def __init__(self, cmd, *args, **kargs):
if isinstance(cmd, unicode):
self.name = str(cmd)
elif isinstance(cmd, str):
self.name = cmd
else:
raise GrassError("Problem initializing the module {s}".format(s=cmd))
try:
# call the command with --interface-description
get_cmd_xml = Popen([cmd, "--interface-description"], stdout=PIPE)
except OSError as e:
print("OSError error({0}): {1}".format(e.errno, e.strerror))
str_err = "Error running: `%s --interface-description`."
raise GrassError(str_err % self.name)
# get the xml of the module
self.xml = get_cmd_xml.communicate()[0]
# transform and parse the xml into an Element class:
# http://docs.python.org/library/xml.etree.elementtree.html
tree = fromstring(self.xml)
for e in tree:
if e.tag not in ('parameter', 'flag'):
self.__setattr__(e.tag, GETFROMTAG[e.tag](e))
#
# extract parameters from the xml
#
self.params_list = [Parameter(p) for p in tree.findall("parameter")]
self.inputs = TypeDict(Parameter)
self.outputs = TypeDict(Parameter)
self.required = []
# Insert parameters into input/output and required
for par in self.params_list:
if par.input:
self.inputs[par.name] = par
else:
self.outputs[par.name] = par
if par.required:
self.required.append(par.name)
#
# extract flags from the xml
#
flags_list = [Flag(f) for f in tree.findall("flag")]
self.flags = TypeDict(Flag)
for flag in flags_list:
self.flags[flag.name] = flag
#
# Add new attributes to the class
#
self.run_ = True
self.finish_ = True
self.env_ = None
self.stdin_ = None
self.stdin = None
self.stdout_ = None
self.stderr_ = None
diz = {'name': 'stdin', 'required': False,
'multiple': False, 'type': 'all',
'value': None}
self.inputs['stdin'] = Parameter(diz=diz)
diz['name'] = 'stdout'
self.outputs['stdout'] = Parameter(diz=diz)
diz['name'] = 'stderr'
self.outputs['stderr'] = Parameter(diz=diz)
self.popen = None
self.time = None
if args or kargs:
self.__call__(*args, **kargs)
self.__call__.__func__.__doc__ = self.__doc__
def __init__(self, cmd, *args, **kargs):
if isinstance(cmd, unicode):
self.name = str(cmd)
elif isinstance(cmd, str):
self.name = cmd
else:
raise GrassError(
"Problem initializing the module {s}".format(s=cmd))
try:
# call the command with --interface-description
get_cmd_xml = Popen([cmd, "--interface-description"], stdout=PIPE)
except OSError as e:
print("OSError error({0}): {1}".format(e.errno, e.strerror))
str_err = "Error running: `%s --interface-description`."
raise GrassError(str_err % self.name)
# get the xml of the module
self.xml = get_cmd_xml.communicate()[0]
# transform and parse the xml into an Element class:
# http://docs.python.org/library/xml.etree.elementtree.html
tree = fromstring(self.xml)
for e in tree:
if e.tag not in ('parameter', 'flag'):
self.__setattr__(e.tag, GETFROMTAG[e.tag](e))
#
# extract parameters from the xml
#
self.params_list = [Parameter(p) for p in tree.findall("parameter")]
self.inputs = TypeDict(Parameter)
self.outputs = TypeDict(Parameter)
self.required = []
# Insert parameters into input/output and required
for par in self.params_list:
if par.input:
self.inputs[par.name] = par
else:
self.outputs[par.name] = par
if par.required:
self.required.append(par.name)
#
# extract flags from the xml
#
flags_list = [Flag(f) for f in tree.findall("flag")]
self.flags = TypeDict(Flag)
for flag in flags_list:
self.flags[flag.name] = flag
#
# Add new attributes to the class
#
self.run_ = True
self.finish_ = True
self.env_ = None
self.stdin_ = None
self.stdin = None
self.stdout_ = None
self.stderr_ = None
diz = {
'name': 'stdin',
'required': False,
'multiple': False,
'type': 'all',
'value': None
}
self.inputs['stdin'] = Parameter(diz=diz)
diz['name'] = 'stdout'
self.outputs['stdout'] = Parameter(diz=diz)
diz['name'] = 'stderr'
self.outputs['stderr'] = Parameter(diz=diz)
self.popen = None
self.time = None
if args or kargs:
self.__call__(*args, **kargs)
self.__call__.__func__.__doc__ = self.__doc__
class Module(object):
"""This class is design to wrap/run/interact with the GRASS modules.
