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README.rst

true_nth_usa_portal

Movember TrueNTH USA Shared Services

INSTALLATION

Pick any path for installation

$ export PROJECT_HOME=~/truenth_ss

Prerequisites (done one time)

Install required packages

$ sudo apt-get install postgresql python3-venv python3-dev
$ sudo apt-get install libffi-dev libpq-dev build-essential redis-server

Clone the Project

$ git clone https://github.com/uwcirg/truenth-portal.git $PROJECT_HOME

Create a Virtual Environment

This critical step enables isolation of the project from system python, making dependency maintenance easier and more stable. It does require that you activate the virtual environment before you interact with python or the installer scripts. The virtual environment can be installed anywhere, using the nested 'env' pattern here.

$ python3 -m venv $PROJECT_HOME/env

Activate the Virtual Environment

Required to interact with the python installed in this virtual environment. Forgetting this step will result in obvious warnings about missing dependencies. This needs to be done in every shell session that you work from.

$ cd $PROJECT_HOME
$ source env/bin/activate

Create the Database

To create the postgresql database that backs your Shared Services issue the following commands:

$ sudo -u postgres createuser truenth-dev --pwprompt # enter password at prompt
$ sudo -u postgres createdb truenth-dev --owner truenth-dev

Building the schema and populating with basic configured values is done via the :ref:`flask sync <flask-sync>` command. See details below.

Update pip

The default version of pip provided in the virtual environment is often out of date. Best to update first, for optimal results:

$ pip install --upgrade pip setuptools

CONFIGURE

Create the configuration file

Create a configuration file if one does not already exist

$ cp $PROJECT_HOME/instance/application.cfg{.default,}

Add Support For 3rd Party Logins

See :ref:`OAuth Config <oauthconfig>`

Install the Latest Package and Dependencies

Instruct pip to install the correct version of all dependencies into the virtual environment. This idempotent step can be run anytime to confirm the correct libraries are installed:

pip install --requirement requirements.txt

To install additional dependencies necessary for development, replace the named requirements file:

pip install --requirement requirements.dev.txt

COMMAND LINE INTERFACE

A number of built in and custom extensions for command line interaction are available via the click command line interface, several of which are documented below.

To use or view the usage of the available commands:

  1. :ref:`activate-venv`
  2. Set FLASK_APP environment variable to point at manage.py
export FLASK_APP=manage.py
  1. Issue the flask --help or flask <cmd> --help commands for more details
flask sync --help

Note

All flask commands mentioned within this document require the first two steps listed above.

Sync Database and Config Files

The idempotent sync function takes necessary steps to build tables, upgrade the database schema and run seed to populate with static data. Safe to run on existing or brand new databases.

flask sync

Add User

Especially useful in bootstrapping a new install, a user may be added and blessed with the admin role from the command line. Be sure to use a secure password.

flask add-user --email user@server.com --password reDacted! --role admin

Password Reset

Users who forget their passwords should be encouraged to use the forgot password link from the login page. In rare instances when direct password reset is necessary, an admin may perform the following:

flask password-reset --email forgotten_user@server.com --password $NEW_PASSWORD --actor $ADMIN_EMAIL

Install the Latest Package, Dependencies and Synchronize DB (via script)

To update your Shared Services installation run the deploy.sh script (this process wraps together pulling the latest from the repository, the :ref:`pip <pip>` and :ref:`flask sync <flask-sync>` commands listed above).

This script will:

  • Update the project with the latest code
  • Install any dependencies, if necessary
  • Perform any database migrations, if necessary
  • Seed any new data to the database, if necessary
$ cd $PROJECT_HOME
$ ./bin/deploy.sh

To see all available options run:

$ ./bin/deploy.sh -h

Run the Shared Services Server

To run the flask development server, run the below command from an activated virtual environment

$ flask run

By default the flask dev server will run without the debugger and listen on port 5000 of localhost. To override these defaults, call flask run as follows

$ FLASK_DEBUG=1 flask run --port 5001 --host 0.0.0.0

Run the Celery Worker

$ celery worker --app portal.celery_worker.celery --loglevel=info

Alternatively, install an init script and configure. See Daemonizing Celery

Should the need ever arise to purge the queue of jobs, run the following destructive command. All tasks should be idempotent by design, so doing this is suggested, especially if the server is struggling.

$ celery purge --force --app portal.celery_worker.celery

Without running purge, celery will resume any unfinished tasks when it restarts

DATABASE

The value of SQLALCHEMY_DATABASE_URI defines which database engine and database to use. Alternatively, the following environment variables may be used (and if defined, will be preferred):

  1. PGDATABASE
  2. PGUSER
  3. PGPASSWORD
  4. PGHOST

At this time, only PostgreSQL is supported.

Migrations

Thanks to Alembic and Flask-Migrate, database migrations are easily managed and run.

