Release 1.2.8b

Updated default GenePattern server URL to https://cloud.genepattern.org/gp

Release 1.2.8a

Updated log4j to 2.17.1 due to log4shell vulnerability

Release 1.2.8

Changed default server to https://cloud.genepattern.org/gp/

Release 1.2.7

Bug fix for PCAViewer command line, -c with improvements for the user data directory

Parts 1 and 2

• fix for substituting input files with command line flags
• bug fix for special-characters in input filenames
• added InputFileInfo helper class
• GP-6584, change default 'log.dir' location
• GP-6585, optionally set custom 'user.data.dir' location
• fix for Windows file path substitutions
• fix for Windows '~' substitutions
• enable 'user.data.dir' as a relative path
• more options for setting the 'user.data.dir' when launching from the maven command line (for testing/development)

    # by default, use 'appdir' folder in project directory
    mvn package exec:java
    # use ./target/appdir, which is deleted with 'mvn clean'
    mvn package exec:exec
    # can customize with a relative path, relative to project dir
    mvn -Duser.data.dir="relative/path" exec:java
    # can customize relative to target (aka build) dir
    mvn -Duser.data.dir="relative/path" exec:exec
    # or fq path
    mvn -Duser.data.dir=/fq/path

• remove unnecessary ant build script and support files
• set workding dir for junit tests to './target/test-run'
• generate junit html report with surefire report plugin, mvn site

Release 1.2.6

VisualizerLauncher v1.2.6, fix for downloading support files bug

• Download data files via the AppDirs framework into platform specific location:

Mac OS X   : /Users/<Account>/Library/Application Support/VisualizerLauncher
Windows XP : C:\Documents and Settings\<Account>/Application Data\Local Settings\GenePattern\VisualizerLauncher
Windows 7  : C:\Users\<Account>\AppData\GenePattern\VisualizerLauncher
Unix/Linux : /home/<account>/.local/share/VisualizerLauncher

• Cache module support files into <appdir>/taskLib
• Cache job input files into <appdir>/jobs

Release 1.2.5

Fix for '/gp/jobResults' substitution parameter

• fixed a bug with input files sent from the job results page, for example, prediction results file=/gp/jobResults/100101/output.pred.odf
• documentation update

Release 1.2.4

Documentation

See https://genepattern.github.io/VisualizerLauncher/

To get started ...

[Mac OS X] Download VisualizerLauncher.app.zip, unzip, and open the app.
[Other java] Download visualizerLauncher.jar and double-click the jar file.

Launching a visualizer ...

Run the visualizer of interest in GenePattern, as you normally would. Once the Job Status page displays, and the visualizer fails to launch in your browser, you will now have the job number to provide to the app.

After opening the app (either by double clicking or opening - see above for OS specific instructions), the VisualizerLauncher opens in a new application window.
You will then need to enter the following information ...

• server, e.g. https://genepattern.broadinstitute.org/gp (this can be copied from the URL bar in your browser)
• your genepattern username
• your genepattern password
• the job number of your visualizer job

Click Submit ... the launcher downloads the application and data files from the server, then opens the visualizer in a new window.

Note: To start from a command line shell (aka Terminal.app on Mac OS X) ...

java -jar visualizerLauncher-1.2.4.jar

Release notes

• Fix for hidden window on startup
• Reorganized documentation files
  • simplified README.md doc page
  • created INSTALL.md doc page
  • moved end-user doc to GitHub pages
• Updated software libraries
  • log4j from 2.8.1 to 2.8.2
  • httpclient from 4.5.2 to 4.5.3
• Added jUnit test suite

Release 1.2.3

VisualizerLauncher

Launch a GenePattern visualizer from the desktop. Use this as a replacement for the 'Open Visualizer' link embedded in the web page to launch (legacy) Java Applet based visualizers such as MultiplotStudio.

To get started ...

[Mac OS X] Download VisualizerLauncher.app.zip, unzip, and open the app.
[Other java] Download visualizerLauncher.jar and double-click the jar file.

Launching a visualizer ...

The VisualizerLauncher opens in a new application window. If for some reason it is hidden, look for the "VisualizerLauncher" java application icon in your dock. Enter ...

• server, e.g. https://genepattern.broadinstitute.org/gp
• your genepattern username
• your genepattern password
• the job number of your visualizer job

Click Submit ... the launcher downloads the application and data files from the server, then opens the visualizer in a new window.

Note: To start from a command line shell (aka Terminal.app on Mac OS X) ...

java -jar visualizerLauncher-1.2.3.jar

Release notes

• fix for Windows <path.separator>
• improved logging and error messages
• use apache-commons-exec library

Release 1.2.2

Release notes

• fix for <GenePatternURL> in visualizerInputFiles.json, e.g.

    GET /rest/v1/jobs/{jobId}/visualizerInputFiles
    {"inputFiles":["<GenePatternURL>jobResults/123/all_aml_train_filt.pred.odf"]}

• set jvmVersion to 1.8+, required for Mac OS X app

VisualizerLauncher

Launch GenePattern visualizer from the desktop. Use this as a replacement for the 'Open Visualizer' link embedded in the web page to launch (legacy) Java Applet based visualizers such as MultiplotStudio.

To get started ...

Mac OS X: Download VisualizerLauncher.app.zip, unzip, and run the app.

Other java: Download the visualizerLauncher.jar file. From a Terminal window

java -jar visualizerLauncher-1.2.2.jar

Launching your visualizer ...

The VisualizerLauncher opens in a new application window. If for some reason it is hidden, look for the "VisualizerLauncher" java application icon in your dock. Enter the server, (e.g. https://genepattern.broadinstitute.org/gp), your username, password, and the job number of your visualizer job. Click 'Submit'. The launcher will connect to the server, download the required application and data files, and launch the visualizer as a new window.

Release 1.2.1

Release notes

• Bug fix for HTTPS servers. Updated the file downloader to work with both HTTP and HTTPS protocols. This fix is required to launch visualizers with files from the public GenePattern Server.
• Switched build tool from ant to maven to make it easier to package as a Mac OS X application
• Removed 'org.json' source code from this repository. Referencing it as a maven dependency instead.

VisualizerLauncher

Launches a GenePattern visualizer from the desktop. Use this as a replacement for the 'Open Visualizer' link embedded in the web page to launch (legacy) Java Applet based visualizers such as MultiplotStudio.

To get started ...

Mac OS X: Download VisualizerLauncher.app.zip, unzip, and run the app.

Other java: Download the visualizerLauncher.jar file. From a Terminal window

java -jar visualizerLauncher-1.2.1.jar

Launching your visualizer ...

The VisualizerLauncher opens in a new application window. If for some reason it is hidden, look for the "VisualizerLauncher" java application icon in your dock. Enter the server, (e.g. http(s)://genepattern.broadinstitute.org/gp), your username, password, and the job number of your visualizer job. Click 'Submit'. The launcher will connect to the server, download the required application and data files, and launch the visualizer as a new window.