Thanks for the rapid response! I managed to sort the second problem out, it seems that an increase in the memory allocated to Tomcat solved it...all samples are now found!
With regards to the termination of my session when working on the main Samples page (with +/- 85 annotation fields visible). I've looked at the Tomcat log, but I'm not to sure what to look for. The log data is included at the end of this msg (first bit is generated when I navigate to the Samples page, 2nd bit is generated when I try and open any window from this page) below. I've tried to do some diagnostics and the problem seems to be related to the number of annotation fields visible in the main view. As soon as I reduce the number of annotation columns to 62 everything works fine. Having looked at why 63 fields seem to produce some limit I found that the URL being passed to backend (URL in address bar of error page) seems to be truncated (with the cmd function, which is Import in this case, being truncated as "impo" (see below). The Web interface also generates an error saying "Invalid command: The command Impo is not recognised as a valid command." (Screenshot can be sent.) http://xx.xx.xx/base2/biomaterials/samples/index.jsp?rowsperpage=10&presetselector=&filter%3ASTRING%3Aname=%25WBA%25.plasma&filter%3ASTRING%3AexternalId=&filter%3AFLOAT%3AoriginalQuantity=&filter%3AFLOAT%3AremainingQuantity=&filter%3ASTRING%3AcreationEvent.protocol.name=&filter%3ADATE%3AcreationEvent.eventDate=&filter%3ADATE%3AcreationEvent.entryDate=&filter%3ABOOLEAN%3Apooled=&filter%3ASTRING%3Aowner.name=&filter%3ASTRING%3Adescription=&permission=&filter%3ADOUBLE%3A%2337=&filter%3ADOUBLE%3A%2338=&filter%3ADOUBLE%3A%2336=&filter%3ADOUBLE%3A%2386=&filter%3ADOUBLE%3A%2385=&filter%3ADOUBLE%3A%2384=&filter%3ADOUBLE%3A%2350=&filter%3ADOUBLE%3A%2349=&filter%3ADOUBLE%3A%2348=&filter%3ADOUBLE%3A%2376=&filter%3ADOUBLE%3A%2377=&filter%3ADOUBLE%3A%2375=&filter%3ADOUBLE%3A%2379=&filter%3ADOUBLE%3A%2380=&filter%3ADOUBLE%3A%2378=&filter%3ADOUBLE%3A%2356=&filter%3ADOUBLE%3A%2355=&filter%3ADOUBLE%3A%2354=&filter%3ADOUBLE%3A%2390=&filter%3ADOUBLE%3A%2391=&filter%3ADOUBLE%3A%2389=&filter%3A DOUBLE%3A%2358=&filter%3ADOUBLE%3A%2359=&filter%3ADOUBLE%3A%2357=&filter%3ADOUBLE%3A%2362=&filter%3ADOUBLE%3A%2361=&filter%3ADOUBLE%3A%2360=&filter%3ADOUBLE%3A%2365=&filter%3ADOUBLE%3A%2364=&filter%3ADOUBLE%3A%2363=&filter%3ADOUBLE%3A%2368=&filter%3ADOUBLE%3A%2367=&filter%3ADOUBLE%3A%2366=&filter%3ADOUBLE%3A%2370=&filter%3ADOUBLE%3A%2371=&filter%3ADOUBLE%3A%2369=&filter%3ADOUBLE%3A%2322=&filter%3ADOUBLE%3A%2323=&filter%3ADOUBLE%3A%2321=&filter%3ADOUBLE%3A%2328=&filter%3ADOUBLE%3A%2329=&filter%3ADOUBLE%3A%2327=&filter%3ADOUBLE%3A%2325=&filter%3ADOUBLE%3A%2326=&filter%3ADOUBLE%3A%2324=&filter%3ADOUBLE%3A%2331=&filter%3ADOUBLE%3A%2332=&filter%3ADOUBLE%3A%2330=&filter%3ADOUBLE%3A%2334=&filter%3ADOUBLE%3A%2335=&filter%3ADOUBLE%3A%2333=&filter%3ADOUBLE%3A%2340=&filter%3ADOUBLE%3A%2341=&filter%3ADOUBLE%3A%2339=&filter%3ADOUBLE%3A%2343=&filter%3ADOUBLE%3A%2344=&filter%3ADOUBLE%3A%2342=&filter%3ADOUBLE%3A%2352=&filter%3ADOUBLE%3A%2353=&filter%3ADOUBLE%3A%2351=&filter%3ADOUBLE%3A%237 3=&filter%3ADOUBLE%3A%2374=&filter%3ADOUBLE%3A%2372=&rowsperpage=10&ID=4721ceb93fa55a04&cmd=Impo As soon as the annotation fields are increased to 64, I get an error saying that Im no longer logged in or that BASE has been restarted. I presume this is because the &ID=xxxxxxxxxxxx bit is being truncated? At 62 annotation fields, the Import screen activated without any problems and the URL in the address bar is: http://xx.xx.xx/base2/common/import/index.jsp?ID=bf0b70ec121da201&cmd=SelectPlugin&item_type=SAMPLE&context_type=LIST&title=Import+sample Any ideas as to how to get around this problem will be greatly appreciated!! TOMCAT LOG #1 [Navigating to Samples view] org.apache.jsp.biomaterials.samples.index_jsp._jspService(index_jsp.java:85) at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:97) at javax.servlet.http.HttpServlet.service(HttpServlet.java:802) at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:332) at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:314) at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:264) at javax.servlet.http.HttpServlet.service(HttpServlet.java:802) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:252) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173) at net.sf.basedb.clients.web.servlet.CharacterEncodingFilter.doFilter(CharacterEncodingFilter.java:72) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.