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Commit d465346d authored by Frédéric Escudié's avatar Frédéric Escudié
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src/jflow/component.py
View file @ d465346d
......@@ -67,10 +67,10 @@ class Component(object):
required=False, flag=None, group="default", display_name=None, add_to=None):
new_param = InputFile(name, help, flag=flag, file_format=file_format, default=default,
type=type, required=required, group=group, display_name=display_name)
new_param.component_nameid = self.get_nameid()
# store where the parameter is coming from
if hasattr(default, "component_nameid"):
new_param.component_nameid = self.get_nameid()
if issubclass( default.__class__, LinkTraceback ):
new_param.parent_component_nameid = default.component_nameid
# if this input should be added to a particular parameter
......@@ -92,18 +92,24 @@ class Component(object):
if default == None:
inputs = []
else:
inputs = [IOFile(file, self.get_nameid(), None, file_format) for file in default]
inputs = [IOFile(file, file_format, self.get_nameid(), None) for file in default]
new_param = InputFileList(name, help, flag=flag, file_format=file_format, default=inputs,
type=type, required=required, group=group, display_name=display_name)
# store where the parameter is coming from
new_param.component_nameid = self.get_nameid()
if issubclass( default.__class__, list ):
for idx, val in enumerate(default):
if hasattr( val, "component_nameid" ):
if issubclass( val.__class__, LinkTraceback ):
new_param[idx].parent_component_nameid = val.component_nameid
elif hasattr( default, "component_nameid" ):
new_param.parent_component_nameid = default.component_nameid
new_param.parent_component_nameid.append( val.component_nameid )
else:
new_param.parent_component_nameid.append( None )
else:
if issubclass( default.__class__, LinkTraceback ):
new_param[0].parent_component_nameid = default.component_nameid
new_param.parent_component_nameid.append( default.component_nameid )
else:
new_param.parent_component_nameid.append( None )
# if this input should be added to a particular parameter
if add_to:
try:
......@@ -147,6 +153,7 @@ class Component(object):
filename = os.path.basename(filename)
new_param = OutputFile(name, help, default=os.path.join(self.output_directory, filename),
file_format=file_format, group=group, display_name=display_name)
# store where the parameter is coming from
new_param.component_nameid = self.get_nameid()
# if this input should be added to a particular parameter
if add_to:
......@@ -160,8 +167,10 @@ class Component(object):
def add_output_file_list(self, name, help, file_format="any", pattern='{basename_woext}.out',
items=None, group="default", display_name=None, add_to=None):
default = [IOFile(file, self.get_nameid(), None, file_format) for file in self.get_outputs(pattern, items)]
default = [IOFile(file, file_format, self.get_nameid(), None) for file in self.get_outputs(pattern, items)]
new_param = OutputFileList(name, help, default=default, file_format=file_format, group=group, display_name=display_name)
# store where the parameter is coming from
new_param.component_nameid = self.get_nameid()
# if this input should be added to a particular parameter
if add_to:
try:
......@@ -176,6 +185,8 @@ class Component(object):
group="default", display_name=None, add_to=None):
new_param = OutputFilesEndsWith(name, help, self.output_directory, pattern, include=(behaviour == "include"),
file_format=file_format, group=group, display_name=display_name)
# store where the parameter is coming from
new_param.component_nameid = self.get_nameid()
# if this input should be added to a particular parameter
if add_to:
try:
......@@ -190,6 +201,8 @@ class Component(object):
group="default", display_name=None, add_to=None):
new_param = OutputFilesPattern(name, help, self.output_directory, pattern, include=(behaviour == "exclude"),
file_format=file_format, group=group, display_name=display_name)
# store where the parameter is coming from
new_param.component_nameid = self.get_nameid()
# if this input should be added to a particular parameter
if add_to:
try:
......
