Can no longer connect to database with IJChem

Hello,

All of a sudden I cannot access my database with IJChem. Under Projects it shows "localdb[Init error]" then "schema broken(double click to repair)". But when I double click a window opens that shows "Schema localdb[Disconnected]" and prompts for a DB User name and password. I never set those. Are there defaults I can use? At the bottom of that window it shows "Connecting to database failed: Could not get JDBC Connection; nested exception is java.sql.SQLException:Failed to start database'........".
Pressing on 'details' brings up a window that shows this:

------
java.lang.NullPointerException
    at org.netbeans.modules.autoupdate.ui.PluginManagerUI.refreshUnits(PluginManagerUI.java:490)
    at org.netbeans.modules.autoupdate.ui.PluginManagerUI.access$200(PluginManagerUI.java:76)
    at org.netbeans.modules.autoupdate.ui.PluginManagerUI$4.run(PluginManagerUI.java:183)
Caused: java.lang.reflect.InvocationTargetException
    at java.awt.EventQueue.invokeAndWait(Unknown Source)
    at javax.swing.SwingUtilities.invokeAndWait(Unknown Source)
    at org.netbeans.modules.autoupdate.ui.PluginManagerUI.initialize(PluginManagerUI.java:181)
    at org.netbeans.modules.autoupdate.ui.PluginManagerUI$1.run(PluginManagerUI.java:94)
    at org.openide.util.RequestProcessor$Task.run(RequestProcessor.java:561)
    at org.netbeans.modules.autoupdate.ui.Utilities.startAsWorkerThread(Utilities.java:335)
    at org.netbeans.modules.autoupdate.ui.Utilities.startAsWorkerThread(Utilities.java:320)
    at org.netbeans.modules.autoupdate.ui.PluginManagerUI.<init>(PluginManagerUI.java:92)
    at org.netbeans.modules.autoupdate.ui.actions.PluginManagerAction.performAction(PluginManagerAction.java:61)
    at com.im.ijc.autoupdate.statusicon.AvailableUpdateVisualizerProvider.showUC(AvailableUpdateVisualizerProvider.java:108)
[catch] at com.im.ijc.autoupdate.CXNUpdateCenterModule$2.run(CXNUpdateCenterModule.java:88)
    at java.awt.event.InvocationEvent.dispatch(Unknown Source)
    at java.awt.EventQueue.dispatchEvent(Unknown Source)
    at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
    at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
    at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
    at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
    at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
    at java.awt.EventDispatchThread.run(Unknown Source)
-----------
Could you please tell me what the problem is?

Thank you very much.

Could you send the complete log file when you start IJC and then try to connect to this database.

You can display it using "View -> Instant JChem log file". Then copy and paste the complete content.

Thanks

Tim

Hello,
Below is the entire IJChem log file.
Thank you.
-kauerbach.

