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View Code? Open in Web Editor NEWGradle project containing insight java client for OMERO
Home Page: https://www.openmicroscopy.org/omero/
License: GNU General Public License v2.0
Gradle project containing insight java client for OMERO
Home Page: https://www.openmicroscopy.org/omero/
License: GNU General Public License v2.0
When running the tasks to create a exe or dmg only insight is created.
Either we package importer too or we discontinue the importer. Note that we did not warn people
bin/omero-importer does not work
Could not find or load main class org.openmicroscopy.shoola.Main
Following the packaging changes introduced in OMERO.insight 5.5.0, the workflow for adding third-party JARs needs to be reviewed and the instructions updated .
Using OMERO.insight 5.5.3 and the external SlideBook JAR shipped by 3i, I was able to add the functionality using the following:
lib/
folderbin/omero-insight
and append :$APP_HOME/lib/SlideBook6Reader.jar
to the CLASSPATH
lineIt might be sufficient to generate the CLASSPATH
to point at the entire content of $APP_HOME/lib/
rather than a list of hardcoded JARs to re-enable the extensibility of OMERO.insight. This strategy might require testing across the supported environments.
Sometimes Insight crashes on network/connection issues, when it actually should be able to recover from them. When it's not possible to recover there should be at least a better error message for the user.
See for example 28982
For OMERO.insight 5.5.2 I'm told:
Version: @VERSION@
Build: @DATE@
... copyright 2006-2017 too.
Currently the version is set to 1.0, it is currently not possible to set it
This is currently not working
See gradle/gradle#1989
QA 27988 records an NPE. I wonder if the gateway's delete
returned a null
callback; is it possible to try to cut no links? Perhaps we can figure out how this happens or handle it better.
Large image can't be exported as ome-tiff. The button shoudl be disabled.
See https://www.openmicroscopy.org/qa2/qa/feedback/27969/
When adding the "Split channels" option to the Crop workflow in ImageJ, see for example Fiji section, crop workflow of https://downloads.openmicroscopy.org/presentations/2019/Dundee-April/Dundee_April_2019_Day2.pdf
The channels names are not preserved correctly when the crop is imported back to OMERO.
Set publisher and description in .exe
push the "create" button in dataset creation dialog and push of "add to the queue" button are in normal but quick succession:
download the tagged plugin under 5.5.7 Tag of insight in this repo, insert the jar into your Fiji plugin folder.
Connect to outreach as trainer-1
Browse to dataset "test", ID Dataset ID: 5951
Click on the dataset.
The error below occurs, the insight-ij plugin is unusable from then on.
This error does not occur on the same dataset with 5.5.6 insight-ij -> regression
This error happens also on the 5.5.7 insight from teh same tag.
cc @jburel @dominikl @joshmoore @manics
no update needed
Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
at omero.model.LengthI.<init>(LengthI.java:1442)
at omero.model.LengthI.<init>(LengthI.java:1467)
at omero.gateway.model.PixelsData.getPixelSizeX(PixelsData.java:261)
at org.openmicroscopy.shoola.agents.util.EditorUtil.transformPixelsData(EditorUtil.java:717)
at org.openmicroscopy.shoola.agents.util.EditorUtil.formatObjectTooltip(EditorUtil.java:2531)
at org.openmicroscopy.shoola.agents.util.browser.TreeViewerTranslator.formatToolTipFor(TreeViewerTranslator.java:833)
at org.openmicroscopy.shoola.agents.util.browser.TreeViewerTranslator.transformImage(TreeViewerTranslator.java:391)
at org.openmicroscopy.shoola.agents.util.browser.TreeViewerTranslator.transformHierarchy(TreeViewerTranslator.java:419)
at org.openmicroscopy.shoola.agents.treeviewer.browser.BrowserComponent.setLeaves(BrowserComponent.java:581)
at org.openmicroscopy.shoola.agents.treeviewer.ExperimenterDataLoader.handleResult(ExperimenterDataLoader.java:250)
at org.openmicroscopy.shoola.env.data.events.DSCallAdapter.eventFired(DSCallAdapter.java:90)
at org.openmicroscopy.shoola.env.data.views.BatchCallMonitor$1.run(BatchCallMonitor.java:124)
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
at java.awt.EventQueue.access$500(EventQueue.java:97)
at java.awt.EventQueue$3.run(EventQueue.java:709)
at java.awt.EventQueue$3.run(EventQueue.java:703)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
[image.sc] OMERO.importer 5.4.10 throws Ice.ObjectNotExistException when importing hundreds of files describes investigation into "servantsPerSession reached" and UI freeze when importing over 3,000 files. Probably need to see why upload is holding servants open.
Rename the zip to OMERO.insight-
The plugin for Fiji has problems.
The connection fails with differing error messages. Typically, this repeats several times.
The messages can alternate between "wrong username/pwd" and "system failure".
The main problems are on Mac and Linux, although there was a problem also reported when testing on Windows (external user) - but the windows problem has a different message "server not responding"/
Typically, after couple of retries and (maybe) a re-install of the Fiji plugin, the problem goes away.
cc @jburel
QA 27885 reports:
java.lang.NullPointerException
at org.openmicroscopy.shoola.env.data.AdminServiceImpl.updateGroupPermissions(AdminServiceImpl.java:408)
at org.openmicroscopy.shoola.agents.metadata.GroupEditor.handleResult(GroupEditor.java:161)
The gateway's updateGroupPermissions
's Javadoc gives no reason to expect a null
from it.
Dialog expects a java.awt.Color
object, can't handle lookup tables (which are Strings).
