Bug #1499 (new)
Opened 15 years ago
Last modified 15 years ago
Import regressions due to refactoring for CLI — at Version 56
Reported by: | jamoore | Owned by: | bwzloranger |
---|---|---|---|
Priority: | blocker | Cc: | jrswedlow, jburel |
Sprint: | n.a. | ||
Total Remaining Time: | n.a. |
Description (last modified by bwzloranger)
To have much of the newer ImportLibrary functionality in both the cli and the gui versions, refactoring was necessary which introduced several bugs:
Fixed
- importer-win.bat fails with NPE. See description below. (fixed r5191)
- feedback no longer uploads files (fixed)
- warning printed: "Couldn't find icon: gfx/warning_msg16.png" (fixed)
- re-login panel has issues (fixed)
- properties on error dialog not saved (fixed)
- history not showing up (fixed)
- history not 'reimporting'(fixed)
- files which fail during importcandidate not showing up on queue (fixed)
- error in filequeue not being added to feedback queue (fixed)
- eclipse builds failing without testng being built (fixed)
- feedback no longer recording some properties (such as 'additional_files_path' and 'additional_files_size') (fixed)
- 'internal errors' not providing required information for feedback such as reader file types (fixed)
- Properties on error feedback not being saved (fixed)
- Properties on project/dataset/spw not being saved (fixed)
- On failed files, popup no longer showing up at the end of the import process. (fixed)
- Some error messages (Internal Errors) no longer appear to be providing the full stack trace to the feedback mechanism (fixed)
- ImportCandidate? interfering with the reader used during imports so clicking on the 'add button' will poison the import reader if its running, causing imports to fail - ImportCandidate? will probably need to be moved to its own reader. (Fixed by disabling the add button for now)
- Added importHandler events for IMPORT_QUEUE_DONE - some code from this class can now be moved back into the classes where they belong. (fixed)
- Added importHandler event for IMPORT_QUEUE_START (fixed)
- Icon for debug message popup wrong (fixed)
- Failure dialog and project/dataset dialog both modal and blocking each other. (fixed)
- UserSpecifiedFileNames? not working (fixed)
- progress bar can get lost behind other windows (fixed)
- It is no longer possible to log into the server more then once from the same machine. (fixed)
- remove logging: "2009-10-06 21:42:32,588 124833 [1-thread-1] INFO me.formats.importer.gui.FileQueueHandler? - Calling event: ome.formats.importer.util.ErrorHandler?$UNKNOWN_FORMAT" (fixed)
- "processing directories..." when I click on a file is confusing. (fixed)
- ImportCandidates? needs to have functionality to cancel as it currently blocks all gui function while running. (fixed)
- Bio-formats version added to about (fixed)
- files do not preserve the name specified for them in the import dialog (fixed)
- mac app and windows exe fail (fixed)
- Properties on filechooser not being saved (fixed)
- Have a popup show up when errors added during candidate phase. (fixed)
- Feedback dialog not showing email address (fixed)
- Change checkbox to remove the send of feedback (fixed)
- OME Tiffs should import as dataset images not spw (for now) (fixed)
- If a file format is picked in the filechooser, only add those file types to the queue (fixed)
Open
- mouseover since multiple files can be added in one click? (see below)
- popup on "unknown format"
- App hangs on !OOM
- #1486 returning null from ImportCandidates.singleFile
- NPE from #1503 (see below)
- popup warning on MISSING_LIBRARY (see r5271)
- re-use ErrorHandler? where possible (see r5271)
- Importer version should be taken from omero.properties
- When ping session dies, app does not properly register as 'logged out'
- cancelling a directory scan can lead to SPW/non-SPW warnings
- frequent updates to Debug tab might be hanging GUI
- Filed added via reimport do nothing when 'import' button clicked.
Change History (56)
comment:1 Changed 15 years ago by jmoore
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comment:2 Changed 15 years ago by bwzloranger
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comment:3 Changed 15 years ago by bwzloranger
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comment:4 Changed 15 years ago by bwzloranger
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comment:5 Changed 15 years ago by bwzloranger
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comment:6 Changed 15 years ago by bwzloranger
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comment:7 Changed 15 years ago by bwzloranger
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comment:8 Changed 15 years ago by bwzloranger
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comment:9 Changed 15 years ago by bwzloranger
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comment:10 Changed 15 years ago by bwzloranger
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comment:11 Changed 15 years ago by bwzloranger
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comment:12 Changed 15 years ago by bwzloranger
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comment:13 Changed 15 years ago by jmoore
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comment:14 Changed 15 years ago by jmoore
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comment:15 Changed 15 years ago by bwzloranger
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comment:16 Changed 15 years ago by bwzloranger
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comment:17 Changed 15 years ago by bwzloranger
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comment:18 Changed 15 years ago by bwzloranger
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comment:19 Changed 15 years ago by bwzloranger
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comment:20 Changed 15 years ago by bwzloranger
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comment:21 Changed 15 years ago by bwzloranger
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comment:22 Changed 15 years ago by bwzloranger
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comment:23 Changed 15 years ago by bwzloranger
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comment:24 Changed 15 years ago by bwzloranger
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comment:25 Changed 15 years ago by jmoore
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comment:26 Changed 15 years ago by bwzloranger
