REST API for Partek Flow

Structure of the URI

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

Authentication

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

The password should be encrypted 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

Parameter	Type	Description
project	string	The name of the project.

Optional parameters

Parameter	Type	Description
owner	string	Sets the project owner
name	string	Sets the project name
description	string	Sets the project description
collaborator	string	If this parameter is specified, then “role” must also be specified. If the role parameter is “remove” then the specified collaborator is removed from the project, otherwise role must be a valid project role (Collaborator or Viewer).

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

Parameter	Type	Description
filename	string	The name of the file being uploaded.
file	string	The file content

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

Parameter	Type	Description
projectIds	string	Project IDs separated by “,”

Optional parameters

Parameter	Type	Description
includeLibraryFiles	boolean	If true, library files will be included in the project zip. Default: false

Responses

200 application/zip

A zip file containing the project content.

/projects/delete

Required parameters

Parameter	Type	Description
projectIds	string	Project IDs separated by “,”

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

Parameter	Type	Description
sample	string	The name of the sample.
project	string	The name of the sample’s project.

Optional parameters

Parameter	Type	Description
vocabulary	string	If both vocabulary and term are specified, then the specified term is applied to the sample
term	string

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

Parameter	Type	Description
project	string	The name of the project.

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

Parameter	Type	Description
filename	string	The name of the file being uploaded.
file	binary	The file content.
project	string	The id of the project to add the sample to.

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

Optional parameters

Parameter	Type	Description
sample	integer	The id of the sample to add file to. Without this parameter a new sample will be created.
owner	string	The username of the user that should be the owner of the data. The data will count against this user’s quota, if one is configured. By default, the owner will be the user account that uploads the data.
upload_folder	string	If the file is uploaded through the servlet it will be put in this directory, if the owner has permission to access it.

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

Parameter	Type	Description
file	binary	The file content.
file_type	string	The type of library file: reference_genome
assembly	string	The assembly of the library file

Optional parameters

Parameter	Type	Description
species	string	The species of the library file. This is looked up based on the assembly, and the assembly is used as the species if the assembly is not associated with any species.

Responses

200 application/json

The id of the imported library file

400

Returned if any required parameters are missing

GET

Required parameters

Parameter	Type	Description
file_type	string	The type of library file: reference_genome
assembly	string	The assembly of the library file

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

Parameter	Type	Description
assembly	string	The assembly.

Optional parameters

Parameter	Type	Description
description	string	Filter the library file list to those that match this description.

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

Parameter	Type	Description
pipeline	string	The name of the pipeline

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

Parameter	Type	Description
pipeline	string	The name of the pipeline
project	string	The project that the pipeline will run in

Optional parameters

Parameter	Type	Default	Description
data	string	Unaligned reads	The data node that the pipeline will run on, as returned by the /projects interface.

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

Parameter	Type	Description
pipeline	string	The name of the pipeline to run.
project	string	The name of the project to run the pipeline in
inputs	integers	The ids of the resources, in the order returned by the /pipeline/inputs interface. The ids of library files are returned by the /library_files interface.

Optional parameters

Parameter	Type	Default	Description
data	string	Unaligned reads	The data node to run the pipeline on, as returned by the /projects interface.

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

Parameter	Type	Description
project_filter	string	Only return tasks in this project
user_filter	string	Only return tasks run by this user

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

Parameter	Type	Description
project_filter	string	Only return tasks in this project
user_filter	string	Only return tasks run by this user

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:

Parameter	Type	Description
user_name	string	The username of the user. If the user does not exist it will be created.
user_id	integer	The ID of the user

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

Parameter	Type	Description
distinguished_name	string	When creating a new user, this parameter specifies the LDAP distinguished name.
user_password	string	When creating a new user, this parameter specifies their initial Flow password. If this parameter is absent and this is not an LDAP user then the user will receive an email with a link to set their initial password.
email	string	The user’s email address. When creating a new user, this parameter is required.
display_name	string	The name that other users will see
enabled	boolean	Whether the user is able to log in.
admin	boolean	Whether the user has the admin role. The system requires at least one admin account.
private_directory	string	If present, the directory will be created and the user will be given permission to use it.
quota	integer	The size of the user’s quota (in gigabytes) or “none” to remove any quota
notify_when_tasks_finish	boolean	Whether the user will receive an email when a task they have queued completes
notify_when_added_to_project	boolean	Whether the user will receive an email when they are added as a collaborator or viewer to a project
decimal_precison	integer	How many digits to show after the decimal point for numeric values in tables

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:

Parameter	Type	Description
user_name	string	The username of the user
user_id	integer	The ID of the user

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

Additional Assistance

If you need additional assistance, please visit our support page to submit a help ticket or find phone numbers for regional support.

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Structure of the URI

Authentication

Projects

/projects

/projects/list

/projects/import

/projects/export

/projects/delete

Samples

Additional Assistance