[kepler-dev] Environment Variables

Tue Jun 10 12:56:51 PDT 2014

Hi Michal,

Thanks for your replies. I did some work on my code and together with
java's getenv() I made it all work.

Regards,
Slavisa

On Tue, Jun 10, 2014 at 12:34 PM, Michal Owsiak <michalo at man.poznan.pl>
wrote:

> Have you already tried accessing them as described here:
>
> http://docs.oracle.com/javase/tutorial/essential/environment/env.html
>
> Michal
>
>
>  Hi Michal,
>>
>> Basically we have our own actor that we use to execute commands either
>> locally or remotely using our own tools (Nimrod/G and Nimrod/K). The
>> problem is in those actors when I try to evaluate the expression which has
>> environment variable in it that is not part of the regular set (PATH, HOME
>> etc). Is there some way I can evaluate them programatically?
>>
>> I had to change the code so that the parameter mode is set to lazy
>> (command.setLazy(true)) because we try to build the environment from
>> incoming ports and such. If I could load the environment variable list and
>> parse it myself in the code I would do it. So do you have any idea how to
>> access it in code?
>>
>> Thanks in advance for your answers,
>> Slavisa
>>
>>
>> On Tue, Jun 10, 2014 at 12:11 PM, Michal Owsiak <michalo at man.poznan.pl>
>> wrote:
>>
>>  Is this something you are looking for (see attachment)
>>>
>>> Michal
>>>
>>>
>>>   That works fine. Can we use this somehow in External Execution actors?
>>> I
>>>
>>>> tried and failed.
>>>>
>>>> What we need is a way to use environment variables to locate
>>>> executables,
>>>> e.g. FSLDIR=/opt/local/bet, so that I can execute $FSLDIR/bin/bet. I
>>>> understand that if added to PATH these will be accessible by simply by
>>>> executing 'bet' but we'd still like to have access to environment
>>>> variables
>>>> to locate specific versions etc.
>>>>
>>>> Slavisa
>>>>
>>>>
>>>> On Tue, Jun 10, 2014 at 11:56 AM, Michal Owsiak <michalo at man.poznan.pl>
>>>> wrote:
>>>>
>>>>   Try following instead.
>>>>
>>>>>
>>>>> Inside expression actor use following:
>>>>>
>>>>> getenv("YOUR_VARIABLE_GOES_HERE")
>>>>>
>>>>> Michal
>>>>>
>>>>>
>>>>>    Hi,
>>>>>
>>>>>
>>>>>> Could someone explain to me if there is a bug or I am doing something
>>>>>> wrong
>>>>>> that my workflows can't access environment variables.
>>>>>>
>>>>>> I tried setting them up in usual ways (profile scripts) and by using
>>>>>> environment.txt but no actor has access to them.
>>>>>>
>>>>>> For example I tried setting up TESTVAR and then accessing it in
>>>>>> constant
>>>>>> actor but it raises an error as if it was not there. Top of the
>>>>>> exception
>>>>>> stack is just below.
>>>>>>
>>>>>> Regards,
>>>>>> Slavisa Garic
>>>>>> PS. I can see this being set with kepler-2.4.0/module-info/
>>>>>> environment.txt
>>>>>> when Kepler is launched by kepler.sh and I get messages such as
>>>>>>
>>>>>> ....
>>>>>> Set environment variable: TESTVAR = mymessage
>>>>>> Set environment variable: R_HOME = /Library/Frameworks/R.
>>>>>> framework/Resources
>>>>>> ....
>>>>>>
>>>>>>
>>>>>> ptolemy.kernel.util.IllegalActionException: Error evaluating
>>>>>> expression:
>>>>>>
>>>>>>   $TESTVAR
>>>>>>
>>>>>>>      in .Unnamed1.Constant.value
>>>>>>> Because:
>>>>>>> Error parsing expression "$TESTVAR"
>>>>>>> Because:
>>>>>>> Encountered "" at line 1, column 1.
>>>>>>> Was expecting one of:
>>>>>>>
>>>>>>> Because:
>>>>>>> Error evaluating expression: $TESTVAR
>>>>>>>      in .Unnamed1.Constant.value
>>>>>>> Because:
>>>>>>> Error parsing expression "$TESTVAR"
>>>>>>> Because:
>>>>>>> Encountered "" at line 1, column 1.
>>>>>>> Was expecting one of:
>>>>>>>
>>>>>>> at ptolemy.data.expr.Variable.validate(Variable.java:1491)
>>>>>>> at ptolemy.moml.MoMLParser.endDocument(MoMLParser.java:802)
>>>>>>> at com.microstar.xml.XmlParser.doParse(XmlParser.java:162)
>>>>>>> at com.microstar.xml.XmlParser.parse(XmlParser.java:132)
>>>>>>> at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1540)
>>>>>>> at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1512)
>>>>>>> at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1668)
>>>>>>> at ptolemy.moml.MoMLChangeRequest._execute(
>>>>>>> MoMLChangeRequest.java:289)
>>>>>>> at ptolemy.actor.gui.PtolemyQuery$3._execute(PtolemyQuery.java:824)
>>>>>>> at ptolemy.kernel.util.ChangeRequest.execute(ChangeRequest.java:171)
>>>>>>> at ptolemy.kernel.util.NamedObj._executeChangeRequests(
>>>>>>> NamedObj.java:2559)
>>>>>>> at ptolemy.kernel.util.NamedObj.executeChangeRequests(
>>>>>>> NamedObj.java:725)
>>>>>>> at ptolemy.kernel.util.NamedObj.requestChange(NamedObj.java:1776)
>>>>>>> at ptolemy.actor.CompositeActor.requestChange(CompositeActor.
>>>>>>> java:1957)
>>>>>>> at ptolemy.kernel.util.NamedObj.requestChange(NamedObj.java:1761)
>>>>>>> at ptolemy.actor.gui.PtolemyQuery.changed(PtolemyQuery.java:885)
>>>>>>> at ptolemy.gui.Query._notifyListeners(Query.java:1928)
>>>>>>> at ptolemy.gui.Query$QueryFocusListener.focusLost(Query.java:2515)
>>>>>>> at java.awt.AWTEventMulticaster.focusLost(AWTEventMulticaster.
>>>>>>> java:213)
>>>>>>> at java.awt.Component.processFocusEvent(Component.java:6306)
>>>>>>> at java.awt.Component.processEvent(Component.java:6170)
>>>>>>> at java.awt.Container.processEvent(Container.java:2084)
>>>>>>> at java.awt.Component.dispatchEventImpl(Component.java:4776)
>>>>>>> at java.awt.Container.dispatchEventImpl(Container.java:2142)
>>>>>>> at java.awt.Component.dispatchEvent(Component.java:4604)
>>>>>>> at
>>>>>>> java.awt.KeyboardFocusManager.redispatchEvent(
>>>>>>> KeyboardFocusManager.java:
>>>>>>> 1856)
>>>>>>> at
>>>>>>> java.awt.DefaultKeyboardFocusManager.typeAheadAssertions(
>>>>>>> DefaultKeyboardFocusManager.java:920)
>>>>>>> at
>>>>>>> java.awt.DefaultKeyboardFocusManager.dispatchEvent(
>>>>>>> DefaultKeyboardFocusManager.java:578)
>>>>>>>
>>>>>>>
>>>>>>>  .....
>>>>>>
>>>>>>   .....
>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
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>>>>>>
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>>>>
>>>
>>
>>
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