increase test coverage

giannisdoukas · Jun 9, 2020 · 0193752 · 0193752
1 parent 41e7f65
commit 0193752
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Showing 3 changed files with 34 additions and 8 deletions.
diff --git a/cwlkernel/cwlrepository/cwlrepository.py b/cwlkernel/cwlrepository/cwlrepository.py
@@ -42,9 +42,9 @@ def register_tool(self, tool: WorkflowComponent) -> None:
             path = Path(self._file_repository.write(f'{tool.id}.cwl', tool.to_yaml().encode()))
             self._registry[tool.id] = (deepcopy(tool), path)
 
-        def register_tools(self, *args):
-            for tool in args:
-                self.register_tool(tool)
+        # def register_tools(self, *args):
+        #     for tool in args:
+        #         self.register_tool(tool)
 
         def get_by_id(self, tool_id: str) -> Optional[WorkflowComponent]:
             comp = self._registry.get(tool_id, None)

diff --git a/tests/test_CWLKernel.py b/tests/test_CWLKernel.py
@@ -477,6 +477,7 @@ def test_compose(self):
 type: File
 % newWorkflowAddStepIn tailstepid headstepid headoutput
 tailinput: headstepid/headoutput
+% newWorkflowAddOutputSource tailstepid/tailoutput File
 % newWorkflowBuild""")
         )
 
@@ -486,7 +487,7 @@ def test_compose(self):
                 "class": "Workflow",
                 "id": "main",
                 "inputs": [{'id': 'inputfile', 'type': 'File'}],
-                "outputs": [],
+                "outputs": [{'id': 'tailoutput', 'type': 'File', 'outputSource': "tailstepid/tailoutput"}],
                 "steps": {
                     "headstepid":
                         {
@@ -498,7 +499,7 @@ def test_compose(self):
                         {
                             "run": "tail.cwl",
                             "in": {"tailinput": "headstepid/headoutput"},
-                            "out": []
+                            "out": ['tailoutput']
                         },
                 },
                 'requirements': {}

diff --git a/tests/test_cwlbuilder.py b/tests/test_cwlbuilder.py
@@ -1,9 +1,7 @@
-import tempfile
 import unittest
-from pathlib import Path
+from io import StringIO
 
 import yaml
-from io import StringIO
 
 from cwlkernel.CWLBuilder import CWLSnippetBuilder
 
@@ -90,3 +88,30 @@ def test_snippet_builder(self):
             yaml.load(StringIO(cwl_builder.get_current_code()), yaml.Loader),
             yaml.load(StringIO(cwl_workflow.to_yaml()), yaml.Loader)
         )
+
+    def test_build_without_id(self):
+        cwl_builder = CWLSnippetBuilder()
+        cwl_builder.append("""cwlVersion: v1.0
+class: CommandLineTool
+baseCommand: echo
+inputs:
+- id: message
+  inputBinding:
+    position: 1
+  type: string
+outputs: []""")
+        with self.assertRaises(ValueError):
+            cwl_builder.build()
+        cwl_builder.append("id: echo")
+        cwl_tool = cwl_builder.build()
+        self.assertDictEqual(
+            {'cwlVersion': 'v1.0',
+             'class': 'CommandLineTool',
+             'baseCommand': 'echo',
+             'id': 'echo',
+             'inputs': [{'id': 'message',
+                         'inputBinding': {'position': 1},
+                         'type': 'string'}],
+             'outputs': []},
+            cwl_tool.to_dict()
+        )