pubmed-paper-fetcher 0.1.0

Fetch and filter PubMed papers based on pharmaceutical/biotech affiliations.

📚 PubMed Paper Fetcher - Python Package

A Python program to fetch research papers from PubMed based on a user-specified query. It identifies papers with at least one author affiliated with pharmaceutical or biotech companies and returns the results as a CSV file.

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🌟 Features

• 🔍 Fetches papers from PubMed API using full query syntax.
• 📄 Outputs results as a CSV file with details:
  • PubmedID: Unique identifier for the paper.
  • Title: Title of the paper.
  • Publication Date: Date of publication.
  • Non-academic Authors: Authors affiliated with non-academic institutions.
  • Company Affiliations: Names of pharmaceutical/biotech companies.
  • Corresponding Author Email: Email of the corresponding author.
• 📦 Packaged with Poetry.
• 📤 Published on TestPyPI.

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📁 Project Structure

📂 pubmed_paper_fetcher/
│
├── 📄 __init__.py      (Makes it a package)
├── 📄 cli.py           (Command-line interface logic)
├── 📄 fetcher.py       (Module containing core functionalities)

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⚙️ Installation

Clone the Repository

$ git clone https://github.com/YourUsername/pubmed-paper-fetcher-supri267.git
$ cd pubmed-paper-fetcher-supri267

Install Dependencies

Ensure you have Poetry installed. If not, install via:

$ pip install poetry

Install project dependencies:

$ poetry install

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🚀 Usage

Command-Line Interface

1. To fetch papers and display them on console:

$ poetry run get-papers-list "COVID-19 vaccine"

2. To save results to a CSV file:

$ poetry run get-papers-list "COVID-19 vaccine" -f results.csv

3. To enable debug mode for detailed logs:

$ poetry run get-papers-list "COVID-19 vaccine" -d

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🔧 Testing the Module (TestPyPI)

Create a virtual environment:

$ python -m venv test-env
$ .\test-env\Scripts\activate  (Windows)
$ source test-env/bin/activate    (Linux/Mac)

Install the package:

$ pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple pubmed-paper-fetcher-supri267

Run the tool:

$ get-papers-list "Machine learning" -d

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📚 Tools & Libraries Used

• Python (>=3.8)
• Requests (API interaction)
• Poetry (Dependency management & Packaging)
• Twine (Publishing to TestPyPI)

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📌 Helpful Links

• PubMed API Documentation
• Poetry Documentation
• TestPyPI

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📢 Contact

For any issues or suggestions, feel free to reach out!