Merge pull request #9 from dleehr/master

General improvements for workflow building

Author: khillion

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

@@ -15,8 +15,10 @@ def __init__(self):
         self.steps = []
         self.inputs = []
         self.outputs = []
+        self.requirements = []
         self._path = None
 
+
     def export(self, outfile=None):
         """
         Export the workflow in CWL either on STDOUT or in outfile.
@@ -46,6 +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='')
@@ -185,7 +195,7 @@ def __init__(self, param_id, outputSource, label=None, secondary_files=None, par
         self.outputSource = outputSource
 
 ############################
-# Workflow contruction classes
+# Workflow construction classes
 
 
 class File:
@@ -196,6 +206,8 @@ def __init__(self, path):
         self.path = path
 
 
+
+
 class Variable:
     """
     An output variable from a workflow step
@@ -216,6 +228,8 @@ def store(self):
         return
 
 
+
+
 class StepRun:
     """
     Result of adding a step into a workflow
@@ -233,10 +247,13 @@ def __init__(self, workflow, id, tool, params):
                 step.inputs.append(WorkflowStepInput(i, default=j))
             elif isinstance(j, Variable):
                 step.inputs.append(WorkflowStepInput(i, src=j.path()))
+            elif isinstance(j, InputParameter):
+                self.workflow.inputs.append(j),
+                step.inputs.append(WorkflowStepInput(j.id, src=j.id))
             elif isinstance(j, File):
+                # This is just used as a stub, the 'path' inside the file doesn't do anything
                 self.workflow.inputs.append(InputParameter(i, param_type="File"))
                 step.inputs.append(WorkflowStepInput(i, src=i))
-
         for o in tool.outputs:
             step.outputs.append(o.id)
 

test/int_tool.cwl

@@ -0,0 +1,32 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.0
+id: tool_id
+label: a_label
+baseCommand: cat
+class: CommandLineTool
+doc: "super_doc"
+stdin: "in"
+stderr: "err"
+stdout: "out"
+inputs:
+  INTEGER:
+    doc: 'documentation_in'
+    inputBinding:
+      loadContents: True
+      position: 0
+      prefix: --input
+      separate: True
+      itemSeparator: ';'
+      valueFrom: here
+      shellQuote: True
+    type: int
+outputs:
+  OUTPUT1:
+    label: label_out
+    doc: 'documentation_out'
+    outputBinding:
+      glob: "find"
+      loadContents: True
+      outputEval: "eval"
+    type: File

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

@@ -10,16 +10,22 @@
 import os
 import filecmp
 import unittest
+from tempfile import NamedTemporaryFile
 
 # External libraries
 import cwlgen
 
 #  Class(es)  ------------------------------
 
-class TestCommandLineTool(unittest.TestCase):
 
+class TestWorkflow(unittest.TestCase):
 
-    def test_build(self):
+    def capture_tempfile(self, func):
+        with NamedTemporaryFile() as f:
+            func(f.name)
+            return f.read()
+
+    def test_generates_workflow_two_steps(self):
 
         w = cwlgen.Workflow()
         tool = cwlgen.parse_cwl("test/import_cwl.cwl")
@@ -29,4 +35,70 @@ def test_build(self):
         o1 = w.add('step-a', tool, {"INPUT1" : f})
         o2 = w.add('step-b', tool, {"INPUT1" : o1['OUTPUT1']})
         o2['OUTPUT1'].store()
-        w.export("test.cwl")
+        generated = self.capture_tempfile(w.export)
+        expected = b"""#!/usr/bin/env cwl-runner
+
+class: Workflow
+cwlVersion: v1.0
+inputs:
+  INPUT1: {id: INPUT1, type: File}
+outputs:
+  step-b_OUTPUT1: {id: step-b_OUTPUT1, outputSource: step-b/OUTPUT1, type: File}
+steps:
+  step-a:
+    id: step-a
+    in: {INPUT1: INPUT1}
+    out: [OUTPUT1]
+    run: test/import_cwl.cwl
+  step-b:
+    id: step-b
+    in: {INPUT1: step-a/OUTPUT1}
+    out: [OUTPUT1]
+    run: test/import_cwl.cwl
+"""
+        self.assertEqual(expected, generated)
+
+    def test_generates_workflow_int_inputs(self):
+
+        w = cwlgen.Workflow()
+        tool = cwlgen.parse_cwl("test/int_tool.cwl")
+
+        i = cwlgen.workflow.InputParameter('INTEGER', param_type='int')
+        o1 = w.add('step', tool, {"INTEGER": i})
+        o1['OUTPUT1'].store()
+
+        expected = b"""#!/usr/bin/env cwl-runner
+
+class: Workflow
+cwlVersion: v1.0
+inputs:
+  INTEGER: {id: INTEGER, type: int}
+outputs:
+  step_OUTPUT1: {id: step_OUTPUT1, outputSource: step/OUTPUT1, type: File}
+steps:
+  step:
+    id: step
+    in: {INTEGER: INTEGER}
+    out: [OUTPUT1]
+    run: test/int_tool.cwl
+"""
+        generated = self.capture_tempfile(w.export)
+        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)
+