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Open Source Clinical Content Analysis and Management System

• Form versioning
• Direct data entry instead of using paper forms
• Data auditing
• Singular data points with multiple references
• Data workflow captured by the system design, but flexible enough to work for multiple use-cases
• Secure, role-based data access control
• A Relational Database that could describe how data are related through structure instead of convention

• Python 2.7+

• npm

  • bower
  • lessc (must be installed globally, i.e. with "-g" option)

• redis
• PostgreSQL 9.3+

These instructions are intended for contributors only.

Make sure you have the required node packages installed:

$ npm install -g bower
$ npm install -g less

Create a virtual environment for your work:

$ virtualenv MYPROJECT
$ source MYPROJECT/bin/activate

Next, create the necesary directories:

$ cd MYPROJECT
$ mkdir -p  etc  var/exports  var/blobs  src

You'll need to git checkout the web application. If you are using your own forks, change younglabs to yours. The reason we checkout each project individually is because pip will replace all git changes/history the next time your run pip install on a git repo, which can lead you to lose a lot of work and sanity:

$ cd src
$ git clone git@github.com:YOURID/occams

If you plan on working on add-ons, it is recommended you install the following as well:

$ git clone git@github.com:YOURID/occams_datastore
$ git clone git@github.com:YOURID/occams_forms
$ git clone git@github.com:YOURID/occams_accounts
$ git clone git@github.com:YOURID/occams_roster
$ git clone git@github.com:YOURID/occams_studies
$ git clone git@github.com:YOURID/occams_lims

Now that your projects are checked out, copy and update the requirements.txt found in the occams project directory.:

$ cd $VIRTUAL_ENV
$ cp src/occams/requirements.txt .
$ vim requirements.txt
$ pip install -U -r requirements.txt

Once everything is installed you'll need to configure the application with your desired development environment settings:

$ cp src/occams/sample.ini etc/development.ini
$ vim etc/development.ini

Install the appropriate database tables:

$ createdb -U DBADMIN -O DBUSER DBNAME
$ occams_initdb etc/development.ini

Start the web service:

$ gunicorn --reload --paste etc/development.ini

If you applications are using asynchronous tasks, you'll need to start the celery worker:

$ celery worker --autoreload --app occams --loglevel INFO --without-gossip --ini etc/development.ini

TODO

If your app depends on OCCAMS's database structure, it is advised you use alembic branchpoints with a dedicated label for your project.

Use alembic history to inspect the current history of OCCAMS application database structures. Ideally, your project should follow it's only independent history, were you might depend on certain dependant database structure changes. If this is the case, please refer to the following scenarios:

If your project begins as an independent database structure:

$ alembic -c /path/to/ini revision -m "MESSAGE" --head=base --branch-label=MYAPP --version-path=/path/to/app/versions

If your project begins depending on a specific database structure:

$ alembic -c /path/to/ini revision -m "MESSAGE" --head=REVISION --splice --branch-label=MYAPP --version-path=/path/to/app/versions

If your project's revision depends on a certain project's revision:

$ alembic -c /path/to/ini revision -m "MESSAGE" --head=MYAPP@base --depends-on=REVISION --version-path=/path/to/app/versions