Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:
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Story Points:2.5
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Epic Link:
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Sprint:Spring 2 : 20 Jan to 31 Jan, Spring 3 : 3 Feb to 14 Feb
Description
IGB uses the Genoviz Software Development Kit (SDK), a Swing-based library that implements animated, one-dimensional zooming and many other useful features for genome visualization.
App developers need better documentation for the Genoviz SDK so that they can make use of its features in Apps. Also, IGB platform developers need better documentation so that they can improve the core IGB infrastructure.
When Genoviz was first released as a commercial product, developer Eric Blossom created an interactive tutorial for Genoviz features that used Java applets. The tutorial consists of several interlinked Web pages with embedded java applets.
However, to run the tutorial, users need to configure their Web browser to enable java applets. Also, the java applet tags within the pages may need to be updated with new classpaths, as we changed how the library is getting built when we moved from ant to maven based build system.
For this task, look into the code base and figure out how to get the applets to run properly in the tutorial.
Note: This paper gives a high-level overview of Genoviz SDK https://www.ncbi.nlm.nih.gov/pubmed/19706180
Attachments
Issue Links
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-1531 [ 17617 ] |
| Rank | Ranked higher |
| Assignee | Ann Loraine [ aloraine ] |
| Rank | Ranked lower |
| Rank | Ranked higher |
| Sprint | Summer 2019 Sprint 10 [ 69 ] | Summer 2019 Sprint 11 [ 70 ] |
| Rank | Ranked higher |
| Sprint | Summer 2019 Sprint 11 [ 70 ] |
| Rank | Ranked lower |
| Workflow | Loraine Lab Workflow [ 18585 ] | Fall 2019 Workflow Update [ 18991 ] |
| Workflow | Fall 2019 Workflow Update [ 18991 ] | Revised Fall 2019 Workflow Update [ 21107 ] |
| Status | Open [ 1 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Summary | Fix or update Genoviz SDK tutorial and javadocs generation | Fix or update Genoviz SDK tutorial |
| Description |
Note: This is a big task - feel free to create sub-tasks as you see fit. This ticket is marked as "Advanced" because it requires a big picture view.
IGB uses the Genoviz Software Development Kit (SDK), a Swing-based library that implements animated, one-dimensional zooming and many other useful features for genome visualization. App developers need better documentation for the Genoviz SDK so that they can make use of its features in Apps. Also, IGB platform developers need better documentation so that they can improve the core IGB infrastructure. When Genoviz was first released as a commercial product, developer Eric Blossom created an interactive tutorial for Genoviz features that used Java applets. Since then, Java has changed a lot, and it is now extremely difficult to get the tutorials to run. It may be impossible! In addition, the Genoviz developers put a lot of effort into writing javadocs. For this task, investigate what it would take to improve the tutorial so that developers can use it to learn about Genoviz SDK and its features. Also, investigate whether, how, and where to build and deploy the javadocs. For example, can we build them as part of pipeline and deploy them on bitbucket itself? Review all previous Jira issues related to the Genoviz tutorial. Also, read the 2009 Genoviz paper: https://www.ncbi.nlm.nih.gov/pubmed/19706180 |
IGB uses the Genoviz Software Development Kit (SDK), a Swing-based library that implements animated, one-dimensional zooming and many other useful features for genome visualization.
App developers need better documentation for the Genoviz SDK so that they can make use of its features in Apps. Also, IGB platform developers need better documentation so that they can improve the core IGB infrastructure. When Genoviz was first released as a commercial product, developer Eric Blossom created an interactive tutorial for Genoviz features that used Java applets. For this task, investigate what it would take to improve the tutorial so that developers can use it to learn about Genoviz SDK and its features. To start: Review all previous Jira issues related to the Genoviz tutorial. Also, read the 2009 Genoviz paper: https://www.ncbi.nlm.nih.gov/pubmed/19706180 |
| Assignee | Srishti Tiwari [ stiwari8 ] |
| Assignee | Srishti Tiwari [ stiwari8 ] |
| Description |
IGB uses the Genoviz Software Development Kit (SDK), a Swing-based library that implements animated, one-dimensional zooming and many other useful features for genome visualization.
App developers need better documentation for the Genoviz SDK so that they can make use of its features in Apps. Also, IGB platform developers need better documentation so that they can improve the core IGB infrastructure. When Genoviz was first released as a commercial product, developer Eric Blossom created an interactive tutorial for Genoviz features that used Java applets. For this task, investigate what it would take to improve the tutorial so that developers can use it to learn about Genoviz SDK and its features. To start: Review all previous Jira issues related to the Genoviz tutorial. Also, read the 2009 Genoviz paper: https://www.ncbi.nlm.nih.gov/pubmed/19706180 |
IGB uses the Genoviz Software Development Kit (SDK), a Swing-based library that implements animated, one-dimensional zooming and many other useful features for genome visualization.
