some of the journal styles are not being installed

nemo8130
edited December 15, 2017
"This item could not be saved because Zotero is not open or is unreachable. Please open Zotero and try again."

I have followed suggestions in the forum relating to this but none seem to work.
Also tried with downloaded .cls files. How to install such files manually ? I have ubuntu 14.04
Shall be grateful to have your help.
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  • adomasven
    What do you do to get the above message? Are you saying that you can install some styles but not all of them? Can you provide a link to one that fails?
  • nemo8130
    edited December 15, 2017
    Yes. I am getting the problem for only some journal styles, not all.

    Example styles which did not work:
    1. BBA - proteins and proteomics
    2. Journal of computer-aided molecular design
    3. Journal of molecular modeling

    Etc.

    One noticable point is that these journals use square brackets ([1] [2, 3] ) in their citation styles. Though I am not sure if that's the reason or that's true for all cases which fail !

    But I have seen many to post similar problems in the forum ! Is there a possible quick fix ? Also, how can one install manually a .cls file after downloading.
  • adomasven
    Please describe exactly what you are doing. https://www.zotero.org/support/reporting_problems

    You can install csl files in Zotero Preferences -> Cite -> Styles
  • adamsmith
    I'm guessing these are all dependent styles (i.e. styles that aren't in themselves complete but contain a link to a more generic style) and I'd guess they don't install because Zotero doesn't have access to the internet and can't download the parent style.

    An error report ID from Zotero after installing should confirm that. If I'm right, see https://www.zotero.org/support/kb/connection_error
  • nemo8130
    edited December 16, 2017
    Internet connection is absolutely fine. Wish I could add a couple of screenshots of what exactly is happening.

    Precisely, I am trying to install (say) the journal citation style BBA - proteins and proteiomics (https://www.zotero.org/styles?q=bba - prot). Upon clicking the link all I am getting is the following error:

    This item is not saved because zotero is not open or is unreachable. Please open zotero and try again.

    - which is strange since the zotero standalone is open and also I have auto-logged-in to my online zotero account.

    I have also tried to install the .csl file manually (zotero -> preferences -> '+' -> redirecting to the .csl file) which returns an even more general error:

    An unexpected error occurred while installing "/home/sankar/Downloads/bba-proteins-and-proteomics.csl"

    I never encountered such troubleshoots before with my earlier versions of zotero and libreoffice. I am currently using the most upgraded versions of both (libreoffice 5 and zotero 5.0.31. I have checked for updates and nothing more is currently available.

    Should these styles have some dependencies how could it be solved ?


  • nemo8130
    One more thing. When I am opening zotero-standalone from a terminal, I am getting these verbose:

    (zotero:8076): GLib-GObject-CRITICAL **: g_object_ref: assertion 'object->ref_count > 0' failed

    (zotero:8076): GLib-GObject-CRITICAL **: g_object_unref: assertion 'object->ref_count > 0' failed

    (zotero:8076): GLib-GObject-CRITICAL **: g_object_ref: assertion 'object->ref_count > 0' failed

    (zotero:8076): GLib-GObject-CRITICAL **: g_object_unref: assertion 'object->ref_count > 0' failed


    should it be of any help to what is happening within
  • adamsmith
    no, those errors are irrelevant.
    We'd want an error report ID after a failed attempt to install a style:
    https://www.zotero.org/support/reporting_problems#provide_a_report_id
  • nemo8130
    edited December 17, 2017
    I followed the instructions to report the error. However, in the pop-up window there was no means of copy-pasting anything. The error report was already written there (in some coded language) and in attempt to press the return button I actually submitted it twice. This is the latest report ID:

    1723360247

    Kindly ignore the duplication.

    Many thanks for your kind attention. Hope this will be fixed soon.
  • nemo8130
    edited December 17, 2017
    The error report started from saying "You have reached your Zotero File Storage quota. Some files were not uploaded. Other Zotero data will continue to sync to the server."

    So, I went to my library (standalone) and deleted / merged about many redundant articles (including pdf), emptied trash and ensured that it auto-synced in the online library.

    The aforementioned problem still remains !

    Then, I also uninstalled several journal styles (preferences -> cite -> '-') but it did not help the cause.

