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Task #11472 (closed)

Opened 11 years ago

Closed 10 years ago

Last modified 10 years ago

BUG: OMERO.scripts can mishandle min/max parameter attributes

Reported by: crueden-x Owned by: crueden-x
Priority: critical Milestone: 5.0.3
Component: Scripting Version: 4.4.8
Keywords: n.a. Cc: wmoore, spli, jburel, jamoore
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: n.a.

Description

If a script has multiple parameters, one with min/max values, and the next without, the OMERO.scripts bounds checking erroneously emits "OUT OF BOUNDS" errors claiming the value of the subsequent parameter is too large.

I ran into this issue while testing the ImageJ "Widget Demo" command as an OMERO script. It has many parameters, so I am not 100% confident that the bug boils down to the situation as simply as described above, but certainly with the Widget Demo the behavior I observed was as follows:

  • A numeric parameter with min=0, max=1000
  • A multiple-choice string parameter with a small set of values

When entering values into the console using omero scripts launch XYZ, an "OUT OF BOUNDS" error was given after entering a valid option for the multiple-choice string parameter.

My guess is that perhaps parameter objects are being reused and min/max from the previous parameter is not being cleared?

If the bug is not easy to reproduce based on this description, let me know and I will do some more research into the exact conditions of the bug.

Change History (12)

comment:1 Changed 11 years ago by jamoore

  • Cc wmoore spli jburel added
  • Milestone changed from Unscheduled to OMERO-4.4.9
  • Owner set to jamoore
  • Priority changed from minor to critical
  • Version changed from 5.0.0-beta1 to 4.4.8

comment:2 Changed 11 years ago by jamoore

First attempt to reproduce:

(ome1)jamoore@blue:/opt/ome3/dist$ bin/omero script cat 1 > 11472.py
Using session 0088617f-4133-43ec-bee0-0b28f920168d (root@localhost:4064). Idle timeout: 10.0 min. Current group: system
Error printing text
(ome1)jamoore@blue:/opt/ome3/dist$ vi 11472.py 
(ome1)jamoore@blue:/opt/ome3/dist$ bin/omero script upload --official 11472.py
Using session 0088617f-4133-43ec-bee0-0b28f920168d (root@localhost:4064). Idle timeout: 10.0 min. Current group: system
Uploaded official script as original file #651
(ome1)jamoore@blue:/opt/ome3/dist$ bin/omero script launch 651
Using session 0088617f-4133-43ec-bee0-0b28f920168d (root@localhost:4064). Idle timeout: 10.0 min. Current group: system
Job 302 ready
Waiting....
Callback received: FINISHED

	*** start stdout (id=653)***
	* object #0 (::omero::RInt)
	* {
	*     _val = 4
	* }
	* object #0 (::omero::RInt)
	* {
	*     _val = 4
	* }
	* 
	*** end stdout ***


	*** out parameters ***
	***  done ***
(ome1)jamoore@blue:/opt/ome3/dist$ bin/omero script launch 651 Line_Width=10 Line_Height=10
Using session 0088617f-4133-43ec-bee0-0b28f920168d (root@localhost:4064). Idle timeout: 10.0 min. Current group: system
Job 303 ready
Waiting....
Callback received: FINISHED

	*** start stdout (id=654)***
	* object #0 (::omero::RInt)
	* {
	*     _val = 10
	* }
	* object #0 (::omero::RInt)
	* {
	*     _val = 10
	* }
	* 
	*** end stdout ***


	*** out parameters ***
	***  done ***
(ome1)jamoore@blue:/opt/ome3/dist$ bin/omero script launch 651 Line_Width=11 Line_Height=11
Using session 0088617f-4133-43ec-bee0-0b28f920168d (root@localhost:4064). Idle timeout: 10.0 min. Current group: system
Bad parameters:
exception ::omero::ValidationException
{
    serverStackTrace = 
    serverExceptionClass = 
    message = Invalid parameters:
OUT OF BOUNDS for "Line_Width": 11 is above max 10

}
(ome1)jamoore@blue:/opt/ome3/dist$ bin/omero script launch 651 Line_Width=10 Line_Height=11
Using session 0088617f-4133-43ec-bee0-0b28f920168d (root@localhost:4064). Idle timeout: 10.0 min. Current group: system
Job 305 ready
Waiting....
Callback received: FINISHED

	*** start stdout (id=655)***
	* object #0 (::omero::RInt)
	* {
	*     _val = 10
	* }
	* object #0 (::omero::RInt)
	* {
	*     _val = 11
	* }
	* 
	*** end stdout ***


