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Task #7764 (closed)

Opened 8 years ago

Closed 7 years ago

BUG:Import xdce

Reported by: omero-qa Owned by: mlinkert
Priority: minor Milestone: OMERO-4.4
Component: Bio-Formats Version: n.a.
Keywords: n.a. Cc: k.j.z.hands@…, jburel
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: 0.0d
Sprint: 2012-02-28 (9)

Description

​http://qa.openmicroscopy.org.uk/qa/feedback/4122/

Comment: Hi, previously I was able to import the .xdce files from my high content screening data all as one, rather than loading all the individual images but today this is not working- is it something I am doing differently? Thanks, Katie

java.lang.NumberFormatException: empty String
	at sun.misc.FloatingDecimal.readJavaFormatString(Unknown Source)
	at java.lang.Double.valueOf(Unknown Source)
	at java.lang.Double.<init>(Unknown Source)
	at loci.formats.in.InCellReader$InCellHandler.startElement(InCellReader.java:908)
	at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.startElement(Unknown Source)
	at com.sun.org.apache.xerces.internal.parsers.AbstractXMLDocumentParser.emptyElement(Unknown Source)
	at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanStartElement(Unknown Source)
	at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl$FragmentContentDriver.next(Unknown Source)
	at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(Unknown Source)
	at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)
	at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(Unknown Source)
	at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(Unknown Source)
	at com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(Unknown Source)
	at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(Unknown Source)
	at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source)
	at javax.xml.parsers.SAXParser.parse(Unknown Source)
	at javax.xml.parsers.SAXParser.parse(Unknown Source)
	at loci.common.xml.XMLTools.parseXML(XMLTools.java:315)
	at loci.common.xml.XMLTools.parseXML(XMLTools.java:301)
	at loci.formats.in.InCellReader.initFile(InCellReader.java:415)
	at loci.formats.FormatReader.setId(FormatReader.java:1072)
	at loci.formats.ImageReader.setId(ImageReader.java:677)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:488)
	at loci.formats.ChannelFiller.setId(ChannelFiller.java:249)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:488)
	at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:257)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:488)
	at ome.formats.importer.ImportLibrary.open(ImportLibrary.java:310)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:486)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6402)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1228)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:85)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:54)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:111)
	at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
	at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
	at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:274)
	at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
	at java.lang.Thread.run(Unknown Source)

Change History (6)

comment:1 Changed 8 years ago by mlinkert

  • Component changed from from QA to Bio-Formats
  • Milestone changed from Unscheduled to OMERO-Beta4.4
  • Sprint set to 2012-01-17 (6)
  • Status changed from new to accepted

Proposed fix: ​http://github.com/openmicroscopy/bioformats/pull/10

comment:2 Changed 8 years ago by jburel

  • Sprint changed from 2012-01-17 (6) to 2012-01-31 (7)

Moved from sprint 2012-01-17 (6)

comment:3 Changed 8 years ago by mlinkert

  • Remaining Time set to 0.1

comment:4 Changed 8 years ago by jmoore

  • Sprint changed from 2012-01-31 (7) to 2012-02-14 (8)

Moved from sprint 2012-01-31 (7)

comment:5 Changed 7 years ago by jburel

  • Sprint changed from 2012-02-14 (8) to 2012-02-28 (9)

Moved from sprint 2012-02-14 (8)

comment:6 Changed 7 years ago by mlinkert

  • Remaining Time changed from 0.1 to 0
  • Status changed from accepted to closed
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