ZotFile - Advanced PDF management for Zotero

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  • Selecting parent items and running extract annotations should work, certainly does for me (there would be a way to select just PDFs with a saved search for attachment file type, but that really shouldn't be necessary.)

    You have tried this for the PDF itself and it works?
    (IIRC, Zotfile creates new notes every time you extract, though, so what you have in mind doesn't work--but Joscha may have improved that for the current versions, so I'm not sure about that).
  • I take your point about the creation of new notes with every extract.
    I took another look, and indeed, selecting the parent item works for PDF extraction. I wasn't picking up on it because of the behavior of the search bar. It seems that the search bar only finds text in notes if you are searching in the sub-folder where the item lives, and not if you have selected the parent folder. Is this behavior that others have encountered?
  • correct, the quick search bar only searches through the items that are currently displayed. (You can change whether items from subcollections are displayed at the parent level with the recursive collections hidden pref:https://www.zotero.org/support/preferences/hidden_preferences#general_preferences )

    For anything more on that topic, please start a new thread so that this one remains about ZotFile.
  • thanks very much!
  • edited November 19, 2014
    Is there any method to use the links generated by zotfile while extracting annotation (i.e. zotero://open-pdf/) from another application.

    I copied the extracted notes including the links into OneNote; now when I click on the link, it opens Zotero but nothing else happens.

    I would expect clicking on the link to:
    1) highlight/select the pdf file.
    2) Even better, open the pdf file pointing to the page where the hightlight is located (exactly in a same way as clicking on the link from within Zotero).

    Zotero 4.0.23
    Zotfile 4.1
    Windows 7 Pro
  • I am having a problem with getting Zotfile to put pdfs in the custom location and to rename the pdfs using the designated wild cards: {%a_}{%I_}{%y_}{%s}. Instead dragged pdfs go into a folder created by Zotero, and the pdf name is {%a-}{y-}{t}I am using Windows 8.1. I loaded Zotero stand alone. Then I put Zotfile as an add in to Firefox. If someone can help me achieve my preferences for pdf file location, and renaming, I would really appreciate it.

    Thanks!
  • if you're using Zotero Standalone that's where you need to install ZotFile. Download the .xpi file and install from Tools --> add-ons.
  • Adam - thanks for your response. I cannot download Zotfile from the link https://addons.mozilla.org/en-US/firefox/addon/zotfile/contribute/roadblock/?src=dp-btn-primary&version=3.1

    It only gives the option to add Zotfile to Firefox (which I already did). I cannot download it per se to then add to Zotero Standalone, as you recommended. Any other place to look for Zotfile.xpi?

    Thanks,

    Sheila Ward
  • you can download it via right-click --> Save link as (that's in Firefox)
  • Adam-
    I just read the instructions very carefully on the Zotfile website for adding it to Zotero standalone, and it all worked. Thanks so much!
  • is there documentation/discussion somewhere of the file types that zotfile will rename? the webpage states that it can "automatically rename, move, and attach PDFs (or other files)" but the range of "other files" is not specified. zip and txt seem to work, but it doesn't like anything microsoft related (os x 10.10, standalone 4.0.23).

    no errors afaict, just quietly fails.
  • This setting is controlled on the Advanced Settings tab of the ZotFile Preferences dialog. The setting is near the bottom and is a checkbox saying "Only work with the following filetypes", and a comma-separated list of file extensions. I have modified mine, but I think the default is pdf,doc,txt,rtf. At a minimum you should probably add docx. Since I also use an ereader, I have also added mobi and epub.

    I guess you can also just uncheck the box to apply renaming to *all* files, regardless of extension, but I haven't tried.
  • d'oh. i *did* look there, but must have glazed right over it. thanks.
  • * How to configure zotfile to work with box and Papership?

    My current workflow is stand-alone Mac version of Zotero, with Zotfile managing attachments (saved to folder on the Mac with my preferred Author-Year-Title naming scheme)... but I wish to switch things around such that PDFs are still managed by Zotfile but are stored in a WebDav server (box) so that I can annotate them on my iPad (and make them available to colleagues, as read-only, via a link to my box directory). My questions are:

    1) How do I move all attachments from my Mac to box whilst retaining the correct links in Zotero?

    2) What Zotfile settings do I need to tweak, if any, such that annotations I add to PDFs on my tablet through Papership will be reflected in Zotero - I have read some about the "Tablet Settings" of "ZotFile Settings" in this forum and at zotfile.com, but am not sure how or if they need to be tweaked, given that I do NOT want to manually select files to be available in my box account but rather want ALL PDF attachments available there?

    3) Has anyone used this setup successfully (or unsuccessfully)?

