girder_wholetale ################

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Girder plugin enabling intergration with tmpnb

Development

Installing Girder

There are a couple of different ways to install Girder which are outlined here <http://girder.readthedocs.io/en/latest/installation.html#sources>_. Note that this should be done in a Python 3 environment.

To create the virtual environment, install pyenv <https://github.com/pyenv/pyenv-installer>. Also see this <https://gist.github.com/jmvrbanac/8793985>.

Run

.. code-block:: shell

sudo apt-get install -y make build-essential libssl-dev zlib1g-dev libbz2-dev \
libreadline-dev libsqlite3-dev wget curl llvm libncurses5-dev libncursesw5-dev \
xz-utils tk-dev libffi-dev

Install Python 3.5.3

.. code-block:: shell

pyenv install 3.5.3

Set Python 3.5.3 to global

.. code-block:: shell

pyenv global 3.5.3

Install Girder

.. code-block:: shell

pip install girder

Install the web interface

.. code-block:: shell

girder-install web --all-plugins --dev

Note: Make sure you are serving on 0.0.0.0. Check the config files in site-package/girder/girder/conf

Start the server

.. code-block:: shell

girder-server

Linking the plugin to Girder ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Once you have the repo cloned, you'll need to create a new folder named wholetale in the /grider/plugins/ directory. The goal of the next step is to copy/link the contents of the cloned girder_wholetale directory into the wholetale directory.

To symbolically link the directory (so that any changes to girder_wholetale are reflected instantly), run girder-install plugin -s /path/to/your/plugin

To copy the contents instead, run girder-install plugin /path/to/your/plugin

For more infomration visit the page on Installing Third Party Plugins <http://girder.readthedocs.io/en/latest/installation.html#installing-third-party-plugins>_

Enabling Plugins ^^^^^^^^^^^^^^^^

To get to the plugins section, navigate to Admin Console-> Plugins. Make sure that the following plugins are enabled.

1. Celery Jobs
2. Gravatar portraits
3. Jobs
4. OAuth2 login
5. Remote worker
6. wholetale

OAuth ^^^^^ Instead of using the login screen in the dashboard, you'll use OAuth with GitHub to handle authentication. In the plugins menu, click the blue gear next to OAuth2 login. Open a new tab with GitHub. Open your settings, and navigate to Developer Settings, which is the last item in the navigation menu. Click the New OAuth App button. Use the settings in the OAuth2 login settings to fill in the required information. Fill out the fields in the OAuth2 login plugin with the information provided by GitHub.

CORS Headers ^^^^^^^^^^^^ You'll want to allow CORS headers in the dashboard. To do this, navigate to Admin Console-> Server Configuration. Scroll to the bottom of the page and click Advanced Settings. Put * in the CORS Allowed Origins and CORS Allowed Headers fields. More information can be found here <http://girder.readthedocs.io/en/latest/security.html#cors-cross-origin-resource-sharing>_.

Create an Assetstore ^^^^^^^^^^^^^^^^^^^^ To allow uploading and registering data files in the dashboard, you'll need to create an assetstore. To do this, navigate to Admin Console-> Assetstores. Click Create new Filesystem assetstore, name the assetstore, specify where on your local machine it will reside, and click the Create button.

Running Tests

This Girder plugin includes a set of tests in ./plugin_tests. To run these, you'll need to get a copy of the WholeTale Fork of Girder_ and run this plugin's test as part of Girder's test suite.

Pre-requisites:

• Python 3
• CMake
• An instance of MongoDB, running at mongodb://localhost:27101

Optional pre-requisites:

• coverage
• flake8

::

$ git clone https://github.com/whole-tale/girder
$ cd girder
$ rm -rf plugins/wholetale
$ cp -r {path_to_your_version_of_this_repo}/ plugins/wholetale
$ # Install dependencies
$ pip install -r requirements-dev.txt
$ pip install -r plugins/wholetale/requirements.txt
$ cd tests
$ # Set up environment variables for CMake
$ export PYTHON="{YOUR_PYTHON_3_BIN_PATH}"
$ export COVERAGE="{YOUR_COVERAGE_BIN_PATH}"
$ export FLAKE8="{YOUR_FLAKE8_BIN_PATH}"
$ cmake \
    -DRUN_CORE_TESTS:BOOL=OFF \
    -DBUILD_JAVASCRIPT_TESTS:BOOL=OFF \
    -DJAVASCRIPT_STYLE_TESTS:BOOL=OFF \
    -DTEST_PLUGINS:STRING=wholetale \
    -DCOVERAGE_MINIMUM_PASS:STRING=4 \
    -DPYTHON_COVERAGE=ON \
    -DPYTHON_STATIC_ANALYSIS=ON \
    -DPYTHON_VERSION="3.6" \
    -DPYTHON_COVERAGE_EXECUTABLE="$COVERAGE" \
    -DFLAKE8_EXECUTABLE="$FLAKE8" \
    -DPYTHON_EXECUTABLE="$PYTHON" \
    ..
$ ctest -VV

..

.. _WholeTale Fork of Girder: https://github.com/whole-tale/girder

Adding a New Test ^^^^^^^^^^^^^^^^^

To add a new test, create a new file in the plugin_tests directory as <testname>_test.py. Then open plugin.cmake and add the line to the file.

add_python_test(<testname> PLUGIN wholetale).

Note that you do not need to add _test at the end of the filename.

Acknowledgements

This material is based upon work supported by the National Science Foundation under Grant No. OAC-1541450.

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.. |build-status| image:: https://circleci.com/gh/whole-tale/girder_wholetale.png?style=shield :target: https://circleci.com/gh/whole-tale/girder_wholetale :alt: Build Status

.. |codecov-badge| image:: https://img.shields.io/codecov/c/github/whole-tale/girder_wholetale.svg :target: https://codecov.io/gh/whole-tale/girder_wholetale :alt: Coverage Status

.. |nsf-badge| image:: https://img.shields.io/badge/NSF-154150-blue.svg :target: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1541450 :alt: NSF Grant Badge