Errors in Malariamine Build Logs

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Errors in Malariamine Build Logs

Norbert Auer
Hi all,

Currently I am working through the malariamine tutorial.

Although I got BUILD SUCCESSFUL for

cd ./malariamine/dbmodel
ant clean build-db

and

cd ./malariamine/integrate
ant -Dsource=uniprot-malaria -v

I found a lot of Errors in the intermine logs.

For example:
# dbmodel/intermine.log

WARN         org.intermine.task.BuildDbTask     - Failed to remove all
tables from database: org.postgresql.util.PSQLException: ERROR: sequence
"serial" does not exist

# integrate/intermine.log

ERROR     org.intermine.util.PropertiesUtil     - Could not find file
uniprot-malaria_keys.properties from
AntClassLoader[/data/intermine/malariamine/integrate/resources:...

ERROR org.intermine.bio.dataconversion.UniprotConverter     - no valid
gene identifiers found for O15770

 ERROR org.intermine.dataloader.IntegrationWriterAbstractImpl     - Data
source should not contain data in the one to many relation
DataSource.dataSets, as it is ignored. Put the data into the reverse
reference instead.

org.postgresql.util.PSQLException: ERROR: relation "dataset__key_title"
already exists

So my question is: Is this is a normal output and can I ignore these
errors or is something wrong with my setup.

Best,

Norbert
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---------------------------------------
DI(FH) Norbert Auer
Staff Scientist

ACIB - Austrian Centre of Industrial Biotechnology
----------------------------------------
Phone: 0043 1 47654 30852

Web: www.acib.at
Office: Muthgasse 11/DG, 1190 Wien
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FB: 224687y FBG: HG Graz UID: ATU 54545504
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Re: Errors in Malariamine Build Logs

Julie Sullivan-2
Hi Norbert!!

Yes, those are fine. Those messages should be labelled as INFO or at the
most a WARN. I'll make a ticket to update!

I'm glad you got MalariaMine working! Please let us know if you have
more questions. We are on discord at chat.intermine.org too.

Cheers,
Julie

On 01/19/2017 10:44 AM, Norbert Auer wrote:

> Hi all,
>
> Currently I am working through the malariamine tutorial.
>
> Although I got BUILD SUCCESSFUL for
>
> cd ./malariamine/dbmodel
> ant clean build-db
>
> and
>
> cd ./malariamine/integrate
> ant -Dsource=uniprot-malaria -v
>
> I found a lot of Errors in the intermine logs.
>
> For example:
> # dbmodel/intermine.log
>
> WARN         org.intermine.task.BuildDbTask     - Failed to remove all
> tables from database: org.postgresql.util.PSQLException: ERROR: sequence
> "serial" does not exist
>
> # integrate/intermine.log
>
> ERROR     org.intermine.util.PropertiesUtil     - Could not find file
> uniprot-malaria_keys.properties from
> AntClassLoader[/data/intermine/malariamine/integrate/resources:...
>
> ERROR org.intermine.bio.dataconversion.UniprotConverter     - no valid
> gene identifiers found for O15770
>
>  ERROR org.intermine.dataloader.IntegrationWriterAbstractImpl     - Data
> source should not contain data in the one to many relation
> DataSource.dataSets, as it is ignored. Put the data into the reverse
> reference instead.
>
> org.postgresql.util.PSQLException: ERROR: relation "dataset__key_title"
> already exists
>
> So my question is: Is this is a normal output and can I ignore these
> errors or is something wrong with my setup.
>
> Best,
>
> Norbert
>
>
>
> _______________________________________________
> dev mailing list
> [hidden email]
> https://lists.intermine.org/mailman/listinfo/dev
>
_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev
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