ckanext-bioschemaharvester

This plug-in is an extension to CKAN Harvester to harvest (bio)schema datasets from repositories using (bio)schema. Example: MassBank Repo

This harvester is developed using the offical CKAN Harvester https://github.com/ckan/ckanext-harvest following the actual Harvest Interface of gather, fetch and import techniques.

When installed, you can see an option to use as BioSchema Scrapper/Harvest

As name suggests, this harvester is more of a web-scrapper. It is developed using Beautiful scoop to harvest/fetch metadata from HTML page of the dataset (tested only on MassBank Repo)

Note: This plugin uses migrated tables from other plugin to store metadata to desired metadata tables without overwriting default ckan tables in the database. So, see that you already have these tables in your ckan instance.

• https://github.com/bhavin2897/ckanext-rdkit-visuals
• https://github.com/bhavin2897/ckanext-related_resources

Requirements

If your extension works across different versions you can add the following table:

Compatibility with core CKAN versions:

CKAN version	Compatible?
2.8 & eariler	not tested
2.9	yes

Installation

To install ckanext-bioschemaharvester:

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-bioschemaharvester.git
cd ckanext-bioschemaharvester
pip install -e .
pip install -r requirements.txt

Add bioschemaharvester 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

Developer installation

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

git clone https://github.com/TIB/ckanext-bioschemaharvester.git
cd ckanext-bioschemaharvester
python setup.py develop
pip install -r requirements.txt

Restart Server if you are using Supervisor and Nginx

sudo service supervisor reload
sudo service nginx reload

Harvesting and Harvesters

NOTE: Before installing and harvesting, it is assummed that you already have installed

• CKAN Harvester
• RDKit Visuals
• Related Resources

1. BioSchema Harvester

The harvest Source CAN be a Sitemap, Sitemaps or single web page, containing BioSchema in JSON-LD format and available to scrap.

No need to add any information to the configuration text.

Choose BioSchema Scrapper/Harvester

Save and Reharvest

Run Harvester ckan -c /etc/ckan/default/ckan.ini harvester run, if you are running on development/production server.

Else if you are running locally, follow regular harvesting process.

ckan -c /etc/ckan/default/ckan.ini harvester gather-consumer

ckan -c /etc/ckan/default/ckan.ini harvester fetch-consumer

ckan -c /etc/ckan/default/ckan.ini harvester run

2. nmrXiv Harvester

NOTE: This harvester is still under development.

This BioSchema Harvester can obtain only from Swagger API, of nmrXiv which is based on BioSchema JSON-LD. The harvester modifies to gather, fetch and harvest in regard to API.

nmrXiv Swagger API Documentation

No Configuration required.

Choose nmrXiv Swagger Harvester

Save and Reharvest

Run Harvester ckan -c /etc/ckan/default/ckan.ini harvester run, if you are running on development/production server.

Else if you are running locally, follow regular harvesting process.

ckan -c /etc/ckan/default/ckan.ini harvester gather-consumer

ckan -c /etc/ckan/default/ckan.ini harvester fetch-consumer

ckan -c /etc/ckan/default/ckan.ini harvester run

3. Chemotion-Repository Harvester

NOTE: This harvester is still under development.

Chemotion Repository Swagger API Documentation

Configuration Required:

{
"type_chem": "Container",
"offset" : 0,
"limit" : 1000, 
"date_from" : "2020-10-10", 
"date_to": ""
}

Releasing a new version of ckanext-bioschemaharvester

If ckanext-bioschemaharvester 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