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.

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

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 <subcommand> <arguments>

To see all available subcommands, run:

girder-cli --help

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 api-url argument to 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 scheme, port, and api-root args.

girder-cli --host girder.example.com ...

Or...

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 --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 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)

Further Examples and Function Level Documentation

class girder_client.GirderClient(host=None, port=None, apiRoot=None, scheme=None, apiUrl=None, cacheSettings=None)[source]

A class for interacting with the Girder RESTful API. Some simple examples of how to use this class follow:

client = GirderClient(apiUrl='http://myhost:8080')
client.authenticate('myname', 'mypass')

folder_id = '53b714308926486402ac5aba'
item = client.createItem(folder_id, 'an item name', 'a description')
client.addMetadataToItem(item['_id'], {'metadatakey': 'metadatavalue'})
client.uploadFileToItem(item['_id'], 'path/to/your/file.txt')

r1 = client.getItem(item['_id'])
r2 = client.sendRestRequest('GET', 'item',
    {'folderId': folder_id, 'sortdir': '-1' })
r3 = client.sendRestRequest('GET', 'resource/search',
    {'q': 'aggregated','types': '["folder", "item"]'})
addFolderUploadCallback(callback)[source]

Saves a passed in callback function that will be called after each folder has completed. Multiple callback functions can be added, they will be called in the order they were added by calling this function. Callback functions will be called after a folder in Girder is created and all subfolders and items for that folder have completed uploading. Callback functions should take two parameters: - the folder in Girder - the full path to the local folder

Parameters:callback – callback function to be called.
addItemUploadCallback(callback)[source]

Saves a passed in callback function that will be called after each item has completed. Multiple callback functions can be added, they will be called in the order they were added by calling this function. Callback functions will be called after an item in Girder is created and all files for that item have been uploaded. Callback functions should take two parameters: - the item in Girder - the full path to the local folder or file comprising the item

Parameters:callback – callback function to be called.
addMetadataToFolder(folderId, metadata)[source]

Takes an folder ID and a dictionary containing the metadata

Parameters:
  • folderId – ID of the folder to set metadata on.
  • metadata – dictionary of metadata to set on folder.
addMetadataToItem(itemId, metadata)[source]

Takes an item ID and a dictionary containing the metadata

Parameters:
  • itemId – ID of the item to set metadata on.
  • metadata – dictionary of metadata to set on item.
authenticate(username=None, password=None, interactive=False, apiKey=None)[source]

Authenticate to Girder, storing the token that comes back to be used in future requests. This method can be used in two modes, either username and password authentication, or using an API key. Username example:

gc.authenticate(username='myname', password='mypass')

Note that you may also pass interactive=True and omit either the username or password argument to be prompted for them in the shell. The second mode is using an API key:

API keys can be created and managed on your user account page in the Girder web client, and can be used to provide limited access to the Girder web API.

Parameters:
  • username – A string containing the username to use in basic authentication.
  • password – A string containing the password to use in basic authentication.
  • interactive – If you want the user to type their username or password in the shell rather than passing it in as an argument, set this to True. If you pass a username in interactive mode, the user will only be prompted for a password. This option only works in username/password mode, not API key mode.
  • apiKey (str) – Pass this to use an API key instead of username/password authentication.
createCollection(name, description='', public=False)[source]

Creates and returns a collection.

createFolder(parentId, name, description='', parentType='folder', public=None)[source]

Creates and returns a folder.

Parameters:parentType – One of (‘folder’, ‘user’, ‘collection’)
createItem(parentFolderId, name, description='', reuseExisting=False)[source]

Creates and returns an item.

createResource(path, params)[source]

Creates and returns a resource.

createUser(login, email, firstName, lastName, password, admin=None)[source]

Creates and returns a user.

delete(path, parameters=None)[source]

Convenience method to call sendRestRequest() with the ‘DELETE’ HTTP method.

downloadFile(fileId, path, created=None)[source]

Download a file to the given local path or file-like object.

Parameters:
  • fileId – The ID of the Girder file to download.
  • path – The path to write the file to, or a file-like object.
downloadFolderRecursive(folderId, dest, sync=False)[source]

Download a folder recursively from Girder into a local directory.

Parameters:
  • folderId (ObjectId or Unix-style path to the resource in Girder.) – Id of the Girder folder or resource path to download.
  • dest (str) – The local download destination.
  • sync (bool) – If True, check if item exists in local metadata cache and skip download provided that metadata is identical.
downloadItem(itemId, dest, name=None)[source]

Download an item from Girder into a local folder. Each file in the item will be placed into the directory specified by the dest parameter. If the item contains multiple files or a single file with a different name than the item, the item will be created as a directory under dest and the files will become files within that directory.

Parameters:
  • itemId – The Id of the Girder item to download.
  • dest – The destination directory to write the item into.
  • name – If the item name is known in advance, you may pass it here which will save a lookup to the server.
downloadResource(resourceId, dest, resourceType='folder', sync=False)[source]

Download a collection, user, or folder recursively from Girder into a local directory.

