DataManagerAPI

Work in progress -Public API

Introduction

Mobyle manages datasets. A dataset is a data element that can contain multiple files and contains meta-information about its type etc...

{uid}: the dataset identifier, the _id parameter of the Dataset element.
*file: file path in the dataset structure (as defined in the dataset information)

Authentication access

Different types of authentications are implemented to access the restricted access resources.

user has been authenticated with the web portal
a token has been created to grant temporary access to a dataset: the apikey parameter must be set in the query string parameters.
Oauth2 access: after getting access token, the Authorization heaber must send the bearer code as per specified in Oauth specification http://tools.ietf.org/html/rfc6749.

Oauth endpoints

The datamanager supports Oauth2 protocol to ask access to the data

/oauth/v2/authorize: authentication endpoint
/oauth/v2/token: access endpoint

Available scope are:

"user:email": access to the user email address
drive: acces to the user datasets

Dataset list

Get user dataset list

GET /my.json

Response example:

[
{"status": 2, "name": "jjjjjdddd", "tags": [], "persistent": false, "project": {"$oid": "5374c4d62e71a8032e9f4447"}, "path": null, "_id": {"$oid": "5375d59e2e71a879abed7497"}, "data": {"files": [{"path": "test.bam", "size": 19}, {"path": "test.bai", "size": 21}], "_type": "StructData", "type": "EDAM_data:0955+EDAM_data:0924", "properties": {"bai_data": {"path": ["test.bai"], "_type": "RefData", "format": "EDAM_format:3327", "type": "EDAM_data:0955", "size": 21}, "bam_data": {"path": ["test.bam"], "_type": "RefData", "format": "EDAM_format:2572", "type": "EDAM_data:0924", "size": 19}}, "format": "EDAM_format:3327+EDAM_format:2572"}, "public": true, "description": "dddd"},
{"status": 2, "name": "seq", "tags": [], "persistent": false, "project": {"$oid": "5374c4d62e71a8032e9f4447"}, "path": null, "_id": {"$oid": "5375d6b02e71a879abed7498"}, "data": {"path": ["seq"], "_type": "RefData", "format": "EDAM_format:2200", "type": "EDAM_data:2044", "size": 1382}, "public": true, "description": "ddd"}
]

In this response we have 2 datasets with:

"data": {"files": [{"path": "test.bam", "size": 19}, {"path": "test.bai", "size": 21}],, "_type": "StructData", ...

This is a case of a "complex" dataset (StructData) i.e. a dataset made of multiple files. Relative path to each file is set in the files parameter.

and

data": {"path": ["seq"], "_type": "RefData", "format": "EDAM_format:2200", "type": "EDAM_data:2044", "size": 1382}

This is a base dataset made of a single file (RefData). Its path is set in the path parameter.

The dataset id is in the "_id" parameter: "_id": {"$oid": "5375d59e2e71a879abed7497"}

Get public dataset list

GET /public.json

This request is the same as my.json but returns only public datasets.

Dataset file download

GET /download/{uid}/*file

Example, for dataset:

data": {"path": ["seq"], "_type": "RefData", "format": "EDAM_format:2200", "type": "EDAM_data:2044", "size": 1382}

GET /download/5375d6b02e71a879abed7498/seq

Dataset upload

File upload - Not yet available in JSON

The file upload creates a new dataset with a list of files embedded in the body request (multipart)

POST /data

Mandatory query parameters are:

type: EDAM type of the data, '|' separator if multiple types
format: EDAM format of the data, '|' separator if multiple formats
project: Id of the project where data should be stored
protocol: one of the supported protocols (ftp, http,...)

Optional query parameters are:

_id: Id of the dataset to update
privacy: is dataset public or not (public/private, default private)
name: name of the dataset
description: text to describe the dataset
uncompress: if parameter is present, uncompress the file (default false)
group: if file has been uncompressed, group the different files in a single dataset (default false, create one dataset per file)

Remote file upload - Not yet in JSON

The remote file upload creates a new dataset with a remote file URL (http, ftp, ...)

POST /remotedata