	*** out parameters ***
	***  done ***
(ome1)jamoore@blue:/opt/ome3/dist$ bin/omero script cat 651
Using session 0088617f-4133-43ec-bee0-0b28f920168d (root@localhost:4064). Idle timeout: 10.0 min. Current group: system
#!/usr/bin/env python
# -*- coding: utf-8 -*-

from omero.gateway import BlitzGateway
import omero
import omero.util.script_utils as scriptUtil
from omero.rtypes import *
import omero.scripts as scripts
from cStringIO import StringIO
from numpy import *
try:
    from PIL import Image
except ImportError:
    import Image


if __name__ == "__main__":

    client = scripts.client('11472.py', """Tests min/max bug""",

    scripts.Int("Line_Width", optional=False, grouping="3", default=4,
        description="With min/max", min=1, max=10),

    scripts.Int("Line_Height", optional=False, grouping="3", default=4,
        description="Without min/max"),

    version = "4.4.8",
    authors = ["Josh Moore", "OME Team"],
    institutions = ["University of Dundee"],
    contact = "ome-users@lists.openmicroscopy.org.uk",
    )

    try:
        print client.getInput("Line_Width")
        print client.getInput("Line_Height")
    finally:
        client.closeSession()

comment:3 Changed 11 years ago by jamoore

Hmmm...changing to List.ofType(rstring()) also didn't work. Curtis: the widget demo reliably reproduces? Could you perhaps attach the output of params for it?

comment:4 Changed 11 years ago by jamoore

  • Milestone changed from OMERO-4.4.9 to OMERO-4.4.x

Moving to 4.4.x

comment:5 Changed 10 years ago by crueden-x

Sorry for letting this sit for so long. I just noticed your request for feedback.

I was able to reproduce this problem today using the latest version of ImageJ-OMERO with OMERO 5.0.1:

  • Install ImageJ into an OMERO 5.0.1 server as ​described online.
  • Download ​widget-demo-1.0.0-SNAPSHOT.jar and place it into your $OMERO_PREFIX/lib/ImageJ.app/jars folder.
  • Download ​this patched imagej-omero-0.1.0-SNAPSHOT.jar and overwrite the one in $OMERO_PREFIX/lib/ImageJ.app/jars/omero. (See bottom of this comment for details on why this patch is needed.)
  • Run $OMERO_PREFIX/lib/ImageJ.app/lib/gen-scripts --force --all to regenerate scripts.
  • Run omero script list to list the scripts.
  • Run omero script params $(omero script list | grep 'Widget' | sed 's/|.*//') to list parameters of the Widget Demo command. You'll notice that the max is populated for several of the parameters, but the mins of zero are not. I don't know if that's related, or a different bug...
  • Run omero script launch $(omero script list | grep 'Widget' | sed 's/|.*//') to execute the widget demo.
  • The values don't matter that much, as long as you hit valid multiple choice values. Here is a sample execution: 
    $ omero script launch 709
Using session deacf984-defd-4cff-8dd6-b8a9904d016f (omero@localhost:4064). Idle timeout: 10.0 min. Current group: LOCI
Enter value for "pBoolean": true
Enter value for "oBoolean": false
Enter value for "pByte": 1
Enter value for "pDouble": 2
Enter value for "pFloat": 3
Enter value for "pInt": 4
Enter value for "pLong": 5
Enter value for "pShort": 6
Enter value for "oByte": 7
Enter value for "oDouble": 8
Enter value for "oFloat": 9
Enter value for "oInt": 10
Enter value for "oLong": 11
Enter value for "oShort": 12
Enter value for "bigInteger": 13
Enter value for "bigDecimal": 14
Enter value for "pChar": z
Enter value for "oChar": q
Enter value for "string": Hi
Enter value for "choice": quick 
Enter value for "file": /tmp/foo
Enter value for "color": yellow
Enter value for "spinnerInteger": 15
Enter value for "sliderInteger": 16
Enter value for "scrollBarInteger": 17
Enter value for "sliderDouble": 18
Enter value for "scrollBarDouble": 19
Enter value for "choiceRadioH": Maybe
Enter value for "choiceRadioV": Loved
Enter value for "x": 20
Enter value for "twoX": 21
Enter value for "message": Done
Bad parameters:
exception ::omero::ValidationException
{
    serverStackTrace = 
    serverExceptionClass = 
    message = Invalid parameters:
OUT OF BOUNDS for "choiceRadioV": Loved is above max 
OUT OF BOUNDS for "message": Done is above max 
OUT OF BOUNDS for "choiceRadioH": Maybe is above max 
OUT OF BOUNDS for "string": Hi is above max 
OUT OF BOUNDS for "choice": quick is above max 

}

As you can see, the max is somehow erroneously applied to later string parameters.

