Enable conversion to CWL v1.1

README.md

@@ -61,6 +61,12 @@ sbg_cwl_upgrader -i admin/sbg-public-data/whole-exome-sequencing-bwa-gatk-4-0 -o
 ```
 You will additionally be asked if you want to decompose the workflow after installation. 
 
+### Save upgraded CWL in version v1.1
+Version of the upgraded app can be controlled with `-c` parameter
+```
+sbg_cwl_upgrader -i admin/sbg-public-data/whole-exome-sequencing-bwa-gatk-4-0 -c v1.1-o username/usernames-demo-project/wes
+```
+
 ### Decompose a Platform workflow
 Sometimes, you want all workflow components to be available in the same project as the workflow. This can be done using the `sbg_cwl_decomposer` tool.  
 This tool will:

requirements.txt

@@ -1,5 +1,5 @@
 setuptools==41.0.1
-sevenbridges-python==0.20.2
+sevenbridges-python==1.0.1
 humanfriendly==7.1.1
 termcolor==1.1.0
 typing==3.6.6

sbg_cwl_upgrader/converter/cwl_converter.py

@@ -20,6 +20,8 @@
 
 logger = logging.getLogger(__name__)
 
+DEFAULT_CWL_VERSION = 'v1.0'
+
 
 def dict_to_yaml(data: dict, out_path: str):
     y = YAML()
@@ -43,6 +45,7 @@ class CWLConverterFacade:
     def __init__(self,
                  input_: str,
                  output: str = None,
+                 cwl_version: str = 'v1.0',
                  token: str = None,
                  platform: str = None,
                  app_revision: str = None,
@@ -64,6 +67,7 @@ def __init__(self,
         self.username = None
         self.input_ = input_
         self.output = output
+        self.cwl_version = cwl_version
         self.validate = validate
         self.update = update
         self.decompose = decompose
@@ -235,12 +239,15 @@ def _load_input_cwl(self):
 
         return raw
 
-    @staticmethod
-    def _parse(data):
+    def _parse(self, data):
         if 'class' in data and isinstance(data['class'], str):
             if data['class'] == 'CommandLineTool':
-                return CWLToolConverter().convert_dict(data)
+                return CWLToolConverter(
+                    cwl_version=self.cwl_version
+                ).convert_dict(data)
             elif data['class'] == 'Workflow':
-                return CWLWorkflowConverter().convert_dict(data)
+                return CWLWorkflowConverter(
+                    cwl_version=self.cwl_version
+                ).convert_dict(data)
         else:
             raise ValueError('Invalid cwl class.')

sbg_cwl_upgrader/converter/sbg_draft2_to_cwl_1_0.py

@@ -4,27 +4,31 @@
                                         configure_logging,
                                         add_logging_to_args)
 from sbg_cwl_upgrader.converter.cwl_converter import CWLConverterFacade
+from sbg_cwl_upgrader.converter.cwl_converter import DEFAULT_CWL_VERSION
 
 
 def create_arg_parser():
     parser = argparse.ArgumentParser(
         description=' This tool converts CWL draft2 applications '
-                    '(workflows, command line tools) to CWL v1.0.')
+                    '(workflows, command line tools) to CWL v1.0 or v1.1')
 
     parser.add_argument('-i', '--input', required=True,
                         help='can be either draft2 file (YAML, JSON, CWL)'
                              ' path or application ID.')
     parser.add_argument('-o', '--output', required=True,
-                        help='can be either cwl v1.0 file (YAML, JSON, CWL)'
+                        help='can be either cwl v1 file (YAML, JSON, CWL)'
                              ' path or application ID.')
+    parser.add_argument('-c', '--cwl-version', default=DEFAULT_CWL_VERSION,
+                        choices=['v1.0', 'v1.1'],
+                        help='set cwl version for output')
     parser.add_argument('-r', '--revision', type=int,
                         help='platform application revision. default: latest')
     parser.add_argument('-v', '--validate', action='store_true',
-                        help='validate JS in the converted CWL v1.0 app.')
+                        help='validate JS in the converted CWL v1 app.')
     parser.add_argument('-u', '--update', dest='update', action='store_true',
                         help='update/install if output is a platform app.')
     parser.add_argument('-d', '--decompose', action='store_true',
-                        help='decompose the converted CWL v1.0 workflow.')
+                        help='decompose the converted CWL v1 workflow.')
