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.
★ Attach New Files to Zotero Items
ZotFile can rename and add the most recently modified file from the Firefox download or a user specified folder as a new attachment to the currently selected Zotero item. It renames the file using metadata from the selected Zotero item (user configurable), and stores the file as a Zotero attachment to this item (or alternatively, moves it to a custom location).
★ (Batch) Rename and Move Attachments based on Zotero Metadata
The user can also select any number of Zotero items and automatically rename and move all attachments of these items according to the user defined rules using metadata of the respective zotero item (batch processing).
★ Sync PDFs with your iPad or Android tablet
To read and annotate PDF attachments on your mobile device, zotfile can sync PDFs from your Zotero library to your (mobile) PDF reader (e.g. an iPad, Android tablet, etc.). Zotfile sends files to a location on your PC or Mac that syncs with your PDF reader App (PDF Expert, iAnnotate, GoodReader etc.), allows you to configure custom subfolders for easy access, and even extracts the annotations and highlighted text to Zotero notes when you get the files back from your tablet. For instruction, click here.
★ Extract Annotations from PDF Files
After highlighting and annotating pdfs on your tablet (or with the PDF reader application on your computer), ZotFile can automatically extract the highlighted text and note annotations from the pdf. The extracted text is saved in a Zotero note. Thanks to Joe Devietti, this feature is now available on all platforms based on the pdf.js library.
HOW TO INSTALL & SET UP ZOTFILE
To start using zotfile, make sure that Zotero is installed and follow these simple steps:
(1) Install ZotFile
For Zotero Firefox, click on the the download link above and follow the instructions on the Mozilla Add-Ons page. For Zotero Standalone, first download the extension file (follow the download link above, click on 'Continue to Download'. In Firefox, right-click 'Add to Firefox' and select 'Save Link As'. In other browsers, click on 'Download Now' (it's greyed out) and then 'download anyway'). Now start Zotero Standalone, and go to 'Tools->Add-ons->Tools for all Add-ons (the small,drop-down wheel in the top right corner)->Install Add-on From File' and pick the downloaded .xpi file.
(2) Change the Source Folder for Attaching new Files
To attach new files to Zotero items, zotfile looks for the most recently modified (e.g. just downloaded) file in a user specified folder. For Zotero Firefox, this option is set to the Firefox download folder by default. For Zotero Standalone, this option has to be changed on the 'General Settings' tab in the preference window (Zotero Actions -> ZotFile Preferences). The source folder can be set to any location but I generally recommend setting it to your browser's download folder such as ~/Downloads on the mac for most browsers.
(3) Changing other Options (optional)
ZotFile offers many other options that can be changed by the user. Most of them are located in the zotfile preference window under Zotero Actions -> ZotFile Preferences.
SYNCING PDF ATTACHMENTS WITH YOUR IPAD OR ANDROID TABLET
To read and annotate PDF attachments on your mobile device, zotfile can sync PDFs from your Zotero library to your (mobile) PDF reader (e.g. an iPad, Android tablet, etc.). For this purpose, Zotfile sends files to a location on your PC or Mac that syncs with your PDF reader App (PDF Expert, iAnnotate, GoodReader etc.), and gets them back when you have finished reading them. To get started, first set up a folder on your PC or Mac that syncs with your tablet reader application. Files that are copied to this folder should automatically appear in your PDF reader application. One possibility is Dropbox, which is free for up to 2GB of space and works with most PDF reader apps. More detailed instructions as well as alternative options should be available on the website of your PDF reader App. Second, open the 'Tablet Settings' tab in the zotfile preference window and enable the option 'Use ZotFile to send and get files from tablet'. Third, change the zotfile location for files on the tablet to the folder that syncs with your pdf reader app ('Base Folder' on the 'Tablet Settings' tab). Forth (optional), set up subfolders that make it easy to sort your files in the tablet folder so that you can easily find them on your tablet.
You can now start sending pdfs (or other files) to your tablet. Simply right-click on a zotero item and select 'Send to Tablet' under 'Manage Attachments'. When you are done reading and annotating your pdf, just get the file back from the tablet by clicking on 'Get from Tablet' under 'Manage Attachments'. ZotFile will automatically remove the file from your tablet folder and extract the annotations from the pdf file to a zotero note. Alternatively, you can use the 'Scan Tablet Files' function in Zotero's Action Menu to automatically check whether any files in the tablet folder have changed. ZotFile then asks the user how to proceed for each modified file.
ZotFile renames files based on bibliographic information from the currently selected Zotero item. You can change the renaming rules in the zotfile preference window under renaming rules (Zotero Actions -> ZotFile Preferences). The option 'Renaming Format' allows you to create custom renaming rules using wildcards, which are replaced by metadata from the selected Zotero item. Zotfile also supports optional and exclusive wild-cards. Optional wild-cards mean that "{-%y}" only includes the seperator "-" in the filename if "%y" is defined. Exclusive wild-cards such as "%s|%j" will generate the entry for %s if that exists and the entry for %j otherwise. Other characters between the wildcards and the bar are ignored ("%s | stuff %j | - more %p" is equivalent to %s|%j|%p). Some examples are below.
Wildcards
%a - last names of authors (not editors etc) or inventors. The maximum number of authors are changed under 'Additional Settings'.
%I - author initials.
%F - author's last name with first letter of first name (e.g. EinsteinA).
