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.
If you have the source directory of Girder, you can find the
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
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
Otherwise you can equivalently just invoke the module directly:
python -m girder_client <subcommand> <arguments>
To see all available subcommands, run:
For help with a specific subcommand, run:
girder-cli <subcommand> --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
girder-cli. For example:
girder-cli --api-url http://localhost:8080/api/v1 <subcommand> ...
You may also specify the URL in parts, using the
host argument, and optional
girder-cli --host girder.example.com ...
girder-cli --host girder.example.com --scheme https --port 443 --api-root /api/v1 ...
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
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
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
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
girder-cli upload 54b6d41a8926486c0cbca367 test_folder --blacklist .DS_Store
Download a Folder hierarchy into a local folder¶
To download a Girder Folder hierarchy rooted at Folder id 54b6d40b8926486c0cbca364 under the local folder download_folder
girder-cli download 54b6d40b8926486c0cbca364 download_folder
Downloading is only supported from a parent type of Folder.
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)