Library disappeared after upgrade

dstillman
This discussion was created from comments split from: Download whole online library?.
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  • penelopecave

    https://www.zotero.org/support/sync seems only to allow sync FROM personal computer (MAC in my case) to the online one. I want to get my online library back into my computer, which has disappeared since the upgrade I misguidedly agreed to allow. I wish I had left well alone.
  • adamsmith
    No, sync goes both ways. Syncing an empty Zotero library with the server will download it.
    Also, for a library disappearing after update see https://www.zotero.org/support/kb/data_missing_after_zotero_5_upgrade

    Are you the same person who posted originally? If so, make sure that you know which of the two accounts actually has your library.
  • penelopecave
    This is my first comment, and before making it, I had tried searching through all my other zotero files in the hope it was misplaced, but without success. Then I tried moving my Zotero folder from Application Support folder into Users/penelopecave/ but this led to it asking to install a new Zotero. Nowhere was there a zotero with a lowercase z. Can I sync the new download or will it clear my online library?
  • adamsmith
    It sounds like you moved the Zotero application folder to Users/penelopecave/ -- you'll want to delete it from there to be safe; it probably won't matter, but not a good idea to have random Zotero files somwhere.

    Then yes, if you see your library here on this site under "Library" you can just sync with a fresh Zotero install.

    If you prefer, we can also give you some additional pointers on where to look for your Zotero library; it's almost certainly still there as Zotero will never delete a local library. But if you are confident you have all information in the online library and just want to be done with it, syncing will work.

    (The reason I asked whether you're the same person is that we generally ask that people start new discussions for their own problems: it's going to be a bit confusing to sort out which advice is for whom once amorant returns to this thread)
  • penelopecave
    Thank you for your help, and apologies for butting in, but now I am within this thread, perhaps I should stay here! I would be glad for additional pointers to find my local library, as it has additional notes etc. although it will need to be spelt out.
  • adamsmith
    Do you know if you previously used Zotero for Firefox, Zotero Standalone, or both?
  • penelopecave
    I assume I used Standalone.
  • adamsmith
    If you open Zotero and click the "Show Data directory" button under "Advanced -- Files and Folders" what's the filepath of the folder that open?

    And do you have Users/penelopecave/Zotero/Profiles/[randomstring]
    as a folder?

    Also, do you have Firefox installed at all or did have it installed on this computer in the past?
  • penelopecave
    Thank you for your patience. I have not installed Firefox. Yesterday I found /Users//Library/Application Support/Zotero/Profiles/
    BUT no 'zotero' subsdirectory - after Profiles is cmiudghs.default folder, which leads to other documents and folders but zotero.squlite is not in this folder (it is in the Users/penelopecave/Zotero folder)
  • adamsmith
    what's in cmiudghs.default ? (if you're up for using terminal you can get that using
    $ cd /Users/penelopecave/Library/Application Support/Zotero/Profiles/cmiudghs.default

    $ls

    and then just do copy & paste here.


    Also, what are the files starting with zotero.sqlite in Users/penelopecave/Zotero and whare are their respective sizes? Is there any one that's significantly larger than 1 MB?
  • penelopecave
    I am very grateful for your assistance. My cmiudghs.default contains 4 folders and 27 files most of which are blank and my computer is unable to open. Not one of the files within folders, or without, apparently has my local library within it.
    When this first happened, I could open my library but there was only ONE entry (instead of over 900), but now if I open Zotero on the laptop, all I get is the offer of a new library, so if I open this up will it still be possible to sync from this new library to the old online one, or will that disappear?
  • penelopecave
    Zotero.sqlite also won't open.
  • adamsmith
    As I say above, if you just sync with an new, empty library, that will download all items from the server to your local copy, so you can absolutely do that.
    . My cmiudghs.default contains 4 folders and 27 files most of which are blank and my computer is unable to open.
    we wouldn't expect your computer to be able to open them, but what are the file and folder names?

  • penelopecave
    Thank you and I will do that if we can't restore any other way. Meanwhile, here with the list!

    FOLDERS: crashes, datareporting, gmp, saved-telemetry-pings

    FILES: AlternateServices.txt, blacklist.xml, cert8.db, compatibility.ini, content-prefs.sqlite, cookies.sqlite, extensions.ini, extensions.json, form history.sqlite, key3.db, localstore.rdf, logins.json, mimeTypes.rdf, permissions.sqlite, places.sqlite, pluginreg.dat, prefs.js, revocations.txt, secmod.db, SecurityPreloadState.txt, sessionCheckpoints.jsn, SiteSecurityServiceState.txt, storage.sqlite, Telemetry.ShutdownTime.txt
  • adamsmith
    OK, definitely no database there.