See https://www.openmicroscopy.org/qa2/qa/feedback/27972/
Add *.csv
filter to the file attachment dialog. See https://forum.image.sc/t/adding-a-file-type-to-file-selection-dialog/34879 . On that occassion others (like *.xls
etc.) could be improved as well. Investigate if it's possible to add a customizable filter.
Import into non-default ports fails with error dialog
Note also ome/omero-py#103
From the insight log:
2019-11-04 16:47:56,434 DEBUG [ o.o.s.env.data.login.LoginServiceImpl] (nitializer) Failed to log onto OMERO.
Reason: Cannot log in. Login credentials not valid
OMERO address: idr1-slot2.openmicroscopy.org
User Name: root -- Password: *****
omero.gateway.exception.DSOutOfServiceException: Cannot log in. Login credentials not valid
at omero.gateway.Gateway.login(Gateway.java:1218)
at omero.gateway.Gateway.connect(Gateway.java:261)
at org.openmicroscopy.shoola.env.data.OMEROGateway.connect(OMEROGateway.java:1423)
at org.openmicroscopy.shoola.env.data.DataServicesFactory.connect(DataServicesFactory.java:491)
at org.openmicroscopy.shoola.env.data.login.LoginServiceImpl.attempt(LoginServiceImpl.java:144)
at org.openmicroscopy.shoola.env.data.login.LoginServiceImpl.login(LoginServiceImpl.java:277)
at org.openmicroscopy.shoola.env.data.login.LoginManager.login(LoginManager.java:98)
at org.openmicroscopy.shoola.env.init.SplashScreenInit.onEnd(SplashScreenInit.java:157)
at org.openmicroscopy.shoola.env.init.Initializer.notifyEnd(Initializer.java:189)
at org.openmicroscopy.shoola.env.Container.runStartupProcedure(Container.java:119)
at org.openmicroscopy.shoola.env.Container.access$000(Container.java:68)
at org.openmicroscopy.shoola.env.Container$1.run(Container.java:164)
at java.lang.Thread.run(Thread.java:745)
Caused by: Glacier2.PermissionDeniedException
reason = "Password check failed for '95b005aa-ba59-491d-8ed4-5e4d8787de22': []"
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
at java.lang.Class.newInstance(Class.java:442)
at IceInternal.BasicStream.createUserException(BasicStream.java:2779)
at IceInternal.BasicStream.access$300(BasicStream.java:14)
at IceInternal.BasicStream$EncapsDecoder11.throwException(BasicStream.java:3614)
at IceInternal.BasicStream.throwException(BasicStream.java:2291)
at IceInternal.OutgoingAsync.throwUserException(OutgoingAsync.java:399)
at Glacier2.RouterPrxHelper.end_createSession(RouterPrxHelper.java:178)
at Glacier2.RouterPrxHelper.createSession(RouterPrxHelper.java:49)
at Glacier2.RouterPrxHelper.createSession(RouterPrxHelper.java:41)
at omero.client.createSession(client.java:810)
at omero.client.joinSession(client.java:744)
at omero.client.createClient(client.java:543)
at omero.gateway.Connector.<init>(Connector.java:229)
at omero.gateway.Connector.<init>(Connector.java:202)
at omero.gateway.Gateway.login(Gateway.java:1208)
... 12 more
Failed to log onto OMERO.
Reason: Cannot log in. Login credentials not valid
OMERO address: idr1-slot2.openmicroscopy.org
User Name: root -- Password: *****
omero.gateway.exception.DSOutOfServiceException: Cannot log in. Login credentials not valid
at omero.gateway.Gateway.login(Gateway.java:1218)
at omero.gateway.Gateway.connect(Gateway.java:261)
at org.openmicroscopy.shoola.env.data.OMEROGateway.connect(OMEROGateway.java:1423)
at org.openmicroscopy.shoola.env.data.DataServicesFactory.connect(DataServicesFactory.java:491)
at org.openmicroscopy.shoola.env.data.login.LoginServiceImpl.attempt(LoginServiceImpl.java:144)
at org.openmicroscopy.shoola.env.data.login.LoginServiceImpl.login(LoginServiceImpl.java:277)
at org.openmicroscopy.shoola.env.data.login.LoginManager.login(LoginManager.java:98)
at org.openmicroscopy.shoola.env.init.SplashScreenInit.onEnd(SplashScreenInit.java:157)
at org.openmicroscopy.shoola.env.init.Initializer.notifyEnd(Initializer.java:189)
at org.openmicroscopy.shoola.env.Container.runStartupProcedure(Container.java:119)
at org.openmicroscopy.shoola.env.Container.access$000(Container.java:68)
at org.openmicroscopy.shoola.env.Container$1.run(Container.java:164)
at java.lang.Thread.run(Thread.java:745)
Caused by: Glacier2.PermissionDeniedException
reason = "Password check failed for '95b005aa-ba59-491d-8ed4-5e4d8787de22': []"
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
at java.lang.Class.newInstance(Class.java:442)
at IceInternal.BasicStream.createUserException(BasicStream.java:2779)
at IceInternal.BasicStream.access$300(BasicStream.java:14)
at IceInternal.BasicStream$EncapsDecoder11.throwException(BasicStream.java:3614)
at IceInternal.BasicStream.throwException(BasicStream.java:2291)
at IceInternal.OutgoingAsync.throwUserException(OutgoingAsync.java:399)
at Glacier2.RouterPrxHelper.end_createSession(RouterPrxHelper.java:178)
at Glacier2.RouterPrxHelper.createSession(RouterPrxHelper.java:49)
at Glacier2.RouterPrxHelper.createSession(RouterPrxHelper.java:41)
at omero.client.createSession(client.java:810)
at omero.client.joinSession(client.java:744)
at omero.client.createClient(client.java:543)
at omero.gateway.Connector.<init>(Connector.java:229)
at omero.gateway.Connector.<init>(Connector.java:202)
at omero.gateway.Gateway.login(Gateway.java:1208)
... 12 more
Exception in thread "Initializer"
Just to keep track of https://www.openmicroscopy.org/qa2/qa/feedback/29162/ .
