Orion CLI Commands

The Orion CLI is a command line interface to the Orion Platform. It is installed as part of the Orion Platform Python package. The CLI is invoked by the command ocli.

Top-Level Options

The Orion CLI has several top-level options, or flags, that modify the behavior of commands.

Timeout

The --timeout flag can be used to set the request timeout in seconds: if the server takes longer to respond to a request than the specified number of seconds, the client disconnects. The default value is 10, but that may be too short in some cases, such as:

Slow or inconsistent internet connections.
Sharing a package with many cubes to many users.
Uploading large files.

Note

All requests to the Orion API have a maximum timeout of 60 seconds.

JSON

The --json flag can be used to make the Orion CLI return JSON rather than plain text, making it easier to parse the results.

ocli --json <command>

Profile

The --profile flag specifies which profile configuration to use while making requests to the Orion API. The default is the default profile.

ocli --profile=testing <command>

OCLI config directory and file permissions are forced to be read/write for the owner.

Max Retries

The --max-retries flag specifies the number of times the client will retry a connection if it fails or gets a 404 error. This is set to 2 by default. The retries back off, so the time increases exponentially (to a certain point) with the number of retries.

Shard uploads and downloads are unaffected by --max-retries.

ocli --max-retries=5 <command>

Configuring Profiles and Projects

Configure an Orion Profile

ocli config profile

Configure an Orion Profile

A profile is made up of an Orion domain, username, token and project. Tokens can be created by logging into Orion with a web browser, going to the user profile, and clicking Create Token under My Tokens.

If a project is not provided, the profile will use the account’s default project.

Usage

ocli config profile [OPTIONS]

Options

--url <url>: Required Url of Orion Stack, ex: orion.eyesopen.com

--username <username>: Required Username to use to login into Orion with

--password <password>: Deprecated. Ignored if provided.

--token <token>: Orion token to use for authentication. If not provided, will be prompted interactively.

--project <project>: Project identifier to use for configuration

Change the Default Project of an Orion Profile

ocli config project

Configure your profile’s current project. Configure either profile’s default project or input desired project. To see available projects, run ocli projects list.

Usage

ocli config project [OPTIONS]

Delete an Orion Profile

ocli config delete

Delete an Orion Profile

Usage

ocli config delete [OPTIONS] PROFILE_NAME

Arguments

PROFILE_NAME: Required argument

Retrieve Information about the Current Profile

ocli config info

Retrieve information about the current profile

Usage

ocli config info [OPTIONS]

List the Configured Profiles

ocli config list

List the configured profiles

Usage

ocli config list [OPTIONS]

Refresh Your Orion Profile Token

ocli config token

Refresh your Orion Profile Token (Deprecated).

Usage

ocli config token [OPTIONS]

Options

--print-token: Deprecated. Print token rather than writing it to your configuration

Storage in Folders

Folder commands interact with Orion’s virtual filesystem. Note that folder commands are at the TOP LEVEL, that is, ocli ls <path> instead of ocli folders ls <path>.

Folders contain files, datasets, ShardCollections, and other folders. They can take the following forms:

/project/<project-id>/user/<username>/<path>

Project folders, which are private to a user with the given username.

/project/<project-id>/team/<path>

Project shared folders. All project members have access to these folders and their contents.

/project/<project-id>/workspace/<workspace-id>/<path>

Project shared workspace folders. Project members are given permission by sharing the workspace with them.

/organization/<path>

Organization shared folders.

List Contents of a Folder or Details of an Item

ocli ls

List contents of Orion folder(s) by path, or details of an Item

Folder paths have the following forms:

/project/<project-id>/user/<username>/<path>

/project/<project-id>/workspace/<workspace-id>/<path>

/project/<project-id>/team/<path>

/organization/<path>

Items can be specified by file://<file_id> or dataset://<dataset_id>

Filters:

path_contains:
name: Exact name to search for
name_contains: Partial name to search for
name_icontains: Case-insensitive partial name to search for
order_by: field to order results by
folders: (name | created )
data: (name | id | created | type | deleted )
types: Comma-separted list of types to show (collection | file | dataset | folder)
tag_filters: Comma-separated list of tags to filter for
systag_filters: Comma-separated list of system tags to filter for
expired: (default: False) List items that are deleted for more than 30 days
limit: Number of results to show

Examples:

ocli ls
ocli ls /project/
ocli ls /project/<project_id>/user/<username>/my/path/to/file
ocli ls file://10254 dataset://12525 collection://5030
ocli ls types=dataset,folder order_by=id /organization /project/10/user/myname/data1 file://12452
ocli ls types=file,collection limit=50 tag_filters=tag1,tag2 order_by=id /organization

Usage

ocli ls [OPTIONS] [FILTERS_AND_PATHS]...

Options

--recurse <recurse>: List folder contents recursively

Arguments

FILTERS_AND_PATHS: Optional argument(s)

Create a Folder

ocli mkdir

Create an Orion Folder

Folder paths have the following forms:

/project/<project-id>/user/<username>/<path>

/project/<project-id>/workspace/<workspace-id>/<path>

/project/<project-id>/team/<path>

/organization/<path>

Usage

ocli mkdir [OPTIONS] [PATHS]...

Arguments

PATHS: Optional argument(s)

Copy to/from Orion

ocli cp

Copy an item to/from Orion

dest must be a path, and items can only be copied from Orion to local or local to Orion.

Folder paths have the following forms:

/project/<project-id>/user/<username>/<path>

/project/<project-id>/workspace/<workspace-id>/<path>

/project/<project-id>/team/<path>

/organization/<path>

Usage

ocli cp [OPTIONS] SOURCE DEST

Options

--recurse <recurse>: Copy folder contents recursively

--dry-run <dry_run>: Run as a dry-run

Arguments

SOURCE: Required argument

DEST: Required argument

Peek Inside a File or Dataset in Orion

ocli head

Peek inside of an Orion dataset or file by path or Item

Folder paths have the following forms:

/project/<project-id>/user/<username>/<path>

/project/<project-id>/workspace/<workspace-id>/<path>

/project/<project-id>/team/<path>

/organization/<path>

Items can be specified by file://<file_id> or dataset://<dataset_id>

Usage

ocli head [OPTIONS] [PATHS]...

Options

-n, --number <number>: Number of entries

Arguments

PATHS: Optional argument(s)

Move a Folder or an Item

ocli mv

Move item to a folder

Folder paths have the following forms:

/project/<project-id>/user/<username>/<path>

/project/<project-id>/workspace/<workspace-id>/<path>

/project/<project-id>/team/<path>

/organization/<path>

ocli mv [TARGET] [DESTINATION]

Examples:

ocli mv file://254 /project/20/user/myname/new_file_name
ocli mv /project/<project_id>/user/<username>/myfile.oeb /project/<project_id>/user/<username>/newname.oeb
ocli mv /project/<project_id>/user/<username>/myfile.oedb /project/<project_id>/user/<username>/afolder/
ocli mv /project/<project_id>/user/<username>/myfile.oeb /project/20/team/trial2/

Usage

ocli mv [OPTIONS] SOURCE DEST

Options

--dry-run <dry_run>: Run as a dry-run

Arguments

SOURCE: Required argument

DEST: Required argument

Remove a Folder or Item

ocli rm

Delete an Orion folder or item by path

Folder paths have the following forms:

/project/<project-id>/user/<username>/<path>

/project/<project-id>/workspace/<workspace-id>/<path>

/project/<project-id>/team/<path>

/organization/<path>

Items can be specified by file://<file_id> or dataset://<dataset_id>

Usage

ocli rm [OPTIONS] [PATHS]...

