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 <[email protected]>
*Lähetetty:* maanantai 14. helmikuuta 2022 13.08
*Vastaanottaja:* Rahkonen Jukka (MML) <[email protected]>; [email protected]
*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) <[email protected]> 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 <[email protected]>
    *Lähetetty:* maanantai 14. helmikuuta 2022 12.53
    *Vastaanottaja:* Rahkonen Jukka (MML)
    <[email protected]>
    *Kopio:* [email protected]
    *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)
    <[email protected]> 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 <[email protected]>
        *Puolesta *Isabel Kiefer
        *Lähetetty:* maanantai 14. helmikuuta 2022 10.17
        *Vastaanottaja:* [email protected]
        *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

        [email protected]


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