pycyapi 0.0.13

Python client for the CyVerse Science APIs

PyCyAPI

unofficial Python/CLI client for the CyVerse Science (a.k.a. Terrain) APIs

• Status
• Requirements
• Installation
• Usage
  • Authenticating
  • Commands
    • Version
    • Token
    • User
    • List
    • Stat
    • Pull
    • Push
    • Exists
    • Create
    • Share
    • Unshare
    • Tag
    • Tags

Status

API coverage is still sparse, focusing mainly on data and fileio endpoints. It will likely stay this way as this project exists predominantly for consumption by plantit and plantit-action.

Requirements

• Python 3.8+

Installation

To install with pip:

pip install pycyapi

Usage

Generally, the CLI is invoked with pycyapi <command>. All commands return JSON except pycyapi token ... (see below), which returns the token in plain text.

Authenticating

The pycyapi CLI must obtain an access token to authenticate with CyVerse. The token may be provided to commands via the --token parameter, or set as an environment variable CYVERSE_TOKEN. An access token can be obtained from the Terrain API by sending a request with basic auth headers (valid CyVerse username and password):

GET https://de.cyverse.org/terrain/token/cas

A token command (see below) is provided as convenient alternative to manually obtaining a token.

Commands

To show available commands help run pycyapi --help. The following commands are available:

• version: Show the current pycyapi version.
• token: Retrieve a CyVerse authentication token.
• user: Retrieve the user's profile information.
• list: List files in a collection.
• stat: Get information about a file or collection.
• pull: Download one or more files from a collection.
• push: Upload one or more files to a collection.
• exists: Check if a path exists in the data store.
• create: Create a collection in the data store.
• share: Share a file or collection with another user.
• unshare: Revoke another user's access to your file or collection.
• tag: Set metadata for a given file or collection.
• tags: Get metadata for a given file or collection.

To show usage information for a specific command, run pycyapi <command> --help.

Version

To show the current version of pycyapi, use the version command:

pycyapi version

Token

To request a CyVerse CAS authentication token, use the token command:

pycyapi token --username <your CyVerse username> --password <your CyVerse password>

The token can be passed via --token (-t) argument to authenticate subsequent commands.

User

The user command can be used to retrieve public profile information for CyVerse users. For instance:

pycyapi user -t <token> wbonelli

List

To list the contents of a collection in the data store, use the list command. For instance:

pycyapi list -t <token> /iplant/home/shared/iplantcollaborative/testing_tools/

Stat

To view metadata for a particular collection or object in the data store, use the stat command. For instance:

pycyapi stat -t <token> /iplant/home/shared/iplantcollaborative/testing_tools/

Pull

To download a single file from the data store to the current working directory, simply provide its full path:

pycyapi pull -t <token> /iplant/home/shared/iplantcollaborative/testing_tools/cowsay/cowsay.txt

To download all files from the /iplant/home/shared/iplantcollaborative/testing_tools/cowsay/ collection to the current working directory, just provide the collection path instead:

pycyapi pull -t <token> /iplant/home/shared/iplantcollaborative/testing_tools/cowsay/

Optional arguments are:

• --local_path (-p): Local path to download files to
• --include_pattern (-ip): File patterns to include (0+)
• --force (-f): Whether to overwrite already-existing files

Push

To upload all files in the current working directory to the /iplant/home/<my>/<directory/ in the CyVerse Data Store, use:

pycyapi push -t <token> /iplant/home/<username>/<collection>/

Optional arguments include:

• --local_path (-p): Local path to download files to
• --include_pattern (-ip): File patterns to include (0+)
• --include_name (-in): File names to include (0+)
• --exclude_pattern (-ep): File patterns to exclude (0+)
• --exclude_name (-en): File names to exclude (0+)

To upload a single file to the data store, provide the --local_path (-p) argument. For instance:

pycyapi push -t <token> /iplant/home/<username>/<collection/ -p /my/local/file.txt

If only include_...s are provided, only the file patterns and names specified will be included. If only exclude_...s section are present, all files except the patterns and names specified will be included. If you provide both include_... and exclude_... sections, the include_... rules will first be applied to generate a subset of files, which will then be filtered by the exclude_... rules.

Exists

To determine whether a particular path exists in the data store, use the exists command. For instance, to check if a collection exists:

pycyapi exists -t <token> /iplant/home/<username>/<collection

The --type option can be provided with value dir or file to verify that the given path is of the specified type.

Create

To create a new collection, use the create command:

pycyapi create -t <token> /iplant/home/<username>/<new collection name>

Share

To share a file or collection with another user, use the share command:

pycyapi share -t <token> /iplant/home/<username>/<collection> --username <user to share with> --permission <'read' or 'write'>

Note that you must provide both the --username and --permission flags.

Unshare

To revoke another user's access to your file or collection, use the unshare command:

pycyapi unshare -t <token> /iplant/home/<username>/<collection> --username <username>

This applies to both read and write permissions for the specified user.

Tag

To set metadata for a given file object or collection in your data store, use the tag command:

pycyapi tag <data object ID> -t <token> -a k1=v1 -a k2=v2

This applies the two given attributes to the data object (attributes must be formatted key=value).

Warning: this command is an overwrite, not an append. We do not support appending tags as there is no Terrain endpoint to add/remove individual metadata attributes. Note also that by default, key/value pairs are passed on the avus attribute of the request body rather than irods-avus, e.g.:

POST https://de.cyverse.org/terrain/secured/filesystem/<ID>/metadata
{
    "irods-avus": [],
    "avus": [
        {
            "attr": "some key"
            "value": "some value",
            "unit": ""
        }
    ]
}

To configure irods-avus attributes as well as or in place of standard attributes, use the --irods_attribute (-ia) option. Both standard and iRODS attributes can be used in the same invocation.

Tags

To retrieve the metadata describing a particular file object or collection, use the tags command:

pycyapi tags <data object ID> -t <token>

This will retrieve standard attributes by default. To retrieve iRODS attributes instead, use the --irods (-i) option.