Hi Heather, Just to add to Marie's reply.
The reason the query failed when fired against a federated ICGC dataset is that the chosen filter does not exist in the ICGC data source (as it is shown in the log). Basically, in your set up the ICGC datasets are from URL sources and your own datasets are local DB source. For any URL source, in a query the client can not specify any attributes or filters that do not exist in the URL source. On the other hand, for local DB source, you can add new attributes/filters using MartConfigurator as long as corresponding database columns exist, and those new attributes/filters can be used in queries. In advanced query interface, the ICGC URL data source does have the filter (snp__simple_somatic_mutation__dm__tumour_sample_id), so the query works. Below is your original 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></Query> This query will fail if you fire it against ICGC data portal. But it will work if you change config from 'snp_config_quick' to 'snp_config', to test that, you can try the following link: http://dcc.icgc.org/martservice/results?query=%3CQuery%20client=%22webbrowser%22%20processor=%22TSV%22%20limit=%22-1%22%20header=%221%22%3E%3CDataset%20name=%22snp_hopkinsBreast%22%20config=%22snp_config%22%3E%3CFilter%20name=%22snp__simple_somatic_mutation__dm__tumour_sample_id%22%20value=%22HCC1008%22/%3E%3CAttribute%20name=%22cancertype%22/%3E%3CAttribute%20name=%22assemblyversion%22/%3E%3CAttribute%20name=%22snp__feature__main__chromosome%22/%3E%3CAttribute%20name=%22snp__feature__main__chromosome_start%22/%3E%3CAttribute%20name=%22snp__feature__main__chromosome_end%22/%3E%3CAttribute%20name=%22snp__simple_somatic_mutation__dm__tumour_sample_id%22/%3E%3CAttribute%20name=%22snp__simple_somatic_mutation__dm__mutation_id%22/%3E%3CAttribute%20name=%22snp__simple_somatic_mutation__dm__mutation_type%22/%3E%3CAttribute%20name=%22snp__simple_somatic_mutation__dm__tumour_genotype%22/%3E%3CAttribute%20name=%22snp__simple_somatic_mutation__dm__mutation%22/%3E%3CAttribute%20name=%22snp__simple_somatic_mutation__dm__aa_mutation%22/%3E%3CAttribute%20name=%22snp__simple_somatic_mutation__dm__is_annotated%22/%3E%3CAttribute%20name=%22snp__simple_somatic_mutation__dm__validation_status%22/%3E%3CAttribute%20name=%22snp__simple_somatic_mutation__dm__gene_affected%22/%3E%3CAttribute%20name=%22snp__simple_somatic_mutation__dm__transcript_affected%22/%3E%3CAttribute%20name=%22snp__simple_somatic_mutation__dm__consequence_type%22/%3E%3C/Dataset%3E%3C/Query%3E In terms of possible solutions, the two Marie suggested may be feasible. It would be nice if this could be fixed at software level, so it won't be any problem for any one wants to do something similar. The root for this issue is that attributes/filters at present are access point specific, this makes sense in terms of GUI rendering, but for querying it may be better to fall back to a default access point where all attributes/filters defined in the source are available. We will definitely consider supporting that in future releases. Hope this explains everything. Let us know if you have any further questions. Junjun From: Marie Wong-Erasmus <[email protected]<mailto:[email protected]>> Date: Wed, 29 Jun 2011 13:10:23 -0400 To: "Estrella, Heather" <[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 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 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: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"/><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></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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