Unable to launch remote IGV session via JNLP

[PKIDNA]

I have been away from this for a while but it had been working but today I needed to do some work and just noticed that IGV is no longer launching from Broad servers via JNLP.

I am seeing an error "JAR resources in JNLP fle are not signed by same certificate"....here is the exception:

JNLPException[category: Launch File Error : Exception: null : LaunchDesc:
<jnlp spec="6.0+" codebase="http://www.broadinstitute.org/igv/projects/current">
  <information>
    <title>IGV 2.0</title>
    <vendor>The Broad Institute</vendor>
    <homepage href="http://www.broadinstitute.org/igv"/>
    <description>IGV Software</description>
    <description kind="short">IGV</description>
    <icon href="IGV_64.png"/>
    <icon kind="splash" href="IGV_64.png"/>
    <offline-allowed/>
    <shortcut/>
  </information>
  <security>
    <all-permissions/>
  </security>
  <update check="always" policy="always"/>
  <resources>
    <java version="1.6+" initial-heap-size="256m" max-heap-size="1000m"/>
    <jar href="igv.jar" download="eager" main="true"/>
    <jar href="batik-codec.jar" download="eager"/>
    <property name="apple.laf.useScreenMenuBar" value="true"/>
    <property name="com.apple.mrj.application.growbox.intrudes" value="false"/>
    <property name="com.apple.mrj.application.live-resize" value="true"/>
    <property name="com.apple.macos.smallTabs" value="true"/>
  </resources>
  <application-desc main-class="org.broad.igv.ui.Main">
    <argument>http://dnaportal.perkinelmerdna.net/xtmp/4433e38c043e566273dba5f3f2d2c796/xml/0120ee7c60a1ccacdb34a3900963dd11.xml</argument>
    <argument>--preferences</argument>
    <argument>http://dnaportal.perkinelmerdna.net/xtmp/prefs.properties</argument>
  </application-desc>
</jnlp> ]
    at com.sun.javaws.security.JNLPSignedResourcesHelper.checkSignedResourcesHelper(Unknown Source)
    at com.sun.javaws.security.JNLPSignedResourcesHelper.checkSignedResources(Unknown Source)
    at com.sun.javaws.Launcher.prepareResources(Unknown Source)
    at com.sun.javaws.Launcher.prepareAllResources(Unknown Source)
    at com.sun.javaws.Launcher.prepareToLaunch(Unknown Source)
    at com.sun.javaws.Launcher.prepareToLaunch(Unknown Source)
    at com.sun.javaws.Launcher.launch(Unknown Source)
    at com.sun.javaws.Main.launchApp(Unknown Source)
    at com.sun.javaws.Main.continueInSecureThread(Unknown Source)
    at com.sun.javaws.Main.access$000(Unknown Source)
    at com.sun.javaws.Main$1.run(Unknown Source)
    at java.lang.Thread.run(Unknown Source)

[Helga Thorvaldsdottir]

Hi,

We recently updated the certificate, but you may need to clear IGV from your Java cache.
If you need help doing that,  please see the entry "How do I clear IGV from my Java cache so that I can update my IGV?" in the FAQ on the IGV website.

Helga

[PKIDNA]

Did not help, I cleared ALL temporary files in both Java control and browser....but get same message

 "JAR resources in JNLP file are not signed by same certificate"

 This is affecting our clients as well...

[Helga Thorvaldsdottir]

Are you launching via the Java Web Start buttons on the IGV Downloads page?

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[Jim Robinson]

Hi,

Where is this jnlp file coming from?  I ask because its content doesn't match the file on our website.  In particular the jar section is incorrect, or well out-of-date, it should read

    <jar href="igv.jar" download="eager" main="true"/>

    <jar href="batik-codec__V1.7.jar" download="eager"/>

    <jar href="goby-io-igv__V1.0.jar" download="eager"/>   

Jim

[PKIDNA]

Actually, I am seeing that the PHP file I had from you from a while back generates an "on-the-fly" jnlp file, but what is odd was that cleared all my caches and launched IGV from the broad web pages then compared the JNLP in the cache to the one in the PHP and did not see a difference.  I will try updating to the below...thanks...

I have been away from this particular part of the code for a long time so need to get refreshed on a few things....

edward

[PKIDNA]

I made the following changes and now I just get an error message that states  "Error: Could not create the Java Virtual Machine.  Error: A fatal exception has occurred. Program will Exit".

Interestingly I see the same trying this link...  http://broadinstitute.org/igv/projects/current/igv_lm.jnlp  (which I spotted in the other message recently posted....)

[James Robinson]

That generally means you are requesting more memory than can be allocated on your platform (the -Xmx parameter).  In the generic php we set this low, 900m,  so that it can be run by users on Windows with 32 bit JVMs.  

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[PKIDNA]

Ok, it appears after a few changes, and looking at the jnlp that seemed to work I corrected the PHP generation script and they program is launching again, though as a note the "<jar href="batik-codec__V1.7.jar" download="eager"/>" notation did not work, but had to use " <jar href="batik-codec.jar" download="eager" version="1.7"/>"

On a side note: I also detected an issue with newer Firefox blocking use of http://localhost:60151/goto?locus= callback due to the new mixed content filter, seen when parent site is HTTPS.  As localhost does not offer security cert you cannot use https.  Workaround is to temporarily deactivate the feature by clicking the "shield" icon in the address bar, which only works on a per-session bases, or completely turning off the feature in the advance config which is a security risk.  I have filed a request with Mozilla to potentially exclude "localhost" from mix mode filtering.

[James Robinson]

You can use versioning or not, if you use it in your generated jnlp you leave  off the explicit __V1.7, etc.

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