Can't replicate, neither with the .exe
nor the .msi
installer.
The purpose of this issue is to keep track of intermittent, hard to reproduce errors.
See https://trello.com/c/AHUmpyN7/21-macosx-clients#action-5e72499bcf2d7853bf15e4fb
When executing a script (channel offsets) from insight on a slower connection, the script report in the activities shows a spinner which never stops spinning. Even after both web and insight are showing the resulting image (the result of the script execution) as expected, the spinner is still spinninng.
cc @dominikl
Using duplicate image then crop is not recognized as a new image preventing the image to be imported
Saving the image does not work with 5.5.0-m1
If you startup Insight a couple of ERROR messages appear in log file, although they don't seem to have any visible implication in the UI. (OSX, Insight 5.5.2)
2019-07-04 13:19:20,172 ERROR [ o.o.s.agents.dataBrowser.IconManager] (entQueue-0) Failed to retrieve icon: <classpath>/images/agents/dataBrowser/red_dot8.png.
2019-07-04 13:19:20,173 ERROR [ o.o.s.agents.dataBrowser.IconManager] (entQueue-0) Failed to retrieve icon: <classpath>/images/agents/dataBrowser/nuvola_knotes8.png.
2019-07-04 13:19:20,200 ERROR [ o.o.s.agents.dataBrowser.IconManager] (entQueue-0) Failed to retrieve icon: <classpath>/images/agents/dataBrowser/knimeIcon16.png.
2019-07-04 13:19:20,200 ERROR [ o.o.s.agents.dataBrowser.IconManager] (entQueue-0) Failed to retrieve icon: <classpath>/images/agents/dataBrowser/imageJ16.png.
2019-07-04 13:19:20,200 ERROR [ o.o.s.agents.dataBrowser.IconManager] (entQueue-0) Failed to retrieve icon: <classpath>/images/agents/dataBrowser/viewer16.png.
2019-07-04 13:19:20,201 ERROR [ o.o.s.agents.dataBrowser.IconManager] (entQueue-0) Failed to retrieve icon: <classpath>/images/agents/dataBrowser/eclipse_copy_edit16.png.
2019-07-04 13:19:20,202 ERROR [ o.o.s.agents.dataBrowser.IconManager] (entQueue-0) Failed to retrieve icon: <classpath>/images/agents/dataBrowser/eclipse_paste_edit16.png.
2019-07-04 13:19:20,202 ERROR [ o.o.s.agents.dataBrowser.IconManager] (entQueue-0) Failed to retrieve icon: <classpath>/images/agents/dataBrowser/eclipse_delete_edit16.png.
2019-07-04 13:19:20,202 ERROR [ o.o.s.agents.dataBrowser.IconManager] (entQueue-0) Failed to retrieve icon: <classpath>/images/agents/dataBrowser/nuvola_editcut16.png.
2019-07-04 13:19:20,203 ERROR [ o.o.s.agents.dataBrowser.IconManager] (entQueue-0) Failed to retrieve icon: <classpath>/images/agents/dataBrowser/eclipse_paste_edit16.png.
2019-07-04 13:19:20,203 ERROR [ o.o.s.agents.dataBrowser.IconManager] (entQueue-0) Failed to retrieve icon: <classpath>/images/agents/dataBrowser/eclipse_copy_edit16.png.
2019-07-04 13:19:20,203 ERROR [ o.o.s.agents.dataBrowser.IconManager] (entQueue-0) Failed to retrieve icon: <classpath>/images/agents/dataBrowser/nuvola_undo16.png.
2019-07-04 13:19:20,203 ERROR [ o.o.s.agents.dataBrowser.IconManager] (entQueue-0) Failed to retrieve icon: <classpath>/images/agents/dataBrowser/nuvola_reload16.png.
2019-07-04 13:19:20,203 ERROR [ o.o.s.agents.dataBrowser.IconManager] (entQueue-0) Failed to retrieve icon: <classpath>/images/agents/dataBrowser/nuvola_rendering_minmax16.png.
2019-07-04 13:19:20,204 ERROR [ o.o.s.agents.dataBrowser.IconManager] (entQueue-0) Failed to retrieve icon: <classpath>/images/agents/dataBrowser/rendering_owner16.png.
2019-07-04 13:19:20,204 ERROR [ o.o.s.agents.dataBrowser.IconManager] (entQueue-0) Failed to retrieve icon: <classpath>/images/agents/dataBrowser/nuvola_filesaveas16.png.
2019-07-04 13:19:20,205 ERROR [ o.o.s.agents.dataBrowser.IconManager] (entQueue-0) Failed to retrieve icon: <classpath>/images/agents/dataBrowser/nuvola_knotes16.png.
2019-07-04 13:19:20,205 ERROR [ o.o.s.agents.dataBrowser.IconManager] (entQueue-0) Failed to retrieve icon: <classpath>/images/agents/dataBrowser/red_dot8.png.
2019-07-04 13:19:20,206 ERROR [ o.o.s.agents.dataBrowser.IconManager] (entQueue-0) Failed to retrieve icon: <classpath>/images/agents/dataBrowser/nuvola_kdmconfig_modified16.png.
2019-07-04 13:19:20,206 ERROR [ o.o.s.agents.dataBrowser.IconManager] (entQueue-0) Failed to retrieve icon: <classpath>/images/agents/dataBrowser/nuvola_kdmconfig_modified_grey16.png.
