Network connectivity issue with Java

[tthompson29]

Hi, I am new to seqmonk and I am having an issue starting a new project because I can't get network connection. Below is the full error. Unfortunately because it won't connect with java, I can just submit the error directly. Please let me know what to do next.

SeqMonk Version:1.48.0

Operating System:Mac OS X - 10.16

Java Version:11.0.10 - 11.0.10+9

java.lang.IllegalStateException javax.net.ssl.SSLException: Couldn't kickstart handshaking

uk.ac.babraham.SeqMonk.Dialogs.GenomeSelector$ButtonListener.actionPerformed(GenomeSelector.java:305) java.desktop/javax.swing.AbstractButton.fireActionPerformed(Unknown Source) java.desktop/javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source) java.desktop/javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source) java.desktop/javax.swing.DefaultButtonModel.setPressed(Unknown Source) java.desktop/javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown Source) java.desktop/java.awt.Component.processMouseEvent(Unknown Source) java.desktop/javax.swing.JComponent.processMouseEvent(Unknown Source) java.desktop/java.awt.Component.processEvent(Unknown Source) java.desktop/java.awt.Container.processEvent(Unknown Source) java.desktop/java.awt.Component.dispatchEventImpl(Unknown Source) java.desktop/java.awt.Container.dispatchEventImpl(Unknown Source) java.desktop/java.awt.Component.dispatchEvent(Unknown Source) java.desktop/java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source) java.desktop/java.awt.LightweightDispatcher.processMouseEvent(Unknown Source) java.desktop/java.awt.LightweightDispatcher.dispatchEvent(Unknown Source) java.desktop/java.awt.Container.dispatchEventImpl(Unknown Source) java.desktop/java.awt.Window.dispatchEventImpl(Unknown Source) java.desktop/java.awt.Component.dispatchEvent(Unknown Source) java.desktop/java.awt.EventQueue.dispatchEventImpl(Unknown Source) java.desktop/java.awt.EventQueue$4.run(Unknown Source) java.desktop/java.awt.EventQueue$4.run(Unknown Source) java.base/java.security.AccessController.doPrivileged(Native Method) java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) java.desktop/java.awt.EventQueue$5.run(Unknown Source) java.desktop/java.awt.EventQueue$5.run(Unknown Source) java.base/java.security.AccessController.doPrivileged(Native Method) java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) java.desktop/java.awt.EventQueue.dispatchEvent(Unknown Source) java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) java.desktop/java.awt.WaitDispatchSupport$2.run(Unknown Source) java.desktop/java.awt.WaitDispatchSupport$4.run(Unknown Source) java.desktop/java.awt.WaitDispatchSupport$4.run(Unknown Source) java.base/java.security.AccessController.doPrivileged(Native Method) java.desktop/java.awt.WaitDispatchSupport.enter(Unknown Source) java.desktop/java.awt.Dialog.show(Unknown Source) java.desktop/java.awt.Component.show(Unknown Source) java.desktop/java.awt.Component.setVisible(Unknown Source) java.desktop/java.awt.Window.setVisible(Unknown Source) java.desktop/java.awt.Dialog.setVisible(Unknown Source) uk.ac.babraham.SeqMonk.Dialogs.GenomeSelector.(GenomeSelector.java:237) uk.ac.babraham.SeqMonk.SeqMonkApplication.startNewProject(SeqMonkApplication.java:355) uk.ac.babraham.SeqMonk.Menu.SeqMonkMenu.actionPerformed(SeqMonkMenu.java:1662) java.desktop/javax.swing.AbstractButton.fireActionPerformed(Unknown Source) java.desktop/javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source) java.desktop/javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source) java.desktop/javax.swing.DefaultButtonModel.setPressed(Unknown Source) java.desktop/javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown Source) java.desktop/java.awt.AWTEventMulticaster.mouseReleased(Unknown Source) java.desktop/java.awt.Component.processMouseEvent(Unknown Source) java.desktop/javax.swing.JComponent.processMouseEvent(Unknown Source) java.desktop/java.awt.Component.processEvent(Unknown Source) java.desktop/java.awt.Container.processEvent(Unknown Source) java.desktop/java.awt.Component.dispatchEventImpl(Unknown Source) java.desktop/java.awt.Container.dispatchEventImpl(Unknown Source) java.desktop/java.awt.Component.dispatchEvent(Unknown Source) java.desktop/java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source) java.desktop/java.awt.LightweightDispatcher.processMouseEvent(Unknown Source) java.desktop/java.awt.LightweightDispatcher.dispatchEvent(Unknown Source) java.desktop/java.awt.Container.dispatchEventImpl(Unknown Source) java.desktop/java.awt.Window.dispatchEventImpl(Unknown Source) java.desktop/java.awt.Component.dispatchEvent(Unknown Source) java.desktop/java.awt.EventQueue.dispatchEventImpl(Unknown Source) java.desktop/java.awt.EventQueue$4.run(Unknown Source) java.desktop/java.awt.EventQueue$4.run(Unknown Source) java.base/java.security.AccessController.doPrivileged(Native Method) java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) java.desktop/java.awt.EventQueue$5.run(Unknown Source) java.desktop/java.awt.EventQueue$5.run(Unknown Source) java.base/java.security.AccessController.doPrivileged(Native Method) java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) java.desktop/java.awt.EventQueue.dispatchEvent(Unknown Source) java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) java.desktop/java.awt.EventDispatchThread.pumpEvents(Unknown Source) java.desktop/java.awt.EventDispatchThread.pumpEvents(Unknown Source) java.desktop/java.awt.EventDispatchThread.run(Unknown Source)

[s-andrews]

Thanks for reporting this. I've had a look at this and tried to reproduce it here but everything seemed to work OK on the macs I have access to. This is also the only report of this issue I've seen (though it does prevent automated crash reporting!), so I suspect this might be something specific to your mac.

Some obvious things to check.

1. Can you go to https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/current_version.txt in a browser and check that that works.

2. Can you go to Edit > Preferences > Network and check that the download URL is https://www.bioinformatics.babraham.ac.uk/seqmonk/genomes/ can you also check that there's nothing in the Proxy server or Proxy port fields.

3. If this is a laptop can you try connecting from a different network (wifi point etc) in case that matters.

I can't think of anything which has changed recently which would have stopped this from working I'm afraid.

[s-andrews]

One more thing - can you check that the time and date are set correctly on your system.

[tthompson29]

Thanks so much for the response.

1. I went to the url you pasted and I got a html with simply 1.48.0
2. The seqmonk genome website works through all of my browsers, and the Proxy field is empty
3. I have tried this on several networks
4. I also checked my clock system and reset it just incase.

Additionally, I have tried:

1. reinstalling seqmonk
2. installing java independently on my system

The error persisted so i manually downloaded the genomes I need and I think I may be able to use this as the work around for now. I think the issue might be associated with my institution's profile manager. I am trying to find if it is blocking the program right now, or if it is associated with the Mac OS third party app accessibility, but I will try to keep you updated and thanks again.

[s-andrews]

The local version of java shouldn't matter as we ship a JVM with seqmonk for all of the recent releases. It looks like your machine can certainly get to the pages it would need to, so the next most obvious thing is that you have some kind of application level firewall running which is blocking the connection.

As you've found you can manually download the genomes you need and unzip them into your genomes folder which should get you up and running, but it might be worth talking to your IT to see if you can find and remove the block.

[s-andrews]

Since I've got nothing else to go on with this issue and it only seems to affect this one user I'm going to close this. If we get any more clues as to what the cause might be we can reopen.