[Kobo] database disk image is malformed

franklekens · 06-29-2021, 12:57 PM

I have two Kobo devices. On one of them I have no problem, the other suddenly can't communicate with Calibre (or vice versa, rather).

The error message is this:

CorruptError: database disk image is malformed

Traceback (most recent call last):
File "calibre\gui2\device.py", line 89, in run
File "calibre\gui2\device.py", line 515, in _books
File "calibre\devices\kobo\driver.py", line 1878, in books
File "calibre\devices\kobo\driver.py", line 2970, in get_bookshelflist
apsw.CorruptError: CorruptError: database disk image is malformed

Is there a remedy for this? The device functions fine, except that the last batch of books I had sideloaded have suddenly been wiped from it. And I now get this message.

(Windows 10. Calibre 5.22.1 (64-bit)

kovidgoyal · 06-29-2021, 12:58 PM

https://manual.calibre-ebook.com/faq...-touch-glo-etc

franklekens · 06-29-2021, 01:14 PM

Well, I hadn't seen that before. That basically amounts to: don't use Kobo devices.

Having just spent hours getting a 1000+ library on the device, I don't relish the thought of spending hours doing that again. Because I assume even logging out and logging back in and letting it rebuild the database means I've lost all of the shelving for the books that are present.

Back to the shop with this stupid Elipsa. The Forma never gave me any such problems.

PeterT · 06-29-2021, 01:59 PM

Sorry but I think Kovid is exaggerating there.

Yes the Kobo relies on a database on the device to keep track of books / collections (shelves) / reading status etc. Yes; this database can become damaged but this is rare, and quite often can be linked to either older mods (for instance at one time 3rd party add-ons installed to the partition where the books / database are located, preventing an unmount of the partition when a USB connection was made), or to crashes of the Kobo.

I've used Kobos for years (since the original Bluetooth version) and have only had a couple of db corruptions (and I've probably seen more f/w builds than most people).

The Kobo utilities plugin has the ability to perform backups of the db, either daily or on every connection, and also can validate and compress the db.

Sent from my Pixel 4a using Tapatalk

JSWolf · 06-29-2021, 04:35 PM

I've been using my H2O for 6 years 7 months and I've never had a corrupt database. I do use Kobo Utilities to backup the database every time I connect to Calibre. While what Kovid pointed out may have been true back when it was written, it's not true now. If it was, many more people would be posting about it.

Most of the time a corrupt database is cause by an incorrect eject.

ownedbycats · 06-29-2021, 05:54 PM

Quote:

Originally Posted by JSWolf

Most of the time a corrupt database is cause by an incorrect eject.

I have noted that on my system Adobe Digital Editions interferes with ejection if it's running. The OS says the device has been safely ejected but the next time I connect it to Calibre there's an angry error. Re-connecting a second time always works though.

Skydog · 06-29-2021, 08:59 PM

Well, add me to @franklekens. The identical problem just happened to me too. I've had five Kobo readers and never have I had this occur. Since it's new, I was in the process of sideloading additional books and did not yet have a backup. I hope this isn't the beginning of a buggy new device!

I hope the logout/login is the answer.

BTW, 1) I always use Kobo's supplied cables, 2) I always confirm there is no activity in progress before ejecting, and 3) never have any other apps open at the time (Win 10).

Code:

CorruptError: database disk image is malformed

Traceback (most recent call last):
  File "calibre\gui2\device.py", line 89, in run
  File "calibre\gui2\device.py", line 515, in _books
  File "calibre\devices\kobo\driver.py", line 1974, in books
apsw.CorruptError: CorruptError: database disk image is malformed

Isurus · 07-22-2021, 10:23 PM

I am seeing the same recurring problem on the Ellipsa. I have tried hard reset, log out/in, and adding books incrementally (instead of all at once). I am still seeing the problem on Calibre 5.23 and Ellipsa firmware 4.28.17925. Most likely a problem with Ellipsa firmware. I have no issues with my Forma.

calibre, version 5.23.0
ERROR: Error: Error communicating with device

CorruptError: database disk image is malformed

Traceback (most recent call last):
File "calibre\gui2\device.py", line 89, in run
File "calibre\gui2\device.py", line 515, in _books
File "calibre\devices\kobo\driver.py", line 1974, in books
apsw.CorruptError: CorruptError: database disk image is malformed

DNSB · 07-22-2021, 11:27 PM

Quote:

Originally Posted by Skydog

Well, add me to @franklekens. The identical problem just happened to me too. I've had five Kobo readers and never have I had this occur. Since it's new, I was in the process of sideloading additional books and did not yet have a backup. I hope this isn't the beginning of a buggy new device!

