installation & Java problems

Hello,


my applet gives back this Code:





java.lang.AbstractMethodError: chemaxon.marvin.view.swing.ViewHandler.a(Lchemaxon/marvin/view/swing/ViewPanel;Ljavax/swing/JFrame;)V


at chemaxon.marvin.view.swing.ViewPanel.E(Unknown Source)


at chemaxon.marvin.common.swing.MolPanel.init(Unknown Source)


at chemaxon.marvin.common.swing.MolPanel.init(Unknown Source)


at JMView.init(Unknown Source)


at sun.applet.AppletPanel.run(Unknown Source)


at java.lang.Thread.run(Unknown Source)





I don't know where I find these files and how to implemtate.





I use:


OS Win2K3 SP2 R1


Coldfusion Server 7.0


J2SE 5.0.7


Java Platform EE 5.0 SDK


Internet Explorer


Apache webserver


MySQL 5


marvin all 4.1.0


JChem 3.1.7.1





Coldfusion CLASS PATH = "D:/www/openlims"





.jar files:


PATH = "D:/www/openlims/"


jchem.jar


jmarvin.jar


marvin.jar





when I run jman.bat I get this message:


An error occured


java.lang.ClassNotFoundException


SQL





I have nearly no clou about Java and so I don't know where to search for the errors.


I would appreciate any suggestion and help.





Thanxs


TimE

Hi,





A quick tip for the java.lang.AbstractMethodError in the applet:





- make sure no ChemAxon jar files are present in the CLASSPATH environment variable on the client computer (where the browser runs)


- clear the JVM cache and also the browser cache if necessary





Let us know if it helps.

Quote:

when I run jman.bat I get this message: An error occured java.lang.ClassNotFoundException SQL

Please always post a full stack trace when available, this can save a lot of time.


So far a I suspect that the JDBC driver is not in your CLASSPATH.


Please visit this link for more detailed explanation:





http://www.chemaxon.com/forum/ftopic944.html





Best regards,





Szilard

Hello,


thanks first, but it's getting worse.


frist: which is the ENVOIMENT VARIABLE NAME

Quote:

You should include the JDBC driver .jar file into your CLASSPATH environment variable. Under Windows XP: Start menu -> Control panel -> System-> Advanced -> Environment variables

I know the value, but not the NAME (??)





second: how do I clear JVM Cache??





third: when starting Jcman, in the window Connecting to Database what should I write into

Quote:

JDBC driver:

here the stack trace:





java.lang.ClassNotFoundException: chemaxon.marvin.view.swing.modules.GridBagView


at sun.applet.AppletClassLoader.findClass(Unknown Source)


at java.lang.ClassLoader.loadClass(Unknown Source)


at sun.applet.AppletClassLoader.loadClass(Unknown Source)


at java.lang.ClassLoader.loadClass(Unknown Source)


at java.lang.ClassLoader.loadClassInternal(Unknown Source)


at java.lang.Class.forName0(Native Method)


at java.lang.Class.forName(Unknown Source)


at chemaxon.marvin.util.MarvinModule.load(Unknown Source)


at chemaxon.marvin.view.swing.ViewPanel.E(Unknown Source)


at chemaxon.marvin.common.swing.MolPanel.init(Unknown Source)


at chemaxon.marvin.common.swing.MolPanel.init(Unknown Source)


at JMView.init(Unknown Source)


at sun.applet.AppletPanel.run(Unknown Source)


at java.lang.Thread.run(Unknown Source)


Caused by: java.io.IOException: open HTTP connection failed.


at sun.applet.AppletClassLoader.getBytes(Unknown Source)


at sun.applet.AppletClassLoader.access$100(Unknown Source)


at sun.applet.AppletClassLoader$1.run(Unknown Source)


at java.security.AccessController.doPrivileged(Native Method)


... 14 more





jchem.jar, jmarvin.jar and marvin.jar are located at : D:\www\openlims\


Coldfusion CLASSPATH is D:\www\openlims





It's getting better - now this.





Here the code of Java Console:





Java Plug-in 1.5.0_07


Verwendung der JRE-Version 1.5.0_07 Java HotSpot(TM) Client VM


Home-Verzeichnis des Benutzers = C:\Dokumente und Einstellungen\Administrator


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


c: Konsolenfenster schließen


f: Objekte in Finalisierungswarteschlange finalisieren


g: Speicherbereinigung


h: Diese Hilfemeldung anzeigen


l: ClassLoader-Liste ausgeben


m: Speicherbelegung anzeigen


o: Protokollierung auslösen


p: Proxy-Konfiguration neu laden


q: Konsole ausblenden


r: Richtlinien-Konfiguration neu laden


s: System- und Bereitstellungseigenschaften ausgeben


t: Threadliste ausgeben


v: Thread-Stack ausgeben


x: ClassLoader-Cache löschen


0-5: Trace-Stufe auf <n> setzen


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


basic: Applet wird angehalten...


