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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).

...

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": [

...

],
"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

...

Partek Flow Documentation

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Versions Compared

Old Version 2

New Version 3

Key

Samples

/samples

/samples/list

Data

/data

Library Files

/library_files

/library_files/list

Pipelines

/pipelines

/pipelines/list

/pipelines/input

/pipelines/run