Gradle build version of insight #1

rgozim · 2019-02-28T10:03:30Z

Requires testing on multiple OS's and on a server account with plenty of data.

Prerequisites to test:

install gradle on your system (via homebrew if mac, via sdkman if linux)

Build and run insight:

cd omero-insight
gradle run
Check that insight works as before, no icons missing etc.

Build insight:

cd omero-insight
gradle build
A build directory should be visible
Go to the distributions folder
Unzip omero-insight.zip
cd omero-insight
Run bin/omero-insight
Now run bin/omero-insight containerImporter.xml. Check that the importer starts

insight-ij

Unzip omero-insight-imagej.zip
Copy the directory to Fiji/plugins
Check that you can connect to OMERO.

joshmoore · 2019-02-28T10:05:22Z

Re-opening for travis status.

jburel

first round

src/main/java/org/openmicroscopy/shoola/env/ui/AbstractIconManager.java

src/main/java/org/openmicroscopy/shoola/util/ui/IconManager.java

build.gradle

src/main/java/org/openmicroscopy/shoola/agents/fsimporter/IconManager.java

src/main/java/org/openmicroscopy/shoola/util/ui/IconFactory.java

src/main/java/org/openmicroscopy/shoola/util/ui/IconManager.java

src/main/java/org/openmicroscopy/shoola/util/ui/login/ScreenLogin.java

src/main/java/org/openmicroscopy/shoola/util/ui/omeeditpane/OMEWikiComponent.java

build.gradle

jburel · 2019-03-01T12:23:05Z

run { args = ["container.xml", "${project.buildDir}"] }
This means that we will not be able to run the importer.
What about insight as ImageJ, we will need another distribution

jburel · 2019-03-01T13:56:12Z

we will also need to be able to create executable

jburel · 2019-03-01T13:57:33Z

I have not been able to connect to any server using the run command
It is looking for ice.config when attempting to connect org.openmicroscopy.shoola.env.data.OMEROGateway.connect(OMEROGateway.java:1448). This should not be necessary

jburel · 2019-03-13T05:45:44Z

@rgozim: gradle build and gradle test should now work

pwalczysko · 2019-03-18T11:04:02Z

Crashed insight (after building it using the build steps, unzipping etc.) via drawing three ROIs on an idr0021 image (trainer-1 on outreach), saving them. Then, reopened the ROI drawing tool and tried to delete one of those ROIs. Full crash of insight ensued.

this Bug is

repeatable
it IS a regression (5.4.10 release insight with the same workflow, even on the same server and the very same image is performing as expected)

