Page History
...
An up-to-date form of this documentation
| Parameter | Type | Description | Default |
|---|---|---|---|
| format | string | markup: confluence markup | json |
Projects
/projects
since 7.0.18.0125
POST, PUT, POST
Add or configure a project
Parameter | Type | Description |
|---|---|---|
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 |
...
Parameter | Type | Description |
|---|---|---|
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
...
Returns metadata about a project
/projects/cells
since 9.0.20.504
POST, PUT, GET
Summarizes the number of input cells in single-cell experiments
/projects/create
since 7.0.19.0120
POST, PUT, GET
Creates a new project
Parameter | Type | Description |
|---|---|---|
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
POST, PUT, GET, POST
Get or set a project-specific error message
Parameter | Type | Description | |
|---|---|---|---|
project_id or project | integer or string | A project specification | |
message | String |
|
/projects/export
since 7.0.16.1101
POST, PUT, GET, POST
Export a specified project to a .zip file
Parameter | Type | Description | Default | |
|---|---|---|---|---|
project_ids | comma-delimited integers | A specification for one or more projects |
| |
includeLibraryFiles | boolean | If equal to true then library files will be included |
| |
toProject | boolean | If true then rather than downloading a zip file, a new project will be created on the server | ||
task | integer | Export this task and any downstream tasks | ||
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
POST, PUT, GET
Returns files associated with projects. Matches the files that can be deleted when the project is deleted
/projects/files
since 7.0.17.1101
POST, PUT, GET, POST
Returns files associated with projects. Matches files used in the calculation of size shown on the homepage
/projects/folders
since 7.0.17.1101
POST, PUT, GET, POST
Returns folders associated with projects
...
/projects/import
since 7.0.16.1101
POST, PUT, GET, POST
Import a project from an exported .zip file
Parameter | Type | Description | Default | |
|---|---|---|---|---|
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
POST, PUT, GET, POST
Returns a list of projects available on the server
...
/projects/output_folders
since 7.0.17.1101
POST, PUT, GET, POST
Returns the output folders for projects
...
/projects/properties
since 7.0.18.0529
POST, PUT, GET, POST
List or configure project-specific properties
...
/projects/report
since 7.0.18.0902
POST, PUT, GET, POST
Generates a tab-delimited report on tasks in a project
...
/projects/resources
since 7.0.18.0910
POST, PUT, GET, POST
Returns meta-data on resources associated with the project
...
/projects/samples
since 7.0.17.1101
POST, PUT, GET, POST
List samples associated with projects
...
/projects/search
since 7.0.18.0529
POST, PUT, GET, POST
Search for projects
Parameter | Type | Description | Default |
|---|---|---|---|
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 | String | Search by attribute name | |
sample | String | Search by sample name |
/projects/
...
transfer
since 7 9.0.1820.08190612
POST, PUT, GET, POST
Get or set project statuses
Parameter | Type | Description |
|---|---|---|
project_id | integer |
|
importing | String |
|
Manages transferring project to remote servers
Samples
/samples
since 7.0.17.0921
POST, PUT, POST
Import a set of attributes
Parameter | Type | Description | Default | |
|---|---|---|---|---|
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 | ||
(attribute or numeric_attribute) and value | String |
|
/samples
since 7.0.17.0921
POST, PUT, GET, POST
Add or query a sample
Parameter | Type | Description |
|---|---|---|
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
POST, PUT, GET, POST
Returns attributes associated with a sample
/samples/list
since 7.0.17.0921
POST, PUT, GET, POST
Returns samples and attributes in a specified project
Parameter | Type | Description |
|---|---|---|
project_id or project | integer or string | A project specification |
/samples/rename
since 7.0.18.1212
POST, PUT, GET
Bulk rename samples
Parameter | Type | Description |
|---|---|---|
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
POST, PUT, GET, POST
Upload data to the server
Parameter | Type | Description | Default | |
|---|---|---|---|---|
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 . The data will count against this user’s quota, if one is configured(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
POST, PUT, GET, POST
Returns attributes associated with a resource
...
/data/files
since 7.0.18.0830
POST, PUT, GET, POST
Returns the list of files associated with a resource
...