Options

--dry-run <dry_run>: Run as a dry-run

Arguments

PATHS: Optional argument(s)

Workspaces

The CLI provides a number of commands to interact with workspaces: shared areas for Orion files, datasets, and collections organized into folders.

ocli workspaces

Orion workspace commands.

Usage

ocli workspaces [OPTIONS] COMMAND [ARGS]...

create

Create a new workspace

Examples:: ocli workspaces create default_project_shared_space ocli workspaces create ‘another shared space’ –project 10

Usage

ocli workspaces create [OPTIONS] WORKSPACE_NAME

Options

--project <project>: Unless specified, the workspace is created in your current default project.

Arguments

WORKSPACE_NAME: Required argument

help

Long format of help CMD, or the first level commands if CMD is not specified.

Usage

ocli workspaces help [OPTIONS] [CMD]...

Arguments

CMD: Optional argument(s)

info

Retrieve information about an Orion workspace.

Usage

ocli workspaces info [OPTIONS] IDENTIFIER

Arguments

IDENTIFIER: Required argument

list

List Orion workspaces.

Examples:: ocli workspaces list –project 10 ocli workspaces list –limit 5 slug=’my shared workspace’

Usage

ocli workspaces list [OPTIONS] [FILTERS]...

Options

--offset <offset>: Offset from the start of the list

--limit <limit>: Number of objects to list

--project <project>: Filter by project identifier.

Arguments

FILTERS: Optional argument(s)

list-users

List users of a workspace.

Examples:: ocli workspaces list-users 123

Usage

ocli workspaces list-users [OPTIONS] IDENTIFIER

Arguments

IDENTIFIER: Required argument

unshare

Unshare a workspace with one or more users.

Examples:: ocli workspaces unshare 123 75

Usage

ocli workspaces unshare [OPTIONS] IDENTIFIER [SHARE_IDS]...

Arguments

IDENTIFIER: Required argument

SHARE_IDS: Optional argument(s)

Datasets

The CLI provides several ways to interact with datasets.

ocli datasets

Orion dataset commands

Usage

ocli datasets [OPTIONS] COMMAND [ARGS]...

delete

Delete a specific dataset

Usage

ocli datasets delete [OPTIONS] IDENTIFIER

Options

--immediate

Arguments

IDENTIFIER: Required argument

download

Download an Orion dataset to the local file system

Will download to any OEchem writable format

Usage

ocli datasets download [OPTIONS] IDENTIFIER FILE

Options

--fieldlist <fieldlist>

Arguments

IDENTIFIER: Required argument

FILE: Required argument

finalize

Finalize a specific dataset

Usage

ocli datasets finalize [OPTIONS] IDENTIFIER

Arguments

IDENTIFIER: Required argument

help

Long format of help CMD, or the first level commands if CMD is not specified.

Usage

ocli datasets help [OPTIONS] [CMD]...

Arguments

CMD: Optional argument(s)

info

Retrieve information about a specific dataset

Usage

ocli datasets info [OPTIONS] IDENTIFIER

Arguments

IDENTIFIER: Required argument

list

List datasets that you have access to.

Filters: (space separated key=value pairs. see example usage.)

owner: user id to filter for (e.g. owner=10)
tags : comma-separated list of tags to filter for (e.g. tags=tag1,tag2)
exclude_tags: comma-separated list of tags to exclude (e.g. exclude_tags=tag3,tag4)
tag_match: Filtering style used for tags [default: exact] (exact | iexact | contains | icontains | startswith | istartswith | endswith | iendswith)
tag_ids: comma-separated list of tag ids to filter for (e.g. tag_ids=5,7…)
order_by: Result ordering field [default: created] (created | name | size | owner | id) (Adding ‘-’ in front will inverse the ordering)
deleted: boolean on whether to filter for deleted collection [default: False] (e.g. deleted=true)
expired: boolean on whether to filter for expired collections [default: False] (e.g. expired=true)

Examples:

ocli datasets list
ocli datasets list –name=aspirin_
ocli datasets list –limit=20 deleted=true tag_match=iexact tags=tag1,tag2

Usage

ocli datasets list [OPTIONS] [FILTERS]...

Options

--offset <offset>: Offset from the start of the list

--limit <limit>: Number of objects to list

--name <name>: Filter by name

--project <project>: Filter by project identifier

Arguments

FILTERS: Optional argument(s)

tag

Tag a dataset

Usage

ocli datasets tag [OPTIONS] IDENTIFIER [TAGS]...

Options

--project <project>

Arguments

IDENTIFIER: Required argument

TAGS: Optional argument(s)

unshare

Unshare a dataset

Usage

ocli datasets unshare [OPTIONS] IDENTIFIER {user|project|organization}
                      [SHARE_IDS]...

Arguments

IDENTIFIER: Required argument

SHARE_TYPE: Required argument

SHARE_IDS: Optional argument(s)

untag

Untag a dataset

Usage

ocli datasets untag [OPTIONS] IDENTIFIER [TAGS]...

Arguments

IDENTIFIER: Required argument

TAGS: Optional argument(s)

upload

Upload a local dataset to Orion

Will automatically convert any OEChem readable format into a dataset

Usage

ocli datasets upload [OPTIONS] FILE

Options

--project <project>

Arguments

FILE: Required argument

File Commands

These commands are used to manage files.

ocli files

Orion file commands

Usage

ocli files [OPTIONS] COMMAND [ARGS]...

delete

Delete an Orion file by id

Usage

ocli files delete [OPTIONS] IDENTIFIER

Options

--immediate

Arguments

IDENTIFIER: Required argument

download

Download a file from Orion to the local file system

Usage

ocli files download [OPTIONS] IDENTIFIER FILE

Arguments

IDENTIFIER: Required argument

FILE: Required argument

help

Long format of help CMD, or the first level commands if CMD is not specified.

Usage

ocli files help [OPTIONS] [CMD]...

