Merge pull request #13 from illusional/optional-types

Optional types

Author: mr-c

cwlgen/elements.py

@@ -10,11 +10,41 @@
                 'draft-3.dev4', 'draft-3.dev5', 'draft-3', 'draft-4.dev1',
                 'draft-4.dev2', 'draft-4.dev3', 'v1.0.dev4', 'v1.0']
 DEF_VERSION = 'v1.0'
+NON_NULL_CWL_TYPE = ['boolean', 'int', 'long', 'float', 'double', 'string', 'File',
+                     'Directory', 'stdout']
 CWL_TYPE = ['null', 'boolean', 'int', 'long', 'float', 'double', 'string', 'File',
             'Directory', 'stdout', None]
 DEF_TYPE = 'null'
 
 
+def parse_param_type(param_type):
+    """
+    Parses the parameter type as one of the required types:
+    :: https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter
+
+
+    :param param_type:
+    :return: CWLType | CommandInputRecordSchema | CommandInputEnumSchema | CommandInputArraySchema | string |
+       array<CWLType | CommandInputRecordSchema | CommandInputEnumSchema | CommandInputArraySchema | string>
+    """
+
+    if isinstance(param_type, str) and len(param_type) > 0:
+        # Must be CWLType
+        optional = param_type[-1] == "?"
+        if optional:
+            _LOGGER.debug("Detected {param_type} to be optional".format(param_type=param_type))
+        cwltype = param_type[:-1] if optional else param_type
+        if cwltype not in CWL_TYPE:
+            _LOGGER.warning("The type '{param_type}' is not a valid CWLType, expected one of: {types}"
+                            .format(param_type=param_type, types=", ".join(str(x) for x in CWL_TYPE)))
+            _LOGGER.warning("type is set to {}.".format(DEF_TYPE))
+            return DEF_TYPE
+        return param_type
+    else:
+        _LOGGER.warning("Unable to detect type of param '{param_type}".format(param_type=param_type))
+        return DEF_TYPE
+
+
 class Parameter(object):
     '''
     Based class for parameters (common field of Input and Output) for CommandLineTool and Workflow
@@ -40,17 +70,13 @@ def __init__(self, param_id, label=None, secondary_files=None, param_format=None
         :param param_type: type of data assigned to the parameter
         :type param_type: STRING corresponding to CWLType
         '''
-        if param_type not in CWL_TYPE:
-            _LOGGER.warning("The type {} is incorrect for the parameter.".format(param_type))
-            _LOGGER.warning("type is set to {}.".format(DEF_TYPE))
-            param_type = DEF_TYPE
         self.id = param_id
         self.label = label
         self.secondaryFiles = secondary_files
         self.format = param_format
         self.streamable = streamable
         self.doc = doc
-        self.type = param_type
+        self.type = parse_param_type(param_type)
 
     def get_dict(self):
         '''

test/test_unit_typing.py

@@ -0,0 +1,21 @@
+import unittest
+from cwlgen.elements import parse_param_type, NON_NULL_CWL_TYPE, CWL_TYPE, DEF_TYPE
+import logging
+
+
+class TestParamTyping(unittest.TestCase):
+
+    def test_types(self):
+        for cwl_type in NON_NULL_CWL_TYPE:
+            self.assertEqual(parse_param_type(cwl_type), cwl_type)
+
+    def test_incorrect_type(self):
+        for cwl_type in NON_NULL_CWL_TYPE:
+            should_be_def_type = parse_param_type(cwl_type.upper())
+            self.assertNotEqual(should_be_def_type, cwl_type)
+            self.assertEqual(should_be_def_type, DEF_TYPE)
+
+    def test_optional_string(self):
+        for cwl_type in NON_NULL_CWL_TYPE:
+            optional_type = cwl_type + "?"
+            self.assertEqual(parse_param_type(optional_type), optional_type)

test/test_unit_workflow.py

@@ -85,7 +85,6 @@ def test_generates_workflow_int_inputs(self):
         generated = self.capture_tempfile(w.export)
         self.assertEqual(expected, generated)
 
-
     def test_add_requirements(self):
         w = cwlgen.Workflow()
         req = cwlgen.InlineJavascriptReq()