-------------------------------------------------------------------------------
>Log Session: Monday, January 24, 2011 11:56:10 AM EST System Info:
  Product Version         = Instant JChem 2.3
  Operating System        = Windows XP version 5.1 running on x86
  Java; VM; Vendor        = 1.6.0_05; Java HotSpot(TM) Client VM 10.0-b19; Sun Microsystems Inc.
  Java Home               = c:\Program Files\ChemAxon\InstantJChem\jre
  System Locale; Encoding = en_US (instantjchem); Cp1252
  Home Directory          = C:\Documents and Settings\kenroy
  Current Directory       = C:\Program Files\ChemAxon\InstantJChem
  User Directory          = C:\Documents and Settings\kenroy\Application Data\.instantjchem\ijc_2_3
  Installation            = C:\Program Files\ChemAxon\InstantJChem\instantjchem
                            C:\Program Files\ChemAxon\InstantJChem\ide8
                            C:\Program Files\ChemAxon\InstantJChem\platform7
  Boot & Ext. Classpath   = c:\Program Files\ChemAxon\InstantJChem\jre\lib\resources.jar;c:\Program Files\ChemAxon\InstantJChem\jre\lib\rt.jar;c:\Program Files\ChemAxon\InstantJChem\jre\lib\sunrsasign.jar;c:\Program Files\ChemAxon\InstantJChem\jre\lib\jsse.jar;c:\Program Files\ChemAxon\InstantJChem\jre\lib\jce.jar;c:\Program Files\ChemAxon\InstantJChem\jre\lib\charsets.jar;c:\Program Files\ChemAxon\InstantJChem\jre\classes;c:\Program Files\ChemAxon\InstantJChem\jre\lib\ext\dnsns.jar;c:\Program Files\ChemAxon\InstantJChem\jre\lib\ext\localedata.jar;c:\Program Files\ChemAxon\InstantJChem\jre\lib\ext\sunjce_provider.jar;c:\Program Files\ChemAxon\InstantJChem\jre\lib\ext\sunmscapi.jar;c:\Program Files\ChemAxon\InstantJChem\jre\lib\ext\sunpkcs11.jar
  Application Classpath   = C:\Program Files\ChemAxon\InstantJChem\platform7\lib\boot.jar;C:\Program Files\ChemAxon\InstantJChem\platform7\lib\org-openide-modules.jar;C:\Program Files\ChemAxon\InstantJChem\platform7\lib\org-openide-util.jar
  Startup Classpath       = C:\Program Files\ChemAxon\InstantJChem\platform7\core\core.jar;C:\Program Files\ChemAxon\InstantJChem\platform7\core\org-openide-filesystems.jar;C:\Program Files\ChemAxon\InstantJChem\instantjchem\core\locale\core_instantjchem.jar
-------------------------------------------------------------------------------
WARNING [org.netbeans.core.modules]: had to upgrade dependencies for module com.im.ijc.core: added = [module org.openide.options > 6.7] removed = []; details: [#88531 Remove SystemOption usage from PrintSettings] WARNING [org.netbeans.core.modules]: had to upgrade dependencies for module com.im.ijc.project: added = [module org.netbeans.modules.options.api/1 > 1.4, module org.openide.options > 6.7] removed = [module org.netbeans.modules.options.api/0-1 > 1.5.1]; details: [#88531 Remove SystemOption usage from PrintSettings, Major release version of module changed from 0 to 1 to signal stability; update your dependencies] WARNING [org.netbeans.core.modules]: had to upgrade dependencies for module com.im.ijc.standardizer: added = [module org.openide.options > 6.7] removed = []; details: [#88531 Remove SystemOption usage from PrintSettings] WARNING [org.netbeans.core.modules]: had to upgrade dependencies for module com.im.ijc.structurefiles: added = [module org.openide.options > 6.7] removed = []; details: [#88531 Remove SystemOption usage from PrintSettings] WARNING [org.netbeans.core.modules]: had to upgrade dependencies for module com.im.ijc.widgets: added = [module org.openide.options > 6.7] removed = []; details: [#88531 Remove SystemOption usage from PrintSettings] WARNING [org.netbeans.core.modules]: the module org.netbeans.modules.db uses org.openide.options which is deprecated: Use org.openide.util.NbPreferences instead.
WARNING [org.netbeans.core.modules]: the module com.im.ijc.core uses org.openide.options which is deprecated: Use org.openide.util.NbPreferences instead.
WARNING [org.netbeans.core.modules]: the module com.im.ijc.structurefiles uses org.openide.options which is deprecated: Use org.openide.util.NbPreferences instead.
WARNING [org.netbeans.core.modules]: the module org.netbeans.modules.editor uses org.openide.options which is deprecated: Use org.openide.util.NbPreferences instead.
