code gardening

Author: khillion

cwlgen/__init__.py

@@ -5,18 +5,15 @@
 #  Import  ------------------------------
 
 # General libraries
-import os
-import argparse
-import sys
 import logging
 
 # External libraries
 import ruamel.yaml
 import six
 from .version import __version__
 
-from .utils import *
-from .elements import Parameter, CWL_VERSIONS
+from .utils import literal, literal_presenter
+from .elements import Parameter, CWL_VERSIONS, DEF_VERSION, CWL_SHEBANG
 from .workflow import Workflow, File
 from .import_cwl import parse_cwl
 
@@ -90,8 +87,8 @@ def export(self, outfile=None):
         """
         # First add representer (see .utils.py) for multiline writting
         ruamel.yaml.add_representer(literal, literal_presenter)
-        cwl_tool = {k: v for k, v in vars(self).items() if v is not None and\
-                                                           type(v) is str}
+        cwl_tool = {k: v for k, v in vars(self).items() if v is not None and
+                    type(v) is str}
         cwl_tool['class'] = self.__CLASS__
         # Treat doc for multiline writting
         if self.doc:
@@ -139,8 +136,6 @@ def export(self, outfile=None):
             out_write.close()
 
 
-
-
 class CommandInputParameter(Parameter):
     '''
     An input parameter for a :class:`cwlgen.CommandLineTool`.
@@ -378,9 +373,7 @@ def _to_dict(self):
         tool generated in an export method.
 
         """
-        return {p:v for p,v in vars(self).items() if p.startswith('docker') and v is not None}
-
-
+        return {p: v for p, v in vars(self).items() if p.startswith('docker') and v is not None}
 
 
 class Namespaces(object):

cwlgen/elements.py

@@ -1,4 +1,7 @@
+import logging
 
+logging.basicConfig(level=logging.INFO)
+_LOGGER = logging.getLogger(__name__)
 
 #  Constant(s)  ------------------------------
 
@@ -11,7 +14,6 @@
             'Directory', None]
 
 
-
 class Parameter(object):
     '''
     Based class for parameters (common field of Input and Output) for CommandLineTool and Workflow
@@ -38,7 +40,7 @@ def __init__(self, param_id, label=None, secondary_files=None, param_format=None
         :type param_type: STRING corresponding to CWLType
         '''
         if param_type not in CWL_TYPE:
-            LOGGER.warning("The type is incorrect for the parameter.")
+            _LOGGER.warning("The type is incorrect for the parameter.")
             param_type = None
         self.id = param_id
         self.label = label
@@ -59,8 +61,8 @@ def get_dict(self):
         if dict_param['type'] != 'File':
             # Remove what is only for File
             for key in ['format', 'secondaryFiles', 'streamable']:
-               try:
-                   del(dict_param[key])
-               except KeyError:
-                   pass
+                try:
+                    del(dict_param[key])
+                except KeyError:
+                    pass
         return dict_param

cwlgen/import_cwl.py

@@ -6,22 +6,27 @@
 
 # General libraries
 import os
-import argparse
-import sys
+import six
 import logging
 
 # External libraries
 import ruamel.yaml as ryaml
-import six
 import cwlgen
 import cwlgen.workflow
 
 logging.basicConfig(level=logging.INFO)
-logger = logging.getLogger(__name__)
+_LOGGER = logging.getLogger(__name__)
 
 #  Class(es)  ------------------------------
 
+
 def parse_cwl(cwl_path):
+    """
+    Method that parse a CWL file.
+
+    :param cwl_path: PATH to the CWL file
+    :type cwl_path: STRING
+    """
     with open(cwl_path) as yaml_file:
         cwl_dict = ryaml.load(yaml_file, Loader=ryaml.Loader)
         cl = cwl_dict['class']
@@ -34,6 +39,7 @@ def parse_cwl(cwl_path):
         return p.import_cwl(cwl_path)
     return None
 
+
 class CWLToolParser(object):
     """
     Class to import content from an existing CWL Tool.
@@ -152,7 +158,7 @@ def _load_class(self, tool, class_el):
         :type class_el: STRING
         """
         if class_el != 'CommandLineTool':
-            logger.warning('cwlgen library only handle CommandLineTool for the moment')
+            _LOGGER.warning('cwlgen library only handle CommandLineTool for the moment')
 
     def _load_inputs(self, tool, inputs_el):
         """
@@ -194,20 +200,26 @@ def import_cwl(self, cwl_path):
             try:
                 getattr(self, '_load_{}'.format(key))(tool, element)
             except AttributeError:
-                logger.warning(key + " content is not processed (yet).")
+                _LOGGER.warning(key + " content is not processed (yet).")
         tool._path = cwl_path
         return tool
 
+
 def dict_or_idlist_items(v):
+    """
+    :param v:
+    :type v: DICT of [DICT]
+    """
     if isinstance(v, dict):
         return v.items()
     o = []
     for i in v:
         e = dict(i)
         del e['id']
-        o.append( (i['id'], e) )
+        o.append((i['id'], e))
     return o
 
