Merge pull request #114 from phac-nml/fix_batch_not_starting

Fixed batch uploads crashing, added unit tests to catch errors

CHANGELOG.md

@@ -1,6 +1,11 @@
 Changes
 =======
 
+Beta 0.6.1
+----------
+Bug fixes:
+* Fixed issue where starting a batch upload from the command line would crash instead of running.
+
 Beta 0.6.0
 ----------
 Added functionality:

iridauploader/__init__.py

@@ -1 +1 @@
-VERSION_NUMBER = "0.6.0"
+VERSION_NUMBER = "0.6.1"

iridauploader/core/cli.py

@@ -232,7 +232,7 @@ def main():
 
     # Start Upload
     if args.batch:
-        return upload_batch(args.directory, args.force, args.upload_mode, args.coninue_partial)
+        return upload_batch(args.directory, args.force, args.upload_mode, args.continue_partial)
     else:
         return upload(args.directory, args.force, args.upload_mode, args.continue_partial)
 

iridauploader/tests/core/test_cli.py

@@ -0,0 +1,122 @@
+import unittest
+from unittest.mock import patch
+from os import path
+
+from iridauploader.core import cli
+
+path_to_module = path.abspath(path.dirname(__file__))
+if len(path_to_module) == 0:
+    path_to_module = '.'
+
+
+class TestCliEntryPoints(unittest.TestCase):
+    """
+    Tests the core.cli package entry points into core.upload via main()
+    """
+
+    def setUp(self):
+        print("\nStarting " + self.__module__ + ": " + self._testMethodName)
+
+    @patch("iridauploader.core.upload.upload_run_single_entry")
+    @patch("iridauploader.core.cli._config_uploader")
+    @patch("iridauploader.core.cli.init_argparser")
+    def test_upload_regular(self, mock_init_argparser, mock_configure_uploader, mock_upload_run_single_entry):
+
+        class StubArgs:
+            """
+            Contains dummy properties that mimic the actual arguments object
+            """
+            @property
+            def directory(self):
+                return path_to_module
+
+            @property
+            def force(self):
+                return False
+
+            @property
+            def continue_partial(self):
+                return False
+
+            @property
+            def batch(self):
+                return False
+
+            @property
+            def upload_mode(self):
+                return None
+
+        stub_args_object = StubArgs()
+        # stub_argparser returns the above args object
+        stub_argparser = unittest.mock.MagicMock()
+        stub_argparser.parse_args.side_effect = [stub_args_object]
+        # mock_init_argparser returns the above stub_argparser, which contains the args object
+        mock_init_argparser.side_effect = [stub_argparser]
+
+        mock_configure_uploader.side_effect = [None]
+        # mock the core code exiting
+        stub_upload_exit = unittest.mock.MagicMock()
+        stub_upload_exit.exit_code.side_effect = 0
+        mock_upload_run_single_entry.side_effect = [stub_upload_exit]
+
+        cli.main()
+
+        # ensure the configuration is called
+        mock_configure_uploader.assert_called_once_with(stub_args_object)
+        # Verify final call
+        mock_upload_run_single_entry.assert_called_once_with(stub_args_object.directory,
+                                                             stub_args_object.force,
+                                                             stub_args_object.upload_mode,
+                                                             stub_args_object.continue_partial)
+
+    @patch("iridauploader.core.upload.batch_upload_single_entry")
+    @patch("iridauploader.core.cli._config_uploader")
+    @patch("iridauploader.core.cli.init_argparser")
+    def test_upload_batch(self, mock_init_argparser, mock_configure_uploader, mock_batch_upload_single_entry):
+
+        class StubArgs:
+            """
+            Contains dummy properties that mimic the actual arguments object
+            """
+            @property
+            def directory(self):
+                return path_to_module
+
+            @property
+            def force(self):
+                return False
+
+            @property
+            def continue_partial(self):
+                return False
+
+            @property
+            def batch(self):
+                return True
+
+            @property
+            def upload_mode(self):
+                return None
+
+        stub_args_object = StubArgs()
+        # stub_argparser returns the above args object
+        stub_argparser = unittest.mock.MagicMock()
+        stub_argparser.parse_args.side_effect = [stub_args_object]
+        # mock_init_argparser returns the above stub_argparser, which contains the args object
+        mock_init_argparser.side_effect = [stub_argparser]
+
+        mock_configure_uploader.side_effect = [None]
+        # mock the core code exiting
+        stub_upload_exit = unittest.mock.MagicMock()
+        stub_upload_exit.exit_code.side_effect = 0
+        mock_batch_upload_single_entry.side_effect = [stub_upload_exit]
+
+        cli.main()
+
+        # ensure the configuration is called
+        mock_configure_uploader.assert_called_once_with(stub_args_object)
+        # Verify final call
+        mock_batch_upload_single_entry.assert_called_once_with(stub_args_object.directory,
+                                                               stub_args_object.force,
+                                                               stub_args_object.upload_mode,
+                                                               stub_args_object.continue_partial)

setup.py

@@ -6,7 +6,7 @@
 
 setuptools.setup(
     name='iridauploader',
-    version='0.6.0',
+    version='0.6.1',
     description='IRIDA uploader: upload NGS data to IRIDA system',
     url='https://github.com/phac-nml/irida-uploader',
     author='Jeffrey Thiessen',

windows-installer.cfg

@@ -1,6 +1,6 @@
 [Application]
 name=IRIDA Uploader GUI
-version=0.6.0
+version=0.6.1
 entry_point=iridauploader.gui.gui:main
 icon=iridauploader/gui/images/icon.ico
 # Uncomment this to have a console show alongside the application