From dag at sonsorol.org Thu Feb 17 08:50:55 2005 From: dag at sonsorol.org (Chris Dagdigian) Date: Thu Feb 17 08:46:18 2005 Subject: [DAS] Important info for all Open-Bio affiliated developers (people with CVS write access...) Message-ID: <4214A13F.6010006@sonsorol.org> Hi folks, apologies for the large cross-posting. Really short summary: We are going to migrate to newer server hardware over the next few months. If you are an OBF developer (someone who has a login account on "pub" with CVS write permission to one or more repositories) then you'll need to make sure we have your most current email address so we can communicate the transition plan directly without spamming N number of mailing lists. We need updated contact info in order to manage the transition. Details below. Long winded details: Our existing servers (the developer CVS repository and the 2nd system that handles websites & mailing lists) are getting a bit old and more importantly are running older Linux distributions that are long past official support dates and are difficult to update, secure and maintain. We have 2 brand new servers sitting online in a Boston area colocation facility and the various OBF sysadmins are starting to think about planning for transitioning services and user accounts. First to move (I suspect) is going to be the pub.open-bio.org system which is the main CVS sourcecode repository for our various projects such as biojava, bioperl, moby, etc. We think the transition will be pretty quick and transparent. It should not be all that hard to migrate the user accounts and copy over the CVS repository tree. We'll be writing scripts to automate the process and can run repeated migration tests before officially switching on the new system. What CVS committers and developers need to do ============================================= 1. SSH login to pub.open-bio.org 2. Run the "chfn" command to edit your user info 3. Make sure a good email address is listed for the Office: or Phone: field. Info about your project and institution would be great as well but is not required. In a week's time I'm going to capture all the email addresses listed and will insert them into a mailing list that we'll use to communicate our plans. This way we can speak to developers directly without cross posting to many mailing lists. Any user account without a full name and working email address will still be migrated but we are going to lockout the password until we hear from the person in question. What OBF Project Leaders need to do ==================================== 1. Login to pub.open-bio.org 2. Check /etc/groups for your project name and examine the users who have write access to your repository -- Email root-l@open-bio.org with the usernames of any inactive members who can safely be deleted. Regards, Chris one of the open-bio admins (root-l@open-bio.org) -- Chris Dagdigian, BioTeam - Independent life science IT & informatics consulting Office: 617-665-6088, Mobile: 617-877-5498, Fax: 425-699-0193 PGP KeyID: 83D4310E iChat/AIM: bioteamdag Web: http://bioteam.net From Jonathan.Warren at agresearch.co.nz Mon Feb 21 22:35:07 2005 From: Jonathan.Warren at agresearch.co.nz (Warren, Jonathan) Date: Mon Feb 21 22:30:24 2005 Subject: [DAS] SEVERE: DazzleServerMain: DAS Error Message-ID: Can anyone point me in the direction of why I would get the following error? We recently upgraded to the new version of dazzle and our old and new data sources now don't work. The reference servers for ensembl versions 25_34 and 18_34 work fine, but our extra annotations in generic feature tables return the following errors when a features?segment=1,1000 or something similar is used. (They show up as sources just fine). 22/02/2005 16:23:44 org.apache.catalina.core.ApplicationContext log SEVERE: DazzleServerMain: DAS Error java.util.NoSuchElementException at java.util.StringTokenizer.nextToken(StringTokenizer.java:259) at org.biojava.servlets.dazzle.DazzleServlet.getSegments(DazzleServlet.java :617) at org.biojava.servlets.dazzle.DazzleServlet.featuresCommand(DazzleServlet. java:906) at org.biojava.servlets.dazzle.DazzleServlet.doGet(DazzleServlet.java:257) at javax.servlet.http.HttpServlet.service(HttpServlet.java:689) at javax.servlet.http.HttpServlet.service(HttpServlet.java:802) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applica tionFilterChain.java:237) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilt erChain.java:157) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValv e.java:214) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValv e.java:178) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java :126) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java :105) at org.apache.catalina.valves.FastCommonAccessLogValve.invoke(FastCommonAcc essLogValve.java:481) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve. java:107) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:1 48) at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:82 5) at org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.processC