2019-07-04 13:19:20,206 ERROR [ o.o.s.agents.dataBrowser.IconManager] (entQueue-0) Failed to retrieve icon: <classpath>/images/agents/dataBrowser/eclipse_transparent16.png.
2019-07-04 13:19:20,207 ERROR [ o.o.s.agents.dataBrowser.IconManager] (entQueue-0) Failed to retrieve icon: <classpath>/images/agents/dataBrowser/nuvola_download_manager_rotated16.png.
2019-07-04 13:19:20,207 ERROR [ o.o.s.agents.dataBrowser.IconManager] (entQueue-0) Failed to retrieve icon: <classpath>/images/agents/dataBrowser/nuvola_download_manager16.png.
2019-07-04 13:19:20,209 ERROR [ o.o.s.agents.dataBrowser.IconManager] (entQueue-0) Failed to retrieve icon: <classpath>/images/agents/dataBrowser/roll_over_image16.png.
2019-07-04 13:19:20,227 ERROR [ o.o.s.agents.dataBrowser.IconManager] (entQueue-0) Failed to retrieve icon: <classpath>/images/agents/dataBrowser/filter_grey16.png.
2019-07-04 13:19:20,228 ERROR [ o.o.s.agents.dataBrowser.IconManager] (entQueue-0) Failed to retrieve icon: <classpath>/images/agents/dataBrowser/eclipse_view_menu16.png.
2019-07-04 13:19:20,228 ERROR [ o.o.s.agents.dataBrowser.IconManager] (entQueue-0) Failed to retrieve icon: <classpath>/images/agents/dataBrowser/nuvola_view_multicolumn16.png.
2019-07-04 13:19:20,229 ERROR [ o.o.s.agents.dataBrowser.IconManager] (entQueue-0) Failed to retrieve icon: <classpath>/images/agents/dataBrowser/nuvola_view_text16.png.
2019-07-04 13:19:20,229 ERROR [ o.o.s.agents.dataBrowser.IconManager] (entQueue-0) Failed to retrieve icon: <classpath>/images/agents/dataBrowser/nuvola_background16.png.
2019-07-04 13:19:20,229 ERROR [ o.o.s.agents.dataBrowser.IconManager] (entQueue-0) Failed to retrieve icon: <classpath>/images/agents/dataBrowser/eclipse_external_tools16.png.
2019-07-04 13:19:20,230 ERROR [ o.o.s.agents.dataBrowser.IconManager] (entQueue-0) Failed to retrieve icon: <classpath>/images/agents/dataBrowser/eclipse_alphab_sort_co16.png.
2019-07-04 13:19:20,230 ERROR [ o.o.s.agents.dataBrowser.IconManager] (entQueue-0) Failed to retrieve icon: <classpath>/images/agents/dataBrowser/eclipse_trace_persp16.png.
2019-07-04 13:19:20,230 ERROR [ o.o.s.agents.dataBrowser.IconManager] (entQueue-0) Failed to retrieve icon: <classpath>/images/agents/dataBrowser/roll_over_image16.png.
2019-07-04 13:19:20,231 ERROR [ o.o.s.agents.dataBrowser.IconManager] (entQueue-0) Failed to retrieve icon: <classpath>/images/agents/dataBrowser/nuvola_folder_image16.png.
2019-07-04 13:19:20,231 ERROR [ o.o.s.agents.dataBrowser.IconManager] (entQueue-0) Failed to retrieve icon: <classpath>/images/agents/dataBrowser/nuvola_style16.png.
I'm having touble opening Insight in Fedora 31. It happens with every version I tried versions (5.4, 5.5.8 and 5.5.9).
Sorry for always having to upgrade my OS to the very latest version. It's a disease.
java -version output is:
openjdk version "1.8.0_242"
OpenJDK Runtime Environment (build 1.8.0_242-b08)
OpenJDK 64-Bit Server VM (build 25.242-b08, mixed mode)
Traceback is:
Abnormal termination due to an uncaught exception.
java.awt.HeadlessException
at java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:204)
at java.awt.Window.<init>(Window.java:536)
at java.awt.Frame.<init>(Frame.java:420)
at javax.swing.JFrame.<init>(JFrame.java:233)
at org.openmicroscopy.shoola.util.ui.login.ScreenLogin.<init>(ScreenLogin.java:805)
at org.openmicroscopy.shoola.env.ui.SplashScreenManager.initializedView(SplashScreenManager.java:171)
at org.openmicroscopy.shoola.env.ui.SplashScreenManager.<init>(SplashScreenManager.java:235)
at org.openmicroscopy.shoola.env.ui.SplashScreenProxy.<init>(SplashScreenProxy.java:123)
at org.openmicroscopy.shoola.env.ui.UIFactory.makeSplashScreen(UIFactory.java:59)
at org.openmicroscopy.shoola.env.init.SplashScreenInit.execute(SplashScreenInit.java:86)
at org.openmicroscopy.shoola.env.init.Initializer.doInit(Initializer.java:275)
at org.openmicroscopy.shoola.env.Container.runStartupProcedure(Container.java:118)
at org.openmicroscopy.shoola.env.Container.access$000(Container.java:68)
at org.openmicroscopy.shoola.env.Container$1.run(Container.java:164)
at java.lang.Thread.run(Thread.java:748)
Abnormal termination due to an uncaught exception.
