[gdal-dev] Corrupted geopackage

[Even Rouault]

I would just suggest using ogr2ogr to generate a new 'clean' GPKG file 
from the corrupted one. This will not recover lost data, but at least 
you'll get something sane. Well I should say "structurally" sane. 
depending on how the corruption happened you could get also get 
corrupted content in the data that tools can't detect (there's no 
checksum mechanism at the row level in sqlite)

Le 14/02/2022 à 12:51, Rahkonen Jukka (MML) a écrit :
>
> Hi,
>
> Maybe you can drop the rtree tables if you first drop the rtree_xxx 
> triggers that belong to the data table. There are probably 6 of them. 
> I don’t know if it helps, though. rtreecheck() 
> https://sqlite.org/rtree.html is probably useless because you know 
> already that the index is corrupted.
>
> -Jukka-
>
> *Lähettäjä:* Isabel Kiefer <isabel at opengis.ch>
> *Lähetetty:* maanantai 14. helmikuuta 2022 13.08
> *Vastaanottaja:* Rahkonen Jukka (MML) 
> <jukka.rahkonen at maanmittauslaitos.fi>; gdal-dev at lists.osgeo.org
> *Aihe:* Re: [gdal-dev] Corrupted geopackage
>
> Hi Jukka,
>
> Yes, exactly, there are only 78 entries in a dump to text file.
>
> In the original .gpkg-file, the rtree_XX_geom table is completely 
> empty (no columns, no entries) - this must be where the problem comes 
> from..
>
> On Mon, Feb 14, 2022 at 11:59 AM Rahkonen Jukka (MML) 
> <jukka.rahkonen at maanmittauslaitos.fi> wrote:
>
>     Hi,
>
>     And when you .dump https://www.sqlitetutorial.net/sqlite-dump/ the
>     damaged table into a text file, do you only get 78 insert entries
>     into it?
>
>     -Jukka-
>
>     *Lähettäjä:* Isabel Kiefer <isabel at opengis.ch>
>     *Lähetetty:* maanantai 14. helmikuuta 2022 12.53
>     *Vastaanottaja:* Rahkonen Jukka (MML)
>     <jukka.rahkonen at maanmittauslaitos.fi>
>     *Kopio:* gdal-dev at lists.osgeo.org
>     *Aihe:* Re: [gdal-dev] Corrupted geopackage
>
>     Thanks for your suggestion, Jukka! I tried all the advice from
>     stackoverflow. I can do ".recover", but get only the features that
>     have been visible all along.
>
>     In the original .gpkg, I cannot DROP the affected RTree-Index. It
>     gives me the same disk malformed error. But that would also have
>     been my initial idea...
>
>     On Mon, Feb 14, 2022 at 9:26 AM Rahkonen Jukka (MML)
>     <jukka.rahkonen at maanmittauslaitos.fi> wrote:
>
>         Hi,
>
>         Without being able to see your database it is hard to give
>         more advice that
>         https://stackoverflow.com/questions/18259692/how-to-recover-a-corrupt-sqlite3-database/18260642
>         gives. Did you try all of them? Because the problem has
>         something to do with the spatial index I would have a try be
>         dropping it and repeating the suggested tricks.
>
>         -Jukka Rahkonen-
>
>         *Lähettäjä:* gdal-dev <gdal-dev-bounces at lists.osgeo.org>
>         *Puolesta *Isabel Kiefer
>         *Lähetetty:* maanantai 14. helmikuuta 2022 10.17
>         *Vastaanottaja:* gdal-dev at lists.osgeo.org
>         *Aihe:* [gdal-dev] Corrupted geopackage
>
>         Hi everyone,
>
>         I've a problem with a corrupted geopackage.
>
>         It should contain a table with 694 entries, but only 78 are
>         visible when opening the file with DB Browser for SQLite or
>         QGIS. The table gpkg_ogr_contents says 694 though. When
>         opening the .gpkg with a Notepad or similar, I can see that
>         there are more than 78 entries.
>
>         The error message in DB Browser is "database disk image is
>         malformed in "PRAGMA "main".TABLE_INFO("rtree_XXX");" So it
>         seems that there is a problem with the index of the concerned
>         table.
>
>         Does anyone know how to fix this? I tried
>         https://stackoverflow.com/questions/18259692/how-to-recover-a-corrupt-sqlite3-database/18260642
>         <https://stackoverflow.com/questions/18259692/how-to-recover-a-corrupt-sqlite3-database/18260642> but
>         without success.
>
>         Thanks in advance for your help!
>
>         Isabel
>
>         -- 
>
>         Isabel Kiefer
>
>         OPENGIS.ch
>
>         isabel at opengis.ch
>
>
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