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

Pengcheng Yang yangpc at biols.ac.cn
Sun Aug 2 10:01:38 BST 2015


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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