Zotero does not link local pdfs

edited October 29, 2020
I am trying to convert from mendeley and have some problems with local pdfs in zotero. In mendeley I could watch a folder and every pdf in that folder would be imported, formatted, and sent to my library. I have zotero configured now that it could read the pdfs from a folder, but it only captures the reference, it does not link the local pdf. Is there a way to achieve this?

For example, I have a pdf without a reference, let's say I am reviewing a thesis of some kind, then I want zotero to create a header with the title, extract the author and link the pdf to that ref without doing manual intervention.
  • I'm not really clear what you're doing now, but what you're describing isn't really the way to think about using Zotero.

    In Zotero, you generally add items from the web, which downloads metadata and saves a PDF if available, storing the file in its own storage.

    If you only have a PDF on disk — say, because you received it via email — you can drag it to Zotero, which will try to retrieve metadata for it and copy the PDF into its own storage. You can then delete the original copy on disk.

    It's also possible to use linked files, generally with the help of the ZotFile extension. But ZotFile will convert the default stored files into linked files in a location of your choosing — it doesn't just link them where they exist now. (You can do that manually in Zotero, but it'd be tedious, and not a recommended workflow.) If you have a file on disk that you were adding to Zotero, it would generally be in a temporary folder such as a download folder, and you would drag it to Zotero — resulting in either a stored file or a linked file in a configured directory — and then delete it.
  • To clarify the workflow I am to mimic is the one from mendeley which is:
    - Watch ~/[target_folder] (automatic)
    - Download a pdf to ~/[target_folder] (manual)
    - extract metadata and copy pdf with cleaned title to the zotero library (automatic)

    I have ZotFile installed, however it does not do the above. I receive manuscripts from students or other pdfs that I need to manage that I wish to put into zotero so that I can easily search for them at some later time or attach other things relating to them. Currently zotero only imports the cleaned information without linking the pdf. With linking I specifically mean the cleaned pdf inside the zotero library folder (under ~/Zotero)
  • edited October 29, 2020
    There's no watch folder functionality, because a PDF-first workflow just isn't a recommended way of using Zotero. When you view a PDF in your browser (directly, not in a web viewer), you can just click the Save to Zotero button, which will show a PDF icon. Otherwise you just need to drag the downloaded file to Zotero.
    Currently zotero only imports the cleaned information without linking the pdf.
    I think this is some sort of misunderstanding. Again, if you add a PDF to Zotero, it copies the PDF into Zotero's storage — or, if you're using ZotFile, you can configure it to create linked files elsewhere. Either way, you would then delete the original PDF in the download folder.
  • Irregardless of what the recommended way of using is, the primary focus of zotero is to be a ref-manager first. This means that it is related to documents of various formats. PDF being science's primary one (al though not in all disciplines). I don't think there is a misunderstanding, I am merely highlighting a lack in the current features that the competitor clearly has, rendering zotero for my workflow useless (i.e. a ref-manager that can actually manage my files). The plugin does work well when I am browsing journals, but unfortunately that is only part of my job and not its entirety.
  • edited October 29, 2020
    Zotero will absolutely manage your files — that's exactly what it does. You just have to understand how it's designed to work. Again, if you have a PDF on disk, you just drag it to Zotero, and it will rename and manage it for you, either within its own stored files or a configured linked-file location via ZotFile.

    If you're absolutely committed to downloading files yourself to a specific permanent folder and then linking those, from that location, into Zotero, it's certainly possible to do that, either via dragging with a system-standard modifier key or using Link to File. There are just better ways to add files to Zotero.
  • Great! Where in the settings can I tell Zotero to automatically link the ref to a file?
    Let's say I have some folder; Reading_group_thermal_dynamics, how can I instruct Zotero to link pdf files locally without manual inputting the files with the gui? i.e. watching the folder as outlined above?
  • You seem more committed to arguing than actually learning how Zotero works, so I'm going to stop trying here.

    Zotero is designed to work a certain way. That may not be precisely how you think it should work, or how some other tool works, but that doesn't mean there aren't reasons it works the way it does or that it's somehow a less capable tool. Zotero makes it trivial to add PDFs from your browser or disk and have those files be copied to a managed folder of your choice — the keyword being "managed", which means it's not a folder where you're directly saving files yourself, which can create a mess. It's absurd to say it can't manage your files when that's exactly what it's designed to do, and when millions of people from across all fields use it to do just that.

    Again, Zotero doesn't have watch-folder functionality, because that's not a workflow we recommend — you're either saving files to a browser download folder, in which case there's no reason to think that every PDF should be automatically added to Zotero, or you're wasting time manually choosing an organized folder to save files to, when that's something Zotero and ZotFile can automate for you, in a way that will work the same whether you're saving from the browser or from disk.

    ZotFile does have an function to add the most recently modified file in a given folder, so you might be interested in that option if you're frequently downloading files to disk — again, to a downloads folder, not the final location — without being able to save them or their article pages to Zotero from the browser.
  • > You seem more committed to arguing than actually learning how Zotero works, so I'm going to stop trying here.

    This seems to be a childish response. I am quite serious in what I am asking. There are numerous of previous posts on this forum specifically that has similar requests in the past. Not all workflows are considered to be going from browser -> zotero.
    Saying things like "this isn't the way to think about Zotero" is very peculiar to me, there is no reason for such austerity.

    A simple answer like Zotero doesn't support that feature but we are welcome a plugin that would implement this feature would suffice. In addition I would like to add that the Zotfile extension "watched folder" implementation does not actually work since version 5. Hence, my question on this issue.

    I am closing this issue now as apparently it is difficult for you to remain professional. Hopefully, the posterity can help me or a feature does get implemented in the future.

  • I am quite serious in what I am asking.
    A sarcastic "Great!" that ignores what I've been repeatedly trying to explain and just asks the same question again is not a serious response. It's a waste of our time to respond to you if you won't engage with what we write and instead just keep asking how to follow the exact workflow you're used to from another program. If you want to use Mendeley, use Mendeley.
    Not all workflows are considered to be going from browser -> zotero.
    At no point did I say the only workflow was browser → Zotero, and if you think it is that's just further evidence that you're not actually making an effort to engage with my responses to you. I've been talking about adding files from disk this entire thread.
    Saying things like "this isn't the way to think about Zotero" is very peculiar to me, there is no reason for such austerity.
    It's not austerity. We make design choices that we think produce the best experience. Zotero is incredibly flexible — I've listed a whole slew of ways to do variations on what you're asking — but we have opinions about what we think works best, and understanding those will help you use Zotero more effectively.
    A simple answer like Zotero doesn't support that feature but we are welcome a plugin that would implement this feature would suffice.
    Because that's not my answer. First, you genuinely seem to not be understanding the things I've been saying, so I've been trying to explain more clearly all the options you have here. And then I explained above why I don't think a watch folder is a good solution for adding things to Zotero.
    In addition I would like to add that the Zotfile extension "watched folder" implementation does not actually work since version 5.
    To be clear, that's not the feature I was referring to, which still exists and is appropriate when pointed to a downloads folder.
This discussion has been closed.