Standalone dropbox sync

2
  • Peter100
    edited September 10, 2012
    I did that. It is in dropbox. But now what? What do I need to do to get DevonThink to see the Zotero attachment library? If I had moved the entire Zotero attachment library folder into Dropbox (which you warn against) then I would have told DT to index the folder... I tried indexing the link_zotero_mac_unix.sh but that just opened a text file of the script?? I know I am missing something but don't see it.

    (edit: move storage symlink - not the script! - duh)
  • adamsmith
    do you see the link that looks like an alias?
    It's very hard to do this blind, we need you to both read closely and describe with some care what you're seeing and what not - remember we don't see your screen.
  • adamsmith
    also, are you sure you can't just point DT to the Zotero storage folder to indexing?
    Also, note that you can move the entire Zotero folder anywhere you want on your harddisk that _doesn't_ sync dropbox-style - there is no risk involved with that (change the location of the folder in the advanced tab of the Zotero preferences, you need to manually move the contents of the Zotero folder to the new location).
  • Peter100
    edited September 11, 2012
    Ok... I think I understand...

    So now if I open a pdf from the "storage" and annotate with a third party app the changes will be automatically synced to the Zotero library simultaneously.

    I wonder if I have understood this correctly now.
  • adamsmith
    exactly.
  • Peter100
    edited September 10, 2012
    A few quick follow-ups. If I delete a pdf from the "storage" is it deleted in Zotero as well? Does this risk corruption? Does it matter if Zotero is running or not?

    I just starting "importing" the "storage" folder when I think I should have "indexed" the "storage" folder. Perhaps it doesn't matter. I would like the annotations I make on pdfs in DevonThink or elsewhere to be visible in Zotero... is this possible?

    Also, does the "storage" folder double the size of the "original" zotero pdf library - in otherwords... if I had 1 gb of pdfs will this method now give me 2 gb?

    Also, do you recommend creating an alias of the "storage" symlink for importing/indexing with DevonThink, or simly import the same "storage" symlink?
  • adamsmith
    edited September 10, 2012
    as mronkko so aptly describes it above, the storage folder in your dropbox is the same folder with a different address.
    That means any file you change - delete, annotate, etc. - in the folder on dropbox will change in exactly the same way in Zotero storage.

    Deleting PDFs from Zotero's storage folder (and hence its symlink in dropbox) isn't recommended as that leaves you with dead links to that file from within Zotero - but it does not corrupt your database beyond that. Whether Zotero is running or not while you do that is irrelevant.
    edit: that also means that you shouldn't rename the file except through Zotero - that, too, will lead to a dead link.

    Any annotations that you make to PDFs in either of those two locations will appear when you open them from Zotero as well, yes. (Provided the annotations are written to the pdf directly as most pdf readers - including adobe, pdfxchange etc. do - I don't know about DT, but I'd expect it follows the standard, best to try it out.).

    edit: no, this does not double the size of the folder. How you handle this with DT I have no advice. I don't think it matters much.
  • Peter100
    edited September 10, 2012
    Sorry I added a bit to my last post ...

    I understand that the symlink produces to essentially the same file in two different locations so if one version is changed both are changed.

    Do you have any advice for indexing vs importing into DevonThink? I was advised elsewhere to "index" via an alias which provides DevonThink with the path to the pdf folder without moving the actual folder into DevonThink. What do you recommend with this method using the symlink? It warps my brain a bit.

    (edit: I will have to experiment a bit.)
  • adamsmith
    see above DT I don't know what DT does exactly, how it works and what you can specify, but generally - using an alias vs. a symlink for this purpose should make very little difference.
  • Peter100
    edited September 10, 2012
    Oh, and if I delete the storage symlink what happens to my Zotero library? Will it also be deleted ?! but that can't be can it?? i.e. what is the best way to delete the symlink without risking loss to the "original" pdf collection?