App developers need better documentation for the Genoviz SDK so that they can make use of its features in Apps. Also, IGB platform developers need better documentation so that they can improve the core IGB infrastructure. When Genoviz was first released as a commercial product, developer Eric Blossom created an interactive tutorial for Genoviz features that used Java applets. The tutorial consists of several interlinked Web pages with embedded java applets. However, to run the tutorial, users need to configure their Web browser to enable java applets. Also, the java applet tags within the pages may need to be updated with new classpaths, as we changed how the library is getting built when we moved from ant to maven based build system. For this task, look into the code base and figure out how to get the applets to run properly in the tutorial. Note: This paper gives a high-level overview of Genoviz SDK https://www.ncbi.nlm.nih.gov/pubmed/19706180 |
| Assignee | Pawan Bole [ pbole ] |
| Sprint | Spring 2 : 20 Jan to 31 Jan [ 85 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Story Points | 3 | 2.5 |
| Reporter | Ann Loraine [ aloraine ] | Pawan Bole [ pbole ] |
| Reporter | Pawan Bole [ pbole ] | Ann Loraine [ aloraine ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Sprint | Spring 2 : 20 Jan to 31 Jan [ 85 ] | Spring 2 : 20 Jan to 31 Jan, Spring 3 : 3 Feb to 14 Feb [ 85, 86 ] |
| Rank | Ranked higher |
Following is the link to enable Java in web browsers.
https://www.digitalcitizen.life/how-enable-java-all-major-web-browsers
Please test to determine this fix works for MacOS Chrome not just Windows Chrome.
Pawan Bole - thanks for the summary yesterday about applet tags. Please document same here.
Applets are no longer supported/deprecated by all major browsers as they do not support the Netscape Plugin API(NPAPI).
The only browser that supports is Internet explorer.
However, I tried an example by building a simple applet.
For example, http://journals.ecs.soton.ac.uk/java/tutorial/getStarted/applet/index.html
I tried loading in Internet Explorer and it failed to load the applet.
Also, using the Appletviewer I was able to load the applet.
The Appletviewer and applet tags are no longer supported from Java 9 and above versions.
https://docs.oracle.com/javase/9/docs/api/java/applet/package-summary.html
https://www.oracle.com/technetwork/java/javase/9-deprecated-features-3745636.html
Thanks Pawan Bole
Please provide detailed step-by-step instructions on how to run the applets using appletviewer.
Some basic information of applets and how to run applets using Appletviewer can be found on the link below.
https://www.geeksforgeeks.org/java-applet-basics/
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
This is good - thanks Pawan Bole
Please can you also give step-by-step instructions explaining to a user what they must do to run the applets in the tutorial?
Hi, Dr. [~aloraine]:
Following are the steps to load the site
1. Build the Genoviz project
2. Open the local repository and navigate to \src\main\resources\html and open index.html
To load the applet.
1. Inspect element for the applet in the web browser.
For example :
<applet codebase="../demo" archive="genoviz.jar" code="genoviz.tutorial.SimpleMap1" height="150" width="570">
2. From the code, attribute select the class you want to load. In the above example, it is SimpleMap1.
3. Using NetBeans load the genoviz tutorial project.
4. In the projects, section click on Source Packages and then click on com.affymetrix.genoviz.tutorial
5. Right-click on the respective class to execute, for example, right-click on "SimpleMap1.java" and click run.
6. The applet is loaded for the class.
If you are using an older version of Netbeans you will not have an option on right-click on the class to run.
Instead, you can use the following command in the command line.
java -Dfile.encoding=UTF-8 -classpath "target classes path;Genoviz jar path" com.affymetrix.genoviz.tutorial.SimpleMap1
For example:
java -Dfile.encoding=UTF-8 -classpath "G:\LoraineLab\genoviz-sdk-demos\target\classes;C:\Users\pawan\.m2\repository\com\affymetrix\genoviz\1.1.8\genoviz-1.1.8.jar" com.affymetrix.genoviz.tutorial.SimpleMap1
| Link | This issue relates to IGBF-2265 [ IGBF-2265 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
Please fork this https://bitbucket.org/lorainelab/genoviz-sdk-demos for next steps.