Hi Rebecca, Depending on the server configuration both DB sources and HTTP could be affected by network issues.
The easiest way to figure this out might be if you do the following: - shut down your server - remove the current log files - add 'log.level = DEBUG' to your biomart.properties file (if it's not already there) - start your server back up - access the server to ensure the server log will contain some of the failing queries If you can then send me the contents of that log file directly to my email address as a file attachment it may help to try to solve the problem having that information. Brett On 5/6/11 11:23 AM, "Rebecca Shepherd" <[email protected]> wrote: >Hi Brett > >Our COSMIC mart data comes from our database and I can't get any data >back for that with rc5, but I can with rc4. > >Thanks > >Rebecca > >On 6 May 2011, at 16:21, Brett Whitty wrote: > >> Hi Rebecca, >> >> Is it possible there may be some network configuration issues with your >> server preventing it from accessing URL-based data sources? >> >> Check the log files for a message that contains the URL that the >> queryEngine was trying to access (should contain the text string 'URL' >>--- >> you may have to set log level to DEBUG). See if you can access the URL >> that the query engine is trying to access manually (via your browser, or >> something like curl or wget on the server itself). If that works fine, >> then at least we know the remote server is not the problem. >> >> Let me know what you find, and if you'd like to include the DEBUG level >> log snippet that includes the failed query URL as well that might be >> helpful. >> >> Regards, >> >> Brett >> >> On 5/6/11 10:53 AM, "Rebecca Shepherd" <[email protected]> wrote: >> >>> Hi >>> >>> I am using Biomart 0.8 rc5. I have sorted out the problem with the >>>server >>> but am unable to get any data. I am getting the following error in the >>> log file: >>> >>> java.net.ConnectException: Connection timed out >>> at java.net.PlainSocketImpl.socketConnect(Native Method) >>> at java.net.PlainSocketImpl.doConnect(PlainSocketImpl.java:333) >>> at java.net.PlainSocketImpl.connectToAddress(PlainSocketImpl.java:195) >>> at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:182) >>> at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:366) >>> at java.net.Socket.connect(Socket.java:519) >>> at java.net.Socket.connect(Socket.java:469) >>> at sun.net.NetworkClient.doConnect(NetworkClient.java:163) >>> at sun.net.www.http.HttpClient.openServer(HttpClient.java:394) >>> at sun.net.www.http.HttpClient.openServer(HttpClient.java:529) >>> at sun.net.www.http.HttpClient.<init>(HttpClient.java:233) >>> at sun.net.www.http.HttpClient.New(HttpClient.java:306) >>> at sun.net.www.http.HttpClient.New(HttpClient.java:323) >>> at >>> >>>sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(HttpURLConn >>>ec >>> tion.java:852) >>> at >>> >>>sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnecti >>>on >>> .java:793) >>> at >>> >>>sun.net.www.protocol.http.HttpURLConnection.connect(HttpURLConnection.ja >>>va >>> :718) >>> at >>> >>>sun.net.www.protocol.http.HttpURLConnection.getOutputStream(HttpURLConne >>>ct >>> ion.java:896) >>> at >>> >>>org.biomart.queryEngine.SubQuery.executeMartServiceQuery(SubQuery.java:7 >>>73 >>> ) >>> at org.biomart.queryEngine.SubQuery.executeQuery(SubQuery.java:698) >>> at >>> >>>org.biomart.queryEngine.QueryRunnerThread.recurseSubQueries(QueryRunnerT >>>hr >>> ead.java:173) >>> at >>> >>>org.biomart.queryEngine.QueryRunnerThread.call(QueryRunnerThread.java:75 >>>) >>> at >>> >>>org.biomart.queryEngine.QueryRunnerThread.call(QueryRunnerThread.java:36 >>>) >>> at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) >>> at java.util.concurrent.FutureTask.run(FutureTask.java:138) >>> at >>> java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:441) >>> at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) >>> at java.util.concurrent.FutureTask.run(FutureTask.java:138) >>> at >>> >>>java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecuto >>>r. >>> java:886) >>> at >>> >>>java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.ja >>>va >>> :908) >>> at java.lang.Thread.run(Thread.java:619) >>> 2011-05-06 15:47:28,880 WARN >>> [1763281041@qtp-1697022030-7:Slf4jLog.java:76]: /martservice/results: >>> java.io.IOException: Closed >>> >>> I am having a similar problem with our COSMIC mart. It seems to work >>>fine >>> using rc4 but I don't get any data using rc5. >>> >>> Do you have any idea what might be wrong? >>> >>> Thanks >>> >>> Rebecca >>> >>> On 5 May 2011, at 15:32, Brett Whitty wrote: >>> >>>> Hi Rebecca, >>>> >>>> That does seem unusual. Can you please tell me what version of BioMart >>>> you're running? >>>> Also, what are the specs if the server you're running on? You should >>>> have >>>> a look at the memory usage of the biomart java process as it's >>>>starting >>>> up >>>> to see if there's a problem with memory usage and available memory on >>>> the >>>> server. >>>> >>>> Also, it might be worth checking the log files under 'dist/logs' for >>>>any >>>> informative messages on startup; maybe post anything unusual you might >>>> find to the list. You can also try increasing the logging level to >>>> 'DEBUG' >>>> by adding 'log.level = DEBUG' in your biomart.properties file and see >>>>if >>>> that reveals anything more. >>>> >>>> Regards, >>>> >>>> Brett >>>> >>>> On 5/5/11 10:05 AM, "Rebecca Shepherd" <[email protected]> wrote: >>>> >>>>> I have our version of the ICGC mart up and running. However, it is >>>>> taking >>>>> over 40 minutes for the server to start. Is there anything I can do >>>>>to >>>>> speed it up? >>>> >>> >>> >>> >>> -- >>> The Wellcome Trust Sanger Institute is operated by Genome Research >>> Limited, a charity registered in England with number 1021457 and a >>> company registered in England with number 2742969, whose registered >>> office is 215 Euston Road, London, NW1 2BE. >> > > > >-- > The Wellcome Trust Sanger Institute is operated by Genome Research > Limited, a charity registered in England with number 1021457 and a > company registered in England with number 2742969, whose registered > office is 215 Euston Road, London, NW1 2BE. _______________________________________________ Users mailing list [email protected] https://lists.biomart.org/mailman/listinfo/users
