Single folder for all pdfs

Chris_mik
Is it possible to have all associated pdfs (and other files) gathered in a single folder?

For example, in Mendeley you can have all the pdfs in a single folder and each file is automatically renamed when imported in the following naming convention:
Author1, Author2_Year_Title of paper.pdf

This is convenient since you can search, index or link the files from this single folder using other applications, i.e. Terminal, Obsidian, etc...
  • dstillman
    Zotero manages stored files in its own folder structure, which allows it to reliably keep them linked, sync them between devices, delete them if you delete the attachment in Zotero, etc. (Mendeley users on Twitter complained constantly over the years about missing and unlinked files.)

    Zotero has always named saved files automatically based on parent metadata. As explained on the linked page, if you want a flat list, you can just create a smart folder in your OS for all PDFs within the 'storage' folder of the Zotero data directory.
  • jazow
    I've wanted to do this too. I didn't realise smart folders were even a thing on mac! Cheers for that. I guess you could also search for .pdf in the storage folder and that should show you a list of the pdfs
  • tim820
    edited October 25, 2022
    This has traditionally been done via the Zotfile add-on.
    https://github.com/jlegewie/zotfile

    It had an update earlier this month so support may be more active again. However the documentation is a bit out of date, eg still refers to annotation extraction, which disappeared as a Zotfile feature when Zotero added the PDF reader/annotations in v6.

  • adamsmith
    Using the ZotFile/linked item route has a number of other implications though, so people need to think about if that's actually what they want: for example, it doesn't work for groups, doesn't work with the iOS app (and won't work with the Android one) and Zotero won't actually manage linked files (e.g., won't delete linked attachments when you delete the item in Zotero).

    If you understand Zotero and ZotFile well enough to be aware of these implications and you don't mind the trade offs, that's great. I'd be careful recommending it to Zotero beginners, who'll find them harder to judge/appreciate, though
  • tim820
    All fair points. I started using Zotfile as soon as I started using Zotero, but I read enough to know exactly what I was doing. It's described along with Zotero on enough university library websites that I assume it has a large user base. PDFs stored in a single folder reflects the use case where people need to access their PDFs directly when outside Zotero. It would be nice if Zotero itself had the option to put them in a single folder. I do now have a Windows saved search ('smart' folder) for the 100 or so PDFs that remain in my local Zotero storage for various reasons (ie located in 100 or so different folders created by Zotero for those PDFs, amongst ~5000 total Zotero folders). I don't know how well a smart folder would scale speed-wise for my ~3500 PDFs (currently in my linked folder), or for people who have many 1000's of PDFs.

    I do almost everything under Windows. I have never/will never use any Apple devices, and don't see myself using Zotero under Android when that arrives. My first reference database program was Reference Manager on floppy disks in the 1980s - so my expectations of reference database programs tend to be modest ! I don't expect them to do everything; in particular I don't expect them to make my PDFs available online on every possible device. I look after making my PDFs portable enough for my needs (same as I did pre-Zotero). I'm just happy when a referencing program doesn't screw up my database like Endnote used to ! My setup is similar to other people I know, but it wouldn't suit everyone.

    BTW the deletion of linked PDF attachments is adequately handled by the Delitem add-on.
    https://github.com/redleafnew/delitemwithatt
  • proteome
    I recommend all Windows users check out a program called "Everything". https://voidtools.com/
    It totally replaces and extends the capabilities of Windows search, and it's practically instant -- feels like magic. Without hyperbole, it's improved my time at the computer more than any other software ever has.

    I use this instead of smart folders for my library of ~4500 Zotero pdfs. At the push of two hotkeys ("Ctrl+Shift+/" and "Ctrl+z"), I have Everything pulled up with a list of all my Zotero pdfs. The first hotkey opens the Everything window from anywhere. The second applies a custom Zotero filter. Now, your cursor is focused in the Everything search box, and anything you type winnows down the pdf file list based on file name (or regular expression or metadata if using special search syntax). You can also easily search or sort by date, size, # times opened, last time opened, etc. Delete, rename, drag and drop, ...

    To create a custom Zotero filter:
    Everything -> Search menu -> Organize Filters -> New
    I named my filter "zotero files [ctrl+z]"
    and set the Search string to
    "_AppData\Zotero\storage ext:pdf;zip;xlsx;xls;docx;txt;pptx"
    and Keyboard shortcut to "Ctrl+Z".
    This finds every file under my Zotero storage directory that has one of the listed extensions.

    There's a lot more power to the Everything software beyond pulling up Zotero files. Can't recommend highly enough.
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