Display a warning message for Beta and Exerimental tools.

[cmnbroad]

Fixes #4367. Includes a sleep for 5 seconds; not sure thats a good idea, although the warning message scrolls off the screen pretty quickly, especially with Spark apps. This will need to be replicated in Picard as well.

Experimental:

Beta:

[lbergelson]

5 seconds of sleep is going to drive me insane. .5 seems much more tolerable but still noticeable. We might want to add a command line option to disable the sleep and apply that to all the tests

[droazen]

Let's remove the sleep delay @cmnbroad. Red text + a border made out of exclamation points should be sufficient.

[lbergelson]

The one problem with using color in the output is that it makes it gross to read logs that aren't on an interactive terminal that supports color. We might want to make an attempt to tell if we're connected to a terminal or an output file and remove the colors if so.

[lbergelson]

I have this class from an ancient branch that makes dealing with colors nicer in some ways. It tries to avoid printing colors to non-interactive things and it makes it harder to forget a reset:

/**
 * Provides ANSI colors for the terminal output *
 */
public final class TerminalColors {

    private TerminalColors(){};

    private enum TerminalColor{
        CYAN("\u001B[36m"),
        RED("\u001B[31m"),
        GREEN("\u001B[32m"),
        WHITE("\u001B[37m"),
        BOLD("\u001B[1m"),
        RESET("\u001B[0m"); // reset the colors

        private final String color;

        TerminalColor(String color){
            this.color = color;
        }

        public String getColorString(){
            return color;
        }

    }

    public static boolean isInteractive(){
        return !(System.console() == null);
    }

    public static String cyan(String toColor){
        return colorString(toColor, TerminalColor.CYAN);
    }

    public static String red(String toColor){
        return colorString(toColor, TerminalColor.RED);
    }

    public static String green(String toColor){
        return colorString(toColor, TerminalColor.GREEN);
    }

    public static String white(String toColor){
        return colorString(toColor, TerminalColor.WHITE);
    }

    public static String bold(String toBold){
        return colorString(toBold, TerminalColor.BOLD);
    }

    public static String colorString(String toColor, TerminalColor color) {
        if(isInteractive()) {
            return color.getColorString() + toColor + TerminalColor.RESET.getColorString();
        } else {
            return toColor;
        }
    }

    public static String stripColorsFromString(String colorString){
        String stripped = colorString;
        for(TerminalColor color : TerminalColor.values()) {
            stripped = stripped.replace(color.getColorString(),"");
        }
        return stripped;
    }
}

[cmnbroad]

@lbergelson What do you think about putting the TerminalColors class in Barclay ? The same changes I'm making here need to be made in Picard. We could put a lot of this behavior into a shared CommandLineProgram base class that uses TerminalColors.

[lbergelson]

@cmnbroad Barclay sounds like the best place for things that have to deal with the command line. Feel free to use that class or not. I'm not sure it's the greatest way to deal with colors, but it seems better than manually adding the escape codes everywhere.

[codecov-io]

Codecov Report

Merging #4429 into master will increase coverage by 0.079%.
The diff coverage is 77.273%.

@@              Coverage Diff               @@
##             master     #4429       +/-   ##
==============================================
+ Coverage     79.04%   79.119%   +0.079%     
- Complexity    16447     16521       +74     
==============================================
  Files          1047      1047               
  Lines         59189     59460      +271     
  Branches       9672      9747       +75     
==============================================
+ Hits          46783     47044      +261     
+ Misses         8644      8639        -5     
- Partials       3762      3777       +15

Impacted Files	Coverage Δ	Complexity Δ
...stitute/hellbender/cmdline/CommandLineProgram.java	81.757% <77.273%> (-0.783%)	43 <9> (+9)
...park/sv/discovery/alignment/AlignmentInterval.java	89.272% <0%> (ø)	73% <0%> (ø)	⬇️
...kers/variantutils/PosteriorProbabilitiesUtils.java	77.966% <0%> (+0.847%)	43% <0%> (+1%)	⬆️
...oadinstitute/hellbender/utils/gcs/BucketUtils.java	80% <0%> (+1.29%)	39% <0%> (ø)	⬇️
...nder/tools/examples/ExampleVariantWalkerSpark.java	76.316% <0%> (+2.242%)	9% <0%> (+4%)	⬆️
...institute/hellbender/engine/FeatureDataSource.java	79.752% <0%> (+3.696%)	66% <0%> (+22%)	⬆️
...oadinstitute/hellbender/utils/test/XorWrapper.java	78.261% <0%> (+4.348%)	9% <0%> (+1%)	⬆️
...kers/variantutils/CalculateGenotypePosteriors.java	91.398% <0%> (+5.482%)	25% <0%> (+12%)	⬆️
...hellbender/utils/test/VariantContextTestUtils.java	89.053% <0%> (+6.621%)	83% <0%> (+23%)	⬆️
...utils/smithwaterman/SmithWatermanIntelAligner.java	90% <0%> (+40%)	3% <0%> (+2%)	⬆️

[magicDGS]

Maybe https://github.com/fusesource/jansi to handle colors?

[droazen]

Maybe warnAboutToolStatus() would be clearer?

[cmnbroad]

Done.

[droazen]

If this check isn't 100% reliable, I would take it out. Printing the literal codes in non-interactive use is not that big of a deal.

[cmnbroad]

Done.

[droazen]

getToolStatusWarning() might be clearer?

[cmnbroad]

Done.

[droazen]

👍 merge after addressing comments