WARNING [org.netbeans.core.modules]: the module org.netbeans.modules.editor.plain uses org.openide.options which is deprecated: Use org.openide.util.NbPreferences instead.
WARNING [org.netbeans.core.modules]: the module com.im.ijc.widgets uses org.openide.options which is deprecated: Use org.openide.util.NbPreferences instead.
WARNING [org.netbeans.core.modules]: the module com.im.ijc.renderers uses org.openide.options which is deprecated: Use org.openide.util.NbPreferences instead.
WARNING [org.netbeans.core.modules]: the module com.im.ijc.welcome uses org.openide.options which is deprecated: Use org.openide.util.NbPreferences instead.
WARNING [org.netbeans.core.modules]: the module org.netbeans.modules.xml.text uses org.openide.options which is deprecated: Use org.openide.util.NbPreferences instead.
WARNING [org.netbeans.core.modules]: the module org.netbeans.modules.db.sql.editor uses org.openide.options which is deprecated: Use org.openide.util.NbPreferences instead.
WARNING [org.netbeans.core.modules]: the module org.netbeans.modules.properties.syntax uses org.openide.options which is deprecated: Use org.openide.util.NbPreferences instead.
WARNING [org.netbeans.core.modules]: the module com.im.ijc.project uses org.openide.options which is deprecated: Use org.openide.util.NbPreferences instead.
WARNING [org.netbeans.core.modules]: the module com.im.ijc.standardizer uses org.openide.options which is deprecated: Use org.openide.util.NbPreferences instead.
WARNING [org.netbeans.core.modules]: the module org.netbeans.modules.editor.codetemplates uses org.openide.options which is deprecated: Use org.openide.util.NbPreferences instead.
WARNING [org.netbeans.core.modules]: the module org.netbeans.modules.options.editor uses org.openide.options which is deprecated: Use org.openide.util.NbPreferences instead.
WARNING [org.openide.loaders.DataLoader]: Use of super(com.im.ijc.core.ds.SchemaConnectionDataObject.class) in com.im.ijc.core.ds.SchemaConnectionDataLoader() should be replaced with super("com.im.ijc.core.ds.SchemaConnectionDataObject") to reduce unnecessary class loading WARNING [org.netbeans.modules.settings.convertors.XMLSettingsSupport]: Warning: unknown module code base: org.netbeans.modules.welcome in MultiFileObject@105eb6f[Services/WelcomeOptions.settings]
WARNING [org.openide.filesystems.Ordering]: Not all children in Services/MIMEResolver/ marked with the position attribute: [CofigurationResolver.xml], but some are: [HtmlResolver.xml, SchemaResolver.xml, org-netbeans-modules-properties-mime-resolver.xml, plain-text-resolver.xml, StandardizerResolver.xml, org-netbeans-modules-editor-settings-storage-mime-resolver.xml, org-netbeans-modules-url-mime-resolver.xml, org-netbeans-modules-pdf-mime-resolver.xml, StructureFileResolver.xml, XMLStructureFileResolver.xml] INFO [com.im.df.localdb.api.ProjectDatabaseSupport]: Creating project db for C:/ICJProjects_backups/IJCProjects_012111/ChemInventory1  of type derby INFO [com.im.df.util.GenericInstancesProvider]: New instance MViewPane created in 16578ms. Thread: MViewPane instances provider INFO [com.im.df.util.GenericInstancesProvider]: New instance MViewPane created in 78ms. Thread: MViewPane instances provider INFO [com.im.df.util.GenericInstancesProvider]: New instance MViewPane created in 63ms. Thread: MViewPane instances provider INFO [com.im.ijc.autoupdate.statusicon.AvailableUpdateVisualizerProvider]: New update: com.im.ijc.versionprovider INFO [com.im.ijc.autoupdate.statusicon.AvailableUpdateVisualizerProvider]: New update: com.im.ijc.io INFO [com.im.ijc.autoupdate.statusicon.AvailableUpdateVisualizerProvider]: New update: com.im.ijc.core INFO [com.im.ijc.autoupdate.statusicon.AvailableUpdateVisualizerProvider]: New update: com.im.ijc.project INFO [com.im.ijc.autoupdate.statusicon.AvailableUpdateVisualizerProvider]: New update: com.im.ijc.branding INFO [com.im.ijc.autoupdate.statusicon.AvailableUpdateVisualizerProvider]: New update: com.im.ijc.update.pack INFO [com.im.ijc.autoupdate.statusicon.AvailableUpdateVisualizerProvider]: New update: com.im.df.core.oracle INFO [com.im.ijc.autoupdate.statusicon.AvailableUpdateVisualizerProvider]: New update: com.im.ijc.welcome INFO [com.im.ijc.autoupdate.statusicon.AvailableUpdateVisualizerProvider]: