macOS Sierra: papers protected?

christianbrodbeck
Since upgrading to macOS Sierra public beta, every time I open a paper from my Zotero library in Preview and try to edit it (e.g. Highlight some text) I get a message (from Preview) that “The original document can’t be changed, so a duplicate with your changes has been created.”. I have also reported this to Apple since it is probably due to a change in the OS?
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  • adamsmith
    I don't know anything about the mac OS update specifically, but judging by the error message, check file permissions in your Zotero data directory.
    https://www.zotero.org/support/zotero_data
  • christianbrodbeck
    the PDF file itself is
    -rw-r--r--@ 1 christian staff ...
    which is the same as other PDFs that I can edit. It's located at
    ~/Library/Application Support/Zotero/Profiles/p4w1twjt.default/zotero/storage/C2ZFSRTT
    The enclosing folders up to `p4w1twjt.default` are drwx------ <n> christian staffthen drwxr-xr-x <n> christian staff

    From what I know this should be ok, but I am not familiar enough to tell for sure?
  • dstillman
    What's the result for 'xattr -l' on the PDF? Do files you can edit have the '@' as well?
  • christianbrodbeck
    xattr shows this:
    $ xattr -l O\'Brien....pdf
    com.apple.quarantine: 0082;57904424;Preview;
    And yes editable files also have the '@'.
  • christianbrodbeck
    edited July 23, 2016
    The issue seems to be fixed by moving the Zotero data directory out of `~/Library`. All I did was change the Data directory to `~/Zotero Library` (in the standalone preferences dialog), and then dragging the files to the new location in Finder.
  • abodywithoutorgans
    I am also having this problem since upgrading to both Sierra and the latest Zotero. Anyone else?
  • dstillman
    Yes, it looks like Apple changed Preview in Sierra to prevent editing of files within ~/Library/Application Support (though I can't actually find any documentation of this). I suspect another PDF program (e.g., Acrobat Reader) would work — even TextEdit doesn't do this — but the easiest option is probably just to move your Zotero data directory out of ~/Library and into ~/Zotero or similar.

    We're going to have Zotero 5.0 use ~/Zotero by default for new installations, and we'll also have it migrate existing data directories out of ~/Library/Application Support to address this (though I'm not sure if that part will happen for 5.0 Final).
  • elavigne
    Same problem with MacOS Sierra and Preview saving edited pdf files as copies. Moving the library to ~/Zotero as suggested worked. Thanks!
  • Erressler
    I am having the same problem.

    If I am reading correctly, the following provides a fix until Zotero 5.0: (quoting from Dan above)

    "the easiest option is probably just to move your Zotero data directory out of ~/Library and into ~/Zotero or similar."

    Please confirm this is all I need to do and if so, kindly give me a little more step by step....having trouble understanding exactly what to do.
  • redcloud111
    edited October 16, 2016
    I can confirm this fixes the problem. I had the same issues after upgrading to Sierra.

    Erressler

    In preferences, you can click a button to take you to your library folder, ~/zotero. Just move this out of the ~/library path. I put it elsewhere along side my /Documents and /Applications in my root user directory.
  • Erressler
    First, thank you!

    Second, this apparently seems simple. However, step one says go to preferences and click on the library folder. When I go to preferences under the apple icon, under Safari, and under Zotero, and I do not see a "library folder". As such, I cannot get past step one. Challenged here in Peachtree Corners.
  • adamsmith
    No, this is the Zotero preferences in the advanced tab:
    https://www.zotero.org/support/preferences
  • Erressler
    OK...embarrassed but here goes: I am now in the Files and Folders, under Advanced, under preferences, in Zotero. How exactly do I "Just move this [~/zotero] out of the ~library path...[and] put it elsewhere...."
  • adamsmith
    There's two things you need to do:
    1. (Disable automatic sync in the sync tab of the preferences then...) Go to show folder, which opens the data directory in Finder. Then close Zotero and move the entire "zotero" folder (in Finder) to the new location.
    2. Restart Zotero. You'll see an empty library. Now again under files and folders, use the custom location button and browse to the new location of the zotero folder. (You'll need to again restart Zotero and you should re-enable auto-sync)
  • Erressler
    edited October 19, 2016
    OK...disabled sync, then moved entire Zotero folder to Applications (on iMac). When I tried to open Zotero again, I received this error msg: "The Zotero data directory could not be found." When I tried to open files and folders, nothing was responsive.

