Update MS2 SpectrumImporter to work with Java 25

[labkey-tchad]

Rationale

Java 25 fixes an inconsistency in the behavior of File.exists where new File("") refers to the working directory in most cases but new File("").exists erroneously returns false. SpectrumImporter depended on the old behavior to determine which file to import.

java.lang.NullPointerException: Cannot invoke "java.io.File.toURI()" because "f" is null
	at org.labkey.vfs.FileSystemLike$Builder.<init>(FileSystemLike.java:135)
	at org.labkey.vfs.FileSystemLike.wrapFile(FileSystemLike.java:257)
	at org.labkey.ms2.SpectrumImporter.<init>(SpectrumImporter.java:77)
	at org.labkey.ms2.PepXmlImporter.processSpectrumFile(PepXmlImporter.java:263)
	at org.labkey.ms2.PepXmlImporter.importRun(PepXmlImporter.java:150)
	at org.labkey.ms2.MS2Importer.upload(MS2Importer.java:201)
	at org.labkey.ms2.MS2Manager.importRun(MS2Manager.java:619)
	at org.labkey.ms2.pipeline.MS2ImportPipelineJob.run(MS2ImportPipelineJob.java:110)

While investigating this issue, I noticed that PepXmlImporter.processSpectrumFile won't ever upload the file returned by getMzXMLFile. This seems to be a regression caused by the latest FileLike changes.

Using FileLike a little more, with null representing non-existent files (instead of empty Strings) fixes both of these issues.

Related Pull Requests

• Continue adopting FileLike instead of File or Path #960

Changes

• Update MS2 SpectrumImporter to work with Java 25
• Restore mzXmlFile import behavior in PepXmlImporter.processSpectrumFile