ZotFile - Advanced PDF management for Zotero

  • Hi Joscha, just wanted to let you know how much time and frustration ZotFile has saved me from - You really have created a plugin which enhances Zotero immensely. Thank you very much! Tom.
  • Hello
    I am trying to use ZotFile to "export" the collection that consists of the multiple hierarchical sub-collections. I am trying to use "Manage Attachments -> Send to Tablet" option to "re-create the "collection hierarchy" at the "Base folder Setting" destination defined in the "Tablet Settings" of ZotFile preferences. I expect to see the hierarchy of the collection folders to be re-created at the "base folder setting destination. However, at best I can can get the folders hierarchy but all the files are located in one particular folder instead of being in the corresponding "collection folders"
    What exactly should be done to get the multiple sub-collections with pdf files to be exported properly preserving the hierarchy ?
    Thanks in advance
  • @sdaexpert / Alex

    it works for me, but instead of using "Manage Attachments -> Send to Tablet", you should use "Manage Attachments -> <name of a collection>".

    At the bottom of "Manage Attachments" contextual menu you should see a list of collections to which an item belongs. I applied it successfully to multiple items that belong to the same collection.
  • Hi jacekg
    Thanks for your post.
    But is it possible to "point" somehow at the "top-level" collection
    (that consists of the multiple sub-collections) and in a single click to "recreate" the whole "hierarchical" collection data structure at the selected tablet location?
  • I don't believe that's possible, no. The send to tablet function is designed to send a limited number of items to the tablet (and get them back), not to move entire collections full of files.

    (note that you _can_ use ZotFile to maintain all Zotero attachments outside of Zotero in a folder hierarchy determined by collections.)
  • edited November 24, 2012
    right, I do not think it is possible. you can send multiple items to a tablet and have the hierarchical structure of folders created on the tablet but you need to do it for each sub-collection or sub-sub-collection separately.

    And the reason is that currently "send to tablet" ignores collections, and to have items sent to a folder in a hierarchy based on your collection hierarchy you need to select one specific collection this items "located in".
  • @jacekg/@adamsmith
    Thanks for the clarifications!

    Now, regarding the following
    (note that you _can_ use ZotFile to maintain all Zotero attachments outside of Zotero in a folder hierarchy determined by collections.)
    from the post of adamsmith

    I understand I can configure ZotFile in GeneralSettings with the directory location for the attachments and it says that that it can move the existing attachments into that location. But what do I do to get it actually moved ?
  • edited November 24, 2012
    Dear Joscha and everybody,

    Is it possible to use ZotFile to have the location of files in a custom location (in a custom directory, as it is now, say with subfolders defined by /%a_%y_%t) but WITHOUT renaming the files themselves (the attachments) inside the subfolders? In particular, renaming attachments with code, or the names of the different parts of supplementary material, is something I'd like to avoid.

    An option that seems to partially work is to disable "Automatically rename new attachments" (under Advanced Settings), while keeping the "Custom location" (under General settings). Then import data, and next do "Rename attachments". This will only move and rename the PDFs, txt, etc, leaving untouched the tar.gz. But it still renames files (so something like supp-mat-1.pdf and supp-mat-2.pdf will have their names changed), and now the location for the storage of files of a single item is under two or more directories.

    I guess what I want to do is to use ZotFile to avoid the default directory naming scheme used by Zotero, but preserving Zotero's approach of not changing the names of the files themselves.
    (I want to do this to make my life as simple as possible when syncing all of my stored PDFs to a tablet.)

  • Hi Joscha, I'm just discovering your great tool. I seems to me there could be one bug:
    The renaming rule option "Add suffix when authors are omitted" ignores some special characters, amongst them the dot. So I get "et al" instead of "et al." (which would be Zotero default).
    Is it possible to fix this behaviour? Perhaps with some quotation character like "et al\."
    Thanks in advance!
  • Hi,

    I'm usig Zotero standalone with zotfile extension, Windows 7. I've got strange square lettres in my pdf annotations extracted such as that exemple :

    "Les phnomnes de base apparaissent  travers les tmoignages ou les rminiscences qui nous reportent aux ges les plus "

    I tried to annotate with Adobe Reader XI and PDF Xchange Viewer and both results are the same...

    Zotero error report (ID 1000900637) gave me that message :
    [JavaScript Error: "The character encoding of the HTML document was not declared. The document will render with garbled text in some browser configurations if the document contains characters from outside the US-ASCII range. The character encoding of the page must be declared in the document or in the transfer protocol." {file: "jar:file:///C:/Program%20Files/Zotero%20Standalone/chrome/zotero.jar!/content/zotero/tinymce/themes/advanced/source_editor.htm" line: 0}]

    How can I fix that problem ? Could you help ?

