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Gradle project containing insight java client for OMERO

Home Page: https://www.openmicroscopy.org/omero/

License: GNU General Public License v2.0

Java 99.76% Groovy 0.24%

omero client gui java

omero-insight's Introduction

OMERO.insight Project

The OMERO.insight Project is a sub-project of the Open Microscopy Environment Project, OME that focuses on delivering a client for the visualization and manipulation of both image data and metadata maintained at an OMERO server site. OMERO.insight is completely written in Java. Technical documentation can be found here.

Directory Contents

This directory is the repository of the software artifacts of the OMERO.insight Project. Its contents are as follows:

+ build.gradle, settings.gradle: build for build system
+ src: Contains the application source files, various configuration
       files required by the application to run and the test code.
+ buildSrc: source files to package the applications
+ README: This file.
+ LICENSE.txt: The license covering this software.
+ CHANGELOG.md: The release history
+ FAQ.md: Commons questions

Building OMERO.insight

The compilation, testing, launch, and delivery of the application are automated by means of a Gradle build file. In order to perform a build, all you need is a JDK -- version 1.8 or later. From the command line, enter:

 gradle build

This will compile, build, test and create a distribution bundle. To run OMERO.insight from the distribution bundle unzip omero-insight.zip then go to the omero-insight directory and from the command line enter, for example:

 bin/omero-insight

To run the OMERO.importer, enter:

 bin/omero-insight containerImporter.xml

To run OMERO.insight, from the command line, enter:

 gradle run

To run OMERO.importer, from the command line, enter:

 gradle runImporter

Packaging OMERO.insight

OMERO.insight uses the Gradle java-packager-plugin and is capable of creating an installer for the platform the deployment task is run on.

Note, a Java runtime is included with the bundled installer. It is recommended to use OpenJDK as the system's JRE to avoid potential licensing issues.

In order to be able to successfully create an installer, a JDK with javapackager or an OpenJFX SDK matching the version of the system JDK is required (particularly if you intend to build with JDK 11 or higher).

OSX

If you are using Homebrew, you can install, for example, OpenJDK 8 which comes bundled with JavaFX. To install run:

  brew tap bell-sw/liberica
  brew install --cask liberica-jdk8-full

Windows

Scoop:

  scoop bucket add java

  scoop install zulufx8

Manually:

To set up a build environment with Windows without using a package manager such as Scoop or Chocolatey perform the following:

JDK:

Download ojdkbuild.
Run the installer.
Once at the custom setup page of the setup select the OpenJDK Runtime drop-down and install the JAVA_HOME feature.
Whilst on the custom setup page, select to include the OpenJFX Runtime.

Inno Setup (required to create .exe installer):

Download and install Inno Setup.
Add the Inno Setup install directory (e.g. C:\Program Files (x86)\Inno Setup 5) to the PATH.

You can install Inno Setup using Chocolatey:

  choco install innosetup

Depending on the Windows version you are using, you might not be able to use the latest version of Inno Setup.

WiX (required to build .msi installer):

Download and install WiX 3.0 or greater.
Add WiX to the PATH.

Packaging

To run the application packager, from the command line enter:

Windows

 gradle packageApplicationExe

OSX

 gradle packageApplicationDmg

Developing OMERO.insight

See https://docs.openmicroscopy.org/latest/omero/developers/index.html#insight.

OMERO.insight extension

To use the metadata extension OMERO.mde, set the following entry in container.xml or in containerImporter.xml to true:

<entry name="omero.client.import.mde.enabled" type="boolean">false</entry>

FAQ

See FAQ.md

Licensing

This software is licensed under the terms of the GNU General Public License (GPL), the full text of which can be found in the top level LICENSE.txt. See https://www.openmicroscopy.org/licensing/ for further details.

Copyright

omero-insight's People

Contributors

Stargazers

Watchers

Forkers

jburel rgozim dominikl joshmoore manics-archive mtbc sukunis sbesson pwalczysko stoffelc emilroz jenswendt tom-tbt

omero-insight's Issues

Bug: Insight import from root folder

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.

Review version checks (not critical)

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).

Improve handling of network errors

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

Insight and Fiji plugin 5.5.7

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)

logback file missing

OMERO.insight-5.5.7-SNAPSHOT/config/logback.xml]. java.io.FileNotFoundException

cc @manics

Fail test Windows

testZipDirectoryWithSubfolder test fails on Windows

Intermittent bugs

The purpose of this issue is to keep track of intermittent, hard to reproduce errors.

NPE when new creating new screen: 28055
NPE when loading tiles: 28070
Multiple image download doesn't work: 28071 - Can't reproduce the issue with 5.5.6
Have to check if Insight has a problem with unicode(?) path names and/or network drives - 28987
Delete attachments: 29016
NPE in importer component: 29049 (might be swingx related)
NPE when propagating ROIs: 29087
NPE in DataServicesFactory 29189
NPE Win32ShellFolderManager2 - looks very Win10 specific 29196
NPE in LayoutUtils 29200
NPE in ImportableFile 29363
ValidationException/SQL linkAnnotation 29366 , 29387
IllegalStateException 29393
IllegalComponentStateException TreeViewerWin.showPopup 29398
NPE AdminServiceImpl.updateGroupPermissions , but apparently not doing anything AdminService related 29408
IllegalArgumentException in MeasurementViewerComponent.setLoadingFromServerClient() LOADING_ROI state 29432
IllegalArgumentException when editing ROI/Folders 29454

Importer launcher fails

$ bin/omero-importer
Error: Could not find or load main class org.openmicroscopy.shoola.Main

Publisher and description .exe

Set publisher and description in .exe

handle NPE in deleting objects

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.

bin/omero-importer

bin/omero-importer does not work
Could not find or load main class org.openmicroscopy.shoola.Main

package version

Currently the version is set to 1.0, it is currently not possible to set it

Download issues

Download of multiple files is not working 29023
ome.tiff export is only possible for one file at a time 29022

Both have to be checked with newer Insight, maybe already fixed.

