Instant JChem hangs when trying to connect to MySQL instance

User 6d24b35814

10-06-2009 13:00:02

Instant JChem 2.5.1 on windows:-

MySQL 5.0.41 on Linux (redhat 64 bit)

I can't connect to my MySQL instance.

After selecting MySQL in the database connection wizard, I enter the jdbc connection string and user name and pwd and then click next and the application hangs - I end up having to kill Instant JChem using task manager.

The connection details are valid - I have other desktop applications connecting to the MySQL instance and I have a valid Instant JChem evaluation license.

Kind regards

Ceara

ChemAxon fa971619eb

10-06-2009 13:26:40

Its not immediately obvious what is wrong here.

Which version of Java are you using? There are some problems with 64 bit versions, so it is best to use a 32 bit version. You can find the version using Help -> About Instant JChem.

Which version of MySQL are you trying to connect to?

Are you using the 'New schema" or 'Connect to schema' wizards? 'New schema' if for creating the IJC schema for the first time. Once it has been created other users connect to it using 'Connect to schema'.

Tim

ChemAxon fa971619eb

10-06-2009 13:29:02

Sorry, I missed the MySQL version info in your post. And as you are running on Windows I assume you are using 32 bit Java. Can you just confirm which wizard you are uisng.

Tim

User 6d24b35814

10-06-2009 15:04:02

Hi Tim

See below the 'about' details. I've tried to connect to the database using file > 'New Schema' and 'Connect to Schema'. I've also tried to create a new project and then try to do it - always the same behaviour.

I did manage to connect to the remote database yesterday just after I first installed the app, as a test. Since then I have :-

- disconnected the laptop and had it on hibernate

- changed the proxy settings to get the news feeds on the front page

- imported an SDF file of 450K compounds into a new project

Please let me know if any of the above will have made a difference. I will reboot the laptop and try again.

I also include the log from the latest session.

Kind regards

Ceara

Instant JChem Version: 2.5.1 (build: 090528)
JChem Version: 5.2.2
JChem Table Version: 5020100
Marvin Version: 5.2.2 (build date: 2009-05-26)
Java: 1.6.0_13; Java HotSpot(TM) Client VM 11.3-b02
System: Windows XP version 5.1 running on x86; Cp1252; en_GB (instantjchem)
NetBeans build: 200903060201
Userdir: C:\Documents and Settings\CR86686\Application Data\.instantjchem\ijc_2_5
Java Web Start: No
Plugins:
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Log details:-

