I suspect this is kind of a klugefest on my part, but I'm working with the Luigi and Sciluigi modules which set a number of critical parameters PRIOR to 'self' being returned by an init. ANd if I try to manhandle these parameters AFTER self is returned, the Luigi.Parameter object masks them in such a way that I cant do what I need to do.
The luigi and sciluigi classes (as one uses them) contain no __init__. And if I try to insert an __init__ or call super(ChildClass, self).__init__(*args, **kwargs) ...I get weird errors 'unexpected parameter' errors.
So a Sciluigi class looks like this...
class MyTask(sciluigi.task):
param1 = sciluigi.Parameter(default='Yes') #String only
param2 = sciluigi.Parameter(default='No') #String only
def out_target(self):
return sciluigi.TargetInfo(self, self.out)
def run(self):
with self.out_target().open('w') as foofile:
foofile.write('foo\n')
SO...I'm hoping I can dynamically set some parameters via setattr PRIOR to 'self' actually being returned. But setattr requires the object.
I was hoping I could do something like...
setattr(inspect.stack()[?][?], 'DynamicVar', sciluigi.Parameter(default='Yes') )
Well, I'm not sure what info would be most helpful.
First issue is; I can't add an init. The actual code is below, with an __init__method added. I've included the resulting error if I try to run it. Its the same error is if I tr to run the super call to __init__
class FileConverter(sciluigi.Task):
"""
"""
in_target = None # Mandatory
out = sciluigi.Parameter() # <file>
exepath = sciluigi.Parameter(default = "")
def __init__(self):
self.var = 'anything'
def out_target(self):
log.debug("In 'FileConverter.out_target'... ")
return sciluigi.TargetInfo(self, self.out)
def run(self):
result = None
command = ''.join([
self.exepath, _slash, "FileConverter ",
" -in ", self.in_target().path,
" -out ", self.out_target().path,
" -out_type ", self.file_type
])
log.info("RUNNING COMMAND: " + command)
result = self.ex(command)
log.info("result: " + result[1])
2017-02-24 17:01:48 | WARNING | Will not run MyWorkflow(instance_name=sciluigi_workflow) or any dependencies due to error in deps() method:
Traceback (most recent call last):
File "/Library/Python/2.7/site-packages/luigi/worker.py", line 697, in _add
deps = task.deps()
File "/Library/Python/2.7/site-packages/luigi/task.py", line 572, in deps
return flatten(self._requires())
File "/Library/Python/2.7/site-packages/luigi/task.py", line 544, in _requires
return flatten(self.requires()) # base impl
File "/Library/Python/2.7/site-packages/sciluigi/workflow.py", line 105, in requires
workflow_output = self.workflow()
File "/Users/mikes/Documents/Eclipseworkspace/Bioproximity/OpenMS-Python-Luigi/site-packages/Bioproximity/sciluigi_tasks/PipelineTest1.py", line 33, in workflow
exepath = "/Applications/OpenMS-2.1.0/TOPP"
File "/Library/Python/2.7/site-packages/sciluigi/workflow.py", line 145, in new_task
newtask = sciluigi.new_task(instance_name, cls, self, **kwargs)
File "/Library/Python/2.7/site-packages/sciluigi/task.py", line 37, in new_task
newtask = cls.from_str_params(kwargs)
File "/Library/Python/2.7/site-packages/luigi/task.py", line 412, in from_str_params
return cls(**kwargs)
File "/Library/Python/2.7/site-packages/luigi/task_register.py", line 99, in __call__
h[k] = instantiate()
File "/Library/Python/2.7/site-packages/luigi/task_register.py", line 80, in instantiate
return super(Register, cls).__call__(*args, **kwargs)
TypeError: __init__() got an unexpected keyword argument 'instance_name'
If I wait for self to return, I can no longer differentiate between (for example using the above code)...
in_target = None # Mandatory
out = sciluigi.Parameter() # <file>
If I do a type(out), type reports that the parameter is just a string (not a sciluigi.Parameter object) so if I try to use a `ìsinstance(out, sciluigi.Parameter)...it returns False.
I need to be able to set the sciluigi.Parameter objects dynamically (programatically) and subsequently be able to differentiate between a sciluigi.Parameter() object variable (like out) and a 'real' str() object (like in_target)
I hope this makes sense.
Just for future reference, the answer to the isolated question, "How to...
setattr(<thisClassObject>, 'DynamicVar', sciluigi.Parameter(default='Yes') )
Is to use the locals() built in function. I.e.
locals()['DynamicVar'] = sciluigi.Parameter(default='Yes') #String only
This is a snippet of how I solved my particular kluge ;)
import sciluigi
class MyFooWriter(sciluigi.Task):
locals()['outfile'] = sciluigi.Parameter(default='./foo.txt') #String only
locals()['normalvar'] = 'Normalstring'
print "pre-self-returned outfile type =", type(outfile)
print "pre-self-returned normalvar type =", type(normalvar)
# locals()['param1'] =
def out_foo(self):
# raw_input("Enter...")
return sciluigi.TargetInfo(self, self.outfile)
def run(self):
print "self.outfile type =", type(self.outfile)
print "self.normalvar type =", type(self.normalvar)
# raw_input("Enter...")
with self.out_foo().open('w') as foofile:
foofile.write('foo\n')
class MyWorkflow(sciluigi.WorkflowTask):
def workflow(self):
print 'Starting workflow...'
foowriter = self.new_task('foowriter', MyFooWriter, outfile = 'testfile.txt')
return foowriter
if __name__ == '__main__':
sciluigi.run_local(main_task_cls=MyWorkflow)
pre-self-returned outfile type = <class 'sciluigi.parameter.Parameter'>
pre-self-returned normalvar type = <type 'str'>
Starting workflow...
2017-02-27 12:08:37 | INFO | --------------------------------------------------------------------------------
2017-02-27 12:08:37 | INFO | SciLuigi: MyWorkflow Workflow Started (logging to log/workflow_myworkflow_started_20170227_110837_278707.log)
2017-02-27 12:08:37 | INFO | --------------------------------------------------------------------------------
2017-02-27 12:08:37 | INFO | Task foowriter started
self.outfile type = <type 'str'>
self.normalvar type = <type 'str'>
2017-02-27 12:08:37 | INFO | Task foowriter finished after 0.001s
Starting workflow...
2017-02-27 12:08:37 | INFO | --------------------------------------------------------------------------------
2017-02-27 12:08:37 | INFO | SciLuigi: MyWorkflow Workflow Finished (workflow log at log/workflow_myworkflow_started_20170227_110837_278707.log)
2017-02-27 12:08:37 | INFO | --------------------------------------------------------------------------------