/data/managed
since 7.0.17.0817
POST, PUT, GET, POST
Returns unmanaged files in a given directory
Parameter | Type | Description | |
|---|---|---|---|
directory | String |
|
/data/reassign
since 7.0.18.0710
POST, PUT, GET, POST
Repair links to data that has changed directories
Parameter | Type | Description |
|---|---|---|
former | String | Old path to the data |
current | String | New path to the data |
/data/recover
since 7.0.19.0520
POST, PUT, GET
Recover disk space by deleting unnecessary files
/data/table
since 7.0.18.1120
POST, PUT, GET, POST
Exports a task result table
Parameter | Type | Description | Default | |
|---|---|---|---|---|
task_id | integer | The ID of the task that produced the table |
| |
table | String | The table to download, if ambiguous for the task. | QuantificationSummary |
/data/unmanaged
since 7.0.17.0817
POST, PUT, GET, POST
Returns unmanaged files in a given directory
Parameter | Type | Description | |
|---|---|---|---|
directory | String |
|
/data/upload
since 9.0.20.0617
POST, PUT, GET
Uploads data to the server and then imports the uploaded data
Parameter | Type | Description | Default |
|---|---|---|---|
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
POST, PUT, GET, POST
Imports a library file
Parameter | Type | Description |
|---|---|---|
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
POST, PUT, GET, POST
Build a library file derived from an existing managed file
/library_files/files
since 7.0.17.0921
POST, PUT, GET, POST
Returns metadata (including file paths) for managed library files
/library_files/list
since 7.0.17.0915
POST, PUT, GET, POST
Returns metadata for managed library files
...
/library_files/snp_eff
since 7.0.18.0619
POST, PUT, GET, POST
Loads a manually downloaded SnpEff database. A SnpEff bin file must be present on the server under library files assembly/database/SnpEff database/database
Parameter | Type | Description | |
|---|---|---|---|
genome_build | String |
| |
database | String |
|
/library_files/types
since 7.0.17.0915
POST, PUT, GET, POST
Returns available library file types
...
/pipelines
since 7.0.17.0921
POST, PUT, GET, POST
Download the specified pipeline specification
...
/pipelines/inputs
since 7.0.17.0921
POST, PUT, GET, POST
List the inputs required by the specified pipeline
Parameter | Type | Description | Default | |
|---|---|---|---|---|
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
POST, PUT, GET, POST
Returns pipelines available on the server
/pipelines/
...
ready
since 7.0.17.0921
POST, PUT, GET
Run the specified pipeline
Parameter | Type | Description | Default |
|---|---|---|---|
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
POST, PUT, GET
Run the specified pipeline
Parameter | Type | Description | Default | |
|---|---|---|---|---|
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
POST, PUT, GET, POST
Returns summary statistics of the task queue
...
/queue/cancel
since 7.0.17.0901
POST, PUT, POST
Cancel tasks in progress
Parameter | Type | Description |
|---|---|---|
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
POST, PUT, GET, POST
Returns information about queued commands
/queue/downloads
since 7.0.17.0901
POST, PUT, GET, POST
Returns the count of downloads in progress
/queue/tasks
since 7.0.17.0901
POST, PUT, GET, POST
Returns information about tasks in the queue
...
Users
/users
since 7.0.17.0901
POST, PUT, POST
Add or configure users
Parameter | Type | Description | Default | |
|---|---|---|---|---|
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. |
| |
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 |
| |
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
...
Parameter | Type | Description | Default |
|---|---|---|---|
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
POST, PUT, GET
List files used by a specified user. Matches files used in the calculation of disk usage as reported on the user management page
/users/list
since 7.0.17.0901
POST, PUT, GET, POST
Returns a list of known users
/users/logins
since 7.0.18.0102
POST, PUT, GET, POST
Returns a list of logged in users and their last activity
/users/preferences
since 7.0.18.0912
POST, PUT, GET, POST
Get and set user preferences
Parameter | Type | Description |
|---|---|---|
key | String | The name of the preference |
value | String | The value of the preference |
/users/preferences/list
since 9.0.20.0625
POST, PUT, GET
Lists system preferences which can be set
/users/roles
since 7.0.18.0323
POST, PUT, GET, POST
Returns a list of roles assigned to users
/users/unset_private_directory
since 7.0.17.1011
POST, PUT, POST
Configures the specified user to no longer use a private directory, instead reverting to the server defaults
...
Roles
/roles
since 7.0.18.0710
POST, PUT, GET, POST
Apply roles to users
Parameter | Type | Description |
|---|---|---|
file | binary | A json file which contains a list of RolePrivileges (as returned by roles/list |
/roles
since 7.0.18.0710
DELETE
Remove roles from users
Parameter | Type | Description |
|---|---|---|
role | integer | the ID of the role to remove |
/roles/list
since 7.0.18.0710
POST, PUT, GET, POST
Returns a list of roles available on the server
/roles/privileges
since 7.0.18.0710
POST, PUT, GET, POST
Returns a list of privileges available on the server
...
/permission
since 7.0.18.0213
POST, PUT, GET, POST
Get or set enforcement of directory permissions
Parameter | Type | Description | |
|---|---|---|---|
enforce | boolean |
|
/permission/add_directory
since 7.0.18.0213
POST, PUT, GET, POST
Add permission to access a directory to a specified user
Parameter | Type | Description | Default | ||
|---|---|---|---|---|---|
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 |
/permission/remove_directory
since 7.0.18.0213
POST, PUT, GET, POST
Remove permission to access a directory from a specified user
Parameter | Type | Description | Default | ||
|---|---|---|---|---|---|
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 |
...
