fix object control

mmeds/tests/unit/test_analysis.py

@@ -15,20 +15,18 @@
 class AnalysisTests(TestCase):
     """ Test running analyses """
     @classmethod
-    def setUpClass(cls):
+    def setUpClass(self):
         """ Set up tests """
         # path to an example study, created from a MMEDs upload of existing test files
         # definied in config.py
-        cls.test_study = fig.TEST_STUDY
-        cls.watcher = Watcher()
-        cls.watcher.connect()
-        cls.queue = cls.watcher.get_queue()
-        cls.config = load_config(fig.DEFAULT_CONFIG, fig.TEST_MIXED_METADATA, 'standard_pipeline')
+        self.test_study = fig.TEST_STUDY
+        self.watcher = Watcher()
+        self.watcher.connect()
+        self.queue = self.watcher.get_queue()
+        self.config = load_config(fig.DEFAULT_CONFIG, fig.TEST_MIXED_METADATA, 'standard_pipeline')
+        self.analysis = []
         with Database(owner=fig.TEST_USER_0, testing=True) as db:
-            cls.analysis_code = db.create_access_code()
-            cls.runs = db.get_sequencing_run_locations(fig.TEST_MIXED_METADATA, fig.TEST_USER_0)
-        cls.analysis = Analysis(cls.queue, fig.TEST_USER_0, cls.analysis_code, fig.TEST_CODE_MIXED,
-                                'standard_pipeline', 'default', 'test_init', cls.config, True, cls.runs, False, threads=2)
+            self.analysis_code = db.create_access_code()
 
     def test_a_upload_sequencing_run(self):
         """ Upload sequencing run for analysis """
@@ -39,6 +37,13 @@ def test_a_upload_sequencing_run(self):
         sleep(5)
         self.assertEquals(result, 0)
 
+    def test_b_analysis_init(self):
+        """ Test analysis object """
+        with Database(owner=fig.TEST_USER_0, testing=True) as db:
+            self.runs = db.get_sequencing_run_locations(fig.TEST_MIXED_METADATA, fig.TEST_USER_0)
+        self.analysis += [Analysis(self.queue, fig.TEST_USER_0, self.analysis_code, fig.TEST_CODE_MIXED,
+                                'standard_pipeline', 'default', 'test_init', self.config, True, self.runs, False, threads=2)]
+
 
     def test_b_standard_pipeline(self):
         """ Test running a standard analysis """
@@ -54,21 +59,24 @@ def test_b_standard_pipeline(self):
 
     def test_c_analysis_class(self):
         """ Test the analysis object """
-        self.analysis.run()
+        analysis = self.analysis[0]
+        analysis.run()
 
-        info = self.analysis.get_info()
+        info = analysis.get_info()
         self.assertEquals(info['owner'], fig.TEST_USER_0)
         self.assertEquals(info['analysis_code'], self.analysis_code)
 
     def test_d_analysis_utils(self):
         """ Test that adding files to the tool object works properly """
-        Logger.info(str(self.analysis))
-        assert 'testfile' not in self.analysis.doc.files.keys()
-        self.analysis.add_path('testfile', '.txt')
-        assert 'testfile' in self.analysis.doc.files.keys()
+        analysis = self.analysis[0]
+        Logger.info(str(analysis))
+        assert 'testfile' not in analysis.doc.files.keys()
+        analysis.add_path('testfile', '.txt')
+        assert 'testfile' in analysis.doc.files.keys()
 
     def test_e_get_job_params(self):
-        params = self.analysis.get_job_params()
+        analysis = self.analysis[0]
+        params = analysis.get_job_params()
         assert params['nodes'] == 2
 
     def test_f_get_files(self):
@@ -77,17 +85,19 @@ def test_f_get_files(self):
 
     def test_g_missing_file(self):
         """ Test that an appropriate error will be raised if a file doesn't exist on disk """
-        files = self.analysis.doc.files
+        analysis = self.analysis[0]
+        files = analysis.doc.files
         # Add a nonexistent file
         files['fakefile'] = '/fake/dir'
-        self.analysis.update_doc(files=files)
+        analysis.update_doc(files=files)
         with self.assertRaises(err.MissingFileError):
-            self.analysis.get_file('fakefile', check=True)
+            analysis.get_file('fakefile', check=True)
         del files['fakefile']
-        self.analysis.update_doc(files=files)
+        analysis.update_doc(files=files)
 
     def test_h_update_doc(self):
-        self.assertEqual(self.analysis.doc.study_name, 'TEST_MIXED_17')
-        self.analysis.update_doc(study_name='Test_Update')
-        self.assertEqual(self.analysis.doc.study_name, 'Test_Update')
+        analysis = self.analysis[0]
+        self.assertEqual(analysis.doc.study_name, 'TEST_MIXED_17')
+        analysis.update_doc(study_name='Test_Update')
+        self.assertEqual(analysis.doc.study_name, 'Test_Update')