Yes, clearing just the items with errors should be enough.


--
Adam Field
Business Relationship Manager and Community Lead
EPrints Services
+44 (0)23 8059 8814

On 22 Oct 2015, at 12:26, Ajunk Pracetio wrote:

> Ok Adam, I will try your suggest.
>
> Or maybe I only clear the item that have the problem?
>
> On Thu, Oct 22, 2015 at 5:29 PM, Field A.N. <af05v@ecs.soton.ac.uk> wrote:
> Issues with PDF files may be reported to the error log when EPrints gets them converted to text for indexing, and I wouldn't worry to much about that (though if you know which pdf files are causing the errors, perhaps you should inspect them and make sure the open successfully).  I'm not sure about the duplicate primary key issue.  You could try clearing out the eprint__rindex table (it's all automatically generated) and then reindexing your whole repository.
>
>
> --
> Adam Field
> Business Relationship Manager and Community Lead
> EPrints Services
> +44 (0)23 8059 8814
>
>
>
>
>
> On 21 Oct 2015, at 12:33, Ajunk Pracetio wrote:
>
> > I already try command bin/epadmin reindex sir eprint 292 --verbose --verbose and below is the result. It's too long, and I cut when error show up.
> >
> > .......
> > Database execute debug: INSERT INTO `eprint__rindex` (`eprintid`,`field`,`word`) VALUES (?,?,?)
> > DBD::mysql::st execute failed: Duplicate entry 'documents--292' for key 'PRIMARY' at /usr/share/eprints3/bin/../perl_lib/EPrints/Database.pm line 1287.
> > Database execute debug: INSERT INTO `eprint__rindex` (`eprintid`,`field`,`word`) VALUES (?,?,?)
> > Database execute debug: INSERT INTO `eprint__index_grep` (`eprintid`,`fieldname`,`grepstring`) VALUES (?,?,?)
> > Database execute debug: INSERT INTO `eprint__rindex` (`eprintid`,`field`,`word`) VALUES (?,?,?)
> > Database execute debug: INSERT INTO `eprint__index_grep` (`eprintid`,`fieldname`,`grepstring`) VALUES (?,?,?)
> > Database execute debug: INSERT INTO `eprint__rindex` (`eprintid`,`field`,`word`) VALUES (?,?,?)
> > Database execute debug: INSERT INTO `eprint__index_grep` (`eprintid`,`fieldname`,`grepstring`) VALUES (?,?,?)
> > Database execute debug: INSERT INTO `eprint__rindex` (`eprintid`,`field`,`word`) VALUES (?,?,?)
> > Database execute debug: INSERT INTO `eprint__index_grep` (`eprintid`,`fieldname`,`grepstring`) VALUES (?,?,?)
> > Database execute debug: INSERT INTO `eprint__rindex` (`eprintid`,`field`,`word`) VALUES (?,?,?)
> > Database execute debug: INSERT INTO `eprint__index_grep` (`eprintid`,`fieldname`,`grepstring`) VALUES (?,?,?)
> > Database execute debug: INSERT INTO `eprint__rindex` (`eprintid`,`field`,`word`) VALUES (?,?,?)
> > Database execute debug: INSERT INTO `eprint__index_grep` (`eprintid`,`fieldname`,`grepstring`) VALUES (?,?,?)
> > Database execute debug: INSERT INTO `eprint__rindex` (`eprintid`,`field`,`word`) VALUES (?,?,?)
> > Database execute debug: INSERT INTO `eprint__index_grep` (`eprintid`,`fieldname`,`grepstring`) VALUES (?,?,?)
> > Database execute debug: INSERT INTO `eprint__rindex` (`eprintid`,`field`,`word`) VALUES (?,?,?)
> > Database execute debug: INSERT INTO `eprint__index_grep` (`eprintid`,`fieldname`,`grepstring`) VALUES (?,?,?)
> > Indexed item: eprint/292
> >
> > It's still error about Duplicate entry, but there is still error like "illegal character", "Error: Restoring state when no valid states to pop", "Error: Missing or invalid 'Bounds' entry in stitching function", "Error: PDF file is damaged - attempting to reconstruct xref table...", "Error: Expected the optional content group list, but wasn't able to find it, or it isn't an Array", and "Error: Bad annotation destination"
