Problems with data directory, locating pdfs, and syncing between computers

phsoh
Hi, I have gone through some past discussions, but couldn't find an answer to the syncing problems I have.

I have been using my laptop Zotero client in firefox without a problem until I tried syncing in Zotero client on my desktop. I didn't get the pdf files on my desktop, so I thought it has to do with the data directory. Back to my laptop,I changed the base directory to one inside 'my document' (outside of firefox profile), thinking that it would be easier to match it on my desktop computer later. It didn't work either, so I revert it back.

After these changes, I found that a lot of Zotero files in 'my library' on the laptop "couldn't be found. It may have been moved or deleted outside of Zotero"! Fortunately, those in 'group library' are not affected.

I also found that some folders in 'my library' are not affected. This has become so messy, I don't know what i can do, but am desperate to save my work from downloading the files again. The alternative is to consider starting a new Zotero account, set up the base directory away from firefox profile and correctly sync my new files on two computers.

Finally, I also learned that we cannot rename folders in Zotero 'my library' as they will not match with the folders under 'my document'. Though I had tried renaming my document folders, the pdf file links will be lost. Is this true?

Could anyone enlighten me the following: 1) how I can locate the pdf files on my laptop that I have lost, 2) how to put all files (from my library and group library) in one directory so that I can sync them between computers? 3) Ideally, I want to sync some Zotero group library folders to my working Box (or dropbox) with colleagues, so that those who don't conduct research/lit review can still read the pdf files I recommend.

Thank you for your patience. I hope to resolve these issues once and for all, and willing to start fresh with a different user account in Zotero to set it up correctly.
  • dstillman
    The base directory setting is an advanced feature that pertains only to linked attachment files and doesn't have anything to do with the data directory. Don't touch that if you don't know what it does.

    For missing files, start here: https://www.zotero.org/support/kb/files_not_syncing
    Finally, I also learned that we cannot rename folders in Zotero 'my library' as they will not match with the folders under 'my document'. Though I had tried renaming my document folders, the pdf file links will be lost. Is this true?
    I don't know what you mean here. What "folders" are you referring to? If you mean the 8-character folders within the 'storage' subdirectory of your Zotero data directory, you absolutely can't rename those, and, in fact, you shouldn't be touching anything within the Zotero data directory by hand.

    I can't help you beyond that, and I think anyone who does will need a lot more details about what exactly you're trying to do and the specifics of the things you're referring to.

    Generally, it sounds like you may have some misconceptions about how various parts of Zotero work, so it might be helpful to read through some parts of the documentation:

    https://www.zotero.org/support/zotero_data
    https://www.zotero.org/support/sync
  • dstillman
    (Regardless of anything else, though, there's no reason to start with a new Zotero account.)
  • phsoh
    Hi Dan, I am a relatively new Zotero user, started using Zotero more frequently in the last few months. I don't understand why some times certain pdf files can be stored in a designated location while others in the default storage (even though I had specified a location using Zotfile preference). In the latter case, the file name appears as 'ContentServer.pdf'.

    I didn't rename folders within storage, only those appear in my Zotero pane. Now I try to make sense of why so many pdf file links cannot be found in Zotero when in fact those files still sit in the designated directory. I will read through the documentations again before checking the sync problem. If there is a way to diagnose the missing links, it would be helpful.

    I am going through the last two URLs you posted. Hope that explains what I did wrong.
  • phsoh
    Hi Dan, I read this https://www.zotero.org/support/sync, so it appears that we can only sync group libraries with attached files on Zotero server, but all other data in 'my library' appear with citation info and not files attached. If this is the case, then I should keep more frequently used files online to benefit from multiple computer access. Correct me if I am wrong.

    The problem left for me is how can I re-establish the links from 'my library' folders in Zotero pane to the originally designated folders under 'my document' on my laptop? Now I have to 'locate' the files one by one by double click each reference in Zotero.

    Thanks again.
  • adamsmith
    how did you link those files in "My Documents" to Zotero in the first place? Are there, actually, any files in there?
  • phsoh
    Hi Adam, I used Zotfile Preference to select the 'custom location' which points to a subfolder in 'My Document', depending on which library collection I use. Yes, there are pdf files still in those subfolders, but in Zotero Firefox Pane, for a couple of the collections in My Library, I could not locate the files anymore unless I locate them one by one.

    In Zotfile Preference the default option for Source Folder for Attaching New Files is 'Use Firefox download folder'. I never touch this.

    Is there a better way to manage file location?

    Thanks for your help.
  • aurimas
    1. Install Zutilo
    2. Find a few file attachments (3 should be a good number) that are not found by Zotero and check where Zotero is looking for these files by right-clicking the attachment and selecting Zutilo -> Show Attachment Path. Find those files manually and note their paths.
    3. Post the paths where Zotero is looking and where the files actually are here. That should help us figure out what happened and how to proceed.
  • phsoh
    Hi, Zutilo is very useful. I pulled out 3 articles and checked the paths. The top directory \Users\xxx has been renamed as I have changed the computer name recently. Do I change the computer name back? I wonder if there is a way to change the Zotero path name in case when I have a new computer that I want to restore Zotero backup?

    Thanks so much for your help!

    (Zutilo)
    C:\Users\Pek\Documents\SFU\RESEARCH\ARTICLES\Zotero Downloads\Nahapiet_Ghoshal_1998_Social Capital, Intellectual Capital, and the Organizational Advantage.pdf
    (Path noted)
    C:\Users\Pek-Hooi\Documents\SFU\RESEARCH\ARTICLES\Zotero Downloads

    (Zutilo)
    C:\Users\Pek\Documents\SFU\RESEARCH\ARTICLES\Zotero Downloads\Gulati_1999_Network Location and Learning.pdf
    (Path noted)
    C:\Users\Pek-Hooi\Documents\SFU\RESEARCH\ARTICLES\Zotero Downloads

    (Zutilo)
    C:\Users\Pek\Documents\SFU\RESEARCH\ARTICLES\Zotero Downloads\Miscellaneous\Strategic Management Journal\McEvily,Zaheer (1999) Bridging Ties.pdf
    (Path noted)
    C:\Users\Pek-Hooi\Documents\SFU\RESEARCH\ARTICLES\Zotero Downloads\Miscellaneous\Strategic Management Journal
  • aurimas
    No, you don't need to change back your user account. You can use Zutilo to fix your pathrs. See the "Modify attachment paths" feature here: https://addons.mozilla.org/en-US/firefox/addon/zutilo-utility-for-zotero/
  • phsoh
    Hi, Zutilo is great. I want to thank you first. I have read the instructions but it will take me a while to try out and know the results.
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