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comment:27 Changed 15 years ago by bwzloranger
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comment:28 Changed 15 years ago by bwzloranger
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comment:29 Changed 15 years ago by bwzloranger
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comment:30 Changed 15 years ago by bwzloranger
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comment:31 Changed 15 years ago by jmoore
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From #1503 error.log:
11 Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException 12 at javax.swing.text.DefaultStyledDocument.getCharacterElement(Unknown Source) 13 at javax.swing.text.StyledEditorKit$AttributeTracker.updateInputAttributes(Unknown Source) 14 at javax.swing.text.StyledEditorKit$AttributeTracker.caretUpdate(Unknown Source) 15 at javax.swing.text.JTextComponent.fireCaretUpdate(Unknown Source) 16 at javax.swing.text.JTextComponent$MutableCaretEvent.fire(Unknown Source) 17 at javax.swing.text.JTextComponent$MutableCaretEvent.stateChanged(Unknown Source) 18 at javax.swing.text.DefaultCaret.fireStateChanged(Unknown Source) 19 at javax.swing.text.DefaultCaret.changeCaretPosition(Unknown Source) 20 at javax.swing.text.DefaultCaret.handleSetDot(Unknown Source) 21 at javax.swing.text.DefaultCaret.setDot(Unknown Source) 22 at javax.swing.text.DefaultCaret.setDot(Unknown Source) 23 at javax.swing.text.JTextComponent.setCaretPosition(Unknown Source) 24 at ome.formats.importer.gui.GuiImporter$5.adjustmentValueChanged(GuiImporter.java:317)
comment:32 Changed 15 years ago by bwzloranger
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comment:33 Changed 15 years ago by jmoore
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Brian, I've reworked ImportConfig? to not load or save as many properties. The login issues were possibly being caused by a session key being persisted. Let's get the blocking of ImportCandidates? fixed ASAP, and then move on to testing all these different code paths. We'll probably need a list.
comment:34 Changed 15 years ago by jmoore
sorry, meant to mention: r5189
comment:35 Changed 15 years ago by jmoore
- Description modified (diff)
- Priority changed from critical to blocker
java.lang.NullPointerException at ome.formats.importer.gui.LoginHandler.displayLoginDialog(LoginHandler .java:277) at ome.formats.importer.gui.LoginHandler.displayLogin(LoginHandler.java: 119) at ome.formats.importer.gui.LoginHandler.<init>(LoginHandler.java:111) at ome.formats.importer.gui.LoginHandler.<init>(LoginHandler.java:93) at ome.formats.importer.gui.GuiImporter.<init>(GuiImporter.java:347) at ome.formats.importer.gui.GuiImporter.main(GuiImporter.java:617) at ome.formats.importer.Main.main(Main.java:34)
comment:36 Changed 15 years ago by jmoore
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I think I fixed one NPE. But the hang on OutOfMemory? is very disturbing!
Exception in thread "Thread-11" java.lang.OutOfMemoryError: Java heap space at loci.common.RandomAccessInputStream.reopen(RandomAccessInputStream.ja va:626) at loci.common.RandomAccessInputStream.<init>(RandomAccessInputStream.ja va:124) at loci.formats.in.MinimalTiffReader.initFile(MinimalTiffReader.java:214 ) at loci.formats.FormatReader.setId(FormatReader.java:366) at loci.formats.in.MIASReader.getTile(MIASReader.java:821) at loci.formats.in.MIASReader.openBytes(MIASReader.java:194) at loci.formats.ImageReader.openBytes(ImageReader.java:339) at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:172) at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:191) at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:273) at loci.formats.MinMaxCalculator.openBytes(MinMaxCalculator.java:246) at loci.formats.MinMaxCalculator.openBytes(MinMaxCalculator.java:229) at ome.formats.importer.OMEROWrapper.openPlane2D(OMEROWrapper.java:109) at ome.formats.importer.ImportLibrary.importData(ImportLibrary.java:451) at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:319 ) at ome.formats.importer.gui.ImportHandler.importImages(ImportHandler.jav a:184) at ome.formats.importer.gui.ImportHandler.access$000(ImportHandler.java: 48) at ome.formats.importer.gui.ImportHandler$1.run(ImportHandler.java:99)
comment:37 Changed 15 years ago by jmoore
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comment:38 Changed 15 years ago by bwzloranger
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comment:39 Changed 15 years ago by bwzloranger
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comment:40 Changed 15 years ago by bwzloranger
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comment:41 Changed 15 years ago by jmoore
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comment:42 Changed 15 years ago by jmoore
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comment:43 Changed 15 years ago by jmoore
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comment:44 Changed 15 years ago by jmoore
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comment:45 Changed 15 years ago by bwzloranger
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comment:46 Changed 15 years ago by bwzloranger
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comment:47 Changed 15 years ago by bwzloranger
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comment:48 Changed 15 years ago by bwzloranger
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comment:49 Changed 15 years ago by bwzloranger
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comment:50 Changed 15 years ago by bwzloranger
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comment:51 Changed 15 years ago by bwzloranger
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comment:52 Changed 15 years ago by bwzloranger
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comment:53 Changed 15 years ago by bwzloranger
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comment:54 Changed 15 years ago by bwzloranger
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comment:55 Changed 15 years ago by bwzloranger
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comment:56 Changed 15 years ago by bwzloranger
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Further explanation on "mouseover since multiple files":
If a user clicks a directory, say "My Plates" for import, then a single file will show up for each plate. Something of the form: mode0001_z001_t0001.tif. The user will have no way to know which one relates to which plate.