JChem upgrade issue

(Previously I have modified and re-generated all the tables in my JChem schema / I have not yet upgraded the cartridge)





I am in the process of upgrading to JChem version 3.0.12 and have completed the following tasks in two (XP / Linux)


tomcat domains:





1) Replaced all .jar files in /shared/lib with the latest versions





2) Placed latest jchemstreams.war file in /webapps





3) Replaced the jchem folder in /webapps so that the URL is referencing the latest 3.0.12 veriosn of the JSP application





4) Re-started TOMCAT server and ensured jchemstreams folder is created.





On my XP tomcat server I can access the JSP pages no problem, however on my Linux tomcat server


I get the following errors on moving from seltable.jsp to initsearch.jsp/searching.jsp, suggesting that


some of the JSP are not compiled correctly / certain methods are not being recognised?





Please find attached the catalina.out





Any ideas as two why my two environments apparently behave differently gratefully received as always!


(XP JAVA_HOME = C:\j2sdk1.4.2_04, Linux JAVA_HOME = j2sdk1.4.2_07)





Below is what I see in "initsearch.jsp"





HTTP Status 500 -





--------------------------------------------------------------------------------





type Exception report





message





description The server encountered an internal error () that prevented it from fulfilling this request.





exception





org.apache.jasper.JasperException: Unable to compile class for JSP





An error occurred at line: 60 in the jsp file: /examples/jsp1_x/searching.jsp


Generated servlet error:


/home/Tomcat5/jakarta-tomcat-5.0.28/work/Catalina/localhost/jchem/org/apache/jsp/examples/jsp1_005fx/searching_jsp.java:202: cannot resolve symbol


symbol : method checkFilter (java.lang.String,chemaxon.struc.Molecule)


location: class chemaxon.sss.search.MolSearch


MolSearch.checkFilter(chemterm, new MolHandler(molfile).getMolecule());


^








An error occurred at line: 113 in the jsp file: /examples/jsp1_x/searching.jsp


Generated servlet error:


/home/Tomcat5/jakarta-tomcat-5.0.28/work/Catalina/localhost/jchem/org/apache/jsp/examples/jsp1_005fx/searching_jsp.java:248: cannot resolve symbol


symbol : variable SUPERSTRUCTURE


location: class chemaxon.jchem.db.JChemSearch


searchType = JChemSearch.SUPERSTRUCTURE;


^








An error occurred at line: 173 in the jsp file: /examples/jsp1_x/searching.jsp


Generated servlet error:


/home/Tomcat5/jakarta-tomcat-5.0.28/work/Catalina/localhost/jchem/org/apache/jsp/examples/jsp1_005fx/searching_jsp.java:335: cannot resolve symbol


symbol : method setTimeout (int)


location: class chemaxon.jchem.db.JChemSearch


searcher.setTimeout(6);


^


3 errors











org.apache.jasper.compiler.DefaultErrorHandler.javacError(DefaultErrorHandler.java:84)


org.apache.jasper.compiler.ErrorDispatcher.javacError(ErrorDispatcher.java:332)


org.apache.jasper.compiler.Compiler.generateClass(Compiler.java:412)


org.apache.jasper.compiler.Compiler.compile(Compiler.java:472)


org.apache.jasper.compiler.Compiler.compile(Compiler.java:451)


org.apache.jasper.compiler.Compiler.compile(Compiler.java:439)


org.apache.jasper.JspCompilationContext.compile(JspCompilationContext.java:511)


org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:295)


org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:292)


org.apache.jasper.servlet.JspServlet.service(JspServlet.java:236)


javax.servlet.http.HttpServlet.service(HttpServlet.java:802)








note The full stack trace of the root cause is available in the Apache Tomcat/5.0.28 logs.

log file attached

Hi,





From the error log it seems your Linux machine still uses the old jar.


Please make sure that





- you have replaced the old jar files with the proper versions


- you do not have jchem.jar anywhere else in the Tomcat directory (e.g. under a WEB-INF/lib directory)


- you have restarted Tomcat





You can also try to delete the content of Tomcat's work directory:


<Tomcat_home>/work/





An other (unrelated) problem:





Sun's j2sdk1.4.2_07 has a JVM bug, which affects certain parts of our code.


(e.g. hit alignment will crash the JVM )


Please upgrade to 1.4.2_08, they have fixed this bug in that version.





Best regards,





Szilard

Yes, sorry, I assumed I had copied the jar files over correctly and had not!