Fix zip parsing and add zipfile parsing test

[alanocallaghan]

The javadocs claim we can parse models without unzipping, but as far as I can tell this is not the case (hence the broken unit test).

When parsing a zip, we try to resolve model names with respect to the root directory of the model zip. However for me this returns "/", so we're looking for files in the filesystem root and this will fail unless somebody's done something really strange.

This PR aims to fix parsing from zipped files without unzipping.

[alanocallaghan]

Relatedly, it'd be good to have better reporting from the unit tests here... Not obvious what's failing

[petebankhead]

Not entirely sure I follow, but there is some weirdness around how zip files are handled generally - because there is a Zip File System Provider I'm less sure that looking relative to "/" is necessarily wrong.

Adding to the fun, since the modularisation of Java you'll need to ensure that jdk.zipfs is available - otherwise it might all compile fine, but fail at the end. I vaguely recall that causing problems with tests or distributions in the past.

[alanocallaghan]

I'm less sure that looking relative to "/" is necessarily wrong.

In theory, if there was a way to pass the filesystem to Files.exists, but otherwise we're just ignoring where the zip is and checking the system/user's filesystem root. The paths returned from fs.getRootDirectories should include the zip path since that's where we're likely to find stuff within the zip.

It's probably that there wrong type of filesystem is being create here:

qupath-bioimageio-spec/src/main/java/qupath/bioimageio/spec/BioimageIoSpec.java

Lines 210 to 218 in 1649e6f

	var fs = FileSystems.newFileSystem(path, (ClassLoader)null);
	for (var dir : fs.getRootDirectories()) {
	for (var name : MODEL_NAMES) {
	var p = dir.resolve(name);
	if (Files.exists(p))
	return p;
	}
	}
	}

but convincing Filesystems.newFileSystem to make a ZipFileSystem seems to be another story entirely.

[alanocallaghan]

Actually, I spoke too soon. It is a zip file system, but we're not resolving paths within the zip.

eg, changing the above quoted block to this:

			// Check zip file
			var fs = FileSystems.newFileSystem(path, null);
			System.out.println(fs.getClass());
			for (var dir : fs.getRootDirectories()) {
				for (var name : MODEL_NAMES) {
					var p = dir.resolve(name);
					System.out.println(p);
					if (Files.exists(p))
						return p;
				}
			}

I get:

class jdk.nio.zipfs.ZipFileSystem
/model.yaml
/model.yml
/rdf.yaml
/rdf.yml

because dir is /, so Files.exists(p) fails for all of these because I don't have any of these files in /.

This stackoverflow post suggests exactly this method, so it's not clear to me if/when something changed here.

[alanocallaghan]

My mistake, the code was right, my zip files were wrong. Could merge this to test zip parsing, or not, doesn't matter much

[alanocallaghan]

Going to can this, might be useful to automatically generate a zipfile then parse it but there's little utility in this

[alanocallaghan]

I've broken zip parsing somehow which I guess demonstrates the utility of this PR