ZotFileCleaner

An utility to find pdf files that are locally stored in Zotero database instead of ZotFile custom locations.

• Filter and clean the attachment PDF files already deleted in Zotero library.
• Filter Zotero items that is without any attachments.
• Filter and clean the empty/orphan folders in ZotFile custom location.

0. Prerequisite

This utility relies on the ZotFile and Better Bibtex plugins. If you use them too, you may face the same problem as me.

Environment: Python3 and bibtexparser

pip install --no-cache-dir --force-reinstall git+https://github.com/sciunto-org/python-bibtexparser@main
pip install send2trash

1. Preparation in Zotero

• Remember the Custom Location setting in the ZotFile Preferences:
  

• In Zotero, click (1)File->(2)Export Library->(3)Select Better BibTex->(3)Check Keep updated option->(4)Save the bib file to any folder your like.
  

2. Run the script

$ python3 ~/github/Zotero/src/zotfileCleaner.py -h
usage: zotfileCleaner.py [-h] -f FILE -c CUSTOMLOCATION [-e] [-d]

ZotFileCleaner: An utility to find pdf files that are locally stored in Zotero
database instead of ZotFile custom locations.

optional arguments:
  -h, --help            show this help message and exit
  -f FILE, --file FILE  Zotero automatic exported better bibtex lib file.
  -c CUSTOMLOCATION, --customlocation CUSTOMLOCATION
                        Custom location defined in ZotFile preferences.
  -e, --empty           Print items without any attachment files.
  -d, --delete          Clean up the zombie files under ZotFile folder .

Examples

1. Find the items that are locally stored in Zotero database instead of ZotFile custom locations

   # Replace with your own path
   python3 ~/github/Zotero/src/zotfileCleaner.py -f "YOUR/PATH/mylib.bib" -c "YOUR/ZOTFILE/CUSTOM/PATH"
   

   # Output
   Citation keys of the files in Zotero database: 2
     labahnLeanBlowoutSimulations
     wangLargeeddySimulationsFlow2020
   ---------------------------------------------
   ZotFile zombie files: 7
   Done!

2. Find the items without any attachment files

   # Replace with your own path
   python3 ~/github/Zotero/src/zotfileCleaner.py -f "YOUR/PATH/mylib.bib" -c "YOUR/ZOTFILE/CUSTOM/PATH" -e

   # Output
   Citation keys of the files in Zotero database: 2
     labahnLeanBlowoutSimulations
     wangLargeeddySimulationsFlow2020
   ---------------------------------------------
   Citation keys of items without attachment files: 123
     ahnHeatReleaseRate2022
     aignerSwirlCounterswirlEffects1988
     aignerSwirlCounterswirlEffects1988a
     andreiniLocalSourceBased2013
     ansysinc.ANSYSFluentTheory
     ...
     zhouyuTongZhouSheLiuRanShaoShiFeiYuHunTuanLiuRanShaoLiuChangTeXingDaWoMoNiYanJiu2017
   ---------------------------------------------
   ZotFile zombie files: 7
   Done!

3. Delete the ZotFile zombie files

   # Replace with your own path
   python3 ~/github/Zotero/src/zotfileCleaner.py -f "YOUR/PATH/mylib.bib" -c "YOUR/ZOTFILE/CUSTOM/PATH" -d

   #Output
   Citation keys of the files in Zotero database: 2
     labahnLeanBlowoutSimulations
     wangLargeeddySimulationsFlow2020
   ---------------------------------------------
   ZotFile zombie files: 7
   ---------------------------------------------
   Moving Zombie Files to Trash...
     /Dropbox/Zotero/_/李林_et_al_一种双预膜气动雾化低污染燃烧室头部结构.pdf
     /Dropbox/Zotero/2018/夏朝阳_et_al_2018_基于FGM的湍流射流扩散火焰超大涡模_拟.pdf
     /Dropbox/Zotero/2015/Zips_et_al_2015_Numerical_simulation_of_a_single-element_GOx-GCH_4_rocket.pdf
     /Dropbox/Zotero/Science China Technological Sciences2015/Zhang_et_al_2015_Large_eddy_simulation_of_unconfined_turbulent_swirling_flow.pdf
     /Dropbox/Zotero/Combustion and Flame2020/Zadsirjan_et_al_2020_Large_eddy_simulation_of_turbulent_diffusion_jet_flames.pdf
     /Dropbox/Zotero/Chinese Journal of Aeronautics2015/Zhiyin_2015_Large-eddy_simulation.pdf
     /Dropbox/Zotero/Combustion and Flame2021/Zhong_et_al_2021_Local_flame_and_flow_properties_of_propagating_premixed.pdf
   Done!

3. Find the items with problems and do your modification

• Click Edit->Advanced Search->Paste the Citation keys to the input field-> Click Search -> Save Search:
  

• The sub collection named Untitled will be shown under My library. Do you modifications and then the Untitled collection can be deleted.