application/json |
| RETURNS | application/json |
GET - Genome configurations
| PARAMETER | DESCRIPTION | PARAMETER TYPE | DATA TYPE/ REPRESENTATION |
|---|---|---|---|
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"
}
POST - Add a genome configuration. You will have to provide DAS server URLs that are used in Dalliance to plot variant details.
| 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>"
}
|
| Code | Reason | Representation |
|---|---|---|
| 200 | success |
{
"success": "true"
}
|
| PATH | <server url>/trc/opmconfigapi/v1.0/config/dalliance/{genomeVersion} |
| ACCEPTS | application/json |
| RETURNS | application/json |
GET - Configuration for a genome version
| PARAMETER | DESCRIPTION | PARAMETER TYPE | DATA TYPE/ REPRESENTATION |
|---|---|---|---|
| genomeVersion | Genome version | path | String |
| Code | Reason | Representation (Example) |
|---|---|---|
| 200 | success |
{
"name":"HG19",
"authority":"GRCh",
"version":"38",
"sequenceTrackUrl":"<URL>",
"genesTrackUrl":"<URL>"
"dnaVersion": "V68"
}
|
PUT - Update an existing genome configuration
| 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>"
}
|
| Code | Reason | Representation |
|---|---|---|
| 200 | success |
{
"success": "true"
}
|
REST APIs to manage credentials for invoking Thomson Reuters genomic APIs. Valid subscription for Thomson Reuters APIs is required for consuming them. You must enable the Thomson Reuters related feature after configuring the credential. For details, see Section 2.4, "Enabling or Disabling Features Related to External Systems".
Admin user can configure the organization level and own (if available) credentials to access Thomson Reuters APIs. Molecular pathologists can add their own credentials to access Thomson Reuters by using this API.
| PATH | <server url>/trc/opmconfigapi/v1.0/config/credential/thomsonReuters |
| ACCEPTS | application/json |
| RETURNS | application/json |
GET - Users configured for Thomson Reuters
| PARAMETER | DESCRIPTION | PARAMETER TYPE | DATA TYPE/ REPRESENTATION |
|---|---|---|---|
| Code | Reason | Representation (Example) |
|---|---|---|
| 200 | success |
{
"id":"1001",
"credentialType":"USER",
"username":"testuser",
"password":"" -- Is not loaded in GET
},
{
"id":"1002",
"credentialType":"ORG",
"username":"testorg",
"password":"" -- Is not loaded in GET
}
|
POST - Add a user credential for invoking Thomson Reuters
| PARAMETER | DESCRIPTION | PARAMETER TYPE | DATA TYPE/ REPRESENTATION |
|---|---|---|---|
| body | body |
{
"credentialType":"USER|ORG",
"username":"<USER_ID>",
"password":"<PASSWORD>"
}
|
| Code | Reason | Representation (Example) |
|---|---|---|
| 200 | success |
{
"id":"1231",
"credentialType":"USER",
"username":"testuser",
"password":"" -- Is not loaded
}
|
PUT - Update user credential for invoking Thomson Reuters
| PARAMETER | DESCRIPTION | PARAMETER TYPE | DATA TYPE/ REPRESENTATION |
|---|---|---|---|
| body | body |
{
"id":"1002",
"credentialType":"ORG",
"username":"testOrg",
"password":"<PASSWORD>"
}
|
| Code | Reason | Representation (Example) |
|---|---|---|
| 200 | success |
{
"success": "true"
}
|
| PATH | <server url>/trc/opmconfigapi/v1.0/config/credential/thomsonReuters/{credentialID} |
| ACCEPTS | application/json |
| RETURNS | application/json |
GET - User details for a user configured for Thomson Reuters
| PARAMETER | DESCRIPTION | PARAMETER TYPE | DATA TYPE/ REPRESENTATION |
|---|---|---|---|
| credentialID | path | integer |
| Code | Reason | Representation (Example) |
|---|---|---|
| 200 | success |
{
"id":"1002",
"credentialType":"USER",
"username":"testorg",
"password":"" -- Is not loaded in GET
}
|
PUT - Update user credential for invoking Thomson Reuters
| PARAMETER | DESCRIPTION | PARAMETER TYPE | DATA TYPE/ REPRESENTATION |
|---|---|---|---|
| credentialID | path | integer | |
| body | body |
{
"id":"1002",
"credentialType":"USER",
"username":"testUser",
"password":"<PASSWORD>"
}
|
| Code | Reason | Representation |
|---|---|---|
| 200 | success |
{
"success": "true"
}
|
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 2.4, "Enabling or Disabling Features Related to External Systems".
| PATH | <server url>/trc/opmconfigapi/v1.0/config/credential/nof1 |
| ACCEPTS | application/json |
| RETURNS | application/json |
GET - User credential for N-of-One
| PARAMETER | DESCRIPTION | PARAMETER TYPE | DATA TYPE/ REPRESENTATION |
|---|---|---|---|
| Code | Reason | Representation |
|---|---|---|
| 200 | success |
{
"id":"1002",
"credentialType":"ORG",
"authorizationToken": null
"productKey":"<productKey>",
"customerId":"<customerId>"
}
|
authorizationToken is not loaded in GET.
POST - Add credential details for invoking N-of-One
| PARAMETER | DESCRIPTION | PARAMETER TYPE | DATA TYPE/ REPRESENTATION |
|---|---|---|---|
| body | body |
{
"authorizationToken": "<AUTH TOKEN>",
"productKey":"<productKey>",
"customerId":"<customerId>"
}
|
| Code | Reason | Representation |
|---|---|---|
| 200 | success |
{
"id":"1231",
"credentialType":"ORG",
"authorizationToken": "<AUTH TOKEN>"
"productKey":"<productKey>",
"customerId":"<customerId>"
}
|
PUT - Update credential details for N-of-One
| PARAMETER | DESCRIPTION | PARAMETER TYPE | DATA TYPE/ REPRESENTATION |
|---|---|---|---|
| body | body |
{
"authorizationToken": "<AUTH TOKEN>",
"productKey":"<productKey>",
"customerId":"<customerId>"
}
|
| Code | Reason | Representation |
|---|---|---|
| 200 | success |
{
"authorizationToken": "<AUTH TOKEN>"
"productKey":"<productKey>",
"customerId":"<customerId>"
}
|
| PATH | <server url>/trc/opmconfigapi/v1.0/config/externalFeaturesState |
| ACCEPTS | application/json |
| RETURNS | application/json |
GET - Returns current features state
| PARAMETER | DESCRIPTION | PARAMETER TYPE | DATA TYPE/ REPRESENTATION |
|---|---|---|---|
| Code | Reason | Representation |
|---|---|---|
| 200 | success |
{
"dalliance":false,
"thomsonReuters":false,
"clinvar":true,
"nof1":false,
"emr":false
}
|
PUT - Enable or disable features in OHPM
| PARAMETER | DESCRIPTION | PARAMETER TYPE | DATA TYPE/ REPRESENTATION |
|---|---|---|---|
| body | body |
{
"dalliance":false,
"thomsonReuters":false,
"clinvar":true,
"nof1":false,
"emr":true
}
|
| Code | Reason | Representation |
|---|---|---|
| 200 | success |
{
"success": "true"
}
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