Hi Richard,
you are right, renaming internal names to lower case and updating
pointer attributes makes it work.
Thank you so much.
Regards,
Jennifer
Richard Holland a écrit :
I'm not sure, but I think internal names are all converted to lower
case when loaded by configure.pl, but I don't think the pointer
attribute names are converted as well before the lookup is done to
find what they are pointing at. If you rename the internal names to
lower case, and also update the pointer attributes to match, it might
work.
cheers,
Richard
On 10 Nov 2009, at 10:27, Jennifer Dupiot wrote:
Hi all,
I need your precious help one more time !
Creating pointer attributes in MartEditor (duplicates attributes
needed), some of them are not displayed in MartView...
Configuration xml file (retreive from meta_conf__xml__dm table)
contains:
<DatasetConfig dataset="draft8" datasetID="1" displayName="Genotypes"
interfaces="default" internalName="default" martUsers="default"
modified="2009-11-10 09:28:22" softwareVersion="0.6"
template="draft8" type="TableSet" visible="1">
...
<AttributePage displayName="SNPs" internalName="snp_page"
outFormats="html,txt,csv,tsv,xls">
...
<AttributeDescription displayName="Chromosome (draft8)"
field="seq_region_name" internalName="seq_region_name"
key="snp_id_key" maxLength="30"
tableConstraint="draft8__snp_details__dm" />
<AttributeDescription displayName="Position on chromosome (bp)
(draft8)" field="position" internalName="position" key="snp_id_key"
maxLength="11" tableConstraint="draft8__snp_details__dm" />
<AttributeDescription displayName="Chromosome (Netherlands draft9)"
field="draft9NL_chr" internalName="seq_region_name_9NL"
key="snp_id_key" maxLength="30"
tableConstraint="draft8__snp_details__dm" />
<AttributeDescription displayName="Position on chromosome (bp)
(Netherlands draft9)" field="draft9NL_pos"
internalName="position_9NL" key="snp_id_key" maxLength="11"
tableConstraint="draft8__snp_details__dm" />
...
</AttributePage>
<AttributePage displayName="DRAFT8" internalName="draft8_page"
outFormats="html,txt,csv,tsv,xls">
...
<AttributeDescription internalName="seq_region_name_draft8"
pointerAttribute="seq_region_name" pointerDataset="draft8"
pointerInterface="default" />
<AttributeDescription internalName="position_draft8"
pointerAttribute="position" pointerDataset="draft8"
pointerInterface="default" />
...
</AttributePage>
<AttributePage displayName="DRAFT9" internalName="draft9_page"
outFormats="html,txt,csv,tsv,xls">
...
<AttributeDescription internalName="chr_draft9NL"
pointerAttribute="seq_region_name_9NL" pointerDataset="draft8"
pointerInterface="default" />
<AttributeDescription internalName="pos_draft9NL"
pointerAttribute="position_9NL" pointerDataset="draft8"
pointerInterface="default" />
...
</AttributePage>
...
</DatasetConfig>
In martview pointer attributes 'seq_region_name_draft8' and
'position_draft8' are displayed, whereas pointer attibutes
'chr_draft9NL' and 'pos_draft9NL' aren't displayed.
Please, note that I exported configuration from MartEditor,
reconfugured biomart with --clean option and restarted apache.
There aren't error message in error.log.
How can I find the source of the problem and solve it ?
Thanks for help.
Regards.
Jennifer
--
Richard Holland, BSc MBCS
Operations and Delivery Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: [email protected]
http://www.eaglegenomics.com/
