With the Partek Flow REST API, you can create custom solutions to query or drive your server. Below are some common use cases for the REST API:
A complete reference for the API can be found on the REST API Command List or by visiting [server]/api/v1/servlets
The referenced Python library can be downloaded here.
An access token can be generated from the System information section of the settings page.
Alternatively, GetToken.py will generate a token:
you will be prompted to enter your password.
This token can be specified as the token parameter.
Flow organizes data by projects and they can be created and managed by the REST API.
To create a project:
The server will respond with JSON data describing the new project:
The new project will appear on the Flow homepage:
UploadSamples.py is a python script that can create samples within a project by uploading files:
This operation will generate a data node on the Analyses tab for the imported samples:
We can associate attributes with samples for use in visualizations and statistical analysis:
The sample attributes can be viewed and managed on the data tab:
A pipeline is a series of tasks used to process and analyze genomic data. You can read more about pipelines here
To run a pipeline, first we need to know its name.
We can get the name of a pipeline from the GUI or from the API:
Many pipelines also require that library files are specified.
You can get the list of required inputs for the pipeline from the API:
http://localhost:8080/flow/api/v1/pipelines/inputs?project_id=0&pipeline=AlignAndQuantify
This particular pipeline requires a bowtie index and an annotation model:
The request to launch the pipeline needs to specify one resource ID for each input.
These IDs can be found using the API:
Get the IDs for the library files that match the required inputs
The pipeline can be launched in any project using RunPython.py
This action will cause two tasks to start running:
Alternatively, UploadSamples.py can create the project, upload the samples and launch the pipeline in one step:
To add a collaborator to a project:
If you need additional assistance, please visit our support page to submit a help ticket or find phone numbers for regional support.
http://example.com:8080/flow/api/v1
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
since 7.0.180726
GET An up-to-date form of this documentation
since 7.0.18.0125
POST, PUT
Add or configure a project
since 7.0.17.0803
DELETE
Delete projects
since 7.0.17.0524
GET
Returns metadata about a project
since 9.0.20.504
GET, POST, PUT
Summarizes the number of input cells in single-cell experiments
since 7.0.19.0120
GET, POST, PUT
Creates a new project
since 7.0.18.0802
GET, POST, PUT
Get or set a project-specific error message
since 7.0.16.1101
GET, POST, PUT
Export a specified project to a .zip file
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
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
since 7.0.17.1101
GET, POST, PUT
Returns folders associated with projects
since 7.0.16.1101
GET, POST, PUT
Import a project from an exported .zip file
since 7.0.17.1101
GET, POST, PUT
Returns a list of projects available on the server
since 7.0.17.1101
GET, POST, PUT
Returns the output folders for projects
since 7.0.18.0529
GET, POST, PUT
List or configure project-specific properties
since 7.0.18.0902
GET, POST, PUT
Generates a tab-delimited report on tasks in a project
since 7.0.18.0910
GET, POST, PUT
Returns meta-data on resources associated with the project
since 7.0.17.1101
GET, POST, PUT
List samples associated with projects
since 7.0.18.0529
GET, POST, PUT
Search for projects
since 9.0.20.0612
GET, POST, PUT
Manages transferring project to remote servers
since 7.0.17.0921
POST, PUT
Import a set of attributes
since 7.0.17.0921
GET, POST, PUT
Add or query a sample
since 7.0.17.0915
GET, POST, PUT
Returns attributes associated with a sample
since 7.0.17.0921
GET, POST, PUT
Returns samples and attributes in a specified project
since 7.0.18.1212
GET, POST, PUT
Bulk rename samples
since 7.0.18.0110
GET, POST, PUT
Upload data to the server
since 7.0.18.0110
GET, POST, PUT
Returns attributes associated with a resource
since 7.0.18.0830
GET, POST, PUT
Returns the list of files associated with a resource
since 10.0.21.2111
GET, POST, PUT
Imports all files in a specified folder
since 7.0.17.0817
GET, POST, PUT
Returns unmanaged files in a given directory
since 7.0.18.0710
GET, POST, PUT