java.awt.HeadlessException
at java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:204)
at java.awt.Window.<init>(Window.java:536)
at java.awt.Frame.<init>(Frame.java:420)
at javax.swing.JFrame.<init>(JFrame.java:233)
at org.openmicroscopy.shoola.util.ui.login.ScreenLogin.<init>(ScreenLogin.java:805)
at org.openmicroscopy.shoola.env.ui.SplashScreenManager.initializedView(SplashScreenManager.java:171)
at org.openmicroscopy.shoola.env.ui.SplashScreenManager.<init>(SplashScreenManager.java:235)
at org.openmicroscopy.shoola.env.ui.SplashScreenProxy.<init>(SplashScreenProxy.java:123)
at org.openmicroscopy.shoola.env.ui.UIFactory.makeSplashScreen(UIFactory.java:59)
at org.openmicroscopy.shoola.env.init.SplashScreenInit.execute(SplashScreenInit.java:86)
at org.openmicroscopy.shoola.env.init.Initializer.doInit(Initializer.java:275)
at org.openmicroscopy.shoola.env.Container.runStartupProcedure(Container.java:118)
at org.openmicroscopy.shoola.env.Container.access$000(Container.java:68)
at org.openmicroscopy.shoola.env.Container$1.run(Container.java:164)
at java.lang.Thread.run(Thread.java:748)
Exception in thread "Initializer"
Exception: java.awt.HeadlessException thrown from the UncaughtExceptionHandler in thread "Initializer"
java.lang.Exception: Abnormal termination due to an uncaught exception.
java.nio.file.InvalidPathException: Illegal char <:> at index 47: C:\Users\cedre\AppData\Local\OMERO.insight\app\::{F02C1A0D-BE21-4350-88B0-7367FC96EF3C}
at sun.nio.fs.WindowsPathParser.normalize(WindowsPathParser.java:182)
at sun.nio.fs.WindowsPathParser.parse(WindowsPathParser.java:153)
at sun.nio.fs.WindowsPathParser.parse(WindowsPathParser.java:77)
at sun.nio.fs.WindowsPath.parse(WindowsPath.java:94)
at sun.nio.fs.WindowsFileSystem.getPath(WindowsFileSystem.java:255)
at java.nio.file.Paths.get(Paths.java:84)
at org.openmicroscopy.shoola.util.ui.filechooser.GenericFileChooser.handleFileSelection(GenericFileChooser.java:67)
at org.openmicroscopy.shoola.util.ui.filechooser.GenericFileChooser.access$100(GenericFileChooser.java:49)
See #65 (comment).
Repasting the error (which comes after you logged in, and the splashscreen vanishes).
[Wed Aug 21 12:21:12 BST 2019] [INFO] [] Reading available sites from https://imagej.net/
[Wed Aug 21 12:23:10 BST 2019] [ERROR] [] null
java.lang.NoSuchMethodException: Could not find method com.sun.jna.Native.load(Ljava/lang/String;Ljava/lang/Class;Ljava/util/Map;)Lcom/sun/jna/Library;
There was a problem with the class com.sun.jna.Native which can be found here:
/C:/Users/petr/DOWNLO~1/FIJI-W~1/Fiji.app/jars/jna-4.5.2.jar
/C:/Users/petr/DOWNLO~1/FIJI-W~1/Fiji.app/plugins/OMERO.imagej-5.5.4-SNAPSHOT/lib/jna-5.3.0.jar
WARNING: multiple locations found!
java.lang.NoSuchMethodError: com.sun.jna.Native.load(Ljava/lang/String;Ljava/lang/Class;Ljava/util/Map;)Lcom/sun/jna/Library;
at com.sun.jna.platform.win32.Version.<clinit>(Version.java:37)
at org.openmicroscopy.shoola.env.data.model.appdata.WindowsApplicationDataExtractor.extractAppData(WindowsApplicationDataExtractor.java:236)
at org.openmicroscopy.shoola.env.data.model.ApplicationData.<init>(ApplicationData.java:112)
at org.openmicroscopy.shoola.agents.treeviewer.view.TreeViewerFactory.readExternalApplications(TreeViewerFactory.java:477)
at org.openmicroscopy.shoola.agents.treeviewer.view.TreeViewerFactory.getTreeViewer(TreeViewerFactory.java:427)
at org.openmicroscopy.shoola.agents.treeviewer.view.TreeViewerFactory.getTreeViewer(TreeViewerFactory.java:193)
at org.openmicroscopy.shoola.agents.treeviewer.TreeViewerAgent.activate(TreeViewerAgent.java:661)
at org.openmicroscopy.shoola.env.Container.activateAgents(Container.java:327)
at org.openmicroscopy.shoola.env.Container.startService(Container.java:360)
at org.openmicroscopy.shoola.env.init.Initializer.notifyEnd(Initializer.java:197)
at org.openmicroscopy.shoola.env.Container.startupInPluginMode(Container.java:488)
at org.openmicroscopy.shoola.env.Container.startupInPluginMode(Container.java:412)
at org.openmicroscopy.shoola.MainIJPlugin.run(MainIJPlugin.java:272)
at ij.IJ.runUserPlugIn(IJ.java:230)
at ij.IJ.runPlugIn(IJ.java:193)
at ij.Executer.runCommand(Executer.java:137)
at ij.Executer.run(Executer.java:66)
at java.lang.Thread.run(Thread.java:748)
at com.sun.jna.platform.win32.Version.<clinit>(Version.java:37)
at org.openmicroscopy.shoola.env.data.model.appdata.WindowsApplicationDataExtractor.extractAppData(WindowsApplicationDataExtractor.java:236)
at org.openmicroscopy.shoola.env.data.model.ApplicationData.<init>(ApplicationData.java:112)
at org.openmicroscopy.shoola.agents.treeviewer.view.TreeViewerFactory.readExternalApplications(TreeViewerFactory.java:477)
at org.openmicroscopy.shoola.agents.treeviewer.view.TreeViewerFactory.getTreeViewer(TreeViewerFactory.java:427)
at org.openmicroscopy.shoola.agents.treeviewer.view.TreeViewerFactory.getTreeViewer(TreeViewerFactory.java:193)
at org.openmicroscopy.shoola.agents.treeviewer.TreeViewerAgent.activate(TreeViewerAgent.java:661)
at org.openmicroscopy.shoola.env.Container.activateAgents(Container.java:327)
at org.openmicroscopy.shoola.env.Container.startService(Container.java:360)
at org.openmicroscopy.shoola.env.init.Initializer.notifyEnd(Initializer.java:197)
at org.openmicroscopy.shoola.env.Container.startupInPluginMode(Container.java:488)
at org.openmicroscopy.shoola.env.Container.startupInPluginMode(Container.java:412)
at org.openmicroscopy.shoola.MainIJPlugin.run(MainIJPlugin.java:272)
at ij.IJ.runUserPlugIn(IJ.java:230)
at ij.IJ.runPlugIn(IJ.java:193)
at ij.Executer.runCommand(Executer.java:137)
at ij.Executer.run(Executer.java:66)
at java.lang.Thread.run(Thread.java:748)
OMERO.insight-5.5.7-SNAPSHOT/config/logback.xml]. java.io.FileNotFoundException
cc @manics
Need to review again, where version checks are happening and fix or remove them. For example the ImageJ plugin still prints out a warning that one should upgrade to the non-existant 5.6.0 version (using 5.5.8/9).