New update: com.im.ijc.sfs INFO [com.im.ijc.autoupdate.statusicon.AvailableUpdateVisualizerProvider]: New update: com.im.df.core.derby INFO [com.im.ijc.autoupdate.statusicon.AvailableUpdateVisualizerProvider]: New update: com.im.ijc.autoupdate INFO [com.im.ijc.autoupdate.statusicon.AvailableUpdateVisualizerProvider]: New update: com.im.ijc.chem.overlap INFO [com.im.ijc.autoupdate.statusicon.AvailableUpdateVisualizerProvider]: New update: com.im.df INFO [com.im.ijc.autoupdate.statusicon.AvailableUpdateVisualizerProvider]: New update: com.im.ijc.widgets INFO [com.im.ijc.autoupdate.statusicon.AvailableUpdateVisualizerProvider]: New update: com.im.df.db.mysql INFO [com.im.df.util.GenericInstancesProvider]: New instance MSketchPane created in 26062ms. Thread: MSketchPane instances provider INFO [com.im.df.util.GenericInstancesProvider]: New instance MSketchPane created in 1313ms. Thread: MSketchPane instances provider INFO [com.im.df.util.GenericInstancesProvider]: New instance MSketchPane created in 344ms. Thread: MSketchPane instances provider INFO [org.netbeans.core.startup.NbEvents]: Turning on modules:
        org.openide.util [7.10.1.1 1 200711261600]
        org.openide.modules [7.3.1 200711261600]
        com.mysql.jdbc/1 [5.0.8 080424]
        org.apache.derby/1 [10.3.2.1 080424]
        oracle.jdbc/1 [11.1.0.6.0 080424]
        org.dom4j/1 [1.3 080424]
        org.netbeans.libs.commons_logging/1 [1.4.1 1.0.4 200711261600]
        org.freehep/1 [1.0 080424]
        org.apache.batik/1 [1.1 080424]
        chemaxon.jchem/1 [5.0.3 080424]
        org.openide.awt [6.11.1.1 200711261600]
        org.netbeans.modules.schema2beans/1 [1.16.1 200711261600]
        org.apache.commons.pool/1 [1.3 080424]
        org.apache.commons.dbcp/1 [1.2.2 080424]
        net.sf.cglib/1 [2.1.3 080424]
        org.springframework/1 [2.0.7 080424]
        com.michaelbaranov.microba/1 [0.4.4 080424]
        org.openide.filesystems [7.3.1 200711261600]
        org.netbeans.api.progress/1 [1.10.1.1 1 200711261600]
        org.openide.dialogs [7.5.1 200711261600]
        org.jdesktop.layout/1 [1.4.1 1.0.3 200711261600]
        org.acegisecurity/1 [1.0.5 080424]
        com.im.df/1 [2.3 080424]
        org.netbeans.modules.editor.util/1 [1.21.1 200711261600]
        org.netbeans.modules.lexer/2 [1.25.1.1 1 200711261600]
        org.netbeans.modules.xml.lexer [1.1.1 200711261600]
        org.openide.nodes [7.2.1.1 200711261600]
        org.openide.explorer [6.12.1 1 200711261600]
        org.openide.windows [6.18.1 200711261600]
        org.netbeans.modules.editor.mimelookup/1 [1.8.1 200711261600]
        org.openide.text [6.16.1 200711261600]
        org.openide.actions [6.6.1.1 200711261600]
        org.openide.io [1.11.1 200711261600]
        org.netbeans.core.output2/1 [1.8.2.1 1 200711261600]
        com.im.commons.db.test [5.3 100225]
        org.netbeans.modules.queries/1 [1.10.1 200711261600]
        org.openide.loaders [6.7.1 200711261600]
        org.netbeans.modules.projectapi/1 [1.13.1 200711261600]
        org.netbeans.modules.projectuiapi/1 [1.24.1.6 6 200711261600]
        com.im.ijc.security/1 [2.2 080424]
        org.netbeans.modules.options.api/1 [1.5.1 200711261600]
        org.netbeans.modules.project.ant/1 [1.17.1 200711261600]
        org.netbeans.api.xml/1 [1.14.1 200711261600]
        org.netbeans.spi.navigator/1 [1.5.1 200711261600]
        org.netbeans.modules.xml.core/2 [1.13.1.4 4 200711261600]
        com.jacob.com [1.0 080424]
        org.apache.poi [3.0.1 080424]
        com.im.ijc.io [2.3 080424]
        org.openide.options [6.7.1 200711261600]
        com.im.df.localdb/1 [2.3 080424]
        org.netbeans.modules.classfile/1 [1.19.1 200711261600]
        org.netbeans.bootstrap/1 [2.7.1 200711261600]
        org.netbeans.core.startup/1 [1.10.1.1 200711261600]
        org.netbeans.modules.javahelp/1 [2.9.1 200711261600]
        org.netbeans.modules.db/1 [1.24.1.5 5 200711261600]
        com.im.ijc.core/1 [2.3 080424]
        com.im.ijc.querytextpanel [2.3 080424]
        org.netbeans.modules.properties/1 [1.21.1 200711261600]
        org.netbeans.modules.editor.settings/1 [1.12.1 200711261600]
        org.netbeans.modules.editor.lib2/1 [1.5.1.2 2 200711261600]
