Python Client and Girder CLI¶
In addition to the web clients, Girder comes with a python client library and a CLI to allow for programmatic interaction with a Girder server, and also to workaround limitations of the web client. For example, the python CLI makes it much easier to upload a large, nested hierarchy of data from a local directory to Girder, and also makes it much easier to download a large, nested hierarchy of data from Girder to a local directory.
Versioning¶
The Girder python client is versioned separately from the Girder server, but not fully independently because the client and server are coupled. The design intent is that every version of the client should work with every version of the server, though this is not an explicit guarantee. Generally you should use the latest version of the Girder python client that is installable from pip.
Installation¶
If you have the source directory of Girder, you can find the girder_client
package within the clients/python directory. If you do not have the source
directory of Girder, you can install the client via pip:
pip install girder-client
After installing the client via pip and if you are using bash,
auto-completion can easily be enabled executing:
eval "$(_GIRDER_CLI_COMPLETE=source girder-cli)"
For convenience, adding this line at the end of .bashrc will make sure
auto-completion is always available.
For more details, see http://click.pocoo.org/6/bashcomplete/
The Command Line Interface¶
The girder_client package ships with a command-line utility that wraps some of
its common functionality to make it easy to invoke operations without having
to write any custom python scripts. If you have installed girder_client via
pip, you can use the special girder-cli executable:
girder-cli <arguments>
Otherwise you can equivalently just invoke the module directly:
python -m girder_client <command> <arguments>
To see all available commands, run:
girder-cli --help
For help with a specific command, run:
girder-cli <command> --help
Specifying the Girder Instance¶
When constructing a Girder client, you must declare what instance of Girder
you wish to connect to. The easiest way to do so is to pass the full URL to the
REST API of the Girder instance you wish to connect to using the api-url
argument to girder-cli. For example:
girder-cli --api-url http://localhost:8080/api/v1 <command> ...
Instead of using api-url argument, you may also specify the URL in parts, using the
host argument, and optional scheme, port, and api-root args.
Specifying credentials¶
The recommended way is to generate an API key and specify
the api-key argument.
girder-cli --api-url https://girder.example.com:443/api/v1 --api-key abcdefghijklmopqrstuvwxyz012345678901234 ...
Setting the GIRDER_API_KEY environment variable is also supported:
export GIRDER_API_KEY=abcdefghijklmopqrstuvwxyz012345678901234
girder-cli --api-url https://girder.example.com:443/api/v1 ...
The client also supports username and password args. If only the
username is specified, the client will prompt the user to interactively
input their password.
Disabling SSL verification¶
Specifying --no-ssl-verify allows to ignore SSL verification. This is
usually required when using the client behind a proxy that is not configured to
accept the certificate of the given host.
Specifying a custom SSL certificate¶
Specifying --certificate /path/to/custom_bundle.pem allows to use a custom “bundle” of
Certificate Authority (CA) public keys (CA certs) for performing the SSL verification
applied when the https scheme is associated with the API url.
By default, the carefully curated collection of Root Certificates from Mozilla is used. See https://pypi.python.org/pypi/certifi
Upload a local file hierarchy¶
To upload a folder hierarchy rooted at test_folder to the Girder Folder with id 54b6d41a8926486c0cbca367
girder-cli upload 54b6d41a8926486c0cbca367 test_folder
When using the upload command, the default --parent-type, meaning the type
of resource the local folder will be created under in Girder, is Folder, so the
following are equivalent
girder-cli upload 54b6d41a8926486c0cbca367 test_folder
girder-cli upload 54b6d41a8926486c0cbca367 test_folder --parent-type folder
To upload that same local folder to a Collection or User, specify the parent type as follows
girder-cli upload 54b6d41a8926486c0cbca459 test_folder --parent-type user
To see what local folders and files on disk would be uploaded without actually
uploading anything, add the --dry-run flag
girder-cli upload 54b6d41a8926486c0cbca367 test_folder --dry-run
To have leaf folders (those folders with no subfolders, only containing files)
be uploaded to Girder as single Items with multiple Files, i.e. those leaf
folders will be created as Items and all files within the leaf folders will be
Files within those Items, add the --leaf-folders-as-items flag
girder-cli upload 54b6d41a8926486c0cbca367 test_folder --leaf-folders-as-items
If you already have an existing Folder hierarchy in Girder which you have a
superset of on your local disk (e.g. you previously uploaded a hierarchy to
Girder and then added more folders and files to the hierarchy on disk), you can
reuse the existing hierarchy in Girder, which will not create new Folders and
Items for those that match folders and files on disk, by using the --reuse flag.
