add workflow test

Author: mr-c

MANIFEST.in

@@ -0,0 +1,2 @@
+include MANIFEST.in
+include tests/*.cwl

cwlupgrader/main.py

@@ -5,12 +5,17 @@
 from collections import Mapping, MutableMapping, Sequence
 import sys
 import copy
-from typing import Any, Dict, List, Text, Union  # pylint:disable=unused-import
+from typing import (Any, Dict, List, Optional,  # pylint:disable=unused-import
+                    Text, Union)
 import ruamel.yaml
 
-def main():  # type: () -> int
+
+def main(args=None):  # type: (Optional[List[str]]) -> int
     """Main function."""
-    for path in sys.argv[1:]:
+    if not args:
+        args = sys.argv[1:]
+    assert args is not None
+    for path in args:
         with open(path) as entry:
             document = ruamel.yaml.safe_load(entry)
             if ('cwlVersion' in document
@@ -36,6 +41,7 @@ def draft3_to_v1_0(document):  # type: (Dict[Text, Any]) -> None
                         value[index] = _draft3_to_v1_0(entry)
     document['cwlVersion'] = 'v1.0'
 
+
 def _draft3_to_v1_0(document):
     # type: (MutableMapping[Text, Any]) -> MutableMapping[Text, Any]
     """Inner loop for transforming draft-3 to v1.0."""
@@ -144,7 +150,7 @@ def shorten_type(type_obj):  # type: (List[Any]) -> Union[Text, List[Any]]
         if 'null' in new_type:
             type_copy = copy.deepcopy(new_type)
             type_copy.remove('null')
-            if isinstance(type_copy[0], Text):
+            if isinstance(type_copy[0], (str, Text)):
                 return type_copy[0] + '?'
     return new_type
 
@@ -160,4 +166,4 @@ def clean_secondary_files(document):
 
 
 if __name__ == "__main__":
-    sys.exit(main())
+    sys.exit(main(sys.argv[:1]))

setup.py

@@ -3,13 +3,13 @@
 import os
 import sys
 
-from setuptools import setup, find_packages
+from setuptools import setup
 
 SETUP_DIR = os.path.dirname(__file__)
 README = os.path.join(SETUP_DIR, 'README.rst')
 
-needs_pytest = {'pytest', 'test', 'ptr'}.intersection(sys.argv)
-pytest_runner = ['pytest-runner', 'pytest-cov'] if needs_pytest else []
+NEEDS_PYTEST = {'pytest', 'test', 'ptr'}.intersection(sys.argv)
+PYTEST_RUNNER = ['pytest-runner', 'pytest-cov'] if NEEDS_PYTEST else []
 
 setup(name='cwl-upgrader',
       version='0.4.0',
@@ -20,8 +20,10 @@
       url="https://github.com/common-workflow-language/cwl-upgrader",
       download_url="https://github.com/common-workflow-language/cwl-upgrader",
       license='Apache 2.0',
-      packages=["cwlupgrader"],
+      packages=["cwlupgrader", "cwlupgrader.tests"],
+      package_dir={'cwlupgrader.tests': 'tests'},
       install_requires=[
+          'setuptools',
           'ruamel.yaml >= 0.14.12, < 0.15',
           'typing'],
       entry_points={
@@ -44,5 +46,6 @@
           'Topic :: Scientific/Engineering',
           'Topic :: Scientific/Engineering :: Bio-Informatics'],
       zip_safe=True,
-      setup_requires=[] + pytest_runner,
-      tests_require=['pytest'])
+      setup_requires=[] + PYTEST_RUNNER,
+      tests_require=['pytest'],
+      test_suite='tests')

tests/__init__.py

@@ -0,0 +1,28 @@
+class: Workflow
+cwlVersion: v1.0
+inputs:
+  input_file: File?
+outputs:
+  md5_report:
+    outputSource: md5/report
+    type: File?
+  validatefiles_report:
+    outputSource: validatefiles/report
+    type: File?
+requirements:
+  InlineJavascriptRequirement: {}
+steps:
+  md5:
+    in:
+      input_file: input_file
+    out:
+    - report
+    run: md5.cwl
+  validatefiles:
+    in:
+      input_file: input_file
+      type: {}
+    out:
+    - report
+    run: validate.cwl
+

tests/draft-3-wf-v1.0.cwl

@@ -0,0 +1,28 @@
+class: Workflow
+cwlVersion: draft-3
+inputs:
+- id: '#input_file'
+  type: ['null', File]
+outputs:
+- id: '#validatefiles_report'
+  source: '#validatefiles.report'
+  type: ['null', File]
+- id: '#md5_report'
+  source: '#md5.report'
+  type: ['null', File]
+requirements:
+- {class: InlineJavascriptRequirement}
+steps:
+- id: '#md5'
+  inputs:
+  - {id: '#md5.input_file', source: '#input_file'}
+  outputs:
+  - {id: '#md5.report'}
+  run: md5.cwl
+- id: '#validatefiles'
+  inputs:
+  - {id: '#validatefiles.input_file', source: '#input_file'}
+  - {id: '#validatefiles.type'}
+  outputs:
+  - {id: '#validatefiles.report'}
+  run: validate.cwl

tests/draft-3-wf.cwl

@@ -0,0 +1,16 @@
+import filecmp
+import os
+from cwlupgrader.main import main
+from .util import get_data
+
+
+def test_draft3_workflow(tmpdir, capsys):
+    main([get_data('tests/draft-3-wf.cwl')])
+    test_path = tmpdir.join("test.cwl")
+    with test_path.open('w') as outfile:
+        outfile.write(capsys.readouterr().out)
+        outfile.flush()
+        outfile.close()
+    result = filecmp.cmp('tests/draft-3-wf-v1.0.cwl', str(test_path),
+                         shallow=False)
+    assert result

tests/test_complete.py

@@ -0,0 +1,23 @@
+from __future__ import absolute_import
+import os
+
+from pkg_resources import (Requirement, ResolutionError,  # type: ignore
+                           resource_filename)
+
+
+def get_data(filename):
+    filename = os.path.normpath(filename)
+    # normalizing path depending on OS or else it will cause problem when
+    # joining path
+    filepath = None
+    try:
+        filepath = resource_filename(Requirement.parse("cwlupgrader"),
+                                     filename)
+    except ResolutionError:
+        pass
+    if not filepath or not os.path.isfile(filepath):
+        filepath = os.path.join(os.path.dirname(__file__), os.pardir, filename)
+        # warning, __file__ is all lowercase on Windows systems, this can
+        # sometimes conflict with docker toolkit. Workaround: pip install .
+        # and run the tests elsewhere via python -m pytest --pyarg cwltool
+    return filepath

tests/util.py

@@ -17,7 +17,7 @@ skipsdist = True
 deps =
   -rrequirements.txt
   lint: flake8
-  unit: pytest-xdist
+  # unit: pytest
   pydoc: pydocstyle
   tyle: diff-cover
   pycode: pycodestyle