[InterMine Dev] Strange behavior with SNP data

Vallejos, Andrew avallejos at mcw.edu
Wed Aug 19 20:01:47 BST 2009


I am not getting primary identifers showing up for my snps.

 

I have a link to the snp report page and the results from the postgres
database query.  The query shows that the primaryidentifier is set, its
equal to the name.  The original dbSNP.pl script set the name to the
name value.  Rather than rerun the XML generating script, I ran an sql
query to set the primaryidentifier equal to the name.  It seems to have
worked, except that we webapp does not want to display the id
information.  I will probably go back and update the dbSNP script, but
this behavior seems odd to me....

 

http://ratmine.mcw.edu/ratmine-webapp/objectDetails.do?id=763929527&trai
l=|query|results.6|763929527

 

production-rat=# select * from snp limit 1;

 secondaryidentifier | chromosomestart | curated | allele2 |
primaryidentifier | length |    id     |       name       | snp |
allele1 | chromosomeend | chromosomeid | chromosomelocationid |
organismid | sequenceid |            class            

---------------------+-----------------+---------+---------+------------
-------+--------+-----------+------------------+-----+---------+--------
-------+--------------+----------------------+------------+------------+
-----------------------------

                     |                 |         | T       |
ENSRNOSNP2336733  |        | 763929527 | ENSRNOSNP2336733 |     | C
|               |    756050611 |            763929526 |  755000000 |
| org.intermine.model.bio.SNP

(1 row)

 

 

======================

Andrew Vallejos

Web Developer II

Biotechnology and Bioengineering Center

Medical College of Wisconsin

414-955-4104

avallejos at mcw.edu

 

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