    Thanx !
  • Hey there!

    Zotfile is great! Really boosts Zotero. Donation ahead!

    But recently troubles started:
    When I first tried to "sent attachments to tablet" (mark, right click, send to subfolder) - it didn't work. I had to do send attachments seperately. After sending some files seperately - all of a sudden I could send attachments of several items (zotfile would ask: "do you really want to send xx attachments to tablet?" -> ok)

    This way I sent all of my papers to "the tablet" (Dropbox folder).

    But then I had to rearrange my search (new papers, new subfolders etc.). Before doing that I GOT ALL ATTACHMENTS BACK from the tablet (to avoid sync conflicts).

    Now my new search is done (new articles and collections) but when I try to send the attachments "to tablet" - it does not work.
    At first not at all. Then single attachments worked, then ONCE (just ONE TIME) I could send 20 attachments at the same time.
    Then two seperate ones -

    NOW I can neither send attachments to nor get them from the tablet.
    Not even the 22 that had just sent.

    I am lost here.

    I use Firefox 17.0.1 with built in Zotero 3.0.11 and Zotfile 2.2.4. on a Mac OSX 10.8.2.

    Following the suggestions on the zotfile website - here's report from the Firefox Error Console:

    Timestamp: 20/12/12 16:17:15
    Error: NS_ERROR_NOT_AVAILABLE: Component returned failure code: 0x80040111 (NS_ERROR_NOT_AVAILABLE) [nsIDOMWindow.confirm]
    Source File: chrome://zotfile/content/zotfile.js
    Line: 1830

    I am not that fit with "terminal slang" etc. so some technical information might be missing.

    Any suggestions what's going on and how to repair it?

    Thanks in advance!
  • joshukn: Your problem is related to this Firefox "bug": https://bugzilla.mozilla.org/show_bug.cgi?id=633154
    I am not going to do something about it until they make up there mind but you can enable the confirm alert boxes again or disable confirmation in zotfile.

    Currently any other reproducible zotfile errors with an error message out there? I am fixing some bugs right now. I will only fix them now if I have an error message, the bug is reproducible and it's not related to the annotation extraction. Feel free to post others too but I won't get to them right now.
  • Hello!

    A couple of questions re. zotfile from a newbie:

    - text extracted from highlighted pdfs and imported into zotero as a note ends up with a lot of words strung together without spaces in my final reports... any way to deal with that?

    - anyone have a suggested workflow to sync zotero-zotfile-(dropbox?-) ipad/tablet? where should i store my zotero documents to avoid messups? more likely to work with ipad or other tablet?

  • As far as I know, there are at least five possible workflows/setups that you can use. (And at least two more that you should not use.)

    I wrote an article about these on the ZotPad website:

  • Hi!
    I'd really like to use Zotfile, however I cannot get it work. I want to have files stored in a defined folder (inside my Dropbox) and configured that in the zotfile options.
    However, when adding a new Zotero item (including attachment), I always get the following mistake: https://dl.dropbox.com/u/4294224/zotero1.jpg or https://dl.dropbox.com/u/4294224/zotero2.jpg
    Any ideas what I'm doing wrong?
    Thank you very much in advance!
  • edited January 18, 2013
    Hi there!

    I just started to use zotero + zotfile two days ago and I'm happy! (I even switched to firefox, because it's such a killer app, after having used konqueror for some 10 years!)

    There is one important feature missing for me, which actually has a ticket
    and a discussion thread

    It appears to me that this might actually fit into zotfile? Namely, zotfile could update (optionally, set via preferences) the metadata in pdf's while renaming them. There is a perl script that I used just before discovering zotero, which works fine:


    the file bibtex2pdfmeta.pl is in the subfolder "pdfmeat".
    The following seems to be an alternative:


    I read that jabref can also do this, but I wasn't really able to get started with jabref.

    I should add: to be really useful for me, it should not only update the XMP stream but also the infofields, since these are what my ereader uses...