Arguments

CMD: Optional argument(s)

info

Retrieve information about a specific file

Usage

ocli files info [OPTIONS] IDENTIFIER

Arguments

IDENTIFIER: Required argument

list

List information about the Files you have access to

Filters: (space separated key=value pairs. see example usage.)

owner: user id to filter for (e.g. owner=10)
tags: comma-separated list of tags to filter for (e.g. tags=tag1,tag2)
exclude_tags: comma-separated list of tags to exclude (e.g. exclude_tags=tag3,tag4)
tag_match: Filtering style used for tags [default: exact] (exact | iexact | contains | icontains | startswith | istartswith | endswith | iendswith)
tag_ids: comma-separated list of tag_ids to filter for (e.g. tag_ids=5,7…)
order_by: Result ordering field [default: created] (created | name | size | owner | id) (Adding ‘-’ in front will inverse the ordering)
deleted: filter for deleted collection [default: False] (e.g. deleted=True)
expired: boolean on whether to filter for expired collections [default: False] (e.g. expired=True)

Examples:

ocli files list

ocli files list –limit=20 name=foo_ deleted=true tag_match=iexact tags=tag1,tag2

Usage

ocli files list [OPTIONS] [FILTERS]...

Options

--offset <offset>: Offset from the start of the list

--limit <limit>: Number of objects to list

--name <name>: Filter by name

--project <project>: Filter by project identifier

Arguments

FILTERS: Optional argument(s)

tag

Tag a specific file

Usage

ocli files tag [OPTIONS] IDENTIFIER [TAGS]...

Options

--project <project>

Arguments

IDENTIFIER: Required argument

TAGS: Optional argument(s)

unshare

Unshare a file

Usage

ocli files unshare [OPTIONS] IDENTIFIER {user|project|organization}
                   [SHARE_IDS]...

Arguments

IDENTIFIER: Required argument

SHARE_TYPE: Required argument

SHARE_IDS: Optional argument(s)

untag

Untag a file

Usage

ocli files untag [OPTIONS] IDENTIFIER [TAGS]...

Arguments

IDENTIFIER: Required argument

TAGS: Optional argument(s)

upload

Upload a file from the local file system to Orion

Note: Slow or inconsistent internet connections may require a longer –timeout to reliably upload large files

Ex: ocli –timeout 90 files upload FILE_TO_UPLOAD

Usage

ocli files upload [OPTIONS] FILE

Options

--project <project>

--name <name>

Arguments

FILE: Required argument

Collections

These are commands for managing collections.

ocli collections

Orion collection commands

Usage

ocli collections [OPTIONS] COMMAND [ARGS]...

close

Close a collection specified by IDENTIFIER

A closed (i.e. ready) collection cannot have shards added to it.

Usage

ocli collections close [OPTIONS] IDENTIFIER

Arguments

IDENTIFIER: Required argument

delete

Delete Orion collections by IDENTIFIER

Usage

ocli collections delete [OPTIONS] IDENTIFIER

Options

--immediate

Arguments

IDENTIFIER: Required argument

delete-shards

Delete parts of an Orion collection specified by collection IDENTIFIER and list of SHARD_IDENTIFIERS.

If no SHARD_IDENTIFIERS are specified, then no operations will be performed. Use ‘ocli collections delete’ to delete a collection.

Usage

ocli collections delete-shards [OPTIONS] IDENTIFIER [SHARD_IDENTIFIERS]...

Arguments

IDENTIFIER: Required argument

SHARD_IDENTIFIERS: Optional argument(s)

download

Download an Orion collection specified by IDENTIFIER to the DEST dir on the local file system

Each shard will be downloaded into DEST.

Usage

ocli collections download [OPTIONS] IDENTIFIER DEST

Options

--overwrite: Overwrite files

--download-attempts <download_attempts>: The number of attempts to try downloading a shard

Arguments

IDENTIFIER: Required argument

DEST: Required argument

download-shards

Download parts of an Orion collection specified by IDENTIFIER to the DEST dir on the local file system

Each shard in SHARD_IDENTIFIERS will be downloaded into DEST.

Usage

ocli collections download-shards [OPTIONS] IDENTIFIER [SHARD_IDENTIFIERS]...
                                 DEST

Options

--overwrite: Overwrite files

--download-attempts <download_attempts>: The number of attempts to try downloading a shard

Arguments

IDENTIFIER: Required argument

SHARD_IDENTIFIERS: Optional argument(s)

DEST: Required argument

help

Long format of help CMD, or the first level commands if CMD is not specified.

Usage

ocli collections help [OPTIONS] [CMD]...

Arguments

CMD: Optional argument(s)

info

Retrieve information about a specific collection

Usage

ocli collections info [OPTIONS] IDENTIFIER

Arguments

IDENTIFIER: Required argument

info-shard

Retrieve information about a specific collection’s shards

Usage

ocli collections info-shard [OPTIONS] IDENTIFIER SHARD_IDENTIFIER

Arguments

IDENTIFIER: Required argument

SHARD_IDENTIFIER: Required argument

list

List information about the collections you have access to.

Filters: (space separated key=value pairs. see example usage.)

name : name to partial search for (eg: name=foo_ will return foo_1, foo_2, etc)
owner: user id to filter for (e.g. owner=10)
project: project id to filter for (e.g. project=10)
tags: comma-separated list of tags to filter for (e.g. tags=tag1,tag2)
tag_match: Filtering style used for tags [default: exact] (exact | iexact | contains | icontains | startswith | istartswith | endswith | iendswith)
tag_ids: comma-separated list of tag_ids to filter for (e.g. tag_ids=5,7…)
order_by: Result ordering field [default: created] (created | name | size | owner | id) (Adding ‘-’ in front will inverse the ordering)
deleted: boolean on whether to filter for deleted collections [default: False] (e.g. deleted=True)
expired: boolean on whether to filter for expired collections [default: False] (e.g. expired=True)
v2: boolean on wheather to search for v1 or v2 collections [default: False] (e.g. v2=True)

Examples:

ocli collections list

ocli collections list –limit=20 name=foo_ deleted=true tag_match=iexact tags=tag1,tag2

Usage

ocli collections list [OPTIONS] [FILTERS]...

Options

--offset <offset>: Offset from the start of the list

--limit <limit>: Number of objects to list

Arguments

FILTERS: Optional argument(s)

list-shards

Retrieve information about a specific collection’s shards

Filters:

name : name to partial search for (eg: name=foo_ will return foo_1, foo_2, etc)

Usage

ocli collections list-shards [OPTIONS] IDENTIFIER [FILTERS]...

Options

--offset <offset>: Offset from the start of the list

--limit <limit>: Number of objects to list

--name <name>: Filter shards by name

Arguments

IDENTIFIER: Required argument

FILTERS: Optional argument(s)

open

Open a collection specified by IDENTIFIER

A open collection can have shards added to it.

Usage

ocli collections open [OPTIONS] IDENTIFIER

Arguments

IDENTIFIER: Required argument

tag

Tag a specific collection

Usage

ocli collections tag [OPTIONS] IDENTIFIER [TAGS]...

Options

--project <project>

Arguments

IDENTIFIER: Required argument

TAGS: Optional argument(s)

unshare

Unshare a collection

Usage

ocli collections unshare [OPTIONS] IDENTIFIER {user|project|organization}
                         [SHARE_IDS]...

Arguments

IDENTIFIER: Required argument

SHARE_TYPE: Required argument

SHARE_IDS: Optional argument(s)

untag

Untag a specific collection

Usage

ocli collections untag [OPTIONS] IDENTIFIER [TAGS]...

