Abstract Retriever

Short description of your project.

Table of Contents

• Installation
• Usage
• Testing
• Contributing
• License

Installation

1. Clone the repository:

git clone https://github.com/yourusername/abstract-retriever.git

1. Navigate to the project directory:

cd abstract-retriever

2.Create and activate a virtual environment:

python -m venv env
source env/bin/activate  # On macOS/Linux
.\env\Scripts\activate   # On Windows

3. Install dependencies:

pip install -r requirements.txt

For parsing some abstracts, you need to use chromedriver. if you want to us that install chromedriver and pass along its path as an environmental variable when you start the app.

Using Chromedriver om a Mac

brew install chromedriver

find the path to chromedriver

which chromedriver

Have an environmental variable for chrome driver path, or when you launch the app or service etc.

CHROMEDRIVER_PATH='/path/to/chromedriver' python example.py

example, using the ptw that is mentioned later

CHROME_DRIVER_PATH=/opt/homebrew/bin/chromedriver ptw tests/abstract_parsers/test_journals_physiology_parser.py abstract_retriever/ -nv

copy .env file and add your apy keys to it

cp .env.example .env

Usage

get_abstract("https://www.sciencedirect.com/science/article/abs/pii/S1005030224000446")

get_abstract("https://doi.org/10.1016/j.jmst.2023.12.007")

get_abstract_from_doi("10.1016/j.jmst.2023.12.007")

A simple Search UI

If you want to see it in action, you can start the gradio app.

You will need gradio

pip install gradio

You can check serch syntax here

python example.py

or if you want to develop the example and reload the app when you change the code, you can start it with:

gradio example.py

Testing

Using ptw for Automated Testing

ptw (pytest-watch) is a tool that automatically runs your tests whenever your code changes. This is useful for maintaining a fast development workflow and ensuring that your tests are always up-to-date.

Installation

You can install ptw using pip:

pip install pytest-watch

Usage

Usage Once installed, you can use ptw from the command line to watch your project directory for changes and automatically run your tests:

ptw

If you for instance wish to just watch one test file while you are working on the parsers code you could do this, so as not having to run all tests when working on one particular parser.

ptw tests/abstract_parsers/test_science_direct_parser.py abstract_retriever/abstract_parsers -nv

Contributing

Contributions are welcome! Please follow these guidelines:

Fork the repository Create your feature branch (git checkout -b feature/your-feature) Commit your changes (git commit -am 'Add some feature') Push to the branch (git push origin feature/your-feature) Create a new Pull Request

License

This project is licensed under the MIT License - see the LICENSE file for details.