add extra data types

common-workflow-lab · Jun 20, 2020 · df64c68 · df64c68
1 parent 39207ff
commit df64c68
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Showing 3 changed files with 39 additions and 3 deletions.
diff --git a/ipython2cwl/cwltool.py b/ipython2cwl/cwltool.py
@@ -11,7 +11,7 @@
 import astor
 import yaml
 
-from .iotypes import CWLFilePathInput, CWLBooleanInput
+from .iotypes import CWLFilePathInput, CWLBooleanInput, CWLIntInput, CWLStringInput
 from .requirements_manager import RequirementsManager
 
 with open(os.sep.join([os.path.abspath(os.path.dirname(__file__)), 'template.dockerfile'])) as f:
@@ -41,7 +41,17 @@ def visit_AnnAssign(self, node):
                 'boolean',
                 'click.BOOL',
                 input_flag,
-            )
+            ),
+            CWLIntInput.__name__: (
+                'int',
+                'click.INT',
+                input_flag,
+            ),
+            CWLStringInput.__name__: (
+                'string',
+                'click.STRING',
+                input_flag,
+            ),
         }
         """Mapping types. First tuple required, second optional"""
         try:

diff --git a/ipython2cwl/iotypes.py b/ipython2cwl/iotypes.py
@@ -7,3 +7,11 @@ class CWLFilePathInput(typing.TextIO):
 
 class CWLBooleanInput:
     pass
+
+
+class CWLStringInput:
+    pass
+
+
+class CWLIntInput:
+    pass
diff --git a/tests/test_cwltool.py b/tests/test_cwltool.py
@@ -7,15 +7,21 @@
 
 
 class TestCWLTool(TestCase):
+    maxDiff = None
 
     def test_AnnotatedIPython2CWLToolConverter_cwl_command_line_tool(self):
         annotated_python_script = os.linesep.join([
             "import csv",
             "input_filename: CWLFilePathInput = 'data.csv'",
             "flag: CWLBooleanInput = true",
+            "num: CWLIntInput = 1",
+            "msg: CWLStringInput = 'hello world'",
             "with open(input_filename) as f:",
             "\tcsv_reader = csv.reader(f)",
             "\tdata = [line for line in reader]",
+            "print(msg)",
+            "print(num)",
+            "print(flag)",
         ])
 
         cwl_tool = AnnotatedIPython2CWLToolConverter(annotated_python_script).cwl_command_line_tool()
@@ -39,7 +45,19 @@ def test_AnnotatedIPython2CWLToolConverter_cwl_command_line_tool(self):
                         'inputBinding': {
                             'prefix': '--flag'
                         }
-                    }
+                    },
+                    'num': {
+                        'type': 'int',
+                        'inputBinding': {
+                            'prefix': '--num'
+                        }
+                    },
+                    'msg': {
+                        'type': 'string',
+                        'inputBinding': {
+                            'prefix': '--msg'
+                        }
+                    },
                 },
                 'outputs': [],
             },