The class during the init phase read the XML description generate using
the ``--interface-description`` in order to understand which parameters
are required which optionals. ::
>>> from grass.pygrass.modules import Module
>>> from subprocess import PIPE
>>> import copy
>>> region = Module("g.region")
>>> region.flags.p = True # set flags
>>> region.flags.u = True
>>> region.flags["3"].value = True # set numeric flags
>>> region.get_bash()
u'g.region -p -3 -u'
>>> new_region = copy.deepcopy(region)
>>> new_region.inputs.res = "10"
>>> new_region.get_bash()
u'g.region res=10 -p -3 -u'
>>> neighbors = Module("r.neighbors")
>>> neighbors.inputs.input = "mapA"
>>> neighbors.outputs.output = "mapB"
>>> neighbors.inputs.size = 5
>>> neighbors.inputs.quantile = 0.5
>>> neighbors.get_bash()
u'r.neighbors input=mapA method=average size=5 quantile=0.5 output=mapB'
>>> new_neighbors1 = copy.deepcopy(neighbors)
>>> new_neighbors1.inputs.input = "mapD"
>>> new_neighbors1.inputs.size = 3
>>> new_neighbors1.inputs.quantile = 0.5
>>> new_neighbors1.get_bash()
u'r.neighbors input=mapD method=average size=3 quantile=0.5 output=mapB'
>>> new_neighbors2 = copy.deepcopy(neighbors)
>>> new_neighbors2(input="mapD", size=3, run_=False)
Module('r.neighbors')
>>> new_neighbors2.get_bash()
u'r.neighbors input=mapD method=average size=3 quantile=0.5 output=mapB'
>>> neighbors = Module("r.neighbors")
>>> neighbors.get_bash()
u'r.neighbors method=average size=3'
>>> new_neighbors3 = copy.deepcopy(neighbors)
>>> new_neighbors3(input="mapA", size=3, output="mapB", run_=False)
Module('r.neighbors')
>>> new_neighbors3.get_bash()
u'r.neighbors input=mapA method=average size=3 output=mapB'
>>> mapcalc = Module("r.mapcalc", expression="test_a = 1",
... overwrite=True, run_=False)
>>> mapcalc.run()
Module('r.mapcalc')
>>> mapcalc.popen.returncode
0
>>> colors = Module("r.colors", map="test_a", rules="-",
... run_=False, stdout_=PIPE,
... stderr_=PIPE, stdin_="1 red")
>>> colors.run()
Module('r.colors')
>>> colors.popen.returncode
0
>>> colors.inputs["stdin"].value
u'1 red'
>>> colors.outputs["stdout"].value
u''
>>> colors.outputs["stderr"].value.strip()
"Color table for raster map <test_a> set to 'rules'"
>>> colors = Module("r.colors", map="test_a", rules="-",
... run_=False, finish_=False, stdin_=PIPE)
>>> colors.run()
Module('r.colors')
>>> stdout, stderr = colors.popen.communicate(input="1 red")
>>> colors.popen.returncode
0
>>> stdout
>>> stderr
>>> colors = Module("r.colors", map="test_a", rules="-",
... run_=False, finish_=False,
... stdin_=PIPE, stderr_=PIPE)
>>> colors.run()
Module('r.colors')
>>> stdout, stderr = colors.popen.communicate(input="1 red")
>>> colors.popen.returncode
