OpenSpecimen exposes REST APIs that can be consumed to developed custom interfaces and for integration with other databases. The REST APIs will be consumed by the OpenSpecimen user interface.

Common Characteristics of REST Resources

The following characteristics apply to all OpenSpecimen API resources:

• You access a resource by sending an HTTP request to the OpenSpecimen server. The server replies with a response that either contains the data you requested or a status indicator, and in some cases both.

• All resources are located at http[s]://<host-name>:<port>/<application name>/rest. 

  E.g. http://demo.openspecimen.org/openspecimen/rest/ng/collection-protocols/1/workflows

• You request a particular resource by appending a particular path to this base URL
• All resources may return any of the below mentioned status codes:

On this page, when a portion of a URL, path, or parameter value is shown in italics, it indicates that you should replace the italicised value with a particular value appropriate to your request.

Authentication

Majority of OpenSpecimen REST APIs can be invoked by only authenticated users. Authentication is done by invoking the sessions API with valid credentials and using the token returned by the API  in subsequent API invocation request headers. The workflow is explained below:

1. Invoke sessions API with valid credentials i.e. username, password, and domain. When domain is not specified, it defaults to 'openspecimen'.
   
   

   HTTP Method	POST
   URL	http[s]://<host>:<port>/openspecimen/rest/ng/sessions
   Body	{ "loginName": "admin@admin.com", "password": "Login!@3", "domainName": "openspecimen" }
   Response	HTTP 200 OK response with following body { "id": 1, "firstName": "Admin", "lastName": "Admin", "loginName": "admin@admin.com", "token": "NTQ1ZjZkYjktNTUyNi00YzM4LTlkNmEtYjllM2VjNDA0ZmIz", "admin": true, "instituteAdmin": false }

2. Use the token field value returned by sessions API as X-OS-API-TOKEN HTTP header value in every API request made to OpenSpecimen. The token value is used by OpenSpecimen to establish - a) the user is authenticated, and b) to retrieve user details from database for authorisation and other purposes in request handling.

Unauthenticated APIs

Given below is list of APIs that do not require user authentication

Date & Time Handling

OpenSpecimen assumes all date/time values specified in API request payload to be in UTC. The UTC time is then converted to server timezone before storing in database. This is best explained using an example:

• Assume OpenSpecimen is running in Mountain time (MT).
• Assume the API caller specified the date field value as "2017-02-20" in API request payload.
• The server interprets the input value ("2017-02-20") to be in UTC timezone and converts it to "2017-02-19" MST. This is because MT is 6 or 7 hrs behind UTC.
• The MT value ("2017-02-19") is then persisted into database.

This is surprising and undesirable behaviour from API users point of view.

In order to solve this problem, the API caller should always provide date/time field values in UTC using either of following options:

• Milliseconds elapsed since epoch. This mode always represents time in UTC. For example: 1487574000000 is 20th February 2017 00:00 in MDT
  
  

  {
    "lastName": "Blackberry",
    "birthDate": 1487574000000,
    "pmis": []
  }
  
  

• Adding appropriate offset to input date/time field value. For example: 2017-02-20T06:00:00.000Z is 20th February 2017 00:00 in MDT
  
  

  {
    "lastName": "Blackberry",
    "birthDate": "2017-02-20T07:00:00.000Z",
    "pmis":[]
  }

Modules