 
     add_logging_to_args(parser)
     add_sbg_auth_to_args(parser)
@@ -48,6 +52,7 @@ def main(args=sys.argv[1:]):
                        app_revision=args['revision'],
                        input_=args['input'],
                        output=args['output'],
+                       cwl_version=args['cwl_version'],
                        validate=args['validate'],
                        update=args['update'],
                        decompose=args['decompose'])

sbg_cwl_upgrader/converter/tool.py

@@ -221,6 +221,10 @@ def __init__(self, sbg_draft2=None):
 
 
 class CWLToolConverter(CWL):
+
+    def __init__(self, cwl_version=None):
+        self.cwl_version = cwl_version
+
     @staticmethod
     def _is_staged_file(sbg_draft2_input):
         if ('sbg:stageInput' in sbg_draft2_input
@@ -520,7 +524,7 @@ def _handle_bash(literal):
     def convert_dict(self, data: dict):
         """Main method for converting draft2 tool to CWL1.0"""
 
-        # Just reuse if tool is already CWLv1.0
+        # Just reuse if tool is already CWLv1
         if data.get('cwlVersion') != 'sbg:draft-2':
             return data
 
@@ -535,8 +539,8 @@ def convert_dict(self, data: dict):
                                  'sbg:revision', 'sbg:revisionsInfo',
                                  'sbg:createdOn']}
 
-        new_data['cwlVersion'] = 'v1.0'
-        new_data['sbg:appVersion'] = ['v1.0']
+        new_data['cwlVersion'] = self.cwl_version
+        new_data['sbg:appVersion'] = [self.cwl_version]
         if 'stdin' in data:
             new_data['stdin'] = self._handle_stream(data['stdin'])
         if 'stdout' in data:

sbg_cwl_upgrader/converter/workflow.py

@@ -11,6 +11,9 @@
 
 class CWLWorkflowConverter(CWL):
 
+    def __init__(self, cwl_version=None):
+        self.cwl_version = cwl_version
+
     @staticmethod
     def handle_source(source: list):
         source = deepcopy(source)
@@ -139,29 +142,29 @@ def default_requirements():
                 {'class': 'StepInputExpressionRequirement'}]
 
     def convert_dict(self, data: dict) -> dict:
-        v1_0_data = {k: deepcopy(v) for k, v in data.items()
+        v1_data = {k: deepcopy(v) for k, v in data.items()
                      if k not in ['x', 'y', 'appUrl']}
-        if v1_0_data.get('cwlVersion') != 'sbg:draft-2':
-
-            return v1_0_data
-        v1_0_data['cwlVersion'] = 'v1.0'
-        v1_0_data['sbg:appVersion'] = [v1_0_data['cwlVersion']]
-        v1_0_data['inputs'] = self.handle_inputs(v1_0_data['inputs'])
-        v1_0_data['outputs'] = self.handle_outputs(v1_0_data['outputs'])
-        v1_0_data['requirements'] = self.default_requirements()
-        if 'description' in v1_0_data:
-            v1_0_data['doc'] = deepcopy(v1_0_data['description'])
-            del v1_0_data['description']
-        for o in v1_0_data['outputs']:
+        if v1_data.get('cwlVersion') != 'sbg:draft-2':
+
+            return v1_data
+        v1_data['cwlVersion'] = self.cwl_version
+        v1_data['sbg:appVersion'] = [self.cwl_version]
+        v1_data['inputs'] = self.handle_inputs(v1_data['inputs'])
+        v1_data['outputs'] = self.handle_outputs(v1_data['outputs'])
+        v1_data['requirements'] = self.default_requirements()
+        if 'description' in v1_data:
+            v1_data['doc'] = deepcopy(v1_data['description'])
+            del v1_data['description']
+        for o in v1_data['outputs']:
             o['id'] = self.handle_id(o['id'])
             o['outputSource'] = self.handle_source(o['source'])
             del o['source']
-        if 'steps' in v1_0_data and isinstance(v1_0_data['steps'], list):
-            v1_0_data['steps'] = self.handle_steps(v1_0_data['steps'])
+        if 'steps' in v1_data and isinstance(v1_data['steps'], list):
+            v1_data['steps'] = self.handle_steps(v1_data['steps'])
         connection_checker = ConnectionChecker()
-        v1_0_data = connection_checker.fix_terminal_output_types(v1_0_data)
-        v1_0_data = connection_checker.fix_connection_matching(v1_0_data)
-        return v1_0_data
+        v1_data = connection_checker.fix_terminal_output_types(v1_data)
+        v1_data = connection_checker.fix_connection_matching(v1_data)
+        return v1_data
 
 
 def get_pool(pool=None):

setup.py

@@ -4,7 +4,7 @@
 
 
 NAME = 'sbg_cwl_upgrader'
-VERSION = '0.2.2'
+VERSION = '0.3.0'
 DIR = os.path.abspath(os.path.dirname(__file__))
 NOW = datetime.utcnow()
 

tests/converter/test_cwl_converter.py

@@ -31,6 +31,7 @@ def test_all_steps(self):
                                'wes_cwl1.json'), 'r') as f:
             result = json.load(f)
         c = object.__new__(CWLConverterFacade)
+        c.cwl_version = 'v1.0'
         converted = c._parse(in_data)
         for cwl_key in ['hints', 'steps', 'inputs', 'outputs', 'requirements']:
             self.assertEqual(len(converted[cwl_key]),

tests/converter/test_sbg_draft2_to_cwl1.py

@@ -18,6 +18,7 @@ def test_optional_defaults(self, mock_facade):
             endpoint=None,
             input_='a.cwl',
             output='b.cwl',
+            cwl_version='v1.0',
             platform='igor',
             profile='default',
             token=None,
@@ -30,13 +31,15 @@ def test_optional_defaults(self, mock_facade):
         'sbg_cwl_upgrader.converter.sbg_draft2_to_cwl_1_0.CWLConverterFacade'
     )
     def test_shorthand_inputs(self, mock_facade):
-        main(['-i', 'a.cwl', '-o', 'b.cwl', '-u', '-d', '-v', '-r', '2'])
+        main(['-i', 'a.cwl', '-o', 'b.cwl', '-c', 'v1.1',
+              '-u', '-d', '-v', '-r', '2'])
         mock_facade.assert_called_once_with(
             app_revision=2,
             decompose=True,
             endpoint=None,
             input_='a.cwl',
             output='b.cwl',
+            cwl_version='v1.1',
             platform='igor',
             profile='default',
             token=None,