I don't quite have ImageJ scripts working yet, or I would pare down this example to make things simpler. If you need a smaller test case let me know and I can work on creating a simpler ImageJ2 command. But this bug is probably not urgent to solve before Paris. We can fix it later this summer.

FWIW, here is the output of params on the Widget Demo:

omero script params 709
Using session deacf984-defd-4cff-8dd6-b8a9904d016f (omero@localhost:4064). Idle timeout: 10.0 min. Current group: LOCI

id:  709
name:  [ImageJ] Widget Demo
version:  1.0.0-SNAPSHOT-87e5e4152d60784e145f44ba4e158fbb51a19258
authors:  
institutions:  
description:  
namespaces:  
stdout:  text/plain
stderr:  text/plain
inputs:
  pBoolean - (no description)
    Optional: False
    Type: ::omero::RBool
    Min: 
    Max: 
    Values: 
  oBoolean - (no description)
    Optional: False
    Type: ::omero::RBool
    Min: 
    Max: 
    Values: 
  pByte - (no description)
    Optional: False
    Type: ::omero::RString
    Min: 
    Max: 
    Values: 
  pDouble - (no description)
    Optional: False
    Type: ::omero::RDouble
    Min: 
    Max: 
    Values: 
  pFloat - (no description)
    Optional: False
    Type: ::omero::RFloat
    Min: 
    Max: 
    Values: 
  pInt - (no description)
    Optional: False
    Type: ::omero::RInt
    Min: 
    Max: 
    Values: 
  pLong - (no description)
    Optional: False
    Type: ::omero::RLong
    Min: 
    Max: 
    Values: 
  pShort - (no description)
    Optional: False
    Type: ::omero::RString
    Min: 
    Max: 
    Values: 
  oByte - (no description)
    Optional: False
    Type: ::omero::RString
    Min: 
    Max: 
    Values: 
  oDouble - (no description)
    Optional: False
    Type: ::omero::RDouble
    Min: 
    Max: 
    Values: 
  oFloat - (no description)
    Optional: False
    Type: ::omero::RFloat
    Min: 
    Max: 
    Values: 
  oInt - (no description)
    Optional: False
    Type: ::omero::RInt
    Min: 
    Max: 
    Values: 
  oLong - (no description)
    Optional: False
    Type: ::omero::RLong
    Min: 
    Max: 
    Values: 
  oShort - (no description)
    Optional: False
    Type: ::omero::RString
    Min: 
    Max: 
    Values: 
  bigInteger - (no description)
    Optional: False
    Type: ::omero::RString
    Min: 
    Max: 
    Values: 
  bigDecimal - (no description)
    Optional: False
    Type: ::omero::RString
    Min: 
    Max: 
    Values: 
  pChar - (no description)
    Optional: False
    Type: ::omero::RString
    Min: 
    Max: 
    Values: 
  oChar - (no description)
    Optional: False
    Type: ::omero::RString
    Min: 
    Max: 
    Values: 
  string - (no description)
    Optional: False
    Type: ::omero::RString
    Min: 
    Max: 
    Values: 
  choice - (no description)
    Optional: False
    Type: ::omero::RString
    Min: 
    Max: 
    Values: The, quick, brown, fox, jumps, over, the, lazy, dog
  file - (no description)
    Optional: False
    Type: ::omero::RString
    Min: 
    Max: 
    Values: 
  color - (no description)
    Optional: False
    Type: ::omero::RString
    Min: 
    Max: 
    Values: 
  spinnerInteger - (no description)
    Optional: False
    Type: ::omero::RInt
    Min: 
    Max: 1000
    Values: 
  sliderInteger - (no description)
    Optional: False
    Type: ::omero::RInt
    Min: 
    Max: 1000
    Values: 
  scrollBarInteger - (no description)
    Optional: False
    Type: ::omero::RInt
    Min: 
    Max: 1000
    Values: 
  sliderDouble - (no description)
    Optional: False
    Type: ::omero::RDouble
    Min: 0.2
    Max: 1000.7
    Values: 
  scrollBarDouble - (no description)
    Optional: False
    Type: ::omero::RDouble
    Min: 0.2
    Max: 1000.7
    Values: 
  choiceRadioH - (no description)
    Optional: False
    Type: ::omero::RString
    Min: 
    Max: 
    Values: Yes, No, Maybe
  choiceRadioV - (no description)
    Optional: False
    Type: ::omero::RString
    Min: 
    Max: 
    Values: Loved, Really liked, Liked, Disliked, Really disliked
  x - (no description)
    Optional: False
    Type: ::omero::RFloat
    Min: 
    Max: 
    Values: 
  twoX - Demonstrates callback functionality. Equal to double x.
    Optional: False
    Type: ::omero::RFloat
    Min: 
    Max: 
    Values: 
  message - Demonstrates preview functionality by displaying the given message in the ImageJ status bar.
    Optional: False
    Type: ::omero::RString
    Min: 
    Max: 
    Values: 
outputs:
  result - (no description)
    Optional: False
    Type: ::omero::RString
    Min: 
    Max: 
    Values:

