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 Usage of the Partek Flow REST API

Projects

/projects

POST, PUT

Creates a project.  Returns data for the specified project.

GET

Returns data for the specified project.

Required parameters

Optional parameters

Responses

200: application/json

The name, id, description, owner, and data of the project

400: Returned if the project parameter is missing.

403: Returned on a PUT request if a project with the specified name already exists.

Returned on a GET request if the user does not have permission to view the specified project.

404: Returned on a GET request if no project with the specified name exists

Example

http://example.com:8080/flow/api/v1/projects?project=My%20Project

{

 "name": "My Project",
 "id": "12",
 "description": "",
 "owner": "0",
 "data": [
   "Unaligned reads"
 ]
}

/projects/list

POST, PUT, GET

Responses

200: application/json

The name, id, description, owner, and data of each project the user has permission to view.

Example

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

[

 {
   "name": "My Project",
   "id": "12",
   "description": "",
   "owner": "0",
   "data": [
     "Unaligned reads"
   ]
 },

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

]

/projects/import

Required parameters

Alternatively, a url can be specified.

Responses

200: application/json

The name, id, description, owner, and data of the project

500: If an error occurs importing the project

/projects/export

Required parameters

Optional parameters

200 application/zip

A zip file containing the project content.

/projects/delete

Required parameters

Responses

200: application/json

The list of projects that were deleted

Samples

/samples

POST, PUT

Creates a sample.  Returns data for the specified sample.

GET

Returns data for the specified sample.

Required parameters

Optional parameters

Responses

200: application/json

The name, id, files, and attributes of the sample

400: Returned if the sample or project parameters are missing.

403: Returned if the user does not have permission to create samples in the project

404: Returned if there is no project with the given id or if a sample with the specified name can not be found

Example

http://example.com:8080/flow/api/v1/samples?project=My%20Project&sample=Sample1

{

 "name": "Sample1",
 "id": "0",
 "files": [

    "FastqFileDataType: 14138"

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

/samples/list

POST, GET

Required parameters

Responses

200: application/json

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

Data

/data

PUT

Uploads a file for analysis.

Supported files:  unaligned reads, alignments, detected variants.

Required parameters

filepath can be specified instead of filename/file if the data is already on the server.

Optional parameters

Responses

200: application/json

id The ID of the data node for the file’s content type.

400: Returned if the specified file is not of a recognized type.

403: Returned if the user does not have permission to create samples in the project

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

Library Files

/library_files

POST, PUT

Uploads and manages a library file

Required parameters

Optional parameters

Responses

200: application/json

The id of the imported library file

400: Returned if any required parameters are missing

GET

Required parameters

Responses

200: application/json

The id of the specified resource

400: Returned if any required parameters are missing

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

/library_files/list

Required parameters

Optional parameters

Responses

200: application/json

The description and id for each library file managed for the specified assembly.

400: Returned if the assembly parameter is missing.

Example

http://example.com:8080/flow/api/v1/library_files/list?assembly=hg19

[
 {
   "description": "Reference sequence",
   "id": 1
 },

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

]

Pipelines

/pipelines

POST, GET

Downloads a pipeline specification.

Required parameters

Responses

200: application/json

The pipeline definition.

400: Returned if the pipeline parameter is missing

403: Returned if the user does not have permission to view the pipeline.

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

/pipelines/list

POST, GET

Responses

200: application/json

The name, description, file, deletable status, creation date, and creator for each pipeline.

Example

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

[

 {
   "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

Required parameters

Optional parameters

Responses

200: application/json

A list of tasks and their required inputs.

403: Returned if the user does not have permission to view the pipeline.

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

Example

http://example.com:8080/flow/api/v1/pipelines/inputs?project=My%20Project&pipeline=My%20Pipeline

{

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

/pipelines/run

POST, GET

Runs the pipeline

Required parameters

Optional parameters

Responses

200: application/json

pipeline_queued:  [the list of queued task IDs]

If there are missing inputs then the list of required inputs will be returned.

400: Returned if a required parameter is missing.

403: Returned if the user does not have permission to run tasks on the specified data node.

404: Returned if the specified project, data, or pipeline can not be found.

500: Returned if there is an error queueing the pipeline

Example

http://example.com:8080/flow/api/v1/pipelines/run?project=My%20Project&pipeline=My%Project&inputs=1,2

pipeline_queued: 1805,1806

Queue

/queue

POST, GET

Downloads summary information about the queue

Optional parameters

Responses

200: application/json

running:  the number of tasks currently running commands

waiting:  the total number of tasks queued, but not running

waitingForDiskSpace:  tasks that won’t run until hard disk space is made available.  

waitingForProject:  tasks that can’t run because of the project limit

waitingForResources:  tasks that require more resources (such as memory) to run

waitingForUpstreamTask:  tasks for which the input is currently unavailable

permanentlyStalled:  tasks that are waitingForDiskSpace or for which there is no worker with sufficient capacity to run

hasPendingCommands:  true if there are commands which can run if more resources are made available

403: Returned if the user does not have permission to view the queue.

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

Example

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

{

 "running": 1,
 "waiting": 4,
 "waitingForDiskSpace": 0,
 "waitingForProject": 0,
 "waitingForResources": 3,
 "waitingForUpstreamTask": 1,
 "permanentlyStalled": 0,

 "hasPendingCommands":"true"

}

/queue/tasks

Downloads information about the queued tasks

Optional parameters

Responses

200: application/json

id, task, runStatus, progress, submitted, started, end

403: Returned if the user does not have permission to view the queue.

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

Example

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

Optional parameters

One of the following may be specified:

If neither is specified, then the user specified by the username parameter (or the logged-in user) will be used

Responses

200: application/json

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

400: Returned if the user_name or user_id parameter is specified, but does not identify a valid user.

GET

Returns information about a specified user

Optional parameters

One of the following may be specified:

if neither is specified, then the user specified by the username parameter (or the logged-in user) will be used

Responses

200: application/json

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

400: Returned if the user_name or user_id parameter is specified, but does not identify a valid user.

Example

http://example.com:8080/flow/api/v1/users?user_id=0

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

/users/list

GET

Returns information about all users on the system

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