Repair links to data that has changed directories
since 7.0.19.0520
GET, POST, PUT
Recover disk space by deleting unnecessary files
since 7.0.18.1120
GET, POST, PUT
Exports a task result table
since 7.0.17.0817
GET, POST, PUT
Returns unmanaged files in a given directory
since 9.0.20.0617
GET, POST, PUT
Uploads data to the server and then imports the uploaded data
since 7.0.16.0826
GET, POST, PUT
Imports a library file
since 7.0.18.0207
GET, POST, PUT
Build a library file derived from an existing managed file
since 7.0.17.0921
GET, POST, PUT
Returns metadata (including file paths) for managed library files
since 7.0.17.0915
GET, POST, PUT
Returns metadata for managed library files
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
since 7.0.17.0915
GET, POST, PUT
Returns available library file types
since 7.0.17.0921
GET, POST, PUT
Download the specified pipeline specification
since 7.0.17.0921
GET, POST, PUT
List the inputs required by the specified pipeline
since 7.0.17.0921
GET, POST, PUT
Returns pipelines available on the server
since 7.0.17.0921
GET, POST, PUT
Run the specified pipeline
since 7.0.17.0921
GET, POST, PUT
Run the specified pipeline
since 7.0.17.0901
GET, POST, PUT
Returns summary statistics of the task queue
since 7.0.17.0901
GET, POST, PUT
Cancel tasks in progress
since 7.0.17.0901
GET, POST, PUT
Returns information about queued commands
since 7.0.17.0901
GET, POST, PUT
Returns the count of downloads in progress
since 10.0.22.0322
GET, POST, PUT
Check the queue status or request it start or stop handling commands
since 7.0.17.0901
GET, POST, PUT
Returns information about tasks in the queue
since 7.0.17.0901
POST, PUT
Add or configure users
since 7.0.17.0901
GET
Returns information about a user
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
since 7.0.17.0901
GET, POST, PUT
Returns a list of known users
since 7.0.18.0102
GET, POST, PUT
Returns a list of logged in users and their last activity
since 9.0.20.1222
GET, POST, PUT
End the session of the specified user
since 7.0.18.0912
GET, POST, PUT
Get and set user preferences
since 9.0.20.0625
GET, POST, PUT
Lists system preferences which can be set
since 7.0.18.0323
GET, POST, PUT
Returns a list of roles assigned to users
since 7.0.17.1011
POST, PUT
Configures the specified user to no longer use a private directory, instead reverting to the server defaults
since 7.0.18.0710
GET, POST, PUT
Apply roles to users
since 7.0.18.0710
DELETE
Remove roles from users
since 7.0.18.0710
GET, POST, PUT
Returns a list of roles available on the server
since 7.0.18.0710
GET, POST, PUT
Returns a list of privileges available on the server
since 7.0.18.0213
GET, POST, PUT
Get or set enforcement of directory permissions
since 7.0.18.0213
GET, POST, PUT
Add permission to access a directory to a specified user
since 7.0.18.0213
GET, POST, PUT
Remove permission to access a directory from a specified user
since 7.0.17.0207
GET, POST, PUT
Returns information about tasks that have run on the server
since 7.0.18.0207
DELETE, GET, POST
Deletes tasks
since 9.0.20.1002
GET, POST, PUT
Returns task input values
since 7.0.18.0920
GET, POST, PUT
Returns a list of available tasks and their license requirements
since 7.0.18.0930
GET, POST, PUT
Returns task logs
since 7.0.18.1120
GET, POST, PUT
Returns task output resource IDs and descriptions
since 10.0.21.0525
GET, POST, PUT
Returns a list of task test specifications
since 7.0.18.1130
GET, POST, PUT
Generates a report on recent tasks
since 7.0.18.0207
GET, POST, PUT
Returns a list of task test specifications
since 7.0.18.0207
GET, POST, PUT
Upload feature filters
since 7.0.17.0901
GET, POST, PUT
Returns information about commands that have run on the server
since 7.0.17.0901
GET, POST, PUT
Returns a description of commands that have run on the server
since 7.0.17.0901
GET, POST, PUT
Returns information about command fits
since 7.0.17.0901
GET, POST, PUT
Returns the memory used by commands
since 7.0.18.1124
GET, POST, PUT
Returns a summary report on pending commands
since 7.0.17.0901
GET, POST, PUT
Returns the predicted utilization of commands
since 7.0.18.0902
GET, POST, PUT
Generates a tab-delimited report on commands in a task
since 7.0.17.0314
GET, POST, PUT
Returns information about license available on the server
since 7.0.17.0901
GET, POST, PUT
Returns a load summary of all connected workers
since 7.0.17.0901
GET, POST, PUT
Returns the number of connected workers
since 7.0.17.0901
GET, POST, PUT