Lastly, the reason for the patched version of the imagej-omero JAR is because the version on master currently has a workaround for this bug. In the patched version, the workaround has been disabled as follows:

git dif
diff --git a/src/main/java/net/imagej/omero/DefaultOMEROService.java b/src/main/java/net/imagej/omero/DefaultOMEROService.java
index 1e1c501..15cc593 100644
--- a/src/main/java/net/imagej/omero/DefaultOMEROService.java
+++ b/src/main/java/net/imagej/omero/DefaultOMEROService.java
@@ -93,12 +93,10 @@ public class DefaultOMEROService extends AbstractService implements
                if (choices != null && !choices.isEmpty()) {
                        param.values = (omero.RList) toOMERO(choices);
                }
-               // TEMP: Disabled until OME issue #11472 is resolved
-               // https://trac.openmicroscopy.org.uk/ome/ticket/11472
-//             final Object min = item.getMinimumValue();
-//             if (min != null) param.min = toOMERO(min);
-//             final Object max = item.getMaximumValue();
-//             if (max != null) param.max = toOMERO(max);
+               final Object min = item.getMinimumValue();
+               if (min != null) param.min = toOMERO(min);
+               final Object max = item.getMaximumValue();
+               if (max != null) param.max = toOMERO(max);
                return param;
        }
Last edited 10 years ago by crueden-x (previous) (diff)

comment:6 Changed 10 years ago by jamoore

  • Milestone changed from 5.x to 5.0.3

comment:7 Changed 10 years ago by jamoore

Referencing ticket #1343 has changed sprint.

comment:8 Changed 10 years ago by jamoore

Referencing ticket #918 has changed sprint.

comment:9 Changed 10 years ago by jamoore

  • Cc jamoore added
  • Owner changed from jamoore to crueden-x

So it looks like what's happening is an empty string is being set as the min/max by imagej-omero. This doesn't show up in the params output (since an empty string displays as nothing). But I can reproduce the same behavior like this:

$ bin/omero script cat /empty-max.py                                                                                                                                                                   
import omero
import omero.scripts as _os
import omero.rtypes as _ot
c = _os.client("test", _os.String("a", max=_ot.rstring(""), optional=False))

$ bin/omero script params /empty-max.py                                                                                                                                                                

id:  14798
name:  test
version:  
authors:  
institutions:  
description:  
namespaces:  
stdout:  text/plain
stderr:  text/plain
inputs:
  a - (no description)
    Optional: False
    Type: ::omero::RString
    Min: 
    Max: 
    Values: 
outputs:


$ bin/omero script launch /empty-max.py a=hi
Bad parameters:
exception ::omero::ValidationException
{
    serverStackTrace = 
    serverExceptionClass = 
    message = Invalid parameters:
OUT OF BOUNDS for "a": hi is above max

With ​https://github.com/openmicroscopy/openmicroscopy/pull/2582, the output of the params command should be:

id:  14654
name:  [ImageJ] Widget Demo
version:  1.0.0-SNAPSHOT-b56d138f9e0757ce9e51815eb5d1c3bfc4ac898d
authors:  
institutions:  
description:  
namespaces:  
stdout:  text/plain
stderr:  text/plain
inputs:
  pBoolean - (no description)
    Optional: False
    Type: ::omero::RBool
    Min: 
    Max: 
    Values: 
  oBoolean - (no description)
    Optional: False
    Type: ::omero::RBool
    Min: 
    Max: 
    Values: 
  pByte - (no description)
    Optional: False
    Type: ::omero::RString
    Min: 
    Max: 
    Values: 
  pDouble - (no description)
    Optional: False
    Type: ::omero::RDouble
    Min: 
    Max: 
    Values: 
  pFloat - (no description)
    Optional: False
    Type: ::omero::RFloat
    Min: 
    Max: 
    Values: 
  pInt - (no description)
    Optional: False
    Type: ::omero::RInt
    Min: 
    Max: 
    Values: 
  pLong - (no description)
    Optional: False
    Type: ::omero::RLong
    Min: 
    Max: 
    Values: 
  pShort - (no description)
    Optional: False
    Type: ::omero::RString
    Min: 
    Max: 
    Values: 
  oByte - (no description)
    Optional: False
    Type: ::omero::RString
    Min: 
    Max: 
    Values: 
  oDouble - (no description)
    Optional: False
    Type: ::omero::RDouble
    Min: 
    Max: 
    Values: 
  oFloat - (no description)
    Optional: False
    Type: ::omero::RFloat
    Min: 
    Max: 
    Values: 
  oInt - (no description)
    Optional: False
    Type: ::omero::RInt
    Min: 
    Max: 
    Values: 
  oLong - (no description)
    Optional: False
    Type: ::omero::RLong
    Min: 
    Max: 
    Values: 
  oShort - (no description)
    Optional: False
    Type: ::omero::RString
    Min: 
    Max: 
    Values: 
  bigInteger - (no description)
    Optional: False
    Type: ::omero::RString
    Min: 
    Max: 
    Values: 
  bigDecimal - (no description)
    Optional: False
    Type: ::omero::RString
    Min: 
    Max: 
    Values: 
  pChar - (no description)
    Optional: False
    Type: ::omero::RString
    Min: 
    Max: 
    Values: 
  oChar - (no description)
    Optional: False
    Type: ::omero::RString
    Min: 
    Max: 
    Values: 
  string - (no description)
    Optional: False
    Type: ::omero::RString
    Min: ''
    Max: ''
    Values: 
  choice - (no description)
    Optional: False
    Type: ::omero::RString
    Min: ''
    Max: ''
    Values: The, quick, brown, fox, jumps, over, the, lazy, dog
  file - (no description)
    Optional: False
    Type: ::omero::RString
    Min: 
    Max: 
    Values: 
  date - (no description)
    Optional: False
    Type: ::omero::RString
    Min: 
    Max: 
    Values: 
  color - (no description)
    Optional: False
    Type: ::omero::RString
    Min: 
    Max: 
    Values: 
  spinnerInteger - (no description)
    Optional: False
    Type: ::omero::RInt
    Min: 0
    Max: 1000
    Values: 
  sliderInteger - (no description)
    Optional: False
    Type: ::omero::RInt
    Min: 0
    Max: 1000
    Values: 
  scrollBarInteger - (no description)
    Optional: False
    Type: ::omero::RInt
    Min: 0
    Max: 1000
    Values: 
  sliderDouble - (no description)
    Optional: False
    Type: ::omero::RDouble
    Min: 0.2
    Max: 1000.7
    Values: 
  scrollBarDouble - (no description)
    Optional: False
    Type: ::omero::RDouble
    Min: 0.2
    Max: 1000.7
    Values: 
  choiceRadioH - (no description)
    Optional: False
    Type: ::omero::RString
    Min: ''
    Max: ''
    Values: Yes, No, Maybe
  choiceRadioV - (no description)
    Optional: False
    Type: ::omero::RString
    Min: ''
    Max: ''
    Values: Loved, Really liked, Liked, Disliked, Really disliked
  x - (no description)
    Optional: False
    Type: ::omero::RFloat
    Min: 
    Max: 
    Values: 
  twoX - Demonstrates callback functionality. Equal to double x.
    Optional: False
    Type: ::omero::RFloat
    Min: 
    Max: 
    Values: 
  message - Demonstrates preview functionality by displaying the given message in the ImageJ status bar.
    Optional: False
    Type: ::omero::RString
    Min: ''
    Max: ''
    Values: 
  button - (no description)
    Optional: True
    Type: ::omero::RString
    Min: 
    Max: 
    Values: 
outputs:
  result - (no description)
    Optional: False
    Type: ::omero::RString
    Min: ''
    Max: ''
    Values:

comment:10 Changed 10 years ago by jmoore <josh@…>

(In [26bf13f2a2835d97bb7cd22d4753bfabb867ee4f/ome.git] on branch develop) Print empty min/max strings in quotes (See #11472)

bin/omero script params was being misleading by showing
no value for min/max of String arguments when the min or
max was the empty string. This adds single quotes to the
empty string to make it clear that a min or max is present.

comment:11 Changed 10 years ago by jamoore

  • Resolution set to fixed
  • Status changed from new to closed

Discussed with Curtis in Paris: next changes are imagej-omero side. Closing this.

comment:12 Changed 10 years ago by crueden-x

Thanks Josh, I filed ​https://github.com/imagej/imagej-omero/issues/46 to track this on the ImageJ-OMERO side.

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