[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 version2.1 (build #2847; schema #20) Web server Apache Tomcat/5.5.20 Database Dialectorg.hibernate.dialect.PostgreSQLDialect JDBC Driver org.postgresql.Driver (version 8.1) Java runtimeJava(TM) 2 Runtime Environment, Standard Edition (1.5.0_06-b05), Sun Microsystems Inc. http://java.sun.com/ Operating systemLinux 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/extravaluetypes/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.java:563) ...at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java: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(ApplicationFilterChain.java:252) ...at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173) ...at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:672) ...at org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:463) ...at org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:398) ...at org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:301) ...at org.apache.jasper.runtime.PageContextImpl.doForward(PageContextImpl.java:688) ...at org.apache.jasper.runtime.PageContextImpl.forward(PageContextImpl.java:658) ...at org.apache.jsp.admin.extravaluetypes.index_jsp._jspService(index_jsp.java: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.java: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(ApplicationFilterChain.java:252) ...at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173) ...at net.sf.basedb.clients.web.servlet.CharacterEncodingFilter.doFilter(CharacterEncodingFilter.java:71) ...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
Re: [base] JEP extra value calculator again...
Emmanuel Courcelle wrote: 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] You can only calculate one extra value of each type per bioassayset. 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 ? Because the extra value type itself can be used in further calculations, filters, by plugins, etc. You then refer to it by the External ID of the extra value type. If there are more than one value for each type, it is not possible to know which one to choose. 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: It looks like some internal Tomcat error. Try removing everything from the /usr/local/apache-tomcat-5.5.20/work/Catalina/localhost/base2/ directory. /Nicklas Base version 2.1 (build #2847; schema #20) Web serverApache 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 MemoryTotal: 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/extravaluetypes/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.java:563) ...at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java: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(ApplicationFilterChain.java:252) ...at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173) ...at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:672) ...at org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:463) ...at org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:398) ...at org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:301) ...at org.apache.jasper.runtime.PageContextImpl.doForward(PageContextImpl.java:688) ...at org.apache.jasper.runtime.PageContextImpl.forward(PageContextImpl.java:658) ...at org.apache.jsp.admin.extravaluetypes.index_jsp._jspService(index_jsp.java: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.java: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(ApplicationFilterChain.java:252) ...at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173) ...at
Re: [base] JEP extra value calculator again...
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 serverApache 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 MemoryTotal: 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
Re: [base] JEP extra value calculator again...
Micha Bayer a écrit : 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. Right, Micha, some files and directories did in fact belong to root The pb is fixed now Thanks for your help ! -- 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.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
