Script parameter #1822

jburel · 2013-11-22T13:19:36Z

Add check to make sure scripts cannot be started w/o parameters

To test:

Trying to run few scripts from the scripts menu

pwalczysko · 2013-11-25T14:10:27Z

Login to gretzky as user-4, group read-only-1, Dataset: dv.

open first image, draw a polyline (long one)
save polyline
the image still selected, start Kymograph
ends up with error (see below)


Traceback (most recent call last):
  File "./script", line 530, in <module>
    newImages, message = processImages(conn, scriptParams)
  File "./script", line 415, in processImages
    tInterval = duration/(sizeT-1)
ZeroDivisionError: float division

pwalczysko · 2013-11-25T14:13:16Z

Additional info to the error above: the Kymograph images were nevertheless created, so the script ran actually successfully.

pwalczysko · 2013-11-25T14:16:04Z

Batch image export script - in the Image field, deleted the default image ID (left empty field = there is no parameter now). Started the script. Got an exception.
OMERO.insight-5.0.0-beta2-RC1-217-50f4372-ice33-b497-mac


java.lang.Exception: Abnormal termination due to an uncaught exception.
java.lang.IllegalArgumentException: No all required fields have been filled.
    at org.openmicroscopy.shoola.env.ui.ScriptActivity.<init>(ScriptActivity.java:105)
    at org.openmicroscopy.shoola.env.ui.UserNotifierImpl.notifyActivity(UserNotifierImpl.java:405)
    at org.openmicroscopy.shoola.agents.treeviewer.view.TreeViewerControl.handleScript(TreeViewerControl.java:974)
    at org.openmicroscopy.shoola.agents.treeviewer.view.TreeViewerControl.propertyChange(TreeViewerControl.java:1501)
    at java.beans.PropertyChangeSupport.firePropertyChange(PropertyChangeSupport.java:339)
    at java.beans.PropertyChangeSupport.firePropertyChange(PropertyChangeSupport.java:276)
    at java.awt.Component.firePropertyChange(Component.java:8287)
    at org.openmicroscopy.shoola.agents.util.ui.ScriptingDialog.runScript(ScriptingDialog.java:325)
    at org.openmicroscopy.shoola.agents.util.ui.ScriptingDialog.actionPerformed(ScriptingDialog.java:814)
    at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2028)
    at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2351)
    at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)
    at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)
    at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:236)
    at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:272)
    at java.awt.Component.processMouseEvent(Component.java:6414)
    at javax.swing.JComponent.processMouseEvent(JComponent.java:3275)
    at java.awt.Component.processEvent(Component.java:6179)
    at java.awt.Container.processEvent(Container.java:2083)
    at java.awt.Component.dispatchEventImpl(Component.java:4776)
    at java.awt.Container.dispatchEventImpl(Container.java:2141)
    at java.awt.Component.dispatchEvent(Component.java:4604)
    at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4619)
    at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4280)
    at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4210)
    at java.awt.Container.dispatchEventImpl(Container.java:2127)
    at java.awt.Window.dispatchEventImpl(Window.java:2489)
    at java.awt.Component.dispatchEvent(Component.java:4604)
    at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:717)
    at java.awt.EventQueue.access$400(EventQueue.java:82)
    at java.awt.EventQueue$2.run(EventQueue.java:676)
    at java.awt.EventQueue$2.run(EventQueue.java:674)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86)
    at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:97)
    at java.awt.EventQueue$3.run(EventQueue.java:690)
    at java.awt.EventQueue$3.run(EventQueue.java:688)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86)
    at java.awt.EventQueue.dispatchEvent(EventQueue.java:687)
    at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
    at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
    at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
    at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
Abnormal termination due to an uncaught exception.
java.lang.IllegalArgumentException: No all required fields have been filled.
    at org.openmicroscopy.shoola.env.ui.ScriptActivity.<init>(ScriptActivity.java:105)
    at org.openmicroscopy.shoola.env.ui.UserNotifierImpl.notifyActivity(UserNotifierImpl.java:405)
    at org.openmicroscopy.shoola.agents.treeviewer.view.TreeViewerControl.handleScript(TreeViewerControl.java:974)
    at org.openmicroscopy.shoola.agents.treeviewer.view.TreeViewerControl.propertyChange(TreeViewerControl.java:1501)
    at java.beans.PropertyChangeSupport.firePropertyChange(PropertyChangeSupport.java:339)
    at java.beans.PropertyChangeSupport.firePropertyChange(PropertyChangeSupport.java:276)
    at java.awt.Component.firePropertyChange(Component.java:8287)
    at org.openmicroscopy.shoola.agents.util.ui.ScriptingDialog.runScript(ScriptingDialog.java:325)
    at org.openmicroscopy.shoola.agents.util.ui.ScriptingDialog.actionPerformed(ScriptingDialog.java:814)
    at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2028)
    at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2351)
    at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)
    at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)
    at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:236)
    at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:272)
    at java.awt.Component.processMouseEvent(Component.java:6414)
    at javax.swing.JComponent.processMouseEvent(JComponent.java:3275)
    at java.awt.Component.processEvent(Component.java:6179)
    at java.awt.Container.processEvent(Container.java:2083)
    at java.awt.Component.dispatchEventImpl(Component.java:4776)
    at java.awt.Container.dispatchEventImpl(Container.java:2141)
    at java.awt.Component.dispatchEvent(Component.java:4604)
    at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4619)
    at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4280)
    at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4210)
    at java.awt.Container.dispatchEventImpl(Container.java:2127)
    at java.awt.Window.dispatchEventImpl(Window.java:2489)
    at java.awt.Component.dispatchEvent(Component.java:4604)
    at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:717)
    at java.awt.EventQueue.access$400(EventQueue.java:82)
    at java.awt.EventQueue$2.run(EventQueue.java:676)
    at java.awt.EventQueue$2.run(EventQueue.java:674)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86)
    at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:97)
    at java.awt.EventQueue$3.run(EventQueue.java:690)
    at java.awt.EventQueue$3.run(EventQueue.java:688)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86)
    at java.awt.EventQueue.dispatchEvent(EventQueue.java:687)
    at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
    at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
    at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
    at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
Exception in thread "AWT-EventQueue-0"

