convert-ome returns 0 upon failure

[johnyaku]

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Bug report

Describe the bug
QuPath convert-ome returns exit code 0 despite failure.

To Reproduce
Steps to reproduce the behavior:

scale=2
tile=1024
comp=ZLIB
input=broken_image.tif
output=broke_omage.ome.tif
QuPath convert-ome $input $output \
    --pyramid-scale=$scale \
    --tile-size=$tile \
    --compression=$comp \
    --parallelize

Output (truncated)

20:39:42.582 [main] [INFO ] q.l.i.s.b.BioFormatsServerOptions - Setting max Bio-Formats readers to 2
20:39:43.272 [main] [ERROR] loci.formats.tiff.TiffParser - Error reading IFD type at: 14
20:39:43.274 [main] [ERROR] loci.formats.tiff.TiffParser - Error reading IFD type at: 14
20:39:43.275 [main] [ERROR] loci.formats.tiff.TiffParser - Error reading IFD type at: 14
...
20:39:43.604 [main] [ERROR] q.l.i.writers.ome.ConvertCommand - Unable to open file:broken_image.tif
java.io.IOException: Unable to open file:broken_image.tif
        at qupath.lib.images.servers.ImageServers.buildServer(ImageServers.java:306)
        at qupath.lib.images.writers.ome.ConvertCommand.run(ConvertCommand.java:147)
        at picocli.CommandLine.executeUserObject(CommandLine.java:2026)
        at picocli.CommandLine.access$1500(CommandLine.java:148)
        at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2461)
        at picocli.CommandLine$RunLast.handle(CommandLine.java:2453)
        at picocli.CommandLine$RunLast.handle(CommandLine.java:2415)
        at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2273)
        at picocli.CommandLine$RunLast.execute(CommandLine.java:2417)
        at picocli.CommandLine.execute(CommandLine.java:2170)
        at qupath.QuPath.main(QuPath.java:202)
        Suppressed: java.io.IOException: Unable to build ImageServer for file:/scratch/a56/jr9959/tmp/xenium-images/unassigned/230629_Xenium_ID4369_Primary_3962_LA-Spots/230629_Xenium_ID4369_Primary_3962_LA-Spot000001.tif with requested provider qupath.imagej.images.servers.ImageJServerBuilder
                at qupath.lib.images.servers.ImageServerBuilder$DefaultImageServerBuilder.buildOriginal(ImageServerBuilder.java:369)
                at qupath.lib.images.servers.ImageServerBuilder$AbstractServerBuilder.build(ImageServerBuilder.java:174)
                at qupath.lib.images.servers.ImageServers.buildServer(ImageServers.java:299)
                ... 10 common frames omitted

Checkout exit code:

echo $?
0

Expected behavior
Expected a non-zero return code

Desktop (HPC):

• OS: Rocky Linux release 8.8 (Green Obsidian)
• QuPath Version: 0.5.0

[petebankhead]

Thanks, I think the solution might be simply to include System.exit(-1) in the catch clause here:

qupath/qupath-extension-bioformats/src/main/java/qupath/lib/images/writers/ome/ConvertCommand.java

Lines 250 to 255 in 864ac71

	long duration = System.currentTimeMillis() - startTime;
	logger.info(String.format("%s written in %.1f seconds", outputFile.getAbsolutePath(), duration/1000.0));
	} catch (Exception e) {
	logger.error(e.getLocalizedMessage(), e);
	}

@Rylern could you check this please?