Potential for better integration with operating system file management?

jasonlustig
I've been using Zotero for a while now but it's kind of a pain for managing PDFs, for a few reasons:

- When I drag a PDF into Zotero to create a new reference, it copies the PDF file to a new "storage" folder on my computer, so now I have two copies (instead of linking to where I have the PDF).
- This "storage" folder is not particularly organized, and the file names retain the original (which could be quite cryptic depending on where I downloaded it from)

I think it would be fantastic if we could set up Zotero in such a fashion that it organized the PDFs in a more logical way. Here's what i'm thinking:

1) PDF names should be based on the reference information (perhaps in an automated way, updating the PDF file name if you update the citation)
2) PDFs in the file system should be organized in accordance with the way that references are organized in Zotero. For instance if I have a folder called "Article 2" then all of the PDFs for references in that folder would end up in "Storage/Article 2"
3) Also if you tag the PDFs with file system tags (e.g. on macOS) then those tags should automatically be applied to the reference itself

One of the advantages with this is that it would allow the PDFs to also be indexed by software like DevonThink, which can index a folder and make it searchable. As it is, if I make DevonThink index the "storage" folder then all the PDFs show up in the app but they are not organized at all.
  • adamsmith
    1) should already be the case. Are you sure Zotero doesn't do that? (The behavior here has changed recently and wasn't retroactively applied)
    2) You can do with ZotFile: http://zotfile.com and Zotero is planning to add more human readable organization in the storage folder, I understand.
    3) While I'm sure possible, I'm a little doubtful of. For a start, this has rarely been requested. I think that's no co-incidence. OS tags aren't terribly useful attributes as things go, Zotero tags can be very extensive etc.
  • jasonlustig
    Hi Adam, thanks for responding. I've experimented with Zotfile and it does rename files, but it still seems to store them in the "Storage" folder (i.e. not organized).

    As for tags - I understand that's not necessarily a frequently requested feature. In general I'm interested in using the OS file management / search features alongside zotero.
  • adamsmith
    ZotFile will move files, alas not automatically if you import them by dragging them to Zotero and then rely on the automated retrieve metadata -- in those cases you'll need to manually run "rename attachments" (which, in the presence of a custom folder in the Zotfile preferences) will move them.
  • jasonlustig
    edited September 22, 2018
    Aha, I see what you're saying. This is fantastic, if I set Zotfile to save files for instance in ~/Research Library/ with a subfolder defined by %c that will use the categorization in Zotero to sort the PDF files.

    However, running "rename attachments" is kind of cumbersome. Is there a keyboard shortcut I can use to make it faster? I haven't been able to find one...
  • adamsmith
    No, but note you can run this on multiple items at once. ZotFile is designed to do this automatically when you import e.g. a PDF attached to an item added via translator, but the developer hasn't been able to automate this for dragging the PDF to Zotero.
  • jasonlustig
    Yeah, I've seen that I can run it on more than one item. It's too bad that I can't create a keyboard shortcut though.
  • bwiernik
    You could contact the developer of the Zutilo plugin about adding a shortcut for that.
  • jasonlustig
    I created a command line script to do some of this: https://github.com/jalustig/zotero

    It takes Zotero information and puts it into macOS file tags. If it were possible to programmatically manipulate the tags of zotero citation items then it would be possible to do it in the opposite direction as well. Right now it's just using the Zotero sqlite file as read-only...
  • bwiernik
    You can use PyZotero with Python to programmatically safely Edit Zotero tags.
  • jasonlustig
    PyZotero looks promising, from what I can tell it modifies a Zotero database via the web API which syncs with your local computer, right? It doesn’t modify the local store directly?
  • adamsmith
    that's correct; there's currently no accessible local API (planned I believe -- it kind of exists in the form of a javascript API, but there's no way to get to it outside of a Zotero add-on)
  • billtubbs
    I'm looking for a document / reference management system and considering Zotera. After reading this discussion, am I right in concluding that Zotero does not leave files in place (in my computer's existing file system structure). Rather it moves or copies them to a Zotera library?
  • dstillman
    @billtubbs: That's incorrect. You can use a linked-file workflow that leaves your files in place and moves new files that you save from the web to an external folder. ZotFile, linked above, can help with that.
  • jasonlustig
    You *can* link files, but it's not done by default.

    It would be great if there was an option of what should be the default, so you could set it to copy files (as is currently the default) or to link to the existing PDF by default (which I'm sure many people would prefer)
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