Structure of the URI

http://example.com:8080/flow/api/v1

Authentication

The username and access token must be supplied, unless the request is made in an authenticated session.

The access token can be generated from the settings page or using the public key included in the PartekFlow-REST.zip as described in REST API

Projects

/projects

POST, PUT

Creates or modifies a project.  Returns data for the specified project.

...

"data": [ "Unaligned reads" ]

}

/projects/list

POST, PUT, GET

Returns the list of visible projects on the server.

...

{
   "name": "DNA-Seq Project",
   "id": "13",
   "description": "",
   "owner": "0",
   "data": [
     "Variants"
   ]
 }

]

/projects/import

POST

Creates a project from the specified zip.

...

500: If an error occurs importing the project

/projects/export

POST, GET

Exports the specified project(s) to a zip.

...

A zip file containing the project content.

/projects/delete

POST

Deletes the specified project.

...

The list of projects that were deleted

Samples

/samples

POST, PUT

Creates a sample.  Returns data for the specified sample.

...

 ],
 "attributes": {
   "Type": [
     "Normal"
   ],
   "Pair": [
     "1"
   ]
 }
}

/samples/list

POST, GET

Returns a list of samples in the specified project.

...

The name, id, files, and attributes of each sample in the project

Data

/data

POST,PUT

Uploads a file for analysis.

...

404: Returned if there is no project with the given id

Library Files

/library_files

POST, PUT

Uploads and manages a library file

...

404: Returned if no library file is managed for the specified library file and assembly

/library_files/list

POST, GET

Returns information about library files managed by the server

...

{
   "description": "Bowtie index",
   "id": 2
 }

]

Pipelines

/pipelines

POST, GET

Downloads a pipeline specification.

...

404: Returned if the specified pipeline can not be found.

/pipelines/list

POST, GET

Returns a list of pipelines managed by the server

...

 {
   "name": "My Pipeline",
   "description": "",
   "protocolFile": {
     "path": "\/home\/flow\/.partekflow\/partek_db\/protocol\/P20150629140508365_0.json"
   },
   "deletable": true,
   "creationDate": "1472850094644",
   "creator": {
     "arg$1": {
       "section": "Pipelines",
       "date": 1435604708365,
       "user": "",
       "userID": 0,
       "name": "My Pipeline",
       "description": ""
     }
   }
 }

]

/pipelines/input

POST, GET

Returns the required inputs for a specified pipeline

...

 "BowtieTask": [
   "ebwt_reference"
 ],
 "SamtoolsTask": [
   "referenceFasta"
 ]
}

/pipelines/run

POST, GET

Runs the pipeline

...

pipeline_queued: 1805,1806

Queue

/queue

POST, GET

Downloads summary information about the queue

...

 "hasPendingCommands":"true"

}

/queue/downloads

POST, GET

Returns the count of files being downloaded to the server from servlets and tasks.

...

servletDownloads, taskDownloads

/queue/commands

POST, GET

Returns the count of commands that are pending and running.

...

200:  application/json

pending, running

/queue/tasks

POST, GET

Downloads information about the queued tasks

...

[
 {
   "id": 2590,
   "task": "Post-alignment QA\/QC",
   "runStatus": "Pending",
   "progress": 0,
   "submitted": "21 Oct 2016, 03:33 PM CDT",
   "started": "NA",
   "end": "NA"
 },
 {
   "id": 2589,
   "task": "TMAP - 5.0.0",
   "runStatus": "Running",
   "progress": 5,
   "submitted": "21 Oct 2016, 03:33 PM CDT",
   "started": "21 Oct 2016, 03:33 PM CDT",
   "end": "21 Oct 2016, 03:38 PM CDT"
 }
]

Users

/users

POST, PUT

Add and configure a specified user

...

[
 {
   "id": 0,
   "name": "admin",
   "displayName": "Administrator",
   "isOnline": true,
   "tasksInQueue": 1,
   "diskUsage": 83516042096
 }
]

/users/list

GET

Returns information about all users on the system

...

id, name, displayName, isOnline, tasksInQueue, diskQuota, diskUsage (in gigabytes)

Tasks

/tasks

GET

Returns a summary of tasks run on the server

...

id, user, project, status, task

Commands

/commands

GET

Returns a summary of commands running on the server.

...

commandId, workerIdentifier, cpu, memoryMbs, startTimeMillis, runTimeMillis, successful, commandLine

Licensing

/license

POST, GET

Returns a summary of the available licenses.

...

accounts, isNodeLocked, isConcurrent, expiration, version

Workers

/workers

POST, GET

Returns a summary of workers on the server.

...

systemIdentifier, workerIdentifier, isInternal, name, commandResourceUsageLimit, systemResourceUsageLimit, timeAtThisStatusInSeconds, responsive, taskIds

/workers/remote

POST, GET

Returns a summary of remote workers on the server.

...

systemIdentifier, workerIdentifier, isInternal, name, commandResourceUsageLimit, systemResourceUsageLimit, timeAtThisStatusInSeconds, responsive, taskIds

/workers/internal

POST, GET

Returns a summary of the internal worker.

...

systemIdentifier, workerIdentifier, isInternal, name, commandResourceUsageLimit, systemResourceUsageLimit, timeAtThisStatusInSeconds, responsive, taskIds

System

POST, PUT

Configure system parameters

...