Arguments

IDENTIFIER: Required argument

TAGS: Optional argument(s)

upload

Upload one or more FILES as new shards in a collection specified by IDENTIFIER to Orion

If IDENTIFIER is an integer id, then FILES are added to an existing collection. Otherwise, a new collection named IDENTIFIER is created.

Usage

ocli collections upload [OPTIONS] IDENTIFIER [FILES]...

Options

--project <project>

--v1

--upload-attempts <upload_attempts>: The number of attempts to try uploading a file as a shard

--verbose

Arguments

IDENTIFIER: Required argument

FILES: Optional argument(s)

Secrets Commands

ocli secrets

Orion secrets are a way of storing values in an encrypted state that can be retrieved for later use.

Usage

ocli secrets [OPTIONS] COMMAND [ARGS]...

create

Create an Orion secret.

Usage

ocli secrets create [OPTIONS] NAME

Options

--value <value>: Required Secret value to store within a secret.

--description <description>

Arguments

NAME: Required argument

delete

Delete an Orion secret

Usage

ocli secrets delete [OPTIONS] IDENTIFIER

Arguments

IDENTIFIER: Required argument

help

Long format of help CMD, or the first level commands if CMD is not specified.

Usage

ocli secrets help [OPTIONS] [CMD]...

Arguments

CMD: Optional argument(s)

info

Retrieve an Orion secret.

This returns the value that you stored on the secret in the form you set it initially.

Usage

ocli secrets info [OPTIONS] IDENTIFIER

Arguments

IDENTIFIER: Required argument

list

List Orion secrets.

This command will not display the value associated with the secrets.

Filters:

owner: user id to filter for (for example, owner=10).

description : description to partial search for (for example, description=’my description’).

Examples:

ocli secrets list

ocli secrets list owner=10

Usage

ocli secrets list [OPTIONS] [FILTERS]...

Options

--name <name>: Filter by name

--offset <offset>: Offset from the start of the list

--limit <limit>: Number of objects to list

Arguments

FILTERS: Optional argument(s)

list-shares

Sharing status of a secret.

Usage

ocli secrets list-shares [OPTIONS] IDENTIFIER

Arguments

IDENTIFIER: Required argument

unshare

Unshare a secret.

Usage

ocli secrets unshare [OPTIONS] IDENTIFIER {user|project|organization}
                     [SHARE_IDS]...

Arguments

IDENTIFIER: Required argument

SHARE_TYPE: Required argument

SHARE_IDS: Optional argument(s)

Projects

These are commands for managing projects.

ocli projects

Orion project commands

Usage

ocli projects [OPTIONS] COMMAND [ARGS]...

create

Create a new Orion project

Usage

ocli projects create [OPTIONS] PROJECT_NAME

Arguments

PROJECT_NAME: Required argument

delete

Delete an Orion project

Usage

ocli projects delete [OPTIONS] IDENTIFIER

Options

--immediate

Arguments

IDENTIFIER: Required argument

help

Long format of help CMD, or the first level commands if CMD is not specified.

Usage

ocli projects help [OPTIONS] [CMD]...

Arguments

CMD: Optional argument(s)

info

Retrieve information about an Orion project

Usage

ocli projects info [OPTIONS] IDENTIFIER

Arguments

IDENTIFIER: Required argument

leave

Leave an Orion project

Usage

ocli projects leave [OPTIONS] IDENTIFIER

Options

--new-owner <new_owner>: ID of user to receive all owned resources in the project

Arguments

IDENTIFIER: Required argument

list

List Orion projects

Filters:

name: name to partial search for (e.g. name=foo_ will return foo_1, foo_2, etc)
deleted: boolean on whether to filter for deleted collections [default: False] (e.g. deleted=True)
expired: boolean on whether to filter for expired collections [default: False] (e.g. expired=True)

Examples:

ocli projects list
ocli projects list name=foo_
ocli projects list deleted=True

Usage

ocli projects list [OPTIONS] [FILTERS]...

Options

--offset <offset>: Offset from the start of the list

--limit <limit>: Number of objects to list

Arguments

FILTERS: Optional argument(s)

list-shares

Sharing status of a specific project

Usage

ocli projects list-shares [OPTIONS] IDENTIFIER

Arguments

IDENTIFIER: Required argument

unshare

Unshare a project

Usage

ocli projects unshare [OPTIONS] IDENTIFIER {user|project|organization}
                      [SHARE_IDS]...

Options

--new-owner <new_owner>: ID of user to receive all owned resources in the project

Arguments

IDENTIFIER: Required argument

SHARE_TYPE: Required argument

SHARE_IDS: Optional argument(s)

Floe Commands (Packages)

The following commands are a set of resources in Orion that relate to the Floe package, which includes packages, WorkFloes, and jobs.

These commands relate to Floe packages.

Initializing a Package

The ocli packages init command:

Sets up a skeleton of an Orion package containing cubes and floes.
Provides a simple example of a cube and a floe.
Supports the testing setup using PyTest including working tests for the example cube and floe.
Provides a setup.py file with commands to run tests or build the package.
Provides version configuration via storing the version only in the module’s __init__.py file.

When creating a package with ocli packages init --service, the generated services boilerplate includes a demo Flask application and a services.json definition.

ocli packages init

Create a Floe package scaffold.

This command can be used to create the structure necessary for a Floe package, but is distinct from the set of package commands which can be used to manage package images.

Usage

ocli packages init [OPTIONS]

Options

--full-name <full_name>: Required Author of the Floe package

--email <email>: Required Email of the Floe package author

--project-name <project_name>: Required Name of the project

--project-slug <project_slug>: Required Short name for the project

--module-name <module_name>: Required Name of the module

--description <description>: Required Description of the project

--version <version>: Required Package version

--service: Include a service directory and boilerplate code

Retrieving the Information about a Floe Package

ocli packages info

Retrieve information about a specific package

Usage

ocli packages info [OPTIONS] IDENTIFIER

Arguments

IDENTIFIER: Required argument

Retrieving the Environment Build Log for a Floe Package

ocli packages environment <resource_id>

Retrieving the Inspection Information for a Floe Package

ocli packages inspection <resource_id>

Deleting a Floe Package

ocli packages delete <resource_id>

Listing Floe Packages

ocli packages list [--limit=<integer>] [--offset=<integer>] \
    [states=<state>,... (ready, deprecated, queued, error)] \
    [name=<name>] [UUID=<uuid>] [owner=<integer>] \
    [<key>=<value>,...]

ex:
    ocli packages list
    ocli packages list states=error
    ocli packages list --limit=20 states=ready,queued

Upload a Floe Package

ocli packages upload <file_or_url>

WorkFloes

These commands allow access to WorkFloe objects in Orion, also known as floes. WorkFloes are collections of cubes that define the flow of data.

