Relocating pdfs using zotfile, relocating the Zotero Database,

MosesMoses
Hello,

(Three questions)

(1) I have some pdfs stored via Firefox Zotero (directly available in Zotero) and others stored via Zotfile (using Zotero Standalone) with links to their custom location in Dropbox. This distribution reflecting a long ago period of transition.

Is it possible to do this: transition all the former to the custom location with links?

(I searched for an answer, but did not come across one, a version was previously asked here:
keith.w.larson@gmail

Jul 31st 2012

Is there a way to have Zotfile automatically rename and relocate previously attached PDFs to the naming convention and folder specified in the Zotfile preferences? I have over 1000 citations and I do not want to re-download them all. Suggestions?)

(Note. ZotFile Preferences > General Settings > Source Folder for Attaching new Files … is set to a custom location(Dropbox) and ZotFile Preferences > General Settings > Location of Files … is set to a different custom location(Dropbox))


(2) My Zotero database in Zotero Preferences -> Advances -> Files and Folders -> Data Directory Location is:



Users/moses/Library/Application Support/Firefox/Profiles/qlcdz25g.default/zotero/



I would also like to transition this to Dropbox, will that cause problems?


(3) In Chrome, Safari and Firefox, Zotfile upon storing an article from e.g., PubMed, Zotfile upon selecting relocate fails to relocate/create link to the associated pdf to my custom location, success requires repeated attempts at retrieving article via the Zotero icon in the address bar, relocate via Zotfile. If anyone has a solution to this, please let me know?

Thanks,
  • adamsmith
    1) You'd need to select the items with stored attachments and the right-click --> manage attachments --> Rename
    This will move them to the location specified by ZotFile
    You can do this in batch, theoretically all at once, but I don't think there's an easy way to search for just stored attachments (might be forgetting about something, though)

    2) Yes. Don't do it.

    3) We'd need a more specific description. E.g. from PubMed, Zotero wouldn't actually download a PDF and ZotFile only moves PDFs, so I'm not quite clear what you're referring to. Start with a specific example and run through what is and what you think should be happening.
  • MosesMoses
    Thanks for the replies,

    On (1) doing them in a batch would be a great time saver, are there any downsides to having items in the batch that do not have pdf attachments, I ask because I can capture the relevant items in a time window, but said time window would also include items without attachments.


    Redraft of (3) In Chrome, Safari and Firefox, Zotero upon downloading an article/pdf from e.g., http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4222107/, Zotfile upon selecting relocate fails to relocate the associated pdf to my custom location … success requires repeated attempts at retrieving article via the Zotero icon in the address bar, and repeated attempts to relocate via Zotfile. … It eventually works. If anyone has a solution to this, please let me know? Thanks.
  • adamsmith
    1) I don't think that should be a problem. Definitely won't break anything, ZotFile might throw an error but I think an inconsequential one (i.e. it will just tell you there are no attachments and move on).

    3) That should just work, but I'm not sure what you're saying here:
    Zotfile upon selecting relocate fails to relocate the associated pdf to my custom location
    the idea is that ZotFile moves every new file, without any selecting. You're saying it doesn't do that?
  • MosesMoses
    Correct, Zotfile does not "move every new file, without any selecting." Rather I get a little window with: click here to move and rename. I probably have Zotfile configured incorrectly; under Renaming Rules, I have tried the various configurations.

    Selecting: click here to move and rename, is frequently not successful (at relocating) on the first attempt,

    Thanks
  • adamsmith
    What do you have under "Source Folder for Attaching New Files"?
  • MosesMoses
    Thanks for replying,

    ZotFile Preferences > General Settings > Source Folder for Attaching new Files … is set to a custom location(Dropbox)

    ... and ZotFile Preferences > General Settings > Location of Files … is set to a different custom location(Dropbox)

    See my initiating post.

    Thanks,
  • MosesMoses
    I tried switching Source Folder for Attaching new Files to

    /Users/moses/Library/Application Support/Firefox/Profiles/qlcdz25g.default/zotero/storage

    ... did not make a difference to behaviour, still get window with: click here to move and rename.

    In my preferences: Use Firefox download folder is not available for selection.
  • adamsmith
    So, it'd first be important to understand that the "Source folder for Attaching new Files" is something that you'd only rarely use.
    It would typically be the download folder of your browser (needn't be Firefox), but all that it does is that when you save a PDF to that folder, you can attach it to an _already existing item_. ZotFile will then -- depending on your preferences -- also move that PDF. So you definitely don't want to set this to your storage folder, that'll just cause Chaos.

    The way you'd normally use Zotfile is to just click on the URL bar icon for PubmedCentral (or any other site that saves data and PDF to Zotero). With ZotFile set to save to a custom location, it would then take that PDF and move it from the storage folder to said custom location. It'd also display a message that it has renamed the attachment.

    So let's start here -- does that all make sense and is that what you're doing?
  • MosesMoses
    Sure it all makes sense, and that is not what is happening. The relocate+rename, is not a smooth, succinct uninvolved step but rather a window with: click here to move and rename, ... frequently failing and requiring repetition via the the URL bar icon,
  • adamsmith
    edited November 13, 2014
    Could you slowly walk me through what you're doing&seeing exactly? The fact that you're getting "Click here to move" even as an option when using the URL bar icon is utterly perplexing and either suggests we're talking past each other or something is very wrong in how your ZotFile works. Also, which browser is that? I know you say all three, but stick to one for the time being, and ideally not Firefox.
  • MosesMoses
    Thanks for staying with this,

    I am working in Chrome,
    Click the Zotero URL bar icon
    Zotero PopUp window: Saving to
    Zotfile Popup window: click here to move and rename,
    (Frequently stalls and does not move and rename)
    Move by rename or delete and
    … try again,
    ___
    ___
    ___

    Zotfile Popup window: click here to move and rename,

    Success
  • adamsmith
    edited November 14, 2014
    Could you uncheck "Watch for new Files..." in the general tab and "Ask user when attaching..." in the Advanced tab of the ZotFile preferences?

    See if that changes anything.

    edit: also, which ZotFile version are you using? Might be worth updating to 4.0 if you haven't done that already (it's not officially up on mozilla, so wouldn't have happened automatically).
  • MosesMoses
    Thank you! Unchecking "Ask user..." worked. I tend to check "Ask user ..." by default.

    For me, in the Zotfile Popup window: click here to move and rename, clicking stalls the flow,

    BTW I am using ZotFile 4.1.

    Thanks again,
  • adamsmith
    OK, so I think that what's happening is that the "attach on click" thing isn't super reliable, so when you ask every time you get the type of behavior you're getting. That's just an educated guess, though, but if things are working for you that's great.
  • MosesMoses
    Thank you for the guidance, much appreciated,

    Best,

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