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ENCODE Metadata Database

Build status

Step 0: (Mac) Verify that homebrew is working properly:

$ sudo brew doctor

Step 1: Encoded requires a UNIX based system (Mac or Linux) and Python 3.4.x or 3.5.x:

For a mac, follow steps 0/1/2/3.  For Linux use apt-get or yum as your Linux flavor demands.  You can consult
cloud-config.yml for other steps.
Note:  Python 3.6 is NOT compatible with this version of encoded but 3.5.x works on OS X.
Production is currently 3.4 so these notes suggest that installation
Linux: apt-get install python3.4-dev or equivalent

Mac OSX install instructions
If you already have a python3 from homebrew:
$ brew uninstall --force python3


$ brew install pyenv
$ pyenv install 3.4.3
$ pyenv global 3.4.3
$ ln -sf /Users/${USER}/.pyenv/shims/python3 /usr/local/bin/python3

Step 2: (Mac) Install or update dependencies:

$ brew install libevent libmagic libxml2 libxslt openssl postgresql graphviz nginx python3
$ brew install freetype libjpeg libtiff littlecms webp chromedriver # Required by Pillow
$ brew install node@6
$ brew tap garrow/homebrew-elasticsearch17
$ brew install elasticsearch@1.7

# for Mac OSX Sierra
$ brew cask install Caskroom/cask/xquartz
$ xcode-select --install

If you need to update dependencies:

$ brew update
$ brew upgrade
$ rm -rf encoded/eggs

Step 3: Run buildout:

$ python3 bootstrap.py --buildout-version 2.4.1 --setuptools-version 18.5
$ bin/buildout

NOTE:
If you have issues with postgres or the python interface to it (psycogpg2) you probably need to install postgresql
via homebrew (as above)
If you have issues with Pillow you may need to install new xcode command line tools:
- First update Xcode from AppStore (reboot)
$ xcode-select --install
If you wish to completely rebuild the application, or have updated dependencies:

$ make clean

Then goto Step 3.

Step 4: Start the application locally

In one terminal startup the database servers and nginx proxy with:

$ bin/dev-servers development.ini --app-name app --clear --init --load

This will first clear any existing data in /tmp/encoded. Then postgres and elasticsearch servers will be initiated within /tmp/encoded. An nginx proxy running on port 8000 will be started. The servers are started, and finally the test set will be loaded.

In a second terminal, run the app with:

$ bin/pserve development.ini

Indexing will then proceed in a background thread similar to the production setup.

Browse to the interface at http://localhost:8000/.

Running tests

To run specific tests locally:

$ bin/test -k test_name

To run with a debugger:

$ bin/test --pdb

Specific tests to run locally for schema changes:

$ bin/test -k test_load_workbook
$ bin/test -k test_load_schema

Run the Pyramid tests with:

$ bin/test -m "not bdd"

Run the Browser tests with:

$ bin/test -m bdd -v --splinter-webdriver chrome

Run the Javascript tests with:

$ npm test

Or if you need to supply command line arguments:

$ ./node_modules/.bin/jest

Building Javascript and CSS

Our Javascript is written using ES6 and JSX, so needs to be compiled using babel and webpack. Our CSS is written in the SCSS variant of Sass and also needs compilation using webpack.

To build production-ready bundles, do:

$ npm run build

(This is also done as part of running buildout.)

To build development bundles and continue updating them as you edit source files, run:

$ npm run dev

The development bundles are not minified, to speed up building. The above command runs continually in your terminal window and watches for changes in Javascript and SCSS files, rebuilding the bundles as you make changes.

Creating a demo machine

After buildout you (if you have the correct permissions) can run for a single-node "cluster":

$ bin/deploy --instance-type c4.8xlarge

To initiate a server in the AWS cloud with the current branch, and with a computed nameserver alias based on the branch and AWS username. Note that this retrieves a Postgres database from the current backup, so "as is" only applies specifically to the ENCODE Project (forkers beware!). There are options to use a different branch and/or different name and also AWS spotinstnaces.

$ bin/deploy --help

For all options, including setting up ES clusters (needed for full production). After indexing (currently 8+hrs) the machine can be downsized at AWS to an m4.2xlarge, unless you are planning to submit significant data to it.

Linting your code within your code editor

To set up linting with Sublime Text 3 or Visual Studio Code, first install the linters:

$ easy_install-2.7 flake8
$ npm install -g eslint
$ npm install -g eslint-plugin-react

Sublime Text 3

After first setting up Package Control (follow install and usage instructions on site), use it to install the following packages in Sublime Text 3:

Visual Studio Code

Go to the Visual Studio Code marketplace and install these extensions:

  • ESLint
  • Python
  • Sass