Visualizer launching problems and other Java related issues

We have recently been getting many reports from users having trouble launching GenePattern visualizers - HeatMapViewer, HierarchicalClusteringViewer, PCAViewer and so on - especially on Mac computers.  There have also been reports of issues with running the GenePattern installer and using the File Uploader.  If you are experiencing any of these problems the following suggestions might help you.  These components use the Java platform and the problems all seem to trace to a recent set of Java updates from Oracle and Apple.  In particular, many problem reports come from users with Java 7 Update 25 on Mac OS X 10.7 and above or Java 6 Update 51 on OS X 10.6.  Issues have been reported with other combinations, but less frequently. 
These are the latest updates of Java available for these platforms and came out within the last several weeks, so you may or may not have already applied this change depending on the update policies of your organization and the settings on your own computer.  Java 7 update 25 may also be known as:
Java 6 update 51 may also be known as:
While it is unclear exactly what is causing the problems, simply re-installing the update has solved the problem for a number of users.  This worked even though Java had reported that it was up to date on the users' system.  We suspect that the issue is not with the Java update itself, but rather with the way that it was installed by the Java or Apple auto-update process.  To re-install, we recommend taking the following steps:
  1. Download the update package in question from either Oracle or Apple:
  2. Uninstall any existing copy of Java 7.  Instructions are here.
  3. Exit all web browsers and any other programs which rely on Java.
  4. Re-install Java from the downloaded package.
  5. Restart the computer.

If this does not solve your visualizer issues, please consult our FAQ for some other known issues regarding visualizers and ComparativeMarkerSelectionViewer.  This earlier blog posting deals with some issues in earlier versions of Java 6 and Java 7.  Note also that we are currently in the process of updating our visualizers to be compatible with Java 7.  Most have been updated, but Multiplot in particular is still being tested.  We anticipate a Beta release shortly.

Known Issues

On the Mac platform, the Java 7 plug-in is not compatible with the Chrome web browser.  This is a general issue with Java 7 and Chrome on Mac OS X and not specific to GenePattern.  Details are here.  We recommend Firefox or Safari to use visualizers on Mac OS X, though special steps are required for Safari to work.
The latest updates to Java and Safari have automatically disabled Java applets on web pages.  On any page with an applet, Safari will display a message asking if you wish to allow it and walk you through the
steps permitting you to re-enable applets for the site.  Unfortunately, a bug in our visualizer pages is preventing these messages from being displayed.  As a work-around, you can instead enable applets through the File Uploader component; doing so will enable all applets on the GenePattern web site.
First, enable Java in the Safari preferences (Safari menu -> Preferences -> Security).  
Click the Uploads tab in the top right corner, then click the context menu button next to the "uploads" folder, choosing the Upload Files menu selection.
This will launch the File Uploader component.  Safari will prompt whether you wish to Block or Allow it.  Click 'Allow'.
Safari will respond with a security warning dialog.  Check the box labeled "I accept the risk and want to run this application".  Clicking "Show Options" gives you the additional option to always allow apps from this location; checking this box will allow all applets from the GenePattern web site.  Doing so should allow the visualizers to work as well.  Click "Run" to apply these changes.
After these steps are complete, the File Uploader component should be open and enabled.  
Feel free to close this and try visualizers from your Job Results.  When you close the window, Safari may bring up an additonal Security Warning, again prompting you whether or not to Block this applet.  Click "Don't Block" at this point.  After this, visualizers and other components should be enabled for you on the GenePattern web site.

GenePattern 3.6

GenePattern 3.6 contains several new features and fixes.

New Features

Updated Job Submit Page

In GenePattern 3.6, the job submit page (the page that appears when you select a module or pipeline) has been revised for ease of use.  The user interface has been streamlined with clearer drag--and-drop targets, updated buttons and other UI elements, and reorganized module information in the header.

Improved File Input

We have improved file input to modules and pipelines in a number of ways:

Drag-and-drop File Lists

We have implemented the ability to drag-and-drop/upload multiple files for a single module run; this provides an alternative to having to make a text file containing the absolute paths or URLs to each file, making it much easier to do a single module run on a set of files.  These files can come from a direct upload, a previous job result, the GenomeSpace tab, or an external URL.  This works for any module or pipeline that has file lists enabled.


The 3.6 release fixes issues in GenePattern, including:



October 2012 Java 6 update and GenePattern visualizer issues

(Originally posted 2012-11-09)

Oracle recently released an update to their Java 6 platform which could cause problems for GenePattern users.  The update disables the underlying technologies used by several of GenePattern components, specifically the visualization modules (such as ComparativeMarkerSelectionViewer and HeatMapViewer) and the file uploader.  The GenePattern team is currently evaluating options to address this issue.

This update came out within the last couple of weeks, so you may or may not have already applied this change depending on the update policies of your organization and the settings on your own computer.  It is known by several different names, including at least the following:
The update removes the Java Plug-in for web browser and Java Web Start features which had been present in earlier versions of Java 6.  The most visible sign that you are affected will be the display of a 'Missing Plug-in' or similar error message when trying to run a visualizer or use the uploader.  Here's an example from Firefox 16.0.1 running on Mac OS X Lion (the exact message may differ depending on your browser and operating system):
You can also check whether the update has been installed by running 'java -version' from the command line (Command Prompt in Windows, Terminal in OS X, or a UNIX shell prompt).  A response similar to:
   java version "1.6.0_37"
indicates that the update has been installed on your computer.
Unfortunately, as it stands we cannot give our users a blanket recommendation about how to proceed as there are disadvantages to any approach.  There are three options:
Oracle has issued release notes and an associated Critical Patch Advisory with Risk Matrix about the update itself and the security implications around it.  For Mac users, Apple has a knowledge base entry on the matter.  We encourage you to review this information before making any decisions and consult with your organization's IT department before making any changes.  For users within the Broad Institute, the IT recommendations can be found here.  We cannot, however, make any recommendations on behalf of other organizations.
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