    I was half tempted to experiment with this all on my own, but in recognition of the complexities involved with juggling so many components (Zotero for Mac, Zotfile plug-in, box WebDAV sever, Papership iPad/iPhone app), I thought it best to ask for some guidance first. Thanks, in advance, for any help that others can provide - and apologies if this has all been addressed elsewhere.
  • what do you mean for PDFs to be "managed by Zotfile"?

    Obviously ZotFile's ability to move files means they'll no longer sync through Zotero and hence not work with either WebDAV or Papership, so that's an either/or choice. Or do you just mean the renaming but not the moving?

    2) the tablet setting won't be relevant, but I think you'll have to manually prompt ZotFile to extract the PDF annotations. ZotFile can't be configured to do that automatically with your set-up.
  • @ adamsmith said "what do you mean for PDFs to be "managed by Zotfile"? Obviously ZotFile's ability to move files means they'll no longer sync through Zotero and hence not work with either WebDAV or Papership, so that's an either/or choice. Or do you just mean the renaming but not the moving?"

    Sorry for the confusion... within "Zotfile Preferences" I have specified a "Custom Location" for "Locations of Files" so I was assuming that that PDFs were being"managed by Zotfile" - perhaps that is not the case, and the files are just being renamed! The bottom line is that it doesn't matter to me whether PDFs are "managed" by Zotero or Zotfile, as long they can be renamed in Author-Year-Title format and synced with a cloud service (like box which my institution supports, or DropBox which I use personally) so that I can annotate them on an iPad.

    So perhaps my question would best be phrased as: how do I best configure Zotero and/or Zotfile so that I can access PDFs on my iPad, and so that annotations I make on the iPad subsequently show up in Zotero (on my Mac)?
  • So there are two options:
    1. If you want to use a webDAV server to sync files, you can't use ZotFile to move files to a custom location, so you'd have to revert that setting to "Attach Stored Copy" and then select all your items and have ZotFile rename them (which will also move them -- from the custom location back to the Zotero folder from which file sync works. You'd then set up the WebDAV server in the sync preferences of Zotero. You can keep using ZotFile to rename them. You can then use PaperShip on your iPad to annotate, add, etc.

    2. You can keep using DropBox, not use WebDAV and not use PaperShip. You'd have to use the DropBox app to access files on the iPad or you can try using ZotPad, which is supposed to support this set-up (and I haven't heard anything to the contrary).

    As I say above, for both set-ups, annotations sync, but to get the annotations into notes, you have to manually run "Extract annotations" from Zotfile.
  • @adamsmith - thanks for the clarification!

    Here are a few follow-up questions:

    1) If I go with your option #1 (using WebDAV) then can I still access my PDFs on my Mac even when offline? I have not used WebDAV much, so am unsure of how it works - but am assuming it syncs a local directory on my Mac to the web.... If I cannot access the PDFs on my Mac offline, then would your option #2 using DropBox allow it? I recognize that under option #1 I likely cannot access my PDFs from my tablet UNLESS connected to the net, but that's ok - as long as I have full access to my saved attachments when offline with at least one of my devices (my Mac is my primary tool).

    2) Assuming I go with option #2, can you please confirm that I have the steps correct for configuring it:
    a) create a folder in box called Zotero
    b) in Zotero, Preferences, Sync, Settings, under File Syncing, check the box labeled "Sync attachment files in My library using" and select WebDAV and then enter relevant details (path = dav.box.com/dav; then enter username and password)
    c) in Zotfile Preferences, General Settings, check the box "Attach stored copy of file(s)"
    d) in Zotfile Preferences, Tablet Settings, make sure the box labeled "Use ZotFile to send and get files from table" is unchecked
    e) from the main Zotero window, select all items in "My Library, then right-click and select Manage Attachments and then Rename Attachments.

    3) What should I specify in Zotero, Preferences, Advanced, Files and Folders for the Linked Attachment Base Directory - and when should I do it, relative to steps a-e above? Currently my base directory is a folder within "Documents" on my Mac called "Research/Zotfile organized papers" (which is also currently specified in Custom Location in Zotfile Preferences, General Settings).
  • 1) you'll have offline access on your mac with both options just like you do now. Whether you'll have offline access on your ipad depends on how you set up papership, but I'd assume you wouldn't normally.

    2) (I'm assuming here you mean option #1) step d) is actually not necessary--but won't hurt, either--, everything else is correct

    3) Since you won't have linked files left after step e) (they're attached files or attachments now, which we distinguish from linked files), it doesn't matter. You can leave it as is or revert to absolute paths.
  • @adamsmith - Thanks for all of your help (and yes re confirming my steps, I indeed meant option #1 using WebDAV - sorry for the typo)! Based upon a cursory look, things are mostly working just fine - from the standpoint of offline access to PDFs from my Mac, and annotations made on iPad (via PaperShip) or on Mac (via Preview, when double-clicking on item in Zotero) sync between devices.