0
>>> stdout
>>> stderr.strip()
"Color table for raster map <test_a> set to 'rules'"
Run a second time
>>> colors.run()
Module('r.colors')
>>> stdout, stderr = colors.popen.communicate(input="1 blue")
>>> colors.popen.returncode
0
>>> stdout
>>> stderr.strip()
"Color table for raster map <test_a> set to 'rules'"
Multiple run test
>>> colors = Module("r.colors", map="test_a",
... color="ryb", run_=False)
>>> colors.run()
Module('r.colors')
>>> colors(color="gyr")
Module('r.colors')
>>> colors.run()
Module('r.colors')
>>> colors(color="ryg")
Module('r.colors')
>>> colors(stderr_=PIPE)
Module('r.colors')
>>> colors.run()
Module('r.colors')
>>> print(colors.outputs["stderr"].value.strip())
Color table for raster map <test_a> set to 'ryg'
>>> colors(color="byg")
Module('r.colors')
>>> colors(stdout_=PIPE)
Module('r.colors')
>>> colors.run()
Module('r.colors')
>>> print(colors.outputs["stderr"].value.strip())
Color table for raster map <test_a> set to 'byg'
Often in the Module class you can find ``*args`` and ``kwargs`` annotation
in methods, like in the __call__ method.
Python allow developers to not specify all the arguments and
keyword arguments of a method or function. ::
def f(*args):
for arg in args:
print arg
therefore if we call the function like:
>>> f('grass', 'gis', 'modules') # doctest: +SKIP
grass
gis
modules
or we can define a new list:
>>> words = ['grass', 'gis', 'modules'] # doctest: +SKIP
>>> f(*words) # doctest: +SKIP
grass
gis
modules
we can do the same with keyword arguments, rewrite the above function: ::
def f(*args, **kargs):
for arg in args:
print arg
for key, value in kargs.items():
print "%s = %r" % (key, value)
now we can use the new function, with:
>>> f('grass', 'gis', 'modules', os = 'linux', language = 'python')
... # doctest: +SKIP
grass
gis
modules
os = 'linux'
language = 'python'
or, as before we can, define a dictionary and give the dictionary to
the function, like:
>>> keywords = {'os' : 'linux', 'language' : 'python'} # doctest: +SKIP
>>> f(*words, **keywords) # doctest: +SKIP
grass
gis
modules
os = 'linux'
language = 'python'
In the Module class we heavily use this language feature to pass arguments
and keyword arguments to the grass module.
"""
def __init__(self, cmd, *args, **kargs):
if isinstance(cmd, unicode):
self.name = str(cmd)
elif isinstance(cmd, str):
self.name = cmd
else:
raise GrassError("Problem initializing the module {s}".format(s=cmd))
try:
# call the command with --interface-description
get_cmd_xml = Popen([cmd, "--interface-description"], stdout=PIPE)
except OSError as e:
print("OSError error({0}): {1}".format(e.errno, e.strerror))
str_err = "Error running: `%s --interface-description`."