Hi,
I've tried opening OMERO.insight on beta install of macOS Catalina 10.15.
It is coming up with same error as noted here: https://www.reddit.com/r/MacOS/comments/cgj1qs/cant_be_opened_because_apple_cannot_check_it_for/
Using the right-click then open (then choosing open again) suggestion works, and I'm able to open ok after that.
The new "Notarization" requirements are likely going to require a little extra work for Mac packages when people are starting to use this release of the OS. This is likely a few months away now.
https://developer.apple.com/documentation/security/notarizing_your_app_before_distribution
Just a friendly heads up on this as I've run into it.
Cheers.
With OMERO.insight 5.5.6 running on Windows 10, QA 28007 reports,
java.lang.IllegalStateException: This method can't be invoked in the DISCARDED or NEW state.
at org.openmicroscopy.shoola.agents.imviewer.view.ImViewerComponent.getActiveChannels(ImViewerComponent.java:1724)
at org.openmicroscopy.shoola.agents.imviewer.util.player.ChannelPlayer.(ChannelPlayer.java:74)
at org.openmicroscopy.shoola.agents.imviewer.view.ImViewerModel$2.run(ImViewerModel.java:1456)
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
...
testZipDirectoryWithSubfolder
test fails on Windows
When OptimisticLockException
occurs it's usually due to an OMERO object being modified at the same time, either in another process or by someone else in a different client. Insight could catch this error and show a more friendly message to a user, though it should still keep the original error message and stacktrace accessible in case it's a real bug.
https://forum.image.sc/t/omero-plugin-to-fiji-not-working/34076/12
"loci.formats.FormatException: omero.ApiUsageException
serverStackTrace = “ome.conditions.ApiUsageException: Converting Long 5064622080 to Integer is an overflow.”
The issue might be opened in an other repository after investigation
Given one has the respective permissions, it should be possible to move other users' data, e.g. Images into another Dataset. This fails silently in Insight, but works as expected in Web and CLI. See forum post: https://forum.image.sc/t/query-for-datasetimagelink-id/37206/4
Insight appears to have trouble when importing files that are at the root of a mount if we try to create a new dataset from the local folder name. We have a server exception from a local Windows user at https://www.openmicroscopy.org/qa2/qa/feedback/27121/ (from their home on DIF) and locally on Linux it gives me an NPE.
When on Windows, an error is thrown when saving the new image as ome-tiff
loci.formats.UnknownFormatException: Unknown file format: C:\Users\Johnny
at loci.formats.ImageWriter.getWriter(ImageWriter.java:158)
at loci.plugins.out.Exporter.run(Exporter.java:343)
at loci.plugins.LociExporter.run(LociExporter.java:75)
at
ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:266)
at
ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunner.java:114)
at ij.IJ.runUserPlugIn(IJ.java:231)
at ij.IJ.runPlugIn(IJ.java:193)
at ij.IJ.runPlugIn(IJ.java:182)
at
org.openmicroscopy.shoola.env.data.model.FileObject.getFileToImport(FileObject.java:294)
at
See https://trello.com/c/9TOOTVrm/356-missing-extension-in-imagej-exporter
When the split image is used in the BF plugin, insight sees it as a new image
The user is then asked to import the image and the ROI
Starting the insight from merge-ci - the terminal opens concurrently. Noticing the above output in the console.
/pwalczysko/Downloads/OMERO.insight-5.5.7-SNAPSHOT/config/logback.xml]. java.io.FileNotFoundException: /Users/pwalczysko/Downloads/OMERO.insight-5.5.7-SNAPSHOT/config/logback.xml (No such file or directory)
at java.io.FileNotFoundException: /Users/pwalczysko/Downloads/OMERO.insight-5.5.7-SNAPSHOT/config/logback.xml (No such file or directory)
at at java.io.FileInputStream.open0(Native Method)
at at java.io.FileInputStream.open(FileInputStream.java:195)
at at java.io.FileInputStream.<init>(FileInputStream.java:138)
at at ch.qos.logback.core.joran.GenericConfigurator.doConfigure(GenericConfigurator.java:75)
at at ch.qos.logback.core.joran.GenericConfigurator.doConfigure(GenericConfigurator.java:68)
at at org.openmicroscopy.shoola.env.log.LoggerImpl.<init>(LoggerImpl.java:90)
Noticed by @pwalczysko in #87 (comment)
$ bin/omero-importer
Error: Could not find or load main class org.openmicroscopy.shoola.Main
see ome/training-scripts#76 (comment) - the problem is not in the script tested there, but in insight itself ome/training-scripts#76 (comment)
See the full output of the error in ome/training-scripts#76 (comment)
See https://docs.google.com/document/d/1MkaqEvts7wPb3CJXHdxJ3BVHowrmkN6JF7lufIEVUXM/edit for background
Playing the z-stack video in lowest zoom is in most cases and trials not working at all.
