zotero.sqlite was damaged after I updated ver 6.0.26 on 2023/4/21

Kazuyoshi Tanaka
As I really appreciate the Zotero product, I have used it for 3 years.

I would be very glad if you could give me a hint to solve the problems below.
If required, I can upload my zotero.sqlite file which is damaged.

- problem occurred

I updated ver 6.0.26 last Friday, there came the message as bellow:

> Database update error
> Error: Error(s) encountered during statement execution:database disk image >malformed[QUERY: PRAGMAforeign_key_check[PARAMS:][ERROR:database diskimage >is malformed] >Zotero.DBConnection.prototype.queryAsync@chrome://zoreteo/contet/xpcom/db.js:680:13
>From previous event:
>ZoteroService@file://C:/Program%20Files%20(x86)/Zotero/components/zotero^service.js:347:7@chome://zotero/content/include/js:4:14

- repair trial 1, sqlite repair system
I tried zotero.sqlite auto repair system, but my 335M sqlite file is too big to be repaired.

- repair trial 2, use exported file

Unfortunately, I don’t have right backup files and I have only exported files a week ago.
I tried to import it, but I got Error report ID:759152012.

- Environment: Windows 10 and I customized Zotero to set up at D drive.
  • dstillman
    database or disk is full
    The upgrade wouldn't have damaged the database. The disk you're using appears to be out of space.

    You'll need to free up space on the disk or move the data directory back to the default location, and you'll likely need to swap in one of the automatic backups Zotero makes in the data directory.
  • Kazuyoshi Tanaka
    Thank you very much for quick response.
    I understood that the trouble came from disk space problem.

    I have read automatic backups page, but I was not able to find right solution in it by myself.

    I have only damaged zotero.sqlite files which size is 335M.
    All .bak files are seemingly damaged.
    I have an exported files a week ago.

    Is there any way to fix current situation?

    Thank you very much in advance.
  • dstillman
    edited April 24, 2023
    How are you determining that all the files are damaged?

    What are the names, dates, and sizes of all the files beginning with "zotero" in the root of your data directory?
  • Kazuyoshi Tanaka
    Thank you for your response.

    There are some reasons I have determined sqlite files are damaged:

    - When I started Zotero, there came error, "Zotero database's zotero.sqlite is damaged".
    - I replaced zotero.sqlite.bak to zotero.sqlite, but I got same message. It seems to be an identical file, which size is 335612KB as of 2023/4/21.
    - There are zotero.sqilte.damaged and zotero.sqlite-1.damaged. They sounds to be damaged. They are 335612KB as of 2023/4/21.
    - Recent files are situation above. One 1 year old zotero.sqilite.111.bak might be alive. The size is 247504KB as of 2022/3/23.
  • dstillman
    How big is the database if you zip it?

  • Kazuyoshi Tanaka
    Zipped file size is 134107KB, original 335612KB.

    If you tell me your mail address, I could give you my google drive access right.

    Thank you in advance.
  • dstillman
    You can upload that to the repair tool.
  • Kazuyoshi Tanaka
    All recovered! Thank you very much indeed.

    I have a related question. My sqlite file could be too large. It shortly may exceed 150M after zipped. Is there any way to solve this situation?
  • dstillman
    Don’t store it in an unreliable location where it might get corrupted, make regular backups of your entire data directory as you would any other important data, and/or use Zotero syncing to make sure you always have a copy of your library online.
  • Kazuyoshi Tanaka
    Thank you very much for your comment.

    I have a difference type of question, so I will set up new discussion soon.

    I really appreciate your support this time, so I will recommend Zotero to my colleague more.

  • Kazuyoshi Tanaka
    Dear Zotero customer support,

    I have been using Zotero well after the previous issue.
    I faced zotero.sqlite index error which said the indices were damaged.
    Both zotero.sqlite.1.bak and zotero.sqlite.bak are damaged,too.
    I have saved previous zotero.sqlite files 1 month ago.

    When the last issue occurred a year ago, zipped damaged zotero.sqlite file was 130M. It is 182M now.
    Is there any way to fix the damaged zotero.sqlite?

    Thank you in advance.

    Kaz
  • dstillman
    Your database should not be getting corrupted in regular usage. If it is, it suggests there's a problem with where you're storing your database, as I say above.

    Best we can suggest is to follow the manual repair instructions. This is much less straightforward on Windows, so if those steps aren't clear to you, you should ask an IT person who's comfortable with command-line tools to help you.

    Beyond that, it's just what I say above:
    Don’t store it in an unreliable location where it might get corrupted, make regular backups of your entire data directory as you would any other important data, and/or use Zotero syncing to make sure you always have a copy of your library online.
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