A Python script that processes journal article XML files from Open Journal Systems (OJS) and transforms them into PubMed-compliant XML format for submission to the PubMed database.

• Batch Processing: Processes multiple XML files from an input directory
• Title Translation: Retrieves English titles from OJS API using Dutch vernacular titles
• Abstract Enhancement: Fetches English abstracts and reorganizes multilingual abstracts
• Keyword Extraction: Extracts DC.Subject metadata as keywords
• XML Restructuring: Reorganizes XML elements to comply with PubMed DTD requirements
• Language Standardization: Converts language codes (e.g., 'dut' to 'NL')
• Metadata Enrichment: Adds publication types, article IDs, and other required elements

pip install beautifulsoup4 requests pandas python-dotenv lxml

Create a .env file in the root directory with the following variables:

api_key=your_ojs_api_key
journal_title=your_journal_name
journal_abbreviation=Journal_Abbreviation

project/
├── input/              # Place XML files to be processed here
├── output/             # Output directory (created automatically)
├── articleset.xml      # Final combined output file
├── json.txt           # API response cache file
├── .env               # Environment variables
├── main.py            # Main script
└── README.md          # This file

1. Place your XML files in the input/ directory
2. Run the script:

python main.py

3. The processed XML will be saved as articleset.xml

You can also use individual functions programmatically:

from main import rewrite_xml, read_xml_file

# Process a single XML file
xml_content = read_xml_file('path/to/file.xml')
processed_xml = rewrite_xml(xml_content, 'journal_name', 'api_key')

• rewrite_xml(): Main function that orchestrates the entire transformation process
• process_all_xml_files(): Batch processes multiple XML files and combines them
• reorganize_article_xml(): Reorders XML elements according to PubMed DTD requirements

• retrieve_json_info(): Fetches article information from OJS API
• get_english_abstract(): Extracts English abstracts from article pages
• get_dc_subjects(): Retrieves keyword metadata from article pages

• add_article_title(): Adds English article titles
• replace_vernacular_title(): Updates vernacular titles with subtitles
• refurbish_abstracts(): Reorganizes abstracts by language
• insert_keywords_after_abstract(): Adds keyword metadata
• add_article_id_list(): Adds DOI information
• add_publication_type(): Adds publication type metadata
• replace_language_tag(): Standardizes language codes

The script performs the following transformations:

1. Title Processing: Retrieves English titles from OJS API
2. Abstract Enhancement: Fetches English abstracts and creates multilingual structure
3. Metadata Addition: Adds keywords, publication types, and article IDs
4. Language Standardization: Updates language codes for PubMed compatibility
5. Structure Reorganization: Reorders elements according to PubMed DTD
6. DOCTYPE Addition: Adds proper DOCTYPE declaration for PubMed submission

The script generates a combined articleset.xml file containing all processed articles with:

• PubMed-compliant DOCTYPE declaration
• Properly ordered XML elements
• English and vernacular titles
• Multilingual abstracts
• Keyword metadata
• Publication type information
• DOI identifiers

The script includes error handling for:

• Network connectivity issues
• API response errors
• XML parsing errors
• Missing metadata
• File I/O operations

1. API Connection Errors: Verify your API key and journal title in .env
2. XML Parsing Errors: Check that input XML files are well-formed
3. Missing Abstracts: Some articles may not have English abstracts available
4. Network Timeouts: Retry processing if network issues occur

The script outputs detailed information during processing:

• API responses are cached in json.txt
• Progress messages are printed to console
• Error messages indicate specific issues

Update the .env file with your specific journal information:

• journal_title: The OJS journal identifier
• journal_abbreviation: PubMed-approved journal abbreviation

Modify the element_order list in reorganize_article_xml() to change element ordering if needed.

For issues or questions:

• Check the troubleshooting section above
• Review the error messages in the console output
• Verify your .env configuration
• Ensure input XML files are properly formatted