REST API Command List
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
Servlets
/servlets
since 7.0.180726
GET An up-to-date form of this documentation
format
string
markup: confluence markup
json
Projects
/projects
since 7.0.18.0125
POST, PUT
Add or configure a project
project_id or project or new_project
integer or string or string
A project specification
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).
my_output_folder
string
Sets the project output folder for the user making the request
output_folder
string
Sets the project output folder for all collaborators the user making the request has permission to affect
/projects
since 7.0.17.0803
DELETE
Delete projects
project_id or project
integer or string
A project specification
delete_files
String
Delete files from this project. valid values: all or output
/projects
since 7.0.17.0524
GET
Returns metadata about a project
/projects/cells
since 9.0.20.504
GET, POST, PUT
Summarizes the number of input cells in single-cell experiments
/projects/create
since 7.0.19.0120
GET, POST, PUT
Creates a new project
project
String
The name of the new project
new_folder
String
Creates a new unique subfolder for this project
/projects/error
since 7.0.18.0802
GET, POST, PUT
Get or set a project-specific error message
project_id or project
integer or string
A project specification
message
String
ggvG
/projects/export
since 7.0.16.1101
GET, POST, PUT
Export a specified project to a .zip file
project_ids
comma-delimited integers
A specification for one or more projects
includeLibraryFiles
boolean
If true then library files will be included
false
toProject
boolean
If true then rather than downloading a zip file, a new project will be created on the server
task
integer
Export project with this task as the root node
includeDownstream
boolean
If true then tasks downstream of the specified will be included
false
outputFolder
String
A path on the server to write the exported projects to.
Stream the project(s) to the requestor
/projects/file_entries
since 8.0.19.0701
GET, POST, PUT
Returns files associated with projects. Matches the files that can be deleted when the project is deleted
/projects/files
since 7.0.17.1101
GET, POST, PUT
Returns files associated with projects. Matches files used in the calculation of size shown on the homepage
/projects/folders
since 7.0.17.1101
GET, POST, PUT
Returns folders associated with projects
project_ids
string
Retrieve specific projects. IDs joined by ,
project_id
integer
Retrieve a single project by ID
project
string
Retrieve a single project by name
sample
string
List projects that contain a sample with the specified name
file_name
string
List projects that contain a file matching the specified sub-string
user_id
integer
List projects for which the specified user is a member
user_name
string
List projects for which the specified user is a member
/projects/import
since 7.0.16.1101
GET, POST, PUT
Import a project from an exported .zip file
url or filepath or file
string or string or binary
The location of a project zip: on a remote server or on the specified server or in the stream
owner_id or owner_name
integer or string
This user will be the owner of the imported project
By default, the user making the API request will be the owner
/projects/list
since 7.0.17.1101
GET, POST, PUT
Returns a list of projects available on the server
project_ids
string
Retrieve specific projects. IDs joined by ,
project_id
integer
Retrieve a single project by ID
project
string
Retrieve a single project by name
sample
string
List projects that contain a sample with the specified name
file_name
string
List projects that contain a file matching the specified sub-string
user_id
integer
List projects for which the specified user is a member
user_name
string
List projects for which the specified user is a member
/projects/output_folders
since 7.0.17.1101
GET, POST, PUT
Returns the output folders for projects
project_ids
string
Retrieve specific projects. IDs joined by ,
project_id
integer
Retrieve a single project by ID
project
string
Retrieve a single project by name
sample
string
List projects that contain a sample with the specified name
file_name
string
List projects that contain a file matching the specified sub-string
user_id
integer
List projects for which the specified user is a member
user_name
string
List projects for which the specified user is a member
/projects/properties
since 7.0.18.0529
GET, POST, PUT
List or configure project-specific properties
key
String
The name of the property
value
String
The value of the property
/projects/report
since 7.0.18.0902
GET, POST, PUT
Generates a tab-delimited report on tasks in a project
project_id or project
integer or string
A project specification
/projects/resources
since 7.0.18.0910
GET, POST, PUT
Returns meta-data on resources associated with the project
project_id or project
integer or string
A project specification
