Skip to content

Latest commit

 

History

History
183 lines (130 loc) · 5.33 KB

README.md

File metadata and controls

183 lines (130 loc) · 5.33 KB
Raw

Provisioning a new site

Required packages:

  • Python 3
  • Git
  • pip

eg, on Ubuntu:

sudo apt-get install git python3 python3-pip

Folder structure:

Assume we have a user account at /home/username

/home/username
└── sites
    └── PROJECT
         ├── database
         ├── source
         ├── static_files
         └── virtualenv

Local Deployment

  1. Create directory structure in ~/sites

    mkdir -p PROJECT/database
mkdir -p PROJECT/source
mkdir -p PROJECT/static_files
mkdir -p PROJECT/virtualenv

  2. Pull down source code into folder named source

    git clone https://github.com/ProteinsWebTeam/interpro7-api.git PROJECT/source
cd PROJECT/source

    From now on all the command assume you are in the PROJECT/source directory.

  3. Start the virtual env in the assigned folder:

    python -m venv virtualenv

  4. Install requirements in the virtual environment

    ../virtualenv/bin/pip install -r requirements.txt

  5. Install requirements for development

    ```bash
../virtualenv/bin/pip install -r dev_requirements.txt
```

  6. Create a local configuration file in config/interpro.local.yml. In this file you can overwite any of the settings included in the read-only file config/interpro.yml. Below is an example of the local config that will run in debug mode using the test DB with SQLite, a local instance of elasticsearch without redis:

    use_test_db: false
debug: true
allowed_host: ["localhost", "127.0.0.1"]
searcher_path: "https://localhost:9200"
searcher_index: "test"
searcher_user: "elastic"
searcher_password: "password"
api_url: "http://localhost:8007/api/"
static_url: "api/static_files/"
searcher_test_path: "https://localhost:9200"
searcher_test_password: "password"
    • This configuration assumes a running instance of elasticsearch in port 9200. For details on how to install elasticsearch go HERE

  7. Migrate the database models (For SQLite)

     ../virtualenv/bin/python manage.py migrate

    If anything goes wrong check that the database directory exists

     ls ../database

  8. Collect the static files. Only necessary for server deployment.

    ../virtualenv/bin/python manage.py collectstatic --noinput

  9. Load the fixture data into the SQLite DB.

    ../virtualenv/bin/python manage.py loaddata webfront/tests/fixtures_*.json

  10. Install Elasticsearch and load index. Currently running version 8.12 with authentication by password

    e.g for OSX: brew install elasticsearch@8.12

    curl -XPUT 'localhost:9200/test?pretty' -H 'Content-Type: application/json' -d @config/elastic_mapping.json

  11. Run the tests. When running the tests, the API loads the fixtures in the existing elasticsearch instance, which is necessary to run the server with fixtures. ../virtualenv/bin/python manage.py test

  12. Start the server ../virtualenv/bin/python manage.py runserver 0.0.0.0:8000

  13. [Optional] Install precommit, black and the pre-commit hook, to enable the formatting of files before each commit. ../virtualenv/bin/pip install pre-commit black ../virtualenv/bin/pre-commit install
    Note 1:It is important to run the test in Python 3.8 because the VMs where the API runs use that version.

Testing

The unit tests are located in [project]/source/webfront/tests/.

To run unit tests use

../virtualenv/bin/python manage.py test webfront

The functional test are in [project]/functional_tests and are configured to Google Chrome (or Chromium), so you need to have it installed in your machine.

To run functional tests use

export BROWSER_TEST="chrome"

# Only required if ChromeDriver is not in your PATH
# or if its binary is not `chromedriver` (e.g. `chromium.chromedriver`)
export BROWSER_TEST_PATH="/path/to/chromedriver"

../virtualenv/bin/python manage.py test functional_tests

As a reference HERE is a graphic describing the fixtures.

All the test can be run at the same time:

../virtualenv/bin/python manage.py test

Setting up real data (MySQL - elasticsearch)

For the next steps you need an installation of MySQL with a database compatible with the defined model.

  1. Remove the line use_test_db: true from the config/interpro.local.yml file. You could also set the value to false, but given that false is the default value, you can just remove it.

  2. Edit the same config/interpro.local.yml file, changing the searcher_path setting for one with the elastic search instance that corresponds with the data in MySQL.

  3. Copy the template mysql configuration file into config/mysql.yml and edit the file with your data.

    cp config/mysql.template.yml config/mysql.yml

  4. Start the server

    ../virtualenv/bin/python manage.py runserver 0.0.0.0:8000