Retrieving the Information about a WorkFloe

ocli workfloes info <resource_id>

Deleting a Workfloe

ocli workfloes delete <resource_id>

Listing Workfloes

ocli workfloes list [--package=<integer>] [--name=<string>] \
    [--limit=<integer>] [--offset=<integer>] \
    [states=<state>,... (ready, deprecated, hidden, invalid)] \
    [systags=<tag>,...] [tags=<tag>,...] [owner=<integer>] \
    [classification=<string> [classification_depth=<integer>]
    [order_by=(recently_used | name)]
    [<key>=<value>,...]

ex:
    ocli workfloes list
    ocli workfloes list tags=tag1,tag2
    ocli workfloes list --name=collection_to_ --limit=10 order_by=recently_used
    ocli workfloes list --package=10 states=ready,deprecated

Listing Classifications

ocli workfloes list-classifications [--name=<string>] [--path=<string>] \
    [--depth=<integer>] [--limit=<integer>] [--offset=<integer>] \
    [<key>=<value>,...]

ex:
    ocli workfloes list-classifications
    ocli workfloes list-classifications --path=Example/Test
    ocli workfloes list-classifications --name=exam --depth=1 --limit=10

Jobs

These are commands for interacting with jobs in Orion. Jobs are an instantiation of a Workfloe that performs the computation defined by the Workfloe.

Retrieving the Information about a Job

ocli jobs info <resource_id>

Retrieve the Logs of a Job

ocli jobs logs <resource_id>

ocli jobs cancel <resource_id>

Deleting a Job

ocli jobs delete <resource_id>

Displaying Size of Logs

This retrieves the size of the logs of an Orion job.

ocli jobs log_size [OPTIONS] JOB_ID

Arguments

JOB_ID: Required argument identifying the job.

Deleting Job Logs

This deletes the logs of an Orion job.

ocli jobs delete_logs [OPTIONS] JOB_ID

Arguments

JOB_ID: Required argument.

Listing Existing Jobs

ocli jobs list [--limit=<integer>] [--offset=<integer>] \
    [name=<name>] [project=<integer>] [workfloe=<integer>] \
    [job_type=(system | user)] [owner=<integer>] \
    [states=<state>,... (queued, running, complete)] \
    [tags=<tag>,...] [<key>=<value>,...]

ex:
    ocli jobs list
    ocli jobs list workfloe=20
    ocli jobs list tags=tag1,tag2 states=complete
    ocli jobs list job_type=user name=aspirin_ states=queued,running

Tag

This tags a specific job.

ocli jobs tag [OPTIONS] IDENTIFIER [TAGS]...

Options

–project <project>

Arguments

IDENTIFIER: Required argument identifying the job.
TAGS: Optional string argument(s) to be used as tags.

The –project` option applies the tags using the project ID.

For example:

ocli jobs tag --project 25412 203761 candidates
Tagged WorkFloeJob 203761 with ('candidates',)

Project tags are displayed in pink in the user interface. Job tags are yellow.

../../../../_images/job_tag.png — **Figure 1.** Project tags (pink) and job tags (yellow).

Both kinds of tag can be used in searches in the user interface.

../../../../_images/job_tag_search.png — **Figure 2.** Searching with a project tag.

Starting a Job

ocli jobs start <workfloe_id> <job_name> [--wait] \
    [--param-file <path>] [FLOE_PARAMETERS]

ex:

ocli jobs start 6836 job_name0 --in 601 --out run_output.oedb

Note

Adding -- --help to the ocli jobs start command will print the parameters that are expected by the workfloe.

Using a Parameter File

The --param-file argument allows you to provide job parameters from a JSON file. This is especially useful for complex floes with multi-level parameters that are difficult to express as command-line arguments.

ocli jobs start <workfloe_id> <job_name> --param-file params.json

The JSON file should contain a dictionary with any of the following keys:

parameters — promoted, cube, and floe parameter overrides.
system_parameters — system-level settings such as project or priority.
notify — whether to send a notification email when the job completes.

Any command-line arguments provided alongside --param-file override values from the file.

# Start using file parameters, but override the project
ocli jobs start 42 "My Job" --param-file params.json --project 99

Exporting Job Parameters

Export the parameters of a previously run job to a JSON file. The exported file can be used with --param-file on ocli jobs start to rerun a job with the same (or modified) parameters.

ocli jobs export-params <job_id> [--output <path>]

ex:

ocli jobs export-params 12345
ocli jobs export-params 12345 --output my_params.json

If --output is not specified, the file is written to job_<job_id>_params.json in the current directory.

The exported JSON contains:

{
  "workfloe": 814,
  "name": "Original Job Name",
  "parameters": {
    "promoted": {},
    "cube": {},
    "floe": {}
  },
  "system_parameters": {
    "project": 99
  },
  "notify": false
}

Watching a Job

ocli jobs watch <workfloe_id> <job_name> [CUBES] [OPTIONS]

Collect Debug Information

ocli jobs debug-export <job_id>

Retrieving Summary of Jobs Within an Organization

ocli jobs summary-export [--package-uuids=<str>] [--workfloe-uuid=<str>] \
    [--job_ids=<str>] [--start-date=<str>] [--end-date=<str>] \
    [--output-path=<str>] [--download=(--download | --no-download)] \
    [--notify=(--notify | --no-notify)]

Examples:

ocli jobs summary-export
ocli jobs summary-export --notify --download
ocli jobs summary-export --start-date 2023-01-01 --end-date "2023-01-01 18:00:00"
ocli jobs summary-export --output-path "/project/<project-id>/users/<user-id>/folder-name/"
ocli jobs summary-export --package-uuids "uuid_A, uuid_B" --workfloe-uuids "uuid_C" --job-ids "6, 19, 47"

This functionality is available only to Stack Admins, Org Admins, and MT Org Admins.

Cost Export

Generating Storage Use Report

The report generated by the following commands contains estimates based on the amount of storage used. They do not reflect the exact billed cost.
The results do not take into account the AWS tiered storage system.
Generating the report does not move anything from a lower cost tier into a higher cost tier.

ocli cost export --report-type=storage_use [USER IDS]

ex:

ocli cost export --report-type=storage_use 10 11 20

Generating Spend Summary Report

This report provides per-user totals for storage, jobs, and services. Costs for user-created Molecule Search databases are included in the services total. Totals are pulled from the ledger entries and aggregated over the previous 7 days (168 hours), current calendar month, and previous calendar month. If no user IDs are provided, data for the current user will be reported (non-admin) or for all organization users (admin).

ocli cost export --report-type=spend_summary [USER IDS]

ex:

ocli cost export --report-type=spend_summary 10 11 20

The resulting CSV has column headers providing content labels, but the schema is not versioned. For programmatic usage, the orionclient LedgerEntry is recommended. All amounts are in dollars.

ocli cost export

Triggers cost report in Orion, optionally downloads the file.

notify: Send an email upon completion.

output-path: The output path to store the cost report in.

report-type: The report type.

redact-project-names: Redact project names from reports.

users: A list of user ids for user data to include in the cost report.