> >
> > Thank you
> >
> > Regards,
> > Agung
> >
> >
> > On Wed, Oct 21, 2015 at 4:18 PM, Field A.N. <af05v@ecs.soton.ac.uk> wrote:
> > This won't fix the problem, it will just gather more information.
> >
> > --
> > Adam Field
> > Business Relationship Manager and Community Lead
> > EPrints Services
> > +44 (0)23 8059 8814
> >
> >
> >
> >
> >
> > On 21 Oct 2015, at 10:16, Ajunk Pracetio wrote:
> >
> > > If after I reindex that error item, and the problem still exist, what I must to do? is there any step that I must to do?
> > >
> > > my hardware spec :
> > > ProLiant ML150 G5
> > > RAM 6GB
> > >
> > > Regards,
> > > Agung
> > >
> > > On Wed, Oct 21, 2015 at 4:11 PM, Field A.N. <af05v@ecs.soton.ac.uk> wrote:
> > > Yes, that should be fine.
> > >
> > > What's the hardware spec of your server?
> > >
> > > --
> > > Adam Field
> > > Business Relationship Manager and Community Lead
> > > EPrints Services
> > > +44 (0)23 8059 8814
> > >
> > >
> > >
> > >
> > >
> > > On 21 Oct 2015, at 10:01, Ajunk Pracetio wrote:
> > >
> > > > but the process very slow. my item only 1330, and it take about 1 day. Is there any problem with my indexer process? or maybe my RAM not enough? But, I will try it
> > > >
> > > > Btw, is it ok if I only reindex that item got error? using bin/epadmin reindex sir eprint 603 --verbose --verbose ?
> > > >
> > > > Regards,
> > > > Agung
> > > >
> > > > On Wed, Oct 21, 2015 at 3:41 PM, Field A.N. <af05v@ecs.soton.ac.uk> wrote:
> > > > Try running:
> > > >
> > > > bin/epadmin reindex sir eprint --verbose --verbose
> > > >
> > > > Two 'verbose' flags will increase the verbosity and show you the mysql query that's failing here.
> > > >
> > > > --
> > > > Adam Field
> > > > Business Relationship Manager and Community Lead
> > > > EPrints Services
> > > > +44 (0)23 8059 8814
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > On 21 Oct 2015, at 00:32, Ajunk Pracetio wrote:
> > > >
> > > > > I'm running EPrints 3.3.12. I already check using phpmyadmin and it's okay. Or maybe I must running mysqlcheck from command line?
> > > > >
> > > > > Is it possible to solve this error one by one, or the item must be reindex or maybe any other way?
> > > > >
> > > > > thank you
> > > > >
> > > > > On Tue, Oct 20, 2015 at 5:25 PM, Field A.N. <af05v@ecs.soton.ac.uk> wrote:
> > > > > What version of EPrints are your running?
> > > > >
> > > > > It looks like a database issue of some kind.  Have you tried running mysqlcheck?
> > > > >
> > > > > --
> > > > > Adam Field
> > > > > Business Relationship Manager and Community Lead
> > > > > EPrints Services
> > > > > +44 (0)23 8059 8814
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > On 20 Oct 2015, at 01:30, Ajunk Pracetio wrote:
> > > > >
> > > > > > Hi,
> > > > > >
> > > > > > Yesterday I running command bin/epadmin reindex sir eprint --verbose
> > > > > > and I get a few like :
> > > > > >
> > > > > > DBD::mysql::st execute failed: Duplicate entry 'documents--604' for key 'PRIMARY' at /usr/share/eprints3/bin/../perl_lib/EPrints/Database.pm line 1287.
> > > > > >
> > > > > > Error (96): Illegal character '}'
> > > > > >
> > > > > > Error: Missing or invalid 'Bounds' entry in stitching function
> > > > > >
> > > > > > How I can fix this error?
> > > > > >
> > > > > > thank you
> > > > > >
> > > > > >
> > > > > > --
> > > > > > Life isn't valuable if you don't have someone to care
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> > > > >
> > > > >
> > > > > --
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> > > >
> > > > --
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