java.lang.Exception: Abnormal termination due to an uncaught exception.
java.lang.IllegalArgumentException: node must be a TreeTableNode managed by this model
	at org.jdesktop.swingx.treetable.DefaultTreeTableModel.isLeaf(DefaultTreeTableModel.java:312)
	at javax.swing.plaf.basic.BasicTreeUI.paint(BasicTreeUI.java:1185)
	at com.apple.laf.AquaTreeUI.paint(AquaTreeUI.java:129)
	at javax.swing.plaf.ComponentUI.update(ComponentUI.java:161)
	at javax.swing.JComponent.paintComponent(JComponent.java:780)
	at javax.swing.JComponent.paint(JComponent.java:1056)
	at org.jdesktop.swingx.JXTreeTable$TreeTableCellRenderer.paint(JXTreeTable.java:3053)
	at javax.swing.CellRendererPane.paintComponent(CellRendererPane.java:151)
	at javax.swing.plaf.basic.BasicTableUI.paintCell(BasicTableUI.java:2115)
	at javax.swing.plaf.basic.BasicTableUI.paintCells(BasicTableUI.java:2016)
	at javax.swing.plaf.basic.BasicTableUI.paint(BasicTableUI.java:1812)
	at javax.swing.plaf.ComponentUI.update(ComponentUI.java:161)
	at javax.swing.JComponent.paintComponent(JComponent.java:780)
	at javax.swing.JComponent.paint(JComponent.java:1056)
	at javax.swing.JComponent.paintToOffscreen(JComponent.java:5210)
	at javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1579)
	at javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1502)
	at javax.swing.RepaintManager.paint(RepaintManager.java:1272)
	at javax.swing.JComponent._paintImmediately(JComponent.java:5158)
	at javax.swing.JComponent.paintImmediately(JComponent.java:4969)
	at javax.swing.RepaintManager$4.run(RepaintManager.java:831)
	at javax.swing.RepaintManager$4.run(RepaintManager.java:814)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
	at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:814)
	at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:789)
	at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:738)
	at javax.swing.RepaintManager.access$1200(RepaintManager.java:64)
	at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1732)
	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:76)
	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.pumpEventsForFilter(EventDispatchThread.java:109)
	at java.awt.WaitDispatchSupport$2.run(WaitDispatchSupport.java:184)
	at java.awt.WaitDispatchSupport$4.run(WaitDispatchSupport.java:229)
	at java.awt.WaitDispatchSupport$4.run(WaitDispatchSupport.java:227)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.awt.WaitDispatchSupport.enter(WaitDispatchSupport.java:227)
	at java.awt.Dialog.show(Dialog.java:1084)
	at java.awt.Component.show(Component.java:1673)
	at java.awt.Component.setVisible(Component.java:1625)
	at java.awt.Window.setVisible(Window.java:1014)
	at java.awt.Dialog.setVisible(Dialog.java:1005)
	at org.openmicroscopy.shoola.util.ui.MessengerDialog.setVisible(MessengerDialog.java:824)
	at org.openmicroscopy.shoola.util.ui.UIUtilities.centerAndShow(UIUtilities.java:577)
	at org.openmicroscopy.shoola.env.ui.UserNotifierImpl.showErrorDialog(UserNotifierImpl.java:197)
	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.measurement.view.MeasurementViewerUI.handleROIException(MeasurementViewerUI.java:1123)
	at org.openmicroscopy.shoola.agents.measurement.view.MeasurementViewerUI.removeROI(MeasurementViewerUI.java:985)
	at org.openmicroscopy.shoola.agents.measurement.view.MeasurementViewerControl.figureRemoved(MeasurementViewerControl.java:601)
	at org.jhotdraw.draw.AbstractDrawing.fireFigureRemoved(AbstractDrawing.java:226)
	at org.jhotdraw.draw.AbstractDrawing.remove(AbstractDrawing.java:142)
	at org.jhotdraw.draw.AbstractDrawing.removeAll(AbstractDrawing.java:96)
	at org.jhotdraw.draw.DefaultDrawingView.delete(DefaultDrawingView.java:835)
	at org.jhotdraw.app.action.DeleteAction.actionPerformed(DeleteAction.java:48)
	at org.jhotdraw.draw.AbstractTool.keyPressed(AbstractTool.java:224)
	at org.jhotdraw.draw.SelectionTool.keyPressed(SelectionTool.java:67)
	at java.awt.AWTEventMulticaster.keyPressed(AWTEventMulticaster.java:250)
	at java.awt.Component.processKeyEvent(Component.java:6493)
	at javax.swing.JComponent.processKeyEvent(JComponent.java:2832)
	at java.awt.Component.processEvent(Component.java:6312)
	at java.awt.Container.processEvent(Container.java:2236)
	at java.awt.Component.dispatchEventImpl(Component.java:4891)
	at java.awt.Container.dispatchEventImpl(Container.java:2294)
	at java.awt.Component.dispatchEvent(Component.java:4713)
	at java.awt.KeyboardFocusManager.redispatchEvent(KeyboardFocusManager.java:1954)
	at java.awt.DefaultKeyboardFocusManager.dispatchKeyEvent(DefaultKeyboardFocusManager.java:806)
	at java.awt.DefaultKeyboardFocusManager.preDispatchKeyEvent(DefaultKeyboardFocusManager.java:1074)
	at java.awt.DefaultKeyboardFocusManager.typeAheadAssertions(DefaultKeyboardFocusManager.java:945)
	at java.awt.DefaultKeyboardFocusManager.dispatchEvent(DefaultKeyboardFocusManager.java:771)
	at java.awt.Component.dispatchEventImpl(Component.java:4762)
	at java.awt.Container.dispatchEventImpl(Container.java:2294)
	at java.awt.Window.dispatchEventImpl(Window.java:2750)
	at java.awt.Component.dispatchEvent(Component.java:4713)
	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:76)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86)
	at java.awt.EventQueue$4.run(EventQueue.java:731)
	at java.awt.EventQueue$4.run(EventQueue.java:729)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
	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)
Abnormal termination due to an uncaught exception.
java.lang.IllegalArgumentException: node must be a TreeTableNode managed by this model
	at org.jdesktop.swingx.treetable.DefaultTreeTableModel.isLeaf(DefaultTreeTableModel.java:312)

jburel · 2019-03-18T13:01:54Z

@pwalczysko the problem should now be fixed. Could you try it again?

pwalczysko · 2019-03-18T14:14:27Z

@jburel Re #1 (comment) - I can confirm the fix of the problem - all works as expected as re-tested 10 minutes ago

pwalczysko · 2019-03-18T16:27:17Z

When trying to connect to eel. Expected ?

jburel · 2019-03-18T16:30:35Z

@pwalczysko thanks i need to check the version

pwalczysko · 2019-03-18T17:12:31Z

Cannot find any more bugs today. We did not do any testing on Linux yet.

jburel · 2019-03-18T21:05:50Z

@pwalczysko The version checked is done at the Java gateway level when insight tries to connect
ExperimenterData exp = omeroGateway.connect(cred);
see https://github.com/ome/omero-blitz/blob/master/src/main/java/omero/gateway/Gateway.java#L1138
cc @dominikl

mtbc · 2019-03-19T08:11:16Z

I've guessed it's the same issue as why we have to disable omero.web.check_version. In the Java Gateway as @jburel points to I've been hacking clientVersion to be null to be able to run integration tests.

dominikl · 2019-03-19T09:52:47Z

I don't get it, why is the build 5.4.10 and not 5.5.0-m_something ?