Returns a load summary of the internal worker, if it is enabled
since 7.0.17.0901
GET, POST, PUT
Returns a summary of the load of remote workers
since 10.21.0723
GET, POST, PUT
Shuts down workers
since 10.21.0723
GET, POST, PUT
Starts the internal worker
since 18.0930
GET, POST, PUT
Get and set information about workers that have been submitted to a cluster, but may not yet have connected
since 7.0.17.0227
GET, POST, PUT
System configuration options
since 10.0.21.0709
GET, POST, PUT
Dumps contents of heap
since 10.0.23.0322
GET, POST, PUT
Configure execution of immediate commands, that support the front-end
since 7.0.18.1020
GET, POST, PUT
Generate an access token for the requesting user
since 7.0.18.0228
POST, PUT
Import a set of server preferences from a json specification
since 7.0.17.1024
GET, POST, PUT
Configure log levels
since 10.0.23.0203
GET, POST, PUT
Download system logs
since 10.0.23.0301
GET, POST, PUT
Query or override package paths
since 7.0.18.0130
DELETE
Delete preferences, reverting the values to default
since 7.0.18.0130
GET, POST, PUT
Get and set system preferences
since 9.0.20.0625
GET, POST, PUT
Lists system preferences which can be set
since 7.0.18.0130
GET, POST, PUT
Returns a list of preference node names
since 7.0.18.1020
GET, POST, PUT
Revoke API access tokens
since 8.0.23.0419
GET, POST, PUT
Return a stack trace of current activity
since 8.0.20.0130
GET, POST, PUT
Report on recent system activity
since 18.07.0930
GET, POST, PUT
Manage access tokens
since 7.0.18.1020
GET, POST, PUT
Lists all managed tokens (Requires View user accounts privilege)
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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format
string
markup: confluence markup
json
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
project_id or project
integer or string
A project specification
delete_files
String
Delete files from this project. valid values: all or output
project
String
The name of the new project
new_folder
String
Creates a new unique subfolder for this project
project_id or project
integer or string
A project specification
message
String
ggvG
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
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
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
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
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
key
String
The name of the property
value
String
The value of the property
project_id or project
integer or string
A project specification
project_id or project
integer or string
A project specification
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
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
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
project_id or project
integer or string
A project specification
sample_id or sample_name
integer or string
A sample specification
project_id or project
integer or string
A project specification
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
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.
resource_id
integer
A resource ID
resource_id
integer
A resource ID
folder
String
path to the data on the server
project
String
Project to import to
Creates a project based on the folder name
directory
String
former
String
Old path to the data
current
String
New path to the data
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
directory
String
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
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
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
genome_build
String
database
String
pipeline
String
The name of the 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
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
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
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
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
op
String
Operation start#
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
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
user_id or user_name
integer or string
A user specification.
If this is not specified, the user making the request will be used
user_id or user_name
integer or string
A user specification.
The user to logoff. If this is not specified, the user making the request will be used
key
String
The name of the preference
value
String
The value of the preference
user_id or user_name
integer or string
A user specification.