+
 class InputsParser(object):
     """
     Class to parse content of inputs from an existing CWL Tool.
@@ -318,7 +330,7 @@ def load_inputs(self, inputs, inputs_el):
                 try:
                     getattr(self, '_load_{}'.format(key))(input_obj, element)
                 except AttributeError:
-                    logger.warning(key + " content for input is not processed (yet).")
+                    _LOGGER.warning(key + " content for input is not processed (yet).")
             inputs.append(input_obj)
 
 
@@ -418,7 +430,7 @@ def load_inbinding(self, input_obj, inbinding_el):
             try:
                 getattr(self, '_load_{}'.format(key))(inbinding_obj, value)
             except AttributeError:
-                logger.warning(key + " content for inputBinding is not processed (yet).")
+                _LOGGER.warning(key + " content for inputBinding is not processed (yet).")
             input_obj.inputBinding = inbinding_obj
 
 
@@ -532,7 +544,7 @@ def load_outputs(self, outputs, outputs_el):
                 try:
                     getattr(self, '_load_{}'.format(key))(output_obj, element)
                 except AttributeError:
-                    logger.warning(key + " content for output is not processed (yet).")
+                    _LOGGER.warning(key + " content for output is not processed (yet).")
             outputs.append(output_obj)
 
 
@@ -588,7 +600,7 @@ def load_outbinding(self, output_obj, outbinding_el):
             try:
                 getattr(self, '_load_{}'.format(key))(outbinding_obj, value)
             except AttributeError:
-                logger.warning(key + " content for outputBinding is not processed (yet).")
+                _LOGGER.warning(key + " content for outputBinding is not processed (yet).")
             output_obj.outputBinding = outbinding_obj
 
 
@@ -597,10 +609,22 @@ class StepsParser(object):
     Class to parse content of steps of workflow from existing CWL Workflow.
     """
     def __init__(self, basedir=None, expand_run=True):
+        """
+        :param basedir:
+        :type basedir:
+        :param expand_run:
+        :type: expand_run:
+        """
         self.basedir = basedir
         self.expand_run = expand_run
 
     def _load_in(self, step_obj, in_el):
+        """
+        :param step_obj:
+        :type step_obj:
+        :param in_el:
+        :type in_el:
+        """
         for key, val in in_el.items():
             o = cwlgen.workflow.WorkflowStepInput(key)
             if isinstance(val, dict) and 'default' in val:
@@ -615,14 +639,13 @@ def _load_out(self, step_obj, in_el):
             step_obj.outputs.append(o)
 
     def _load_run(self, step_obj, in_el):
-        if isinstance(in_el, basestring) and self.expand_run:
+        if isinstance(in_el, six.string_types) and self.expand_run:
             path = os.path.join(self.basedir, in_el)
-            #logger.info("Parsing: %s", path)
+            # logger.info("Parsing: %s", path)
             step_obj.run = parse_cwl(path)
         else:
             step_obj.run = in_el
 
-
     def load_steps(self, steps_obj, steps_elm):
         """
         Load the content of step into the output object.
@@ -638,7 +661,7 @@ def load_steps(self, steps_obj, steps_elm):
                 try:
                     getattr(self, '_load_{}'.format(key))(step_obj, element)
                 except AttributeError:
-                    logger.warning(key + " content for input is not processed (yet).")
+                    _LOGGER.warning(key + " content for input is not processed (yet).")
             steps_obj.append(step_obj)
 
 
@@ -674,7 +697,7 @@ def import_cwl(self, cwl_path):
             try:
                 getattr(self, '_load_{}'.format(key))(tool, element)
             except AttributeError:
-                logger.warning(key + " workflow content is not processed (yet).")
+                _LOGGER.warning(key + " workflow content is not processed (yet).")
         tool._path = cwl_path
         return tool
 
@@ -700,7 +723,6 @@ def _load_cwlVersion(self, tool, cwl_version_el):
         """
         tool.cwlVersion = cwl_version_el
 
-
     def _load_class(self, tool, class_el):
         """
         Display message to inform that cwlgen only deal with Workflow for the moment.
@@ -711,7 +733,7 @@ def _load_class(self, tool, class_el):
         :type class_el: STRING
         """
         if class_el != 'Workflow':
-            logger.warning('cwlgen library only handle Workflow for the moment')
+            _LOGGER.warning('cwlgen library only handle Workflow for the moment')
 
     def _load_requirements(self, tool, req_el):
         pass
@@ -740,7 +762,6 @@ def _load_outputs(self, tool, outputs_el):
         inp_parser = OutputsParser()
         inp_parser.load_outputs(tool.outputs, outputs_el)
 
-
     def _load_steps(self, tool, outputs_el):
         """
         Load the content of inputs into the tool.

cwlgen/utils.py

@@ -2,7 +2,9 @@
 Set of util functions and classes
 """
 
+
 class literal(str): pass
 
+
 def literal_presenter(dumper, data):
-    return dumper.represent_scalar('tag:yaml.org,2002:str', data, style = "|")
+    return dumper.represent_scalar('tag:yaml.org,2002:str', data, style="|")

cwlgen/version.py

@@ -1,2 +1,2 @@
-version_info = (0,2,8)
+version_info = (0, 2, 8)
 __version__ = '.'.join(str(c) for c in version_info)