ZotFile

Advanced PDF management for Zotero

Download

View the Project on GitHub

         


Content

Features Install Zotfile Renaming Rules User-Defined Wildcards Extract PDF Annotations Hidden Options Reporting a Bug Changelog


FEATURES

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. Instructions are below.

★ 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.

INSTALL 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.

RENAMING RULES

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

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.

USER-DEFINED WILDCARDS

All wildcards are now defined in the hidden preference zotfile.wildcards.default and can be changed by the user. But I strongly suggest that you do not change this preference. Instead, there is a second hidden preference zotfile.wildcards.user, which allows you to add and overwrite wildcards (hidden preference can be changed in about:config). This is a preference for advanced users without any error checking. Be careful what you do and validate your JSON using this site! By default, zotfile.wildcards.user is set to {} so that no user wildcards are defined. Below is an example JSON that defines wildcards for %1, %2, %3, %4, and %5 illustrating all the possibilities:

  1. String with the name of Zotero field (%1)
  2. JSON with item type specific field names (%2)

    Always include a default value. Otherwise this is not going to work. A list of all item types is available here.

  3. JSON with field element and transformations based on regular expressions (%3 and %4)

    ZotFile uses the specified field as an input string and then applies the transformations specified in operations. The value of field can either be the name of a Zotero field (see 1) or a javascript object with item type specific field names (see 2). operations is an array of javascript objects and supports three types of transformations that are identified by the function element:

    • exec: Search for matches using regular expressions (%3). Zotfile uses the exec() function based on the regular expression defined in regex, and returns the element specified in group so that 0 returns the matched text and higher values the corresponding capturing parenthesis. If the match fails, this operation returns the input data.

      Required parameters: regex

      Optional parameters: group (default 0), flags (default "g")

    • replace: Replaces matches of a pattern using regular expressions (%4). Zotfile uses the replace() function with the regular expression regex and replacement string replacement. The replacement string can include $n for the nth parenthesized sub-match string and other special replacement patterns (see replace() documentationn). The wildcard %4, for example, takes the date when an item was added (format 2012-02-18 02:31:37) and returns the reformatted date as 20120218.

      Required parameters: regex, replacement

      Optional parameters: flags (default "g")

    • toLowerCase etc: Simple string functions that that do not require any additional arguments(%5). Currently supported are toLowerCase, toUpperCase, and trim.

    flags is an optional parameter for both searching and replacing and corresponds to flags for regular expressions in javascript (default: "g").

  4. Finally, the wildcard %5 illustrates a complex combination of operations (completely arbitrary).

Example for user-defined wildcards

{
    "1": "publicationTitle",
    "2": {
        "default": "publicationTitle",
        "book": "publisher",
        "bookSection": "publisher"
    },
    "3": {
        "field": "title",
        "operations": [{
            "function":"exec",
            "regex": "([\\w ,-]{1,50})[:\\.?!]?",
            "group": 1
        }]
    },
    "4": {
        "field":"dateAdded",
        "operations": [{
            "function": "replace",
            "regex": "(\\d{4})-(\\d{2})-(\\d{2})(.*)",
            "replacement": "$1$2$3",
            "flags":"g"
        }]
    },
    "5": {
        "default": {
            "field": "title",
            "operations": [
                {
                    "function":"replace",
                    "regex": "\\d",
                    "replacement": ""
                },
                {
                    "function": "exec",
                    "regex": "([\\w ,-]{1,10})[:\\.?!]?",
                    "group": 1
                },
                {
                    "function": "toUpperCase"
                },
                {
                    "function": "trim"
                }
            ]
        },
        "journalArticle": "publicationTitle"
    }
}

Item types and field names

A complete list of Zotero fields is available here (dateModified and dateAdded seem to be missing from that list) and all the item types are here. The fields for each item type are listed on this page. Zotfile defines a number of additional fields that can be used as part of wildcards: itemType is the language specific item type, formatedTitle is the title formatted using the options defined in the zofile preferences, author is the author string formatted using the zotfile preferences, authorLastF is the author string formatted as LastnameF, and authorInitials are the initial of the authors.

