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ckanext-rdkit-visuals

RDKit Module is an Open source toolkit for cheminformatics and Machine Learning. Here Rdkit python module is used as an important library extension to CKAN venv to create various cheminformatics, perform and provide various chemical solution from metadata harvested (fetched) from different chemistry repositories.

More information about RDKit: https://www.rdkit.org/

In this plugin, the major rdkit library must be installed giving an assess to perform chemical logics to create: InChI Smiles InChIKey Molecule Molecular Image Molecular Formula Exact Mass

Most of the chemistry repository provide standard InChI key in their metadata fields. We have used this field to create other chemical information to enrich the dataset display and provide more information of the sample or research dataset, as the user can easily go through.

Not only on the "dataset" page of CKAN, but also on "resource" page.

Apporach while harvesting (For more information about the harvester OAI-PMH Harvester):

  • InChI → Smiles
  • InChI → InChIKey
  • InChI → Molecule
  • Molecule → Molecular Image
  • Molecule → Molecular Formula
  • Molecule → Exact Mass

Data Models and Migration

This Plugin also contains database migration tables to store molecule data of each dataset molecule in molecule table. Name of the database tables: molecules & molecules_rel_data

Database Migration is done, to establish new tables within the CKAN PostgreSQL database. For more information please check offical documenation: https://docs.ckan.org/en/2.9/extensions/best-practices.html

Data Models Two data models scripts are sued for interaction with database tables of Molecules and MolecularRelationData.

  1. Molecules Table: The data table schema is indexed to store molecule data while harvesting using RDKit Python Library, which contains id for every entry and their molecules information. (Highly based on InChIKey)

  2. Molecules Relation Data Table : The data table schema is indexed to store moleculesID and their corresponding package ID.

The classmethods are designed to store/create rows during each harvesting and also get information via packageID and their moelcular information.

Note: If you are creating your own migration tables then, Please follow official documentation preciesly. (https://docs.ckan.org/en/2.9/extensions/best-practices.html)

You can copy migration python file and version control files, after creating migration is done. if you are using different table names & column names, please name them using "lower_cases" instead of CamelCase.

Requirements

Compatibility with core CKAN versions:

CKAN version Compatible?
2.8 & eariler not tested
2.9 yes

Installation

To install ckanext-rdkit-visuals:

Activate your CKAN virtual environment, for example:

. /usr/lib/ckan/default/bin/activate

Clone the source and install it on the virtualenv

git clone https://github.com/bhavin2897/ckanext-rdkit-visuals.git
cd ckanext-rdkit-visuals
pip install -e .
	pip install -r requirements.txt

Add rdkit-visuals to the ckan.plugins setting in your CKAN config file (by default the config file is located at /etc/ckan/default/ckan.ini).

Restart CKAN. For example if you've deployed CKAN with Apache on Ubuntu:

sudo service apache2 reload

To upgrade ckan database, for the tables you have created:

ckan -c /etc/ckan/default/ckan.ini db upgrade -p rdkit-visuals

You will get a message Upgrading DB: SUCCESS

Later, check the database list of tables for the ckan user to see the table for the migrated/generated table.

Config settings

None at present

Developer installation

To install ckanext-rdkit-visuals for development, activate your CKAN virtualenv and do:

git clone https://github.com/bhavin2897/ckanext-rdkit-visuals.git
cd ckanext-rdkit-visuals
python setup.py develop
pip install -r dev-requirements.txt

Add Plugin-in int he confirguation file

sudo nano /etc/ckan/default/ckan.ini 

ckan.plugin: <other plugins> rdkit_visuals

Restart Server if you are using Supervisor and Nginx

sudo service supervisor reload
sudo service nginx reload

To upgrade ckan database, for the tables you have created:

ckan -c /etc/ckan/default/ckan.ini db upgrade -p rdkit_visuals

You will get a message Upgrading DB: SUCCESS

Later, check the database list of tables for the ckan user to see the table for the migrated/generated table.

Tests

To run the tests, do:

pytest --ckan-ini=test.ini

Releasing a new version of ckanext-rdkit-visuals

If ckanext-rdkit-visuals should be available on PyPI you can follow these steps to publish a new version:

  1. Update the version number in the setup.py file. See PEP 440 for how to choose version numbers.

  2. Make sure you have the latest version of necessary packages:

    pip install --upgrade setuptools wheel twine

  3. Create a source and binary distributions of the new version:

    python setup.py sdist bdist_wheel && twine check dist/*

    Fix any errors you get.

  4. Upload the source distribution to PyPI:

    twine upload dist/*

  5. Commit any outstanding changes:

    git commit -a
git push

  6. Tag the new release of the project on GitHub with the version number from the setup.py file. For example if the version number in setup.py is 0.0.1 then do:

    git tag 0.0.1
git push --tags

License

AGPL