Merge pull request #17 from illusional/fix-base-command

Ensures base command is exported if it's a list

Author: mr-c

cwlgen/__init__.py

@@ -39,7 +39,7 @@ def __init__(self, tool_id=None, base_command=None, label=None, doc=None,
         :param tool_id: unique identifier for this tool
         :type tool_id: STRING
         :param base_command: command line for the tool
-        :type base_command: STRING
+        :type base_command: STRING | list[STRING]
         :param label: label of this tool
         :type label: STRING
         :param doc: documentation for the tool, usually longer than the label
@@ -82,19 +82,17 @@ def __init__(self, tool_id=None, base_command=None, label=None, doc=None,
         self._path = path
         self.namespaces = Namespaces()
 
-    def export(self, outfile=None):
-        """
-        Export the tool in CWL either on STDOUT or in outfile.
-        """
-        # First add representer (see .utils.py) for multiline writting
-        ruamel.yaml.add_representer(literal, literal_presenter)
+    def get_dict(self):
         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:
             cwl_tool['doc'] = literal(self.doc)
 
+        if self.baseCommand:
+            cwl_tool['baseCommand'] = self.baseCommand
+
         # Add Arguments
         cwl_tool['arguments'] = [in_arg.get_dict() for in_arg in self.arguments]
 
@@ -108,6 +106,13 @@ def export(self, outfile=None):
         for out_param in self.outputs:
             cwl_tool['outputs'][out_param.id] = out_param.get_dict()
 
+        if self.successCodes:
+            cwl_tool['successCodes'] = self.successCodes
+        if self.temporaryFailCodes:
+            cwl_tool['temporaryFailCodes'] = self.temporaryFailCodes
+        if self.permanentFailCodes:
+            cwl_tool['permanentFailCodes'] = self.permanentFailCodes
+
         # If metadata are present in the description
         if getattr(self, 'metadata', None):
             for key, value in self.metadata.__dict__.items():
@@ -125,6 +130,15 @@ def export(self, outfile=None):
 
         if requirements:
             cwl_tool['requirements'] = requirements
+        return cwl_tool
+
+    def export(self, outfile=None):
+        """
+        Export the tool in CWL either on STDOUT or in outfile.
+        """
+        # First add representer (see .utils.py) for multiline writting
+        ruamel.yaml.add_representer(literal, literal_presenter)
+        cwl_tool = self.get_dict()
 
         # Write CWL file in YAML
         if outfile is None:

test/test_unit_cwlgen.py

@@ -22,6 +22,8 @@ def setUp(self):
         self.cwl = cwlgen.CommandLineTool(tool_id='an_id', label='a description '+\
                                          'with spaces.', base_command='a_command')
 
+        self.array_basecommand = cwlgen.CommandLineTool(tool_id="base-command-array", base_command=["base", "command"])
+
     def test_init(self):
         self.assertEqual(self.cwl.id, 'an_id')
         self.assertEqual(self.cwl.label, 'a description with spaces.')
@@ -30,6 +32,23 @@ def test_init(self):
         self.assertListEqual(self.cwl.outputs, [])
         self.assertIsNone(self.cwl.doc)
 
+    def test_array_basecommand(self):
+        dict_test = self.array_basecommand.get_dict()
+        self.assertIn('baseCommand', dict_test)
+
+    def test_codes(self):
+        code_tool = cwlgen.CommandLineTool()
+        code_tool.permanentFailCodes.extend([400, 401, 500])
+        code_tool.temporaryFailCodes.append(408)
+        code_tool.successCodes = []     # empty (falsy)
+
+        dict_test = code_tool.get_dict()
+        self.assertIn('permanentFailCodes', dict_test)
+        self.assertEqual(len(dict_test['permanentFailCodes']), 3)
+        self.assertIn('temporaryFailCodes', dict_test)
+        self.assertEqual(len(dict_test['temporaryFailCodes']), 1)
+        self.assertNotIn('successCodes', dict_test)
+
     """
     def test_export(self):
         tmp_file = 'test_export.tmp'