raise GrassError(str_err % self.name)
# get the xml of the module
self.xml = get_cmd_xml.communicate()[0]
# transform and parse the xml into an Element class:
# http://docs.python.org/library/xml.etree.elementtree.html
tree = fromstring(self.xml)
for e in tree:
if e.tag not in ('parameter', 'flag'):
self.__setattr__(e.tag, GETFROMTAG[e.tag](e))
#
# extract parameters from the xml
#
self.params_list = [Parameter(p) for p in tree.findall("parameter")]
self.inputs = TypeDict(Parameter)
self.outputs = TypeDict(Parameter)
self.required = []
# Insert parameters into input/output and required
for par in self.params_list:
if par.input:
self.inputs[par.name] = par
else:
self.outputs[par.name] = par
if par.required:
self.required.append(par.name)
#
# extract flags from the xml
#
flags_list = [Flag(f) for f in tree.findall("flag")]
self.flags = TypeDict(Flag)
for flag in flags_list:
self.flags[flag.name] = flag
#
# Add new attributes to the class
#
self.run_ = True
self.finish_ = True
self.env_ = None
self.stdin_ = None
self.stdin = None
self.stdout_ = None
self.stderr_ = None
diz = {'name': 'stdin', 'required': False,
'multiple': False, 'type': 'all',
'value': None}
self.inputs['stdin'] = Parameter(diz=diz)
diz['name'] = 'stdout'
self.outputs['stdout'] = Parameter(diz=diz)
diz['name'] = 'stderr'
self.outputs['stderr'] = Parameter(diz=diz)
self.popen = None
self.time = None
if args or kargs:
self.__call__(*args, **kargs)
self.__call__.__func__.__doc__ = self.__doc__
def __call__(self, *args, **kargs):
"""Set module paramters to the class and, if run_ is True execute the
module, therefore valid parameters are all the module parameters
plus some extra parameters that are: run_, stdin_, stdout_, stderr_,
env_ and finish_.
"""
if not args and not kargs:
self.run()
return self
#
# check for extra kargs, set attribute and remove from dictionary
#
if 'flags' in kargs:
for flg in kargs['flags']:
self.flags[flg].value = True
del(kargs['flags'])
# set attributs
for key in ('run_', 'env_', 'finish_', 'stdout_', 'stderr_'):
if key in kargs:
setattr(self, key, kargs.pop(key))
# set inputs
for key in ('stdin_', ):
if key in kargs:
self.inputs[key[:-1]].value = kargs.pop(key)
#
# check args
#
for param, arg in zip(self.params_list, args):
param.value = arg
for key, val in kargs.items():
if key in self.inputs:
self.inputs[key].value = val
elif key in self.outputs:
self.outputs[key].value = val
elif key in self.flags:
# we need to add this, because some parameters (overwrite,
# verbose and quiet) work like parameters
self.flags[key].value = val
else:
raise ParameterError('%s is not a valid parameter.' % key)
#
# check if execute
#
if self.run_:
#
# check reqire parameters
#
for k in self.required:
if ((k in self.inputs and self.inputs[k].value is None) or
(k in self.outputs and self.outputs[k].value is None)):
msg = "Required parameter <%s> not set."
raise ParameterError(msg % k)
return self.run()
return self
def get_bash(self):
"""Return a BASH rapresentation of the Module."""
return ' '.join(self.make_cmd())
def get_python(self):
"""Return a Python rapresentation of the Module."""
prefix = self.name.split('.')[0]
name = '_'.join(self.name.split('.')[1:])
params = ', '.join([par.get_python() for par in self.params_list
if par.get_python() != ''])
flags = ''.join([flg.get_python()
for flg in self.flags.values()
if not flg.special and flg.get_python() != ''])
special = ', '.join([flg.get_python()
for flg in self.flags.values()
if flg.special and flg.get_python() != ''])
# pre name par flg special
if flags and special:
return "%s.%s(%s, flags=%r, %s)" % (prefix, name, params,
flags, special)
elif flags:
return "%s.%s(%s, flags=%r)" % (prefix, name, params, flags)
elif special:
return "%s.%s(%s, %s)" % (prefix, name, params, special)
else:
return "%s.%s(%s)" % (prefix, name, params)
def __str__(self):