Parameters:
  • resourceId (ObjectId or Unix-style path to the resource in Girder.) – ID or path of the resource to download.
  • dest (str) – The local download destination. Can be an absolute path or relative to the current working directory.
  • resourceType (str) – The type of resource being downloaded: ‘collection’, ‘user’, or ‘folder’.
  • sync (bool) – If True, check if items exist in local metadata cache and skip download if the metadata is identical.
get(path, parameters=None)[source]

Convenience method to call sendRestRequest() with the ‘GET’ HTTP method.

getCollection(collectionId)[source]

Retrieves a collection by its ID.

Parameters:collectionId – A string containing the ID of the collection to retrieve from Girder.
getFile(fileId)[source]

Retrieves a file by its ID.

Parameters:fileId – A string containing the ID of the file to retrieve from Girder.
getFolder(folderId)[source]

Retrieves a folder by its ID.

Parameters:folderId – A string containing the ID of the folder to retrieve from Girder.
getFolderAccess(folderId)[source]

Retrieves a folder’s access by its ID.

Parameters:folderId – A string containing the ID of the folder to retrieve access for from Girder.
getItem(itemId)[source]

Retrieves a item by its ID.

Parameters:itemId – A string containing the ID of the item to retrieve from Girder.
getResource(path, id=None, property=None)[source]

Returns a resource based on id or None if no resource is found; if property is passed, returns that property value from the found resource.

getUser(userId)[source]

Retrieves a user by its ID.

Parameters:userId – A string containing the ID of the user to retrieve from Girder.
inheritAccessControlRecursive(ancestorFolderId, access=None, public=None)[source]

Take the access control and public value of a folder and recursively copy that access control and public value to all folder descendants, replacing any existing access control on the descendant folders with that of the ancestor folder.

Parameters:
  • ancestorFolderId – Id of the Girder folder to copy access control from, to all of its descendant folders.
  • access – Dictionary Access control target, if None, will take existing access control of ancestor folder
  • public – Boolean public value target, if None, will take existing public value of ancestor folder
isFileCurrent(itemId, filename, filepath)[source]

Tests whether the passed in filepath exists in the item with itemId, with a name of filename, and with the same length. Returns a tuple (file_id, current) where file_id = id of the file with that filename under the item, or None if no such file exists under the item. current = boolean if the file with that filename under the item has the same size as the file at filepath.

Parameters:
  • itemId – ID of parent item for file.
  • filename – name of file to look for under the parent item.
  • filepath – path to file on disk.
listCollection(limit=None, offset=None)[source]

This is a generator that will yield all collections in the system.

Parameters:
  • limit – If requesting a specific slice, the length of the slice.
  • offset – Starting offset into the list.
listFile(itemId, limit=None, offset=None)[source]

This is a generator that will yield files under the given itemId.

Parameters:
  • itemId – the item’s ID
  • limit – the result set size limit.
  • offset – the result offset.
listFolder(parentId, parentFolderType='folder', name=None, limit=None, offset=None)[source]

This is a generator that will yield a list of folders based on the filter parameters.

Parameters:
  • parentId – The parent’s ID.
  • parentFolderType – One of (‘folder’, ‘user’, ‘collection’).
  • name – query for exact name match of items.
  • limit – If requesting a specific slice, the length of the slice.
  • offset – Starting offset into the list.
listItem(folderId, text=None, name=None, limit=None, offset=None)[source]

This is a generator that will yield all items under a given folder.

Parameters:
  • folderId – the parent folder’s ID.
  • text – query for full text search of items.
  • name – query for exact name match of items.
  • limit – If requesting a specific slice, the length of the slice.
  • offset – Starting offset into the list.
listResource(path, params=None, limit=None, offset=None)[source]

This is a generator that will yield records using the given path and params until exhausted. Paging of the records is done internally, but can be overriden by manually passing a limit value to select only a single page. Passing an offset will work in both single-page and exhaustive modes.

listUser(limit=None, offset=None)[source]

This is a generator that will yield all users in the system.

Parameters:
  • limit – If requesting a specific slice, the length of the slice.
  • offset – Starting offset into the list.
loadLocalMetadata(dest)[source]

Reads item metadata from a local folder.

Parameters:dest – The local download destination.
loadOrCreateFolder(folderName, parentId, parentType)[source]

Returns a folder in Girder with the given name under the given parent. If none exists yet, it will create it and return it.

Parameters:
  • folderName – the name of the folder to look up.
  • parentId – id of parent in Girder
  • parentType – one of (collection, folder, user)
Returns:

The folder that was found or created.

loadOrCreateItem(name, parentFolderId, reuseExisting=True)[source]

Create an item with the given name in the given parent folder.

