Make a new IGB "demo" App that shows how Apps can get access to track data

This is closely related to IGBF-1351 .
Review the comments there.

Most importantly:
draft documentation:
https://docs.google.com/document/d/1qYb0MSAV3kiKmv0EZdfS2hqImDMb3FRGG09h-WmkrQI

Helpful notes from Ann related to this topic:

Questions:

• How does an App find out what tracks are currently selected?
• How does an App get access to currently loaded data currently in view for a track?

To understand IGB graphics, see paper describing the GenoViz SDK and how it works:
https://www.ncbi.nlm.nih.gov/pubmed/19706180

Also, see:

• ProtAnnot paper - https://www.ncbi.nlm.nih.gov/pubmed/27153567
• IGB platform paper - https://www.ncbi.nlm.nih.gov/pubmed/27153568
• MI Bundle App paper from Dr. Arnaud Céol -
  https://www.ncbi.nlm.nih.gov/pubmed/26209801

Dr. Céol's App adds a new track to IGB. It may be useful to look at how he did this, and how the platform supports it.

I think this ticket has taken such a long time to close because the task description is too vague. Instead of creating documentation, we should instead create a demonstration of how an App can get access to the data loaded into a track. Also, we did not have very good infrastructure for supporting Apps until recently.

To answer the potential App developer's question, let's write simple demonstration App that implements an example feature that he has suggested.

First pass at a specification:

Develop App: "Get Average Score" (start a new repo for it, configured like the others)
Description: This App calculates the average score for all items in the current view for selected annotation tracks.

On installation:

• App adds an item to Tools menu - "Get Average Score"
• If user selects "Get Average Score" and no tracks are selected, a window opens explaining how the Get Average Score function works.
• If user selects "Get Average Score" with one or more annotation tracks selected, the App calculates the average score for every item currently on view in the display that has a score.
• The output is printed to the IGB console or to a new window that appears on the user's desktop. (You should decide based your own best judgement – rule of thumb: fewer clicks are better.)

Note: BED, GFF, and many other formats have numeric "score" field. When IGB reads these files and creates data objects, many times these data objects have a "score" attribute - try to access this. Don't go back to the original file – use the internal data models in IGB.

I have been checking into the code to learn how the app can access the tracks or part of tracks that are selected. ProtAnnot app has a similar functionality and I am trying to implement the logic in my demo app. After this, I shall work on calculating the average score with some guidance from Dr. Loraine.

The app is working as required, without making any major code changes in the IGB code. Now, I am working on creating an icon for the app and displaying it a shortcut button for the same.

The app is functional and can be found in the following repository. For now, the icon for the app is kept fairly simple just for demonstration but can be changed if required. The README.md file consists of step to test the functionality of the app. I shall also be adding a document which includes all the approaches that I as an app developer considered while working on this app. This document will also include steps to test. Kindly refer the document if you need more information. Kindly let me know your opinions and suggestions to make this a better demo app. Thank you.

https://bitbucket.org/skulka2710/get-average-score/src/master/

To review:

• Look at the code. Developer should be able to read the code and know (1) how to build it (2) how to run and test the App in IGB
• Run the code. Developer should be able to install the App and try it out in IGB.

Please make comments here for SK.

Goal: This App is meant to serve as an example for how an App developer can get access to items in the IGB display. Developers (e.g., people like us) are the target audience for this App.

Shamika Gajanan Kulkarni, I have reviewed the code for the Demo App. It is very easy to understand.
IGB service is used to get sequence map view. After that a for loop is ran on the sequence map to get selected syms. And for each score entry for the sym, you have calculated average.
When I was reviewing your code, I have noticed that the target folder is accidentally pushed to the app repository which shouldn't be there. Along with that there is git.properties file in the resource directory of the source folder which also should be removed from the repository.
Other than that, everything is fine. Even the message popup that you are showing on click of Tools>"Get Average Score" is perfect.
Moving the ticket to TO DO. Once you're done removing this folder/file from the repository, let me know so that I can move it forward to Ready for pull request.
Thanks.

I am sorry I overlooked this fact and I have made the necessary changes.
Also, Dr. Loraine suggested a few changes:
1) To add a new AppDecription.md file that will be visible in the App Manager and provide instructions to the user on how to use the app.
2) To modify the existing README.md file providing the user with instructions on how to install the app. The README.md file will only be visible on bitbucket. The App Manager should show the AppDescription.md data.
The changes have been implemented and usability testing has been conducted for the same.
Kindly check the link below and let me know if you observe any more changes that need to be done. Thank you for the review.
https://bitbucket.org/skulka2710/get-average-score/src/master/

Shamika Gajanan Kulkarni, I have checked both markdown files, the one after adding plugin to the IGB app manager which is AppDescription as well as the one which is displayed on the bitbucket i.e. README.
Moving the ticket forward. You can now submit a PR for the same.

Thank you for the reviews.
Since the repository is a separate one for the Demo App - Get Average Score, the ownership to the repo is transferred to LoraineLabs. Moving the ticket to PR Submitted. Kindly review.