Open Microscopy Environment

It might be that the logging level needs updated in order to return the same level of logging as the command line tools. You can change the logger level as below:

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loci.common.DebugTools.setRootLevel('INFO');

or for even more detail:

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loci.common.DebugTools.setRootLevel('DEBUG');

When I analyze purposefully distorted OME-XML file using the command line tools, the command line output looks like this.

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>> [status,res]= system(sprintf('%s "%s"',xmlvalid,"C:\xxxxxxxxxx\Desktop\boats.ome.xml"))
status =
     0
res =
    'Parsing schema path
     Error parsing schema path from C:\xxxxxxxxxx\Desktop\boats.ome.xml
     org.xml.sax.SAXParseException: Attribute "PhysicalSizeXUnit" was already specified for element "Pixels".
        at org.apache.xerces.util.ErrorHandlerWrapper.createSAXParseException(Unknown Source) ~[bioformats_package.jar:5.8.2]
        at org.apache.xerces.util.ErrorHandlerWrapper.fatalError(Unknown Source) ~[bioformats_package.jar:5.8.2]
        at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) ~[bioformats_package.jar:5.8.2]
        at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) ~[bioformats_package.jar:5.8.2]
        at org.apache.xerces.impl.XMLScanner.reportFatalError(Unknown Source) ~[bioformats_package.jar:5.8.2]
        at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanAttribute(Unknown Source) ~[bioformats_package.jar:5.8.2]
        at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanStartElement(Unknown Source) ~[bioformats_package.jar:5.8.2]
        at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source) ~[bioformats_package.jar:5.8.2]
        at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source) ~[bioformats_package.jar:5.8.2]
        at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) ~[bioformats_package.jar:5.8.2]
        at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) ~[bioformats_package.jar:5.8.2]
        at org.apache.xerces.parsers.XMLParser.parse(Unknown Source) ~[bioformats_package.jar:5.8.2]
        at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source) ~[bioformats_package.jar:5.8.2]
        at org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source) ~[bioformats_package.jar:5.8.2]
        at org.apache.xerces.jaxp.SAXParserImpl.parse(Unknown Source) ~[bioformats_package.jar:5.8.2]
        at javax.xml.parsers.SAXParser.parse(Unknown Source) ~[na:1.8.0_191]
        at loci.common.xml.XMLTools.validateXML(XMLTools.java:653) [bioformats_package.jar:5.8.2]
        at loci.common.xml.XMLTools.validateXML(XMLTools.java:627) [bioformats_package.jar:5.8.2]
        at loci.formats.tools.XMLValidate.process(XMLValidate.java:60) [bioformats_package.jar:5.8.2]
        at loci.formats.tools.XMLValidate.main(XMLValidate.java:81) [bioformats_package.jar:5.8.2]
     '

The most of the stack tace is not useful, but the line "org.xml.sax.SAXParseException: Attribute "PhysicalSizeXUnit" was already specified for element "Pixels"." is crucial.

At the moment, when I run `res = loci.common.xml.XMLTools.validateXML(xml, "XML");` instead, initially there was no command line output.

Using this

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loci.common.DebugTools.enableLogging();


resulted in the command line output as below (much simpler than the above):

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Parsing schema path

Error parsing schema path from XML


futher executing

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loci.common.DebugTools.setRootLevel('DEBUG');

or

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loci.common.DebugTools.setRootLevel('INFO');

or

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loci.common.DebugTools.enableIJLogging(true);

doesn't seem to make a difference.


Looking at the source code (https://github.com/ome/ome-common-java/ ... .java#L788), perhaps I need to specify the third input argument `schemaReader` to get a detailed error message??? I don't really know what `schemaReader` is about, though.

You shouldn't need to specify the schemaReader, this should be automatically parsed from the XML itself, however it seems to have resulted in the exception while parsing the schema path.

If you open the XML do any of the Pixels elements have multiple 'PhysicalSizeXUnit' attributes?

If you open the XML do any of the Pixels elements have multiple 'PhysicalSizeXUnit' attributes?

Yes, I duplicated it for the testing purpose.

The duplicate attributes on Pixels look as though they are causing the issue. If they are removed it should run without the Exception which you are seeing.

Sorry, but I'm afraid that you might have missed the point of this testing.

By directly using Java API, I want to retrieve the same command line output as the one we obtain with Command Line Tools. If I validate a correct OME-XML, the output is much shorter without a stack trace.

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Parsing schema path
     http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd
     Validating C:\Users\xxxxxx\Desktop\tpc2a8e01c_d4f2_4276_9cc3_e110b708be07.ome.tif
     No validation errors found.


But when I validate a wrong OME-XML, I get detailed command line output with Command Line Tools.

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'Parsing schema path
     Error parsing schema path from C:\Users\xxxxxxx\Desktop\boats.ome.xml
     org.xml.sax.SAXParseException: Attribute "PhysicalSizeXUnit" was already specified for element "Pixels".
        at org.apache.xerces.util.ErrorHandlerWrapper.createSAXParseException(Unknown Source) ~[bioformats_package.jar:5.8.2]
        at org.apache.xerces.util.ErrorHandlerWrapper.fatalError(Unknown Source) ~[bioformats_package.jar:5.8.2]
        at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) ~[bioformats_package.jar:5.8.2]
        at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source) ~[bioformats_package.jar:5.8.2]
        at org.apache.xerces.impl.XMLScanner.reportFatalError(Unknown Source) ~[bioformats_package.jar:5.8.2]
        at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanAttribute(Unknown Source) ~[bioformats_package.jar:5.8.2]
        at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanStartElement(Unknown Source) ~[bioformats_package.jar:5.8.2]
        at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source) ~[bioformats_package.jar:5.8.2]
        at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source) ~[bioformats_package.jar:5.8.2]
        at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) ~[bioformats_package.jar:5.8.2]
        at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) ~[bioformats_package.jar:5.8.2]
        at org.apache.xerces.parsers.XMLParser.parse(Unknown Source) ~[bioformats_package.jar:5.8.2]
        at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source) ~[bioformats_package.jar:5.8.2]
        at org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source) ~[bioformats_package.jar:5.8.2]
        at org.apache.xerces.jaxp.SAXParserImpl.parse(Unknown Source) ~[bioformats_package.jar:5.8.2]
        at javax.xml.parsers.SAXParser.parse(Unknown Source) ~[na:1.8.0_191]
        at loci.common.xml.XMLTools.validateXML(XMLTools.java:653) [bioformats_package.jar:5.8.2]
        at loci.common.xml.XMLTools.validateXML(XMLTools.java:627) [bioformats_package.jar:5.8.2]
        at loci.formats.tools.XMLValidate.process(XMLValidate.java:60) [bioformats_package.jar:5.8.2]
        at loci.formats.tools.XMLValidate.main(XMLValidate.java:81) [bioformats_package.jar:5.8.2]



And this is what I want to reproduce by accessing Java API from MATLAB. At the moment, using `loci.common.DebugTools.enableLogging();`, it looks like:

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Parsing schema path

Error parsing schema path from XML


Of course, this is not very informative.

Sorry, I may have misunderstood, I have been trying today to see if I can reproduce the issue and get the stack trace to display but so far have had no such luck. I will continue to investigate and keep you update if I find a solution.