src/jflow/parameter.py
View file @ d465346d
......@@ -372,23 +372,27 @@ class AbstractParameter(object):
return create_test_function(self.type)
class AbstractIOFile(object):
class LinkTraceback(object):
def __init__(self, file_format="any"):
def __init__(self, component_nameid=None, parent_component_nameid=[]):
self.component_nameid = component_nameid
self.parent_component_nameid = parent_component_nameid
class AbstractIOFile(LinkTraceback):
def __init__(self, file_format="any", component_nameid=None, parent_component_nameid=[]):
LinkTraceback.__init__(self, component_nameid, parent_component_nameid)
self.file_format = file_format
self.component_nameid = None
self.parent_component_nameid = None
class IOFile(str):
class IOFile(str, AbstractIOFile):
def __new__(self, val="", component_nameid=None, parent_component_nameid=[], file_format="any"):
def __new__(self, val="", file_format="any", component_nameid=None, parent_component_nameid=None):
return str.__new__(self, val)
def __init__(self, val, component_nameid=None, parent_component_nameid=[], file_format="any"):
self.component_nameid = component_nameid
self.parent_component_nameid = parent_component_nameid
self.file_format = file_format
def __init__(self, val="", file_format="any", component_nameid=None, parent_component_nameid=None):
AbstractIOFile.__init__(self, file_format, component_nameid, parent_component_nameid)
class MultiParameter(dict, AbstractParameter):
......@@ -985,9 +989,11 @@ class OutputFilesEndsWith(DynamicOutput):
output_files = list()
for file in os.listdir( self.output_directory ):
if file.endswith( self.end_str ) and self.include :
output_files.append( IOFile(os.path.join(self.output_directory, file), None, None, self.file_format) )
output_files.append( IOFile(os.path.join(self.output_directory, file), self.file_format, self.component_nameid, None) )
self.component_parent_nameid.append(None)
elif not file.endswith( self.end_str ) and not self.include:
output_files.append( IOFile(os.path.join(self.output_directory, file), None, None, self.file_format) )
output_files.append( IOFile(os.path.join(self.output_directory, file), self.file_format, self.component_nameid, None) )
self.component_parent_nameid.append(None)
list.__init__(self, output_files)
......@@ -1015,7 +1021,9 @@ class OutputFilesPattern(DynamicOutput):
output_files = list()
for file in os.listdir( self.output_directory ):
if self.include and re.search( self.pattern, file ) is not None:
output_files.append( IOFile(os.path.join(self.output_directory, file), None, None,self.file_format) )
output_files.append( IOFile(os.path.join(self.output_directory, file), self.file_format, self.component_nameid, None) )
self.component_parent_nameid.append(None)
elif not self.include and re.search( self.pattern, file ) is None:
output_files.append( IOFile(os.path.join(self.output_directory, file), None, None,self.file_format) )
output_files.append( IOFile(os.path.join(self.output_directory, file), self.file_format, self.component_nameid, None) )
self.component_parent_nameid.append(None)
return list.__init__(self, output_files)
\ No newline at end of file
src/jflow/workflow.py
View file @ d465346d
......@@ -338,13 +338,14 @@ class Workflow(threading.Thread):
gr.add_node_attribute(cpt.get_nameid(), self.COMPONENT_GRAPH_LABEL)
for cpt in self.components:
for ioparameter in cpt.__dict__.values():
if issubclass( ioparameter.__class__, InputFile ) and hasattr(ioparameter, "component_nameid"):
try: gr.add_edge((ioparameter.parent_component_nameid, ioparameter.component_nameid))
except: pass
if issubclass( ioparameter.__class__, InputFile ):
if ioparameter.parent_component_nameid != None:
try: gr.add_edge((ioparameter.parent_component_nameid, ioparameter.component_nameid))
except: pass
if issubclass( ioparameter.__class__, InputFileList):
for io in ioparameter:
if hasattr(io, "component_nameid"):
try: gr.add_edge((io.parent_component_nameid, io.component_nameid))
for iofile in ioparameter:
if iofile.parent_component_nameid != None:
try: gr.add_edge((iofile.parent_component_nameid, ioparameter.component_nameid))
except: pass
return gr
......@@ -620,8 +621,6 @@ class Workflow(threading.Thread):
# update outputs
for output in cmpt_object.get_dynamic_outputs():
output.update()
for file in output:
file.component_id = cmpt_object.get_nameid()
else:
if self._component_is_duplicated(cmpt_object):
raise ValueError("Component " + cmpt_object.__class__.__name__ + " with prefix " +
......
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