Developer Cookbook

This cookbook consists of a set of examples of common tasks that developers may encounter when developing Girder applications.

Client cookbook

The following examples are for common tasks that would be performed by a Girder client application.

Authenticating to the web API

Clients can make authenticated web API calls by passing a secure temporary token with their requests. Tokens are obtained via the login process; the standard login process requires the client to make an HTTP GET request to the api/v1/user/authentication route, using HTTP Basic Auth to pass the user credentials. For example, for a user with login “john” and password “hello”, first base-64 encode the string "john:hello" which yields "am9objpoZWxsbw==". Then take the base-64 encoded value and pass it via the Girder-Authorization header (The Authorization header will also work):

Girder-Authorization: Basic am9objpoZWxsbw==

If the username and password are correct, you will receive a 200 status code and a JSON document from which you can extract the authentication token, e.g.:

{
  "authToken": {
    "token": "urXQSHO8aF6cLB5si0Ch0WCiblvW1m8YSFylMH9eqN1Mt9KvWUnghVDKQy545ZeA",
    "expires": "2015-04-11 00:06:14.598570"
  },
  "message": "Login succeeded.",
  "user": {
    ...
  }
}

The authToken.token string is the token value you should pass in subsequent API calls, which should either be passed as the token parameter in the query or form parameters, or as the value of a custom HTTP header with the key Girder-Token, e.g.

Girder-Token: urXQSHO8aF6cLB5si0Ch0WCiblvW1m8YSFylMH9eqN1Mt9KvWUnghVDKQy545ZeA

Note

When logging in, the token is also sent to the client in a Cookie header so that web-based clients can persist its value conveniently for its duration. However, for security reasons, merely passing the cookie value back is not sufficient for authentication.

Note

If you are using Girder’s JavaScript web client library in a CORS environment, be sure to set girder.corsAuth = true; in your application prior to calling girder.login. This will allow users’ login sessions to be saved on the origin site’s cookie.

Upload a file

If you are using the Girder javascript client library, you can simply call the upload method of the girder/models/FileModel. The first argument is the parent model object (an ItemModel or FolderModel instance) to upload into, and the second is a browser File object that was selected via a file input element. You can bind to several events of that model, as in the example below.

import FileModel from 'girder/models/FileModel';

var fileModel = new FileModel();
fileModel.on('g:upload.complete', function () {
    // Called when the upload finishes
}).on('g:upload.chunkSent', function (info) {
    // Called on each chunk being sent
}).on('g:upload.progress', function (info) {
    // Called regularly with progress updates
}).on('g:upload.error', function (info) {
    // Called if an upload fails partway through sending the data
}).on('g:upload.errorStarting', function (info) {
    // Called if an upload fails to start
});
fileModel.upload(parentFolder, fileObject);

If you don’t feel like making your own upload interface, you can simply use the girder/views/widgets/UploadWidget to provide a nice GUI interface for uploading. It will prompt the user to drag and drop or browse for files, and then shows a current and overall progress bar and also provides controls for resuming a failed upload.

Using the Girder upload widget in a custom app

Your custom javascript application can easily reuse the existing upload widget provided in the Girder javascript library if you don’t want to write your own upload view. This can save time spent duplicating functionality, since the upload widget provides current and overall progress bars, file displays, a drag-and-droppable file selection button, resume behavior in failure conditions, and customizable hooks for various stages of the upload process.

The default behavior of the upload widget is to display as a modal dialog, but many users will want to simply embed it underneath a normal DOM element flow. The look and behavior of the widget can be customized when the widget is instantiated by passing in options like so:

import UploadWidget from 'girder/views/widgets/UploadWidget';

new UploadWidget({
    option: value,
    ...
});

The following options are not required, but may be used to modify the behavior of the widget:

