Zotero storage folder duplicates pdf

edited 2 days ago
Hi there.
I am using Zotero 7 on Windows 11.
I have attached local pdf to all books in my collection and made many annotations on the pdf files using zotero with adobe acrobat reader. I al not using fulltext sync.
Now I have discovered that in this way annotations are made on a copy file of the pdf I have attached and not on my files. And these copies are stored in Zotero folder.
I dont want any copy of my files. I want annotations directly on the local file in the precise folder where it is when I have attached it.
Do I have to use LINKED FILES plus selecting a relative-link folder in settings?
Thanks


  • Working entirely within the Zotero ecosystem just "works" for most people. It is possible to work somewhat outside that, but it can get complicated.

    When you add a PDF to Zotero from your OS (by drag and drop for example), a *copy* of that file is what is added to Zotero storage (under Zotero\storage). That's a "stored" PDF file. Any annotations in the PDF at that time will be visible within Zotero, but 'locked' (unless you import them - then they will be added to the Zotero database and wiped from the PDF file in Zotero storage).
    https://www.zotero.org/support/kb/annotations_in_database

    If instead you do the drag and drop of the PDF file into Zotero while holding down Ctrl+Shift (Windows/Linux) or Cmd+Option (Mac), Zotero will instead add the PDF as a "linked" file in its current location (the PDF must remain in that location so Zotero can continue to find it). There are other ways to add linked PDF files (eg by right click menu, or via the web connector plus the Zotmoov plugin). Any existing annotations in the PDF (and any added later in an external viewer) will be locked unless imported.
    https://www.zotero.org/support/attaching_files#adding_files_via_the_browser

    Linked files have limitations - they don't work with the mobile Zotero apps, Groups, or the online web library. You can move files from stored to linked (using Zotmoov for example), or linked to stored (using Zotero or Zotmoov), at any time. But it is best to have all your files in one scheme. Stored files count towards your online file storage quota, if you want Zotero to sync them to other devices. Linked files do not count towards that quota (if you want to sync them across computers, you need to a cloud service for that). WebDAV is another syncing option for stored files.
    https://www.zotero.org/support/attaching_files#stored_files_and_linked_files

    For both stored and linked files, any annotations you add in the Zotero reader will be saved in the Zotero database, not the PDF itself (they can be exported back to the PDF for a single PDF, but that is not intended to be a routine operation - see the reasons for annotations being in the database, at the first link above).

    Many people come to Zotero with their PDFs stored in their OS in a way they wish to maintain (for example in a structured OS folder hierarchy). Some people decide to use linked files (but often with those linked files all in a single folder), sometimes because they cannot afford Zotero online storage for syncing (and don't need, or have workarounds for mobile access). Some in the first group soon decide that trying to organize everything in *both* their OS and under Zotero is redundant and inefficient, so they move to working in Zotero only. Part of the reason for that is that most people use the Zotero reader rather than an external PDF reader (you can however open a PDF in an external viewer from Zotero, for example using the Open PDF plugin).
  • Thank you. A complete and detailed explanation, thanks!!
    But with a clarification/correction: you said that annotations are locked and not impressed in the pdf file. That is true ONLY if you use Zotero reader.
    With adobe as zotero standard pdf reader annotations are impressed in the original pdf even with linked files.

    Another question: if I have my pdf in two subfolders of C:\users\name\PDF, if I want Zotero to find the same linked files in a second pc with files present in the same path and subfolder, is it ok in settings to point the attachment folder to just the main one ( C:\users\name\PDF) and not the subfolder? Will it work?


  • If the paths are exactly the same, the Linked Attachment Base directory doesn't do anything -- its function is for you to have files at paths that differ in the beginning (e.g. a.different username or even Mac vs PC).
    Setting this up the way you describe will let you open the files, but suggests you aren't fully understanding how linked files work (yet), which may cause you problems down the road
  • Ok thanks.
    I don't perfectly understand what you mean by "differ in the beginning" of the path. It is just sufficient that final folder name is the same while the rest of the path is totally different?
    For example the Linked Attachment Base directory will work in the case I have on pc1 C:\users\name\PDF and on pc2 C:\users\documents\AM\study\PDF?

    Plus my second question regards subsolders. If I have linked files in 2 subfolders of the above mentioned "PDF" folder they will be recognized also on a second pc?

    Thanks
  • For example the Linked Attachment Base directory will work in the case I have on pc1 C:\users\name\PDF and on pc2 C:\users\documents\AM\study\PDF?
    exactly, yes.

    For subfolders, not sure exactly what you mean by 'recognized' -- but if the path is the same starting from the PDF folder (so PDF\subfolder) then yes, you can have any number and depth of subfolders in there and Zotero will be able to open the files in them.
  • Ok great! Thank you
Sign In or Register to comment.