        org.netbeans.modules.editor.fold/1 [1.6.1 200711261600]
        org.netbeans.modules.editor.lib/1 [1.20.1.4.2 4 200711261600]
        org.netbeans.modules.editor.plain.lib/1 [1.4.1 200711261600]
        org.netbeans.swing.dirchooser [1.0.1 200711261600]
        com.im.ijc.structurefiles/1 [2.2 080424]
        org.netbeans.modules.db.core [1.5.1 200711261600]
        org.netbeans.modules.sendopts/2 [2.1.1 200711261600]
        com.im.ijc.chem.overlap/1 [2.3 080424]
        org.netbeans.swing.tabcontrol [1.9.1 200711261600]
        org.openidex.util/3 [3.13.1 200711261600]
        org.netbeans.modules.editor/3 [1.35.1.4.2 200711261600]
        org.netbeans.modules.editor.plain/1 [1.4.1 200711261600]
        com.im.ijc.widgets/1 [2.3 080424]
        com.im.ijc.gridview/1 [2.3 080424]
        org.netbeans.swing.plaf [1.6.1 200711261600]
        org.netbeans.core/2 [3.6.1.1 200711261600]
        org.netbeans.modules.settings/1 [1.13.1 200711261600]
        com.im.ijc.renderers/1 [2.3 080424]
        com.im.ijc.branding/1 [2.3 080424]
        com.im.ijc.versionprovider [2.3 080424]
        com.im.ijc.welcome/1 [2.3 080424]
        org.netbeans.modules.editor.indent/2 [1.6.1.4 200711261600]
        org.netbeans.modules.editor.structure/1 [1.15.1.1 1 200711261600]
        org.netbeans.modules.editor.completion/1 [1.9.1 200711261600]
        org.netbeans.modules.xml.text/2 [1.13.1.4.4 4 200711261600]
        org.netbeans.modules.xml.xam/1 [1.2.1 1 200711261600]
        org.apache.xml.resolver [1.2.1 1.2 200711261600]
        org.netbeans.modules.xml.retriever/1 [1.1.1 200711261600]
        org.netbeans.modules.progress.ui [1.0.1.0.0.1 080409]
        org.netbeans.core.windows/2 [2.8.1.1 200711261600]
        org.netbeans.modules.editor.mimelookup.impl/1 [1.1.1 200711261600]
        com.im.ijc.examples.ijcrenderers [2.3 080424]
        org.openide.execution [1.10.1 200711261600]
        com.im.ijc.sfs [2.3 080424]
        org.netbeans.modules.editor.settings.storage/1 [1.10.1 200711261600]
        org.netbeans.modules.dbapi [1.5.1.5 200711261600]
        org.netbeans.modules.db.sql.editor [1.5.1.5 200711261600]
        org.netbeans.core.ui/1 [1.10.1 200711261600]
        org.netbeans.modules.editor.errorstripe.api/1 [2.3.1.1 1 200711261600]
        org.netbeans.modules.editor.errorstripe/2 [2.3.1.1.1 1 200711261600]
        org.netbeans.modules.defaults/1 [1.3.1 200711261600]
        org.netbeans.modules.lexer.nbbridge/1 [1.2.1.1 200711261600]
        org.netbeans.modules.autoupdate.services [1.3.1.0.1 080214]
        org.netbeans.modules.editor.bracesmatching/0 [1.3.1 200711261600]
        org.netbeans.modules.xml.schema.model/1 [1.2.1 1 200711261600]
        org.netbeans.modules.xml.axi [1.2.1 200711261600]
        org.netbeans.modules.xml.schema.completion [1.0.1 200711261600]
        com.im.ijc.autoupdate/1 [2.2 080424]
        org.netbeans.modules.properties.syntax/1 [1.18.1 200711261600]
        com.im.df.db.mysql/1 [2.3 080424]
        org.apache.commons.beanutils/1 [1.7.0 080424]
        org.netbeans.api.visual [2.9.1 200711261600]
        org.netbeans.modules.xml.catalog/2 [1.12.1.4.4 4 200711261600]
        org.netbeans.modules.extbrowser/1 [1.11.1 200711261600]
        com.im.ijc.examples.addfield [2.2 080424]
        com.im.df.core.derby/1 [2.3 080424]
        com.im.ijc.project/1 [2.3 080424]
        com.im.ijc.examples.mathcomputationactions [2.2 080424]
        com.im.ijc.formview/1 [2.3 080424]
        chemaxon.ijc.updatecenter [2.2.1 080424]
        com.im.ijc.extraloaders [2.2 080424]
        com.im.df.core.oracle/1 [2.3 080424]
        com.im.ijc.standardizer/1 [2.3 080424]
        com.im.ijc.update.pack [2.3 080424]
        org.netbeans.core.execution/1 [1.10.1.1 200711261600]
        org.netbeans.modules.masterfs/1 [1.11.1 200711261600]
        org.netbeans.modules.favorites/1 [1.12.1 200711261600]
        org.netbeans.modules.projectui [1.12.1.1.6 1 200711261600]
        org.netbeans.modules.editor.bookmarks/1 [1.4.1 200711261600]
        org.netbeans.spi.editor.hints/0 [1.2.1.5 5 200711261600]
        org.netbeans.modules.editor.codetemplates/1 [1.5.1.1.5 1 200711261600]
        org.netbeans.modules.jumpto/1 [1.3.1 200711261600]