If this is not specified, the user making the request will be used
file
binary
A json file which contains a list of RolePrivileges (as returned by roles/list
role
integer
the ID of the role to remove
enforce
boolean
directory
String
user_id or user_name or group_id or group_name
integer or string or integer or string
A member specification
If a user or group is not specified, this action will apply to all users
directory
String
user_id or user_name or group_id or group_name
integer or string or integer or string
A member specification
If a user or group is not specified, this action will apply to all users
project_id or project
integer or string
A project specification
id
integer
A single task ID
user_name or user_id
string or integer
The username or ID of a user that has run tasks
status
String
A task status: Pending, Waiting, Running, Done, Canceled, Failed
task
String
A sub-string of the task name & version as it appears in the Task entry on the task details page
project_id
integer
id
integer
keep_output
boolean
false
task_type
String
slots
String
A comma-delimited list of input slots to query
project_id or project
integer or string
A project specification
id
integer
A single task ID
user_name or user_id
string or integer
The username or ID of a user that has run tasks
status
String
A task status: Pending, Waiting, Running, Done, Canceled, Failed
task
String
A sub-string of the task name & version as it appears in the Task entry on the task details page
recent
boolean
Set to false to report on all tasks
true
filepath or filter
String
filepath: a file on the server with filter content or filter: the filter content in json format
task
integer
Filter commands to those belonging to the specified task ID
worker_identifier
integer
Filter commands to those run on the specified worker
successful
boolean
Filter commands based on whether they successfully completed
command_line
String
Filter commands based on their command-line representation
id
String
A specific command identifier
task
integer
Filter results based on a task ID
command
String
Filter results based on the command
conservative
boolean
Include/exclude results based on whether they are flagged as conservative
id
String
A specific command identifier
task
integer
Filter results based on a task ID
command
String
Filter results based on the command
conservative
boolean
Include/exclude results based on whether they are flagged as conservative
id
String
A specific command identifier
task
integer
Filter results based on a task ID
command
String
Filter results based on the command
conservative
boolean
Include/exclude results based on whether they are flagged as conservative
description
String
CommandDescription in json format
feature
String
Filters results based on feature name
internal
boolean
Shut down the internal worker
true
external
boolean
Shut down all external workers
true
id
integer
Shut down only the worker matching this identifier
submitted_workers
integer
max_memory_mb
integer
page_load_log_threshold
integer
If specified and greater than 0 a warning will be written to logs/page_load.log whenever a page-load takes longer than this value (in seconds)
reload_import_config
boolean
Reload the partek_db/import.config file
reload_help_config
boolean
Reload the partek_db/help.config file
update_command_resources
boolean
Download and update command resource estimates
reload_feature_lists
boolean
Reload the feature lists for the user
file
String
Path to write the hprof heap dump
synchronous_threadpool
integer
Number of threads to use for the synchronous executor
dispatch_method
String
An optional method for dispatching commands that must run immediately
user_id or user_name
integer or string
A user specification.
If this is not specified, the user making the request will be used
expiration
String
never for no expiration, otherwise: d-M-yyyy h:mm a
duration
integer
duration of the token, in hours
logger
String
The name of a logger or "commands" to configure multiple command-related logs.
log_level
String
Sets the level of the specified logger: ALL, TRACE, DEBUG, INFO, WARN, ERROR, OFF
get
String
Return current path to package
package
String
Set the path of the specified package
node
String
Required unless deleting from the root node
key
String
The ID of the preference to delete
node
String
The node name
key
String
The preference name
value
String
The preference value
api_key
String
An API token to revoke. "mine" to revoke the requestors tokens, "all" to revoke all managed tokens (requires Change user accounts privilege)
all_threads
boolean
Show all threads (rather than just those with partek in the class name)
false
heap_dump
boolean
Write heap dump to the logs
false
io
boolean
Measure the time to write & read a file from mount points
false
gc
boolean
Request System.gc before reporting memory usage
true
log
boolean
Include the last section of content from various log files
true
tasks
boolean
Include the section on running / pending tasks
true
top
boolean
Write the output of top to the output
false
cpu_load_threshold
integer
Print a warning if the system load average exceeds this value
mem_load_threshold
integer
Print a warning if the percent of heap used exceeds this value
api_key
String
The token to configure
Return a list of all tokens managed for the requestor
expiration
String
never for no expiration, otherwise: d-M-yyyy h:mm a