Zooming: zooming works and is quite fast.
Scrolling through z in high zoom levels: It takes ca 10 secs for the new z plane to appear at 25% zoom. But, this is a z-plane of insight's choosing (very hard to force insight to scroll to a z plane of your choice.)
insight-error:
After a time of testing in full viewer, tried to expand the dataset in the same project (containing the other 2 Anatole's images). This elicited an error on idr-testing which appeared in insight as
java.lang.Exception: omero.gateway.exception.DSAccessException: Cannot access data.
Cannot load hierarchy for class omero.gateway.model.DatasetData.
at org.openmicroscopy.shoola.env.data.OMEROGateway.handleException(OMEROGateway.java:772)
at org.openmicroscopy.shoola.env.data.OMEROGateway.loadContainerHierarchy(OMEROGateway.java:1633)
at org.openmicroscopy.shoola.env.data.OmeroDataServiceImpl.loadContainerHierarchy(OmeroDataServiceImpl.java:233)
at org.openmicroscopy.shoola.env.data.views.calls.DMLoader$1.doCall(DMLoader.java:82)
at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
at java.lang.Thread.run(Thread.java:745)
Caused by: omero.gateway.exception.DSAccessException: Cannot access data.
Could not load hierarchy
at omero.gateway.facility.Facility.handleException(Facility.java:305)
at omero.gateway.facility.BrowseFacility.getHierarchy(BrowseFacility.java:151)
at org.openmicroscopy.shoola.env.data.OMEROGateway.loadContainerHierarchy(OMEROGateway.java:1630)
... 9 more
Caused by: omero.InternalException
serverStackTrace = "ome.conditions.InternalException: Wrapped Exception: (org.springframework.dao.DataAccessResourceFailureException):
Hibernate operation: could not execute query; SQL [select image0_.id as id60_, image0_.acquisitionDate as acquisit2_60_, image0_.archived as archived60_, image0_.description as descript4_60_, image0_.creation_id as creation10_60_, image0_.external_id as external11_60_, image0_.group_id as group12_60_, image0_.owner_id as owner13_60_, image0_.permissions as permissi5_60_, image0_.update_id as update14_60_, image0_.experiment as experiment60_, image0_.fileset as fileset60_, image0_.format as format60_, image0_.imagingEnvironment as imaging18_60_, image0_.instrument as instrument60_, image0_.name as name60_, image0_.objectiveSettings as objecti20_60_, image0_.partial as partial60_, image0_.series as series60_, image0_.stageLabel as stageLabel60_, image0_.version as version60_, annotation1_.Image_id as Image1_60_0__, annotation1_.count as count0__, annotation1_.owner_id as owner3_0__ from image image0_ left outer join count_Image_annotationLinks_by_owner annotation1_ on image0_.id=annotation1_.Image_id where (
( image0_.group_id = ? AND
( 1 = ? OR
1 = ? OR
image0_.owner_id = ?
)
) OR
image0_.group_id = 1 OR
1 = ?
) and (image0_.id in (? , ?))]; ERROR: canceling statement due to statement timeout; nested exception is org.postgresql.util.PSQLException: ERROR: canceling statement due to statement timeout
at org.springframework.jdbc.support.SQLStateSQLExceptionTranslator.doTranslate(SQLStateSQLExceptionTranslator.java:105)
at org.springframework.jdbc.support.AbstractFallbackSQLExceptionTranslator.translate(AbstractFallbackSQLExceptionTranslator.java:73)
at org.springframework.jdbc.support.AbstractFallbackSQLExceptionTranslator.translate(AbstractFallbackSQLExceptionTranslator.java:82)
at org.springframework.jdbc.support.AbstractFallbackSQLExceptionTranslator.translate(AbstractFallbackSQLExceptionTranslator.java:82)
at org.springframework.orm.hibernate3.HibernateAccessor.convertJdbcAccessException(HibernateAccessor.java:428)
at org.springframework.orm.hibernate3.HibernateAccessor.convertHibernateAccessException(HibernateAccessor.java:414)
at org.springframework.orm.hibernate3.HibernateTemplate.doExecute(HibernateTemplate.java:416)
at org.springframework.orm.hibernate3.HibernateTemplate.execute(HibernateTemplate.java:342)
at ome.logic.QueryImpl.execute(QueryImpl.java:176)
at ome.logic.QueryImpl.findAllByQuery(QueryImpl.java:419)
at ome.logic.PojosImpl.loadContainerHierarchy(PojosImpl.java:248)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
at ome.security.basic.EventHandler.invoke(EventHandler.java:154)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:282)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)
at com.sun.proxy.$Proxy95.loadContainerHierarchy(Unknown Source)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:93)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)
at com.sun.proxy.$Proxy95.loadContainerHierarchy(Unknown Source)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at ome.services.blitz.util.IceMethodInvoker.invoke(IceMethodInvoker.java:172)
at ome.services.throttling.Callback.run(Callback.java:56)
at ome.services.throttling.InThreadThrottlingStrategy.callInvokerOnRawArgs(InThreadThrottlingStrategy.java:56)
at ome.services.blitz.impl.AbstractAmdServant.callInvokerOnRawArgs(AbstractAmdServant.java:140)