        org.netbeans.modules.project.libraries/1 [1.15.1 200711261600]
        com.im.ijcs.test [5.3 100225]
        org.netbeans.modules.options.keymap [1.1.1 200711261600]
        org.netbeans.modules.web.flyingsaucer/1 [1.0.1 1 200711261600]
        org.netbeans.modules.utilities/1 [1.25.1 200711261600]
        org.netbeans.core.ide/1 [1.10.1 200711261600]
        org.netbeans.modules.options.editor/1 [1.4.1 200711261600]
        org.netbeans.modules.db.sql.visualeditor/1 [2.1.1.5 200711261600]
        org.netbeans.modules.autoupdate.ui [1.2.1 200711261600] WARNING [org.openide.loaders.InstanceDataObject]: Use of [] in MultiFileObject@19b97c[Shortcuts/DELETE[org-openide-actions-DeleteAction].instance] is deprecated.
WARNING [org.openide.loaders.InstanceDataObject]: (Please use the string-valued file attribute instanceClass instead.) WARNING [org.openide.loaders.InstanceDataObject]: Use of [] in MultiFileObject@1b57dcb[Shortcuts/D-P[org-openide-actions-PrintAction].instance] is deprecated.
WARNING [org.openide.loaders.InstanceDataObject]: (Please use the string-valued file attribute instanceClass instead.) WARNING [org.openide.loaders.InstanceDataObject]: Use of [] in MultiFileObject@81d783[Shortcuts/D-Z[org-openide-actions-UndoAction].instance] is deprecated.
WARNING [org.openide.loaders.InstanceDataObject]: (Please use the string-valued file attribute instanceClass instead.) WARNING [org.openide.loaders.InstanceDataObject]: Use of [] in MultiFileObject@e5307e[Shortcuts/D-C[org-openide-actions-CopyAction].instance] is deprecated.
WARNING [org.openide.loaders.InstanceDataObject]: (Please use the string-valued file attribute instanceClass instead.) WARNING [org.openide.loaders.InstanceDataObject]: Use of [] in MultiFileObject@1086036[Shortcuts/D-R[org-openide-actions-ReplaceAction].instance] is deprecated.
WARNING [org.openide.loaders.InstanceDataObject]: (Please use the string-valued file attribute instanceClass instead.) WARNING [org.openide.loaders.InstanceDataObject]: Use of [] in MultiFileObject@13887c2[Shortcuts/D-S[org-openide-actions-SaveAction].instance] is deprecated.
WARNING [org.openide.loaders.InstanceDataObject]: (Please use the string-valued file attribute instanceClass instead.) WARNING [org.openide.loaders.InstanceDataObject]: Use of [] in MultiFileObject@1ffccd6[Shortcuts/D-Y[org-openide-actions-RedoAction].instance] is deprecated.
WARNING [org.openide.loaders.InstanceDataObject]: (Please use the string-valued file attribute instanceClass instead.) WARNING [org.openide.loaders.InstanceDataObject]: Use of [] in MultiFileObject@94cbe2[Shortcuts/D-F4[org-openide-actions-CloseViewAction].instance] is deprecated.
WARNING [org.openide.loaders.InstanceDataObject]: (Please use the string-valued file attribute instanceClass instead.) WARNING [org.openide.loaders.InstanceDataObject]: Use of [] in MultiFileObject@39b27b[Shortcuts/D-X[org-openide-actions-CutAction].instance] is deprecated.
WARNING [org.openide.loaders.InstanceDataObject]: (Please use the string-valued file attribute instanceClass instead.) WARNING [org.openide.loaders.InstanceDataObject]: Use of [] in MultiFileObject@128cad[Shortcuts/D-V[org-openide-actions-PasteAction].instance] is deprecated.
WARNING [org.openide.loaders.InstanceDataObject]: (Please use the string-valued file attribute instanceClass instead.) WARNING [org.openide.filesystems.Ordering]: Not all children in Toolbars/ marked with the position attribute: [Edit, File, Memory, Debugging.xml, Standard.xml], but some are: [Navigation, Sorting] SEVERE [global] java.lang.NullPointerException
        at org.netbeans.modules.autoupdate.ui.PluginManagerUI.refreshUnits(PluginManagerUI.java:490)
        at org.netbeans.modules.autoupdate.ui.PluginManagerUI.access$200(PluginManagerUI.java:76)
        at org.netbeans.modules.autoupdate.ui.PluginManagerUI$4.run(PluginManagerUI.java:183)
Caused: java.lang.reflect.InvocationTargetException
        at java.awt.EventQueue.invokeAndWait(Unknown Source)
        at javax.swing.SwingUtilities.invokeAndWait(Unknown Source) [catch] at org.netbeans.modules.autoupdate.ui.PluginManagerUI.initialize(PluginManagerUI.java:181)
        at org.netbeans.modules.autoupdate.ui.PluginManagerUI$1.run(PluginManagerUI.java:94)
