Hi Emmanuel, The Catalina/work directory caches copies of your compiled JSP pages. It looks from the stacktrace like the JSP compiler can't write to the work directory because you don't have permissions to it -- check what they are set to.
Cheers Micha ================================== Dr Micha M Bayer Bioinformatics Specialist Genetics Programme The Scottish Crop Research Institute Invergowrie Dundee DD2 5DA Scotland, UK Telephone +44(0)1382 562731 ext. 2309 Fax +44(0)1382 562426 http://www.scri.sari.ac.uk/MichaBayer.htm ============================= > -----Original Message----- > From: [EMAIL PROTECTED] [mailto:basedb-users- > [EMAIL PROTECTED] On Behalf Of Emmanuel Courcelle > Sent: 30 November 2006 09:23 > To: BASE ML > Subject: [base] JEP extra value calculator again... > > Hi all. > Sorry to bother you again with this point, but I still does not > understand everything... > > I tried to define a new type, called "float colored": it is a float, > colored with min value as 0, max as 0, mid as 5 > I want to add 2 values to my data: > -2 * (ch(1) / ch(2)) > -3 * (ch(1) / ch(2)) > (Probably stupid for the analysis, but I just want to check the > functionality) > > So, I tried the JEP extra value calculator, specifying float coloured as > a data type, and 2 * (ch(1) / ch(2)) as the expression. Then, I give a > look to the data, and it works: the numbers are preceded with a little > coloured square, the colour depends on the value. > Great, indeed. > > So, I tried a second run, this time with 3 * (ch(1) / ch(2)) as > expression. It got the following error message: > > "The bioassay set already has extra values of the type: Extra value > type[id=2824; name=float colored]" > > This sounds very strange to me: If "float colored" is an "Extra Value > Type", (this sounds to me as some data type, it's not right ?) why > should it be applied ONLY one time ? > > -------------------------------------------- > > Something else, which is probably a bug. When I go to > Administrate/Types/Extra value types, I click on any extra type declared > (for instance for editing the type), I get the following: > > Base version 2.1 (build #2847; schema #20) > Web server Apache Tomcat/5.5.20 > Database Dialect org.hibernate.dialect.PostgreSQLDialect > JDBC Driver org.postgresql.Driver (version 8.1) > Java runtime Java(TM) 2 Runtime Environment, Standard Edition > (1.5.0_06-b05), Sun Microsystems Inc. <http://java.sun.com/> > Operating system Linux i386 2.6.16-2-em64t-p4-smp > Memory Total: 155.3 MB > Free: 30.9 MB > Max: 986.1 MB > Browser Mozilla/5.0 (X11; U; Linux i686; fr; rv:1.8.1) Gecko/20061010 > Firefox/2.0 > Error message > /usr/local/apache-tomcat- > 5.5.20/work/Catalina/localhost/base2/org/apache/jsp/admin/extravaluetype s/ > view_005fextravaluetype_jsp.java > (Permission denied) > Stack trace > > ...at java.io.FileOutputStream.open(Native Method) > ...at java.io.FileOutputStream.(Unknown Source) > ...at java.io.FileOutputStream.(Unknown Source) > ...at org.apache.jasper.compiler.Compiler.generateJava(Compiler.java:140) > ...at org.apache.jasper.compiler.Compiler.compile(Compiler.java:295) > ...at org.apache.jasper.compiler.Compiler.compile(Compiler.java:276) > ...at org.apache.jasper.compiler.Compiler.compile(Compiler.java:264) > ...at > org.apache.jasper.JspCompilationContext.compile(JspCompilationContext.ja va > :563) > > ...at > org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.ja va > :305) > ...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(Applica ti > onFilterChain.java:252) > ...at > org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilt er > Chain.java:173) > ...at > org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatc he > r.java:672) > ...at > org.apache.catalina.core.ApplicationDispatcher.processRequest(Applicatio nD > ispatcher.java:463) > ...at > org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDisp at > cher.java:398) > ...at > org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispat ch > er.java:301) > ...at > org.apache.jasper.runtime.PageContextImpl.doForward(PageContextImpl.java :6 > 88) > ...at > org.apache.jasper.runtime.PageContextImpl.forward(PageContextImpl.java:6 58 > ) > ...at > org.apache.jsp.admin.extravaluetypes.index_jsp._jspService(index_jsp.jav a: > 278) > ...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.ja va > :334) > ...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(Applica ti > onFilterChain.java:252) > ...at > org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilt er > Chain.java:173) > ...at > net.sf.basedb.clients.web.servlet.CharacterEncodingFilter.doFilter(Chara ct > erEncodingFilter.java:71) > ...at > org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applica ti > onFilterChain.java:202) > ...at > org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilt er > Chain.java:173) > ...at > org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValv e. > java:213) > ...at > org.apache.catalina.core.StandardContextValve.invoke(StandardContextValv e. > java:178) > ...at > org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java :1 > 26) > ...at > org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java :1 > 05) > ...at > org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve. ja > va:107) > ...at > org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:1 48 > ) > ...at > org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:86 9) > ...at > org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.proc es > sConnection(Http11BaseProtocol.java:664) > ...at > org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint .j > ava:527) > ...at > org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollow er > WorkerThread.java:80) > ...at > org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool .j > ava:684) > ...at java.lang.Thread.run(Unknown Source) > > > > -- > Emmanuel COURCELLE [EMAIL PROTECTED] > L.I.P.M. (UMR CNRS-INRA 2594/441) tel (33) 5-61-28-54-50 > B.P.52627 - 31326 CASTANET TOLOSAN Cedex - FRANCE > ------ > > > > ------------------------------------------------------------------------ - > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share > your > opinions on IT & business topics through brief surveys - and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDE V > _______________________________________________ > The BASE general discussion mailing list > basedb-users@lists.sourceforge.net > unsubscribe: send a mail with subject "unsubscribe" to > [EMAIL PROTECTED] _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ DISCLAIMER: This email is from the Scottish Crop Research Institute, but the views expressed by the sender are not necessarily the views of SCRI and its subsidiaries. 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