Bug: Scripts CLI inputs

[wmoore]

default=True

If I have a script with a Bool parameter like this:

    scripts.Bool("Use_All_Timepoints", default=True)

And in the script launch command I use 'False', printing out the unwrapped script parameters gives me 'True'...

wjm:scripts will$ omero script launch 1055 IDs=601 Use_All_Timepoints=False
Using session 0183460d-3f73-4448-91ee-78969b37d806 (will@localhost:4064). Idle timeout: 10.0 min. Current group: JRS-collab
Job 719 ready
Waiting....
Callback received: FINISHED

	*** start stdout ***
	* {'Line_Width': 4, 'Use_All_Timepoints': True, 'IDs': [601L], 'Data_Type': 'Image'}

Int to Float

I have a parameter where I want a list of ints:

    scripts.List("Channels", grouping="4",
        description="List of Channels to process. E.g 1, 2").ofType(rint(0)),

But when I pass integers in the command line OR via Insight, I get these converted to Floats:

jrs-macbookpro-25107:scripts will$ omero script launch 559 IDs=158 Channels=1,4
Using session ea00a81e-13e3-40c1-99d9-85c6d5037096 (will@localhost:4064). Idle timeout: 10.0 min. Current group: Swedlow lab
Job 268 ready
Waiting....
Callback received: FINISHED

	*** start stdout ***
	* {'Channels': [1.0, 4.0], 'Line_Width': 1, 'IDs': [158L], 'Data_Type': 'Image'}

[wmoore]

Adding Int -> Float bug to this ticket, since it covers the same issues. NB: Noticed this from Insight too (not just CLI)

[jmoore]

Will, I've pushed this to ​https://github.com/joshmoore/openmicroscopy/tree/7003-scripts can you review?

I've fixed the boolean issue. You might want to take a look at the test case and see if there are any other specific values you'd like to have parsed to "false".

For the channel int list to float issue, I can't reproduce. Neither with the test nor with the command-line:

~/git/dist $ bin/omero script launch 567 Channels=1,4
Using session 777fa5d6-39ee-4a2e-90b8-aa2d2cbd7e46 (root@localhost:4064). Idle timeout: 10.0 min. Current group: system
Job 317 ready
Waiting....
Callback received: FINISHED

	*** start stdout ***
	* {'Channels': [1, 4], 'Use_All_Timepoints': True}
	* 
	*** end stdout ***


	*** out parameters ***
	***  done ***

~/git/dist $ cat lib/scripts/7003.py 
import omero
import omero.scripts as scripts


def runAsScript():
    client = scripts.client('7003.py',
        """Test various param types which seem to be failing""",
    scripts.Bool("Use_All_Timepoints", default=True),
    scripts.List("Channels").ofType(omero.rtypes.rint(0)),
    version="4.3.3",
    authors=["Josh Moore", "OME Team"],
    institutions=["Glencoe Software, Inc."],
    contact="ome-users@lists.openmicroscopy.org.uk",
    )

    try:
        parameterMap = {}
        for key in client.getInputKeys():
            if client.getInput(key):
                parameterMap[key] = client.getInput(key, unwrap=True)
        print parameterMap

    finally:
        client.closeSession()

if __name__ == "__main__":
    runAsScript()

If you could find a way to reproduce, that'd be great.

[wmoore]

OK, the rint -> rfloat issue is NOT a bug. It just turns out that numpy.rint is not the same as omero.model.rint! ;)

>>> from numpy import *
>>> rint
<ufunc 'rint'>

The default=True bug seems to be fixed.

[wmoore]

Josh - do you know if your 7003-scripts branch got merged into develop?
Just cleaning up my local branches and couldn't be sure that it had.

Cheers.

[jmoore]

Will, nope, didn't go in. Does that mean your ok with a PR for it?

[wmoore]

I haven't tested recently, but from the comments above I'd say it's good to go.

Cheers

[jmoore <josh@…>]

(In [d1fc0e3e9e065fe1a08af46f883fc22df2001840/ome.git] on branch develop) Parse rbool specially (See #7003)

[jmoore <josh@…>]

(In [1f431f0bfe787bb836f72cfbcbcf90de9da48280/ome.git] on branch develop) Passing test for list of rints (See #7003)