[InterMine Dev] kegg-pathway load: genespathways table is empty

Julie Sullivan julie at flymine.org
Mon Aug 3 08:32:46 BST 2015


Sorry you are having problems with the kegg source!

Can you clarify what is different about the two project XML files?

On 02/08/15 10:01, Pengcheng Yang wrote:
> Hi InterMiner developers,
>
> Thank you all who answered my questions. Here is another question that
> blocked my way to deploy my InterMine.
>
> To load kegg-pathway data, I set the project.xml as that in malariamine
> and prepared the two files map_title.tab and org_gene_map.tab. When I
> load the data using "ant -Dsource=kegg-pathway -v 1> kegg-pathway.log1
> 2> kegg-pathway.log2", the kegg-pathway.log1 said at the end [1].
> However, when I query in the postgres database using SQL language:
> "select * from genespathways", nothing returned.
>
> But when I do the same thing for malariamine after loading kegg-pathway
> data, I got the pathways to genes information as [2] listed. So I
> compared the log information between my mine and malariamine, and found
> my mine hasn't build several the indexes as [3] listed.
>
> Because I have used the same sources kegg-pathway as malariamine, so
> what the problem here?
>
> Any suggestions and comments are welcom! Thanks a lot!
>
> Best,
> Pengcheng Yang
>
>
> ---------------------------------
> [1] build successful log information from my mine after load kegg-pathway
> /BUILD SUCCESSFUL//
> //Total time: 21 seconds//
> //[Thread-16] INFO com.zaxxer.hikari.pool.HikariPool - HikariCP pool
> db.common-tgt-items is being shutdown.//
> //[Thread-8] INFO com.zaxxer.hikari.pool.HikariPool - HikariCP pool
> db.common-tgt-items is being shutdown.//
> //[Thread-16] INFO com.zaxxer.hikari.pool.HikariPool - HikariCP pool
> db.production is being shutdown./
>
> [2] genespathways table from malariamine database.
>
>   pathways |  genes
> ----------+---------
>    2000002 | 1002796
>    2000002 | 1003874
>    2000002 | 1004075
>
> [3] the log information not appeared in my mine but in malariamine.
>   [integrate] Creating index: CREATE INDEX Gene__key_secondaryidentifier
> ON Gene (secondaryIdentifier, organismid)
>   [integrate] Creating index: CREATE INDEX Gene__key_symbol_org ON Gene
> (symbol, organismid)
>   [integrate] Creating index: CREATE INDEX Gene__key_primaryidentifier
> ON Gene (primaryIdentifier)
>   [integrate] Creating index: CREATE INDEX Organism__key_taxonid ON
> Organism (taxonId)
>   [integrate] Creating index: CREATE INDEX SOTerm__key ON SOTerm (name,
> ontologyid)
>
>
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