ZotFile - Advanced PDF management for Zotero

  • edited March 2, 2012
    (Heckscher, I am not sure what you are asking for with the zotero collections. Do you mean that this feature is not only available for sending pdfs to the tablet but also for linked attachments in zotero?)

    Not just attachments -- it seems to be able to identify the collections that any item is in. That would be a great feature, but I certainly understand that it's not in your main line of development.
  • Version 2.1 is under review now, which will probably only take a couple of days.

    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
  • In my hand a growing number of saved searches "Files on Tablet" are generated. At present I see about 30 lines "Files on Tablet"

    I have Zotero 3.0.3 and Zotfile 2.0, German

    Any hints what I could check?
  • sorry for the trouble. There was a bug in 2.0, which also created the saved search for people who are not using the tablet feature. Not sure whether that is related.

    You should try 2.1. Delete the saved searches and let me know whether the problem persists. Here is the link for 2.1:
  • Again got into Trouble when trying to work with patents (imported from Google patents)

    Zotfil wont move to file.

    My Settings are:

    move to "Target" /%y/%A
    Renaming by zotero

    The file is just attached from the download-directory, not moved and not renamed

    can someone help please?
  • edited March 8, 2012
    Hi Joscha,
    I have a question regarding the "rename/move/link" option of Zotfile:
    During this process, is there (implicitly) a call for the PDF to be (re)indexed?
    I suspect it may be one of the reasons Firefox hang some time even after the file has been renamed and moved (i.e., after the file is visible in its folder-structure).

    Schuessi, maybe you have the same problem I already mentioned, concerning unauthorized characters (such as :) in a field that is used to rename/move the file.
  • Hi Joscha,

    Really great addon.
    Question/suggestion: The extract annotation from PDF only extract the:

    I mostly use the
    -callout tool
    -and typewriter

    callout gives much better visibility then the note tool (at least to me).
    Is there an easy way to insert the extraction of these too?
    Or it is an unimplemented function of pds.js?
    I tried to look at the code of zotfile.js, but my java is very meager.

    best wishes
  • schuessi, I was going to ask the same as Thierry. Is that the problem? Do you have special characters in the %y or %A?

    Thierry.C, yes I think that is why it sometimes hangs. I am not controlling when pdfs get indexed so. It just happens automatically when new attachments are added and that is basically the case when you do certain renaming actions (they reattach the file). There is one case for which a future version of zotfile will help though. Here are all the possible renaming possibilities. Currently, all expect 4 should trigger a reindexing. A future version might avoid reindexing for 1 but the other cases always require to reattach the file, which triggers the indexing as far as I know. I am not sure about these things though because I never used the indexing feature.

    1 Linked att -> Linked att
    2 Linked att -> imported att
    3 imported att -> Linked att
    4 imported att - > imported att

    szallomany, sorry, I don't have any plans to add the extraction of other annotation types right now...
  • Thanks for the information Joscha. Good to know my impression wasn't wrong.
    I adjusted parameters of the indexing feature such that it doesn't hang too much.
    I do not understand what the 2) option corresponds to (i.e., how to trigger it).

    By curiosity, why are you not using the indexing feature? This is the only way to be able to search within docs, right?
  • Which iPad PDF apps work best with zotfile via DropBox? It isn't clear to me which iPad PDF produce a PDF from which zotfile can extract notes via pdf.js. Thanks for the information.

    Joscha, I am new to zotfile -- it appears I'll be using it quite a bit (and making a donation). Thanks for all the hard work you've put into it.
  • turner-es, I tried PDF Expert and iAnnotate, which both work fine. I assume that goodreader or something like that also works but I haven't tried it. My own experience is that recent journal article work pretty well but older once are often problematic. pdf.js still has problems with spaces and the poppler based extraction (mac only) with umlaute.
    In the end, the quality of extraction will depend on the pdf documents you use...
  • Hi all.
    I downloaded the plugin hoping it will be the heavenly answer to my prayers for a tool that will do a "batch remove zotero file attachment",as this came up at the google search with these terms...Unfortunately it probably isn't, unless i am doing something wrong, so please enlighten me...
    The real problem is that after i started using zotero i thought it would be a good idea to attach pdf files as files (not links) which resulted in a huge database which now cannot be synced with main server, so only used locally.Since they are more than a 1000 entries,i am looking for a tool to batch remove the attached files and turn them to local links instead...would that be possible via the plugin? if not any ideas would be most welcome...
    Thanks beforehand for any answers.
  • anginar: The easiest solution to your problem is to just disable file syncing in the Zotero preferences. Also, even if you get error messages about exceeding your quota, I believe that the data are synced to Zotero regardless.
  • I think anginara is looking for a way to actually remove all of those PDFs from the Zotero directory and place them in a folder elsewhere, attached by links, no?