girder-cli upload 54b6d41a8926486c0cbca367 test_folder --reuse
To include a blacklist of file patterns that will not be uploaded, pass a comma
separated list to the --blacklist arg
girder-cli upload 54b6d41a8926486c0cbca367 test_folder --blacklist .DS_Store
Download a hierarchy of data into a local folder¶
Folder¶
To download a Girder Folder hierarchy rooted at Folder id 54b6d40b8926486c0cbca364 under the local folder download_folder
girder-cli download 54b6d40b8926486c0cbca364 download_folder
Collection¶
To download the Girder Folder hierarchies associated with a Girder Collection with id 57b5c9e58d777f126827f5a1 under the local folder download_folder
girder-cli download --parent-type collection 57b5c9e58d777f126827f5a1 download_folder
User¶
To download the Girder Folder hierarchies associated with a Girder User with id 54f8ac238d777f69813604af under the local folder download_folder
girder-cli download --parent-type user 54b6d40b8926486c0cbca364 download_folder
Item¶
To download the file(s) associated with a Girder Item with if 58b8eb798d777f0aef5d0f78 under the local folder download_folder:
girder-cli download --parent-type item 8b8eb798d777f0aef5d0f78 download_folder
File¶
To download a specific file from girder with id 58b8eb798d777f0aef5d0f78 to the local file local_file
girder-cli download --parent-type file 8b8eb798d777f0aef5d0f78 local_file
Auto-detecting parent-type¶
Both download and upload commands accept a –parent-type argument allowing the users to specify the type (folder, collection, user, or item) associated with the chosen object id.
If the argument is omitted, the client will conveniently try to autodetect the type by iteratively invoking the resource/%id/path?type=%type API end point and checking if a resource is found.
Note that relying on auto-detection incurs extra network requests, which will slow down the script, so it should be avoided for time-sensitive operations.
Synchronize local folder with a Folder hierarchy¶
If the download_folder is a local copy of a Girder Folder hierarchy rooted at Folder id 54b6d40b8926486c0cbca364, any change made to the Girder Folder remotely can be synchronized locally by
girder-cli localsync 54b6d40b8926486c0cbca364 download_folder
This will only download new Items or Items that have been modified since the last download/localsync. Local files that are no longer present in the remote Girder Folder will not be removed. This command relies on a presence of metadata file .metadata-girder within download_folder, which is created upon girder-cli download. If .metadata-girder is not present, localsync will fallback to download.
The Python Client Library¶
For those wishing to write their own python scripts that interact with Girder, we recommend using the Girder python client library, documented below.
Recursively inherit access control to a Folder’s descendants¶
This will take the access control and public value in the Girder Folder with id 54b43e9b8926486c0c06cb4f and copy those to all of the descendant Folders
import girder_client
gc = girder_client.GirderClient(apiUrl='https://data.kitware.com/api/v1')
gc.authenticate('username', 'password')
gc.inheritAccessControlRecursive('54b43e9b8926486c0c06cb4f')
Set callbacks for Folder and Item uploads¶
If you have a function you would like called upon the completion of an Item or Folder upload, you would do the following.
N.B. The Item callbacks are called after the Item is created and all Files are uploaded to the Item. The Folder callbacks are called after the Folder is created and all child Folders and Items are uploaded to the Folder.
import girder_client
gc = girder_client.GirderClient()
def folderCallback(folder, filepath):
# assume we have a folderMetadata dict that has
# filepath: metadata_dict_for_folder
gc.addMetadataToFolder(folder['_id'], folderMetadata[filepath])
def itemCallback(item, filepath):
# assume we have an itemMetadata dict that has
# filepath: metadata_dict_for_item
gc.addMetadataToItem(item['_id'], itemMetadata[filepath])
gc.authenticate('username', 'password')
gc.addFolderUploadCallback(folderCallback)
gc.addItemUploadCallback(itemCallback)
gc.upload(localFolder, parentId)