The MOLGENIS REST API allows you to retrieve and modify your data model entities and entity collections. The API supports all CRUD (create, read, update and delete) methods as well as resource collections paging & filtering and resource field expansion. At the moment of writing JSON and form data are supported as request content types and JSON is the only supported response content type.

Your MOLGENIS data model defines the resources and resource collections that can be accessed and modified. Lets assume that your data model contains the entities DataSet, Protocol and Feature. The REST API will consist of the following endpoints:

Collections

MOLGENIS entity collections are available as end-points:

Endpoints

Retrieve collection

Each entity collection has its own end-point:

Request

GET http://your.molgenis.url/api/v1/dataset

Response

200 OK

{
    "href": "/api/v1/dataset",
    "start": 0,
    "num": 100,
    "total": 2,
    "items": [{
        "href": "/api/v1/dataset/1",
        "name": "my first data set",
        "protocol": {
            "href": "/api/v1/dataset/1/protocol"
        },{
        "href": "/api/v1/dataset/2",
        "name": "my second data set",
        "protocol": {
            "href": "/api/v1/dataset/2/protocol"
        }
    }]
}

Delete collection

Datasets can be completely deleted (Nb. the meta data will be kept):

Request

DELETE http://your.molgenis.url/api/v1/dataset

Response

204 No Content

Query a collection

Key Type Description
start int Offset in resource collection
num int Number of resources to retrieve starting at start
q list of molgenis query rule objects Query to filter the resource collection list

start and num

Request

GET http://your.molgenis.url/api/v1/dataset?start=1&num=1

Response

200 OK

{
    "href": "/api/v1/dataset",
    "start": 1,
    "num": 1,
    "total": 3,
    "prevHref":"/api/v1/dataset?start=0&num=1"
    "nextHref":"/api/v1/dataset?start=2&num=1"
    "items": [{
        "href": "/api/v1/dataset/2",
        "name": "my second data set",
        "protocol": {
            "href": "/api/v1/dataset/2/protocol"
        }
    }]
}

prevHref is the location of the previous page of resources, nextHref is the location of the next page of resources.

q

Request

POST http://your.molgenis.url/api/v1/dataset?_method=GET
Content-Type: application/json

{
    "q": [{
       "field": "name",
       "operator": "EQUALS",
       "value": "my first data set"
    }]
}

Response

200 OK

{
    "href": "/api/v1/dataset",
    "start": 0,
    "num": 100,
    "total": 1,
    "items": [{
        "href": "/api/v1/dataset/1",
        "name": "my first data set",
        "protocol": {
            "href": "/api/v1/dataset/1/protocol"
        }
    }]
}

Instances

Each data row within a collection (i.e. entity instance) can be accessed via its identifier:

Endpoints

Retrieve

Request

GET http://your.molgenis.url/api/v1/dataset/1

Response

200 OK

{
    "href": "/api/v1/dataset/1",
    "name": "my first data set",
    "protocol": {
        "href": "/api/v1/dataset/1/protocol"
    }
}

href is the location of this resource, name is a string value and protocol is the location of the entity that this dataset refers to.

Create

By psoting a JSON message that matches the meta data attributes you can add new instances:

Request

POST http://your.molgenis.url/api/v1/person
Content-Type: application/json

{
    "age": "17",
    "driverslicence": true
}

Response

201 Created

In the response headers you can find the id of the newly created resource:
Example: Location: /api/v1/person/AAAACTUMDL2N4BTTSWWS6PQAAE

Update

Existing instances can be updated by putting a complete changed record to the entity instance endpoint:

Request

PUT http://your.molgenis.url/api/v1/dataset/3
Content-Type: application/json

{
    "name": "renamed data set"
}

Response

204 No Content

Update one value

If you only want to change one attribute without needing to provide all other attributes you can put values to the attributes seperately:

Request

PUT http://your.molgenis.url/api/v1/dataset/3/name
Content-Type: application/json

{
    "name": "renamed data set"
}

Response

204 No Content

Delete

Request

DELETE http://your.molgenis.url/api/v1/dataset/3

Response

204 No Content

Advanced options

Instance end-points have the following options:

Key Type Description
attributes Comma-separated string Defines which fields in the API response to select
expand Comma-separated string Defines which fields in the API response to (partially) expand
_method HTTP method Tunnel request through defined method over default API operation
callback string Callback function name used as JSON padding to allow cross domain requests

select attributes

In a query you can specify what attributes to return, useful when having thousands of attributes:

