Hi,
I'm trying to add a tumour_sample_id to both the somatic mutation and
CNV quick searches in our local ICGC-formatted biomart. The queries work
OK for local datasets, but not for any of the datasets that are
federated in from dcc.icgc.org. The queries filtered on
"snp__simple_somatic_mutation__dm__tumour_sample_id" also work OK for
advanced queries on both federated ICGC datasets and internal datasets.
Again, technically this should work fine as can be seen in the advanced
queries, but for some reason, adding the filter to the quick search
doesn't work for federated queries. I've even compared the configs for
the advanced tumour_sample_id filter (that works) and what I have in the
quick search and they are the same.
I only get the error when adding the filter to the quick search that it
is not working. Here's the error message it returns:
2011-06-29 09:14:22,923 DEBUG [pool-1-thread-2:Log.java:143]: SENDING
INSECURE(non-OAUTH) request
text
org.biomart.common.exceptions.BioMartException: HTTP Error 400 - Filter
snp__simple_somatic_mutation__dm__tumour_sample_id not found in Breast
Cancer (JHU, US)
at
org.biomart.queryEngine.SubQuery.executeMartServiceQuery(SubQuery.java:8
14)
at
org.biomart.queryEngine.SubQuery.executeQuery(SubQuery.java:726)
at
org.biomart.queryEngine.QueryRunnerThread.recurseSubQueries(QueryRunnerT
hread.java:171)
at
org.biomart.queryEngine.QueryRunnerThread.call(QueryRunnerThread.java:73
)
at
org.biomart.queryEngine.QueryRunnerThread.call(QueryRunnerThread.java:37
)
at
java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
at java.util.concurrent.FutureTask.run(FutureTask.java:166)
at
java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
at
java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
at java.util.concurrent.FutureTask.run(FutureTask.java:166)
at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.jav
a:1110)
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.ja
va:603)
at java.lang.Thread.run(Thread.java:636)
2011-06-29 09:14:23,442 INFO [1943435117@qtp-881305036-8:Log.java:165]:
Total query time is 520 ms
2011-06-29 09:16:13,319 INFO [689021860@qtp-881305036-4:Log.java:165]:
Incoming XML query: <!DOCTYPE Query><Query client="webbrowser"
processor="TSV" limit="-1" header="1"><Dataset name="snp_hopkinsBreast"
config="snp_config_quick"><Filter
name="snp__simple_somatic_mutation__dm__tumour_sample_id"
value="HCC1008"/><Attribute name="cancertype"/><Attribute
name="assemblyversion"/><Attribute
name="snp__feature__main__chromosome"/><Attribute
name="snp__feature__main__chromosome_start"/><Attribute
name="snp__feature__main__chromosome_end"/><Attribute
name="snp__simple_somatic_mutation__dm__tumour_sample_id"/><Attribute
name="snp__simple_somatic_mutation__dm__mutation_id"/><Attribute
name="snp__simple_somatic_mutation__dm__mutation_type"/><Attribute
name="snp__simple_somatic_mutation__dm__tumour_genotype"/><Attribute
name="snp__simple_somatic_mutation__dm__mutation"/><Attribute
name="snp__simple_somatic_mutation__dm__aa_mutation"/><Attribute
name="snp__simple_somatic_mutation__dm__is_annotated"/><Attribute
name="snp__simple_somatic_mutation__dm__validation_status"/><Attribute
name="snp__simple_somatic_mutation__dm__gene_affected"/><Attribute
name="snp__simple_somatic_mutation__dm__transcript_affected"/><Attribute
name="snp__simple_somatic_mutation__dm__consequence_type"/></Dataset></Q
uery>
2011-06-29 09:16:13,323 INFO [689021860@qtp-881305036-4:Log.java:165]:
PSEUDO attribute's value: Breast Cancer (JHU, US)
2011-06-29 09:16:13,323 INFO [689021860@qtp-881305036-4:Log.java:165]:
PSEUDO attribute's value: NCBI36
2011-06-29 09:16:13,324 DEBUG [689021860@qtp-881305036-4:Log.java:143]:
Start prepareLinks
2011-06-29 09:16:13,324 DEBUG [689021860@qtp-881305036-4:Log.java:143]:
End prepareLinks
2011-06-29 09:16:13,325 DEBUG [689021860@qtp-881305036-4:Log.java:143]:
Unplanned:
========================================================================
=============
snp_hopkinsBreast
Attributes: snp__feature__main__chromosome
snp__feature__main__chromosome_start snp__feature__main__chromosome_end
snp__simple_somatic_mutation__dm__tumour_sample_id
snp__simple_somatic_mutation__dm__mutation_id
snp__simple_somatic_mutation__dm__mutation_type
snp__simple_somatic_mutation__dm__tumour_genotype
snp__simple_somatic_mutation__dm__mutation
snp__simple_somatic_mutation__dm__aa_mutation
snp__simple_somatic_mutation__dm__is_annotated
snp__simple_somatic_mutation__dm__validation_status
snp__simple_somatic_mutation__dm__gene_affected
snp__simple_somatic_mutation__dm__transcript_affected
snp__simple_somatic_mutation__dm__consequence_type
Filters: snp__simple_somatic_mutation__dm__tumour_sample_id:
HCC1008
------------------------------------------------------------------------
-------------
Any insight would be great.
Thanks,
Heather
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