giorginolab / zotfile_doctor

Zotfile directory consistency checker

Zotfile directory consistency checker

Zotfile is an extension for Zotero reference manager software which maintains an organized directory of literature PDF files.

This small script checks the consistency between Zotfile's file storage and the corresponding Zotero's view.

It compares the annotations stored in zotero.sqlite file with the PDF files in your chosen Zotfile directory. Both should be passed as arguments. The output should be self-explanatory. It does not modify the files nor the zotero DB. If you want to do clean-ups, you should do it yourself.

Requirements

Python 3.5 or higher.

Usage

Display differences only

python zotfile_doctor.py zotero.sqlite zotfile_directory

Display disfferences and clean zotfile directory

python zotfile_doctor.py zotero.sqlite zotfile_directory -c

Example output

There were 2 files in DB but not in zotfile directory:
   Statistics/Socio/Herrera et al_2010_Mapping the Evolution of Scientific Fields.PDF
   [...]

There were 8 files in zotfile directory but not in DB:
   MD/MM-PBSA/Chen et al_2016_Assessing the performance of the MM-PBSA and MM-GBSA methods.pdf
   [...]

See also

These issues

• jlegewie/zotfile#96
• https://forums.zotero.org/discussion/41179/zotfile-does-not-delete-pdf-files-when-a-database-entry-is-deleted

Known issues

• Files not ending in .pdf will be false positives (which includes capitalized .PDF etc.).
• Zotero must be closed (a locked DB can't be opened).
• Current as of 9/2019. May stop working if Zotero's internal storage format changes.
• Syncing case-insensitive filesystems occasionally causes confusion (not a problem originated by this script though).

Author

Toni Giorgino, <www.giorginolab.it>

License

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see https://www.gnu.org/licenses/.