Transferring a few thousand PDFs into zotero

adshiller
I already have a large library of files in dropbox.
I see that I can drag things into zotero, though apparently that's not recommended. But it's not likely that I can go back to their webpages to download. Any other comments about doing this intelligently?

Also, when I drag something into Zotero, or download it from the browser plug in, does Zotero make a copy in its own folder? Or does it merely index the PDF (or other file) and allow me to keep the file wherever I want it to live?

Thanks
:-)
  • bwiernik
    1) You can drag them from Dropbox to Zotero. That’s fine. What’s not recommended is storing your whole Zotero data folder in Dropbox or another cloud storage folder. That will lead to database corruption.

    2) When you drag files into Zotero, it by default make a copy in Zotero’s internal storage folder, leaving the original in place. To _move_ the files to Zotero instead and delete the original, hold down Shift (Windows/Linux) or Cmd (Mac) as you drag.

    3) I recommend you let Zotero manage the location of your files in its internal storage folder. You can sync files using either Zotero’s sync servers or a WebDAV cloud provider. If you want to keep using Dropbox, see the last section on this page: https://Zotero.org/support/sync
  • adshiller
    Thank You @bwiernik
    I'm a bit confused by the language used on the link you shared. It says:
    "Data syncing merges library items, notes, links, tags, etc.—everything except attachment files—between your local computer and the Zotero servers, allowing you to work with your data from any computer with Zotero installed. It also allows you to view your library online on zotero.org. Data syncing is free, has no storage limit, and can be used without file syncing"

    If I read correctly, that means that Zotero syncs all of the information **about** my PDFs, but not the files themselves.
    If I want to sync the files too, I need to "set up file syncing". And then Zotero will store my 6.7GB of PDFs in its internal folder, and sync the PDFs themselves to other computers with which I sync, and I will pay Zotero for that storage.

    It sounds like if I want to keep my PDFs stored and syncing to to other computers in Dropbox, and have Zotero sync just the "library items, notes, links, tags, etc.—everything except attachment files", then I need to use Zotfile Plugin, or something similar, to tel Zotero to put and store PDFs in dropbox. And then dropbox could sync my PDFs, and Zotero will sync all the Zotera data that is related to the PDFs. Is that right?

    In your experience do both of those approaches work just as well in terms of efficiency, accuracy, potential glitches?

    thanks
  • bwiernik
    That’s right, though you can also use a different cloud provider to sync the files with the first option. Any provider that supports WebDAV will work. Here are a few options: https://www.zotero.org/support/kb/webdav_services

    Personally, I recommend using the first option with Zotero storage space. It is the easiest option to set up and doesn’t depend on other sites also working to sync, so less potential for glitches or downtime. The second option, using Dropbox, has the disadvantages that it takes more effort to set up, may require more manual file maintenance in the future, and items you delete in Zotero will not have their files automatically removed from the Dropbox folder.

    Using Zotero storage rather than WebDAV or linked files in Dropbox also has two more advantages: File syncing in Group Libraries is only possible using Zotero Storage (for technical reasons), and using Zotero file storage will let you view the files from the Zotero.org web library.
  • adamsmith
    Yes, your description/summary is exactly right.
    In your experience do both of those approaches work just as well in terms of efficiency, accuracy, potential glitches?
    No. Zotfile+fileLinks+Dropbox works fine and is absolutely useable, but there are more moving parts and more things that can go wrong and require accurate set-up so if you're looking for a "care free" (so to speak) experience and the costs aren't a significant issue for you, Zotero file sync is what you'd want to use.