Examples:

ocli cost export –notify=true –report-type=spend_summary 10

ocli cost export –report-type=spend_summary 10 11 20

ocli cost export –report-type=storage_use 10 11 20

Usage

ocli cost export [OPTIONS] [USERS]...

Options

--notify <notify>: Notify upon completion via email

--output-path <output_path>: Project path

--report-type <report_type>

Required Report type

Options:: storage_use | spend_summary

--redact-project-names <redact_project_names>: Redact project names

--download, --no-download: Wait for export to complete and download the result

Arguments

USERS: Optional argument(s)

../../../../_images/cost_export_table.png — **Figure 3.** Sample cost export table.

Molecule Search Database Commands

These commands are used to manage molecule search databases.

ocli molsearch db

Orion molecule search database commands.

Usage

ocli molsearch db [OPTIONS] COMMAND [ARGS]...

create

Submit a job to create a molecule search database.

Optionally, specify the resources required for the job.
Please note, if you do not use the –gpu flag, a 3D database will default to 1 GPU and a 2D database will default to 0.
If a molsearch database uses a fraction of an AWS GPU instance, then its cost will only be for the portion of the instance it is allocated,
but the Organization will still be charged for the full cost of the instance. While cost is not as big a factor for the cdns-g1 instances,
it would still be best practice to make them in sets. This will increase the likelihood that the scheduler will place them on the same instance.
If you do not pin –instance-type, the scheduler may place the database on any instance whose resources satisfy it. When the lowest-cost
instance has no available capacity, the scheduler falls back to progressively larger, more expensive instances. Set –instance-type to limit the compatible instances and avoid unexpected charges.
Examples:
ocli molsearch db create –collection=123
ocli molsearch db create –collection=123 –pools=[system]
ocli molsearch db create –collection=123 –memory-mb=24000 –disk-space=200 {requests 24 GB memory and 200GB disk}
ocli molsearch db create –collection=123 –cpu=16
ocli molsearch db create –collection=123 –gpu=0.125 –instance-type cdns-g1 {requests 1/8th of a GPU on a cdns-g1, or 1/96th of the instance}
ocli molsearch db create –collection=123 –display-name=”my database”
ocli molsearch db create –server-is-remote –verify-ssl-cert –auth-secret=mysecret –server-address=http://mydomain.com:1234
See Dominant Resource Factor for examples of what resources are given, especially when requesting fractional GPUs.

Usage

ocli molsearch db create [OPTIONS]

Options

--collection <collection>: Collection with molecule search database.

--cpu <cpu>: Number of CPUs.

--memory-mb <memory_mb>: Memory (in MB).

--disk-space <disk_space>: Disk (in GB).

--gpu <gpu>: Number of GPUs.

--instance-type <instance_type>: Instance type.

--pools <pools>: Pools to run the job in.

--search-type <search_type>

Search type ‘2D’ or ‘3D’

Options:: 2D | 3D

--server-is-remote: Is the server being manually managed?

--server-address <server_address>: Address of the remote server.

--auth-secret <auth_secret>: Authorization secret of the remote server.

--verify-ssl-cert: Should the remote server verify its SSL certificate?

--display-name <display_name>: User provided display name for the database

--section <section>: Value of database section - OE provided or Customer Managed

--is-proxy: Flag to use proxy or not

delete

Delete a molecule search database.

Usage

ocli molsearch db delete [OPTIONS] DATABASE

Arguments

DATABASE: Required argument

help

Long format of help CMD, or the first level commands if CMD is not specified.

Usage

ocli molsearch db help [OPTIONS] [CMD]...

Arguments

CMD: Optional argument(s)

info

Information about a specific molecule search database.

Usage

ocli molsearch db info [OPTIONS] DATABASE

Arguments

DATABASE: Required argument

list

List all molecule search databases.

Filters: (space separated key=value pairs. see example usage.)

search_type: e.g. 2D or 3D

state: state to filter for (e.g. QUEUED, DOWNLOADING, LOADING, LOADED,

UNLOADING, UNLOADED, FAILED, STOPPED)

section: section for which to filter for, (e.g. “Customer Managed” or “OE provided”)

Usage

ocli molsearch db list [OPTIONS] [FILTERS]...

Options

--offset <offset>: Offset from the start of the list

--limit <limit>: Number of objects to list

Arguments

FILTERS: Optional argument(s)

list-shares

Sharing status of a specific molecule search database.

Usage

ocli molsearch db list-shares [OPTIONS] IDENTIFIER

Arguments

IDENTIFIER: Required argument

load

Load a molecule search database.

Usage

ocli molsearch db load [OPTIONS] DATABASE

Arguments

DATABASE: Required argument

logs

Retrieve the logs of a molecule search database

Get logs based on date:

$ ocli molsearch db logs 1 –from “2024-04-28” –until “2024-05-01”

Usage

ocli molsearch db logs [OPTIONS] IDENTIFIER

Options

--from <from_dt>: start date for the logs

--until <until>: end date for the logs

Arguments

IDENTIFIER: Required argument

unload

Unload a molecule search database.

Usage

ocli molsearch db unload [OPTIONS] DATABASE

Arguments

DATABASE: Required argument

unshare

Unshare a molecule search database.

Usage

ocli molsearch db unshare [OPTIONS] IDENTIFIER {user|project|organization}
                          [SHARE_IDS]...

Arguments

IDENTIFIER: Required argument

SHARE_TYPE: Required argument

SHARE_IDS: Optional argument(s)

update

Update a molecule search database.

Usage

ocli molsearch db update [OPTIONS] DATABASE

Options

--section <section>: Value of database section - OE provided or Customer Managed

--display-name <display_name>: User provided display name for the database

Arguments

DATABASE: Required argument

Molecule Search Query Commands

These commands are used to manage Molecule Search queries.

ocli molsearch query

Orion molecule search query commands.

Usage

ocli molsearch query [OPTIONS] COMMAND [ARGS]...

cancel

Cancel a substructure molecule search query.

Applies only to searches with query_type=substructure.

Example: ocli molsearch query cancel <query_id>

Usage

ocli molsearch query cancel [OPTIONS] QUERY

Arguments

QUERY: Required argument

create

Create a molecule search query.

Usage

ocli molsearch query create [OPTIONS] COMMAND [ARGS]...

exact

2D exact search using a SMILES string. If a file is provided, it will be converted into smiles.

Examples:

ocli molsearch query create exact <database_id> “CC(=O)Oc1ccccc1C(=O)O”

ocli molsearch query create exact <database_id> /path/to/molecule/file

Usage

ocli molsearch query create exact [OPTIONS] DATABASE QUERY

Options

--search-type <search_type>

How to search.

