Task #6332 (closed)
Opened 13 years ago
Closed 10 years ago
BUG: HTD import - Feedback 3884
Reported by: | omero-qa | Owned by: | mlinkert |
---|---|---|---|
Priority: | major | Milestone: | 5.0.0-rc1 |
Component: | Bio-Formats | Version: | 4.4.9 |
Keywords: | n.a. | Cc: | jay_copeland@… |
Resources: | n.a. | Referenced By: | n.a. |
References: | n.a. | Remaining Time: | n.a. |
Sprint: | n.a. |
Description (last modified by jmoore)
http://qa.openmicroscopy.org.uk/qa/feedback/3884/
Comment: I attempted these imports using the 4.3.1 client against our new 4.3.0 server.
(stack below)
Change History (8)
comment:1 Changed 13 years ago by jmoore
- Component changed from from QA to Import
- Description modified (diff)
comment:2 Changed 11 years ago by jamoore
- Milestone changed from Unscheduled to 5.0.0-beta2
- Resolution set to fixed
- Status changed from new to closed
- Version set to 4.4.9
Bug has subsequently been fixed in the 4.4 and 5.0 lines. Thanks for the feedback.
comment:3 Changed 11 years ago by pwalczysko
Huh, sorry, I was just trying to re-import the file from Apache 3884 using Insight and got a failed import.
java.lang.ArrayIndexOutOfBoundsException: -1 at loci.formats.in.CellWorxReader.getFile(CellWorxReader.java:546) at loci.formats.in.CellWorxReader.initFile(CellWorxReader.java:386) at loci.formats.FormatReader.setId(FormatReader.java:1360) at loci.formats.ImageReader.setId(ImageReader.java:781) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:576) at loci.formats.ChannelFiller.setId(ChannelFiller.java:263) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:576) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:274) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:576) at loci.formats.Memoizer.setId(Memoizer.java:471) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:576) at ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:414) at ome.formats.importer.ImportCandidates.handleFile(ImportCandidates.java:595) at ome.formats.importer.ImportCandidates.execute(ImportCandidates.java:371) at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:229) at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:180) at org.openmicroscopy.shoola.env.data.OMEROGateway.getImportCandidates(OMEROGateway.java:6469) at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1194) at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:77) at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:53) at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:102) at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144) at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226) at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126) at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165) at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276) at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91) at java.lang.Thread.run(Thread.java:680) at org.openmicroscopy.shoola.env.data.util.StatusLabel.update(StatusLabel.java:662) at ome.formats.importer.ImportCandidates.safeUpdate(ImportCandidates.java:555) at ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:463) at ome.formats.importer.ImportCandidates.handleFile(ImportCandidates.java:595) at ome.formats.importer.ImportCandidates.execute(ImportCandidates.java:371) at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:229) at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:180) at org.openmicroscopy.shoola.env.data.OMEROGateway.getImportCandidates(OMEROGateway.java:6469) at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1194) at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:77) at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:53) at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:102) at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144) at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226) at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126) at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165) at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276) at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91) at java.lang.Thread.run(Thread.java:680) Caused by: java.lang.ArrayIndexOutOfBoundsException: -1 at loci.formats.in.CellWorxReader.getFile(CellWorxReader.java:546) at loci.formats.in.CellWorxReader.initFile(CellWorxReader.java:386) at loci.formats.FormatReader.setId(FormatReader.java:1360) at loci.formats.ImageReader.setId(ImageReader.java:781) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:576) at loci.formats.ChannelFiller.setId(ChannelFiller.java:263) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:576) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:274) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:576) at loci.formats.Memoizer.setId(Memoizer.java:471) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:576) at ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:414) ... 16 more
comment:4 Changed 11 years ago by pwalczysko
And on Howe as well:
ava.lang.ArrayIndexOutOfBoundsException: -1 at loci.formats.in.CellWorxReader.getFile(CellWorxReader.java:523) at loci.formats.in.CellWorxReader.initFile(CellWorxReader.java:372) at loci.formats.FormatReader.setId(FormatReader.java:1244) at loci.formats.ImageReader.setId(ImageReader.java:727) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:529) at loci.formats.ChannelFiller.setId(ChannelFiller.java:263) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:529) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:274) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:529) at ome.formats.importer.ImportLibrary.open(ImportLibrary.java:323) at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:499) at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6375) at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1347) at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:77) at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:53) at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:102) at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144) at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226) at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126) at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165) at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276) at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91) at java.lang.Thread.run(Thread.java:680) at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6429) at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1347) at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:77) at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:53) at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:102) at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144) at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226) at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126) at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165) at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276) at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91) at java.lang.Thread.run(Thread.java:680) Caused by: java.lang.ArrayIndexOutOfBoundsException: -1 at loci.formats.in.CellWorxReader.getFile(CellWorxReader.java:523) at loci.formats.in.CellWorxReader.initFile(CellWorxReader.java:372) at loci.formats.FormatReader.setId(FormatReader.java:1244) at loci.formats.ImageReader.setId(ImageReader.java:727) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:529) at loci.formats.ChannelFiller.setId(ChannelFiller.java:263) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:529) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:274) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:529) at ome.formats.importer.ImportLibrary.open(ImportLibrary.java:323) at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:499) at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6375) ... 11 more
comment:5 Changed 11 years ago by pwalczysko
- Resolution fixed deleted
- Status changed from closed to reopened
comment:6 Changed 11 years ago by pwalczysko
Sorry, although I was saying something else in Jabber, I got an e-mail from this ticket suggesting I should try and re-import the file. Which I did and it failed on bot branches => reopening the ticket.
comment:7 Changed 10 years ago by jamoore
- Component changed from Import to Bio-Formats
- Owner changed from cxallan to mlinkert
- Priority changed from minor to major
- Status changed from reopened to accepted
Melissa: could you take a quick look?
comment:8 Changed 10 years ago by mlinkert
- Resolution set to fixed
- Status changed from accepted to closed
Should be fixed with: https://github.com/openmicroscopy/bioformats/pull/800
Note that QA 3884 is expected not to import (since all of the pixel data is missing), but that PR fixes the exception that is thrown.