It would appear that all the posts about database corruption in the last while have been connected to using a Kobo Elipsa.

For what it's worth, my current experience with an Elipsa is a customer who is looking at them as replacements for their aging Sony DPT eNote devices. After sideloading the corporate content and "safely" ejecting the Elipsa, they have been shutting the connected computer down before unplugging the USB cable. Not exactly the speediest process but so far they have not seen any database corruption.

davidfor · 07-23-2021, 03:14 AM

Quote:

Originally Posted by Isurus

I am seeing the same recurring problem on the Ellipsa. I have tried hard reset, log out/in, and adding books incrementally (instead of all at once). I am still seeing the problem on Calibre 5.23 and Ellipsa firmware 4.28.17925. Most likely a problem with Ellipsa firmware. I have no issues with my Forma.

calibre, version 5.23.0
ERROR: Error: Error communicating with device

CorruptError: database disk image is malformed

Traceback (most recent call last):
File "calibre\gui2\device.py", line 89, in run
File "calibre\gui2\device.py", line 515, in _books
File "calibre\devices\kobo\driver.py", line 1974, in books
apsw.CorruptError: CorruptError: database disk image is malformed

Unfortunately, I can't help. As @DNSB said, it seems to be an issue with the Elipsa, or the firmware on it. There is discussion on it in the Kobo forum. I have posted some suggestions that might help to track down when it happens, but, at the moment, we don't know. But, I do not believe it is a problem caused by calibre. I believe that something else is causing the problem, and calibre just happens to be the only thing that explicitly shows an error about it.

dem1980fr · 08-14-2021, 08:30 AM

Hello,

i have the same issue with my Kobo Libra HD (4.26.16704) :

Quote:

calibre, version 5.25.0
ERREUR : Erreur: Erreur pendant la communication avec le périphérique

CorruptError: database disk image is malformed

Traceback (most recent call last):
File "calibre\gui2\device.py", line 89, in run
File "calibre\gui2\device.py", line 515, in _books
File "calibre\devices\kobo\driver.py", line 1974, in books
apsw.CorruptError: CorruptError: database disk image is malformed

There are some news about this problem ?
I'm uisng KoboUtilities pour read/update the reading status of books on my Kobo.
Do you also using this function ?

dem1980fr · 08-14-2021, 03:00 PM

I have hard reset my Kobo (no more kmon, no more nickelmenu, no more ebook).
I have then copy my ebooks from calibre to the Kobo and everything is working.
I ask the KoboUtilities plugin to synchronise reading status and the i have the error.
I think when this plugins try to read or write the reading status of ebbok, something is wrong.

davidfor · 08-14-2021, 10:57 PM

Quote:

Originally Posted by dem1980fr

Hello,

i have the same issue with my Kobo Libra HD (4.26.16704) :

There are some news about this problem ?
I'm uisng KoboUtilities pour read/update the reading status of books on my Kobo.
Do you also using this function ?

Quote:

Originally Posted by dem1980fr

I have hard reset my Kobo (no more kmon, no more nickelmenu, no more ebook).
I have then copy my ebooks from calibre to the Kobo and everything is working.
I ask the KoboUtilities plugin to synchronise reading status and the i have the error.
I think when this plugins try to read or write the reading status of ebbok, something is wrong.

If you are still seeing the above error, then it is has nothing to do with Kobo Utilities plugin. That error is happening while the driver is trying to get the list of books from the device. And it is probably happening when the database on the device is first accessed. If the Kobo Utilities plugin is causing a problem, it happened when you last connected the device. And it doesn't write to the database except when you manually start one of the functions that do updates.

