cd /home/daytona/workspace && pandoc --track-changes=all "/home/daytona/workspace/attachments/d8c76e06-3222-421b-bf84-aa3af677479e/teaching intervention on gut microbiota and mental wellbeing-1.docx" -o /tmp/doc_content.md 2>&1 && cat -n /tmp/doc_content.md

ls /home/daytona/workspace/scripts/office/ 2>/dev/null || echo "no scripts dir"

ls /home/daytona/skills/docx/scripts/office/ 2>/dev/null && ls /home/daytona/skills/docx/ 2>/dev/null

mkdir -p /home/daytona/workspace/gut-microbiota-correction && python /home/daytona/skills/docx/scripts/office/unpack.py "/home/daytona/workspace/attachments/d8c76e06-3222-421b-bf84-aa3af677479e/teaching intervention on gut microbiota and mental wellbeing-1.docx" /home/daytona/workspace/gut-microbiota-correction/unpacked/ 2>&1

mkdir -p /home/daytona/workspace/gut-microbiota-correction/unpacked && cd /home/daytona/workspace/gut-microbiota-correction && cp "/home/daytona/workspace/attachments/d8c76e06-3222-421b-bf84-aa3af677479e/teaching intervention on gut microbiota and mental wellbeing-1.docx" ./original.docx && unzip -q ./original.docx -d ./unpacked/ && echo "Done"

ls -la "/home/daytona/workspace/attachments/d8c76e06-3222-421b-bf84-aa3af677479e/"

cp "/home/daytona/workspace/attachments/d8c76e06-3222-421b-bf84-aa3af677479e/teaching intervention on gut microbiota and mental wellbeing-1.docx" /home/daytona/workspace/gut-microbiota-correction/original.docx && echo "copied"

cd /home/daytona/workspace/gut-microbiota-correction && unzip -q original.docx -d unpacked/ && echo "unpacked ok" && ls unpacked/word/

python3 -c "import zipfile; z=zipfile.ZipFile('/home/daytona/workspace/gut-microbiota-correction/original.docx'); z.extractall('/home/daytona/workspace/gut-microbiota-correction/unpacked'); print('done'); print(z.namelist()[:10])"

pandoc "/home/daytona/workspace/attachments/d8c76e06-3222-421b-bf84-aa3af677479e/teaching intervention on gut microbiota and mental wellbeing-1.docx" -o /home/daytona/workspace/gut-microbiota-correction/content.md --wrap=none 2>&1 && echo "SUCCESS"

