Clara HD Database disk image is malformed?

JDesat · 01-25-2022, 11:09 PM

I've been trying to find a way to fix this issue without having to reset the Kobo entirely. I have no idea what caused the database error; I have only ever used Calibre to load books and haven't had any issues with it before (I use the Kobo program only for updating the device).

When I run an integrity check I get this:

Spoiler:

I've tried deleting and recreating the content_bookid_index like I saw suggested on an older thread here, but that doesn't seem to do anything.

I've noticed that this only really seems to be affecting one book at a time (ones that I've added recently - I've got thousands of books and fanfics on the Kobo so I don't know if it's affecting things i Haven't opened in a while), and when I try to open the affected book on the Kobo I get told that it has Adobe DRM on it and I can't open it on the Kobo.

Can anyone think of anything I can do to fix this without a factory reset?
Thanks!

P.S. I really know pretty much nothing about SQL files/editing, I had SQLite Studio and I've downloaded SQL Tools but don't really know how to use it.

DNSB · 01-25-2022, 11:40 PM

Have you tried vacuuming the file? That and re-indexing are about the only non-destructive suggestions I can come up with.

davidfor · 01-26-2022, 01:04 AM

@JDesat: The database gets corrupted because something went wrong. It could be a bug in the software, it could be that you didn't eject the device safely one time, it could have been a crash.

The only case I have been able to prove a reason for a corrupt database has been when reading CBZ or CBR files and then connecting to the PC. That was a bug on the device not freeing things properly. This was fixed recently in either the 4.28 or 4.30 firmware.

Looking at the errors, the only way that might fix it is the VACUUM, or compress, of the database. That basically dumps the database out and reloads it. It should clean up everything. But, there is a chance that some data will be lost. Most of those errors should be harmless and a sign that some cleanup wasn't done. The first two are

Rebuilding an index won't help. When that has been suggested, it was because the check showed that there was an index problem. And it named the index that needed to be rebuilt.

JDesat · 01-26-2022, 01:39 AM

Unfortunately, when I try to VACUUM the database (in SQLite Studio or with the Kobo Utilities plugin in Calibre) that's when I get the 'disk image is malformed' error and it doesn't work.

Any other ideas, maybe a way to force the VACUUM, or am I SOL?

icallaci · 01-26-2022, 08:57 AM

Quote:

Originally Posted by JDesat

Unfortunately, when I try to VACUUM the database (in SQLite Studio or with the Kobo Utilities plugin in Calibre) that's when I get the 'disk image is malformed' error and it doesn't work.

Any other ideas, maybe a way to force the VACUUM, or am I SOL?

Is vacuuming the same thing as "compressing the database"? I don't see an option to "vaccum" and I am having the same problem.

Edit: Oops, I see davidfor's suggestion above is to "VACUUM, or compress" the database, so I assume they are the same thing. Never mind.

davidfor · 01-26-2022, 06:20 PM

Quote:

Originally Posted by icallaci

Is vacuuming the same thing as "compressing the database"? I don't see an option to "vaccum" and I am having the same problem.

Edit: Oops, I see davidfor's suggestion above is to "VACUUM, or compress" the database, so I assume they are the same thing. Never mind.

Different databases use different terms. I am used to "compress" so that is the term I used. I can see why they called it vaccum, but, it just doesn't feel right to me.

icallaci · 01-26-2022, 08:21 PM

Quote:

Originally Posted by davidfor

Different databases use different terms. I am used to "compress" so that is the term I used. I can see why they called it vaccum, but, it just doesn't feel right to me.

Thanks for the verification.

JDesat · 01-26-2022, 09:55 PM

I think I read somewhere that logging out of my Kobo account (on the Kobo itself) and logging back in will rebuild the database... would that work? And if so, I seem to remember doing that once and nothing was in my collections or had covers anymore, is there a way to fix that?

davidfor · 01-26-2022, 10:03 PM

Quote:

Originally Posted by JDesat

I think I read somewhere that logging out of my Kobo account (on the Kobo itself) and logging back in will rebuild the database... would that work? And if so, I seem to remember doing that once and nothing was in my collections or had covers anymore, is there a way to fix that?

That would work. Afterwards, the device will import any sideloaded books. You will lose the reading status, annotations and collections for the sideloaded books. The actual collections will be synced from the Kobo server during the setup, but, they do not sync anything about the sideloaded books.