        at org.openide.util.RequestProcessor$Task.run(RequestProcessor.java:561)
        at org.netbeans.modules.autoupdate.ui.Utilities.startAsWorkerThread(Utilities.java:335)
        at org.netbeans.modules.autoupdate.ui.Utilities.startAsWorkerThread(Utilities.java:320)
        at org.netbeans.modules.autoupdate.ui.PluginManagerUI.<init>(PluginManagerUI.java:92)
        at org.netbeans.modules.autoupdate.ui.actions.PluginManagerAction.performAction(PluginManagerAction.java:61)
        at com.im.ijc.autoupdate.statusicon.AvailableUpdateVisualizerProvider.showUC(AvailableUpdateVisualizerProvider.java:108)
        at com.im.ijc.autoupdate.CXNUpdateCenterModule$2.run(CXNUpdateCenterModule.java:88)
        at java.awt.event.InvocationEvent.dispatch(Unknown Source)
        at java.awt.EventQueue.dispatchEvent(Unknown Source)
        at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
        at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
        at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
        at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
        at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
        at java.awt.EventDispatchThread.run(Unknown Source) Diagnostic information Input arguments:
        -Xms48m
        -Xmx128m
        -Dderby.system.home=derby
        -Dnetbeans.logger.console=true
        -ea
        -Dorg.netbeans.ProxyClassLoader.level=1000
        -DuseGtk=false
        -Djdk.home=c:\Program
        Files\ChemAxon\InstantJChem\jre
        -Dnetbeans.home=C:\Program
        Files\ChemAxon\InstantJChem\platform7
        -Dnetbeans.dirs=C:\Program
        Files\ChemAxon\InstantJChem\instantjchem;C:\Program
        Files\ChemAxon\InstantJChem\ide8
        -Dnetbeans.user=C:\Documents
        and
        Settings\kenroy\Application
        Data\.instantjchem\ijc_2_3
        -Dnetbeans.system_http_proxy=DIRECT
        -Dnetbeans.system_http_non_proxy_hosts=
        -Dsun.awt.keepWorkingSetOnMinimize=true
Compiler: HotSpot Client Compiler
Heap memory usage: initial 48.0MB maximum 127.1MB Non heap memory usage: initial 32.2MB maximum 116.0MB Garbage collector: Copy (Collections=66 Total time spent=0s) Garbage collector: MarkSweepCompact (Collections=2 Total time spent=0s)
Classes: loaded=6294 total loaded=6313 unloaded 19 INFO [org.netbeans.core.ui.warmup.DiagnosticTask]: Total memory 2,146,398,208 INFO [null]: Total physical memory 2,146,398,208 INFO [org.netbeans.modules.autoupdate.updateprovider.AutoupdateCatalogCache]: Processing URL: http://www.chemaxon.com/instantjchem/updatecenter/updates1/updates.xml />INFO [org.netbeans.modules.editor.settings.storage.SettingsProvider]: Won't provide any settings for text/base It's been deprecated, use MimePath.EMPTY instead.
WARNING [org.netbeans.modules.autoupdate.ui.actions.AutoupdateCheckScheduler]: Plugin Instant JChem Pack[com.im.ijc.update.pack/2.3.1] cannot be installed, some dependencies can be satisfied: [module org.netbeans.modules.projectuiapi/1 > 1.35.1.6, module org.openide.nodes > 7.9.1.1, module com.im.df/1 > 3.1, module org.openide.windows > 6.26.1, module org.openide.dialogs > 7.10.1, module org.netbeans.modules.projectapi/1 > 1.24.1, module org.openide.awt > 7.8.1.1, module chemaxon.jchem/1 > 5.3, module org.jdesktop.layout/1 > 1.7.1.103, module org.netbeans.modules.settings/1 > 1.18.1.1, module org.openide.util > 7.22.1.1, module com.im.ijc.server.api > 3.1, module com.im.ijc.core/1 > 3.1, module com.im.commons.db > 3.1, module org.openide.actions > 6.9.1.1, module com.im.commons > 3.1, module org.openide.explorer > 6.18.1.1, module com.im.df.api > 3.1] WARNING [org.netbeans.modules.editor.impl.KitsTracker]: Inconsistent mime type declaration for the kit: org.netbeans.modules.xml.text.syntax.XMLKit@b97275; mimeType from the kit is 'text/xml, but the kit is registered for 'text/xml-external-parsed-entity'
WARNING [org.netbeans.modules.editor.impl.KitsTracker]: No mime type uses editor kit implementation class: class org.netbeans.editor.BaseKit WARNING [org.openide.filesystems.Ordering]: Found same position 1700 for both Menu/Tools/org-netbeans-modules-options-OptionsWindowAction.shadow and Menu/Tools/sep-4.instance