Formatting rules

There are a couple of formatting rules for the user-defined wildcards:

Most importantly, validate your json. Check out zotfile.wildcards.default for more examples (see below). Finally, the JSON has to be reformatted to one line that can be pasted into the preference field in about:config. Here is the example from above:

{"1": "publicationTitle", "2": {"default": "publicationTitle", "book": "publisher", "bookSection": "publisher"}, "3": {"field": "title", "operations": [{"function":"exec", "regex": "([\\w ,-]{1,50})[:\\.?!]?", "group": 1 }] }, "4": {"field":"dateAdded", "operations": [{"function": "replace", "regex": "(\\d{4})-(\\d{2})-(\\d{2})(.*)", "replacement": "$1$2$3", "flags":"g"}] }, "5": {"default": {"field": "title", "operations": [{"function":"replace", "regex": "\\d", "replacement": ""}, {"function": "exec", "regex": "([\\w ,-]{1,10})[:\\.?!]?", "group": 1 }, {"function": "toUpperCase"}, {"function": "trim"} ] }, "journalArticle": "publicationTitle"} }

You can use a javascript console such as Firefox’s Scratchpad to test whether the JSON is properly formatted:

wildcard = '{"1": "publicationTitle"}';
JSON.parse(wildcard)

Default setting for zotfile.wildcards.default

The information in this file might not be up to date but you can look at the default wildcards and learn something about user-defined wildscards here. The minified version in one line is here so that you can copy it to zotfile.wildcards.default if you screw up.

EXTRACT PDF ANNOTATIONS

Zotfile can extracted annotations and highlighted text from many PDF files. The extracted annotations are saved in Zotero notes and you can go back to the annotation in the pdf by clicking on the link after the extracted text. PDFs are a very complex format and the extraction will never work for 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. When you have a pdf file that does not work or with clear spacing problems, feel free to share the file on the zotfile thread in the Zotero forum or upload it to the zotfile Zotero group in the PUT FILES HERE folder. But only share files for which you can copy and paste text! Otherwise you are wasting everyone’s time.
On Mac OS, you can also use poppler to extract pdf annotations (ZotFile Preferences -> Advanced Settings). Currently, pdf.js is more reliable and should be the default in most cases. The poppler-based tool, however, is faster and might handle certain pdf standards that are not yet supported by pdf.js.

Goto Annotation in PDF

Zotfile adds a link to extracted annotations that allows you to open the pdf file at the page with the annotation. Just click on the link after some extracted text and your pdf should open on the correct location. On Windows, zotfile detects the default pdf viewer and opens the pdf on the correct page (not tested for Windows 8). Adobe Reader, Foxit and PDF-XChange all work (other might as well but are untested). Adobe Reader, however, does not jump to the correct page when the file is already open (Foxit and PDF-XChange do). If zotfile is unable to detect the default viewer or you want to force zotfile to use a different viewer, simply change the hidden option zotfile.pdfExtraction.openPdfWin to the desired path (e.g. C:\Program Files\Adobe\Reader 11.0\Reader\AcroRd32.exe). On Mac OS, zotfile works with Preview (the default) and Skim. Preview, however, does not support scripting very well and has certain limitations. Don’t press any keys while the pdf is opening, for example. Skim, an alternative pdf viewer for Mac OS, works much better! Just set the hidden option zotfile.pdfExtraction.openPdfMac_skim to true and zotfile will open the pdf in Skim. For Linux, zotfile first tries okular and then evince but you can also set the zotfile.pdfExtraction.openPdfLinux option to change the default behavior. One example would be /usr/bin/okular -p, which tell zotfile the path and the argument for the page number.

HIDDEN OPTIONS

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):

REPORTING A BUG

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.

CHANGELOG

Changes in 4.0

Changes in 3.1

Changes in 3.0.3

Other small fixes mainly for Italian translation, restriction of saved searches and renaming based on collections.

Changes in 3.0

Changes in 2.3.4

Changes in 2.3.1

Changes in 2.3

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 renaming rules.

Changes in 2.2.3

Changes in 2.2.2

Changes in 2.2

Changes in 2.1

Changes in 2.0