BioTek: refine field and channel name regexes

[melissalinkert]

This allows a negative field index and more punctuation characters in the channel name.

[muhanadz]

Testing with some issue example files.
Without PR:

Exception in thread "main" picocli.CommandLine$ExecutionException: Error while calling command (com.glencoesoftware.bioformats2raw.Converter@53fe15ff): java.lang.IllegalArgumentException: Invalid series: 0
	at picocli.CommandLine.executeUserObject(CommandLine.java:1962)
	at picocli.CommandLine.access$1300(CommandLine.java:145)
	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2352)
	at picocli.CommandLine$RunLast.handle(CommandLine.java:2346)
	at picocli.CommandLine$RunLast.handle(CommandLine.java:2311)
	at picocli.CommandLine$AbstractParseResultHandler.handleParseResult(CommandLine.java:2172)
	at picocli.CommandLine.parseWithHandlers(CommandLine.java:2550)
	at picocli.CommandLine.parseWithHandler(CommandLine.java:2485)
	at picocli.CommandLine.call(CommandLine.java:2761)
	at com.glencoesoftware.bioformats2raw.Converter.main(Converter.java:2013)
Caused by: java.lang.IllegalArgumentException: Invalid series: 0
	at loci.formats.FormatReader.seriesToCoreIndex(FormatReader.java:1298)
	at loci.formats.FormatReader.setSeries(FormatReader.java:969)
	at loci.formats.MetadataTools.populatePixels(MetadataTools.java:203)
	at loci.formats.MetadataTools.populatePixels(MetadataTools.java:116)
	at com.glencoesoftware.bioformats2raw.BioTekReader.initFile(BioTekReader.java:398)
	at loci.formats.FormatReader.setId(FormatReader.java:1443)
	at loci.formats.ImageReader.setId(ImageReader.java:849)
	at com.glencoesoftware.bioformats2raw.Converter.getBaseReaderClass(Converter.java:1961)
	at com.glencoesoftware.bioformats2raw.Converter.convert(Converter.java:517)
	at com.glencoesoftware.bioformats2raw.Converter.call(Converter.java:493)
	at com.glencoesoftware.bioformats2raw.Converter.call(Converter.java:97)
	at picocli.CommandLine.executeUserObject(CommandLine.java:1953)
	... 9 more

With PR:
Problem example files convert successfully which then could be converted to ome.tiff using raw2ometiff and imported to OMERO successfully.

[chris-allan]

Before we merge this I'd like to see the regexes unit tested so we know exactly what we're matching and don't end up with regressions down the line when we inevitably need to update them.

[melissalinkert]

f3fe218 adds tests that should fail if we break regex handling in the future. We can obviously add more tests cases there as needed.

@muhanadz, for reviewing the latest commit:

gradlew clean build will automatically run the new tests, since the new test class is under src/test/java. See https://docs.gradle.org/current/userguide/java_testing.html#using_junit5 for more details on how Gradle finds tests.

Once the build finishes, a report of which tests were run and whether they passed or failed will be in build/reports/tests/test. The easiest way to read those is to open build/reports/tests/test/index.html in a web browser and then click through to the specific class name you want to check. In this case, make sure that the BioTekTest class shows up in the report. Each test that appears in the source code should be listed in the class report, and should be listed as passing. You can definitely experiment locally with modifying the tests or the reader slightly to see what happens when things fail (e.g. change an assertFalse to assertTrue, check that a plate count is negative, modify one of the reader's regexes).

getTestCases() lists all of the file names that will be checked; it would be a good idea to check our existing BioTek data and verify that I didn't miss any known naming conventions.

[muhanadz]

Build is successful with all the tests passing.

To the best of my knowledge, and looking at our biotek data, these tests are sufficient, however, would be good to get someone else's opinion on it.