Merge pull request #3 from joezuntz/master

Export DockerRequirement and always include input/output dicts

Author: khillion

cwlgen/__init__.py

@@ -102,16 +102,14 @@ def export(self, outfile=None):
         if self.doc:
             cwl_tool['doc'] = literal(self.doc)
         # Add Inputs
-        if self.inputs:
-            cwl_tool['inputs'] = {}
-            for in_param in self.inputs:
-                cwl_tool['inputs'][in_param.id] = in_param.get_dict()
+        cwl_tool['inputs'] = {}
+        for in_param in self.inputs:
+            cwl_tool['inputs'][in_param.id] = in_param.get_dict()
 
         # Add Outputs
-        if self.outputs:
-            cwl_tool['outputs'] = {}
-            for out_param in self.outputs:
-                cwl_tool['outputs'][out_param.id] = out_param.get_dict()
+        cwl_tool['outputs'] = {}
+        for out_param in self.outputs:
+            cwl_tool['outputs'][out_param.id] = out_param.get_dict()
 
         # If metadata are present in the description
         if getattr(self, 'metadata', None):
@@ -122,6 +120,14 @@ def export(self, outfile=None):
             for k, v in self.namespaces.__dict__.items():
                 if '$' not in v:
                     cwl_tool[self.namespaces.name][k] = v
+
+        # Add requirements.
+        requirements = {}
+        for requirement in self.requirements:
+            requirement.add(requirements)
+
+        if requirements:
+            cwl_tool['requirements'] = requirements
 
         # Write CWL file in YAML
         if outfile is None:
@@ -367,6 +373,13 @@ def __init__(self, req_class):
         '''
         self.req_class = req_class
 
+    def add(self, tool):
+        tool[self.req_class] = self._to_dict()
+
+    def _to_dict(self):
+        raise NotImplementedError("Requirement subclass {} not fully implemented".format(
+            self.req_class))
+
 
 class InlineJavascriptReq(Requirement):
     '''
@@ -412,6 +425,16 @@ def __init__(self, docker_pull=None, docker_load=None, docker_file=None,
         self.dockerImageId = docker_image_id
         self.dockerOutputDir = docker_output_dir
 
+    def _to_dict(self):
+        """
+        Add this requirement to a dictionary description of a 
+        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}
+
+
+
 
 class Namespaces(object):
     """

test/test_unit_cwlgen.py

@@ -208,6 +208,12 @@ def test_init(self):
         self.assertEqual(self.dock_req.dockerImageId, 'id')
         self.assertEqual(self.dock_req.dockerOutputDir, 'dir')
 
+    def test_export(self):
+        d = self.dock_req._to_dict()
+        assert d == dict(dockerPull='pull', dockerLoad='load',\
+                         dockerFile='file', dockerImport='import',\
+                         dockerImageId='id', dockerOutputDir='dir')
+
 
 ###########  Main  ###########