The covers should come from the books and should be regenerated by the device as they are needed. If you use calibre and use the option to send the covers to the device, the cover might not match or exist for some formats.

JDesat · 01-26-2022, 11:24 PM

Hmm... I have the Kobo Utilities plugin, so I could get my reading positions back on those, and the covers aren't a huge issue, really... but I sideload absolutely everything through Calibre, so losing the collections would be a pain... and I'd be annoyed at the fact that everything was messed up in my book list(s) because I always have it set for me to see recent books at the top... I'd say something like 80% of the 8,000 or so 'books' on my Kobo are fanfiction, and I tend to read things I've added recently more often than I do older stuff, so having to try to remember a name of a fic or author and trying to hunt it down would be an issue.

I suppose if this is my only option I'll have to do it, but for the moment, if no one can think of anything I can do to fix the database, I think I might just tough it out. So far it's only been 2 books that have caused an issue, both fanfic. One downloaded with FanFicFare, and another made into a docx file and then converted to epub in Calibre by me. Calibre doesn't let me delete them, but I can delete them on the Kobo itself without a problem. And, oddly, I've been able to get the docx one to work after several delete and resend attempts... that's when the other story started glitching.

Anyway, thanks everyone so far for your suggestions, even if nothing has worked yet.

davidfor · 01-26-2022, 11:48 PM

If you are using calibre to sideload the books, are you using it for collection management? If so, that should happen automatically as you get the books on the device. If you are not using it for collection management, there is a way to fetch the collections from the device to a column in calibre. Which needs calibre to still be able to connect to the device.

Reloading the device is also something I don't like because of the "Recent" sort. It is based on when the book was added and then the title within the batch. But, the Kobo Utilities plugin can set one of the date used by this (the other is the last read timestamp). I generally set it to the "Date" column in calibre as that is when the book was first added to the library. And will be reasonably close to when I first put it on the device. It isn't quite so good for books downloaded with FFF, as that will update the date when you update the book. But, the plugin can use any date column in the library.

You can keep going as you are. But, I would expect this to get worse, not better. If it is working, at the least you can do some preparation and maybe choose when you do it, rather than get forced into it. And if it is more serious that it currently appears, it will be seen if you restart the device. That will mean the database is reread, and if there were problems writing it, then you may end up with old data.

JSWolf · 01-27-2022, 04:36 AM

You can setup the Kobo Utilities plugin with Calibre to backup your Kobo database to the computer every time you connect your Kobo to your library. That way you'll have a fairly updated database backup. That way you can restore it if you have another database corruption.

Joliet Jake · 01-29-2022, 10:25 PM

I had to deal with this issue recently (for only the second time in three years, that I recall), probably due to a loose cable. I haven't set Kobo Utilities to backup the database because I don't know what happens if the cable gets loose during the backup process.

davidfor · 01-30-2022, 05:07 AM

Quote:

Originally Posted by Joliet Jake

I had to deal with this issue recently (for only the second time in three years, that I recall), probably due to a loose cable. I haven't set Kobo Utilities to backup the database because I don't know what happens if the cable gets loose during the backup process.

The backup would fail and the backup would be no good. But, it is a simple file copy, so the database on the device should not be affected.

aymeric106 · 01-30-2022, 06:12 PM

Strange I have the same issue.
Never happened before.

Just after upgrading to the latest firmware and uploading a new book with calibre.

Tried with various SQLLite editor without success.
I reseted my Kobo, but the error came back eventually, after a few transfer.

Will try with another USB cable, but file copy had no issue.