Parameters:
  • name – The name of the item to load or create.
  • parentFolderId – id of parent folder in Girder
  • reuseExisting – boolean indicating whether to load an existing item of the same name in the same location, or create a new one.
patch(path, parameters=None, data=None, json=None)[source]

Convenience method to call sendRestRequest() with the ‘PATCH’ HTTP method.

post(path, parameters=None, files=None, data=None, json=None)[source]

Convenience method to call sendRestRequest() with the ‘POST’ HTTP method.

put(path, parameters=None, data=None, json=None)[source]

Convenience method to call sendRestRequest() with the ‘PUT’ HTTP method.

resourceLookup(path, test=False)[source]

Look up and retrieve resource in the data hierarchy by path.

Parameters:
  • path – The path of the resource. The path must be an absolute Unix path starting with either “/user/[user name]” or “/collection/[collection name]”.
  • test – Whether or not to return None, if the path does not exist, rather than throwing an exception.
saveLocalMetadata(dest)[source]

Dumps item metadata collected during a folder download.

Parameters:dest – The local download destination.
sendRestRequest(method, path, parameters=None, data=None, files=None, json=None)[source]

This method looks up the appropriate method, constructs a request URL from the base URL, path, and parameters, and then sends the request. If the method is unknown or if the path is not found, an exception is raised, otherwise a JSON object is returned with the Girder response.

This is a convenience method to use when making basic requests that do not involve multipart file data that might need to be specially encoded or handled differently.

Parameters:
  • method (str) – The HTTP method to use in the request (GET, POST, etc.)
  • path (str) – A string containing the path elements for this request. Note that the path string should not begin or end with the path separator, ‘/’.
  • parameters (dict) – A dictionary mapping strings to strings, to be used as the key/value pairs in the request parameters.
  • data – A dictionary, bytes or file-like object to send in the body.
  • files (dict) – A dictonary of ‘name’ => file-like-objects for multipart encoding upload.
  • json (dict) – A JSON object to send in the request body.
setFolderAccess(folderId, access, public)[source]

Sets the passed in access control document along with the public value to the target folder.

Parameters:
  • folderId – Id of the target folder.
  • access – JSON document specifying access control.
  • public – Boolean specificying the public value.
setResourceTimestamp(id, type, created=None, updated=None)[source]

Set the created or updated timestamps for a resource.

transformFilename(name)[source]

Sanitize a resource name from Girder into a name that is safe to use as a filesystem path.

Parameters:name (str) – The name to transform.
upload(filePattern, parentId, parentType='folder', leafFoldersAsItems=False, reuseExisting=False, blacklist=None, dryRun=False)[source]

Upload a pattern of files.

This will recursively walk down every tree in the file pattern to create a hierarchy on the server under the parentId.

Parameters:
  • filePattern (str) – a glob pattern for files that will be uploaded, recursively copying any file folder structures.
  • parentId (ObjectId or Unix-style path to the resource in Girder.) – Id of the parent in Girder or resource path.
  • parentType (str) – one of (collection,folder,user), default of folder.
  • leafFoldersAsItems (bool) – bool whether leaf folders should have all files uploaded as single items.
  • reuseExisting (bool) – bool whether to accept an existing item of the same name in the same location, or create a new one instead.
  • dryRun (bool) – Set this to True to print out what actions would be taken, but do not actually communicate with the server.
uploadFile(parentId, stream, name, size, parentType='item', progressCallback=None, reference=None, mimeType=None)[source]

Uploads a file into an item or folder.

Parameters:
  • parentId (str) – The ID of the folder or item to upload into.
  • stream (file-like) – Readable stream object.
  • name (str) – The name of the file to create.
  • size (str) – The length of the file. This must be exactly equal to the total number of bytes that will be read from stream, otherwise the upload will fail.
  • parentType (str) – ‘item’ or ‘folder’.
  • progressCallback (callable) – If passed, will be called after each chunk with progress information. It passes a single positional argument to the callable which is a dict of information about progress.
  • reference (str) – optional reference to send along with the upload.
  • mimeType (str or None) – MIME type to set on the file. Attempts to guess if not explicitly passed.
Returns:

The file that was created on the server.

uploadFileContents(fileId, stream, size, reference=None)[source]

Uploads the contents of an existing file.

Parameters:
  • fileId – ID of file to update
  • stream (file-like) – Readable stream object.
  • size (str) – The length of the file. This must be exactly equal to the total number of bytes that will be read from stream, otherwise the upload will fail.
  • reference (str) – optional reference to send along with the upload.
uploadFileToItem(itemId, filepath, reference=None, mimeType=None, filename=None)[source]

Uploads a file to an item, in chunks. If ((the file already exists in the item with the same name and size) or (if the file has 0 bytes), no uploading will be performed.

Parameters:
  • itemId – ID of parent item for file.
  • filepath – path to file on disk.
  • reference (str) – optional reference to send along with the upload.
  • mimeType (str or None) – MIME type for the file. Will be guessed if not passed.
  • filename – path with filename used in Girder. Defaults to basename of filepath.
Returns:

the file that was created.

exception girder_client.HttpError(status, text, url, method)[source]

Raised if the server returns an error status code from a request.