  • Chell, missing spaces between words is a problem with certain PDF files in the pdf.js based extraction method. A lot of files won't have that problem. The poppler based extraction (mac only) is better in terms of separating spaces but has problems with special characters. It would be great if anyone wants to work on and improve the pdf.js based extraction.

    msteffen, you can't rename and move links and snapshots. It only works for pdf, docs etc. You still shouldn't get such an error. Which version are you using? Try the current beta and let me know whether you still get this error.

    axiomize, there is a ticket for this but I won't implement it for now. So contributions are welcome.
  • OK, thanks for letting me know. I'm afraid I cannot contribute though.
  • Hi,

    Zotfile prevents my Firefox from opening the tab-groups (cmd + shift + E). Even when deactivated it would do so; I had to uninstall the plugin completely to get that functionality to work again. I am on OS X 10.8.2 and Firefox 18.0. I use Zotfile in the standalone app for now, works fine.

  • Tschoepler,I can't reproduce that problem (same OS, same version) and I don't think zotfile is the problem...
  • I see. Well at least it is part of the problem: I installed it and the problem appeared. I uninstalled it and the problem disappeared. There was nothing else done in between. I have quite a few plug-ins installed, so I'll investigate further and let you know if I find a plug-in that screws up when Zotfile is installed.
  • edited January 21, 2013
    I find Zotfile very usefull, and the new renaming rules are almost perfect.But, for books with long title, or beginning with a "the" "On" "Le" etc, if the title is limited to 10-15 letters, the name of the file something like:
    It's not very useful to search, find, send, etc the file.
    Can you add a renaming variant based on TAG or short title?
    In such way that I can have filename like this:

    (and please excuse my english... )
  • Dansimati: What's the original complete title?
    M. BESSON, Nos origines chrétiennes, études sur les origines du christianisme en Suisse Romande, Fribourg, 1921 ?
  • edited January 21, 2013
    Yes... but it's not the only one...
    For exemple, I have :
    Legoux R., « Époque mérovingienne : les objets de parure en verre », dans Verre et merveilles : mille ans de verre dans le Nord-Ouest de la Gaule : exposition, 17 octobre 1993-31 janvier 1994, Musée départemental du Val-d’Oise, Guiry-en-Vexin., Guiry-en-Vexin : Musée archéologique départemental du Val-d’Oise, 1993, pp. 103‑108.

    ---> Legoux_Epoque_1993... not very useful...
  • Are you aware that you can change in the ZotFile prefs the "Maximum length of the title" ("Renaming rule" tab)? That does not address your issue though.
  • edited January 21, 2013
    I know... The problem is not the length of the title, but the fact that the relevant term may be at the end of the title. In the case of Legoux, "verre" is more usefull than "époque mérovingienne". I have many books with title like "époque mérovingienne"... And I don't like files with name like "Besson_L_art_barbare_dans_l_ancien_diocèse_1921"

    Before I use Zotero, I renamed the file with Name_Keyword_date...

    (Legoux is not a good exemple... beaucause it's an article...)
  • A short title wildcard is possible but how would it work for tag? If there is more than one tag ("marqueur" in Zotero French version), which one has to be chosen?
  • The first one I suppose? It was just an idea
    But I tink that wilcard based on the short title is simpler to code and write, and very usefull for a lot of people. In addition, this field is used in short citation style...
  • Yes, it's very easy to add (one line in the code). But would it be really useful? In zotero, the short title field is automatically created in some cases, e.g. when there's a colon (:) in the title. In the same way, Zotfile truncates the title when there's a colon.
    Thus, with your example:
    "Époque mérovingienne : les objets de parure en verre" => shortTitle is "Époque mérovingienne" in Zotero (if you didn't add the item manually and didn't edit the shortTitle field manually) and the title used by Zotfile, at the moment, is "Époque mérovingienne" too. Introducing a shortTitle wildcard in zotfile would not add any benefit in these cases (but doesn't hurt either). It would only be interesting if the user edited the shortTitle field: not an automatic solution.

    What about a wildcard which would use the xx first relevant words (i.e: Legoux_Époque_mérovingienne_objets_parure_verre_1993)? (a bit complicated to code though).

    (I don't speak for Joscha, the Zotfile developer)
  • edited January 21, 2013
    I have added short title as a wildcard. The wildcard is %h (the actual letter used for the wildcard are pretty abitrary by now). I recommend that you use it with the new exclusive wildcards like this `%h|%t` so that you get the normal title when the short title does not exists.

    It's going to be in the next version, which I will submit to mozilla soon. The beta is here and it would be good if some people test this version. Here is the changelog.

    ps: I agree with gracile that the tags don't make sense as a wildcard. The short title was a one line addition and it might be useful if the short title is different than the normal title. gracile's other suggestions might be a good idea but it won't make it in the next version unless someone implements it.
This discussion has been closed.