OrcidXtract 0.0.6

This Python library extracts ORCID information from a file containing ORCID IDs and generates reports in various formats (TXT, PDF, JSON, CSV, Excel).

ORCID Data Extractor and Report Generator

This Python script extracts ORCID information from a file containing ORCID IDs and generates reports in various formats (TXT, PDF, JSON, CSV, Excel).

Table of Contents

• Installation
• Usage
  • Command-Line Usage
  • Using in Python Code
• Features
• Dependencies
• License
• Contributions

Installation

1. To install the OrcidXtract library, simply use pip:

   pip install OrcidXtract
   

Usage

Once the library is installed, you can use it from the command line with the orcidxtract command.

Command-Line Arguments

  orcidxtract --help

  Options:
    -h, --help            show this help message and exit
    --inputfile INPUTFILE
                          Path to the input file containing ORCID IDs.
    --orcid_ids [ORCID_IDS ...]
                          List of ORCID IDs (e.g., 0000-0001-...).
    --output-format {txt,pdf,json} [{txt,pdf,json} ...]
                          Specify one or more output formats (txt, pdf, json).
                          Example: --output-format txt pdf json
    --report {csv,excel}  Specify if you want to generate a CSV or Excel report.
                          Example: --report csv

The script accepts the following command-line arguments:

• --inputfile: Path to the input file containing ORCID IDs.
• --orcid_ids: A list of ORCID IDs (e.g., 0000-0001-5109-3700).
• --output-format: Specify one or more output formats (txt, pdf, json). Example: --output-format txt pdf json.
• --report: Specify if you want to generate a CSV or Excel report.

Example Commands

1. Extract ORCID data and generate TXT, PDF, and JSON reports:

   orcidxtract --inputfile orcid_ids.txt --output-format txt pdf json
   

2. Extract ORCID data and generate a CSV report:

   orcidxtract --inputfile orcid_ids.txt --output-format txt --report csv
   

3. Extract ORCID data and generate an Excel report:

   orcidxtract --inputfile orcid_ids.txt --output-format json --report excel
   

4. Extract ORCID directly from the command line (Work only for one ORCID id at a time):

   orcidxtract --orcid_ids xxxx-xxxx-xxxx-xxxx --output-format txt pdf json  --report csv   
   

5. Generate only Report

   orcidxtract --orcid_ids xxxx-xxxx-xxxx-xxxx --report csv
   

Function Details

Fetching ORCID Data: get_orcid_data(orcid_id: str)

This function fetches ORCID profile information using an ORCID ID.

Parameters:

• orcid_id (str): The ORCID ID of the researcher.

Returns:

• An OrcidData object containing ORCID profile details.

Generate File: create_report(orcid_data: list, format: str)

he library provides multiple functions to generate files in different formats: TXT, PDF, and JSON.

Functions:

• create_txt(file_path: str, orcid_info: OrcidData)
• create_pdf(file_path: str, orcid_info: OrcidData)
• create_json(file_path: str, orcid_info: OrcidData)

Parameters:

• file_path (str): The output path where the JSON file should be saved.
• orcid_info (OrcidData): The ORCID data object.

Generating Reports: create_report(orcid_data: list, format: str)

Generates a report in CSV or Excel format, containing multiple ORCID profiles.

Parameters:

• orcid_data (list): A list of OrcidData objects.
• format (str): The format of the report (csv or excel).

Using in Python Code

To integrate the library into a Python script, follow these steps.

1. Import the Required Functions

   from OrcidXtract.orcid_extractor import get_orcid_data
   from OrcidXtract.report_generator import create_txt, create_pdf, create_json, create_report
   

2. Define the ORCID IDs

   You can manually define ORCID IDs or read them from a file.

   # Define ORCID IDs to fetch data for
   orcid_ids = ["0000-0002-2140-1538", "0009-0003-9071-3804"]
   
   # Read ORCID IDs from a file
   input_file = "input_file.txt"
   with open(input_file, "r") as f:
         orcid_ids = [line.strip() for line in f if line.strip()]
   

3. Set Output Formats

   Specify the output formats (txt, pdf, json) and report type (csv or excel).

   output_formats = ["txt", "json", "pdf"]  # Choose desired formats
   report_format = "csv"  # Change to "excel" if needed
   

4. Fetch ORCID Data and Generate Reports

   orcid_data = []
   for orcid_id in orcid_ids:
       orcid_info = get_orcid_data(orcid_id)
       orcid_data.append(orcid_info)
   
       # Save reports only in the specified formats
       if "txt" in output_formats:
           create_txt(f"{orcid_id}.txt", orcid_info)
       if "pdf" in output_formats:
           create_pdf(f"{orcid_id}.pdf", orcid_info)
       if "json" in output_formats:
           create_json(f"{orcid_id}.json", orcid_info)
   

5. Generate a Summary Report (CSV/Excel)

   create_report(orcid_data, report_format)  # Generates a CSV or Excel report
   

Input File Format

The input file should contain one ORCID ID per line. Example (orcid_ids.txt):

0000-0000-0000-0001
0000-0000-0000-0002
0000-0000-0000-0003

Output Files

The generated reports will be saved in the Result directory. The directory structure will look like this:

Result
  - 0000-0000-0000-0001.txt
  - 0000-0000-0000-0002.pdf
  - 0000-0000-0000-0003.json
  - orcid_report.csv
  - orcid_report.xlsx

Features

• ORCID Data Extraction: Extracts detailed information from ORCID IDs.
• Multiple Output Formats: Supports TXT, PDF, JSON, CSV, and Excel formats.
• Customizable Reports: Generate reports based on specific requirements.
• Error Handling: Handles missing or invalid data gracefully.
• Automatic Output Handling: All reports are saved in the Result folder.

Dependencies

• argparse: For parsing command-line arguments.
• reportlab: For generating PDF reports.
• pandas: For generating CSV and Excel reports.
• requests: For making HTTP requests to ORCID's API.
• openpyxl: For working with Excel files.

These dependencies will be automatically installed when you install the package via pip.

License

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

Contributions

For any questions or issues, please open an issue on the GitHub repository. If you'd like to contribute, please fork the repository and submit a pull request.