Invoking the Python program
Copy this command to the command line to start processing the input data to get the abstracts.
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Sample working run of the 4th version:
`` $ python extractor4.py --input_file ../data/data.csv --output_file output.csv --email dan.mccreary@gmail.com 2025-05-29 14:13:51,874 - INFO - Starting PubMed abstract extraction 2025-05-29 14:13:51,874 - INFO - Input file: ../data/data.csv 2025-05-29 14:13:51,874 - INFO - Output file: output.csv 2025-05-29 14:13:51,874 - INFO - Batch size: 100 2025-05-29 14:13:51,874 - INFO - Max workers: 1 2025-05-29 14:13:51,874 - INFO - Specified encoding: Auto-detect 2025-05-29 14:13:51,914 - INFO - Detected encoding: utf-8 (confidence: 0.99) 2025-05-29 14:13:51,914 - INFO - Trying to read file with encoding: utf-8 2025-05-29 14:13:51,933 - INFO - Successfully read file with encoding: utf-8 2025-05-29 14:13:51,933 - INFO - Processing 7338 articles Fetching abstracts: 100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 74/74 [01:15<00:00, 1.01s/it] 2025-05-29 14:15:34,578 - INFO - File saved with UTF-8 encoding 2025-05-29 14:15:34,578 - INFO - Successfully saved 7338 articles with abstracts to output.csv 2025-05-29 14:15:34,580 - INFO - Articles with abstracts: 7289/7338 (99.33%) 2025-05-29 14:15:34,581 - INFO - Extraction completed ```