The reasons for the database being corrupted are unknown. It can happen if the device is not ejected properly. I think it would also happen if two applications tried to access the database at the same time. So running calibre and the Kobo desktop application at the same time is not recommended. Otherwise, it is something happening when using the device. Something might be crashing and corrupting the database. But, I don't know what. In the Kobo forum I recently made some suggestions for trying to find when it happens, but, there have been no results from that yet.

And for the record, it would be a rare day where I didn't plug one or more of my Kobo ereaders in. And I fetch the reading status from them when I do. I rarely see a corrupt database. And mostly I know because I messed up and accidentally unplugged the device. I would love to be able to say what it is that is causing this, but, I just don't know.

dem1980fr · 08-15-2021, 04:55 AM

Thank you for your answer.
I have only one Kobo and i don't use the Kobo Desktop, only Calibre.
I always disconnect the Kobo from the Calibre device option or from the Eject option from Win10.
I was able to reproduce it because i had the problem on my previous setup and i thought that hard reset the device will help.
So i start from a device that was hard reset (no more ebooks on it, no more custom program, the device was "formated") and i then have the same problem on the "new" device.

davidfor · 08-15-2021, 05:14 AM

Quote:

Originally Posted by dem1980fr

Thank you for your answer.
I have only one Kobo and i don't use the Kobo Desktop, only Calibre.
I always disconnect the Kobo from the Calibre device option or from the Eject option from Win10.
I was able to reproduce it because i had the problem on my previous setup and i thought that hard reset the device will help.
So i start from a device that was hard reset (no more ebooks on it, no more custom program, the device was "formated") and i then have the same problem on the "new" device.

As stated above, I have no real idea what causes the problem. I know certain ways to cause it a I mentioned. I also know, from heavy use of calibre and the Kobo Utilities plugin, that that is not the cause. If it is happening after a factory reset, then it could be a hardware fault. For the device with an internal SD card, I would suggest changing the card. But, the Libra H2O has fixed internal memory, so that cannot be done.

I mentioned discussion in the Kobo forum about working out the cause. This is inhttps://www.mobileread.com/forums/showthread.php?t=340260. There are suggestions that in that for trying to determine when the corruption happens.

06-29-2021, 12:57 PM	#1
franklekens Addict Posts: 392 Karma: 3421956 Join Date: Sep 2009 Device: Kobo Forma, Sage, Elipsa, Onyx Note2, Pocketbook 360, Kindle Keyboard	[Kobo] database disk image is malformed I have two Kobo devices. On one of them I have no problem, the other suddenly can't communicate with Calibre (or vice versa, rather). The error message is this: CorruptError: database disk image is malformed Traceback (most recent call last): File "calibre\gui2\device.py", line 89, in run File "calibre\gui2\device.py", line 515, in _books File "calibre\devices\kobo\driver.py", line 1878, in books File "calibre\devices\kobo\driver.py", line 2970, in get_bookshelflist apsw.CorruptError: CorruptError: database disk image is malformed Is there a remedy for this? The device functions fine, except that the last batch of books I had sideloaded have suddenly been wiped from it. And I now get this message. (Windows 10. Calibre 5.22.1 (64-bit)

06-29-2021, 08:59 PM	#7
Skydog Wizard Posts: 2,243 Karma: 7400001 Join Date: Mar 2009 Location: Circling Earth @ Mach .83 Device: Elipsa 2E, Sage, Forma, Libra 2, Clara 2E, Kindle Oasis3, Voyage	ARRRRRGH!!! Well, add me to @franklekens. The *identical* problem just happened to me too. I've had five Kobo readers and never have I had this occur. Since it's new, I was in the process of sideloading additional books and did not yet have a backup. I hope this isn't the beginning of a buggy new device! I hope the logout/login is the answer. BTW, 1) I always use Kobo's supplied cables, 2) I always confirm there is no activity in progress before ejecting, and 3) never have any other apps open at the time (Win 10). Code: CorruptError: database disk image is malformed Traceback (most recent call last): File "calibre\gui2\device.py", line 89, in run File "calibre\gui2\device.py", line 515, in _books File "calibre\devices\kobo\driver.py", line 1974, in books apsw.CorruptError: CorruptError: database disk image is malformed Last edited by Skydog; 06-29-2021 at 09:27 PM. Reason: Added info.