    Not sure what system you are on, anginara. For windows, searching the zotero directory for filetype:pdf would at least give you all the pdfs themselves, which could then be removed. But that doesn't solve the problem. Does this link help?: http://forums.zotero.org/discussion/15503/workflow-for-importing-a-large-folder-of-pdfs-as-links/#Item_5

    I've long considered changing all of my links in my zotero database, but have held off because there are no tools to do it unless one works on the sqlite database itself. There's information about that here:

    and a discussion of editing the database in several places (search the forum) including here:

    This probably all deserves a new thread, rather than the zotfile thread
  • edited March 19, 2012
    JonEP is right but I'm concerned that this
    The real problem is that after i started using zotero i thought it would be a good idea to attach pdf files as files (not links) which resulted in a huge database which now cannot be synced with main server, so only used locally.
    is based on a misunderstanding. You can still sync your Zotero database for free if you disable PDF syncing. Whether you have your PDFs linked or attached does not play any role in that.
    If you do need your pdfs synced, obviously batch-removal is a bad idea anyway. In that case you can either pay for additional file storage through Zotero or use a third party WebDav server - with a bit of searching you should be able to find WebDAV providers who provide up to at least 2GB for free and more for relatively little money. Many people have much more than 1000 attachments synced with Zotero.
  • anginara, you should consider the comments from mronkko and adamsmith. If you still want to change your imported attachments to linked attachments, zotfile can take care of that. Just go to the zotfile preferences, change the 'Location of Files' to 'Custom Location' enter the path you want to use for your linked attachments and you are ready to move your attachments to this location. Just select as many attachments as you want, right-click and select 'Manage Attachments->Rename Attachments'. They should be moved to the specified location and changed to linked attachment. First test with a couple of attachments before you try to move all of them. For large batch processing I also recommend that you first backup. Again, check the other comments to determine whether it's really necessary before doing that.
  • For starters,thank you all for the quick reply (JonEP,mronkko and Joscha).
    The truth is that i hadn't seen the option for the file syncing mronko proposed, which does actually partially solve my problem and also was one of these tips that make you feel really silly....
    What i was trying to do is what adamsmith proposed, and to achieve that, i did fiddle around with the SQLite manager addon in firefox,but i admit that i did get scared with the option (too much work to play around).
    My instinct was right though, as joscha proposed, it can be done with the zotfile ext (i tried it with a couple) but since it is a slow process and i am really scared of losin everything, i will stick to the primary solution
    once again, thanks everybody....
  • Joscha,

    I have 2 (related) newbie questions that I'm hoping you'll be able to answer. I am currently naming my PDF files according to the convention (Journal)(Volume)-(Start Page)-(End Page).pdf. As page numbers are not yet included as wildcard options in Zotfile, I'd like to move these files WITHOUT renaming them in order to not lose the page number information. While this is possible as an additional checkbox option under Tablet Settings ("Rename files when they are sent to the tablet"), it does not appear to possible to move files without renaming when relocating files locally. Am I overlooking something here, or this this option lacking in the current iteration of Zotfile? If this (and/or page number wildcards) could be easily implemented in the next revision, this would certainly be appreciated.
  • edited March 24, 2012
    anthonybrucewilson, I have added a ticket to disable any renaming. It's not a big thing but it will take a while before I work on zotfile the next time.
  • Joscha,

    Thanks for your reply... I look forward to the change - Great work on the program!

