ZotFile: Advanced PDF management for Zotero

Joscha Legewie

Zotfile is a Zotero plugin to manage your attachments: automatically rename, move, and attach PDFs (or other files) to Zotero items, sync PDFs from your Zotero library to your (mobile) PDF reader (e.g. an iPad, Android tablet, etc.) and extract annotations from PDF files.

Detailed information are available from the zotfile website.

Installation

The currently released version (3.x) is available here.

To install the development version on github:

1. download .zip file from github
2. extract .zip file
3. recreate .zip file containing all the files at the top level, i.e., install.rdf and the chrome directory need to be at the root of the .zip file and not under zotfile/
4. rename the file to .xpi
5. Install

• For zotero firefox: drag & drop on firefox
• For zotero standalone: In Zotero Standalone go to 'Tools->Add-ons->Tools for all Add-ons (the small, drop-down wheel menu next to the 'Search all Add-ons' box)->Install Add-on From File' and pick the .xpi file.

For Linux, Mac OS X or Cygwin users, there is a Makefile which takes care of creating the .xpi file. Simply run make instead of steps 3 and 4 above.

Extraction of PDF Annotations

Zotfile can extracted annotations and highlighted text from many PDF files. But it will never be able to handle all files. If you can not copy & paste meaningful text from the file in your pdf viewer (open your pdf viewer (not the browser plugin), select text, copy and paste it somewhere), zotfile won't be able to extract the highlighted text either. If you can, there is a chance that future versions of zotfile will solve the problem. In general, these files depend on the pdf standards supported by pdf.js, which is the pdf library used by zotfile to extract annotations.

License

The source code is released under GNU General Public License, version 3.0

Contributions preferably through pull requests are welcome!

Changelog

Changes in 3.0

• Improved extraction of annotation

  The extraction of pdf annotations using pdf.js works much better now! Zotfile uses a modified version of the updated pdf.js library (here is the fork). The new version supports more pdf standards, detects spaces more precisely, sorts annotations in the correct order, and future updates to new versions of pdf.js are relatively easy. There are still pdfs that won't work though! Some pdf standards are not yet supported and if you can not copy & paste text from the pdf file using your pdf viewer (e.g. Preview), it's unlikely that zotfile can help.

• Goto annotation in pdf

  The extracted annotations now include a link that opens the pdf file on the corresponding page. For the extracted annotation "This is my text" (zotfile 2013: 4), zotfile 2013: 4 is a link that opens the pdf on the page with the annotation. Currently, this feature only works from reports (right-click on item and select generate report) but future version of Zotero might be able to open the links directly from the note (see discussion here and here)

• Tablet feature: Restrict saved search for tablet files to sub-folders

  You can now right-click on the two saved searches for tablet files and restrict them to one of your custom sub-folders. This is very helpful to quickly see the files that are in a specific sub-folder.

• Tablet feature: Support of colored tags in Zotero 4

  Zotfile now tags the parent item when an attachment is send to the tablet so that you can easily see which items are on the tablet. Simply assign colors to the two tablet tags (_tablet and _tablet_modified). But DO NOT manually add the tag to items or attachments (also not using the keys for colored tags).

• Italian localization (thanks to Roberto Caviglia)

• Remove empty sub-folders when getting files from tablet

• Fix alert window (headline was missing in Zotero 4)

• Fix automatic renaming option "Only ask if..."

• Fix for zotfile item menu on Zotero as a tab

Changes in 2.3.4

• compatible with Zotero 4.0
• Annotation extraction compatible with FF 20

Changes in 2.3.1

• adding attachments from watched folder now works when child item is selected
• language improvements for French and German
• bug fix for subfolders based on wildcards

Changes in 2.3

• enhanced renaming rules (thanks to Midnighter)

  1. Optional wild-cards: {-%y} only includes - if %y is defined.

  2. Exclusive wild-cards: %s|%j journal abbr. or if not defined full journal name.

  (for examples see below)

• additional wild-cards for author formating (author initials %I and lastnameF %F), pages (%f) and short title (%h)

• watch source folder for new files

  Whenever the focus changes to the item list in Zotero, Zotfile checks for new files in the source folder. If a new file was added to the folder, zotfile uses a clickable, non-disruptive window to ask the user whether s/he wants to attach that file to the currently selected Zotero item.

• revised auto rename with additional options

  Four options: Never, Always ask, Only ask if item has other atts, Always rename. The 'asking' uses a clickable, non-disruptive window that appears in the bottom right corner - same as previous info window but clickable.

• revised notifications and error handling

• Zotfile translation to German (thanks to wuffi) and French (thanks to gracile-fr)

• Allow periods as delimiter in filenames (thanks to jjatria)

• new option: "lower case" filenames (thanks to jjatria)

• new option: disable renaming so that attachments are only moved (hidden: .disable_renaming)

• new option: set opening and closing quotation mark for extracted annotations (hidden: .openingQuotationMarks, .closingQuotationMarks)

• new option: remove periods from filenames (hidden: removePeriods)

• bug fix: download of poppler tool was broken

• bug fix: preview of renaming rules for Unix and Windows

• bug fix: sending to and getting from tablet deleted note content

Examples for enhanced renaming rules %j - journal; %s - journal abbreviation

{%a}{-%y}{-%j (%s)} - author-2001-Proceedings of the National Academy of Sciences (PNAS) (if either %j or %s is empty, author-2001)

{%a-}{%y-}{%s|%j} - author-2001-PNAS or author-2001-Proceedings... if %s is empty

For full description, see updated zotfile website.

Changes in 2.2.3

• bug fix: check whether selected attachments are valid (no top-level item, no web attachments and attachment exists)
• bug fix: editing custom folder created error if user had maximum number of custom folders

Changes in 2.2.2

• Add option to change delimiter between multiple authors (thanks to gracile-fr)

Changes in 2.2

• New feature: automatic renaming of attachment files (thanks to Robin Wilson)
• Bug fix: zotfile produced error when trying to move open files on Windows (thanks to Dominik)

Changes in 2.1

• Important: the tag for tablet files was changed from '_READ' to '_tablet'
• New saved search for modified files on tablet (updates automatically, replaces 'Scan Tablet Files' function, which has been removed)
• Zotfile menu items only appear for bibliographic items and attachments (not for notes)
• Bug fix: allow the extraction of annotations in group libraries
• Other bug fixes

Changes in 2.0

• Sync Zotero Attachments with your iPad or Android tablet
• Extract Annotations from PDF Files (thanks to Joe Devietti)
• redesigned preference pane
• many more features and bug fixes