Aymeric

01-25-2022, 11:09 PM	#1
JDesat Connoisseur Posts: 90 Karma: 32768 Join Date: Dec 2012 Device: Kobo Glo HD, Kobo Clara HD	Database disk image is malformed? I've been trying to find a way to fix this issue without having to reset the Kobo entirely. I have no idea what caused the database error; I have only ever used Calibre to load books and haven't had any issues with it before (I use the Kobo program only for updating the device). When I run an integrity check I get this: Spoiler: * in database main * On tree page 379894 cell 0: Rowid 1353997 out of order On tree page 378735 cell 54: 2nd reference to page 358273 Page 300 is never used Page 846 is never used Page 953 is never used Page 954 is never used Page 955 is never used Page 956 is never used Page 957 is never used Page 958 is never used Page 959 is never used Page 960 is never used Page 3548 is never used Page 4112 is never used Page 4751 is never used Page 4885 is never used Page 4886 is never used Page 4887 is never used Page 4888 is never used Page 4889 is never used Page 4890 is never used Page 4891 is never used Page 4892 is never used Page 4893 is never used Page 4894 is never used Page 4895 is never used Page 4896 is never used Page 4897 is never used Page 4898 is never used Page 4899 is never used Page 4900 is never used Page 4901 is never used Page 4902 is never used Page 4903 is never used Page 5812 is never used Page 5813 is never used Page 6854 is never used Page 6857 is never used Page 6859 is never used Page 6863 is never used Page 6867 is never used Page 6870 is never used Page 6871 is never used Page 6874 is never used Page 6877 is never used Page 6880 is never used Page 6883 is never used Page 6887 is never used Page 6895 is never used Page 6896 is never used Page 6897 is never used Page 6919 is never used Page 6929 is never used Page 7766 is never used Page 7770 is never used Page 7771 is never used Page 7789 is never used Page 8745 is never used Page 8746 is never used Page 9321 is never used Page 9329 is never used Page 9332 is never used Page 9507 is never used Page 10578 is never used Page 10599 is never used Page 10679 is never used Page 10683 is never used Page 10687 is never used Page 10694 is never used Page 10716 is never used Page 10731 is never used Page 10898 is never used Page 11463 is never used Page 11474 is never used Page 11475 is never used Page 11477 is never used Page 11802 is never used Page 11803 is never used Page 11805 is never used Page 11806 is never used Page 11807 is never used Page 11809 is never used Page 11810 is never used Page 11812 is never used Page 11813 is never used Page 11814 is never used Page 11817 is never used Page 11820 is never used Page 11821 is never used Page 11825 is never used Page 11826 is never used Page 11827 is never used Page 11828 is never used Page 11835 is never used Page 11836 is never used Page 11841 is never used Page 11845 is never used Page 14348 is never used Page 14384 is never used Page 14387 is never used I've tried deleting and recreating the content_bookid_index like I saw suggested on an older thread here, but that doesn't seem to do anything. I've noticed that this only really seems to be affecting one book at a time (ones that I've added recently - I've got thousands of books and fanfics on the Kobo so I don't know if it's affecting things i Haven't opened in a while), and when I try to open the affected book on the Kobo I get told that it has Adobe DRM on it and I can't open it on the Kobo. Can anyone think of anything I can do to fix this without a factory reset? Thanks! P.S. I really know pretty much nothing about SQL files/editing, I had SQLite Studio and I've downloaded SQL Tools but don't really know how to use it.

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01-25-2022, 11:40 PM	#2
DNSB Bibliophagist Posts: 37,344 Karma: 149856306 Join Date: Jul 2010 Location: Vancouver Device: Kobo Sage, Libra Colour, Lenovo M8 FHD, Paperwhite 4, Tolino epos	Have you tried vacuuming the file? That and re-indexing are about the only non-destructive suggestions I can come up with.

01-26-2022, 01:04 AM	#3
davidfor Grand Sorcerer Posts: 24,906 Karma: 47303822 Join Date: Jul 2011 Location: Sydney, Australia Device: Kobo:Touch,Glo, AuraH2O, GloHD,AuraONE, ClaraHD, Libra H2O; tolinoepos	@JDesat: The database gets corrupted because something went wrong. It could be a bug in the software, it could be that you didn't eject the device safely one time, it could have been a crash. The only case I have been able to prove a reason for a corrupt database has been when reading CBZ or CBR files and then connecting to the PC. That was a bug on the device not freeing things properly. This was fixed recently in either the 4.28 or 4.30 firmware. Looking at the errors, the only way that might fix it is the VACUUM, or compress, of the database. That basically dumps the database out and reloads it. It should clean up everything. But, there is a chance that some data will be lost. Most of those errors should be harmless and a sign that some cleanup wasn't done. The first two are Rebuilding an index won't help. When that has been suggested, it was because the check showed that there was an index problem. And it named the index that needed to be rebuilt.

01-26-2022, 01:39 AM	#4
JDesat Connoisseur Posts: 90 Karma: 32768 Join Date: Dec 2012 Device: Kobo Glo HD, Kobo Clara HD	Unfortunately, when I try to VACUUM the database (in SQLite Studio or with the Kobo Utilities plugin in Calibre) that's when I get the 'disk image is malformed' error and it doesn't work. Any other ideas, maybe a way to force the VACUUM, or am I SOL?

