fix errors

qiita-spots · Apr 3, 2017 · 17e8db1 · 17e8db1
1 parent 88c1358
commit 17e8db1
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Showing 4 changed files with 127 additions and 101 deletions.
diff --git a/qiita_db/test/test_artifact.py b/qiita_db/test/test_artifact.py
@@ -966,8 +966,8 @@ def test_visibility_setter(self):
         #              /- 2 (private) -|- 5 (private)
         # 1 (private) -|               \- 6 (private)
         #              \- 3 (private)
-        # By changing the visibility of 4 to public, the visibility of 1 and
-        # 2 also changes to public
+        # By changing the visibility of 4 to public, the visibility of all
+        # should change
         a1 = qdb.artifact.Artifact(1)
         a2 = qdb.artifact.Artifact(2)
         a3 = qdb.artifact.Artifact(3)
@@ -979,17 +979,16 @@ def test_visibility_setter(self):
 
         self.assertEqual(a1.visibility, "public")
         self.assertEqual(a2.visibility, "public")
-        self.assertEqual(a3.visibility, "private")
+        self.assertEqual(a3.visibility, "public")
         self.assertEqual(a4.visibility, "public")
-        self.assertEqual(a5.visibility, "private")
-        self.assertEqual(a6.visibility, "private")
+        self.assertEqual(a5.visibility, "public")
+        self.assertEqual(a6.visibility, "public")
 
-        # However, if we change it back to private,
-        # it should remain public
+        # Same if we go back
         a4.visibility = 'private'
 
-        self.assertEqual(a1.visibility, "public")
-        self.assertEqual(a2.visibility, "public")
+        self.assertEqual(a1.visibility, "private")
+        self.assertEqual(a2.visibility, "private")
         self.assertEqual(a3.visibility, "private")
         self.assertEqual(a4.visibility, "private")
         self.assertEqual(a5.visibility, "private")

diff --git a/qiita_db/test/test_util.py b/qiita_db/test/test_util.py
@@ -968,89 +968,119 @@ def test_generate_study_list(self):
 
         qdb.artifact.Artifact(4).visibility = 'public'
         exp_info[0]['status'] = 'public'
-        exp_info[0]['proc_data_info'] = [{
-            'data_type': '18S',
-            'algorithm': 'QIIME (Pick closed-reference OTUs)',
-            'pid': 4,
-            'processed_date': '2012-10-02 17:30:00',
-            'params': {
-                'similarity': 0.97,
-                'reference_name': 'Greengenes',
-                'sortmerna_e_value': 1,
-                'sortmerna_max_pos': 10000,
-                'threads': 1,
-                'sortmerna_coverage': 0.97,
-                'reference_version': '13_8'},
-            'samples': ['1.SKB1.640202', '1.SKB2.640194', '1.SKB3.640195',
-                        '1.SKB4.640189', '1.SKB5.640181', '1.SKB6.640176',
-                        '1.SKB7.640196', '1.SKB8.640193', '1.SKB9.640200',
-                        '1.SKD1.640179', '1.SKD2.640178', '1.SKD3.640198',
-                        '1.SKD4.640185', '1.SKD5.640186', '1.SKD6.640190',
-                        '1.SKD7.640191', '1.SKD8.640184', '1.SKD9.640182',
-                        '1.SKM1.640183', '1.SKM2.640199', '1.SKM3.640197',
-                        '1.SKM4.640180', '1.SKM5.640177', '1.SKM6.640187',
-                        '1.SKM7.640188', '1.SKM8.640201', '1.SKM9.640192']}]
+        exp_info[0]['proc_data_info'] = [
+            {'data_type': '18S',
+             'algorithm': 'QIIME (Pick closed-reference OTUs)', 'pid': 4,
+             'processed_date': '2012-10-02 17:30:00',
+             'params': {'similarity': 0.97, 'reference_name': 'Greengenes',
+                        'sortmerna_e_value': 1, u'sortmerna_max_pos': 10000,
+                        'threads': 1, u'sortmerna_coverage': 0.97,
+                        'reference_version': '13_8'},
+             'samples': ['1.SKB1.640202', '1.SKB2.640194', '1.SKB3.640195',
+                         '1.SKB4.640189', '1.SKB5.640181', '1.SKB6.640176',
+                         '1.SKB7.640196', '1.SKB8.640193', '1.SKB9.640200',
+                         '1.SKD1.640179', '1.SKD2.640178', '1.SKD3.640198',
+                         '1.SKD4.640185', '1.SKD5.640186', '1.SKD6.640190',
+                         '1.SKD7.640191', '1.SKD8.640184', '1.SKD9.640182',
+                         '1.SKM1.640183', '1.SKM2.640199', '1.SKM3.640197',
+                         '1.SKM4.640180', '1.SKM5.640177', '1.SKM6.640187',
+                         '1.SKM7.640188', '1.SKM8.640201', '1.SKM9.640192']},
+            {'data_type': '18S',
+             'algorithm': 'QIIME (Pick closed-reference OTUs)', 'pid': 5,
+             'processed_date': '2012-10-02 17:30:00',
+             'params': {'similarity': 0.97, 'reference_name': 'Greengenes',
+                        'sortmerna_e_value': 1, u'sortmerna_max_pos': 10000,
+                        'threads': 1, 'sortmerna_coverage': 0.97,
+                        'reference_version': '13_8'},
+             'samples': ['1.SKB1.640202', '1.SKB2.640194', '1.SKB3.640195',
+                         '1.SKB4.640189', '1.SKB5.640181', '1.SKB6.640176',
+                         '1.SKB7.640196', '1.SKB8.640193', '1.SKB9.640200',
+                         '1.SKD1.640179', '1.SKD2.640178', '1.SKD3.640198',
+                         '1.SKD4.640185', '1.SKD5.640186', '1.SKD6.640190',
+                         '1.SKD7.640191', '1.SKD8.640184', '1.SKD9.640182',
+                         '1.SKM1.640183', '1.SKM2.640199', '1.SKM3.640197',
+                         '1.SKM4.640180', '1.SKM5.640177', '1.SKM6.640187',
+                         '1.SKM7.640188', '1.SKM8.640201', '1.SKM9.640192']},
+            {'data_type': '16S',
+             'algorithm': 'QIIME (Pick closed-reference OTUs)', 'pid': 6,
+             'processed_date': '2012-10-02 17:30:00',
+             'params': {'similarity': 0.97, 'reference_name': 'Silva',
+                        'sortmerna_e_value': 1, u'sortmerna_max_pos': 10000,
+                        'threads': 1, 'sortmerna_coverage': 0.97,
+                        'reference_version': 'test'},
+             'samples': ['1.SKB1.640202', '1.SKB2.640194', '1.SKB3.640195',
+                         '1.SKB4.640189', '1.SKB5.640181', '1.SKB6.640176',
+                         '1.SKB7.640196', '1.SKB8.640193', '1.SKB9.640200',
+                         '1.SKD1.640179', '1.SKD2.640178', '1.SKD3.640198',
+                         '1.SKD4.640185', '1.SKD5.640186', '1.SKD6.640190',
+                         '1.SKD7.640191', '1.SKD8.640184', '1.SKD9.640182',
+                         '1.SKM1.640183', '1.SKM2.640199', '1.SKM3.640197',
+                         '1.SKM4.640180', '1.SKM5.640177', '1.SKM6.640187',
+                         '1.SKM7.640188', '1.SKM8.640201', '1.SKM9.640192']}]
         obs_info = qdb.util.generate_study_list([1, 2, 3, 4], True,
                                                 public_only=True)
         self.assertEqual(obs_info, exp_info)
 