  • Hi Joscha,

    I've got a quick question about whether Zotfile is meant to be able to copy and rename files that aren't added through Zotfile itself.

    Basically, I don't always want to add attachments to my Zotero items by using the Zotfile "Attach new file" menu option, as the relevant PDF is not always the most recently downloaded PDF. However, when I attach a file using the standard Zotero "Attach stored copy of file" button, it doesn't get picked up by Zotfile and copied/renamed to my selected output folder. Similarly, if I drag a PDF file into the Zotero window and then right-click and choose Get PDF Metadata, Zotfile doesn't pick it up.

    Is this by design? Or is this a bug? Or is it a feature that hasn't been added yet that is in the works?

    In case it matters, I'm using Zotero Standalone.


  • robintw, it's not happening automatically (which is on my list) but you can use the 'Manage Attachmants->Rename Attachment' option to rename and move existing attachments. Hope that helps.
  • I recently installed zotfile plugin, it works fine. I thanks the developers for the same.

    I have a small problem in remaning pdfs. When i save a pdf corresponding to a particular zotero item from net (using save to zotero option) and then rename it (through manage attachments option), zotfile renames the file.

    However if i attach a stored copy of a file (pdf) to the zotero item and then try to rename the pdf, zotlite fails to rename the pdf. Why is it so ?.

  • snsidea, I am not sure whether your problem is related to the way in which you add an attachment. Can you try both ways with the same zotero item and report? (i.e. use 'attach a stored copy of a file' with the same zotero item)

    Also, please check the FF error console as described here:
  • Joscha, I tried both ways for the same zotero item and the problem persists. However i dnt see any error in firefox 'error console'.
  • I will need a little more information to bug fix this because I can't reproduce it... your set up (OS, zotero version, zotfile version etc), the exact steps, a link to the reference you are using etc... It would also be good if you can try a different computer and see whether the same problem occurs...
  • Hi,
    I have provided below some more informations that you have asked.
    Os: Ubuntu 11.10, Zotero: V-3.0.3 , Zotfile: V-2, firefox: V-11.0
    zotero item: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1184292/

    I tried in another computer as per your suggestion and i found the renaming by zotfile works perfectly when a zotero item is attached to stored copy of a file. The only difference is that this system has firefox 7.0 and ubuntu 11.04. Versions of zotero and zotfile are the same.
  • edited April 1, 2012
    Just one question.

    I used to "send file to tablet" function to a folder in sugar sync which I synchronize with my ipad.

    After reading however, I can "get file from tablet".

    The pdf is no longer in the sugar sync folder. However, on zotero, the file is still listed under file in tablet.

    Any clues?
  • snsidea, I am not having any problems with FF 11 and this particular item regardless of the way in which the attachment is added. When I understand you correctly, the problem does not exist at the other computer, right? So it seems to be something related to the configuration at your computer. FF 11 is not the reason and I would be surprised if the ubuntu version matters. I suggest that you first try updating to zotfile to 2.1, restarting FF, restarting your computer and if these things do not help check the preferences carefully (comparing them to the set-up at the other computer). But to be honest, I don't know how they should make a difference for the way in which the attachment is added...

    Star7, I assume you mean "I can not 'get file from tablet'"? Whether a file is on the tablet is determined by the '_tablet' tag. So it looks like the location of the file somehow changed but the tag was not removed. It would be good if you can reproduce this and post the exact steps. If it only happened with this one file, just remove the tag manually (and possibility the stuff in the note field but I think that is not necessary).
  • Hmm, let me reproduce the steps here.

    1) I send several files using the "Send to tablet" function to a folder on sugar sync.
    2) After reading in on ipad, I decide to use the "Get from tablet" function.
    3) I selected a tag, selected all 14 (I think) articles, and click "get from tablet".
    4) A confirmation box ask me if I'm sure and I said yes.
    5) Subsequently, I check the folder in sugar sync and the pdfs are gone, which is good.
    6) However, according to zotero, this files are still in tablet and the "get from tablet" function is still available.
    7) Trying to use the "get from tablet" does not elicit any response however.

    That's all.
This discussion has been closed.