"""Return the command string that can be executed in a shell"""
return ' '.join(self.make_cmd())
def __repr__(self):
return "Module(%r)" % self.name
@docstring_property(__doc__)
def __doc__(self):
"""{cmd_name}({cmd_params})
"""
head = DOC['head'].format(cmd_name=self.name,
cmd_params=('\n' + # go to a new line
# give space under the function name
(' ' * (len(self.name) + 1))).join([', '.join(
# transform each parameter in string
[str(param) for param in line if param is not None])
# make a list of parameters with only 3 param per line
for line in zip_longest(*[iter(self.params_list)] * 3)]),)
params = '\n'.join([par.__doc__ for par in self.params_list])
flags = self.flags.__doc__
return '\n'.join([head, params, DOC['flag_head'], flags, DOC['foot']])
def get_dict(self):
"""Return a dictionary that includes the name, all valid
inputs, outputs and flags
"""
dic = {}
dic['name'] = self.name
dic['inputs'] = [(k, v.value) for k, v in self.inputs.items()
if v.value]
dic['outputs'] = [(k, v.value) for k, v in self.outputs.items()
if v.value]
dic['flags'] = [flg for flg in self.flags if self.flags[flg].value]
return dic
def make_cmd(self):
"""Create the command string that can be executed in a shell
:returns: the command string
"""
skip = ['stdin', 'stdout', 'stderr']
args = [self.name, ]
for key in self.inputs:
if key not in skip and self.inputs[key].value:
args.append(self.inputs[key].get_bash())
for key in self.outputs:
if key not in skip and self.outputs[key].value:
args.append(self.outputs[key].get_bash())
for flg in self.flags:
if self.flags[flg].value:
args.append(str(self.flags[flg]))
return args
@mdebug(1, extra=_get_bash)
def run(self):
"""Run the module
:param node:
:type node:
This function will wait for the process to terminate in case
finish_==True and sets up stdout and stderr. If finish_==False this
function will return after starting the process. Use
self.popen.communicate() of self.popen.wait() to wait for the process
termination. The handling of stdout and stderr must then be done
outside of this function.
"""
if self.inputs['stdin'].value:
self.stdin = self.inputs['stdin'].value
self.stdin_ = PIPE
cmd = self.make_cmd()
start = time.time()
self.popen = Popen(cmd,
stdin=self.stdin_,
stdout=self.stdout_,
stderr=self.stderr_,
env=self.env_)
if self.finish_:
stdout, stderr = self.popen.communicate(input=self.stdin)
self.outputs['stdout'].value = stdout if stdout else ''
self.outputs['stderr'].value = stderr if stderr else ''
self.time = time.time() - start
if self.popen.poll():
raise CalledModuleError(returncode=self.popen.returncode,
code=self.get_bash(),
module=self.name, errors=stderr)
return self
class Module(object):
"""This class is design to wrap/run/interact with the GRASS modules.
The class during the init phase read the XML description generate using
the ``--interface-description`` in order to understand which parameters
are required which optionals. ::
>>> from grass.pygrass.modules import Module
>>> from subprocess import PIPE
>>> import copy
>>> region = Module("g.region")
>>> region.flags.p = True # set flags
>>> region.flags.u = True
>>> region.flags["3"].value = True # set numeric flags
>>> region.get_bash()
u'g.region -p -3 -u'
>>> new_region = copy.deepcopy(region)
>>> new_region.inputs.res = "10"
>>> new_region.get_bash()
u'g.region res=10 -p -3 -u'
>>> neighbors = Module("r.neighbors")
>>> neighbors.inputs.input = "mapA"
>>> neighbors.outputs.output = "mapB"
>>> neighbors.inputs.size = 5
>>> neighbors.inputs.quantile = 0.5
>>> neighbors.get_bash()
u'r.neighbors input=mapA method=average size=5 quantile=0.5 output=mapB'
>>> new_neighbors1 = copy.deepcopy(neighbors)
>>> new_neighbors1.inputs.input = "mapD"
>>> new_neighbors1.inputs.size = 3
>>> new_neighbors1.inputs.quantile = 0.5
>>> new_neighbors1.get_bash()