    How about this question:
    Also, what are the files starting with zotero.sqlite in Users/penelopecave/Zotero and whare are their respective sizes? Is there any one that's significantly larger than 1 MB?
  • penelopecave
    I cannot now find Users/penelopecave/Zotero. Within my Zotero folder, which is all I can locate, are the unreadable zotero sqlite, zotero sqlitejournal, and zotero sqlite.bak

    I don't know how large these files are as I can't open them.
  • adamsmith
    You don't need to open a file to check its size. See e.g. the first option here: https://support.apple.com/kb/PH25363?locale=en_US
    We'd be interested in zotero.sqlite and zotero.sqlite.bak
    Also, is there a storage folder in Zotero? And where is that folder if it's not at Users/penelopecave/Zotero ?
  • penelopecave
    The 3 sqlite files above are 2.5 MB each! If this is my missing library, how do I open it? Also slightly concerned that the first says modified on 3 April and the 2nd 2 modified on 18 and 19 March respectively.

    There is a 'storage' folder in the folder we re-named 'old' and it has 23 folders each of which contains just one reference (they are authors in my own library, but why so few?).
  • adamsmith
    How big is your library online (i.e. how many items)?
  • penelopecave
    922 items
  • dstillman
    If this is my missing library, how do I open it?
    If you don't mind uploading that to the DB Repair Tool and providing the Upload ID, we can confirm whether there's data in it.

    But basically, if you used Zotero previously on this computer, you almost certainly have a Zotero data directory somewhere on your computer, with a zotero.sqlite file and a 'storage' directory containing all the attachments that either you saved on this computer or that were synced. I'm not sure why you have a 'storage' directory with only 23 folders, but the dates on those folders should be instructive in terms of when this data directory is from.

    Even if you think you haven't used Firefox, I would verify that you don't have a Firefox profile directory with a 'zotero' directory in it. That's the most likely reason for Zotero to get confused when you upgrade to 5.0 — it has multiple data directories to choose from and it doesn't choose the one you want.
  • dstillman
    Well, and the other thing I'm a bit confused about is what exactly you did with regard to the /Users/penelopecave/Zotero directory. You said:
    Then I tried moving my Zotero folder from Application Support folder into Users/penelopecave/ but this led to it asking to install a new Zotero.
    But the folder from Application Support would be your profile directory, not your data directory. It's the latter that contains zotero.sqlite and 'storage'. So, to start, you want to make sure that you have a /Users/penelopecave/Zotero folder containing — directly within it, not within any other folders — the 2.5 MB zotero.sqlite and the 'storage' folder with 27 folders. The old profile directory you moved from Application Support you can ignore and keep out of the way for now, assuming there's no other 'zotero.sqlite' file within that.
  • penelopecave
    Thank you, I can find no evidence of Firefox on my computer.

    Because we tried to follow the instructions on the website, we moved what I think is my /Users/penelopecave/Zotero folder and re-named it Zotero-Old
    This is the folder which has within it, the 3 files above, each of 2.5MBs. It also contains the folder named Storage with the 23 files, the 1st is dated 'created 31 March 2016, modified 20 March 2018', the second was obviously entered later, "1 May 2017, but modified 3 April 2018. Another says it was modified yesterday. None of which makes sense to me, as I would not have thought these could be modified on different days, as I have not accessed my library since the upgrade.
  • penelopecave
    Also the sqlite file in the new Zotero (without the 'old'), has a content of 918 KB.
  • dstillman
    And if you temporarily change the Zotero data directory setting in the Advanced → Files and Folders pane of the preferences to point to the Zotero-Old directory, what do you see when it starts up?
  • dstillman
    Also, have you searched your computer for other zotero.sqlite files?

    If you open Terminal from Spotlight, type mdfind -name zotero.sqlite, and press Return, does anything show up other than /Users/peneleopecave/Zotero and /Users/peneleopecave/Zotero-Old?
  • penelopecave
    Thank you, but I'm afraid your 'mdfind' suggestion hasn't worked, it came up with 'no results'.
    I also went to the Advanced → Files and Folders pane of the preferences, with Default as (/Users/penelopecave/Zotero). Opening the Data Directory, I find both Zotero-Old and Zotero. In Zotero-Old has the 3 sqlite files that I have already mentioned with 2.5MB. In the (new) Zotero, are 4 sqlite files: zotero.sqlite of 918KB, zotero.sqlite-journal 91KB, then two zotero.sqlite.bak. and bak1 that are 918KB again.
    Is that what you needed to know?
  • dstillman
    Can you paste the full output of what you typed and what it returned here? Unless you've disabled Spotlight, that should at least find the files you've been looking at.
    Opening the Data Directory, I find both Zotero-Old and Zotero. […] Is that what you needed to know?
    No. This is what I said:
    And if you temporarily change the Zotero data directory setting in the Advanced → Files and Folders pane of the preferences to point to the Zotero-Old directory, what do you see when it starts up?
  • penelopecave
    I fear I am wasting your time, and becoming increasingly frustrated by my own complete ignorance of computer-speak, as I don't understand the instruction: how to temporarily change the data directory setting.

    I typed mdfind - penelopecave zotero.sqlite
    I also tried exactly as you gave it, and also with /s between the words.

  • dstillman
    Just copy and paste what I wrote above. Don’t retype anything.

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