Incomplete implementation, leads to many downstream bugs

[StephanPreibisch]

Hi @tpietzsch,

this line fails:

spimdata/src/main/java/mpicbg/spim/data/generic/sequence/XmlIoBasicImgLoader.java

Line 74 in 9dbb4b3

basePath = basePathURI == null ? null : new File( basePathURI );

if the URI file path does not start with "file:/", which is the normal case in the legacy code, the path will be e.g. "/home/data.xml" and not "file:/home/data.xml" ... My solution is this:

https://github.com/PreibischLab/multiview-reconstruction/blob/b102f2e3092f620a6e23f80061b547d362200548/src/main/java/util/URITools.java#L497-L506

Let's chat how to move forward, for now I implement it like that in my XMLIO's ... PreibischLab/multiview-reconstruction@38f1645

Alternatively, we could also always add "file:/" if it is missing ...

[tpietzsch]

From your explanation, I don't understand what the problem is? What is "the URI file path"? basePathURI? and if that does not start with "file:/" it fails in what way?

[tpietzsch]

Ok, I think I understand now.
The problem is actually in

spimdata/src/main/java/mpicbg/spim/data/XmlHelpers.java

Lines 287 to 310 in ec9eaa1

	public static URI loadPathURI( final Element parent, final String name, final String defaultRelativePath, final URI basePath )
	{
	final Element elem = parent.getChild( name );
	final String path = ( elem == null ) ? defaultRelativePath : elem.getText();
	final boolean isRelative = ( elem == null ) || elem.getAttributeValue( "type" ).equals( "relative" );
	if ( isRelative )
	{
	if ( basePath == null )
	return null;
	else
	return basePath.resolve( path );
	}
	else
	{
	try
	{
	return new URI( path );
	}
	catch ( URISyntaxException e )
	{
	return null;
	}
	}
	}

in particular

spimdata/src/main/java/mpicbg/spim/data/XmlHelpers.java

Line 303 in ec9eaa1

return new URI( path );

This should add the "file:/" prefix for absolute paths (if no prefix is given). Otherwise, it will construct a URI (but a relative URI, without a scheme). And that's wrong.
In the location that you pointed out, everything is ok like it is. We can expect that the basePathURI is absolute, with scheme and all.

[StephanPreibisch]

we also need to consider older XML's that do not start with a scheme ...

[StephanPreibisch]

we'll figure the best way out tomorrow ...