    To confirm, it doesn't matter whatsoever if Zotero is running while I'm working with the pdfs in different apps..
  • adamsmith
    I don't actually know what deleting a symlink does. I'd be careful, but I _think_ it just deletes the link, not the original folder - but maybe someone else can confirm.
    To confirm, it doesn't matter at all if Zotero is running when I'm working with the pdfs in other apps..
    correct. Simultaneous access is only a problem with the zotero.sqlite (hence the warning against putting that into dropbox), not any of the attachments.
  • Peter100
    You've been a wonderful help! Thanks.

    Hopefully someone can confirm the symlink delete issue but for now I'll assume that deleting the symlink just deletes the "container" not the contents.
  • bernard_ivo
    edited September 10, 2012
    Well, thanks for all the comments and clarifications, however, I'm still not sure whether I understood all I had to make things work.

    It looks that the only way Zotero works with (external)storage is:
    a) I create a link targeting /Zotero/storage to path Dropbox/Articles "ln -s xxx/Zotero/storage yyy/Dropbox/Articles"
    b) this so far creates "link to folder" /Dropbox/Articles/storage though my articles are in Articles
    c) if I copy/move one PDF from Articles to Articles/storage then it also appears in /Zotero/storage
    d) however Zotero does not see this file as I still have to either drag and drop it to Zotero application or use Save a copy?
    e) which basically means I have to copy all my PDFs into a new folder /Articles/storage
    f) and mannually add every pdf one by one through Zotero interface so it can build its library

    Did I get it correctly?

    edit: and here http://www.zotero.org/support/retrieve_pdf_metadata it says " Begin by dragging your existing PDFs into your Zotero library (currently broken on linux) or use the “Store Copy of File” option from the add new item menu (green plus sign)." though I haven't tried it yes since I try to get my storage folder fixed first.
  • adamsmith
    edited September 10, 2012
    no. Forget about a-e.
    You just do f) and the files appear both in Zotero and in Zotero/storage. Again, though, you don't have to do that "one by one" - you can do that in pretty large chunks.

    You can _then_ do a) to place a symlink of Zotero/storage to dropbox or anywhere else.

    I'd recommend to just try out some things rather than doing this all on paper.
  • adamsmith
    and again, to be 100% clear: keep you hands off the Zotero/storage folder. If anything you do involves moving files into or out of that folder you're doing something wrong.

    And yes re: your edit - those instructions from the documentation are correct. It's what I've been telling you all along -

    also, note that the entire discussion I have here with Peter100 is almost completely irrelevant for your situation - Peter already has his PDFs in Zotero.
  • bernard_ivo
    Thanks,
    I'm dragging existing PDFs to Zotero so it builds its library. It will double my collection before the whole transfer is done (something I wanted to avoid) then I can delete the one I'm copying from.
  • mronkko2
    Seems that the problems have been solved. However, because this thread will likely com up with searches, I want to add one more thing:

    Using Dropbox to synchronize Zotero files is a bad idea. You should almost always use WebDAV instead.

    Even if you set it up using a symbolic link, there are in general no advantages over WebDAV. Let's compare Dropbox with symlink to using cloudme.com WebDAV:

    - It is easier to register a free account at cloudme.com and configuring the WebDAV URL in Zotero than it is to set up a symbolic link
    - You get more free space in WebDAV and this is dedicated to Zotero leaving your full Dropbox quota for other uses.
    - With Dropbox, you are using two different servers (Dropbox and Zotero) to coordinate synchronization, where as with WebDAV all synchronization logic is performed by a single server (Zotero) resulting in more robust synchronization
    - Many tablet software that support Dropbox as file storage solution also support WebDAV
    - Symbolic links may confuse some disk space analyzer software to incorrectly report the disk usage
  • Peter100
    edited September 11, 2012
    ... and just when I thought I found the optimal solution! ;) I'll have a look.
  • bernard_ivo
    Yeap partially the problems were solved. Now however my PDF are stored in Zotero/Storage and my original order of PDFs into subject folders is lost. I know I can use collections and tags (already experimenting), however I have to count on Zotero to show me where specific PDF is, since browsing the storage folder does not make really sense any longer.