  • [parent] - If the parent object is known when instantiating this upload widget, pass the object here.
  • [parentType=folder] - If the parent type is known when instantiating this upload widget, pass the object here. Otherwise set noParent: true and set it later, prior to starting the upload.
  • [noParent=false] - If the parent object being uploaded into is not known at the time of widget instantiation, pass noParent: true. Callers must ensure that the parent is set by the time uploadNextFile() actually gets called.
  • [title="Upload files"] - Title for the widget. This is highly recommended when rendering as a modal dialog. To disable rendering of the title, simply pass a falsy object.
  • [modal=true] - This widget normally renders as a modal dialog. Pass modal: false to disable the modal behavior and simply render underneath a parent element.
  • [overrideStart=false] - Some callers will want to hook into the pressing of the start upload button and add their own logic prior to actually sending the files. To do so, set overrideStart: true and bind to the g:uploadStarted event of this widget. The caller is then responsible for calling uploadNextFile() on the widget when they have completed their actions and are ready to actually send the files.

For general documentation on embedding Girder widgets in a custom application, see the section on client development.

Server cookbook

The following examples refer to tasks that are executed by the Girder application server.

Creating a REST route

The process of creating new REST resources and routes is documented here.

The API docs of the route method can be found here.

Loading a resource by its ID

This is a fundamental element of many REST operations; they receive a parameter representing a resource’s unique ID, and want to load the corresponding resource from that ID. This behavior is known as model loading. As a brief example, if we had the ID of a folder within our REST route handler, and wanted to load its corresponding document from the database, it would look like:

from girder.models.folder import Folder
folder = Folder().load(theFolderId, user=self.getCurrentUser(), level=AccessType.READ)

The load method of each model class takes the resource’s unique ID as its first argument (this is the _id field in the documents). For access controlled models like the above example, it also requires the developer to specify which user is requesting the loading of the resource, and what access level is required on the resource. If the ID passed in does not correspond to a record in the database, None is returned.

Sometimes models need to be loaded outside the context of being requested by a specific user, and in those cases the force flag should be used:

Folder().load(theFolderId, force=True)

Send a raw or streaming HTTP response body

For consistency, the default behavior of a REST endpoint in Girder is to take the return value of the route handler and encode it in the format specified by the client in the Accepts header, usually application/json. However, in some cases you may want to force your endpoint to send a raw response body back to the client.

If you want to send a raw response, you can simply decorate your route handler with the girder.api.rest.rawResponse decorator, or call girder.api.rest.setRawResponse() within the body of the route handler. For example:

from girder.api import access, rest

@access.public
@rest.rawResponse
def rawExample(self, params):
    return 'raw string'

That will make the response body precisely the string raw string. If the data size being sent to the client is large or unbounded, you should use a streaming response.

If you want to send a streaming response, simply make your route handler return a generator function. A streaming response is automatically sent as a raw response. Developers have full control of the buffer size of the streamed response body; each time you yield data in your generator function, the buffer will be flushed to the client. As a minimal example, the following route handler would flush 10 chunks to the client, and the full response body would be 0123456789.

from girder.api import access

@access.public
def streamingExample(self, params):
    def gen():
        for i in range(10):
            yield str(i)
    return gen

Serving a static file

If you are building a plugin that needs to serve up a static file from a path on disk, you can make use of the staticFile utility, as in the following example:

import os
from girder.utility.server import staticFile

def load(info):
    path = os.path.join(PLUGIN_ROOT_DIR, 'static', 'index.html')
    info['serverRoot'].static_route = staticFile(path)

The staticFile utility should be assigned to the route corresponding to where the static file should be served from.

Note

If a relative path is passed to staticFile, it will be interpreted relative to the current working directory, which may vary. If your static file resides within your plugin, it is recommended to use the special PLUGIN_ROOT_DIR property of your server module, or the equivalent info['pluginRootDir'] value passed to the load method.