python3 << 'EOF' with open('/home/daytona/workspace/gut-microbiota-correction/content.md', 'r', encoding='utf-8') as f: content = f.read() corrections = [ # 1. Title typo: BEETWEEN -> BETWEEN ("BEETWEEN", "BETWEEN"), # 2. Misplaced bold on "Microbial diversity" ("M**icrobial diversity**", "**Microbial diversity**"), # 3. Misplaced bold on "Ghrelin" ("G**hrelin**", "**Ghrelin**"), # 4. Misplaced bold/lowercase on "probiotics" definition ("p**robiotics**", "**Probiotics**"), # 5. EVeryone -> Everyone ("EVeryone", "Everyone"), # 6. Instructor note: incomplete sentence in Nervous Pathway section ("A diagram of the Gut--Brain Axis to illustrate these pathways.", "Display a diagram of the Gut--Brain Axis to illustrate these pathways."), # 7. Instructor note: "The major functions of the ENS." incomplete ("The major functions of the ENS.", "Explain the major functions of the ENS."), # 8. Instructor note: "Common probiotic foods and discuss each one." ("Common probiotic foods and discuss each one.", "Display common probiotic foods and discuss each one."), # 9. Instructor note: "Prebiotic-rich foods." ("Prebiotic-rich foods.\n\nExamples include:", "Display prebiotic-rich foods.\n\nExamples include:"), # 10. Instructor note: "Simple dietary examples." ("Simple dietary examples.", "Provide simple dietary examples."), # Fix reference 13/14 - merge DOI into ref 13 # Fix reference 15/16 - merge DOI into ref 15 # Fix reference 17/18 - merge DOI into ref 17 # Fix duplicate reference 19/20 (same as ref 1) ] for old, new in corrections: if old in content: content = content.replace(old, new) print(f"Fixed: {old[:50]!r}") else: print(f"NOT FOUND: {old[:50]!r}") # Fix references - merge DOIs into parent refs and remove duplicates import re # Fix ref 13: Thursby & Juge - merge the DOI (ref 14) into ref 13 content = content.replace( "13. Thursby, E., & Juge, N. (2017). Introduction to the human gut microbiota. Biochemical Journal, 474(11), 1823--1836.\n\n14. https://doi.org/10.1042/BCJ20160510", "13. Thursby, E., & Juge, N. (2017). Introduction to the human gut microbiota. Biochemical Journal, 474(11), 1823--1836. https://doi.org/10.1042/BCJ20160510" ) # Renumber: old 15 becomes 14, old 16 becomes 15, etc. # But first, let's just merge DOIs into their refs and remove duplicate Cryan ref content = content.replace( "15. Lynch, S. V., & Pedersen, O. (2016). The human intestinal microbiome in health and disease. New England Journal of Medicine, 375(24), 2369--2379.\n\n16. https://doi.org/10.1056/NEJMra1600266", "14. Lynch, S. V., & Pedersen, O. (2016). The human intestinal microbiome in health and disease. New England Journal of Medicine, 375(24), 2369--2379. https://doi.org/10.1056/NEJMra1600266" ) content = content.replace( "17. Sender, R., Fuchs, S., & Milo, R. (2016). Revised estimates for the number of human and bacterial cells in the body. PLoS Biology, 14(8), e1002533.\n\n18. https://doi.org/10.1371/journal.pbio.1002533", "15. Sender, R., Fuchs, S., & Milo, R. (2016). Revised estimates for the number of human and bacterial cells in the body. PLoS Biology, 14(8), e1002533. https://doi.org/10.1371/journal.pbio.1002533" ) # Remove duplicate Cryan ref (was 19/20, now becomes nothing - it duplicates ref 1) content = content.replace( "\n19. Cryan, J. F., O\\'Riordan, K. J., Cowan, C. S. M., et al. (2019). The microbiota--gut--brain axis. Physiological Reviews, 99(4), 1877--2013.\n\n20. https://doi.org/10.1152/physrev.00018.2018\n\n21.", "\n16." ) # Renumber remaining references after 20 for old_num, new_num in [(21,16),(22,17),(23,18),(24,19),(25,20),(26,21),(27,22),(28,23),(29,24),(30,25),(31,26),(32,27),(33,28),(34,29),(35,30),(36,31),(37,32),(38,33),(39,34),(40,35),(41,36),(42,37),(43,38),(44,39),(45,40)]: # Replace reference numbers at start of lines content = content.replace(f"\n{old_num}. ", f"\n{new_num}. ") with open('/home/daytona/workspace/gut-microbiota-correction/content_corrected.md', 'w', encoding='utf-8') as f: f.write(content) print("Done writing corrected file") EOF

pandoc /home/daytona/workspace/gut-microbiota-correction/content_corrected.md -o "/home/daytona/workspace/gut-microbiota-correction/teaching intervention on gut microbiota and mental wellbeing-CORRECTED.docx" --reference-doc="/home/daytona/workspace/attachments/d8c76e06-3222-421b-bf84-aa3af677479e/teaching intervention on gut microbiota and mental wellbeing-1.docx" 2>&1 && echo "SUCCESS"

python3 -c " with open('/home/daytona/workspace/gut-microbiota-correction/content_corrected.md','r') as f: lines = f.readlines() # Check key corrections checks = ['BETWEEN', 'Microbial diversity', 'Ghrelin', 'Probiotics are', 'Everyone should', 'Display a diagram', 'Explain the major', 'Display common probiotic', 'Display prebiotic-rich', 'Provide simple'] for c in checks: found = any(c in l for l in lines) print(f'[{\"OK\" if found else \"MISSING\"}] {c}') # Check reference section cleanup import re ref_lines = [l.strip() for l in lines if re.match(r'^\d+\. ', l.strip())] print('\nFirst few and last few references:') for r in ref_lines[:3]: print(' ', r[:80]) print(' ...') for r in ref_lines[-3:]: print(' ', r[:80]) print(f'Total references: {len(ref_lines)}') "