Ticket #421 (closed defect: invalid)

Opened 10 years ago

Last modified 9 years ago

Feedback 853: flex reader finds other directories

Reported by: omero-qa Owned by: melissa
Priority: critical Milestone:
Component: from QA Severity: serious
Keywords: Cc: josh.moore@…
Blocked By: Blocking:

Change History

comment:1 Changed 10 years ago by melissa

Comment from the feedback:

Flex reader seems to get confused.
I've copied mea/res files to my Desktop for 12133945. My server maps are configured. But for some reason, other directories on my desktop (Here "Flex 3D") are found.
2009-10-14 10:14:23,902 1044664 [2-thread-1] DEBUG loci.common.Log - 1255511663902: java.lang.Thread: findFiles(C:\Documents and Settings\hudson.GRE-MPORTER\Desktop\12133945\Meas_01\Meas_01(2009-08-26_19-24-59).mea)
2009-10-14 10:14:23,902 1044664 [2-thread-1] DEBUG loci.common.Log - 1255511663902: java.lang.Thread: Looking for files with the suffix 'flex' or 'res'.
2009-10-14 10:14:23,902 1044664 [2-thread-1] DEBUG loci.common.Log - 1255511663902: java.lang.Thread: Looking for files in C:\Documents and Settings\hudson.GRE-MPORTER\Desktop\12133945\Meas_01
2009-10-14 10:14:23,902 1044664 [2-thread-1] DEBUG loci.common.Log - 1255511663902: java.lang.Thread: Found file C:\Documents and Settings\hudson.GRE-MPORTER\Desktop\12133945\Meas_01\An_01_Me01_12133945(2009-08-26_19-24-59).res
2009-10-14 10:14:23,902 1044664 [2-thread-1] DEBUG loci.common.Log - 1255511663902: java.lang.Thread: Found file C:\Documents and Settings\hudson.GRE-MPORTER\Desktop\12133945\Meas_01\An_02_Me01_12133945(2009-08-26_19-24-59).res
2009-10-14 10:14:23,902 1044664 [2-thread-1] DEBUG loci.common.Log - 1255511663902: java.lang.Thread: Checking to see if at least one file with each suffix was found...
2009-10-14 10:14:23,902 1044664 [2-thread-1] DEBUG loci.common.Log - 1255511663902: java.lang.Thread: Did not find required files.
2009-10-14 10:14:23,918 1044680 [2-thread-1] DEBUG loci.common.Log - 1255511663918: java.lang.Thread: Looking for files in C:\Documents and Settings\hudson.GRE-MPORTER\Desktop\12133945
2009-10-14 10:14:23,918 1044680 [2-thread-1] DEBUG loci.common.Log - 1255511663918: java.lang.Thread: First attempt at finding measurement file directory failed. Looking for an appropriate measurement directory in C:\Documents and Settings\hudson.GRE-MPORTER\Desktop.
2009-10-14 10:14:23,918 1044680 [2-thread-1] DEBUG loci.common.Log - 1255511663918: java.lang.Thread: Expect measurement files to be in C:\Documents and Settings\hudson.GRE-MPORTER\Desktop\Flex 3D
2009-10-14 10:14:23,918 1044680 [2-thread-1] DEBUG loci.common.Log - 1255511663918: java.lang.Thread: Measurement files are in a subdirectory of C:\Documents and Settings\hudson.GRE-MPORTER\Desktop\Flex 3D
2009-10-14 10:14:23,918 1044680 [2-thread-1] DEBUG loci.common.Log - 1255511663918: java.lang.Thread: Determining which subdirectory contains the measurements for plate Meas_01
2009-10-14 10:14:23,918 1044680 [2-thread-1] DEBUG loci.common.Log - 1255511663918: java.lang.Thread: Checking Meas_01
2009-10-14 10:14:23,918 1044680 [2-thread-1] DEBUG loci.common.Log - 1255511663918: java.lang.Thread: Measurement files are in C:\Documents and Settings\hudson.GRE-MPORTER\Desktop\Flex 3D\Meas_01
2009-10-14 10:14:23,934 1044696 [2-thread-1] DEBUG loci.common.Log - 1255511663934: java.lang.Thread: Returning file list:
2009-10-14 10:14:23,934 1044696 [2-thread-1] DEBUG loci.common.Log - 1255511663934: java.lang.Thread: C:\Documents and Settings\hudson.GRE-MPORTER\Desktop\12133945\Meas_01\An_01_Me01_12133945(2009-08-26_19-24-59).res
2009-10-14 10:14:23,934 1044696 [2-thread-1] DEBUG loci.common.Log - 1255511663934: java.lang.Thread: C:\Documents and Settings\hudson.GRE-MPORTER\Desktop\12133945\Meas_01\An_02_Me01_12133945(2009-08-26_19-24-59).res
2009-10-14 10:14:23,934 1044696 [2-thread-1] DEBUG loci.common.Log - 1255511663934: java.lang.Thread: C:\Documents and Settings\hudson.GRE-MPORTER\Desktop\Flex 3D\Meas_01\Analysis_01.apr
2009-10-14 10:14:23,934 1044696 [2-thread-1] DEBUG loci.common.Log - 1255511663934: java.lang.Thread: C:\Documents and Settings\hudson.GRE-MPORTER\Desktop\Flex 3D\Meas_01\An_01_Me01_20090618-onco-04(2009-06-18_16-46-32).res