basic: Informationen werden gesucht...


basic: ClassLoader wird freigegeben: sun.plugin.ClassLoaderInfo@1f9dc36, refcount=0


basic: ClassLoader wird im Cache abgelegt: sun.plugin.ClassLoaderInfo@1f9dc36


basic: Aktuelle Größe des ClassLoader-Cache: 1


basic: Fertig...


basic: Applet-Thread wird beigetreten...


basic: Applet wird zerstört...


basic: Applet wird verworfen...


basic: Applet wird beendet...


basic: Applet-Thread wurde beigetreten...


basic: Nicht registrierter Modality-Listener


basic: Registrierter Modality-Listener


liveconnect: JS-Methode wird gestartet: document


liveconnect: JS-Methode wird gestartet: URL


basic: ClassLoader wird referenziert: sun.plugin.ClassLoaderInfo@1f9dc36, refcount=1


basic: Applet wird geladen...


basic: Applet wird initialisiert...


basic: Applet wird gestartet...


java.lang.NoClassDefFoundError


at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)


at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)


at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)


at java.lang.reflect.Constructor.newInstance(Unknown Source)


at java.lang.Class.newInstance0(Unknown Source)


at java.lang.Class.newInstance(Unknown Source)


at sun.applet.AppletPanel.createApplet(Unknown Source)


at sun.plugin.AppletViewer.createApplet(Unknown Source)


at sun.applet.AppletPanel.runLoader(Unknown Source)


at sun.applet.AppletPanel.run(Unknown Source)


at java.lang.Thread.run(Unknown Source)


basic: Ausnahme: java.lang.NoClassDefFoundError

Quote:

frist: which is the ENVOIMENT VARIABLE NAME

CLASSPATH





(As I have stated in my previous comment)

Quote:

second: how do I clear JVM Cache??

When a Java applet is loaded, you should see a coffee cup in you tray.


Right click -> Open console


In the console press "x" to clear the cache.

Quote:

third: when starting Jcman, in the window Connecting to Database what should I write into "JDBC driver:"

The name of the JDBC driver class.


You can find examples here:





http://www.chemaxon.com/jchem/FAQ.html#dburl





In your case (MySQL) "org.gjt.mm.mysql.Driver" should be fine.





I did not mean the applet (which runs in a browser) stack trace from the Java console.


You were complaining of the jcman.bat application, I was referring to the stack trace of that.

Quote:

jchem.jar, jmarvin.jar and marvin.jar are located at : D:\www\openlims\ Coldfusion CLASSPATH is D:\www\openlims

You should not mix multiple ChemAxon jar files in your classpath.


(this can cause nasty version mix-ups)


jchem.jar contains all the relevant marvin classes too.


Furthermore, to be effective, the jar file should be explicitly listed in the classpath, e.g:


D:\www\openlims\jchem.jar





Best regards,





Szilard

Hello,


now I understand a little bit more.





here the error code from jcam in prompt:





java.lang.ClassNotFoundException: org.gjt.mm.mysql.Driver


at java.net.URLClassLoader$1.run(Unknown Source)


at java.security.AccessController.doPrivileged(Native Method)


at java.net.URLClassLoader.findClass(Unknown Source)


at java.lang.ClassLoader.loadClass(Unknown Source)


at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source)


at java.lang.ClassLoader.loadClass(Unknown Source)


at java.lang.ClassLoader.loadClassInternal(Unknown Source)


at java.lang.Class.forName0(Native Method)


at java.lang.Class.forName(Unknown Source)


at chemaxon.util.ConnectionHandler.setConnected(ConnectionHandler.java:2


05)


at chemaxon.util.ConnectionHandler.connect(ConnectionHandler.java:246)


at chemaxon.jchem.gui.Connector.go(Connector.java:64)


at chemaxon.jchem.gui.JChemFrame.connect(JChemFrame.java:561)


at chemaxon.jchem.JChemManager.init(JChemManager.java:89)


at chemaxon.jchem.JChemManager.main(JChemManager.java:106)





Thanxs


Tim

Quote:

here the error code from jcam in prompt: java.lang.ClassNotFoundException: org.gjt.mm.mysql.Driver

Ok, so my guess was right, you do not have the JDBC driver listed in your CLASSPATH system environment variable (the Windows variable, not the Cold Fusion setting).





Please read this page in the documentation on how to set the environment variable:





http://www.chemaxon.com/jchem/doc/admin/prepscripts.html





Currently this is the latest stable JDBC driver for MySQL:





http://dev.mysql.com/downloads/connector/j/5.0.html





The package contains a jar file:





"mysql-connector-java-5.0.3-bin.jar"





You should include this file (and not the containing directory) in to you system CLASSPATH.