    at org.openmicroscopy.shoola.env.ui.UserNotifierImpl.showErrorDialog(UserNotifierImpl.java:191)
    at org.openmicroscopy.shoola.env.ui.UserNotifierImpl.notifyError(UserNotifierImpl.java:291)
    at org.openmicroscopy.shoola.env.AbnormalExitHandler.doTermination(AbnormalExitHandler.java:147)
    at org.openmicroscopy.shoola.env.AbnormalExitHandler.terminate(AbnormalExitHandler.java:85)
    at org.openmicroscopy.shoola.env.AWTExceptionHanlder.handle(AWTExceptionHanlder.java:99)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
    at java.lang.reflect.Method.invoke(Method.java:597)
    at java.awt.EventDispatchThread.handleException(EventDispatchThread.java:412)
    at java.awt.EventDispatchThread.processException(EventDispatchThread.java:318)
    at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:312)
    at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
    at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
    at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)

jburel · 2013-11-25T18:11:06Z

@pwalczysko
I can see 2 problems.

One in the script itself division by 0 (Ticket to be created, not for this PR)
Insight error (to be fixed in this PR)

pwalczysko · 2013-11-26T10:32:15Z

Login to Gretzky, user-4, group read-only-1, dataset dv, first image. Tried to run Kymograph script on the image on which I have created a polyline region yesterday.
Build OMERO.insight-5.0.0-beta2-RC1-233-bf07066-ice33-b498-mac

open Kymograph
the ID of the image (2903) is pre-populated as expected
the button "Run script" is greyed out = not expected
try to delete the ID - "Run script" still greyed out
try to paste the ID back - "Run script" still greyed out

pwalczysko · 2013-11-26T10:48:10Z

Unlike Kymograph (see above) which behaves strangely, the following scripts are fine:

Batch image export,
Channel Offsets,
Images from ROIs,
Movie ROI Figure,
Dataset to Plate

The only RFE would be:

Input nonsensical ID (e.g. "0" for the Batch image export script) into the box
the "Run script" button becomes enabled
the image will not be created, but there is no info saying "I could not find such ID"

jburel · 2013-11-26T22:33:36Z

@pwalczysko: you will have to show me the issue with "0" since I cannot reproduce it
The notification will have to be added to the script itself. Out of the scope of this PR.

pwalczysko · 2013-11-27T13:33:28Z

User-6 on Gretzky, dataset dv. Tried to run Channel Offset script. Failure.


java.lang.Exception: java.lang.Exception: org.openmicroscopy.shoola.env.data.ProcessException: Cannot run script with ID:17012
    at org.openmicroscopy.shoola.env.data.views.ProcessBatchCall.doStep(ProcessBatchCall.java:101)
    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:680)
Caused by: org.openmicroscopy.shoola.env.data.ProcessException: Cannot run script with ID:17012
    at org.openmicroscopy.shoola.env.data.OMEROGateway.runScript(OMEROGateway.java:587)
    at org.openmicroscopy.shoola.env.data.OMEROGateway.runScript(OMEROGateway.java:6957)
    at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.runScript(OmeroImageServiceImpl.java:1594)
    at org.openmicroscopy.shoola.env.data.views.calls.ScriptRunner$1.initialize(ScriptRunner.java:77)
    at org.openmicroscopy.shoola.env.data.views.ProcessBatchCall.doStep(ProcessBatchCall.java:99)
    ... 6 more
Caused by: omero.InternalException
    serverStackTrace = "Traceback (most recent call last):
                          File "/home/omero/slave/workspace/OMERO-merge-develop/src/dist/lib/python/omero/util/decorators.py", line 61, in exc_handler
                            rv = func(*args, **kwargs)
                          File "/home/omero/slave/workspace/OMERO-merge-develop/src/dist/lib/python/omero/processor.py", line 866, in processJob
                            prx, process = self.process(client, session, job, current, params, iskill = True)
                          File "/home/omero/slave/workspace/OMERO-merge-develop/src/dist/lib/python/omero/util/decorators.py", line 28, in handler
                            return func(*args, **kwargs)
                          File "/home/omero/slave/workspace/OMERO-merge-develop/src/dist/lib/python/omero/processor.py", line 923, in process
                            process.activate()
                          File "/home/omero/slave/workspace/OMERO-merge-develop/src/dist/lib/python/omero/util/decorators.py", line 81, in with_lock
                            return func(*args, **kwargs)
                          File "/home/omero/slave/workspace/OMERO-merge-develop/src/dist/lib/python/omero/processor.py", line 209, in activate
                            stdout=self.stdout, stderr=self.stderr)
                          File "/home/omero/slave/workspace/OMERO-merge-develop/src/dist/lib/python/killableprocess.py", line 102, in __init__
                            subprocess.Popen.__init__(self, *args, **kwargs)
                          File "/usr/lib/python2.6/subprocess.py", line 633, in __init__
                            errread, errwrite)
                          File "/usr/lib/python2.6/subprocess.py", line 1139, in _execute_child
                            raise child_exception
                        OSError: [Errno 13] Permission denied
                        "
    serverExceptionClass = ""
    message = "Internal exception"
    at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
    at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
    at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
    at java.lang.Class.newInstance0(Class.java:357)
    at java.lang.Class.newInstance(Class.java:310)
    at IceInternal.BasicStream$DynamicUserExceptionFactory.createAndThrow(BasicStream.java:2243)
    at IceInternal.BasicStream.throwException(BasicStream.java:1632)
    at IceInternal.Outgoing.throwUserException(Outgoing.java:442)
    at omero.api._IScriptDelM.runScript(_IScriptDelM.java:508)
    at omero.api.IScriptPrxHelper.runScript(IScriptPrxHelper.java:662)
    at omero.api.IScriptPrxHelper.runScript(IScriptPrxHelper.java:634)
    at org.openmicroscopy.shoola.env.data.OMEROGateway.runScript(OMEROGateway.java:583)
    ... 10 more