u'r.neighbors input=mapD method=average size=3 quantile=0.5 output=mapB'
>>> new_neighbors2 = copy.deepcopy(neighbors)
>>> new_neighbors2(input="mapD", size=3, run_=False)
Module('r.neighbors')
>>> new_neighbors2.get_bash()
u'r.neighbors input=mapD method=average size=3 quantile=0.5 output=mapB'
>>> neighbors = Module("r.neighbors")
>>> neighbors.get_bash()
u'r.neighbors method=average size=3'
>>> new_neighbors3 = copy.deepcopy(neighbors)
>>> new_neighbors3(input="mapA", size=3, output="mapB", run_=False)
Module('r.neighbors')
>>> new_neighbors3.get_bash()
u'r.neighbors input=mapA method=average size=3 output=mapB'
>>> mapcalc = Module("r.mapcalc", expression="test_a = 1",
... overwrite=True, run_=False)
>>> mapcalc.run()
Module('r.mapcalc')
>>> mapcalc.popen.returncode
0
>>> colors = Module("r.colors", map="test_a", rules="-",
... run_=False, stdout_=PIPE,
... stderr_=PIPE, stdin_="1 red")
>>> colors.run()
Module('r.colors')
>>> colors.popen.returncode
0
>>> colors.inputs["stdin"].value
u'1 red'
>>> colors.outputs["stdout"].value
u''
>>> colors.outputs["stderr"].value.strip()
"Color table for raster map <test_a> set to 'rules'"
>>> colors = Module("r.colors", map="test_a", rules="-",
... run_=False, finish_=False, stdin_=PIPE)
>>> colors.run()
Module('r.colors')
>>> stdout, stderr = colors.popen.communicate(input="1 red")
>>> colors.popen.returncode
0
>>> stdout
>>> stderr
>>> colors = Module("r.colors", map="test_a", rules="-",
... run_=False, finish_=False,
... stdin_=PIPE, stderr_=PIPE)
>>> colors.run()
Module('r.colors')
>>> stdout, stderr = colors.popen.communicate(input="1 red")
>>> colors.popen.returncode
0
>>> stdout
>>> stderr.strip()
"Color table for raster map <test_a> set to 'rules'"
Run a second time
>>> colors.run()
Module('r.colors')
>>> stdout, stderr = colors.popen.communicate(input="1 blue")
>>> colors.popen.returncode
0
>>> stdout
>>> stderr.strip()
"Color table for raster map <test_a> set to 'rules'"
Multiple run test
>>> colors = Module("r.colors", map="test_a",
... color="ryb", run_=False)
>>> colors.run()
Module('r.colors')
>>> colors(color="gyr")
Module('r.colors')
>>> colors.run()
Module('r.colors')
>>> colors(color="ryg")
Module('r.colors')
>>> colors(stderr_=PIPE)
Module('r.colors')
>>> colors.run()
Module('r.colors')
>>> print(colors.outputs["stderr"].value.strip())
Color table for raster map <test_a> set to 'ryg'
>>> colors(color="byg")
Module('r.colors')
>>> colors(stdout_=PIPE)
Module('r.colors')
>>> colors.run()
Module('r.colors')
>>> print(colors.outputs["stderr"].value.strip())
Color table for raster map <test_a> set to 'byg'
Often in the Module class you can find ``*args`` and ``kwargs`` annotation
in methods, like in the __call__ method.
Python allow developers to not specify all the arguments and
keyword arguments of a method or function. ::
def f(*args):
for arg in args:
print arg
therefore if we call the function like:
>>> f('grass', 'gis', 'modules') # doctest: +SKIP
grass
gis
modules
or we can define a new list:
>>> words = ['grass', 'gis', 'modules'] # doctest: +SKIP
>>> f(*words) # doctest: +SKIP
grass
gis
modules
we can do the same with keyword arguments, rewrite the above function: ::
def f(*args, **kargs):
for arg in args:
print arg
for key, value in kargs.items():
print "%s = %r" % (key, value)
now we can use the new function, with:
>>> f('grass', 'gis', 'modules', os = 'linux', language = 'python')
... # doctest: +SKIP
grass
gis
modules
os = 'linux'
language = 'python'
or, as before we can, define a dictionary and give the dictionary to
the function, like:
>>> keywords = {'os' : 'linux', 'language' : 'python'} # doctest: +SKIP
>>> f(*words, **keywords) # doctest: +SKIP
grass
gis
modules
os = 'linux'
language = 'python'
In the Module class we heavily use this language feature to pass arguments
and keyword arguments to the grass module.