/projects/samples
since 7.0.17.1101
GET, POST, PUT
List samples associated with projects
project_ids
string
Retrieve specific projects. IDs joined by ,
project_id
integer
Retrieve a single project by ID
project
string
Retrieve a single project by name
sample
string
List projects that contain a sample with the specified name
file_name
string
List projects that contain a file matching the specified sub-string
user_id
integer
List projects for which the specified user is a member
user_name
string
List projects for which the specified user is a member
/projects/search
since 7.0.18.0529
GET, POST, PUT
Search for projects
exact
boolean
If true, the search term must match exactly, otherwise sub-string matches are allowed
false
category
String
Search for categories applied to samples
/projects/transfer
since 9.0.20.0612
GET, POST, PUT
Manages transferring project to remote servers
Samples
/samples
since 7.0.17.0921
POST, PUT
Import a set of attributes
attribute_json
String
A set of attributes in the same format as returned by /samples/attributes
attribute_txt
String
A set of attributes in a tab-delimited file
force
boolean
false
Attribute files with more than 10,000 samples are assumed to be for single cell data, specify force=true to override this
sample_id or sample_name
integer or string
A sample specification
/samples
since 7.0.17.0921
GET, POST, PUT
Add or query a sample
project_id or project
integer or string
A project specification
sample_id or sample_name
integer or string
A sample specification
/samples/attributes
since 7.0.17.0915
GET, POST, PUT
Returns attributes associated with a sample
/samples/list
since 7.0.17.0921
GET, POST, PUT
Returns samples and attributes in a specified project
project_id or project
integer or string
A project specification
/samples/rename
since 7.0.18.1212
GET, POST, PUT
Bulk rename samples
project_id or project
integer or string
A project specification
remove
String
Remove this substring from each sample name
trim_left
integer
Remove this many characters from the beginning of the sample name
trim_right
integer
Remove this many characters from the end of the sample name
Data
/data
since 7.0.18.0110
GET, POST, PUT
Upload data to the server
project_id or project or new_project
integer or string or string
A project specification
filepath and/or filepath1 and/or filepath2
String
The location of the file on the server. Up to three files can by imported at once.
count_matrix
String
The location of a count matrix file on the server.
sample_id or sample or new_sample
integer string string
The id or name of the sample to add data to. If new_sample is specified and the sample already exists characters will be added to disambiguate the new sample
owner or owner_id
string integer
The username or ID of the user that should be the owner of the data (and the project if it is created by this call).
The owner will be the user account that uploads the data
duplicate_handling
String
For a count matrix, how to handle any duplicated features: Mean, Maximmum, Sum
Mean
sample
String
The name of the sample to associate this data with
The filename
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.
/data/attributes
since 7.0.18.0110
GET, POST, PUT
Returns attributes associated with a resource
resource_id
integer
A resource ID
/data/files
since 7.0.18.0830
GET, POST, PUT
Returns the list of files associated with a resource
resource_id
integer
A resource ID
/data/import_folder
since 10.0.21.2111
GET, POST, PUT
Imports all files in a specified folder
folder
String
path to the data on the server
project
String
Project to import to
Creates a project based on the folder name
/data/managed
since 7.0.17.0817
GET, POST, PUT
Returns unmanaged files in a given directory
directory
String
/data/reassign
since 7.0.18.0710
GET, POST, PUT
Repair links to data that has changed directories
former
String
Old path to the data
current
String
New path to the data
/data/recover
since 7.0.19.0520
GET, POST, PUT
Recover disk space by deleting unnecessary files
/data/table
since 7.0.18.1120
GET, POST, PUT
Exports a task result table
task_id
integer
The ID of the task that produced the table
table
String
The table to download, if ambiguous for the task. QuantificationSummary, TranscriptQuantificationSummary, GeneQuantificationSummary, transcript_feature_distribution, gene_feature_distribution
QuantificationSummary
/data/unmanaged
since 7.0.17.0817
GET, POST, PUT
Returns unmanaged files in a given directory
directory
String
/data/upload
since 9.0.20.0617
GET, POST, PUT
Uploads data to the server and then imports the uploaded data
project_id or project or new_project
integer or string or string
A project specification
owner or owner_id
string integer
The username or ID of the user that should be the owner of the data (and the project if it is created by this call).
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.
