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

In order to develop Girder, you should first refer to prerequisites, virtual environment, install from Git, and run sections to setup a basic local 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. This will install npm modules eslint and pug-lint, which are needed to run tests. This will also build the web client code:

girder-install web --dev

For more options for building the web client, run:

girder-install web --help

Vagrant

A shortcut to going through the development environment configuration steps is to use Vagrant to setup the environment on a VirtualBox virtual machine. For more documentation on how to set this up, see Developer Installation

See also

For more information on provisioning Girder, see Provisioning.

During Development

Once Girder is started via girder-server, the server will reload itself whenever a Python file is modified.

If you are doing front-end development, it’s much faster to use a watch process to perform automatic fast rebuilds of your code whenever you make changes to source files.

If you are making changes to Girder’s core web client, run the following watch command:

girder-install web --watch

If you are developing a web client of a plugin, run:

girder-install web --watch-plugin your_plugin_name

With watch option, sourcemaps will be generated, which helps debugging front-end code in browser. When you want to end the watch process, press Ctrl+C (or however you would normally terminate a process in your terminal).

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, edit the girder.local.cfg file. 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 local file, so your local settings will override the defaults.

Server Development

All commits to the core python code must work in both python 2.7 and 3.4. Python code in plugins should also work in both, but some plugins may depend on third party libraries that do not support python 3. If that is the case, those plugins should declare "python3": false in their plugin.json or plugin.yml file to indicate that they do not support being run in python 3. Automated testing of those plugins should also be disabled for python3 if those tests would fail in a python 3 environment. This can be achieved by passing an additional flag PY2_ONLY to add_python_test in your plugin.cmake file.

Python Style

We use flake8 to test for Python style on the server side.

Use % instead of format

Use % or some other string formatting operation that coerces to unicode, and avoid format, since it does not coerce to unicode and has caused bugs.

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 relative to the server root. 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/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

Running the Tests

First, you will need to configure the project with CMake.

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

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

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. More information about CTest can be found here.

ctest -V -R server_user

If you run into errors on any of the packaging tests, two possible fixes are

1) run make inside your girder-build directory, which will create a special virtualenv needed to build the packages.

2) delete any of the files generated by the packaging tests, which will be in your source dir girder and could include girder-<version>.tar.gz, girder-web-<version>.tar.gz, and girder-plugins-<version>.tar.gz.

Running the Tests with Coverage Tracing

To run Python coverage on your tests, configure with CMake and run CTest. The coverage data will be automatically generated. After the tests are run, you can find the HTML output from the coverage tool in the source directory under /clients/web/dev/built/py_coverage.

Client Side Testing

Using the same setup as above for the Server Side Tests, your environment will be set up The client side tests and server side tests are both harnessed with CTest, so use the following commands to run both

cd girder-build
ctest

will run all of the tests, which include the client side tests. Our client tests use the Jasmine JS testing framework.

If you encounter errors regarding ESLINT or PUG_LINT, there is a chance you missed certain steps for setting up development dependencies. You could use ccmake to change CMake configuration. Or, it might be easier to recreate the environment from the beginning.

When running client side tests, if you try to SIGINT (ctrl+c) the CTest process, CTest won’t pass that signal down to the test processes for them to handle. This can result in orphaned python unittest processes and can prevent future runs of client tests. If you run a client side test and see an error message similar to IOError: Port 30015 not free on '0.0.0.0', then look for an existing process similar to /usr/bin/python2.7 -m unittest -v tests.web_client_test, kill the process, and then try your tests again.

Adding a New Client Side Test

To add a new client side test, add a new spec file in /clients/web/test/spec/, add a line referencing your spec file to /girder/tests/CMakeLists.txt using the add_web_client_test function, and then run in your build directory

cmake ../girder

before running your tests.

An example of a very simple client side test would be as follows

add_web_client_test(some_client_test "someSpec.js" PLUGIN "my_plugin")

The PLUGIN argument indicates that “my_plugin” is the owner of some_client_test, at the time of the test my_plugin and all of its dependencies will be loaded.

If additional plugins are needed for a specific test, that can be achieved using the ENABLEDPLUGINS argument

add_web_client_test(another_client_test "anotherSpec.js" PLUGIN "my_plugin" ENABLEDPLUGINS "my_plugin" "jobs")

Here ENABLEDPLUGINS ensures that my_plugin and the jobs plugin are loaded, along with their dependencies at the time of another_client_test.

Note

Core functionality shouldn’t depend on plugins being enabled, this test definition is more suitable for a plugin. Information for testing plugins can be found under Plugin Development.

You will find many useful methods for client side testing in the girderTest object defined at /clients/web/test/testUtils.js.

Initializing the Database for a Test

When running tests in Girder, the database will initially be empty. Often times, you want to be able to start the test with the database in a particular state. To avoid repetitive initialization code, Girder provides a way to import a folder hierarchy from the file system using a simple initialization file. This file is in YAML (or JSON) format and provides a list of objects to insert into the database before executing your test. A typical example of this format is as follows

---
users:
  - login: 'admin'
    password: 'password'
    firstName: 'First'
    lastName: 'Last'
    email: 'admin@email.com'
    admin: true
    import: 'files/user'

collections:
  - name: 'My collection'
    public: true
    creator: 'admin'
    import: 'files/collection'

This will create one admin user and a public collection owned by that user. Both the generated user and collection objects will contain folders imported from the file system. Relative paths provided by the import key will be resolved relative to the location of the YAML file on disk. You can also describe the full hierarchy in the YAML file itself for more complicated use cases. See the test spec in tests/cases/setup_database_test.yml for a more complete example.

Note

When importing from a local path into a user or collection, files directly under that path are ignored because items can be only inserted under folders.

