BUG:XmlAnnotation sample is invalid

[omero-qa]

​http://qa.openmicroscopy.org.uk/qa/feedback/2743/

Comment: Sent from CLI

loci.formats.FormatException: Malformed OME-XML
	at loci.formats.in.OMEXMLReader.initFile(OMEXMLReader.java:223)
	at loci.formats.FormatReader.setId(FormatReader.java:1074)
	at loci.formats.ImageReader.setId(ImageReader.java:650)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:480)
	at loci.formats.ChannelFiller.setId(ChannelFiller.java:244)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:480)
	at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:238)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:480)
	at ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:406)
	at ome.formats.importer.ImportCandidates.handleFile(ImportCandidates.java:567)
	at ome.formats.importer.ImportCandidates.execute(ImportCandidates.java:370)
	at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:228)
	at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:179)
	at ome.formats.importer.cli.CommandLineImporter.<init>(CommandLineImporter.java:74)
	at ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter.java:357)
Caused by: java.io.IOException: Server returned HTTP response code: 503 for URL: http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1313)
	at com.sun.org.apache.xerces.internal.impl.XMLEntityManager.setupCurrentEntity(XMLEntityManager.java:677)
	at com.sun.org.apache.xerces.internal.impl.XMLEntityManager.startEntity(XMLEntityManager.java:1315)
	at com.sun.org.apache.xerces.internal.impl.XMLEntityManager.startDTDEntity(XMLEntityManager.java:1282)
	at com.sun.org.apache.xerces.internal.impl.XMLDTDScannerImpl.setInputSource(XMLDTDScannerImpl.java:283)
	at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$DTDDriver.dispatch(XMLDocumentScannerImpl.java:1194)
	at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$DTDDriver.next(XMLDocumentScannerImpl.java:1090)
	at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$PrologDriver.next(XMLDocumentScannerImpl.java:1003)
	at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:648)
	at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:511)
	at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:808)
	at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:737)
	at com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:119)
	at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1205)
	at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(SAXParserImpl.java:522)
	at javax.xml.parsers.SAXParser.parse(SAXParser.java:395)
	at javax.xml.parsers.SAXParser.parse(SAXParser.java:198)
	at loci.common.xml.XMLTools.parseXML(XMLTools.java:293)
	at loci.common.xml.XMLTools.parseXML(XMLTools.java:269)
	at loci.formats.in.OMEXMLReader.initFile(OMEXMLReader.java:219)
	... 14 more

[ajpatterson]

The file looks to be valid - it looks like this may have been a temporary problem with one of the files pulled in from the w3 site used to validate the file against. Chris and I tried converting it both with and without a network connection and it gave no error.

[jmoore]

Just downloaded ​http://www.ome-xml.org/browser/Documentation/Samples/OmeFiles/2010-06/6x4y1z1t1c8b-swatch-tagged.ome again. "bin/omero import" still fails.

[ajpatterson]

That file is not the XML Annotation sample.
That is in
​http://www.ome-xml.org/browser/Documentation/Samples/OmeFiles/2010-06/6x4y1z1t1c8b-swatch-xmlannotation-svg.ome

File you have failing is the tagged example which uses ListAnnotation and CommentAnnotation.

[ajpatterson]

File that failed in the QA ticket was /tmp/6x4y1z1t1c8b-swatch-xmlannotation-svg.ome and it appears to work.

[jburel]

Moved from sprint 2010-09-30 (17)

[jmoore]

As Melissa pointed out, this happens when the trac page and not the "original format" is downloaded for the sample files. She's never seen it otherwise. At this point, I'll have to assume that that was my mistake. Closing.