Merge pull request #8 from dleehr/workflow-requirements

Support for workflow requirements

Author: dleehr

cwlgen/__init__.py

@@ -337,6 +337,12 @@ def __init__(self, expression_lib=None):
         Requirement.__init__(self, 'InlineJavascriptRequirement')
         self.expressionLib = expression_lib
 
+    def _to_dict(self):
+        if self.expressionLib:
+            return {'expressionLib': [self.expressionLib]}
+        else:
+            return {}
+
 
 class DockerRequirement(Requirement):
     '''
@@ -377,6 +383,15 @@ def _to_dict(self):
         return {p: v for p, v in vars(self).items() if p.startswith('docker') and v is not None}
 
 
+class SubworkflowFeatureRequirement(Requirement):
+
+    def __init__(self):
+        Requirement.__init__(self, 'SubworkflowFeatureRequirement')
+
+    def _to_dict(self):
+        return dict()
+
+
 class Namespaces(object):
     """
     Define different namespace for the description.

cwlgen/workflow.py

@@ -15,6 +15,7 @@ def __init__(self):
         self.steps = []
         self.inputs = []
         self.outputs = []
+        self.requirements = []
         self._path = None
 
 
@@ -47,6 +48,14 @@ def export(self, outfile=None):
             for out in self.outputs:
                 cwl_workflow['outputs'][out.id] = out.get_dict()
 
+        # Add requirements.
+        requirements = {}
+        for requirement in self.requirements:
+            requirement.add(requirements)
+
+        if requirements:
+            cwl_workflow['requirements'] = requirements
+
         # Write CWL file in YAML
         if outfile is None:
             six.print_(CWL_SHEBANG, "\n", sep='')

test/test_unit_cwlgen.py

@@ -193,6 +193,18 @@ def test_init(self):
         self.assertEqual(self.js_req.req_class, 'InlineJavascriptRequirement')
         self.assertEqual(self.js_req.expressionLib, 'expression')
 
+    def test_add(self):
+        tool = {}
+        self.js_req.add(tool)
+        self.assertEqual(tool, {'InlineJavascriptRequirement': {'expressionLib': ['expression']}})
+
+    def test_add_without_lib(self):
+        tool = {}
+        req = cwlgen.InlineJavascriptReq()
+        req.add(tool)
+        self.assertEqual(tool, {'InlineJavascriptRequirement': {}})
+
+
 class TestDockerRequirement(unittest.TestCase):
 
     def setUp(self):
@@ -215,6 +227,17 @@ def test_export(self):
                          dockerImageId='id', dockerOutputDir='dir')
 
 
+class TestSubworkflowFeatureRequirement(unittest.TestCase):
+
+    def setUp(self):
+        self.req = cwlgen.SubworkflowFeatureRequirement()
+
+    def test_add(self):
+        tool = {}
+        self.req.add(tool)
+        self.assertEqual(tool, {'SubworkflowFeatureRequirement': {}})
+
+
 ###########  Main  ###########
 
 if __name__ == "__main__":

test/test_unit_workflow.py

@@ -86,5 +86,19 @@ def test_generates_workflow_int_inputs(self):
         self.assertEqual(expected, generated)
 
 
+    def test_add_requirements(self):
+        w = cwlgen.Workflow()
+        req = cwlgen.InlineJavascriptReq()
+        w.requirements.append(req)
+        generated = self.capture_tempfile(w.export)
+        expected = b"""#!/usr/bin/env cwl-runner
 
+class: Workflow
+cwlVersion: v1.0
+inputs: {}
+outputs: {}
+requirements:
+  InlineJavascriptRequirement: {}
+"""
+        self.assertEqual(expected, generated)