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06-29-2021, 12:58 PM	#2
kovidgoyal creator of calibre Posts: 43,842 Karma: 22666666 Join Date: Oct 2006 Location: Mumbai, India Device: Various	https://manual.calibre-ebook.com/faq...-touch-glo-etc

06-29-2021, 01:14 PM	#3
franklekens Addict Posts: 392 Karma: 3421956 Join Date: Sep 2009 Device: Kobo Forma, Sage, Elipsa, Onyx Note2, Pocketbook 360, Kindle Keyboard	Well, I hadn't seen that before. That basically amounts to: don't use Kobo devices. Having just spent hours getting a 1000+ library on the device, I don't relish the thought of spending hours doing that again. Because I assume even logging out and logging back in and letting it rebuild the database means I've lost all of the shelving for the books that are present. Back to the shop with this stupid Elipsa. The Forma never gave me any such problems.

06-29-2021, 01:59 PM	#4
PeterT Grand Sorcerer Posts: 12,155 Karma: 73448616 Join Date: Nov 2007 Location: Toronto Device: Nexus 7, Clara, Touch, Tolino EPOS	Sorry but I think Kovid is exaggerating there. Yes the Kobo relies on a database on the device to keep track of books / collections (shelves) / reading status etc. Yes; this database can become damaged but this is rare, and quite often can be linked to either older mods (for instance at one time 3rd party add-ons installed to the partition where the books / database are located, preventing an unmount of the partition when a USB connection was made), or to crashes of the Kobo. I've used Kobos for years (since the original Bluetooth version) and have only had a couple of db corruptions (and I've probably seen more f/w builds than most people). The Kobo utilities plugin has the ability to perform backups of the db, either daily or on every connection, and also can validate and compress the db. Sent from my Pixel 4a using Tapatalk

06-29-2021, 04:35 PM	#5
JSWolf Resident Curmudgeon Posts: 73,887 Karma: 128597114 Join Date: Nov 2006 Location: Roslindale, Massachusetts Device: Kobo Libra 2, Kobo Aura H2O, PRS-650, PRS-T1, nook STR, PW3	I've been using my H2O for 6 years 7 months and I've never had a corrupt database. I do use Kobo Utilities to backup the database every time I connect to Calibre. While what Kovid pointed out may have been true back when it was written, it's not true now. If it was, many more people would be posting about it. Most of the time a corrupt database is cause by an incorrect eject.

07-22-2021, 10:23 PM	#8
Isurus Member Posts: 14 Karma: 138 Join Date: Nov 2010 Device: Quaderno A4 Gen2; Sage; Elipsa	I am seeing the same recurring problem on the Ellipsa. I have tried hard reset, log out/in, and adding books incrementally (instead of all at once). I am still seeing the problem on Calibre 5.23 and Ellipsa firmware 4.28.17925. Most likely a problem with Ellipsa firmware. I have no issues with my Forma. calibre, version 5.23.0 ERROR: Error: Error communicating with device CorruptError: database disk image is malformed Traceback (most recent call last): File "calibre\gui2\device.py", line 89, in run File "calibre\gui2\device.py", line 515, in _books File "calibre\devices\kobo\driver.py", line 1974, in books apsw.CorruptError: CorruptError: database disk image is malformed

08-14-2021, 03:00 PM	#12
dem1980fr Enthusiast Posts: 29 Karma: 10 Join Date: Aug 2020 Device: Kobo Libra	I have hard reset my Kobo (no more kmon, no more nickelmenu, no more ebook). I have then copy my ebooks from calibre to the Kobo and everything is working. I ask the KoboUtilities plugin to synchronise reading status and the i have the error. I think when this plugins try to read or write the reading status of ebbok, something is wrong.

08-15-2021, 04:55 AM	#14
dem1980fr Enthusiast Posts: 29 Karma: 10 Join Date: Aug 2020 Device: Kobo Libra	Thank you for your answer. I have only one Kobo and i don't use the Kobo Desktop, only Calibre. I always disconnect the Kobo from the Calibre device option or from the Eject option from Win10. I was able to reproduce it because i had the problem on my previous setup and i thought that hard reset the device will help. So i start from a device that was hard reset (no more ebooks on it, no more custom program, the device was "formated") and i then have the same problem on the "new" device.

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