To use the initialization mechanism, you should add the YAML file next to your test file. For example, if your test is defined in tests/cases/my_test.py, then the initialization spec should go in tests/cases/my_test.yml. This file will be automatically detected and loaded before executing your test code. This is true for both python and javascript tests added in core or inside plugins.

The python module setup_database.py that generates the database can also be run standalone to help in development. To use it, you should point girder to an empty database

GIRDER_MONGO_URI='mongodb://127.0.0.1:27017/mytest' python tests/setup_database.py tests/test_database/spec.yml

You can browse the result in Girder by running

GIRDER_MONGO_URI='mongodb://127.0.0.1:27017/mytest' girder-server

Note

The setup_database module is meant to provision fixures for tests only. If you want to provision a Girder instance for deployment, see the Girder ansible client.

Ansible Testing

Girder provides infrastructure for using Ansible to provision machines to run and configure Girder and its various plugins. Vagrant is used to create development environments and spin up virtual machines as a means of testing the Ansible provisioning infrastructure.

See also

Details for usage of our provisioning infrastructure can be found on Provisioning.

Girder’s Ansible infrastructure can be thought of as 2 components:

1. The Girder Ansible Role (the girder_ansible CTest label)

   This is primarily responsible for deploying Girder

2. The Girder Ansible Client (the girder_ansible_client CTest label)

   This is primarily responsible for configuring Girder through its REST API.

Testing the Ansible Role

The Ansible role is tested simply by starting and provisioning a virtual machine with Vagrant and ensuring it returns a zero exit code.

The tests for these by default are running Vagrant with each of the Ansible playbooks in devops/ansible/examples.

To test these one can run CMake with the ANSIBLE_TESTS option enabled, and test only the correct CTest label

cmake -D ANSIBLE_TESTS=ON /path/to/girder
ctest -L girder_ansible

Note

Since these tests require creating and provisioning several virtual machines, they take a long time to run which is why they’re disabled by default.

Testing the Ansible Client

The Ansible client is tested by provisioning a single Girder virtual machine and running Ansible playbooks against it.

To test these one can run CMake with the ANSIBLE_CLIENT_TESTS option enabled, and test only the correct CTest label

cmake -D ANSIBLE_CLIENT_TESTS=ON /path/to/girder
ctest -L girder_ansible_client

Note

Due to how dependencies are handled in CMake, it’s currently not possible to individually run an Ansible Client test without also running the test that starts the virtual machine.

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 Linux development environment (macOS causes npm to produce slightly different outputs) with version >=5.3 of npm installed:

   npm install -g 'npm@>=5.3'
   

2. Update dependencies or devDependencies in package.json to add a new abstract specifier for the package:

• Packages that are bundled into the web client should generally use the tilde range to specify versions.
• Packages that are part of the build or testing process should generally use the caret range to specify versions.

3. Run from the root Girder directory:

   npm update
   

4. Commit the updated package.json and package-lock.json files.

Creating a new release

Girder releases are uploaded to PyPI for easy installation via pip. In addition, the python source packages are stored as releases inside the official github repository. The recommended process for generating a new release is described here.

1. From the target commit, set the desired version number in package.json, clients/web/src/package.json, and girder/__init__.py. Create a new commit and note the SHA; this will become the release tag.

2. Ensure that all tests pass.

3. Clone the repository in a new directory and checkout the release SHA. (Packaging in an old directory could cause files and plugins to be mistakenly included.)

4. Run python setup.py sdist --dist-dir=.. This will generate the source distribution tarball with a name like girder-<version>.tar.gz.

5. Create a new virtual environment and install the python package into it and build the web client. This should not be done in the repository directory because the wrong Girder package will be imported.

   mkdir test && cd test
   virtualenv release
   source release/bin/activate
   pip install ../girder-<version>.tar.gz
   girder-install web
   

6. Now start up the Girder server and ensure that you can browse the web client, plugins, and swagger docs.

7. When you are confident everything is working correctly, generate a new release on GitHub. You must be sure to use a tag version of v<version>, where <version> is the version number as it exists in package.json. For example, v0.2.4. Attach the tarball you generated to the release.

8. Add the tagged version to readthedocs and make sure it builds correctly.

9. Finally, upload the release to PyPI with the following command:

   python setup.py sdist upload
   

10. Publish the new girder source package on npm.

    cd clients/web/src && npm publish

Releasing the python client package

The design intent behind the python client package is to work with as many versions of the Girder server as possible; think carefully before breaking this compatibility. There isn’t a formal rule for releasing versions of the python client package, releases tend to be made when a significant change is made to the client that people want to use in production.

Normal semantic versioning is not in use for the python client package because its version is partially dependent on the Girder server package version. The rules for versioning the python client package are as follows:

• The major version of the python client should be the same as the major version of the Girder server package, assuming it is compatible with the server API.
• The minor version should be incremented if there is any change in backward compatibility within the python client API, or if significant new features are added.
• If the release only includes bug fixes or minor enhancements, just increment the patch version token.

The process for releasing the python client is as follows:

1. Set the version number inside clients/python/girder_client/__init__.py according to the above rules. It is set in the line near the top of the file that looks like __version__ = 'x.y.z'

2. Change to the clients/python directory of the source tree and build the package using the following commands.

   cd clients/python
   python setup.py sdist --dist-dir .
   

3. That should have created the package tarball as girder-client-<version>.tar.gz. Install it locally in a virtualenv and ensure that you can call the girder-cli executable.

   mkdir test && cd test
   virtualenv release
   source release/bin/activate
   pip install ../girder-client-<version>.tar.gz
   girder-cli
   

4. Go back to the clients/python directory and upload the package to pypi:

   cd ..
   python setup.py sdist upload