JChem updates

Hi,


COuld you enlist the changes that need to be done when one installs a new version of JChem(e.g regenrating tables, replacing jchem.jar etc). Also, if for some reason, if I would like to download an earlier version of JChem, is there a link where you place your archives for download


Thanks!

Hi,

Quote:

COuld you enlist the changes that need to be done when one installs a new version of JChem(e.g regenrating tables, replacing jchem.jar etc).

Please see the following topic, let me know if you have further questions:





http://www.chemaxon.com/forum/viewpost3959.html width="90%" cellspacing="0" cellpadding="3" border="0" align="center"> Quote:


Also, if for some reason, if I would like to download an earlier version of JChem, is there a link where you place your archives for download You can find this link on our regular download page:


http://www.chemaxon.com/download.php?d=/data/download/jchem





Please note, that downgrading to an older version is not supported in JChem - you should create a new property table and new tables if testing an older version.





Best regards,





Szilard

Hi,


I just updated to JChem5 and did all that you suggested when doing the update. I get this error:

Code:

JChem version : 5.0.0 JVM : Apple Computer, Inc. 1.4.2_09 OS  : ppc Mac OS X 10.4.2 Stack trace: ------------ java.lang.SecurityException: class "chemaxon.util.DotfileUtil"'s signer information does not match signer information of other classes in the same package    at java.lang.ClassLoader.checkCerts(ClassLoader.java:611)    at java.lang.ClassLoader.defineClass(ClassLoader.java:532)    at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:123)    at org.apache.catalina.loader.WebappClassLoader.findClassInternal(WebappClassLoader.java:1679)    at org.apache.catalina.loader.WebappClassLoader.findClass(WebappClassLoader.java:968)    at org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java:1409)    at org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java:1289)    at org.apache.jasper.servlet.JasperLoader.loadClass(JasperLoader.java:197)    at org.apache.jasper.servlet.JasperLoader.loadClass(JasperLoader.java:131)    at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:302)    at org.apache.jsp.setup_jsp._jspService(setup_jsp.java:53)    at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:137)    at javax.servlet.http.HttpServlet.service(HttpServlet.java:853)    at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:210)    at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:295)    at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:241)    at javax.servlet.http.HttpServlet.service(HttpServlet.java:853)    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:247)    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:193)    at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:256)    at org.apache.catalina.core.StandardPipeline$StandardPipelineValveContext.invokeNext(StandardPipeline.java:643)    at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:480)    at org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java:995)    at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191)    at org.apache.catalina.core.StandardPipeline$StandardPipelineValveContext.invokeNext(StandardPipeline.java:643)    at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:480)    at org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java:995)    at org.apache.catalina.core.StandardContext.invoke(StandardContext.java:2417)    at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:180)    at org.apache.catalina.core.StandardPipeline$StandardPipelineValveContext.invokeNext(StandardPipeline.java:643)    at org.apache.catalina.valves.ErrorDispatcherValve.invoke(ErrorDispatcherValve.java:171)    at org.apache.catalina.core.StandardPipeline$StandardPipelineValveContext.invokeNext(StandardPipeline.java:641)    at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:172)    at org.apache.catalina.core.StandardPipeline$StandardPipelineValveContext.invokeNext(StandardPipeline.java:641)    at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:480)    at org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java:995)    at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:174)    at org.apache.catalina.core.StandardPipeline$StandardPipelineValveContext.invokeNext(StandardPipeline.java:643)    at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:480)    at org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java:995)    at org.apache.ajp.tomcat4.Ajp13Processor.process(Ajp13Processor.java:457)    at org.apache.ajp.tomcat4.Ajp13Processor.run(Ajp13Processor.java:576)    at java.lang.Thread.run(Thread.java:552)

Hi,





The jchem.jar in 5.0.0 was not signed, and it can cause problems in certain circumstances.


This has been fixed, please upgrade to 5.0.1.





Please also make sure that only jchem.jar is present in the lib directory of the web server (e.g. Tomcat), you should NOT place MarvinBeans.jar there (jchem already contains all the the classes of this jar).





Best regards,





Szilard

Thanks! However, after updating to 5.0.1, I am getting a new error message:

Code:

JChem version : 5.0.1 JVM : Apple Computer, Inc. 1.4.2_09 OS  : ppc Mac OS X 10.4.2 Stack trace: ------------ java.lang.InternalError: Can't connect to window server - not enough permissions.    at java.lang.ClassLoader$NativeLibrary.load(Native Method)    at java.lang.ClassLoader.loadLibrary0(ClassLoader.java:1586)    at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1503)    at java.lang.Runtime.loadLibrary0(Runtime.java:788)    at java.lang.System.loadLibrary(System.java:834)    at sun.security.action.LoadLibraryAction.run(LoadLibraryAction.java:50)    at java.security.AccessController.doPrivileged(Native Method)    at java.awt.Toolkit.loadLibraries(Toolkit.java:1437)    at java.awt.Toolkit.(Toolkit.java:1458)    at java.awt.Color.(Color.java:250)    at chemaxon.util.HitColoringAndAlignmentOptions.(HitColoringAndAlignmentOptions.java:85)    at org.apache.jsp.searchresults_jsp._jspService(searchresults_jsp.java:861)    at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:137)    at javax.servlet.http.HttpServlet.service(HttpServlet.java:853)    at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:210)    at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:295)    at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:241)    at javax.servlet.http.HttpServlet.service(HttpServlet.java:853)    at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:684)    at org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:432)    at org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:356)    at org.apache.jasper.runtime.PageContextImpl.forward(PageContextImpl.java:430)    at org.apache.jsp.searching_jsp._jspService(searching_jsp.java:523)    at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:137)    at javax.servlet.http.HttpServlet.service(HttpServlet.java:853)    at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:210)    at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:295)    at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:241)    at javax.servlet.http.HttpServlet.service(HttpServlet.java:853)    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:247)    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:193)    at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:256)    at org.apache.catalina.core.StandardPipeline$StandardPipelineValveContext.invokeNext(StandardPipeline.java:643)    at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:480)    at org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java:995)    at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191)    at org.apache.catalina.core.StandardPipeline$StandardPipelineValveContext.invokeNext(StandardPipeline.java:643)    at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:480)    at org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java:995)    at org.apache.catalina.core.StandardContext.invoke(StandardContext.java:2417)    at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:180)    at org.apache.catalina.core.StandardPipeline$StandardPipelineValveContext.invokeNext(StandardPipeline.java:643)    at org.apache.catalina.valves.ErrorDispatcherValve.invoke(ErrorDispatcherValve.java:171)    at org.apache.catalina.core.StandardPipeline$StandardPipelineValveContext.invokeNext(StandardPipeline.java:641)    at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:172)    at org.apache.catalina.core.StandardPipeline$StandardPipelineValveContext.invokeNext(StandardPipeline.java:641)    at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:480)    at org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java:995)    at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:174)    at org.apache.catalina.core.StandardPipeline$StandardPipelineValveContext.invokeNext(StandardPipeline.java:643)    at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:480)    at org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java:995)    at org.apache.ajp.tomcat4.Ajp13Processor.process(Ajp13Processor.java:457)    at org.apache.ajp.tomcat4.Ajp13Processor.run(Ajp13Processor.java:576)    at java.lang.Thread.run(Thread.java:552)

Hi,





This error seems to be an environment specific problem.





Please run the Tomcat JVM in headless mode.

Quote:

export CATALINA_OPTS="-Djava.awt.Headless=true"

If this doesn't help here is an other suggestion that seems to work for Mac users:

Quote:

You can run Xvfb, the X virtual frame buffer, as the tomcat user on display 1 (or any other number besides 0) and then set DISPLAY=:1 in Tomcat's environment. It's basically a mini X server, and AWT will be perfectly happy with it. I've done this instead of using headless mode. Works great for testing GUI code, too.

http://saloon.javaranch.com/cgi-bin/ubb/ultimatebb.cgi?ubb=get_topic&f=2&t=011572





Best regards,





Szilard

I almost never seem to get it right when updating to a newer version of JChem. I have updated to 5.3.1; regenerated tables using jcman (5.3.1); loaded everything in the /lib directory to Tomcat /lib directory; deleted the .java and .class files in the Tomcat /work directory; restarted Tomcat. Tried to access /examples/db_search/

The error :

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

An error occurred at line: 60 in the generated java file
The method getJspApplicationContext(ServletContext) is undefined for the type JspFactory

Stacktrace:
	org.apache.jasper.compiler.DefaultErrorHandler.javacError(DefaultErrorHandler.java:92)
	org.apache.jasper.compiler.ErrorDispatcher.javacError(ErrorDispatcher.java:330)
	org.apache.jasper.compiler.JDTCompiler.generateClass(JDTCompiler.java:439)
	org.apache.jasper.compiler.Compiler.compile(Compiler.java:334)
	org.apache.jasper.compiler.Compiler.compile(Compiler.java:312)
	org.apache.jasper.compiler.Compiler.compile(Compiler.java:299)
	org.apache.jasper.JspCompilationContext.compile(JspCompilationContext.java:589)
	org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:317)
	org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:313)
	org.apache.jasper.servlet.JspServlet.service(JspServlet.java:260)
	javax.servlet.http.HttpServlet.service(HttpServlet.java:853)

Hi,

 

deleted the .java and .class files in the Tomcat /work directory;

We advise to simply delete all contents of the work directory.

The method getJspApplicationContext(ServletContext) is undefined for the type JspFactory

This looks like a sign of conflicting servlet.jar versions.

If deleting everything from the work directory and restart does not help:

- Make sure no conflicting .jar versions are found in different lib directories of Tomcat (e.g. "global" v.s. WEB-INF/lib)

- Make sure you do not have  a servlet jar in your lib/ext directory of your JRE or SDK used by Tomcat

- Although it is usually not necessary, you may try to remove the servlet.jar from the lib directory of Tomcat which was shipped with Jchem. If this helps please let us know your exact Tomcat versions, and which lib directory you have used.

Best regards,

Szilard