    Update: Had to relocate and then restart...everything OK now! Thank you.
  • Oliver Kuehn
    I tried this, but for me it did not work. It looks as if Zotero (standalone) does not recognize the new location of the directory. In fact upon startup it just creates a new one under Application Support.
  • Erressler
    Hi Oliver:

    As I recall, I had to restart the computer/Zotero or both. I do recall that it did not immediately appear as if it was fixed, but it ended up fixed. Keep fiddling with it! There is enough information in this discussion to make it work.

    Blessings, Eric
  • Oliver Kuehn
    Thanks Eric, fiddling looked as follows: I just moved the directory "storage" somewhere else and generated a soft link to this new place instead.
    Now it works.
    Oliver
  • Erressler
    Awesome!
  • adomasven
    adamsmith:
    There's two things you need to do:
    1. (Disable automatic sync in the sync tab of the preferences then...) Go to show folder, which opens the data directory in Finder. Then close Zotero and move the entire "zotero" folder (in Finder) to the new location.
    2. Restart Zotero. You'll see an empty library. Now again under files and folders, use the custom location button and browse to the new location of the zotero folder. (You'll need to again restart Zotero and you should re-enable auto-sync)
    @Oliver%20Kuehn you probably missed step 2. No symlinks are necessary, Zotero can use any data directory as long as you move the whole thing (not just storage).

    While your setup works now, we are planing to perform a data directory migration on Zotero 5.0 release, which could potentially break it.
  • sekidemoodo
    Changing the location of Zotero database helped me, as well! Thank you so much. :)
  • toz
    edited December 6, 2016
    These four simple steps fixed the issue for me:

    1. Clicked on the "Show Data Directory" button in Advanced > "Files and Folders".
    Finder opened a window in which a folder named "zotero" was selected.

    2. Copied that zotero folder to ~.
    In my case, the folder was in /Users/toz/Library/Application Support/Zotero/Profiles/mi3eo0kb.default, i.e. I copied the folder /Users/toz/Library/Application Support/Zotero/Profiles/mi3eo0kb.default/zotero
    and pasted it to ~, i.e. now there is a new folder as /home/toz/zotero.

    BEWARE: There is another folder named Zotero (capitalized) in the full path, I did not copy that folder, instead I copied the folder named "zotero" three directories below it.

    3. Set the Data Directory Location to Custom and pointed it to the new folder.

    NOTE: As soon as I clicked on the OK button, Zotero asked me to restart.

    4. Removed the old "zotero" folder in /Users/toz/Library/Application Support/Zotero/Profiles/mi3eo0kb.default
  • dstillman
    edited March 14, 2017
    Just to note, the Zotero 5.0 beta now does this migration automatically, so if you prefer you can install the beta version. (We'll be releasing 5.0 to everyone soon.)
  • dominicv
    Hi, following Dan Stillman's statement about migration to 5.0 to fix the issue, I migrated my standalone mac version to the latest beta, but that did not fix the issue.
    I then tried the option in settings to migrate the database to the new default location, Zotero restarted but it didn't move the database...
  • dstillman
    @dominicv: Make sure Zotero for Firefox isn't open at the time. If it is, the installation will be skipped. We'll clarify that for the manual option.
  • hamfeh
    @dstillman Worked for me. Thanks a lot!
  • johnsmithtexas
    @toz Thanks a lot for the clear and step by step explanation. For anyone having this problem, I recommend user toz explanation.
  • sem
    I gave up waiting for 5.0 gold and used the explanation of toz. It worked, thanks!
  • cptwomey
    edited February 13, 2017
    The explanation from toz and adamsmith worked for me too. Thanks much, all.
  • shairbek
    I followed toz and all worked fine. I copy-pasted, and once done, wanted to delete the old storage. But strangely, I cannot find it. I know the path, but when trying to locate in the Finder, there is simply no "Library" folder under user (path says it should be there). Any ideas?
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