Sending Emails

Girder has a utility module that make it easy to send emails from the server. For the sake of maintainability and reusability of the email content itself, emails are stored as Mako templates in the girder/mail_templates directory. By convention, email templates should include _header.mako above and _footer.mako below the content. If you wish to send an email from some point within the application, you can use the utility functions within girder.utility.mail_utils, as in the example below:

from girder.utility import mail_utils

...

def my_email_sending_code():
    html = mail_utils.renderTemplate('myContentTemplate.mako', {
        'param1': 'foo',
        'param2': 'bar'
    })
    mail_utils.sendEmail(to=email, subject='My mail from Girder', text=html)

If you wish to send email from within a plugin, simply create a server/mail_templates directory within your plugin, and it will be automatically added to the mail template search path when your plugin is loaded. To avoid name collisions, convention dictates that mail templates within your plugin should be prefixed by your plugin name, e.g., my_plugin.my_template.mako.

If you want to send email to all of the site administrators, there is a convenience keyword argument for that. Rather than setting the to field, pass toAdmins=True.

mail_utils.sendEmail(toAdmins=True, subject='...', text='...')

Note

All emails are sent as rich text (text/html MIME type).

Logging a Message

Girder application servers maintain an error log and an information log and expose a utility module for sending events to them. Any 500 error that occurs during execution of a request will automatically be logged in the error log with a full stack trace. Also, any 403 error (meaning a user who is logged in but requests access to a resource that they don’t have permission to access) will also be logged automatically. All log messages automatically include a timestamp, so there is no need to add your own.

If you want to log your own custom error or info messages outside of those default behaviors, use the following examples:

from girder import logger

try:
    ...
except Exception:
    # Will log the most recent exception, including a traceback, request URL,
    # and remote IP address. Should only be called from within an exception handler.
    logger.exception('A descriptive message')

# Will log a message to the info log.
logger.info('Test')

Adding Automated Tests with CTest

Note

Girder is transitioning towards using pytest for its testing. The section below describes how to add automated tests using pytest.

The server side Python tests are run using unittest. All of the actual test cases are stored under tests/cases.

Adding to an Existing Test Case

If you want to add tests to an existing test case, just create a new function in the relevant TestCase class. The function name must start with test. If the existing test case has setUp or tearDown methods, be advised that those methods will be run before and after each of the test methods in the class.

Creating a New Test Case

To create an entirely new test case, create a new file in cases that ends with _test.py. To start off, put the following code in the module (with appropriate class name of course):

from .. import base

def setUpModule():
    base.startServer()

def tearDownModule():
    base.stopServer()

class MyTestCase(base.TestCase):

Note

If your test case does not need to communicate with the server, you do not need to call base.startServer() and base.stopServer() in the setUpModule() and tearDownModule() functions. Those functions are called once per module rather than once per test method.

Then, in the MyTestCase class, just add functions that start with test, and they will automatically be run by unittest.

Finally, you’ll need to register your test in the CMakeLists.txt file in the tests directory. Just add a line like the ones already there at the bottom. For example, if the test file you created was called thing_test.py, you would add:

add_python_test(thing)

Re-run CMake in the build directory, and then run CTest, and your test will be run.

Note

By default, add_python_test allows the test to be run in parallel with other tests, which is normally fine since each python test has its own assetstore space and its own mongo database, and the server is typically mocked rather than actually binding to its port. However, some tests (such as those that actually start the cherrypy server) should not be run concurrently with other tests that use the same resource. If you have such a test, use the RESOURCE_LOCKS argument to add_python_test. If your test requires the cherrypy server to bind to its port, declare that it locks the cherrypy resource. If it also makes use of the database, declare that it locks the mongo resource. For example:

add_python_test(my_test RESOURCE_LOCKS cherrypy mongo)

Adding Automated Tests with pytest

Test cases for pytest are stored in girder/test.

Provided Fixtures

All helper utilities for developing tests with pytest are stored in the pytest_girder package within Girder. A list of fixtures provided can be viewed by running pytest --fixtures from the Girder directory.

Adding to an Existing Test Case

If you want to add tests to an existing test case, just create a new function in the file. The function name must start with test.

Creating a New Test Case

To create an entirely new test, create a new file in girder/test that starts with test_. To start off, put the following code in the module (with appropriate function name of course):

def testCase(server):
    pass

Note

If your test case does not need to communicate with the server, you do not need include server as an argument to your test. Refer to pytest fixtures for more information on using dependency injection in this manner.

