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
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Link | This issue relates to IGBF-2265 [ IGBF-2265 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Rank | Ranked higher |
| 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 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Reporter | Pawan Bole [ pbole ] | Ann Loraine [ aloraine ] |
| Reporter | Ann Loraine [ aloraine ] | Pawan Bole [ pbole ] |
| Story Points | 3 | 2.5 |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Sprint | Spring 2 : 20 Jan to 31 Jan [ 85 ] |
| Assignee | Pawan Bole [ pbole ] |
| 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 | Srishti Tiwari [ stiwari8 ] |
| Assignee | Srishti Tiwari [ stiwari8 ] |
| 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 |
| Summary | Fix or update Genoviz SDK tutorial and javadocs generation | Fix or update Genoviz SDK tutorial |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Workflow | Fall 2019 Workflow Update [ 18991 ] | Revised Fall 2019 Workflow Update [ 21107 ] |
| Status | Open [ 1 ] | In Progress [ 3 ] |
| Workflow | Loraine Lab Workflow [ 18585 ] | Fall 2019 Workflow Update [ 18991 ] |
| Rank | Ranked lower |
| Sprint | Summer 2019 Sprint 11 [ 70 ] |
| Rank | Ranked higher |
| Sprint | Summer 2019 Sprint 10 [ 69 ] | Summer 2019 Sprint 11 [ 70 ] |
| Rank | Ranked higher |
| Rank | Ranked lower |
| Assignee | Ann Loraine [ aloraine ] |
| Rank | Ranked higher |
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-1531 [ 17617 ] |