{"id":26295613,"url":"https://github.com/akash-kumar-2/full-stack-developer-aganitha-cognitive-solutions","last_synced_at":"2025-03-15T04:14:32.869Z","repository":{"id":282304180,"uuid":"948141335","full_name":"Akash-Kumar-2/Full-Stack-Developer-Aganitha-Cognitive-Solutions","owner":"Akash-Kumar-2","description":"A Python-based CLI tool that fetches PubMed research papers, filters non-academic authors affiliated with pharmaceutical/biotech companies, and saves results in a structured CSV file.","archived":false,"fork":false,"pushed_at":"2025-03-13T20:32:02.000Z","size":12,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-03-13T21:33:30.242Z","etag":null,"topics":["academic-research-data-processing","biotech","cli-tool","pharma","pubmed","python","research-project"],"latest_commit_sha":null,"homepage":"https://github.com/Akash-Kumar-2/Full-Stack-Developer-Aganitha-Cognitive-Solutions.git","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/Akash-Kumar-2.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2025-03-13T20:21:37.000Z","updated_at":"2025-03-13T20:32:05.000Z","dependencies_parsed_at":"2025-03-13T21:43:53.281Z","dependency_job_id":null,"html_url":"https://github.com/Akash-Kumar-2/Full-Stack-Developer-Aganitha-Cognitive-Solutions","commit_stats":null,"previous_names":["akash-kumar-2/full-stack-developer-aganitha-cognitive-solutions"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Akash-Kumar-2%2FFull-Stack-Developer-Aganitha-Cognitive-Solutions","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Akash-Kumar-2%2FFull-Stack-Developer-Aganitha-Cognitive-Solutions/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Akash-Kumar-2%2FFull-Stack-Developer-Aganitha-Cognitive-Solutions/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Akash-Kumar-2%2FFull-Stack-Developer-Aganitha-Cognitive-Solutions/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Akash-Kumar-2","download_url":"https://codeload.github.com/Akash-Kumar-2/Full-Stack-Developer-Aganitha-Cognitive-Solutions/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":243681077,"owners_count":20330155,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["academic-research-data-processing","biotech","cli-tool","pharma","pubmed","python","research-project"],"created_at":"2025-03-15T04:14:32.177Z","updated_at":"2025-03-15T04:14:32.863Z","avatar_url":"https://github.com/Akash-Kumar-2.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# 📚 PubMed Paper Fetcher\n\nA Python-based CLI tool that fetches research papers from PubMed, extracts authors affiliated with pharmaceutical/biotech companies, and saves the results as a CSV file.\n\n## 🚀 Features\n- ✅ Fetches PubMed papers based on a user query  \n- ✅ Filters non-academic authors affiliated with **pharmaceutical/biotech companies**  \n- ✅ Extracts **corresponding author emails** (if available)  \n- ✅ Saves results in a structured **CSV file**  \n- ✅ CLI supports **query, debug mode, and custom file output**  \n- ✅ Uses **venv for virtual environment** and **Poetry for dependency management \u0026 operations**  \n- ✅ Implements **robust error handling and modular code structure**  \n\n---\n\n## 📂 Project Structure\n```bash\npubmed_fetcher/\n│── pubmed_fetcher/  # Package directory\n│   ├── __init__.py\n│   ├── fetch_papers.py  # Fetches PubMed papers\n│   ├── filter_authors.py  # Identifies non-academic authors\n│   ├── csv_writer.py  # Writes filtered data to CSV\n│   ├── cli.py  # CLI command-line interface\n│── .gitignore\n│── README.md\n│── pyproject.toml  # Poetry configuration file\n```\n\n---\n\n## 🛠 Installation \u0026 Setup\n\n### **1️⃣ Clone the Repository**\n```bash\ngit clone https://github.com/Akash-Kumar-2/Full-Stack-Developer-Aganitha-Cognitive-Solutions.git\ncd pubmed\n```\n\n### **2️⃣ Create a Virtual Environment**\n```bash\npython -m venv venv\n```\n\n### **3️⃣ Activate the Virtual Environment**\n- **Windows:**\n  ```bash\n  venv\\Scripts\\activate\n  ```\n- **Mac/Linux:**\n  ```bash\n  source venv/bin/activate\n  ```\n\n### **4️⃣ Install Poetry** (if not installed)\nPoetry is used for dependency management.\n```bash\npip install poetry\n```\n\n### **5️⃣ Install Dependencies Using Poetry**\n```bash\npoetry install\n```\n\n---\n\n## 🎯 Usage\n\n### **Run the CLI to Fetch PubMed Papers**\n```bash\npoetry run get-papers-list \"deep learning\"\n```\n\n### **Save Results to a Specific CSV File**\n```bash\npoetry run get-papers-list \"cancer research\" -f cancer_papers.csv\n```\n\n### **Enable Debug Mode for More Details**\n```bash\npoetry run get-papers-list \"machine learning\" --debug\n```\n\n### **Show Help Menu**\n```bash\npoetry run get-papers-list --help\n```\n\n---\n\n## 🛠 Scripts \u0026 Commands\n| Command | Description |\n|---------|-------------|\n| `python -m venv venv` | Create a virtual environment |\n| `venv\\Scripts\\activate` (Windows) / `source venv/bin/activate` (Mac/Linux) | Activate the virtual environment |\n| `pip install poetry` | Install Poetry |\n| `poetry install` | Install dependencies |\n| `poetry run get-papers-list \"query\"` | Run the CLI with a query |\n| `poetry run get-papers-list \"query\" -f output.csv` | Save results to a file |\n| `poetry run get-papers-list \"query\" --debug` | Run in debug mode |\n| `pytest` | Run tests (if added) |\n\n---\n\n## 🛠 Dependencies\n- **Python 3.8+** (Ensure Python is installed)\n- **venv** (For virtual environment management)\n- **Poetry** (For dependency management \u0026 operations)\n- **Requests** (For API calls)\n\n---\n\n## 📜 License\nThis project is licensed under the **MIT License**.\n\n---\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fakash-kumar-2%2Ffull-stack-developer-aganitha-cognitive-solutions","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fakash-kumar-2%2Ffull-stack-developer-aganitha-cognitive-solutions","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fakash-kumar-2%2Ffull-stack-developer-aganitha-cognitive-solutions/lists"}