onnection(Http11Protocol.java:731) at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint .java:526) at org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollow erWorkerThread.java:80) at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool .java:684) at java.lang.Thread.run(Thread.java:534) Config snippet below: ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= From td2 at sanger.ac.uk Tue Feb 22 04:16:39 2005 From: td2 at sanger.ac.uk (Thomas Down) Date: Tue Feb 22 04:16:31 2005 Subject: [DAS] SEVERE: DazzleServerMain: DAS Error In-Reply-To: References: Message-ID: <911c858d92ccde68f306d33cca697ebd@sanger.ac.uk> On 22 Feb 2005, at 03:35, Warren, Jonathan wrote: > Can anyone point me in the direction of why I would get the following > error? > > We recently upgraded to the new version of dazzle and our old and new > data sources now don't work. > > The reference servers for ensembl versions 25_34 and 18_34 work fine, > but our extra annotations in generic feature tables return the > following > errors when a features?segment=1,1000 or something similar is used. > (They show up as sources just fine). I think there's an error in the request there. You can do either: features?segment=1 (all features on the sequence named "1") or: features?segment=1:1,1000 (features overlapping positions 1-1000 on "1") But I don't know of any valid request type which just uses two numbers. The error you're showing comes from the code which parses the "segment=" part of the request. Am I missing something here? Thomas. From Jonathan.Warren at agresearch.co.nz Tue Feb 22 17:06:10 2005 From: Jonathan.Warren at agresearch.co.nz (Warren, Jonathan) Date: Tue Feb 22 17:02:03 2005 Subject: [DAS] SEVERE: DazzleServerMain: DAS Error Message-ID: Hi Thomas Amazingly I do seem to have used the wrong request consistently with the annotation servers but not with the reference server - I apologise. We are getting another error with our new annotations to the new reference server however ? SEVERE: Servlet.service() for servlet DazzleServerMain threw exception java.lang.IndexOutOfBoundsException: max must exceed min: min=2147400001, max=-2147467296 at org.biojava.bio.symbol.RangeLocation.(RangeLocation.java:61) at org.ensembl.das.GenericSeqFeatureSource$TiledFeatures.(GenericSeqF eatureSource.java:403) at org.ensembl.das.GenericSeqFeatureSource.getFeatures(GenericSeqFeatureSou rce.java:225) at org.biojava.servlets.dazzle.DazzleServlet.featuresCommand(DazzleServlet. java:933) at org.biojava.servlets.dazzle.DazzleServlet.doGet(DazzleServlet.java:257) at javax.servlet.http.HttpServlet.service(HttpServlet.java:689) at javax.servlet.http.HttpServlet.service(HttpServlet.java:802) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applica tionFilterChain.java:237) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilt erChain.java:157) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValv e.java:214) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValv e.java:178) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java :126) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java :105) at org.apache.catalina.valves.FastCommonAccessLogValve.invoke(FastCommonAcc essLogValve.java:481) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve. java:107) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:1 48) at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:82 5) at org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.processC onnection(Http11Protocol.java:731) at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint .java:526) at org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollow erWorkerThread.java:80) at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool .java:684) at java.lang.Thread.run(Thread.java:534) -----Original Message----- From: Thomas Down [mailto:td2@sanger.ac.uk] Sent: Tuesday, February 22, 2005 10:17 PM To: Warren, Jonathan Cc: das@biodas.org Subject: Re: [DAS] SEVERE: DazzleServerMain: DAS Error On 22 Feb 2005, at 03:35, Warren, Jonathan wrote: > Can anyone point me in the direction of why I would get the following > error? > > We recently upgraded to the new version of dazzle and our old and new > data sources now don't work. > > The reference servers for ensembl versions 25_34 and 18_34 work fine, > but our extra annotations in generic feature tables return the > following > errors when a features?segment=1,1000 or something similar is used. > (They show up as sources just fine). I think there's an error in the request there. You can do either: features?segment=1 (all features on the sequence named "1") or: features?segment=1:1,1000 (features overlapping positions 1-1000 on "1") But I don't know of any valid request type which just uses two numbers. The error you're showing comes from the code which parses the "segment=" part of the request. Am I missing something here? Thomas. ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. =======================================================================