    The same problem remains for other journals as well:
    1. https://www.zotero.org/styles?q=journal of computer-aided
    2. https://www.zotero.org/styles?q=journal of molecular mode
    3. https://www.zotero.org/styles?q=journal of molecular bio


    Is there a way to monitor continuously the size after each insertion / deletion ? What minimum size is required to install new styles ?
  • adamsmith
    this has nothing to do with syncing, that's a coincidenence.
  • nemo8130
    edited December 17, 2017
    I didn't mean it has something to do with syncing but it seems that it has something to do with "quota". So, I had to ensure that the deleted / uninstalled items were synced in both the (online and standalone) versions. Anyway, I shall be much grateful to have some definite hints addressing the specific queries (for example the one copy-pasted below) so that the problem could be fixed soon. Also kindly follow the error report (ID: 1723360247).

    Is there a way to monitor continuously the size after each insertion / deletion ? What minimum size is required to install new styles ?
  • LiborA
    There is no qouta to install new style. Qouta is affected only by new items. Styles are not synced to the Zotero cloud.
  • nemo8130
    Ok, Can you kindly give me any other hints on how to fix this (maybe after going through the error report) ?
  • dstillman
    I have also tried to install the .csl file manually (zotero -> preferences -> '+' -> redirecting to the .csl file) which returns an even more general error:

    An unexpected error occurred while installing "/home/[…]/Downloads/bba-proteins-and-proteomics.csl"
    Can you provide a Debug ID (different from a Report ID) for this?
  • nemo8130
    Yes I also got the same error. From where to retrieve a debug id ?
  • bwiernik
    In Zotero, in the Help menu, choose Debug Logging -> Enable Logging. Then immediately try to install a style manually. After you get the error, click Help -> Debug Logging -> Submit Log. Then copy the Debug ID it shows and paste it here.
  • nemo8130
    edited December 17, 2017
    Here is the debug ID: D934329224
  • dstillman
    [JavaScript Error: "Unix error 13 during operation open on file /home/[…]/.mozilla/firefox/gdeemnqx.default/zotero/styles/algorithms.csl (Permission denied)" {file: "chrome://zotero/content/xpcom/style.js" line: 177}]
    It looks like your Zotero data directory is still located in your Firefox profile directory, and I'd guess that security software (AppArmor, SELinux, etc.) is preventing Zotero from being able to write to that directory. Zotero 5.0 attempts to migrate that to ~/Zotero automatically, and I believe it should've warned you if it wasn't able to.

    In any case, you should close Zotero and move /home/[…]/.mozilla/firefox/gdeemnqx.default/zotero to ~/Zotero (capitalized), and then make sure all folders and files in that directory are writable by your current user account (but again, it's probably security software).
  • nemo8130
    Thanks. Yes it did give me such warning and I did chmod 777 to /usr/bin/zotero

    Didn't help the cause. Let me try this and get back to you.
  • dstillman
    I did chmod 777 to /usr/bin/zotero
    That has nothing to do with the data files, and you should change that back to 755.
  • nemo8130
    In "/home/[…]/.mozilla/firefox/gdeemnqx.default/zotero" - should the 'dot' before mozila be there ? Is it a hidden folder ?
  • dstillman
    Yes.
  • dstillman
    edited December 17, 2017
    @nemo8130: You can just run this from the terminal with Zotero closed (assuming you don't have a ~/Zotero directory already):

    mv ~/.mozilla/firefox/gdeemnqx.default/zotero ~/Zotero
  • nemo8130
    Found the folder: /home/[...]/.mozilla/firefox/gdeemnqx.default/zotero/
  • nemo8130
    edited December 17, 2017
    should I then create (mkdir) ~/Zotero (Z in caps) ? I don't have it pre-existing.
  • dstillman
    I gave you the command to run.
  • nemo8130
    edited December 17, 2017
    moved. Now I suppose I should do sudo chmod -R 777 ~/Zotero
  • dstillman
    edited December 17, 2017
    No. That's absolutely not something you should be running indiscriminately (or ever, really). I would strongly discourage you from running commands you don't understand.

    Just try running Zotero. If the problem still exists, you'd need to fix permissions, but what you're doing is absolutely not the way to do it.
  • nemo8130
    edited December 17, 2017
    Actually it worked that way :)

    sudo chmod -R 777 ~/Zotero

    and then after running zotero I could install manually the style.

    And now I could install all other desired styles from the online repository as well.

    Though I understand it might have been possible without changing the permissions as well.
    Actually I had already run the chmod command before your last message arrived.

    Many many thanks.
  • dstillman
    It's an incorrect and dangerous command to run — that's the point.

    Generally speaking, folders should be 755, files should be 644, and they should be owned by the right user. Using 777 is pretty much never a proper fix.
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