Options:: ISM | ABS | ISOMORPH | UNCOLOR

--name <name>

--max-hits <max_hits>

--wait

--project <project>

Arguments

DATABASE: Required argument

QUERY: Required argument

fastrocs

3D similarity search using a fastrocs query

query_mol_file_path can be any file supported by 3D search:

.sdf, .mol, .mol2, or .oeb

Example:

ocli molsearch query create fastrocs <database_id> <file>

Usage

ocli molsearch query create fastrocs [OPTIONS] DATABASE QUERY_MOL_FILE_PATH

Options

--name <name>

--max-hits <max_hits>

--shape-only

--sim-type <sim_type>

Options:: tanimoto | tversky

--tversky-alpha <tversky_alpha>

--orientation <orientation>

WARNING: ‘inertialAtHeavyAtoms’, ‘inertialAtColorAtoms’, and ‘subrocs’ orientations are extremely memory intensive and can cause the database to exceed available memory. Use with caution.

Options:: inertial | random

--random-starts <random_starts>

--wait

--project <project>

Arguments

DATABASE: Required argument

QUERY_MOL_FILE_PATH: Required argument

graphsim

2D similarity search using a GraphSim query. If a file is provided, it will be converted into smiles.

Examples:

ocli molsearch query create graphsim <database_id> “c1ccccc1”

ocli molsearch query create graphsim <database_id> /path/to/molecule/file

Usage

ocli molsearch query create graphsim [OPTIONS] DATABASE QUERY

Options

--fpname <fpname>: Fingerprint to use.

--cutoff <cutoff>: Cutoff.

--measure <measure>

Similarity measure to use.

Options:: Tanimoto | Tversky | Dice | Cosine

--name <name>

--max-hits <max_hits>

--wait

--project <project>

Arguments

DATABASE: Required argument

QUERY: Required argument

help

Long format of help CMD, or the first level commands if CMD is not specified.

Usage

ocli molsearch query create help [OPTIONS] [CMD]...

Arguments

CMD: Optional argument(s)

substructure

2D substructure search using an OEChem substructure query.

Constraints only applicable for MDL queries.
Supported file types are: .mol, .sdf, .sd, .json
If using a generic molecule as a query, .smi, .ism, .usm, .can, .cxsmiles, .oeb, .oez are also supported.
Any file provided will be converted to json before the query is created.
Examples:
ocli molsearch create substructure 1 path/to/file
ocli molsearch create substructure 1 c1cocc1 –subsearch_query_type SMARTS

Usage

ocli molsearch query create substructure [OPTIONS] DATABASE INPUT_QUERY

Options

--subsearch_query_type <subsearch_query_type>

Options:: MDL | SMARTS

--aliphatic-constraint: only applicable for MDL queries

--topology-constraint: only applicable for MDL queries

--stereo-constraint: only applicable for MDL queries

--isotope-constraint: only applicable for MDL queries

--name <name>

--max-hits <max_hits>

--wait

--cancel-after <cancel_after>

--project <project>

Arguments

DATABASE: Required argument

INPUT_QUERY: Required argument

title

Search a 2D database using a space separated list of titles.

If providing a file as the query, file type must be .txt and should contain only titles separated by newlines.

Example:

ocli molsearch query create title <database_id> <titles_list>

ocli molsearch query create title <database_id> /path/to/molecule/file.txt

Usage

ocli molsearch query create title [OPTIONS] DATABASE [TITLE]...

Options

--name <name>

--project <project>

Arguments

DATABASE: Required argument

TITLE: Optional argument(s)

delete

Delete a molecule search query.

Example: ocli molsearch query delete <query_id>

Usage

ocli molsearch query delete [OPTIONS] QUERY

Arguments

QUERY: Required argument

download

Download molecule search results and query to separate local files.

File format is determined by filename extension. Supported formats are csv, smi, sdf, oeb

Downloaded query file will be named <result_file_name>-query.<ext>

Example:

ocli molsearch query download 1 search-results.csv –ids 1234,1236

Usage

ocli molsearch query download [OPTIONS] QUERY FILE

Options

--ids <ids>: Comma-separated list of result IDs to export.

--exclude: Exclude ids from results.

Arguments

QUERY: Required argument

FILE: Required argument

export

Export search results to a dataset.

The optional --path will place the export output in a non-default location, as with:

--path /project/<project-id>/user/<username>/<custom_path>/

if unset, this value defaults to: /project/<project-id>/user/<username>/

The optional --project will place the export output in a non-default project, as with:

--project <project-id>

A list of currently-available projects can be found with:

ocli projects list

Example:

ocli molsearch query export <id> –path /project/<project_id>/user/<username>/<path> –project <project_id> –ids=1,2,3

Usage

ocli molsearch query export [OPTIONS] QUERY

Options

--path <path>: Orion path where exported dataset is placed

--project <project>

--name <name>: Name of output dataset.

--format <format>: Output format.

--background: Export in async mode?

--ids <ids>: Comma-separated list of result IDs to export.

Arguments

QUERY: Required argument

help

Long format of help CMD, or the first level commands if CMD is not specified.

Usage

ocli molsearch query help [OPTIONS] [CMD]...

Arguments

CMD: Optional argument(s)

info

Information about a specific molecule search query.

Example: ocli molsearch query info <query_id>

Usage

ocli molsearch query info [OPTIONS] QUERY

Arguments

QUERY: Required argument

list

List all molecule search queries.

Example: ocli molsearch query list

Usage

ocli molsearch query list [OPTIONS]

Options

--offset <offset>: Offset from the start of the list

--limit <limit>: Number of objects to list

--query-type <query_type>: Type of query to list

--project <project>

--programmatic <programmatic>: Filter queries created by ocli (True), UI (False), or all queries (None)

list-results

List results for a single molecule search query.

Example: ocli molsearch query list-results <query_id>

Usage

ocli molsearch query list-results [OPTIONS] QUERY

Options

--offset <offset>: Offset from the start of the list

--limit <limit>: Number of objects to list

Arguments

QUERY: Required argument

smiles

Get SMILES string for the molecule with the given title.

Searches all loaded 2D databases.

Example: ocli molsearch query smiles aspirin

Usage

ocli molsearch query smiles [OPTIONS] TITLE

Arguments

TITLE: Required argument

update

Update a molecule search query.

Example: ocli molsearch query update <query_id> –name=<query_name> –saved=<True|False>

Usage

ocli molsearch query update [OPTIONS] QUERY

Options

--name <name>: Query name.

--saved <saved>: Save query.

Arguments

QUERY: Required argument

Token Commands

These commands are used to manage tokens.

ocli tokens

Orion token commands

A token is used to authenticate a client when communicating with Orion

Usage

ocli tokens [OPTIONS] COMMAND [ARGS]...

create

Create an Orion token

Usage

ocli tokens create [OPTIONS] DESCRIPTION

Arguments

DESCRIPTION: Required argument

delete

Delete an Orion token

Usage

ocli tokens delete [OPTIONS] IDENTIFIER

Arguments

IDENTIFIER: Required argument

help

Long format of help CMD, or the first level commands if CMD is not specified.

Usage

ocli tokens help [OPTIONS] [CMD]...

