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Old 12-24-2023, 01:55 PM   #1
Josieb1
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Database Malformed error

I'm suddenly seeing the Database Malformed error on my Kobo Forma when trying to add new books via Calibre. I don't have this problem with my Libra or Clara. Does anyone know if a factory reset would fix the problem?

I can still add books to my Forma but it doesn't add them to collections, I can work around that manually going forwards but I wouldn't want to do a factory reset and have the same problem for over 3000 books.

This is the calibre error message

CorruptError: database disk image is malformed

Traceback (most recent call last):
File "calibre\gui2\device.py", line 104, in run
File "calibre\gui2\device.py", line 558, in _books
File "calibre\devices\kobo\driver.py", line 2028, in books
File "C:\t\t\apsw-42s16m2x\src\cursor.c", line 240, in resetcursor
apsw.CorruptError: CorruptError: database disk image is malformed
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Old 12-24-2023, 02:48 PM   #2
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Yes a factory reset will solve the issue by removing the database from the device. Do you have backups created by Calibre / Kobo utilities? If so you could restore the last good backup (if I remember correctly backups of corrected databases have a different name from non corrupted ones).

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Old 12-24-2023, 03:34 PM   #3
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Originally Posted by PeterT View Post
Yes a factory reset will solve the issue by removing the database from the device. Do you have backups created by Calibre / Kobo utilities? If so you could restore the last good backup (if I remember correctly backups of corrected databases have a different name from non corrupted ones).

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Yes, corrupted databases backup look like KoboReader-KoboClaraHD-N249840008209-20201107-172337_CORRUPT.
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Old 12-24-2023, 06:05 PM   #4
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Originally Posted by PeterT View Post
Yes a factory reset will solve the issue by removing the database from the device. Do you have backups created by Calibre / Kobo utilities? If so you could restore the last good backup (if I remember correctly backups of corrected databases have a different name from non corrupted ones).


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Thank you. No I doubt I have backups, I’ve never set it up but I can just reload from Calibre, it’s not a problem. Thanks again.
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Old 12-24-2023, 06:05 PM   #5
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Yes, corrupted databases backup look like KoboReader-KoboClaraHD-N249840008209-20201107-172337_CORRUPT.
Thank you.
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Old 12-25-2023, 01:47 AM   #6
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One item that may help until Kobo releases their next firmware update is to reboot your Forma before connecting to your computer.
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Old 12-25-2023, 05:19 AM   #7
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One item that may help until Kobo releases their next firmware update is to reboot your Forma before connecting to your computer.
Thank you. I’ll try that today. Merry Christmas x
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Old 12-25-2023, 05:49 AM   #8
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One item that may help until Kobo releases their next firmware update is to reboot your Forma before connecting to your computer.
Again, that does not have to be done. Make sure an ePub was least displayed and then go to the home page before plugging in.
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Old 12-25-2023, 10:37 AM   #9
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Again, that does not have to be done. Make sure an ePub was least displayed and then go to the home page before plugging in.
Sorry, but rebooting IS required for some people. I always go to the home page before connecting my Kobo and if I don't reboot, I get the "database malformed" issue more than half the time. Not sure what triggered the problem to begin with, but once it starts, it continues. (Plus, Kobo has acknowledged that there is a problem and that it will be fixed in the next firmware release.)

Last edited by icallaci; 12-25-2023 at 10:57 AM.
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Old 12-25-2023, 11:04 AM   #10
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It's baffling. No problem here. Just checked database again. Regularly updating two Sage and occasionally 3 other Sage, Libra, Elipsa, Libra2 and Nia.
I make sure it's at "My Books"
I eject from Calibre and wait not just for bargraph importing, but also the brief screen flash after "My Books" reappears, before disconnecting or reconnecting.

SideloadedMode=true (so "My Books" is the "home page")

Linux Mint + Mate desktop. Various versions Calibre up to just before 7.2
Current FW.

But that doesn't seem to work for everyone. It's very strange. No doubt that's why it's a bug, it's maybe not repeatable for the developers.
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Old 12-25-2023, 01:37 PM   #11
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Using SideloadedMode may avoid the issue. For me, the consistent item when I got the database errors was the presence of the -shm and -wal files for the KoboReader.sqlite and BookReader.sqlite databases. Those files tells me the database had not been closed before the USB connection completed. I had wondered if my Sage is trying to sync to Kobo and that is taking too long.
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Old 12-25-2023, 05:01 PM   #12
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Using SideloadedMode may avoid the issue. For me, the consistent item when I got the database errors was the presence of the -shm and -wal files for the KoboReader.sqlite and BookReader.sqlite databases. Those files tells me the database had not been closed before the USB connection completed. I had wondered if my Sage is trying to sync to Kobo and that is taking too long.
Even when I didn't have SideloadedMode=true I'd never have WiFi on nor have any sort of auto sync in settings.
In theory when you tap on "Connect", the developers should have arranged that everything is closed, sync ceased, Wifi suspended etc before enabling the USB connection. So what ever way you look at it the problem is "in Kobo", not "how you are holding it". MS had to recently roll back a W10 WiFi update as they han't yet figured how to fix what they broke. Really compared to most consumer items with SW the Kobo track record isn't that bad. I remember MS DOS 4.x and MSDOS 5.x, People had to stay with DOS 3.3 for years till DOS 6.22. And the sheer volume of PCs I replaced Windows ME with either Win98SE or NT 4.0.
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Old 12-25-2023, 07:55 PM   #13
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Sorry, but rebooting IS required for some people. I always go to the home page before connecting my Kobo and if I don't reboot, I get the "database malformed" issue more than half the time. Not sure what triggered the problem to begin with, but once it starts, it continues. (Plus, Kobo has acknowledged that there is a problem and that it will be fixed in the next firmware release.)
Do you go to the home screen always after displaying ePub? Have you been going to the home page after displaying KePub and getting the database corrupted?

My thought is that with KePub, once you are at the home screen, something may be still open. But with ePub, everything is closed. It works for me going to the home screen after displaying an ePub. I have no tried going to the home screen after a KePub and then connecting to the computer.

Last edited by JSWolf; 12-25-2023 at 08:00 PM.
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Old 12-25-2023, 08:02 PM   #14
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Using SideloadedMode may avoid the issue. For me, the consistent item when I got the database errors was the presence of the -shm and -wal files for the KoboReader.sqlite and BookReader.sqlite databases. Those files tells me the database had not been closed before the USB connection completed. I had wondered if my Sage is trying to sync to Kobo and that is taking too long.
Have you ever seen these files after viewing ePub or only after KePub?
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Old 12-25-2023, 08:22 PM   #15
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I thought a factory reset wasn't necessary, just logging out and back in will solve the problem?
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