default file extension for graph tracks

The graph file extension options are .gr and .bedgraph.
The value when the pop up window opens is randomly picked between those.

Likewise, in saving annotation files,
The annotation file options are bed (.bed) or bed detail (.bed).
The value when the pop up window opens is randomly picked between those.

I never did get mvn clean install to work, it keeps failing tests.

But the same tests fail from master, so I really don't think the changes in this issue are causing any problems, but it would be best if the first level reviewer could get the tests to run (at least the ones that don't fail on the master branch).

I have implemented and tested a solution on a branch called IGBF-1149.
I'm moving this to get first level review.

In the current IGB, click Save Track As... several times, notice that the default file type is randomly picked from the two options.
You can do this very quickly by selecting a track and using control+S, and click cancel, and repeat.

With this fix, the graph tracks consistently get the "bedgraph" default and annotation tracks get the "bed" default. This is not based on the most recent selection or the recommendation, but it is consistent. And it so happens that the first type when you sort this way is the option I would recommend for each case.

I'm assigning to Mason for first level review.

My branch for this issue is called IGBF-1149.

https://bitbucket.org/IvoryBlak/integrated-genome-browser/branch/IGBF-1149

1st Level Testing:

• Does not fail any additional tests
• Save As... file extension drop down menu showed 'BED (bed)' first when saving an annotation, and 'Graph (bedgraph)' first when saving a graph, as expected.
• All four choices saved files successfully ( BED (bed), bed detail (bed), Graph (bedgraph), Graph (gr) )
• Documentation comments in AbstractExportFileAction.java is clear enough that someone adding a new file extension will know that they will be sorted alphabetically.

I rebased from main master and created a pull request.

I'm reassigned this issue to Ann so she can look at the pull request.

@Ivory:

I started testing this issue by trying to reproduce the original problem on IGB 9.0.0, however, I was not able to do so. I tried several different files and used the method of hitting Ctrl "S" to quickly bring up the save menu and then selecting cancel but I always saw "BED" come up for annotations and "BEDGRAPH" come up for graphs; I never saw "BED_Detail" or "Gr" come up first. The issue is functioning as expected, but I feel uncomfortable closing an issue when I was not able to reproduce the original problem. Any idea on why I am not able to do this? I tested on Windows and Mac, by the way. Please let me know if you have any advice on this.

That is odd. Perhaps try a fresh install of IGB 9.0.0, just to be sure that you are testing it on the live bioviz.org IGB, and not the main master IGB (both of which show version 9.0.0).

Not mind-blowing or anything, but that's all I can think of. I've seen the random-choice on every machine I've looked at (my mac, my windows, Jenn's linux).

After testing this issue it appears that the story is resolved:

*Save As... file extension drop down menu showed 'BED (bed)' first when saving an annotation, and 'Graph (bedgraph)' first when saving a graph, as expected.
*All four choices saved files successfully ( BED (bed), bed detail (bed), Graph (bedgraph), Graph (gr) )

• There is no missing data or additional artifacts seen when opening the saved files.
  *There seems to be no additional behavior caused by this code change.

Since the issue is resolved, it will now be closed.