  • adshiller
    @bwiernik Thanks for all your help and followup. One thing you said didn't seem to work, though....
    "2) When you drag files into Zotero, it by default make a copy in Zotero’s internal storage folder, leaving the original in place. To _move_ the files to Zotero instead and delete the original, hold down Shift (Windows/Linux) or Cmd (Mac) as you drag."
    I'm on a mac, and held down that "command" key next to the spacebar and dragged a few files. It didn't delete the old ones in dropbox.
    What do you suggest?
  • bwiernik
    Sorry, I might have misremembered which key it was on Mac. Try Shift or Alt instead.
  • dstillman
    https://www.zotero.org/support/attaching_files#adding_linked_files
    By default, files dragged into Zotero are added as copies of the original files. To instead add links to the original files, hold down Ctrl+Shift (Windows/Linux) or Cmd+Option (Mac) while dropping.
    (You might need to pause briefly until the Zotero comes to the front for the modified keys to take effect.)
  • bwiernik
    Isn’t there also a shortcut to move the files (add as stored attachments, delete the original)?
  • dstillman
    edited December 10, 2019
    Oh, yes, sorry, I misread. You were correct — it's Cmd. The same thing I said above about hovering over the window applies to that as well.
  • adshiller
    OK
    Amazing
    @dstillman @bwiernik
    Dstillman line drive.
    I tried all the combinations of all the special keys, including shift+[key]
    In the end, what works, is a. select file b. hold down Cmd, c. bring cursor to zotero library d. wait until the zotero window comes in front of the finder window e. let go.
    yay!
    Thanks you too for staying with it.
    :-)
  • adshiller
    @dstillman @bwiernik
    Another question
    The transfer is proceeding well.
    What I notice is that some entries show up as a PDF symbol where I can open the article. But there doesn't seem to be any data except the name.
    And the huge majority of entries show up as a generic-looking document icon that has a 'rightarrow' next to it. When I click on the nondescript document icon I see document name and authors and abstract and so on. When I click on rightarrow, I see the PDF icon with the document.
    Is that because the former group doesn't have that other data available? Is there a fix for that besides manual entry?
    Thanks
  • dstillman
    What I notice is that some entries show up as a PDF symbol where I can open the article.
    Those are PDFs that no metadata could be retrieved for. You can 1) find those items online, save them, and drag the relevant PDFs on top of them, 2) do the same with Add Item by Identifier if you have a DOI, or 3) right-click and choose Create Parent Item and enter the metadata manually.
    And the huge majority of entries show up as a generic-looking document icon
    For those Zotero was able to extract some basic info from the PDF, but it wasn't able to find high-quality metadata. As above, if you can find better metadata, you can transfer the PDF over, or else you'll need to fill out the metadata manually.

    Zotero should be able to find high-quality metadata for most academic PDFs, particularly if there's a DOI in the first few pages.
  • adshiller
    @dstillman
    Thanks again.
    I did my big import and got many man duplicates.
    How do I deal with that?
    Can I go into 'duplicates' and easily delete the extras?
  • dstillman
    Just to clarify, you'd only get duplicates if you imported files more than once.

    You can merge via Duplicates Items, but that currently only merges parent items, so if you have multiple copies of the same PDF those will just be combined under a single item.

    Depending on how much work you've done, you may be better off starting from scratch — by closing Zotero and deleting your Zotero data directory — and making sure you only import things once.
  • adshiller
    @dstillman I see what you mean. I stumbled down the road of 'merging' and it makes for a HUGE folder full of duplicate files. Part of the problem is that it seems that Zotero was inconsistent in 'deleting' from dropbox when I moved a bunch of files at once. So I thought I was transfering once, but it was really time 2 or 3.

    Practical issue now--in an attempt to avoid the issue you described of multiple copies of a file underneath the merged record, I thought to manually delete the redundant files themselves in the Zotero folder.
    I thought that would fix the problem, but it doesn't seem to remove those from the 'duplicates' folder.
    Is there a workaround for that?
    thanks
  • dstillman
    If you delete a file on disk, that still leaves the attachment item behind in Zotero, and has no effect on the parent bibliographic item. You can use the Attachment (blue circle) column to see which items are missing their associated files and delete those manually, though.
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