Arguments

CMD: Optional argument(s)

info

Retrieve an Orion token

A token is used to authenticate orionclient when communicating with Orion

Usage

ocli tokens info [OPTIONS] IDENTIFIER

Arguments

IDENTIFIER: Required argument

list

List Orion tokens

This command will not display the value associated with the tokens

Usage

ocli tokens list [OPTIONS]

Options

--offset <offset>: Offset from the start of the list

--limit <limit>: Number of objects to list

update

Update an Orion Token

Allows for modification of an Orion Token

Usage

ocli tokens update [OPTIONS] IDENTIFIER

Options

-d, --description <description>

Arguments

IDENTIFIER: Required argument

User Commands

These commands are used to manage users.

ocli users

Orion user commands

Provides information about Orion users within the same organization.

Usage

ocli users [OPTIONS] COMMAND [ARGS]...

help

Long format of help CMD, or the first level commands if CMD is not specified.

Usage

ocli users help [OPTIONS] [CMD]...

Arguments

CMD: Optional argument(s)

info

Retrieve information about an Orion user

Usage

ocli users info [OPTIONS] IDENTIFIER

Arguments

IDENTIFIER: Required argument

list

List Orion users

Filters:

–show-inactive : Also show inactive users in the output (only available for admin users)

Usage

ocli users list [OPTIONS] [FILTERS]...

Options

--offset <offset>: Offset from the start of the list

--limit <limit>: Number of objects to list

--show-inactive: Include inactive users in output

Arguments

FILTERS: Optional argument(s)

Scaling Group Commands

These commands are used to manage scaling groups.

ocli scaling-groups

Orion scaling group commands

Usage

ocli scaling-groups [OPTIONS] COMMAND [ARGS]...

list

List Orion Scaling Groups

Usage

ocli scaling-groups list [OPTIONS]

update

Update the allowed size, reserve, and various states of a scaling group.

The –gpu-only flag can be used to modify scaling group behavior. For AWS resources, this flag is set to TRUE by default and should not be changed, so that CPU jobs do not run on costly GPU instances. You can modify this to FALSE for CDNS groups to allow a mixture of CPU and GPU work.

Usage

ocli scaling-groups update [OPTIONS] GROUP

Options

--max-size <max_size>

--min-size <min_size>

--min-reserve <min_reserve>

--affinity <affinity>

--state <state>

--gpu-only <gpu_only>

Arguments

GROUP: Required argument

Service Commands

Orion Services is a registry of internal and external services integrated within the larger Orion system.

Service Specifications

These commands create and manipulate service specifications.

ocli services spec

Specification of Orion Service.

Orion services is a registry of internal or external services integrated with the larger Orion system.

Usage

ocli services spec [OPTIONS] COMMAND [ARGS]...

help

Long format of help CMD, or the first level commands if CMD is not specified.

Usage

ocli services spec help [OPTIONS] [CMD]...

Arguments

CMD: Optional argument(s)

info

Retrieve an Orion service specification

Usage

ocli services spec info [OPTIONS] IDENTIFIER

Arguments

IDENTIFIER: Required argument

list

List available specifications of Orion services

Filters:

owner: id of owner (e.g. owner=10)

examples:

ocli services spec list
ocli services spec list
ocli services spec list –limit=5 owner=10

Usage

ocli services spec list [OPTIONS] [FILTERS]...

Options

--name <name>: Filter by name

--offset <offset>: Offset from the start of the list

--limit <limit>: Number of objects to list

Arguments

FILTERS: Optional argument(s)

list-shares

Sharing status of a specificatgion

Usage

ocli services spec list-shares [OPTIONS] IDENTIFIER

Arguments

IDENTIFIER: Required argument

unshare

Unshare a service specification

Usage

ocli services spec unshare [OPTIONS] IDENTIFIER {user|project|organization}
                           [SHARE_IDS]...

Arguments

IDENTIFIER: Required argument

SHARE_TYPE: Required argument

SHARE_IDS: Optional argument(s)

Service Tasks

These commands create and manipulate service tasks from service specifications.

ocli services task

Management of Orion Services.

Orion services is a registry of internal or external services integrated with the larger Orion system.

Usage

ocli services task [OPTIONS] COMMAND [ARGS]...

create

Create an Orion service

Usage

ocli services task create [OPTIONS]

Options

--name <name>

--description <description>

--specification <specification>

--external <external>

--url <url>

delete

Delete an Orion service

Usage

ocli services task delete [OPTIONS] IDENTIFIER

Arguments

IDENTIFIER: Required argument

help

Long format of help CMD, or the first level commands if CMD is not specified.

Usage

ocli services task help [OPTIONS] [CMD]...

Arguments

CMD: Optional argument(s)

info

Retrieve an Orion service

Usage

ocli services task info [OPTIONS] IDENTIFIER

Arguments

IDENTIFIER: Required argument

list

List Orion services

Filters:

owner: id of owner (e.g. owner=10)

examples:

ocli services list

ocli services list –limit=5 owner=10

Usage

ocli services task list [OPTIONS] [FILTERS]...

Options

--name <name>: Filter by name

--offset <offset>: Offset from the start of the list

--limit <limit>: Number of objects to list

Arguments

FILTERS: Optional argument(s)

list-shares

Sharing status of a service

Usage

ocli services task list-shares [OPTIONS] IDENTIFIER

Arguments

IDENTIFIER: Required argument

logs

Retrieve the logs of a service task

Get logs based on date:

$ ocli services task logs 1 –from “2024-04-28” –until “2024-05-01”

Usage

ocli services task logs [OPTIONS] IDENTIFIER

Options

--from <from_dt>: start date for the logs

--until <until>: end date for the logs

Arguments

IDENTIFIER: Required argument

unshare

Unshare a service

Usage

ocli services task unshare [OPTIONS] IDENTIFIER {user|project|organization}
                           [SHARE_IDS]...

Arguments

IDENTIFIER: Required argument

SHARE_TYPE: Required argument

SHARE_IDS: Optional argument(s)

update

Update an Orion service

Usage

ocli services task update [OPTIONS] IDENTIFIER

Options

--name <name>

--description <description>

--state <state>

Arguments

IDENTIFIER: Required argument

Orion CLI Commands

Top-Level Options

Timeout

JSON

Profile

Max Retries

Configuring Profiles and Projects

Configure an Orion Profile

ocli config profile

Change the Default Project of an Orion Profile

ocli config project

Delete an Orion Profile

ocli config delete

Retrieve Information about the Current Profile

ocli config info

List the Configured Profiles

ocli config list

Refresh Your Orion Profile Token

ocli config token

Storage in Folders

List Contents of a Folder or Details of an Item

ocli ls

Create a Folder

ocli mkdir

Copy to/from Orion

ocli cp

Peek Inside a File or Dataset in Orion

ocli head

Move a Folder or an Item

ocli mv

Remove a Folder or Item

ocli rm

Workspaces

ocli workspaces

create

help

info

list

list-users

share

unshare

Datasets

ocli datasets

delete

download

finalize

help

info

list

list-tags

share

tag

unshare

untag

upload

File Commands

ocli files

delete

download

help

info

list

list-tags

share

tag

unshare

untag

upload

Collections

ocli collections

close

delete

delete-shards

download

download-shards

help

info

info-shard

list

list-shards