For some non archived images (OMERO version < 5) the download action is enabled which results in throwing a NPE 29045

Handle OptimisticLockException with a nicer message

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.

download image file

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

Java version

Make clear what the min java version supported
see https://forum.image.sc/t/installing-omero-insight-5-5-9-on-linux/36695/8

NullPointerException from group editor

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.

launch script

Previous batch script could be launched from any location
This is no longer the case with bin/omero-insight

Fiji: save new image

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

Bug: Fresh Fiji on Win7 does not work with insight-ij

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)

No enum constant omero.gateway.LoginCredentials.DefaultPort.SSL

Just to keep track of https://www.openmicroscopy.org/qa2/qa/feedback/29162/ .
Can't replicate, neither with the .exe nor the .msi installer.

Fiji: duplicate image

Using duplicate image then crop is not recognized as a new image preventing the image to be imported

zip rename

Rename the zip to OMERO.insight-

bat file

This is currently not working
See gradle/gradle#1989

Fiji: split image

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

Path error in FileChooser windows 10

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 https://www.openmicroscopy.org/qa2/qa/feedback/29147/

Improve file attachment dialog

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.

Hangs when importing very many files: servants held open

[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.

Import wrong dataset

push the "create" button in dataset creation dialog and push of "add to the queue" button are in normal but quick succession:

select a dataset, create new dataset A,click import;
while import 1 is running: select a dataset, create new dataset B, click import;
while import 1 is running: select a dataset, create new dataset C, click import;
After the import:
import 1 and import 2 are imported to dataset A; import 3 is imported to dataset C. Dataset B was created but empty. I had put a log messages to the LocationDialog::getImportSettings method and it seems so, that the LocationDialog doesn't get the right dataset destination if the time between creating a new dataset and add to queue event is very short and the connection to the server is slow

cc @sukunis @dominikl

OMERO.insight: fix addition of third-party JARs

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:

download the external JAR and add it under the lib/ folder
edit bin/omero-insight and append :$APP_HOME/lib/SlideBook6Reader.jar to the CLASSPATH line
start OMERO.insight and try importing a Slidebook file that fails with the legacy OME Slidebook reader

It 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.

Fiji: crop image

Saving the image does not work with 5.5.0-m1

Admin tasks

There are several bugs in Insight with respect to "admin" tasks (like managing user - group relationships).

Make sure a user really can be removed from a group before enabling the respective actions, see QA 29040, QA 29039 and QA 29055
NPE in UserProfile view/editor: 29228
SQLException 29367

Bug: ImageJ plugin 5.5.3 release works only in Fiji

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)

5.5.3 release insight-ij plugin does not work in ImageJ - the menu item OMERO is present, but "Connect to OMERO" does not elicit any action (no obvious error is popping up)
5.4.10 release insight-ij plugin does work in the same ImageJ - Connect to OMERO pops up a splashscreen as expected

Fiji:

5.5.3 release insight-ij plugin works fine
5.4.10 release insight-ij plugin worked fine (tested during outreaches repeatedly)

cc @rgozim @jburel

ImageJ plugin - channels

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.

lets have an image in OMERO with channels A, B, C
lets use the insight-ij plugin to open this image in Fiji and when in B-F dialog
lets select the "Split channels" checkbox
in Fiji, draw a rectangle on the image from channel C, then Image > Crop
Select Plugins > OMERO > Save image to OMERO and import the cropped image
in OMERO, observe that the crop is having one channel only (expected), but the name of this channels is "A" (not expected, "C" should be the name)

"Movie export" dialog can't handle lookup tables

Dialog expects a java.awt.Color object, can't handle lookup tables (which are Strings).
See https://www.openmicroscopy.org/qa2/qa/feedback/27972/

Fiji does not connect

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

insight win shortcut

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

Version is not reported in Help → About

For OMERO.insight 5.5.2 I'm told:

Version: @VERSION@
Build: @DATE@

ChannelPlayer causes IllegalStateException from ImViewerComponent

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)
...

insight crashes when BDV is browsed

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)

settings.setStroke

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)

cc @jburel @dominikl

package importer

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

Failed to retrieve icon

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.

Move other users' data fails

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

Notarization requirements for package install on macOS Catalina Beta

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.

Endless spinner activities script execution

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

Fedora31 java.awt.HeadlessException

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"

"Export as ome-tiff" option should be disabled for large images

Large image can't be exported as ome-tiff. The button shoudl be disabled.
See https://www.openmicroscopy.org/qa2/qa/feedback/27969/

Bug: import into non-default ports

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"

cc @jburel @dominikl @joshmoore

logback.xml FileNotFound

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)