Data download directory configured on the System preferences page
*
string
1 or more files to receive and import
Library files
/library_files
since 7.0.16.0826
GET, POST, PUT
Imports a library file
file or filepath
binary or string
The file content or the path of the file on the server
file_type
String
The type of library file. The list of available library file types is returned by /library_files/types
assembly
String
The assembly of the library file
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
/library_files/build
since 7.0.18.0207
GET, POST, PUT
Build a library file derived from an existing managed file
/library_files/files
since 7.0.17.0921
GET, POST, PUT
Returns metadata (including file paths) for managed library files
/library_files/list
since 7.0.17.0915
GET, POST, PUT
Returns metadata for managed library files
file_type
String
Filters results based on file type
annotation_model
String
Filters results based on annotation model
descriptions
String
Filters results based on the description
id
String
Return a result for a specific library file
/library_files/snp_eff
since 7.0.18.0619
GET, POST, PUT
Loads a manually downloaded SnpEff database. A SnpEff bin file must be present on the server under library files assembly/database/SnpEff database/database
genome_build
String
database
String
/library_files/types
since 7.0.17.0915
GET, POST, PUT
Returns available library file types
Pipelines
/pipelines
since 7.0.17.0921
GET, POST, PUT
Download the specified pipeline specification
pipeline
String
The name of the pipeline
/pipelines/inputs
since 7.0.17.0921
GET, POST, PUT
List the inputs required by the specified pipeline
pipeline
String
The name of the pipeline
project_id or project
integer or string
A project specification
data
String
The data node that the pipeline will run on, as returned by the /projects interface.
Unaligned reads
/pipelines/list
since 7.0.17.0921
GET, POST, PUT
Returns pipelines available on the server
/pipelines/ready
since 7.0.17.0921
GET, POST, PUT
Run the specified pipeline
pipeline
String
The name of the pipeline
project_id or project
integer or string
A project specification
data
String
The data node that the pipeline will run on, as returned by the /projects interface.
Unaligned reads
/pipelines/run
since 7.0.17.0921
GET, POST, PUT
Run the specified pipeline
pipeline
String
The name of the pipeline
project_id or project
integer or string
A project specification
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.
data
String
The data node that the pipeline will run on, as returned by the /projects interface.
Unaligned reads
Queue
/queue
since 7.0.17.0901
GET, POST, PUT
Returns summary statistics of the task queue
project or project_name or project_filter
String
Only return tasks in this project
project_id
integer
Only return tasks in this project
user_name or user_filter
String
Only return tasks run by this user
user_id
integer
Only return tasks run by this user
status
String
Only return tasks matching this status
/queue/cancel
since 7.0.17.0901
GET, POST, PUT
Cancel tasks in progress
project or project_name or project_filter
String
Only return tasks in this project
project_id
integer
Only return tasks in this project
user_name or user_filter
String
Only return tasks run by this user
user_id
integer
Only return tasks run by this user
status
String
Only return tasks matching this status
/queue/commands
since 7.0.17.0901
GET, POST, PUT
Returns information about queued commands
/queue/downloads
since 7.0.17.0901
GET, POST, PUT
Returns the count of downloads in progress
/queue/status
since 10.0.22.0322
GET, POST, PUT
Check the queue status or request it start or stop handling commands
op
String
Operation start#
/queue/tasks
since 7.0.17.0901
GET, POST, PUT
Returns information about tasks in the queue
project or project_name or project_filter
String
Only return tasks in this project
project_id
integer
Only return tasks in this project
user_name or user_filter
String
Only return tasks run by this user
user_id
integer
Only return tasks run by this user
status
String
Only return tasks matching this status
Users
/users
since 7.0.17.0901
POST, PUT
Add or configure users
user_id or user_name
integer or string
A user specification. If user_name is specified the account will be created if it does not already exist
If this is not specified, the configuration will apply to the user making the request
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.
display_name
String
The name that other users will see.
enabled
boolean
Whether the user is able to log in
add_role_name or add_role_id
string or integer
Add the user to the specified role
remove_role_name or remove_role_id
string or integer
Remove the user from the specified role
private_directory
String
If present, the directory will be created and the user will be given permission to use it.
add_directory
String
Add permission for the user to browse files in this directory.
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_precision
integer
How many digits to show after the decimal point for numeric values in tables
/users
since 7.0.17.0901
GET
Returns information about a user
user_id or user_name
integer or string
A user specification.
If this is not specified, the user making the request will be used
/users/files
since 8.0.19.0701
GET, POST, PUT
List files used by a specified user. Matches files used in the calculation of disk usage as reported on the Users settings page
/users/list
since 7.0.17.0901
GET, POST, PUT
Returns a list of known users