Downloading External Data Artifacts for Test Cases

In some cases, it is necessary to perform a test on an artifact that is too big to store inside a repository. For tests such as these, Girder provides a way to link to test artifacts served at https://data.kitware.com (or any Girder instance with the hashsum_download plugin enabled) and have them automatically downloaded and cached during the build stage, while storing only the SHA512 hashsum of the test artifact in the source repository as a “key file”.

To add a new external artifact, first make an account at https://data.kitware.com and upload a publicly accessible file (ideally to the Girder collection, which you can request access to in your feature’s GitHub pull request). Then, while viewing the newly created item page, open the file info dialog for the test artifact (by clicking the “i” icon to “Show info”, next to the file link), then click the “SHA-512” field’s key icon to “Download key file”. Save and commit this downloaded key file to the tests/data/ directory of Girder’s repository. This file can then be listed as an optional EXTERNAL_DATA argument to the add_python_test function to have the artifact downloaded as an extra build step. As an example, consider the artifact currently used for testing called tests/data/test_file.txt.md5. To use this artifact in you test, you would add the test as follows:

add_python_test(my_test EXTERNAL_DATA test_file.txt)

The EXTERNAL_DATA keyword argument can take a list of files or even directories. When a directory is provided, it will download all files that exist in the given path. Inside your test, you can access these artifact files under the path given by the environment variable GIRDER_TEST_DATA_PREFIX as follows

import os
test_artifact = os.path.join(
    os.environ['GIRDER_TEST_DATA_PREFIX'],
    'test_file.txt'
)
with open(test_artifact, 'r') as f:
    content = f.read() # The content of the downloaded test artifact

Setting python code coverage paths

By default, python tests added via the add_python_test cmake function will only report coverage for python files within certain paths. For core tests, the following paths are used:

  • girder
  • clients/python/girder_client

For tests created within a plugin, the plugin’s server directory is added to this list. If you wish to report coverage on files residing outside of one of these directories, you can add a COVERAGE_PATHS argument to the add_python_test call. This argument accepts one or more comma-separated paths. For example, to add coverage reporting to to python files in a plugin’s utils directory for a given test:

add_python_test(cat
    PLUGIN cats
    COVERAGE_PATHS "${PROJECT_SOURCE_DIRECTORY}/plugins/cats/utils"
)

Mounting a custom application

Normally, the root node (/) of the server will serve up the Girder web client. A plugin may contain an entire application separate from the default Girder web client. This plugin may be written in a way which enables administrators to mount the application at a configured endpoint, including the option of replacing the root node with the plugin application.

To achieve this, you simply have to register your own root and configure your routes as you wish. In your plugin’s load method, you would follow this convention:

from girder.utility.plugin_utilities import registerPluginWebroot
registerPluginWebroot(CustomAppRoot(), info['name'])

This will register your CustomAppRoot with Girder so that it can then be mounted wherever an Administrator specifies using the Server Configuration Panel. See Managing Routes.

Supporting web browser operations where custom headers cannot be set

Some aspects of the web browser make it infeasible to pass the usual Girder-Token authentication header when making a request. For example, if using an EventSource object for SSE, or when you must redirect the user’s browser to a download endpoint that serves its content as an attachment.

In such cases, you may allow specific REST API routes to authenticate using the Cookie. To avoid vulnerabilities to Cross-Site Request Forgery attacks, you should only do this if the endpoint is “read-only” (that is, the endpoint does not make modifications to data on the server). Accordingly, only routes for HEAD and GET requests allow cookie authentication to be enabled (without an additional override).

In order to allow cookie authentication for your route, simply add the cookie decorator to your route handler function. Example:

from girder.api import access

@access.cookie
@access.public
def download(self, params):
    ...

As a last resort, if your endpoint is not read-only and you are unable to pass the Girder-Token header to it, you can pass a token query parameter containing the token , but in practice this will probably never be the case.