%A - first letter of author (useful for subfolders)
%y - year (extracted from Date field)
%t - title. Usually truncated after : . ? The maximal length of the remaining part of the title can be changed.
%T - item type (localized)
%j - name of the journal
%p - name of the publisher
%w - name of the journal or publisher (same as "%j|%p")
%s - journal abbreviation
%v - journal volume
%e - journal issue
%f - pages
%n - patent number (patent items only)
%i - assignee (patent items only)
%u - issue date (patent items only)
Examples
Abbott, Andrew, and Alexandra Hrycak (1990): Measuring Resemblance in Sequence Data: An Optimal Matching Analysis of Musicians' Careers. American Journal of Sociology 96:144-185.
{%a}{-%y}{-%j (%s)} - Abbott-1990-American Journal of Sociology (AJS)
(if either "%j" or "%s" is empty, "Abbott-1990")
{%a-}{%y-}{%s|%j} - "Abbott-1990-AJS" or "Abbott-1990-American Journal of Sociology" if "%s" is empty
{%a_}{%y_}{%t}: Abbott_Hrycak_1990_Measuring Resemblance in Sequence Data
%a-%y %t: Abbott_Hrycak-1990 Measuring Resemblance in Sequence Data
{%w_}{%y_}{%a}: American Journal of Sociology_1990_Abbott_Hrycak
With 'Maximum number of authors' set to 1 and 'Add suffix ...' set to 'et al'
%a_%y_%t: Abbott et al_1990_Measuring Resemblance in Sequence Data
With 'Maximum number of authors' set to 1, 'Add suffix ...' disabled, and 'Maximum length of title' set to 10
%a_%y_%t: Abbott_1990_Measuring
Zotfile has a number of hidden options that allow you to further configure zotfile. You can access the hidden options through about:config. In Zotero Firefox, type 'about:config' in the url bar. In Zotero Standalone, go to 'Actions->Preferences->Advanced->Open about:config'.
Search for 'extensions.zotfile' to see a list of the hidden zotfile options. Here is a list of the options that can be changed by the user (I strongly discourage to change any of the other options):
.allFiles
By default, zotfile's 'Attach New File' function attaches the most recently modified file from the user defined folder. With this option set to true, zotfile attaches all files in the user defined folder to the currently selected zotero item. (Note: I haven't tested this for a while but it should still work)
.disable_renaming
Disable any renaming of files - just moves them to the specified location.
.tablet.mode
In background mode (mode=1, default), zotfile leaves zotero attachments at their current location and moves a copy of the file to the tablet folder (set in the zotfile preference window) when they are send to the tablet. Getting the file back from the tablet replaces the zotero attachment file and removes it from the tablet folder. This mode is recommended when you sync attachment files in your zotero library across multiple computers or when you index your attachments.
The foreground mode (mode=2) moves the attachment file to the tablet folder and links to this location from zotero. In this mode there is always only one copy of the file. You can not, however, sync linked attachments to the zotero server.
.confirmRepush
By default, zotfile asks the user whether an attachment should be send to the tablet that is already on the tablet, which can be useful to move it to a different subfolder. This user confirmation can be disabled with this option.
.tablet.tagParentPush
.tablet.tagParentPush_tag
.tablet.tagParentPull
.tablet.tagParentPull_tagThese options allow the user to tag the parent item when sending (push) or getting back (pull) attachments to or from the tablet.
.pdfExtraction.NoteHtmlTagStart
.pdfExtraction.NoteHtmlTagEnd
.pdfExtraction.HighlightHtmlTagStart
.pdfExtraction.HighlightHtmlTagEnd
.pdfExtraction.UnderlineHtmlTagStart
.pdfExtraction.UnderlineHtmlTagEndThese options allow the user to fine-tune the formatting of the extracted PDF annotations in the zotero note. They define the opening and closing html tag for different types of annotations. The default settings format highlighted text from the pdf normally, note text in italics (<i> for start and </i> for end), and underline underlined text (<u> for start and </u> for end). The end options for note, highlight and underline have to be the closing tag for the corresponding start option.
.pdfExtraction.NoteRemoveHyphens
By default, zotfile removes hyphens from extracted text. Setting NoteRemoveHyphens to false, disables this option.
.UsePDFJSandPoppler
With this option, zotfile extracts PDF annotations twice using both pdf.js and poppler. This option only works on Mac OS when the poppler based extraction script is installed.
.openingQuotationMarks, .closingQuotationMarks
Set the opening and closing quotation mark for extracted annotations.
You can report bugs on the Zotfile thread in the Zotero forum. Please provide information about about your system (Windows, Mac OS, Linux etc) as well as your Zotfile, Zotero and Firefox version. Also make sure that you can reproduce the bug and describe the steps as closely as possible. In addition, any information from the Error Console are very helpful. You can check the Error Console in Zotero for Firefox by going to 'Tools->Web Dev.->Error Console' in Firefox and look for any zotfile related stuff after the bug occurred. For zotfile bugs, the 'Source File' should be something like 'chrome://zotfile/content/...' (most likely zotfile.js). You can also clear the console, execute the actions that caused the problem and then check again. If I ask you to provide a Report ID, follow the instructions here.
Zotfile is a Zotero plugin that is based on the Zotero API. It uses code from the pdf.js and the poppler project for the extraction of annotations from pdf files. Joe Devietti has implemented the extraction based on pdf.js. The small icons in the preference window are from famfamfam.