Hi Josef,
In the current query, there is some problem with web service type
request indeed. Please use the following registry (that connects to
database directly). This will work and will be much faster.
/////////////////////////
<MartRegistry>
<MartDBLocation databaseType="mysql" host="martdb.ensembl.org"
database="ensembl_mart_57" name="ensembl" displayName="ENSEMBL 57 GENE
(SANGER UK)" port="5316" schema="ensembl_mart_57" user="anonymous"
password="" visible="1" default="1" martUser=""
includeDatasets="mmusculus_gene_ensembl" />
<MartDBLocation databaseType="mysql" host="martdb.ensembl.org"
database="ontology_mart_57" name="ont" displayName="ENSEMBL 57 ONTOLOGY
(SANGER UK)" port="5316" schema="ontology_mart_57" user="anonymous"
password="" visible="0" default="1" martUser="" includeDatasets="" />
<MartDBLocation databaseType="mysql" host="martdb.ensembl.org"
database="genomic_features_mart_57" name="gf" displayName="ENSEMBL 57
GEN FEAT (SANGER UK)" port="5316" schema="genomic_features_mart_57"
user="anonymous" password="" visible="0" default="1" martUser=""
includeDatasets="" />
<MartDBLocation databaseType="mysql" host="martdb.ensembl.org"
database="sequence_mart_57" name="seq" displayName="ENSEMBL 57 SEQ
(SANGER UK)" port="5316" schema="sequence_mart_57" user="anonymous"
password="" visible="1" default="1" martUser=""
includeDatasets="mmusculus_genomic_sequence" />
</MartRegistry>
/////////////////////////
Best
Syed
Josef Anrather wrote:
Sorry,
the code in my previous post should read
$query->addAttribute("gene_flank");
instead of
$query->addAttribute("cdna");
I was playing around a little to much.
Cheers, Josef