    Will check the WebDav and cloud.me option.
    Thanks
  • simondedman
    For those who are now interested in cloudme's webDAV solution, this is potentially of interest as your next thing to read:
    http://forum.cloudme.com/viewtopic.php?id=416
  • zed
    I have spent all day trying to understand how the zotero and dropbox link works and am getting very confused. I'm also not a very "computery" person unfortunately(I'm trying!).Hence I need some very very basic advice. I would like to able to access my pds from home and office computers. Is using dropbox the only way to do this? Other people I know recommend this. Can I just save the citation on zotero and the actual pdf on dropbox?
    many thanks
    Zed
  • adamsmith
    The easiest way to get your PDFs on multiple computers using Zotero is to use Zotero file storage. The downside is that you'll have to pay once you have >300MB of files.

    You can also sync via a WebDAV service such as cloudme - see a list here:
    http://www.zotero.org/support/kb/webdav_services

    While it's possible to use Dropbox, that does require more set-up. If you really want to do that start a new thread and describe what you've done so far.
  • zed
    Hi Adam,



    Many thank for your rapid reply.

    I have been trying to follow these http://libguides.princeton.edu/content.php?pid=31604&sid=3799749
    instructions in zotero standalone.

    I got to the point of "change directory location" when I changed it to this C:\Users\**\AppData\Roaming\Mozilla\Firefox etc in "custom" but didn't go any further in case I lost all the pdfs that I currently have saved in zotero.



    Best



    Zed
  • adamsmith
    edited June 7, 2013
    The custom setting for the data directory isn't part of those instructions - it's just something that happens to be the case in the profile of the author of the guide. Ignore it & leave your data directory in it's default location.

    Edit: If you're at Princeton, go to the library and ask for help there - this is much easier in person.
  • zed
    Ok thanks. That's simply enough. And if I do that then a copy of everything will go to my dropbox zotero folder?

    Unfortunately I'm in rainy London!
  • adamsmith
    no. none of this happens automatically, see steps 5-7.
    You can use Zotfile to help with doing this automatically,
    http://www.jlegewie.com/zotfile.html
    but you'll have to do most of the legwork of reading documentation and trying things out.

    As I say above, if you want a simple, one-click solution, use zotero's own file storage.
  • zed
    Thanks Adam. I will have a read to see what the best solution is.



    You may see me back here...



    Best
    Zed
  • edgimar
    Why is it difficult or undesirable for Zotero to include an additional configuration option which allows a user to select the location of the *storage* directory (not data directory) they wish to use? This would provide users with more choices about how to store their documents, without requiring them to understand and implement "workarounds" (e.g. symlinks).

    It's unreasonable to expect that all the people in a zotero 'group' will necessarily know how to jump through the hoops to make zotero work with systems like dropbox. Therefore not making such an option available is in essence 'forcing' those who use zotero for group collaboration to use either a WebDAV service or Zotero's storage service.

    Is such a configuration option option in the works?
  • adamsmith
    no it's not. It also wouldn't work with groups even if it were possible. The only way to share files in groups is via Zotero file storage, WebDAV doesn't work either.
  • mronkko2
    I could think of at least two reasons:

    1) The problem that you describe is already well addressed with Zotero storage. There are other, important problems that do not have solutions yet and these are therefore prioritized.

    2) Zotero is funded by selling storage subscription and it is not in the interest of the project or the users that this funding is removed.

    3) Technical difficulties. Take for example Dropbox conflict management. Files that are marked as conflicted by Dropbox would need to somehow be processed with Zotero and I can see how this can be problematic.

    As far as I know, not in the works and very unlikely to ever be.

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