Xapian discuss - Jun 2021 - How to recover from this permanent fatal error?

On Fri, Jun 4, 2021 at 8:37 PM David Bremner <david at tethera.net>
wrote:
> Felipe Contreras <felipe.contreras at gmail.com> writes:
> > I can't use notmuch anymore, I get this error:
> >
> > A Xapian exception occurred opening database: The revision being read
> > has been discarded - you should call Xapian::Database::reopen() and
> > retry the operation
> >
> > Context. In order to investigate a bug about mbsync I moved away the
> > folder ~/mail/.notmuch. I have a timer that calls notmuch new after
> > mbsync, so I paused that timer.
> >
> > Initially I used notmuch, only to see everything empty. Then I
> > recalled what I did, removed all the files, and moved back the .nomuch
> > directory.
> >
> > IIRC I was able to use notmuch without problems once, and then I got
the issue.
>
> Maybe the Xapian folk will have a more concrete suggestion, but I would
> start by running xapian-check on the database. In your case I guess that
> should be "xapian-check ~/mail/.notmuch".
Actually `xapian-check ~/mai/.notmuch/xapian`, but I already did that:

Database couldn't be opened for reading: DatabaseModifiedError: The
revision being read has been discarded - you should call
Xapian::Database::reopen() and retry the operation
Continuing check anyway
docdata:
xapian-check: DatabaseCorruptError: Db block overwritten - are there
multiple writers?

`xapian-check ~/mail/.notmuch/xapian F` doesn't seem to change anything.

Thanks for the prompt response though.

Cheers.

-- 
Felipe Contreras

On Fri, Jun 04, 2021 at 08:40:56PM -0500, Felipe Contreras
wrote:
> On Fri, Jun 4, 2021 at 8:37 PM David Bremner <david at tethera.net>
wrote:
> > Felipe Contreras <felipe.contreras at gmail.com> writes:
> 
> > > I can't use notmuch anymore, I get this error:
> > >
> > > A Xapian exception occurred opening database: The revision being
read
> > > has been discarded - you should call Xapian::Database::reopen()
and
> > > retry the operation
> > >
> > > Context. In order to investigate a bug about mbsync I moved away
the
> > > folder ~/mail/.notmuch. I have a timer that calls notmuch new
after
> > > mbsync, so I paused that timer.
> > >
> > > Initially I used notmuch, only to see everything empty. Then I
> > > recalled what I did, removed all the files, and moved back the
.nomuch
> > > directory.
Perhaps a process had the database or the empty replacement open for
writing over the moving aside or the moving back?  That could result
in a broken database.
> `xapian-check ~/mail/.notmuch/xapian F` doesn't seem to change
anything.
With some filing systems and older format (chert) Xapian databases a
system crash or power failure could result in truncating to zero size
the files which tracked which blocks were in use and where the root of a
particular revision of the tree; the xapian-check's "fix" mode was
added
to recreate those files by scanning the whole database to work out what
they should contain.

In newer format databases (glass) we eliminated these files and
currently the "fix" mode doesn't actually do anything for glass.

The plan was to teach xapian-check how to recreate the `iamglass` file,
but that doesn't seem to suffer from the truncation problem and so it
hasn't actually been implemented yet and so "F" currently does
nothing
for glass databases.
> > > IIRC I was able to use notmuch without problems once, and then I
got the issue.
> >
> > Maybe the Xapian folk will have a more concrete suggestion, but I
would
> > start by running xapian-check on the database. In your case I guess
that
> > should be "xapian-check ~/mail/.notmuch".
I'd suggest trying this simple tool I wrote that can probably rescue the
tags from a broken notmuch database (the tags are the part notmuch can't
just recreate by reindexing):

https://git.xapian.org/?p=xapian;a=blob;f=README.notmuch;hb=refs/heads/notmuch-tag-rescue-hack

Once you have those, you can reindex your mail and then restore the
tags.

Cheers,
    Olly