Developer Guide

Girder is a platform-centric web application whose client and server are very loosely coupled. As such, development of Girder can be divided into the server (a CherryPy-based Python module) and the primary client (a Backbone-based) web client. This section is intended to get prospective contributors to understand the tools used to develop Girder.

Configuring Your Development Environment

Next, you should install the Python development dependencies with pip, to provide helpful development tools and to allow the test suite to run:

pip install -r requirements-dev.txt

Install front-end web client development dependencies and build the web client code:

cd girder/web && yarn && yarn build

This will build the core web client. Any plugins you plan to install that have front-end code will need to be built as well. For example, to build the jobs plugin:

cd plugins/jobs/girder_jobs/web_client && yarn && yarn build

Finally, you’ll want to set your server into development mode. Add the following entry into your local config file (see Configuration for instructions):

[server]
mode="development"

Girder Shell

To test various functionality in a typical REPL (Python, IPython, etc) some bootstrapping is required to configure the Girder server. This sets up an “embedded” server, meaning no TCP ports are actually bound but requests can still be performed via Python. Bootstrapping the server involves running girder.utility.server.configureServer with the plugins to be enabled.

Girder provides a utility script for entering into a shell with the server preconfigured. Once Girder is installed the script can be run using girder shell which optionally takes a comma separated list of plugins to enable.

Utilities

Girder has a set of utility modules and classes that provide handy extractions for certain functionality. Detailed API documentation can be found here.

Configuration Loading

The Girder configuration loader allows for lazy-loading of configuration values in a CherryPy-agnostic manner. The recommended idiom for getting the config object is:

from girder.utility import config
cur_config = config.getConfig()

There is a configuration file for Girder located in girder/conf. The file girder.dist.cfg is the file distributed with the repository and containing the default configuration values. This file should not be edited when deploying Girder. Rather, create a custom girder.cfg file and place it in one of the supported locations (see Configuration). You only need to edit the values in the file that you wish to change from their default values; the system loads the dist file first, then the custom file, so your local settings will override the defaults.

Client Development

If you are writing a custom client application that communicates with the Girder REST API, you should look at the Swagger page that describes all of the available API endpoints. The Swagger page can be accessed by navigating a web browser to /api/v1. If you wish to consume the Swagger-compliant API specification programmatically, the JSON listing is served out of /api/v1/describe.

If you are working on the main Girder web client, either in core or extending it via plugins, there are a few conventions that should be followed. Namely, if you write code that instantiates new View descendant objects, you should pass a parentView property when constructing it. This will allow the child view to be cleaned up recursively when the parent view is destroyed. If you forget to set the parentView property when constructing the view, the view will still work as expected, but a warning message will appear in the console to remind you. Example:

import View from '@girder/core/views/View';

MySubView = View.extend({
   ...
});

new MySubView({
    el: ...,
    otherProperty: ...,
    parentView: this
});

If you use View in custom Backbone apps and need to create a new root view object, set the parentView to null. If you are using a Girder widget in a custom app that does not use the View as the base object for its views, you should pass parentView: null and make sure to call destroy() on the view manually when it should be cleaned up.

Server Side Testing

Most of Girder’s server tests are run via tox, which provides virtual environment isolation and automatic dependency installation for test environments. The tox Python package must be installed:

pip install tox

To run the basic test suite, ensure that a MongoDB instance is ready on localhost:27017, then run:

tox

To destroy and recreate all virtual environments used for testing, pass the -r flag to tox.

Static Analysis Tests

Girder’s static analysis (linting) tests are fast to execute, run on all code, and don’t require a running MongoDB. It’s recommended to run them locally before any Python code changes are committed. To execute them, run:

tox -e lint

pytest Tests

Girder’s modern automated tests are written with pytest. To execute them, ensure MongoDB is ready, then run:

tox -e pytest

Specific arguments can be passed through tox to pytest by adding them after a --.

For example, pytest uses -k to filter tests; to run only the testLoadModelDecorator test, run:

tox -e pytest -- -k testLoadModelDecorator

Legacy unittest Tests

Girder’s legacy automated tests are written with Python’s unittest framework and executed with CMake. All new tests should be written with pytest, but many important test cases are still covered only by unitest.

Note

Unless debugging code that is already coverered by a legacy test case, it may be more convenient to allow these tests to be run by Girder’s CI environment, instead of configuring them locally.

