ENCODE Metadata Database

System Installation (OSX Catlina 10.15.2)

See Snovault OSX System Installation. ENCODE installs Snovault as it is a dependency. The System Installation is the same for both. However, you do not need to set up a running Snovault instance yourself.

Application Installation

For issues see Snovault OSX App Installation first.

1. Create a virtual env in your work directory. This example uses the python module venv. Other options would also work, like conda or pyenv

   $ cd your-work-dir
   $ python3 -m venv encoded-venv
   $ source encoded-venv/bin/activate
   

2. Clone the repo and install requirements

   # Make sure you are in the encoded-venv
   $ cd encoded
   $ pip install -r requirements.osx.txt
   

3. Build Application

   $ make clean && buildout bootstrap && bin/buildout
   

4. Run Application

   $ bin/dev-servers development.ini --app-name app --clear --init --load
   # In a separate terminal, make sure you are in the encoded-venv
   $ bin/pserve development.ini
   

5. Browse to the interface at http://localhost:6543

6. Run Tests

   # Make sure you are in the encoded-venv
   $ ./circle-tests.sh bdd
   $ ./circle-tests.sh indexing
   $ ./circle-tests.sh indexer
   $ ./circle-tests.sh not-bdd-non-indexing
   $ ./circle-tests.sh npm
   

Configuration Installation (In Progress)

The configuration repo is set by 'conf_dir = ./cloud-config' in the 'demo-config.ini' file.  The
'deploy.py' compiles yaml files from 'cloud-config' for use with aws instances.  There is a
very specific file structure at the moment.  We are working to generalize the use case.

To use a different directory for cloud configuration copy 'demo-config.ini' to '.dev-config.ini'.
Then change the 'conf_dir=../your-conf-repo/cloud-config' in the hidden file to your 
configuration directory.

'deploy.py' uses configuration in 'demo-config.ini:deployment' section.  Those are overwritten
by '.dev-config.ini:deployment' if it exists.  Currently command line arguments will be
overwritten by the ini files.  Eventaully that may be swtiched so the command line arguments
overwrite ini files.

For temporary backwards compatibility the default config repo is set to this repos cloud-config.
Eventually, the demo-config.ini will default to a demonstration configuration