Phenote Webstart

Phenote is a Java application, that can be launched from the web using Java Webstart. 

Downloading and Running Phenote

You can access Phenote webstart at the website, http://www.phenote.org/content/software/.  Clicking on the "Webstart" link will download the application and place a link 'phenote.jnlp' in your download location (typically your Desktop) and run.  The indication that a link works is that you get a popup that says "Java Loading", or something like that and then a bunch of files get downloaded and eventually the application actually comes up.  It will ask you to verify a security certificate from the National Center for Biomedical Ontology. 

If nothing happens, this may indicate that your browser is not properly configured.  See instructions below for configuring your browser.

In the future, you can start the software by clicking the 'phenote.jnlp' link.

 

Phenote might take a few minutes to get started.  Since many ontolgies are updated everyday, it is important to keep in synch with the resources.  So, every time you start Phenote it checks to see if there are newer versions of ontologies available for download.  If so, it will automatically download the newest versions to your local computer.  (This feature can be disabled in the future.  See the Customizing Phenote section for more information.)

 

Configuring your MacOS or Windows browser for Webstart

You must have Java 1.5 or later installed on your computer. Your browser must be configured to recognize webstart appications with the 'jnlp' extension. Most Mac and Windows browsers tend to have webstart pre-installed on their browsers, but you may be asked to update the Java that is installed.

Configuring your Linux browser for Webstart

Linux browsers tend not to have webstart pre-installed.  You must set up an association between the MIME type, which is an "application/x-java-jnlp-file".

These are the steps I had to go through to get webstart installed on my Mozilla browser on Linux, which does not come with webstart pre-installed:

Download/Install Java Webstart

First you need to see if you have webstart already installed on your computer. If you have java on your computer then usually webstart comes with java so you should have it. So if you have java you first need to find out where it is installed. In linux you type "which java" at the command line. For me this comes back with

/usr/lib/java/bin/java

Since Phenote requires Java 1.5, you need to make sure you are using java 1.5. Do a "java-version" at the command line. If you have anything less than 1.5, you need to install java 1.5, or if you have 1.5 installed somewhere (but its not the default) you need to find it and grab its javaws. If you try to webstart phenote with a java less than 1.5 nothing will happen and it won't even indicate that its the wrong java, you just have to know.

So what I found is in java 1.5 javaws is in both the bin and jre directory. So cd to /usr/lib/java and do a "ls jre" and "ls bin" (on windows "dir jre" & "dir bin") and look for a file called "javaws", which is the webstart application. The full path plus javaws is what you will need below. So for me its "/usr/lib/java/jre/javaws"

If webstart is not on your computer (or network) you can download it from(make sure its from java 1.5):

http://java.sun.com/products/javawebstart/download.jsp

Associating the MIME type

Now that we've found the webstart application we are ready to associate it with a mime type in the browser. Here is how it is done in Mozilla on linux, I hope other browsers are somewhat similar.

Hit the "Edit" menu, and its "Preferences" sub menu to get the Preferences dialog.  Expand the "Navigator" category, and under that click on "Helper Application", which is where mime types get associated with applications. Click the "New Type" button, which brings up a New Type dialog box. In the "MIME Type" field enter "application/x-java-jnlp-file".  Under "Description" you can just put "Java Webstart". Under "Extension" put "jnlp". Click on "Open it with:" and in the associated field either entor or browse for the location of webstart on your computer. This is what you were digging for above. For my computer I enter "/usr/lib/java/jre/javaws", the location of my webstart app. then deselect "Always ask me before handling files of this type", as who wants to keep being asked, and hit "OK" and hit "OK" as well in the Helper Applications dialog.

You now need to restart your browser for it to pick up the new mime type association for webstart and hopefully the above link should now work.

Other Hints

One thing thats also handy if there are problems bringing up webstart is to bring up the browser's java console (this may not be supported by all browsers). This should give some feedback on things happening behind the scenes of the webstart application, so its good for trouble shooting. In mozilla this can be brought up with menu Tools->Web Development->Java Console.