Parameter | Type | Description | Default | ||
|---|---|---|---|---|---|
id | integer |
|
| ||
keep_output | boolean |
| false |
/tasks
since 7.0.17.0207
POST, PUT, GET, POST
Returns information about tasks that have run on the server
...
/tasks/license
since 7.0.18.0920
POST, PUT, GET, POST
Returns a list of available tasks and their license requirements
/tasks/logs
since 7.0.18.0930
POST, PUT, GET, POST
Returns task logs
Parameter | Type | Description |
|---|---|---|
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 |
/tasks/outputs
since 7.0.18.1120
POST, PUT, GET, POST
Returns task output resource IDs and descriptions
/tasks/report
since 7.0.18.1130
POST, PUT, GET
Generates a report on recent tasks
/tasks/specs
since 7.0.18.0207
POST, PUT, GET, POST
Returns a list of task test specifications
Filters
/filters
since 7.0.18.0207
POST, PUT, GET, POST
Upload feature filters
Parameter | Type | Description |
|---|---|---|
filepath or filter | String | filepath: a file on the server with filter content or filter: the filter content in json format |
...
/commands
since 7.0.17.0901
POST, PUT, GET, POST
Returns information about commands that have run on the server
...
/commands/description
since 7.0.17.0901
POST, PUT, GET, POST
Returns a description of commands that have run on the server
Parameter | Type | Description |
|---|---|---|
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 |
/commands/fit
since 7.0.17.0901
POST, PUT, GET, POST
Returns information about command fits
/commands/memory
since 7.0.17.0901
POST, PUT, GET, POST
Returns the memory used by commands
Parameter | Type | Description |
|---|---|---|
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 |
/commands/pending
since 7.0.18.1124
POST, PUT, GET
Returns a summary report on pending commands
/commands/prediction
since 7.0.17.0901
POST, PUT, GET, POST
Returns the predicted utilization of commands
Parameter | Type | Description |
|---|---|---|
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 |
description_file | String | A file on the server with a set of CommandDescriptions in json format |
/commands/report
since 7.0.18.0902
POST, PUT, GET, POST
Generates a tab-delimited report on commands in a task
License
/license
since 7.0.17.0314
POST, PUT, GET, POST
Returns information about license available on the server
...
Workers
/workers
since 7.0.17.0901
POST, PUT, GET, POST
Returns a load summary of all connected workers
/workers/count
since 7.0.17.0901
POST, PUT, GET, POST
Returns the number of connected workers
/workers/internal
since 7.0.17.0901
POST, PUT, GET, POST
Returns a load summary of the internal worker, if it is enabled
/workers/remote
since 7.0.17.0901
POST, PUT, GET, POST
Returns a summary of the load of remote workers
/workers/submitted
since 18.0930
POST, PUT, GET, POST
Get and set information about workers that have been submitted to a cluster, but may not yet have connected
Parameter | Type | Description | |
|---|---|---|---|
submitted_workers | integer |
| |
max_memory_mb | integer |
|
System
/system
since 7.0.17.0227
POST, PUT, GET, POSTGet and set page load log threshold
System configuration options
Parameter | Type | Description |
|---|---|---|
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 |
update_command_resources | boolean | Download and update command resource estimates |
reload_feature_lists | boolean | Reload the feature lists for the user |
/system/generate_token
since 7.0.18.1020
POST, PUT, GET, POST
Generate an access token for the requesting user
Parameter | Type | Description | Default | |
|---|---|---|---|---|
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 | 1 hour |
/system/import
since 7.0.18.0228
POST, PUT, POST
Import a set of server preferences from a json specification
/system/logging
since 7.0.17.1024
POST, PUT, GET, POST
Configure log levels
Parameter | Type | Description |
|---|---|---|
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 |
...
/system/preferences
since 7.0.18.0130
POST, PUT, GET, POST
Get and set system preferences
Parameter | Type | Description |
|---|---|---|
node | string | The node name |
key | string | The preference name |
value | string | The preference value |
/system/preferences/list
since 9.0.20.0625
POST, PUT, GET
Lists system preferences which can be set
/system/preferences/nodes
since 7.0.18.0130
POST, PUT, GET, POST
Returns a list of preference node names
/system/revoke
since 7.0.18.1020
POST, PUT, GET, POST
Revoke API access tokens
Parameter | Type | Description |
|---|---|---|
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) |
/system/status_report
since 8.0.20.0130
POST, PUT, GET
Report on recent system activity
Parameter | Type | Description | Default |
|---|---|---|---|
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 |
/system/token
since 18.07.0930
POST, PUT, GET, POST
Manage access tokens
Parameter | Type | Description | Default | |
|---|---|---|---|---|
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 |
|
/system/token/list
since 7.0.18.1020
POST, PUT, GET, POST
Lists all managed tokens (Requires View user accounts privilege)
| Additional assistance |
|---|
| Rate Macro | ||
|---|---|---|
|
...
Overview
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