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.core.StandardEngineValve.invoke(StandardEngineValve.java:107) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:148) at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:869) at org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:664) at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:527) at org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:80) at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:684) at java.lang.Thread.run(Thread.java:595) #2[Clicking on Import button (opens new window which gives not logged in error)] 12:14:43,458 ERROR [jsp]:253 - Servlet.service() for servlet jsp threw exception net.sf.basedb.core.NotLoggedInException: Permission denied: Not logged in. at net.sf.basedb.clients.web.Base.getExistingSessionControl(Base.java:155) at org.apache.jsp.biomaterials.samples.index_jsp._jspService(index_jsp.java:85) at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:97) at javax.servlet.http.HttpServlet.service(HttpServlet.java:802) at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:332) at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:314) at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:264) at javax.servlet.http.HttpServlet.service(HttpServlet.java:802) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:252) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173) at net.sf.basedb.clients.web.servlet.CharacterEncodingFilter.doFilter(CharacterEncodingFilter.java:72) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.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.core.StandardEngineValve.invoke(StandardEngineValve.java:107) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:148) at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:869) at org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:664) at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:527) at org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:80) at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:684) at java.lang.Thread.run(Thread.java:595) Regards, Johan van Heerden --- Nicklas Nordborg <[EMAIL PROTECTED]> wrote: > Johan van Heerden wrote: > > Hi all, > > > > I've been experiencing strange problems (BASE > V2.4.5) > > with sample annotations. The first problem seems > to > > be related to a limit on the number of annotation > > fields allowed (I'm not sure if there is a > limit?). I > > have been trying to attach non-array type data to > > samples as annotations. Specifically, I have 83 > > annotation fields per sample. I managed to create > all > > annotation types without any hitches, but as soon > as I > > go to the Samples page and try to initiate any > other > > action (e.g. importing of annotation data) from > this > > page I get a msg saying that I'm not logged in, OR > > that the server has been restarted. I've manage to > > avoid this problem, however, if I reduce the > number of > > annotation fields to somewhere < 50 (I haven't > > determined the exact limit yet). Any ideas why > this > > should happen? > > There is no special limit. Have you checked Tomcat's > logfile for any > error messages? The message about being logged out > is typical when an > unexpected error happens during the page generation > befor the session ID > has been written to the output. You have not > actually been logged out. > Going back to the previous page would allow you to > continue working. > > > > > The second problem relates to the annotation > importer > > (this might be related to the first). Once I've > > reduced the number of annotation fields to enable > me > > to initialise the importer wizard, I manage to > start > > the importing of data, but keep on getting a msg > > saying that: > > "Item not found: Sample[name=T10656.b1.WBA.plasma] > on > > line 2: T10656.b1.WBA.pla..." > > > > I've tried to create simpler sample entries (i.e. > Not > > seperated by "."), but this generates the same > error > > msg. I've previously had this working, which > leaves > > me somewhat baffled? Any ideas? > > The samples must exists before running the > annotation importer. If they > do, make sure that you set the options where the > annotation importer > should look for them (owned by you, in the current > projects, etc...) > > /Nicklas > > ------------------------------------------------------------------------- > Check out the new SourceForge.net Marketplace. > It's the best place to buy or sell services for > just about anything Open Source. > http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace > _______________________________________________ > The BASE general discussion mailing list > basedb-users@lists.sourceforge.net > unsubscribe: send a mail with subject "unsubscribe" > to > [EMAIL PROTECTED] > ____________________________________________________________________________________ Looking for last minute shopping deals? Find them fast with Yahoo! Search. http://tools.search.yahoo.com/newsearch/category.php?category=shopping ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