at ome.services.blitz.impl.ContainerI.loadContainerHierarchy_async(ContainerI.java:177)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
at omero.cmd.CallContext.invoke(CallContext.java:85)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)
at com.sun.proxy.$Proxy96.loadContainerHierarchy_async(Unknown Source)
at omero.api._IContainerTie.loadContainerHierarchy_async(_IContainerTie.java:120)
at omero.api._IContainerDisp.___loadContainerHierarchy(_IContainerDisp.java:537)
at omero.api._IContainerDisp.__dispatch(_IContainerDisp.java:980)
at IceInternal.Incoming.invoke(Incoming.java:221)
at Ice.ConnectionI.invokeAll(ConnectionI.java:2536)
at Ice.ConnectionI.dispatch(ConnectionI.java:1145)
at Ice.ConnectionI.message(ConnectionI.java:1056)
at IceInternal.ThreadPool.run(ThreadPool.java:395)
at IceInternal.ThreadPool.access$300(ThreadPool.java:12)
at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)
at java.lang.Thread.run(Thread.java:748)
"
serverExceptionClass = "ome.conditions.InternalException"
message = " Wrapped Exception: (org.springframework.dao.DataAccessResourceFailureException):
Hibernate operation: could not execute query; SQL [select image0_.id as id60_, image0_.acquisitionDate as acquisit2_60_, image0_.archived as archived60_, image0_.description as descript4_60_, image0_.creation_id as creation10_60_, image0_.external_id as external11_60_, image0_.group_id as group12_60_, image0_.owner_id as owner13_60_, image0_.permissions as permissi5_60_, image0_.update_id as update14_60_, image0_.experiment as experiment60_, image0_.fileset as fileset60_, image0_.format as format60_, image0_.imagingEnvironment as imaging18_60_, image0_.instrument as instrument60_, image0_.name as name60_, image0_.objectiveSettings as objecti20_60_, image0_.partial as partial60_, image0_.series as series60_, image0_.stageLabel as stageLabel60_, image0_.version as version60_, annotation1_.Image_id as Image1_60_0__, annotation1_.count as count0__, annotation1_.owner_id as owner3_0__ from image image0_ left outer join count_Image_annotationLinks_by_owner annotation1_ on image0_.id=annotation1_.Image_id where (
( image0_.group_id = ? AND
( 1 = ? OR
1 = ? OR
image0_.owner_id = ?
)
) OR
image0_.group_id = 1 OR
1 = ?
) and (image0_.id in (? , ?))]; ERROR: canceling statement due to statement timeout; nested exception is org.postgresql.util.PSQLException: ERROR: canceling statement due to statement timeout"
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
at java.lang.Class.newInstance(Class.java:442)
at IceInternal.BasicStream.createUserException(BasicStream.java:2779)
at IceInternal.BasicStream.access$300(BasicStream.java:14)
at IceInternal.BasicStream$EncapsDecoder11.throwException(BasicStream.java:3614)
at IceInternal.BasicStream.throwException(BasicStream.java:2291)
at IceInternal.OutgoingAsync.throwUserException(OutgoingAsync.java:399)
at omero.api.IContainerPrxHelper.end_loadContainerHierarchy(IContainerPrxHelper.java:1994)
at omero.api.IContainerPrxHelper.loadContainerHierarchy(IContainerPrxHelper.java:1858)
at omero.api.IContainerPrxHelper.loadContainerHierarchy(IContainerPrxHelper.java:1845)
at omero.gateway.facility.BrowseFacility.getHierarchy(BrowseFacility.java:147)
... 10 more
at org.openmicroscopy.shoola.env.ui.UserNotifierImpl.showErrorDialog(UserNotifierImpl.java:189)
at org.openmicroscopy.shoola.env.ui.UserNotifierImpl.notifyError(UserNotifierImpl.java:289)
at org.openmicroscopy.shoola.env.ui.UserNotifierImpl.notifyError(UserNotifierImpl.java:257)
at org.openmicroscopy.shoola.agents.treeviewer.DataBrowserLoader.handleException(DataBrowserLoader.java:148)
at org.openmicroscopy.shoola.env.data.events.DSCallAdapter.eventFired(DSCallAdapter.java:84)
at org.openmicroscopy.shoola.env.data.views.BatchCallMonitor$1.run(BatchCallMonitor.java:124)
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)
at java.awt.EventQueue.access$500(EventQueue.java:97)
at java.awt.EventQueue$3.run(EventQueue.java:709)
at java.awt.EventQueue$3.run(EventQueue.java:703)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:726)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
See https://forum.image.sc/t/pb-connectiong-to-omero-with-imagej-but-not-fiji-omero-server-5-5-3/28756
Confirmed the observations from the post (tested on Mac):
ImageJ(downloaded freshly from https://imagej.nih.gov/ij/download.html)
Fiji:
Make clear what the min java version supported
see https://forum.image.sc/t/installing-omero-insight-5-5-9-on-linux/36695/8
as already discussed with @rgozim , it would be good if there would be a shortcut created on the installation step - the other programmes ask about this when I am trying to install them on Windows (something like : should a shortcut be created on Desktop and or in Start menu ?). Otherwise it is a challenge to find where insight was installed.
cc @jburel
See discussion on ome/www.openmicroscopy.org#296
Previous batch script could be launched from any location
This is no longer the case with bin/omero-insight
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