Move console to lower tabbed panel for display

For Ease of Development, we can use my Branch

https://bitbucket.org/sshanbh1/sameer-igb/commits/branch/IGBF-1864

Prof. [~aloraine], I am done with the development of the same.
Shall I go ahead and remove the View console option under help menu in IGB along with the code from the IGB codebase?
Please let me know.

I have made the changes and moved the IGB console to the bottom tabbed panel in IGB.
Code changes are available at :
https://bitbucket.org/sshanbh1/sameer-igb/src/IGBF-1864/

Looking good!!!!

I have a couple of change and "new feature" requests.

This is increasing the scope of the task, so please adjust the Story Points upward to reflect the extra effort.

A bit of history:
Some years ago we put some effort into creating a tabbed panel API so that it would be super-easy to add new tabs. You are the first to do this in quite some time, so I'm eager to find out if our re-architecting effort has achieved its goal Your comments – and updates to the Story Points – will be very welcome!

Requests:

• Can you modify the tabbed panel so that the "Copy to Clipboard" button appears in the lower left corner?
• Is this possible? Can you modify the text area so that if the user increases the size of the enclosing window, the Console tab's text area will grow to use up the available horizontal space?
• Please change the "Copy to Clipboard" button label to read "Copy All to Clipboard" (if this is what it does?)
• Make it so that all log messages during the session are printed and kept available in the tab.
• Add a new Button "Open in New Window" that performs the same action as Tab > Console > Window
• Add a new Button "Clear" that deletes all text currently shown. (So that a user can easily see when something new is printed.)
• Allow it to show all text printed from the logs. (Is it doing that now?)

A comment: I like that the Console is editable. Don't change that

And these last two are probably going to be the most complex — if you run into problems or have doubts about it, let's talk!

• Change Help > Show Console menu so that it simply performs the "Open in New Window" action as in above. Also, please remove any code that is duplicated.
• Add and export a service (in the OSGi sense) that lets an App developer cause a message to be printed to the Console. Also, check to see if such a service already exists in the IgbServices class.

Last but not least:

Please check the POM carefully for unused imported packages. I noticed genometry is imported ... but I'm not sure it needs to be!

Prof. [~aloraine], yes. It is showing all text printed from the logs.
I'll work on the changes suggested and will provide an update on this soon. Also, I'll let you know if I run into any problem.
Thanks.

Made some changes in the console tab code.
Now it is resizing as the user resizes the enclosing window.
Changed the "Copy to Clipboard" button label to read "Copy All to Clipboard".
All the log messages were already made available on the console.
Added a clear button which clears the console logs.
There wasn't any using which user can print a message to the console. So, added a service in IgbServices class.
Also, Cleaned up the pom and removed the dependencies which weren't used in the code.
The code changes are present at:
https://bitbucket.org/sshanbh1/sameer-igb/src/IGBF-1864/

I tried almost everything to open console tab in window mode on click of of "Show Console" but was unable to do it. Not removing console-gui package because of that. Once the "Show Console" click functionality is implemented, I will remove it.

Thanks a lot Prutha for looking for a way to implement console tab in window mode on click of "Show Console"

I think it will be OK to go ahead and remove console-gui package. Please go ahead and do that unless you have a doubt about that. We can do it on a different ticket/topic branch if you like. It's your call.

Prutha Kulkarni

I have taken the Sameer's branch and tested the functionality.

Test Results:
1. Console section is not shown in IGB
2. IGB has the following errors[AWT] while execution.

Fixed the AWT error.
Code changes are available at :
https://bitbucket.org/sshanbh1/sameer-igb/src/IGBF-1864/

The code changes are working fine. The console section is shown in lower tabbed panel. Kindly submit a pull request for the same.

Pull request is submitted.
Code changes are available at :
https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/722/igbf-1864/diff
[~aloraine], could you please merge it onto the master?
Thanks.

(Please also see comment on pull request.)

Code looks very nice - I just had one request to add more description to the top of one file.

I also have some doubts about the commit chain. It looks like this pull request is coming from the master branch on a fork - the fork you and Sameer were using to work on this together?

It looks like when you guys were developing, you (Prutha) were submitting pull requests to Sameer's fork, and he was merging them into that fork's master branch. As the team repository acquired new commits, he merged those into master on his fork.

This is making it tricky for me to see which of the commits in the pull request are already part of the team repository's master branch or not, and also it looks like the source master branch is way behind upstream master. It's a little worrying to see such a complex scenario because backing out of it (if we need to) could be very challenging.

Can you make this easier to follow?

What I would love to see is the commit history, pull request, and branch simplified ... a single commit on a topic branch where its parent commit is the last or close-to-last commit on master.

Prof. [~aloraine], I have submitted a new pull request for the same.
Code changes are present at:
https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/725/igbf-1864/diff

Merged to master. Also, deployed as "Early Access Release" on BioViz.org.

Testing results :

1. The tab is seen at the bottom
2. Within the console, the text is not scrollable till the last log.
3. Once the console is cleared ,the logs are not appearing.

Noor Zahara, Please attach a screenshot of the test cases for the same.

Once the console is cleared, the logs are appearing . Maybe when I tested there was some delay.

But once the console area is full it does not let you see the latest logs i.e it is not scrollable. It might be an existing issue.

Noor Zahara, Okay. I'll look into it.
Thanks for letting me know.

Prof. [~aloraine], I have fixed the issue which Noor Zahara has found in the console tab.
I have created a pull request for the fix.
Could you please merge it into the master?
The code diff is present at:
https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/730/igbf-1864-display-text-properly-when-the/diff
Moving the ticket to Needs testing as I am not able to move it to the pull request submitted.

Noor Zahara, could you please test it once again after the fix is merged into the master?

Thank you Prutha Kulkarni!

For the next steps, can you please move it to "Needs First Level Review" ?

The next step should be for some-one - Noor Zahara or possibly someone else who is familiar with the new feature - to download your new installer and try it out. They should also look at how the code has changed. While this is happening, they should assign the Jira issue to themselves and

If all is fine, they should then move it to "Ready for Pull Request". At that point, you can submit a PR and move it to the next phase.

If you have any problems moving things please let me know. This workflow is a new version and it's possible there are kinks. Please take a look at the workflow – if you see an arrow going from state A to state B, it means you can move the item from A to B.

I looked at the history. Looks like a step got missed. When Noor Zahara noted the problem, the issue should have been moved to "To-Do". But since I have been making changes to the workflow, she might not have been able to do that. Prutha Kulkarni, you can do that now. Just pull it back to To-Do, forward to In Progress, and then forward again to Needs First Level Review. At that point you can leave for Noor Zahara or others to do testing.

I am looking forward to using this new feature

Prof. [~aloraine], I am still not able to move the ticket to anywhere before Needs testing column.

Noor Zahara, I have moved it to Needs first level review. Could you please go through the code changes and let me know if I can move it further.
Thanks.

Please review next time you are in the office.

I reviewed the code . It is working as expected.

[~aloraine], Pull request is submitted for the same.
The code changes are present at:
https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/730/igbf-1864-display-text-properly-when-the/diff
Could you please merge it into the master?
Thanks.

Merged. Works as expected (see comment for https://jira.transvar.org/browse/IGBF-1930).