"""
def __init__(self, cmd, *args, **kargs):
if isinstance(cmd, unicode):
self.name = str(cmd)
elif isinstance(cmd, str):
self.name = cmd
else:
raise GrassError(
"Problem initializing the module {s}".format(s=cmd))
try:
# call the command with --interface-description
get_cmd_xml = Popen([cmd, "--interface-description"], stdout=PIPE)
except OSError as e:
print("OSError error({0}): {1}".format(e.errno, e.strerror))
str_err = "Error running: `%s --interface-description`."
raise GrassError(str_err % self.name)
# get the xml of the module
self.xml = get_cmd_xml.communicate()[0]
# transform and parse the xml into an Element class:
# http://docs.python.org/library/xml.etree.elementtree.html
tree = fromstring(self.xml)
for e in tree:
if e.tag not in ('parameter', 'flag'):
self.__setattr__(e.tag, GETFROMTAG[e.tag](e))
#
# extract parameters from the xml
#
self.params_list = [Parameter(p) for p in tree.findall("parameter")]
self.inputs = TypeDict(Parameter)
self.outputs = TypeDict(Parameter)
self.required = []
# Insert parameters into input/output and required
for par in self.params_list:
if par.input:
self.inputs[par.name] = par
else:
self.outputs[par.name] = par
if par.required:
self.required.append(par.name)
#
# extract flags from the xml
#
flags_list = [Flag(f) for f in tree.findall("flag")]
self.flags = TypeDict(Flag)
for flag in flags_list:
self.flags[flag.name] = flag
#
# Add new attributes to the class
#
self.run_ = True
self.finish_ = True
self.env_ = None
self.stdin_ = None
self.stdin = None
self.stdout_ = None
self.stderr_ = None
diz = {
'name': 'stdin',
'required': False,
'multiple': False,
'type': 'all',
'value': None
}
self.inputs['stdin'] = Parameter(diz=diz)
diz['name'] = 'stdout'
self.outputs['stdout'] = Parameter(diz=diz)
diz['name'] = 'stderr'
self.outputs['stderr'] = Parameter(diz=diz)
self.popen = None
self.time = None
if args or kargs:
self.__call__(*args, **kargs)
self.__call__.__func__.__doc__ = self.__doc__
def __call__(self, *args, **kargs):
"""Set module paramters to the class and, if run_ is True execute the
module, therefore valid parameters are all the module parameters
plus some extra parameters that are: run_, stdin_, stdout_, stderr_,
env_ and finish_.
"""
if not args and not kargs:
self.run()
return self
#
# check for extra kargs, set attribute and remove from dictionary
#
if 'flags' in kargs:
for flg in kargs['flags']:
self.flags[flg].value = True
del (kargs['flags'])
# set attributs
for key in ('run_', 'env_', 'finish_', 'stdout_', 'stderr_'):
if key in kargs:
setattr(self, key, kargs.pop(key))
# set inputs
for key in ('stdin_', ):
if key in kargs:
self.inputs[key[:-1]].value = kargs.pop(key)
#
# check args
#
for param, arg in zip(self.params_list, args):
param.value = arg
for key, val in kargs.items():
if key in self.inputs:
self.inputs[key].value = val
elif key in self.outputs:
self.outputs[key].value = val
elif key in self.flags:
# we need to add this, because some parameters (overwrite,
# verbose and quiet) work like parameters
self.flags[key].value = val
else:
raise ParameterError('%s is not a valid parameter.' % key)
#
# check if execute
#
if self.run_:
#
# check reqire parameters
#
for k in self.required:
if ((k in self.inputs and self.inputs[k].value is None) or
(k in self.outputs and self.outputs[k].value is None)):
msg = "Required parameter <%s> not set."