Szilard

Hello Szilard,


jman.bat works now.


further problem was that the Database URL wasn't right.





Now I have only this:





java.lang.RuntimeException: java.lang.NullPointerException


at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source)


at sun.net.www.protocol.http.HttpURLConnection.getHeaderField(Unknown Source)


at java.net.HttpURLConnection.getResponseCode(Unknown Source)


at sun.applet.AppletClassLoader.getBytes(Unknown Source)


at sun.applet.AppletClassLoader.access$100(Unknown Source)


at sun.applet.AppletClassLoader$1.run(Unknown Source)


at java.security.AccessController.doPrivileged(Native Method)


at sun.applet.AppletClassLoader.findClass(Unknown Source)


at java.lang.ClassLoader.loadClass(Unknown Source)


at sun.applet.AppletClassLoader.loadClass(Unknown Source)


at java.lang.ClassLoader.loadClass(Unknown Source)


at java.lang.ClassLoader.loadClassInternal(Unknown Source)


at java.lang.Class.getDeclaredConstructors0(Native Method)


at java.lang.Class.privateGetDeclaredConstructors(Unknown Source)


at java.lang.Class.getConstructor0(Unknown Source)


at java.lang.Class.newInstance0(Unknown Source)


at java.lang.Class.newInstance(Unknown Source)


at sun.applet.AppletPanel.createApplet(Unknown Source)


at sun.plugin.AppletViewer.createApplet(Unknown Source)


at sun.applet.AppletPanel.runLoader(Unknown Source)


at sun.applet.AppletPanel.run(Unknown Source)


at java.lang.Thread.run(Unknown Source)


Caused by: java.lang.NullPointerException


at sun.plugin.cache.Cache.updateTable(Unknown Source)


at sun.plugin.cache.FileCache.getMatchingFile(Unknown Source)


at sun.plugin.cache.CachedFileLoader$2.run(Unknown Source)


at java.security.AccessController.doPrivileged(Native Method)


at sun.plugin.cache.CachedFileLoader.getCacheFile(Unknown Source)


at sun.plugin.cache.CachedFileLoader.load(Unknown Source)


at sun.plugin.cache.FileCache.get(Unknown Source)


at sun.plugin.cache.PluginCacheHandler.get(Unknown Source)


at sun.net.www.protocol.http.HttpURLConnection.plainConnect(Unknown Source)


at sun.net.www.protocol.http.HttpURLConnection.connect(Unknown Source)


at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source)


... 20 more





greetings


TimE

Quote:

my applet gives back this Code: java.lang.AbstractMethodError: chemaxon.marvin.view.swing.ViewHandler.a(Lchemaxon/marvin/view/swing/ViewPanel;Ljavax/swing/JFrame;)V at chemaxon.marvin.view.swing.ViewPanel.E(Unknown Source) at chemaxon.marvin.common.swing.MolPanel.init(Unknown Source) at chemaxon.marvin.common.swing.MolPanel.init(Unknown Source) at JMView.init(Unknown Source) at sun.applet.AppletPanel.run(Unknown Source) at java.lang.Thread.run(Unknown Source)

Probably, one or more files are missing for running Marvin applets.


Are you sure that the whole "marvin" directory is available in the codebase?


Please read this topic: required files to run Marvin applets


If all files are available, the problem may be in your HTML code.


Can you show me your html source where you have got applet error?

Hi and thanxs,


that was my fault, I took all other marvin .jar files and decompressed, etc. chemaxon Folder out of the server root.


Now I put marvin-all into the root (D:/www/openlims/marvin/...), but still get an error:





Java Plug-in 1.5.0_07


Verwendung der JRE-Version 1.5.0_07 Java HotSpot(TM) Client VM


Home-Verzeichnis des Benutzers = C:\Dokumente und Einstellungen\Administrator


network: Benutzerdefinierte Proxy-Konfiguration wird geladen ...


network: Fertig.


network: Proxy-Konfiguration wird aus Internet Explorer geladen ...


network: Fertig.


network: Direkte Proxy-Konfiguration wird geladen ...


network: Fertig.