01-26-2022, 09:55 PM	#8
JDesat Connoisseur Posts: 90 Karma: 32768 Join Date: Dec 2012 Device: Kobo Glo HD, Kobo Clara HD	I think I read somewhere that logging out of my Kobo account (on the Kobo itself) and logging back in will rebuild the database... would that work? And if so, I seem to remember doing that once and nothing was in my collections or had covers anymore, is there a way to fix that?

01-26-2022, 11:24 PM	#10
JDesat Connoisseur Posts: 90 Karma: 32768 Join Date: Dec 2012 Device: Kobo Glo HD, Kobo Clara HD	Hmm... I have the Kobo Utilities plugin, so I could get my reading positions back on those, and the covers aren't a huge issue, really... but I sideload absolutely everything through Calibre, so losing the collections would be a pain... and I'd be annoyed at the fact that everything was messed up in my book list(s) because I always have it set for me to see recent books at the top... I'd say something like 80% of the 8,000 or so 'books' on my Kobo are fanfiction, and I tend to read things I've added recently more often than I do older stuff, so having to try to remember a name of a fic or author and trying to hunt it down would be an issue. I suppose if this is my only option I'll have to do it, but for the moment, if no one can think of anything I can do to fix the database, I think I might just tough it out. So far it's only been 2 books that have caused an issue, both fanfic. One downloaded with FanFicFare, and another made into a docx file and then converted to epub in Calibre by me. Calibre doesn't let me delete them, but I can delete them on the Kobo itself without a problem. And, oddly, I've been able to get the docx one to work after several delete and resend attempts... that's when the other story started glitching. Anyway, thanks everyone so far for your suggestions, even if nothing has worked yet.

01-26-2022, 11:48 PM	#11
davidfor Grand Sorcerer Posts: 24,906 Karma: 47303822 Join Date: Jul 2011 Location: Sydney, Australia Device: Kobo:Touch,Glo, AuraH2O, GloHD,AuraONE, ClaraHD, Libra H2O; tolinoepos	If you are using calibre to sideload the books, are you using it for collection management? If so, that should happen automatically as you get the books on the device. If you are not using it for collection management, there is a way to fetch the collections from the device to a column in calibre. Which needs calibre to still be able to connect to the device. Reloading the device is also something I don't like because of the "Recent" sort. It is based on when the book was added and then the title within the batch. But, the Kobo Utilities plugin can set one of the date used by this (the other is the last read timestamp). I generally set it to the "Date" column in calibre as that is when the book was first added to the library. And will be reasonably close to when I first put it on the device. It isn't quite so good for books downloaded with FFF, as that will update the date when you update the book. But, the plugin can use any date column in the library. You can keep going as you are. But, I would expect this to get worse, not better. If it is working, at the least you can do some preparation and maybe choose when you do it, rather than get forced into it. And if it is more serious that it currently appears, it will be seen if you restart the device. That will mean the database is reread, and if there were problems writing it, then you may end up with old data.

01-27-2022, 04:36 AM	#12
JSWolf Resident Curmudgeon Posts: 74,839 Karma: 131375596 Join Date: Nov 2006 Location: Roslindale, Massachusetts Device: Kobo Libra 2, Kobo Aura H2O, PRS-650, PRS-T1, nook STR, PW3	You can setup the Kobo Utilities plugin with Calibre to backup your Kobo database to the computer every time you connect your Kobo to your library. That way you'll have a fairly updated database backup. That way you can restore it if you have another database corruption.

01-29-2022, 10:25 PM	#13
Joliet Jake Zealot Posts: 110 Karma: 3098438 Join Date: Feb 2021 Location: Canada Device: Kobo Sage	I had to deal with this issue recently (for only the second time in three years, that I recall), probably due to a loose cable. I haven't set Kobo Utilities to backup the database because I don't know what happens if the cable gets loose during the backup process.

01-30-2022, 06:12 PM	#15
aymeric106 Junior Member Posts: 4 Karma: 10 Join Date: Aug 2015 Device: kobo aura	Strange I have the same issue. Never happened before. Just after upgrading to the latest firmware and uploading a new book with calibre. Tried with various SQLLite editor without success. I reseted my Kobo, but the error came back eventually, after a few transfer. Will try with another USB cable, but file copy had no issue. Aymeric

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