[kepler-dev] Environment Variables

Tue Jun 10 03:34:01 PDT 2014

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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>>>>> Kepler-dev at kepler-project.org
>>>>> http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-dev
>>>>>
>>>>>
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>>>>
>>>
>>
>
>
>
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