-------------------------------------------------------------------------------
>Log Session: Wednesday, June 10, 2009 2:00:52 PM BST
>System Info:
Product Version         = Instant JChem 2.5.1
Operating System        = Windows XP version 5.1 running on x86
Java; VM; Vendor        = 1.6.0_13; Java HotSpot(TM) Client VM 11.3-b02; Sun Microsystems Inc.
Runtime                 = Java(TM) SE Runtime Environment 1.6.0_13-b03
Java Home               = c:\Program Files\ChemAxon\InstantJChem\jre
System Locale; Encoding = en_GB (instantjchem); Cp1252
Home Directory          = C:\Documents and Settings\CR86686
Current Directory       = C:\Program Files\ChemAxon\InstantJChem
User Directory          = C:\Documents and Settings\CR86686\Application Data\.instantjchem\ijc_2_5
Installation            = C:\Program Files\ChemAxon\InstantJChem\instantjchem
                            C:\Program Files\ChemAxon\InstantJChem\ide10
                            C:\Program Files\ChemAxon\InstantJChem\platform9
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\platform9\lib\boot.jar;C:\Program Files\ChemAxon\InstantJChem\platform9\lib\org-openide-modules.jar;C:\Program Files\ChemAxon\InstantJChem\platform9\lib\org-openide-util.jar
Startup Classpath       = C:\Program Files\ChemAxon\InstantJChem\platform9\core\core.jar;C:\Program Files\ChemAxon\InstantJChem\platform9\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.widgets: 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.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.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.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.structurefiles: 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.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.project 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 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.xml.text uses org.netbeans.modules.editor.deprecated.pre61completion which is deprecated.
WARNING [org.netbeans.core.projects.cache]: Inefficient to include an empty layer in a module: jar:file:/C:/Program%20Files/ChemAxon/InstantJChem/instantjchem/modules/com-im-df.jar!/com/im/df/layer.xml
WARNING [org.netbeans.core.projects.cache]: Inefficient to include an empty layer in a module: jar:file:/C:/Program%20Files/ChemAxon/InstantJChem/instantjchem/modules/com-im-ijc-security.jar!/com/im/ijc/security/layer.xml
WARNING [org.netbeans.core.projects.cache]: Inefficient to include an empty layer in a module: jar:file:/C:/Program%20Files/ChemAxon/InstantJChem/instantjchem/modules/com-im-df-server-local.jar!/com/im/df/server/local/layer.xml
WARNING [org.netbeans.core.projects.cache]: Inefficient to include an empty layer in a module: jar:file:/C:/Program%20Files/ChemAxon/InstantJChem/instantjchem/modules/com-im-df-localdb.jar!/com/im/df/localdb/layer.xml
WARNING [org.netbeans.core.projects.cache]: Inefficient to include an empty layer in a module: jar:file:/C:/Program%20Files/ChemAxon/InstantJChem/instantjchem/modules/com-im-ijc-jrprinting.jar!/com/im/ijc/jrprinting/layer.xml
WARNING [org.netbeans.core.projects.cache]: Inefficient to include an empty layer in a module: jar:file:/C:/Program%20Files/ChemAxon/InstantJChem/instantjchem/modules/com-im-ijc-versionprovider.jar!/com/im/ijc/versionprovider/layer.xml
WARNING [org.netbeans.core.projects.cache]: Inefficient to include an empty layer in a module: jar:file:/C:/Program%20Files/ChemAxon/InstantJChem/instantjchem/modules/com-im-ijc-autoupdate.jar!/com/im/ijc/autoupdate/layer.xml
WARNING [org.netbeans.core.projects.cache]: Inefficient to include an empty layer in a module: jar:file:/C:/Program%20Files/ChemAxon/InstantJChem/instantjchem/modules/com-im-ijc-update-pack.jar!/com/im/ijc/update/pack/layer.xml
License could not be verified:
B/S/P/E=
Expiration Date=2009-07-09
License Term=Evaluation
Licensee=GSK
Number of Users=Unlimited
Server Use=Allowed
Software=Reactor
Support Expiration Date=2009-07-09
------------------------------License could not be verified:
B/S/P/E=
Expiration Date=2009-07-09
License Term=Evaluation
Licensee=GSK
Number of Users=Unlimited
Server Use=Allowed
Software=Reactor
Support Expiration Date=2009-07-09
------------------------------License could not be verified:
B/S/P/E=
Expiration Date=2009-07-09
License Term=Evaluation
Licensee=GSK
Number of Users=Unlimited
Server Use=Allowed
Software=Reactor
Support Expiration Date=2009-07-09
------------------------------License could not be verified:
B/S/P/E=
Expiration Date=2009-07-09
License Term=Evaluation
Licensee=GSK
Number of Users=Unlimited
Server Use=Allowed
Software=Reactor
Support Expiration Date=2009-07-09
------------------------------License could not be verified:
B/S/P/E=
Expiration Date=2009-07-09
License Term=Evaluation
Licensee=GSK
Number of Users=Unlimited
Server Use=Allowed
Software=Reactor
Support Expiration Date=2009-07-09
------------------------------License could not be verified:
B/S/P/E=
Expiration Date=2009-07-09
License Term=Evaluation
Licensee=GSK
Number of Users=Unlimited
Server Use=Allowed
Software=Reactor
Support Expiration Date=2009-07-09
------------------------------WARNING: LibraryDeclarationHandlerImpl: Cannot create library: jaxb of unknown type: j2se
INFO [org.netbeans.core.startup.NbEvents]: Turning on modules:
        org.openide.util [7.18.1.1 1 200903060201]
        org.openide.modules [7.7.1 200903060201]
        org.openide.awt [7.3.1.1 200903060201]
        org.jdesktop.layout/1 [1.6.1 1.0.3 200903060201]
        org.netbeans.api.progress/1 [1.12.1.1 1 200903060201]
        org.openide.dialogs [7.8.1 200903060201]
        org.netbeans.swing.outline [1.1.1 200903060201]