Note

Alembic tracks the current version of the database to determine which migration scripts to apply. After the initial install, stamp the current version for subsequent upgrades to succeed:

flask db stamp head

Note

The :ref:`flask sync <flask-sync>` command covers this step automatically.

Upgrade

Anytime a database (might) need an upgrade, run the manage script with the db upgrade arguments (or run the deployment script)

This is idempotent process, meaning it's safe to run again on a database that already received the upgrade.

flask db upgrade

Note

The :ref:`flask sync <flask-sync>` command covers this step automatically.

Schema Changes

Update the python source files containing table definitions (typically classes derived from db.Model) and run the manage script to sniff out the code changes and generate the necessary migration steps:

flask db migrate

Then execute the upgrade as previously mentioned:

flask db upgrade

Testing

To run the tests, repeat the postgres createuser && postgres createdb commands as above with the values for the {user, password, database} as defined in the TestConfig class within portal\config\config.py

All test modules under the tests directory can be executed via py.test (again from project root with the virtual environment activated)

$ py.test

Alternatively, run a single modules worth of tests, telling py.test to not suppress standard out (vital for debugging) and to stop on first error:

$ py.test tests/test_intervention.py

Tox

The test runner Tox is configured to run the portal test suite and test other parts of the build process, each configured as a separate Tox "environment". To run all available environments, execute the following command:

$ tox

To run a specific tox environment, "docs" or the docgen environment in this case, invoke tox with the -e option eg:

$ tox -e docs

Tox will also run the environment specified by the TOXENV environment variable, as configured in the TravisCI integration.

Tox will pass any options after -- to the test runner, py.test. To run tests only from a certain module (analogous the above py.test invocation):

$ tox -- tests/test_intervention.py

Continuous Integration

This project includes integration with the TravisCI continuous integration platform. The full test suite (every Tox virtual environment) is automatically run for the last commit pushed to any branch, and for all pull requests. Results are reported as passing with a ✔ and failing with a ✖.

UI/Integration (Selenium) Testing

UI integration/acceptance testing is performed by Selenium and is included in the test suite and continuous integration setup. Specifically, Sauce Labs integration with TravisCI allows Selenium tests to be run with any number of browser/OS combinations and captures video from running tests.

UI tests can also be run locally (after installing xvfb and geckodriver) by passing Tox the virtual environment that corresponds to the UI tests (ui).

Setup

$ wget https://github.com/mozilla/geckodriver/releases/download/v0.21.0/geckodriver-v0.21.0-linux64.tar.gz
$ tar -xvzf geckodriver-v0.21.0-linux64.tar.gz
$ rm geckodriver-v0.21.0-linux64.tar.gz
$ chmod +x geckdriver
$ sudo mv geckodriver /usr/local/bin/

Run Tests

$ tox -e ui

Dependency Management

Project dependencies are hard-coded to specific versions (see requirements.txt) known to be compatible with Shared Services to prevent dependency updates from breaking existing code.

If pyup.io integration is enabled the service will create pull requests when individual dependencies are updated, allowing the project to track the latest dependencies. These pull requests should be merged without need for review, assuming they pass continuous integration.

Documentation

Docs are built separately via sphinx. Change to the docs directory and use the contained Makefile to build - then view in browser starting with the docs/build/html/index.html file

$ cd docs
$ make html

POSTGRESQL WINDOWS INSTALLATION GUIDE

Download

Download PostgreSQL via: https://www.postgresql.org/download/windows/

Creating the Database and User

To create the postgresql database, in pgAdmin click "databases" and "create" and enter the desired characteristics of the database, including the owner. To create the user, similarly in pgAdmin, click "login roles" and "create" and enter the desired characteristics of the user. Ensure that it has permission to login.

Configuration

Installing requirements

Ensure that C++ is installed -- if not, download from: https://www.microsoft.com/en-us/download/details.aspx?id=44266

Ensure that setuptools is up-to-date by running:

$ python -m pip install --upgrade pip setuptools

Ensure that ez_setup is installed by running:

$ pip install ez_setup

Install requirements by running:

$ pip install --requirement requirements.txt

Configuration files

In $PATH\\data\pg_hba.conf , change the bottom few lines to read:

# TYPE  DATABASE        USER            ADDRESS                 METHOD

# IPv4 local connections:

host    all             all             127.0.0.1/32            trust

# IPv6 local connections:

host    all             all             ::1/128                 trust

Copy the default configuration file to the named configuration file

$ copy $PROJECT_HOME/instance/application.cfg.default $PROJECT_HOME/instance/application.cfg

In application.cfg, (below), fill in the values for SQLALCHEMY_DATABASE_URI for user, password, localhost, portnum, and dbname.

user, password, and dbname were setup earlier in pgAdmin.

portnum can also be found in pgAdmin.

localhost should be 127.0.0.1

SQLALCHEMY_DATABASE_URI = 'postgresql://user:password@localhost:portnum/dbname'

Testing

To test that the database is set up correctly, from a virtual environment run:

$ python ./bin/testconnection.py
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