raise ParameterError(msg % k)
return self.run()
return self
def get_bash(self):
"""Return a BASH rapresentation of the Module."""
return ' '.join(self.make_cmd())
def get_python(self):
"""Return a Python rapresentation of the Module."""
prefix = self.name.split('.')[0]
name = '_'.join(self.name.split('.')[1:])
params = ', '.join([
par.get_python() for par in self.params_list
if par.get_python() != ''
])
flags = ''.join([
flg.get_python() for flg in self.flags.values()
if not flg.special and flg.get_python() != ''
])
special = ', '.join([
flg.get_python() for flg in self.flags.values()
if flg.special and flg.get_python() != ''
])
# pre name par flg special
if flags and special:
return "%s.%s(%s, flags=%r, %s)" % (prefix, name, params, flags,
special)
elif flags:
return "%s.%s(%s, flags=%r)" % (prefix, name, params, flags)
elif special:
return "%s.%s(%s, %s)" % (prefix, name, params, special)
else:
return "%s.%s(%s)" % (prefix, name, params)
def __str__(self):
"""Return the command string that can be executed in a shell"""
return ' '.join(self.make_cmd())
def __repr__(self):
return "Module(%r)" % self.name
@docstring_property(__doc__)
def __doc__(self):
"""{cmd_name}({cmd_params})
"""
head = DOC['head'].format(
cmd_name=self.name,
cmd_params=(
'\n' + # go to a new line
# give space under the function name
(' ' * (len(self.name) + 1))).join([
', '.join(
# transform each parameter in string
[str(param) for param in line if param is not None])
# make a list of parameters with only 3 param per line
for line in zip_longest(*[iter(self.params_list)] * 3)
]),
)
params = '\n'.join([par.__doc__ for par in self.params_list])
flags = self.flags.__doc__
return '\n'.join([head, params, DOC['flag_head'], flags, DOC['foot']])
def get_dict(self):
"""Return a dictionary that includes the name, all valid
inputs, outputs and flags
"""
dic = {}
dic['name'] = self.name
dic['inputs'] = [(k, v.value) for k, v in self.inputs.items()
if v.value]
dic['outputs'] = [(k, v.value) for k, v in self.outputs.items()
if v.value]
dic['flags'] = [flg for flg in self.flags if self.flags[flg].value]
return dic
def make_cmd(self):
"""Create the command string that can be executed in a shell
:returns: the command string
"""
skip = ['stdin', 'stdout', 'stderr']
args = [
self.name,
]
for key in self.inputs:
if key not in skip and self.inputs[key].value:
args.append(self.inputs[key].get_bash())
for key in self.outputs:
if key not in skip and self.outputs[key].value:
args.append(self.outputs[key].get_bash())
for flg in self.flags:
if self.flags[flg].value:
args.append(str(self.flags[flg]))
return args
@mdebug(1, extra=_get_bash)
def run(self):
"""Run the module
:param node:
:type node:
This function will wait for the process to terminate in case
finish_==True and sets up stdout and stderr. If finish_==False this
function will return after starting the process. Use
self.popen.communicate() of self.popen.wait() to wait for the process
termination. The handling of stdout and stderr must then be done
outside of this function.
"""
if self.inputs['stdin'].value:
self.stdin = self.inputs['stdin'].value
self.stdin_ = PIPE
cmd = self.make_cmd()
start = time.time()
self.popen = Popen(cmd,
stdin=self.stdin_,
stdout=self.stdout_,
stderr=self.stderr_,
env=self.env_)
if self.finish_:
stdout, stderr = self.popen.communicate(input=self.stdin)
self.outputs['stdout'].value = stdout if stdout else ''
self.outputs['stderr'].value = stderr if stderr else ''
self.time = time.time() - start
if self.popen.poll():
raise CalledModuleError(returncode=self.popen.returncode,
code=self.get_bash(),
module=self.name,
errors=stderr)
return self