        org.openide.nodes [7.7.3.1 200903060201]
        org.openide.explorer [6.16.3 1 200903060201]
        org.openide.windows [6.24.1 200903060201]
        org.openide.filesystems [7.13.1.1.1 1 200903060201]
        org.netbeans.modules.editor.mimelookup/1 [1.10.1 200903060201]
        org.openide.text [6.21.2 200903060201]
        org.openide.actions [6.8.1.1 200903060201]
        org.netbeans.spi.quicksearch [1.0.1 200903060201]
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WARNING [org.openide.loaders.InstanceDataObject]: Use of [] in MultiFileObject@aee320[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@94b146[Shortcuts/D-F4[org-openide-actions-CloseViewAction].instance] is deprecated.
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WARNING [org.openide.loaders.InstanceDataObject]: Use of [] in MultiFileObject@1af328[Shortcuts/D-P[org-openide-actions-PrintAction].instance] is deprecated.
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WARNING [org.openide.loaders.InstanceDataObject]: Use of [] in MultiFileObject@1988886[Shortcuts/DELETE[org-openide-actions-DeleteAction].instance] is deprecated.
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WARNING [org.openide.filesystems.Ordering]: Not all children in ProjectsTabActions/ marked with the position attribute: [org-netbeans-modules-project-ui-NewProject.instance], but some are: [org-netbeans-modules-project-ui-NewProject.shadow, org-netbeans-modules-project-ui-NewFile.shadow, sep-1.instance, com-im-workbench-project-simpleview-RecentProjectsAction.shadow, com-im-workbench-project-simpleview-OpenProject.shadow, com-im-workbench-project-configuration-OpenConfigurationAction.shadow, com-im-workbench-project-configuration-ConfigurationGenerateAction.shadow, org-netbeans-modules-project-ui-groups-GroupsMenu.shadow]
INFO [com.im.workbench.project.StartupWindowInstaller]: do not initialize schema
INFO [com.im.df.localdb.api.ProjectDatabaseSupport]: Creating project db for C:/Documents and Settings/CR86686/My Documents/IJCProjects/tryagain of type derby
INFO [org.netbeans.ui.metrics.projects]: USG_PROJECT_OPEN
Diagnostic information
Input arguments:
        -Xms48m
        -Xmx300m
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        -Dderby.system.home=derby
        -Dnetbeans.logger.console=true
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        -Dorg.netbeans.ProxyClassLoader.level=1000
        -DuseGtk=false
        -Djdk.home=c:\Program
        Files\ChemAxon\InstantJChem\jre
        -Dnetbeans.home=C:\Program
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        -Dnetbeans.dirs=C:\Program
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        -Dnetbeans.user=C:\Documents
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        -Dnetbeans.system_http_non_proxy_hosts=
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Compiler: HotSpot Client Compiler
Heap memory usage: initial 48.0MB maximum 297.8MB
Non heap memory usage: initial 32.2MB maximum 172.0MB
Garbage collector: Copy (Collections=97 Total time spent=0s)
Garbage collector: MarkSweepCompact (Collections=1 Total time spent=0s)
Classes: loaded=5391 total loaded=5391 unloaded 0
INFO [org.netbeans.core.ui.warmup.DiagnosticTask]: Total memory 2,147,483,647
INFO [null]: Total physical memory 2,147,483,647
INFO [com.im.df.util.GenericInstancesProvider]: MViewPane instances provider created. Initial instance count:3, initial delay 5sec.
INFO [com.im.df.util.GenericInstancesProvider]: MSketchPane instances provider created. Initial instance count:3, initial delay 10sec.
INFO [com.im.df.util.GenericInstancesProvider]: ConfigBuilderPanel instances provider created. Initial instance count:2, initial delay 20sec.
INFO [org.netbeans.modules.autoupdate.updateprovider.AutoupdateCatalogCache]: Processing URL: http://www.chemaxon.com/instantjchem/updatecenter/updates3/updates.xml />INFO [com.im.df.util.GenericInstancesProvider]: New instance MViewPane created in 219ms. Thread: MViewPane instances provider
INFO [com.im.df.util.GenericInstancesProvider]: New instance MViewPane created in 0ms. Thread: MViewPane instances provider
INFO [com.im.df.util.GenericInstancesProvider]: New instance MViewPane created in 16ms. Thread: MViewPane instances provider
INFO [com.im.df.util.GenericInstancesProvider]: New instance MSketchPane created in 531ms. Thread: MSketchPane instances provider
INFO [com.im.df.util.GenericInstancesProvider]: New instance MSketchPane created in 94ms. Thread: MSketchPane instances provider
INFO [org.netbeans.ui.metrics.javahelp]: Showing help ID: ijc
INFO [com.im.df.util.GenericInstancesProvider]: New instance MSketchPane created in 93ms. Thread: MSketchPane instances provider
INFO [com.im.df.util.GenericInstancesProvider]: New instance Standardizer created in 328ms. Thread: ConfigBuilderPanel instances provider
INFO [com.im.df.util.GenericInstancesProvider]: New instance Standardizer created in 94ms. Thread: ConfigBuilderPanel instances provider
License could not be verified:
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License Term=Evaluation
Licensee=GSK
Number of Users=Unlimited
Server Use=Allowed
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INFO [com.im.ijc.core.ui.ProductInformationPanel]: C:\Documents and Settings\CR86686\Application Data\.instantjchem\ijc_2_5\var\log\ws_stderr.log, exists = false
Warning: use of system property netbeans.home in com.im.ijc.core.ui.ProductInformationPanel has been obsoleted in favor of InstalledFileLocator
INFO [com.im.ijc.core.ui.ProductInformationPanel]: C:\Documents and Settings\CR86686\Application Data\.instantjchem\ijc_2_5\var\log\ws_stderr.log, exists = false