joshmoore · 2019-03-20T10:13:56Z

/opt/omero-insight $gradle properties | grep version
version: unspecified

pwalczysko · 2019-03-20T12:37:15Z

HEAD is now at df8908b... remove version check. Move to Java gateway
[pwalczysko@ls31619 ~/Work/omero-insight]$ gradle run

jburel · 2019-03-20T12:54:59Z

@pwalczysko the version check that was in insight is no longer needed since the check is happening at the gateway level. It does not solve the problem. Sorry I should have been clearer in the commit message

rgozim · 2019-03-20T12:58:16Z

looks like gateway gets its version from

set: https://github.com/ome/omero-server/blob/59ea2a80708c3f1c743b0a61380707088c06830c/src/main/resources/omero.properties#L963

used: https://github.com/ome/omero-blitz/blob/b6957e1eb53e999989c03d389fdfc175bd9091e8/src/main/java/omero/gateway/Gateway.java#L1139

pwalczysko · 2019-03-20T13:26:06Z

I have some discrepancy in the script menu. When connected to nightshade.

Insight

but web knows nothing about "mero" script

Either this script is really there, but then, what is that script doing there ? (do not dare to execute) and Why does web not show it ?
Or, the script is not there, and insight shows bogus ?

Edit: This is nothing to do with the PR, the release insight shows the same script menu.

pwalczysko · 2019-03-20T13:46:54Z

Created https://trello.com/c/JSjcrW4H/16-nightshade-public-and-iviewer-missing for the problem of #1 (comment)

pwalczysko · 2019-03-20T16:11:46Z

Went today through all the icons and insight workflows including

search
filtering
RHP annotations
screens
full viewer
admin panel
metadata
downloads

Did the ROI tool previously.

All on Mac. How pressing is the Linux test ?

joshmoore · 2019-03-20T16:14:28Z

@pwalczysko : if you are otherwise happy, I'd propose that that suffices for m1. I'm concerned about the version issue (how are you connecting to the server?) but if we can get that fixed, I'd propose we go ahead and get this PR merged and released and iterate from there.

The 3 excluded tests check the interruption of the thread. The thread was no longer interrupted due to ice issue. The problem might have been fixed with newer versions of Ice (to be checked later). When we move to "no Ice" or if the problem is solved, the above commit and this commit should be rolled back.

joshmoore · 2019-03-20T20:47:48Z

A heads up that I'm force pushing the current branch in order to resurrect the ant build in case it's needed for M2.

joshmoore · 2019-03-20T21:02:04Z

Travis is green again.

jburel · 2019-03-21T12:16:52Z

Travis is green
Merging and tagging m1

Make mde configurable

InvalidPathException

check the visibility of the component

joshmoore closed this Feb 28, 2019

joshmoore reopened this Feb 28, 2019

jburel reviewed Mar 1, 2019

View reviewed changes

jburel force-pushed the develop branch from fc8bd93 to 5a85604 Compare March 13, 2019 04:26

jburel force-pushed the develop branch 2 times, most recently from 74787d9 to 793c2a4 Compare March 14, 2019 21:57

jburel changed the title ~~Gradle build version of insight~~ WIP: Gradle build version of insight Mar 18, 2019

joshmoore self-assigned this Mar 18, 2019

jburel added 18 commits March 20, 2019 21:36

Pass properties to run tests

7f10773

Add task to run the importer

f08d128

update jar name

d8f9703

remove jhotdraw git

bd03fd6

update file

87d7428

remove file

a376585

add instructions

81fda26

add repo

29e0c81

add travis file

fdef0f8

bump to m4 to pass travis

2fd215d

delete files no longer needed

7c6a4cf

set jvm arg to match old files

cd85e80

prep jar for imageJ

eff2f1c

bundle ij plugin

c738920

upload zip to gh on tag

2042dba

downgrade swingx to avoid potential issue

7675d08

remove version check. Move to Java gateway

5dfa29c

joshmoore force-pushed the develop branch from df8908b to 5dfa29c Compare March 20, 2019 20:52

jburel changed the title ~~WIP: Gradle build version of insight~~ Gradle build version of insight Mar 20, 2019

rgozim and others added 3 commits March 21, 2019 09:01

Added version and java compile compat

e38499c

bump version to m1 before tagging

66776e3

Add changelog

9fb2593

jburel merged commit 47e40da into ome:master Mar 21, 2019

jburel referenced this pull request in jburel/omero-insight Sep 17, 2019

Merge pull request #1 from jburel/feat_MDE

b4b5407

Make mde configurable

snoopycrimecop pushed a commit to snoopycrimecop/omero-insight that referenced this pull request Jan 20, 2022

Merge pull request ome#1 from dominikl/issue_111_2

d71338d

InvalidPathException

snoopycrimecop pushed a commit to snoopycrimecop/omero-insight that referenced this pull request Feb 3, 2023

Merge pull request ome#1 from jburel/issue_313_2_adjustment

98a9200

check the visibility of the component

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Gradle build version of insight #1

Gradle build version of insight #1

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Gradle build version of insight #1

Gradle build version of insight #1

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