Create EDAM objects

Author: khillion

cwlgen/__init__.py

@@ -43,7 +43,7 @@ class CommandLineTool(object):
     __CLASS__ = 'CommandLineTool'
 
     def __init__(self, tool_id=None, base_command=None, label=None, doc=None,
-                 cwl_version=None, stdin=None, stderr=None, stdout=None):
+                 cwl_version=None, stdin=None, stderr=None, stdout=None, edam=None):
         '''
         :param tool_id: unique identifier for this tool
         :type tool_id: STRING
@@ -80,6 +80,7 @@ def __init__(self, tool_id=None, base_command=None, label=None, doc=None,
         self.outputs = []  # List of [CommandOutputParameter] objects
         self.baseCommand = base_command
         self.arguments = []  # List of [CommandLineBinding] objects
+        self.edam = None
         self.doc = doc
         self.stdin = stdin
         self.stderr = stderr
@@ -98,6 +99,9 @@ def export(self, outfile=None):
         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__
+        # EDAM ?
+        if self.edam:
+            cwl_tool['edam'] = self.edam.get_dict()
         # Treat doc for multiline writting
         if self.doc:
             cwl_tool['doc'] = literal(self.doc)
@@ -433,3 +437,18 @@ class Metadata(object):
     def __init__(self, **kwargs):
         for key, value in kwargs.items():
             setattr(self, key, value)
+
+class Edam(object):
+    """
+    Represent edam terms
+    """
+
+    def __init__(self):
+        """
+        """
+        self.name = "edam"
+        self.topics = []
+        self.operations = []
+
+    def get_dict(self):
+        return {'topics': self.topics, 'operations': self.operations}

cwlgen/version.py

@@ -1,2 +1,2 @@
-version_info = (0,2,3)
+version_info = (0,2,4)
 __version__ = '.'.join(str(c) for c in version_info)