ChemAxon fa971619eb

10-06-2009 16:09:20

I've go no immediate idea what is wrong here. I have just tried doing this on an almost identical environment and it all works fine. I don't think any of those things you said you did would have caused a problem.

Can you try a restart and see what happens?

Tim

User 6d24b35814

11-06-2009 08:01:42

I think it's the proxy settings. I rebooted my laptop and fired up Instant JChem - again I'm back to the "Cannot connect to the internet - configure proxy settings" boxes on the front page for the newsfeeds.

This time I didn't configure them, I went straight to file > connect to schema and entered the details and it looks like I connect (at least it doesn't hang). So does that mean if you do configure a proxy server then all communication from the software gets sent via that server? not that I know much about proxy servers but I'm assuming that the server I've entered is outside the firewall.

Of course I can live without the news feeds but is there someway that I might be able to configure it to have both? I've tried manually configuring the proxy server to get the news feeds and then going back into the settings and choosing 'No proxy' and if I do that I can connect to the MySQL server but it's a bit of a pain if I have to do this every time.

ChemAxon fa971619eb

11-06-2009 09:26:06

Your understanding is the same as mine - I don't see why the proxy server settings should be interfering with the MySQL connection.

We will investigate this.

Tim

ChemAxon e189db4705

11-06-2009 14:26:16

We are finally able to reproduce this problem. It looks that your proxy is set for all services and all servers. There could be two ways to fix this:
a. Set proxy only for http
b. Exclude mysql server from proxy settings

Could you please try this:

1. Go to main menu Tools-> Options

2. In proxy settings (tab General) click on button "More..."

3a. Deselect checkbox "Use the same proxy settings for all protocols"
OR
3b. Add mysql server's IP address or domain name to "No Proxy hosts" (comma separated values)

Both options should resolve the problem.
Please let us know if this helps.

Thanks
Petr

User 6d24b35814

12-06-2009 09:40:00

Hi

I unchecked the box "use same settings for all protocols" and deleted the address from the other 2 boxes and I can now connect to the MySQL database - thanks

Ceara