 

Thanks for the info. I notice immediately that you are using Instnat JChem version 2.3, which is a very old version (current version if 5.4.0).

I suspect that the problem is caused by connecting to the database with a more recent version. This would in some cases have upgraded the database that is being used in the local database, and make in no longer openable in the version you are using. Is this possible? If so then the only solution would being either to go back to a backup version of the database if you have one and then open it with the 2.3 version, or to open it with the newer version.

EIther way, before you do anything I would generate a backup of the project in its current state before you do anything else (the project contains all the database files). You will probably find you project in your "My Documents\IJC Projects" directory. The easiest way is probably to zip up the complete directory using WinZip or equivalent so that you have a copy.

In addition, could you please provide more info on the actual error. You mention that it says: "Connecting to database failed: Could not get
JDBC Connection; nested exception is java.sql.SQLException:Failed to
start database'........". Is there any more info available. If so then details will be useful.

Thanks

Tim

 

 

 

I downloaded the latest versions (5.4) of Jchem and IJChem but I still get the same error. I'm not able to open my database with either the old version (2.3) or the new one (5.4). I always get this same error: (see below)

---

Connecting to database failed: null
Error creating bean with name 'ijcMetadataDao' defined in URL [jar:file:/C:/Program%20Files/ChemAxon/InstantJChem/instantjchem/modules/com-im-df-server-local.jar!/META-INF/spring/server-duplicate-temporary-context.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [com.im.ijcs.impl.dao.IJCMetadataDao]: Constructor threw exception; nested exception is java.lang.RuntimeException: org.springframework.jdbc.UncategorizedSQLException: StatementCallback; uncategorized SQLException for SQL [CREATE TABLE IJC_SCHEMA_AUTHORITIES (
SCHEMA_ID               VARCHAR(32) NOT NULL,
ITEM_ID                 VARCHAR(32) NOT NULL,
PROPERTY                VARCHAR(32) NOT NULL,
AUTHORITY               VARCHAR(50) NOT NULL,
CONSTRAINT PK_IJC_SCHEMA_AUTHS PRIMARY KEY (SCHEMA_ID, ITEM_ID, AUTHORITY),
CONSTRAINT FK_IJC_SCHEMA_AUTHS_AUTHS FOREIGN KEY (AUTHORITY)
REFERENCES IJC_AUTHORITIES (AUTHORITY) ON DELETE CASCADE,
CONSTRAINT FK_IJC_SCHEMA_AUTHS_SCHEMA FOREIGN KEY (SCHEMA_ID, ITEM_ID)
REFERENCES IJC_SCHEMA (SCHEMA_ID, ITEM_ID) ON DELETE CASCADE
)]; SQL state [X0Y46]; error code [30000]; Constraint 'FK_IJC_SCHEMA_AUTHS_SCHEMA' is invalid: referenced table IJC_SCHEMA does not exist.; nested exception is java.sql.SQLException: Constraint 'FK_IJC_SCHEMA_AUTHS_SCHEMA' is invalid: referenced table IJC_SCHEMA does not exist.

------

That error looks quite different to the one you reported earlier for the 2.3 version. IJC is able to connect to the DB, so it does look like the database was updated to a later version somehow.

The easiest was to resolve this is probably for us to look at the database ourselves. If you are happy for us to do so then let us know and we can arrange a way for you to send the zipped project (as described earlier) in a secure manner.

Thanks
Tim

 

That sounds fine. I have zipped a folder with 2  IJC databases. The size of the zipped file is only a little over 1meg. Where shall I send the file?

Thank you.

Here is the zipped file with 2 databases that I can no longer open.

Thank you.

Here are the projects that can be opened in IJC 5.4.

The probelm seemed to be that somehow a username and password had been specified and were incorrect. For local databases there is typcially no username or password for the database.

It may be possible to restore these some that they can be opened in an earlier version of IJC, but that would need investigating further. Hopfully IJC 5.4 (the current version) will be OK for you.

Tim

Hi Tim,

I have a similar (or the same) problem with 4 of my schemes.

Initially I got the "Could not connect to IJC DB" with version 5.3.8.

I have now updated IJC to 5.4 and the problem persists. (please see attached files).

I can send you the db and log files if that would help in locating the problem.

I would rather not post them here.

This is a rather serious isue for me...

Thanks in advance for your help.

Anna

This seems to be a problem with the database having become corrupt for some reason. If you send the database to us we can take a look and see if it can be fixed. If its small enough you could email it (tdudgeon at chemaxon dot com). If not them we can send you details for an ftp site that it can be securely uploaded to.

We suggest keeping backups of all databases in case of problems.

Tim

We obtained one of these databases and it seems that the database had become corupted, maybe as a result of a power cut, crash, disk error.... In this particular case it seems that it can be fixed by deleting the log files (found within the .config/localdb/db/log directory of the IJC project). More information abotu this problem can be found here:
http://mail-archives.apache.org/mod_mbox/db-derby-user/200602.mbox/%[email protected]%3E

Do not use this as a general fix. Only for this particular problem and only as a last ditch emergency, and create a copy of the DB files first.

We do strongly advice to keep regular backups of your local databases just in case your computer goes crazy.

Tim