    But there is one remaining problem... When i view the files via the box website, they still have bizarre, Zotero names like ESM8PHJW.zip rather than Author-Year-Title. I am guessing the problem is because in Zotero Preferences, Renaming Rules, the Use Zotero to Rename box is currently unchecked - perhaps I toggled it off accidentally?

    To rectify this, can I simply check the box, then once again from the main Zotero window, select all items in "My Library, then right-click and select Manage Attachments and then Rename Attachments? Or is there something else I need to to do?
  • that's expected--that's how Zotero saves items on the webDAV (for various technical reasons). You wouldn't be accessing the items through box but rather through Zotero (on your Mac) or through papership (on your iPad).
    Changing the rename settings for files won't have any affect on that.
  • ugh... per my original post, I was hoping this setup would allow Zotfile-type custom naming within box, so that I could share the box directory as read-only to some colleagues or grad students in my lab.

    As a workaround,
    a) how can I send select items in Zotero to someone INCLUDING the annotated PDFs (either manually chosen, or perhaps an entire collection)?
    b) how can I export ALL of my annotated PDFs, renamed as Author-Year-Title (as an archival backup, or to be shared with others)?
  • this is going to far for this thread - could you start a new one?
  • Hi Josha,
    I've been trying to setup zotero to work with dropbox using zotfile and it keeps retrieving an error when I ask it to rename the files and move to the dropbox folder. What happens is: the pdf is deleted from the data folder but is not moved nor renamed. This is the screenshot:

    https://drive.google.com/file/d/0B3AZf7Qxo2bfX3liUVdlclR0Unc/view

    I tried with one file at a time and the same error is appearing.
    I'm using the 4.1 version, suggested by adamsmith in another thread.

    Thanks!
  • After a gruesome review process, ZotFile 4.1.1 is finally out! New features include full support for jumping to annotations in pdfs, much improves extraction of pdf annotations, extraction of the table of content from pdf files to zotero notes and many more. The full change log is here.

    patriciarossini, I not going to be able look into your problem before February. You should also provide much more details. See here about reporting a bug: http://zotfile.com/#reporting-a-bug and try to describe what you are doing and what your settings are in much more detail.
  • Hi Joscha,

    Thanks for all your work with ZotFile. I actually just started using it today, so I have the new 4.1.1 version! I really like how it can go through and take highlights and comments from pdfs and insert them as a note in Zotero. My question is regarding compatibility with different pdf documents. In particular, this pdf document:
    https://www.dropbox.com/s/5g4ngyw5rmfb7vh/Lawrence_Vorderstrasse_2013_New%20insights%20into%20the%20aryl%20hydrocarbon%20receptor%20as%20a%20modulator%20of%20host.pdf?dl=0
    Looking at the document properties, it seems to be produced by acrobat 1.7 on a linux machine. When I try to extract annotations, the extraction starts, fills about a quarter of the status bar, and then just quits with no error message or anything that I can see. I am using Zotero Standalone 4.0.21.2. Are you familiar with any incompatibility for different versions of acrobat?

    Thanks!
  • I briefly looked at the file but wasn't able to pinpoint what is going on. pdf.js can read the file and the extraction of annotations works when I run it from a test webpage. The Zotfile integration, however, seems to crash in a part that is running without a problem in the test webpage. That makes debugging pretty hard and I won't get to it for a while. The good thing is that the file works in a test webpage. Thanks for sharing the file and feel free to post others are upload them to the "zotfile" zotero group.
  • Since this morning at least, the rename function is broken for me. When I try to rename an attachment, the process fails with the popup reporting only "Unknown Error!". If I click the popup to copy the details of the error, it only copies empty brackets "{}".

    I'm running Zotfile 4.1.1 installed from GitHub, Zotero 4.0.25.2-beta.r2+af775e6, and Firefox 35. The same error also happens with Zotero Standalone version 4.0.25.2 and Zotfile 4.1.1.
  • edited January 21, 2015
    Somewhat similar error to bwiernik's. Send/get from tablet throws up an error. I'm running zotfile 4.1.1, zotero 4.0.23, ubuntu 14.04. For me the issue might a bad slash. I get the following error:

    The file "/home/user/Dropbox/Papers/@To Read P1\Gershman et al - 2014 - Decomposing spatiotemporal brain patterns into topographic latent sources.pdf" does not exists.

    Notice the slash in front of Gershman.
  • Got a different error just now as I was trying to rename a pdf:

    Error: Invalid field '" for base field in ItemFields.getFieldIDFromTypeAndBase()
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