Import regressions due to refactoring for CLI

[jamoore]

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)
• Importer version should be taken from omero.properties (fixed)
• popup warning on MISSING_LIBRARY (see r5271) (fixed)
• popup on "unknown format" (fixed)
  • cancelling a directory scan can lead to SPW/non-SPW warnings (fixed)
• #1486 returning null from ImportCandidates.singleFile (fixed)
• NPE from #1503 (see below) (fixed)
• Filed added via reimport do nothing when 'import' button clicked. (fixed)
• mouseover since multiple files can be added in one click? (moved to r1550)
• App hangs on !OOM (moved to r1551)
• re-use ErrorHandler? where possible (see r5271) (moved to r1552)
• When ping session dies, app does not properly register as 'logged out'
  (moved to r1553)
• frequent updates to Debug tab might be hanging GUI (moved to r1554)

[jmoore]

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.

[jmoore]

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) 

[jmoore]

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.

[jmoore]

sorry, meant to mention: r5189

[jmoore]

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)

[jmoore]

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)