Hi Heather, From: "Estrella, Heather" <[email protected]<mailto:[email protected]>> Date: Wed, 29 Jun 2011 13:22:24 -0400 To: Marie Wong-Erasmus <[email protected]<mailto:[email protected]>>, "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: Re: [BioMart Users] Adding tumour sample ID to somatic mutation quick search in ICGC
Hi Marie, Thanks, so, if I can re-phrase what I think you’re saying, if the originating source (i.e. dcc.icgc.org) has an attribute hidden, even if I unhide it on my end or create a new filter from the attribute, it won’t work because it’s hidden on their end. The quick and advanced queries are all pre-defined by the consortium. For example, the filter under quick is not the same as the filter under advanced meaning I can’t “import from source” for the federated queries. Is that correct? Yes, it's correct that at present for URL source, the attribute/filter are access point (quick, advanced) specific. But this can be changed in the software, as I mentioned in the previous email, for querying purpose, we could have a default access point where all filters/attributes are available. Hence, why it works for advanced (set in original icgc5.xml file), but not when I go to import and add it to quick. It works for advanced because the 'advanced' access point does have this filter exposed. Junjun Thanks, Heather From: Marie Wong-Erasmus [mailto:[email protected]] Sent: Wednesday, June 29, 2011 10:10 AM To: Estrella, Heather; [email protected]<mailto:[email protected]> Subject: Re: [BioMart Users] Adding tumour sample ID to somatic mutation quick search in ICGC Hi Heather, This functionality is "correct". So if the filter is hidden in the federated source's config, even if you turn it on locally, you will not be able to see the filter. the only way to get around this is to import the data to a local database and then turn the filter you want on for all datasets using the mysql connection rather than the URL connection as you have currently. Otherwise, the other option is to ask the consortium if they don't mind to have the filter unhidden. hope this helps, Marie From: "Estrella, Heather" <[email protected]<mailto:[email protected]>> Date: Wed, 29 Jun 2011 12:34:37 -0400 To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: [BioMart Users] Adding tumour sample ID to somatic mutation quick search in ICGC Hi, I’m trying to add a tumour_sample_id to both the somatic mutation and CNV quicksearches in our local ICGC-formatted biomart. The queries work OK for localdatasets, 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:814) at org.biomart.queryEngine.SubQuery.executeQuery(SubQuery.java:726) at org.biomart.queryEngine.QueryRunnerThread.recurseSubQueries(QueryRunnerThread.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$Sync.innerRun(FutureTask.java:334) at java.util.concurrent.FutureTask.run(FutureTask.java:166) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java: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"/><Attributename="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></Query> 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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