Request

GET http://your.molgenis.url/api/v1/dataset/1?attributes=identifier,name

Response

200 OK

{
    "href": "/api/v1/DataSet/1",
    "Identifier": "celiacsprue",
    "Name": "Celiac Sprue"
}

expand xref attributes

MOLGENIS can have attributes of type xref (foreign key) that you can follow and expand attributes of:

Request

GET http://your.molgenis.url/api/v1/dataset/1?expand=protocol

Response

200 OK

{
    "href": "/api/v1/dataset/1",
    "name": "my first data set",
    "protocol": {
        "href": "/api/v1/protocol/10",
        "name": "protocol for dataset #1",
        "features": {
            "href":"/api/v1/protocol/37265/features"
        }
    }
}

partial expand

Within the expansion you can again specify the attributes to be included:

Request

GET http://your.molgenis.url/api/v1/dataset/1?expand=protocol[name]

Response

200 OK

{
    "href": "/api/v1/dataset/1",
    "name": "my first data set",
    "protocol": {
        "href": "/api/v1/protocol/10",
        "name": "protocol for dataset #1"
    }
}

_method

Some browsers do not support operations such as PUT and DELETE. The _method parameter can be used to tunnel the request over a POST operation.

Request

POST http://your.molgenis.url/api/v1/dataset/3?_method=PUT
Content-Type: application/json

{
    "name": "renamed data set"
}

Response

204 No Content

callback

Request

GET http://your.molgenis.url/api/v1/dataset/1?callback=myfunction

Response

200 OK
myfunction(
{
    "href": "/api/v1/dataset/1",
    "name": "my first data set",
    "protocol": {
        "href": "/api/v1/dataset/1/protocol"
    }
}
)

Meta data

Meta data provides details on the attributes within your collection. This allows for client side generation of user interfaces. Assuming that you have entities 'datasets', 'protocol' and 'features' then you can retrieve the metadata as follows:

Endpoints

Retrieve meta data

You can retrieve meta data for each collection:

Request

GET http://your.molgenis.url/api/v1/dataset/meta

Response

200 OK

{
    "href": "/api/v1/DataSet/meta",
    "name": "DataSet",
    "label": "",
    "attributes": {
        "Identifier": {
            "href": "/api/v1/DataSet/meta/Identifier"
        },
        "Name": {
            "href": "/api/v1/DataSet/meta/Name"
        },
        "description": {
            "href": "/api/v1/DataSet/meta/description"
        },
        "ProtocolUsed": {
            "href": "/api/v1/DataSet/meta/ProtocolUsed"
        },
        "startTime": {
            "href": "/api/v1/DataSet/meta/startTime"
        },
        "endTime": {
            "href": "/api/v1/DataSet/meta/endTime"
        }
    },
    "labelAttribute": "Identifier",
    "languageCode": "en"
}

Delete meta data

Deletes resource meta data and all data associated with this resource.

Request

DELETE http://your.molgenis.url/api/v1/dataset/meta

Response

204 No Content

Authentication

Login

Request

POST http://your.molgenis.url/api/v1/login
Content-Type: application/json

{
    "username": "your username",
    "password": "your password"
}

Response

200 OK
{
    "token": "4296ef4fd9324360aa5c-bf8a849003da",
    "username": "admin",
    "firstname": "John",
    "lastname": "Doe"
}

OR
401 Unauthorized

The token can be used as authentication token in subsequent api calls. The token must be added to the http header:

x-molgenis-token: 4296ef4fd9324360aa5c-bf8a849003da

Logout

Request

GET http://your.molgenis.url/api/v1/logout

header:
x-molgenis-token: 4296ef4fd9324360aa5c-bf8a849003da

Response

200 OK

Response codes

Code Description
200 Request ok, returned content in body
201 Resource succesfully created
204 Request ok
400 Your request was not valid
401 You are not authorized to perform this operation, did you authenticate?
404 Resource does not exist
500 Request ok but something went wrong on the server

FAQ

How to resolve a 400 Bad Request error?

Did you specify the Content-Type header if your body contains content?

What options exist to define query rules for resource collection requests?

The query rules are serialized Java QueryRule objects, take a look at the source code of the QueryRule class to see what options are available.

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