2009-10-14 10:14:23,934 1044696 [2-thread-1] DEBUG loci.common.Log - 1255511663934: java.lang.Thread: C:\Documents and Settings\hudson.GRE-MPORTER\Desktop\Flex 3D\Meas_01\Meas_01(2009-06-18_16-46-32).cpr
2009-10-14 10:14:23,934 1044696 [2-thread-1] DEBUG loci.common.Log - 1255511663934: java.lang.Thread: C:\Documents and Settings\hudson.GRE-MPORTER\Desktop\Flex 3D\Meas_01\Meas_01(2009-06-18_16-46-32).mea
2009-10-14 10:14:23,949 1044711 [2-thread-1] ERROR importer.gui.ErrorHandler$MyErrorHandler - FILE_EXCEPTION: C:\Documents and Settings\hudson.GRE-MPORTER\Desktop\12133945\Meas_01\Meas_01(2009-08-26_19-24-59).mea
loci.formats.FormatException: .flex files were not found. Did you forget to specify the server names?
at loci.formats.in.FlexReader.initMeaFile(FlexReader.java:300)
at loci.formats.in.FlexReader.initFile(FlexReader.java:256)
at loci.formats.FormatReader.setId(FormatReader.java:366)
at loci.formats.ImageReader.setId(ImageReader.java:588)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:155)
at loci.formats.ChannelFiller.setId(ChannelFiller.java:177)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:155)
at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:101)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:155)
at ome.formats.importer.ImportLibrary.open(ImportLibrary.java:185)
at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:281)
at ome.formats.importer.gui.ImportHandler.importImages(ImportHandler.java:182)
at ome.formats.importer.gui.ImportHandler.access$100(ImportHandler.java:45)
at ome.formats.importer.gui.ImportHandler$2.run(ImportHandler.java:97)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:441)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
at java.util.concurrent.FutureTask.run(FutureTask.java:138)
at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(ScheduledThreadPoolExecutor.java:98)
at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:207)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:885)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
at java.lang.Thread.run(Thread.java:619)
2009-10-14 10:14:23,949 1044711 [2-thread-1] ERROR e.formats.importer.gui.GuiCommonElements - Couldn't find icon: null
2009-10-14 10:14:23,949 1044711 [2-thread-1] ERROR e.formats.importer.gui.GuiCommonElements - Couldn't find icon: null
2009-10-14 10:14:23,949 1044711 [2-thread-1] DEBUG ome.formats.OMEROMetadataStoreClient - Creating root!
2009-10-14 10:14:23,980 1044742 [2-thread-1] ERROR ome.formats.importer.gui.ImportHandler - Format exception while importing image.
loci.formats.FormatException: .flex files were not found. Did you forget to specify the server names?
at loci.formats.in.FlexReader.initMeaFile(FlexReader.java:300)
at loci.formats.in.FlexReader.initFile(FlexReader.java:256)
at loci.formats.FormatReader.setId(FormatReader.java:366)
at loci.formats.ImageReader.setId(ImageReader.java:588)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:155)
at loci.formats.ChannelFiller.setId(ChannelFiller.java:177)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:155)
at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:101)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:155)
at ome.formats.importer.ImportLibrary.open(ImportLibrary.java:185)
at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:281)
at ome.formats.importer.gui.ImportHandler.importImages(ImportHandler.java:182)
at ome.formats.importer.gui.ImportHandler.access$100(ImportHandler.java:45)
at ome.formats.importer.gui.ImportHandler$2.run(ImportHandler.java:97)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:441)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
at java.util.concurrent.FutureTask.run(FutureTask.java:138)
at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(ScheduledThreadPoolExecutor.java:98)
at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:207)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:885)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
at java.lang.Thread.run(Thread.java:619)

comment:2 Changed 9 years ago by melissa

  • Status changed from new to closed
  • Resolution set to invalid
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