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otindex

A pyramid + postgres implementation of a treestore index for Open Tree of Life. Provides API access to the JSON files in the OpenTree phylesystem data store.

These instructions assume you are doing development setup on your local machine. For deploying otindex on a server, we have ansible playbook.

Tech used in development

  • python 2.7.10
  • pyramid v 1.5.7
  • postgres v 9.5.2
  • peyotl: opentree python library for interacting with the opentree tree store

Tracking dependencies and their versions

The top-level dependencies for otindex are listed in requirements.in. These are generally listed without versions, so a simple installation or update will fetch the latest stable version of everything.

In practice, peyotl will also be run from the same virtual environment, so its dependencies will mix with those of otindex. Hopefully this won't cause conflicts going forward.

For actual ("known good") versions and a full list of lower-level dependencies, look in requirements.txt. Assuming these versions have undergone some testing, using this file is the safest path for deployment.

This version of requirements.txt clearly separates top-level from lower-level dependencies, and ignores packages introduced by peyotl and dev tools. This is better for fool-proof deployment, assuming you follow a similar practice for peyotl in this venv. To update this file, use

$VENV/bin/pip freeze –r requirements.in > requirements.txt

For more insight into the full dependency tree, use pipdeptree to see all installed packages and dependencies. You can save updates to pipdeptree.out.

Setup your postgres database

See the README file in that directory for more detailed setup information.

Postgres setup ubuntu version (draft)

sudo apt-get install postgresql  
service postgresql start  
sudo -u postgres createdb -O postgres -E utf8 otindex  
sudo -u postgres createuser opentree -D -S -P  
<create password>
sudo su - postgres  
psql otindex  
otindex=> GRANT ALL ON DATABASE otindex TO opentree;

Postgres setup on MacOS (draft)

This assumes we're installing a particular Postgres version using Homebrew. % brew install [email protected] If it's an older/deprecated version, postgres binaries might not be linked in the usual. Let's modify the PATH in ~/.zshenv: # add temporary support for [email protected] (for otindex) PATH="/usr/local/opt/[email protected]/bin:${PATH}" Now any new terminal should recognize its binaries. To confirm: % which psql /usr/local/opt/[email protected]/bin/psql Homebrew's postgres setup might not create the usual postgres superuser account. We can do that now, so that other commands will be consistent with the exmples here: % createuser -s postgres You'll need to make sure this OS user has the same PATH adjustment above, so that it can find the expected binaries. Or just use your own OS (login) account to manage postgres, instead of user postgres. Let's take the latter approach to match the ubuntu setup above: % brew services start postgresql % createdb -E utf8 otindex % createuser opentree -D -S -P % psql otindex otindex=> GRANT ALL ON DATABASE otindex TO opentree;

Configuration

First copy the configuration template:

`$ cp development-example.ini development.ini`

Then adjust the new file for your local settings:

  • In the connection_info section, add the database username, database name
    and password
  • In the [app:main] section, edit sqlalchemy.url to match the settings in connection_info
  • Optionally, change the logging level for various components

Installation

Install otindex and set up the database tables

You probably want to be using a virtualenv.

$ pip install -r requirements.in
$ python setup.py develop
$ initialize_otindex_db development.ini

where initialize_otindex_db is in the bin directory of your virtualenv. This last step creates the database tables defined in models.py. It clears any existing tables.

Load data into the database The otindex/scripts directory contains scripts for loading data into the database. See the README file in that directory for detailed setup information.

Note: if running locally, relies on "home/user/.peyotl/config" to find taxonomy and phylesystem It will also write out logs to peyotl log file

cd otindex/scripts bash run_setup_scripts.sh ../../development.ini 100

Running the application

In the top-level directory, run:

$ pserve development.ini --reload

You should now be able to access the methods on http://0.0.0.0:6543.

Running tests

See TESTING.md in this repo.

Development notes

The top-level dev_scripts directory contains scripts for testing out new features. Some implement peyotl functions, while others allow database testing from the CLI without deploying pyramid. No promises that anything in that directory works property.