    at org.openmicroscopy.shoola.env.ui.UserNotifierImpl.showErrorDialog(UserNotifierImpl.java:191)
    at org.openmicroscopy.shoola.env.ui.UserNotifierImpl.notifyError(UserNotifierImpl.java:291)
    at org.openmicroscopy.shoola.env.ui.UserNotifierImpl.notifyError(UserNotifierImpl.java:259)
    at org.openmicroscopy.shoola.env.ui.ActivityComponent.showException(ActivityComponent.java:413)
    at org.openmicroscopy.shoola.env.ui.ActivityComponent.actionPerformed(ActivityComponent.java:926)
    at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2028)
    at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2351)
    at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)
    at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)
    at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:236)
    at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:272)
    at java.awt.Component.processMouseEvent(Component.java:6414)
    at javax.swing.JComponent.processMouseEvent(JComponent.java:3275)
    at java.awt.Component.processEvent(Component.java:6179)
    at java.awt.Container.processEvent(Container.java:2083)
    at java.awt.Component.dispatchEventImpl(Component.java:4776)
    at java.awt.Container.dispatchEventImpl(Container.java:2141)
    at java.awt.Component.dispatchEvent(Component.java:4604)
    at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4619)
    at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4280)
    at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4210)
    at java.awt.Container.dispatchEventImpl(Container.java:2127)
    at java.awt.Window.dispatchEventImpl(Window.java:2489)
    at java.awt.Component.dispatchEvent(Component.java:4604)
    at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:717)
    at java.awt.EventQueue.access$400(EventQueue.java:82)
    at java.awt.EventQueue$2.run(EventQueue.java:676)
    at java.awt.EventQueue$2.run(EventQueue.java:674)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86)
    at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:97)
    at java.awt.EventQueue$3.run(EventQueue.java:690)
    at java.awt.EventQueue$3.run(EventQueue.java:688)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86)
    at java.awt.EventQueue.dispatchEvent(EventQueue.java:687)
    at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
    at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
    at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
    at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)

pwalczysko · 2013-11-27T13:36:35Z

All the scripts fail the same, except Kymograph. Kymograph which fails as well, does not fail in Activities, but with a separate popup:

pwalczysko · 2013-11-27T13:40:45Z

The scripts fail also when started in web or CLI.

jburel · 2013-11-27T14:05:54Z

@pwalczysko: the problem is not related to that PR.

pwalczysko · 2013-11-27T16:42:37Z

@joshmoore fixed the problem (thank you). Now the workflow is as expected, both for Kymograph as well as other scripts.
The "0" problem I was mentioning is not a bug, just an RFE and not connected to this PR I guess. It is about input of non-existent ID into the scripts parameters. If you do this, the script will "succeed" but you obviously have no results and no info why that is so.
The division by zero problem of Kymograph is still there, possibly because ome/omero-scripts#55 is not in the merge as i understand it (why ? what is the supposed workflow here ?).
I think that these problems are not related and this PR works fine.

jburel · 2013-11-27T17:07:44Z

Passing id like 0, will need to be handled by the scripts. No information currently returned.
The Kymograph issue is not covered by this PR.

joshmoore · 2013-12-03T10:18:52Z

Primary changes around:

(script.isParametersLoaded() && !script.allRequiredValuesPopulated())

look good. Merging.

Script parameter

jburel · 2013-12-04T08:18:45Z

--rebased-to #1862

jburel added 4 commits November 22, 2013 10:23

Clean up code.

fa6b2c4

Remove tabs and whitespace.

07bd16a

Add check if all required fields are entered.

91df759

Add check and remove tab/whitespace.

50bb510

jburel added 3 commits November 25, 2013 20:24

Remove tabs and whitespace.

3a19ac2

Improve code.

3c1709b

Make sure required parameters are populated.

878fc9e

joshmoore mentioned this pull request Nov 26, 2013

Prevent ZeroDivisionError on sizeT=1 ome/omero-scripts#55

Closed

Handle all the types returned.

54b1204

joshmoore added a commit that referenced this pull request Dec 3, 2013

Merge pull request #1822 from jburel/script-parameter

834cda6

Script parameter

joshmoore merged commit 834cda6 into ome:develop Dec 3, 2013

jburel mentioned this pull request Dec 4, 2013

Script parameter dev 4 4 #1862

Merged

jburel deleted the script-parameter branch February 3, 2014 10:39

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Script parameter #1822

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Script parameter #1822

Script parameter #1822

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