network: Proxy-Konfiguration: Kein Proxy





basic: Cache ist aktiviert


basic: Speicherort: C:\Dokumente und Einstellungen\Administrator\Anwendungsdaten\Sun\Java\Deployment\cache\javapi\v1.0


basic: Maximale Größe: unlimited


basic: Kompressionsstufe: 0





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


c: Konsolenfenster schließen


f: Objekte in Finalisierungswarteschlange finalisieren


g: Speicherbereinigung


h: Diese Hilfemeldung anzeigen


l: ClassLoader-Liste ausgeben


m: Speicherbelegung anzeigen


o: Protokollierung auslösen


p: Proxy-Konfiguration neu laden


q: Konsole ausblenden


r: Richtlinien-Konfiguration neu laden


s: System- und Bereitstellungseigenschaften ausgeben


t: Threadliste ausgeben


v: Thread-Stack ausgeben


x: ClassLoader-Cache löschen


0-5: Trace-Stufe auf <n> setzen


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





basic: Registrierter Modality-Listener


liveconnect: JS-Methode wird gestartet: document


liveconnect: JS-Methode wird gestartet: URL


basic: ClassLoader wird referenziert: sun.plugin.ClassLoaderInfo@e86da0, refcount=1


network: Verbindung von http://localhost/openlims/img/loading.gif mit Proxy=DIRECT wird hergestellt


network: Verbindung http://localhost/openlims/img/loading.gif mit Cookie "CFADMIN_LASTPAGE=%2FCFIDE%2Fadministrator%2Freports%2Findex%2Ecfm; ANALYZER_DIRECTORY=D%3A%5Cwww%5CCFIDE%5Cadministrator%5Canalyzer; CFID=4110; CFTOKEN=56968214; JSESSIONID=0e30495b53e668306418"


basic: Applet wird geladen...


basic: Applet wird initialisiert...


basic: Applet wird gestartet...


basic: httpCompression = true


network: Verbindung von http://localhost/openlims/jmarvin.jar mit Proxy=DIRECT wird hergestellt


network: Verbindung http://localhost/openlims/jmarvin.jar mit Cookie "CFADMIN_LASTPAGE=%2FCFIDE%2Fadministrator%2Freports%2Findex%2Ecfm; ANALYZER_DIRECTORY=D%3A%5Cwww%5CCFIDE%5Cadministrator%5Canalyzer; CFID=4110; CFTOKEN=56968214; JSESSIONID=0e30495b53e668306418"


network: Verbindung von http://localhost/openlims/JMView.class mit Proxy=DIRECT wird hergestellt


network: Verbindung http://localhost/openlims/JMView.class mit Cookie "CFADMIN_LASTPAGE=%2FCFIDE%2Fadministrator%2Freports%2Findex%2Ecfm; ANALYZER_DIRECTORY=D%3A%5Cwww%5CCFIDE%5Cadministrator%5Canalyzer; CFID=4110; CFTOKEN=56968214; JSESSIONID=0e30495b53e668306418"


basic: http://localhost/openlims/JMView.class wird aus dem Cache geladen


network: Verbindung von http://localhost/openlims/chemaxon/struc/MoleculeGraph.class mit Proxy=DIRECT wird hergestellt


network: Verbindung http://localhost/openlims/chemaxon/struc/MoleculeGraph.class mit Cookie "CFADMIN_LASTPAGE=%2FCFIDE%2Fadministrator%2Freports%2Findex%2Ecfm; ANALYZER_DIRECTORY=D%3A%5Cwww%5CCFIDE%5Cadministrator%5Canalyzer; CFID=4110; CFTOKEN=56968214; JSESSIONID=0e30495b53e668306418"


java.lang.NoClassDefFoundError: chemaxon/struc/MoleculeGraph


at java.lang.Class.getDeclaredConstructors0(Native Method)


at java.lang.Class.privateGetDeclaredConstructors(Unknown Source)


at java.lang.Class.getConstructor0(Unknown Source)


at java.lang.Class.newInstance0(Unknown Source)


at java.lang.Class.newInstance(Unknown Source)


at sun.applet.AppletPanel.createApplet(Unknown Source)


at sun.plugin.AppletViewer.createApplet(Unknown Source)


at sun.applet.AppletPanel.runLoader(Unknown Source)


at sun.applet.AppletPanel.run(Unknown Source)


at java.lang.Thread.run(Unknown Source)


basic: Ausnahme: java.lang.NoClassDefFoundError: chemaxon/struc/MoleculeGraph





Where should this folder "chemaxon/struc/MoleculeGraph" came from,


Out of the jchem.jar ? Or out of the Marvin-all folder? Any other .jar file ? or do I need another application I don't know about?





Is the path I used for marvin-all right ? Or should it be :


D:/www/openlims/... - without the basic folder "marvin"


And how does the application knows where to look ?


Do I have to define the path somewhere?





It's realy confusing that folders like "marvin" or "chemaxon" exist in so many way, with different use and data. For me it is not clear which is which and where to put.





Thanxs again for your help.


Greeting


TimE

Probably, it is a caching problem. "chemaxon/struc/MoleculeGraph" is in the core jar ("jmarvin.jar"). You should clean both browser's and Java's cache.


Please see the following topic how to do this: How I can clear JRE cache?