To initialize the legacy tests, from the root girder repo, run:

mkdir ../girder-build
cd ../girder-build
cmake ../girder
make

You only need to do this once. From then on, whenever you want to run the tests, run:

cd girder-build
ctest

There are many ways to filter tests when running CTest or run the tests in parallel. For example, this command will run tests with name matches regex server_user with verbose output:

ctest -V -R server_user

Client Side Testing

Static Analysis Tests

To run static analysis tests on client side code, run from the top-level Girder directory:

npm i
npm run lint

Running the client end-to-end tests

Girder’s web client test suite are setup as end-to-end tests that make use of an actual server and database. To run them, make sure you are within your Girder virtual environment, and make sure mongod is running locally on port 27017. You’ll also need to make sure you’ve built all the plugin web client code, which can be done with:

python .circleci/build_plugins.py ./plugins

Once that is done, then run:

cd girder/web
npm i
npm run test

Adding a New Client Side Test

To add a new client side test, add a new spec file in girder/web/test/spec/. We recommend copying an existing test case for setting up the server, and then using VSCode’s Playwright plugin to record your interactions.

Test Coverage Reporting

When Girder’s full test suite is run in the CI environment, a test coverage report for both server and client code is generated and uploaded to Codecov. This may be viewed online at any time.

Code Review

Contributions to Girder are done via pull requests with a core developer approving the PR with GitHub review system. At this point, the topic branch can be merged to master. This is meant to be a simple, low-friction process; however, code review is very important. It should be done carefully and not taken lightly. Thorough code review is a crucial part of developing quality software. When performing a code review, ask the following:

  1. Is the continuous integration server happy with this?

  2. Are there tests for this feature or bug fix?

  3. Is this documented (for users and/or developers)?

  4. Are the commits modular with good notes?

  5. Will this merge cleanly?

  6. Does this break backward compatibility? Is that okay?

  7. What are the security implications of this change? Does this open Girder up to any vulnerabilities (XSS, CSRF, DB Injection, etc)?

Third-Party Libraries

Girder’s standard procedure is to use a tool like piprot to check for out-of-date third-party library requirements on a quarterly basis (typically near the dates of the solstices and equinoxes). Library packages should generally be upgraded to the latest released version, except when:

  • Doing so would introduce any new unfixable bugs or regressions.

  • Other closely-affiliated projects (e.g. Romanesco, Minerva) use the same library and the other project cannot also feasibly be upgraded simultaneously.

  • The library has undergone a major API change, and development resources do not permit updating Girder accordingly or Girder exposes parts of the library as members of Girder’s API surface (e.g. CherryPy) and upgrading would cause incompatible API changes to be exposed. In this case, the library should still be upgraded to the highest non-breaking version that is available at the time.

Note

In the event that a security vulnerability is discovered in a third-party library used by Girder, the library must be upgraded to patch the vulnerability immediately and without regard to the aforementioned exceptions. However, attempts should still be made to maintain API compatibility via monkey patching, wrapper classes, etc.

Modifying core web client libraries

Web client libraries in Girder core are managed via npm. When a new npm package is required, or an existing package is upgraded, the following should be done:

  1. Ensure that you are using a development environment with version >=5.6 of npm installed:

    npm install -g 'npm@>=5.6'

  2. Update girder/web_client/package.json.template or girder/web_client/src/package.json to add a new abstract specifier for the package:

  • Packages that are bundled into the web client must be listed under the dependencies field of girder/web_client/src/package.json and should generally use the tilde range to specify versions.

  • Packages that are part of the build or testing process should be listed under either the dependencies or devDependencies fields of girder/web_client/package.json.template and should generally use the caret range to specify versions.

If updating npm libraries related to linting or documentation, you should instead modify the top-level package.json file, run npm update, then commit the modified files.

Creating a new release

Girder releases are uploaded to PyPI for easy installation via pip. Each time a pull request is merged to master, an incremental “dev” release is created during CI as a pre-release package and published to PyPI, making it easy for downstreams to install bleeding edge packages without needing to clone the Girder repository.

The major, minor, and patch version are inferred automatically using setuptools-scm based on the latest git tag. Hence, creating a new release is as simple as pushing a new git tag. For example, from the target commit, you could simply run:

git tag v4.5.6
git push --tags

That will trigger CircleCI to run, and if all tests pass, the 4.5.6 release will be uploaded to PyPI.