Task #2891 (closed)
Opened 14 years ago
Closed 14 years ago
BUG:XmlAnnotation sample is invalid
| Reported by: | omero-qa | Owned by: | jamoore |
|---|---|---|---|
| Priority: | critical | Milestone: | OMERO-Beta4.2.1 |
| Component: | from QA | Version: | 4.1 |
| Keywords: | n.a. | Cc: | |
| Resources: | n.a. | Referenced By: | n.a. |
| References: | n.a. | Remaining Time: | 0.0d |
| Sprint: | 2010-10-28 (18) |
Description
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
Change History (13)
comment:1 Changed 14 years ago by jmoore
- Milestone changed from Unscheduled to OMERO-Beta4.2.1
comment:2 Changed 14 years ago by jmoore
- Remaining Time set to 0.25
comment:3 Changed 14 years ago by ajpatterson
comment:4 Changed 14 years ago by jmoore
Just downloaded http://www.ome-xml.org/browser/Documentation/Samples/OmeFiles/2010-06/6x4y1z1t1c8b-swatch-tagged.ome again. "bin/omero import" still fails.
comment:5 Changed 14 years ago by 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.
comment:6 Changed 14 years ago by ajpatterson
File that failed in the QA ticket was /tmp/6x4y1z1t1c8b-swatch-xmlannotation-svg.ome and it appears to work.
comment:7 Changed 14 years ago by cxallan
- Priority changed from minor to critical
- Remaining Time changed from 0.25 to 1.0
comment:8 Changed 14 years ago by cxallan
- Sprint set to 2010-09-09 (16)
comment:9 Changed 14 years ago by jburel
- Sprint changed from 2010-09-09 (16) to 2010-09-30 (17)
comment:10 Changed 14 years ago by jburel
- Sprint changed from 2010-09-30 (17) to 2010-10-28 (18)
Moved from sprint 2010-09-30 (17)
comment:11 Changed 14 years ago by jmoore
- Owner changed from ajpatterson to jmoore
comment:12 Changed 14 years ago by jmoore
- Status changed from new to assigned
comment:13 Changed 14 years ago by jmoore
- Remaining Time changed from 1.0 to 0
- Resolution set to invalid
- Status changed from assigned to closed
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.
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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.