-        exp_info[0]['proc_data_info'].extend(
-           [{
-            'data_type': '18S',
-            'algorithm': 'QIIME (Pick closed-reference OTUs)',
-            'pid': 5,
-            'processed_date': '2012-10-02 17:30:00',
-            'params': {
-                'similarity': 0.97,
-                'reference_name': 'Greengenes',
-                'sortmerna_e_value': 1,
-                'sortmerna_max_pos': 10000,
-                'threads': 1,
-                'sortmerna_coverage': 0.97,
-                'reference_version': '13_8'},
-            'samples': ['1.SKB1.640202', '1.SKB2.640194', '1.SKB3.640195',
-                        '1.SKB4.640189', '1.SKB5.640181', '1.SKB6.640176',
-                        '1.SKB7.640196', '1.SKB8.640193', '1.SKB9.640200',
-                        '1.SKD1.640179', '1.SKD2.640178', '1.SKD3.640198',
-                        '1.SKD4.640185', '1.SKD5.640186', '1.SKD6.640190',
-                        '1.SKD7.640191', '1.SKD8.640184', '1.SKD9.640182',
-                        '1.SKM1.640183', '1.SKM2.640199', '1.SKM3.640197',
-                        '1.SKM4.640180', '1.SKM5.640177', '1.SKM6.640187',
-                        '1.SKM7.640188', '1.SKM8.640201', '1.SKM9.640192']}, {
-            'data_type': '16S',
-            'algorithm': 'QIIME (Pick closed-reference OTUs)',
-            'pid': 6,
-            'processed_date': '2012-10-02 17:30:00',
-            'params': {
-                'similarity': 0.97,
-                'reference_name': 'Silva',
-                'sortmerna_e_value': 1,
-                'sortmerna_max_pos': 10000,
-                'threads': 1,
-                'sortmerna_coverage': 0.97,
-                'reference_version': 'test'},
-            'samples': ['1.SKB1.640202', '1.SKB2.640194', '1.SKB3.640195',
-                        '1.SKB4.640189', '1.SKB5.640181', '1.SKB6.640176',
-                        '1.SKB7.640196', '1.SKB8.640193', '1.SKB9.640200',
-                        '1.SKD1.640179', '1.SKD2.640178', '1.SKD3.640198',
-                        '1.SKD4.640185', '1.SKD5.640186', '1.SKD6.640190',
-                        '1.SKD7.640191', '1.SKD8.640184', '1.SKD9.640182',
-                        '1.SKM1.640183', '1.SKM2.640199', '1.SKM3.640197',
-                        '1.SKM4.640180', '1.SKM5.640177', '1.SKM6.640187',
-                        '1.SKM7.640188', '1.SKM8.640201', '1.SKM9.640192']}, {
-            'processed_date': '2012-10-02 17:30:00',
-            'pid': 7,
-            'samples': ['1.SKB1.640202', '1.SKB2.640194', '1.SKB3.640195',
-                        '1.SKB4.640189', '1.SKB5.640181', '1.SKB6.640176',
-                        '1.SKB7.640196', '1.SKB8.640193', '1.SKB9.640200',
-                        '1.SKD1.640179', '1.SKD2.640178', '1.SKD3.640198',
-                        '1.SKD4.640185', '1.SKD5.640186', '1.SKD6.640190',
-                        '1.SKD7.640191', '1.SKD8.640184', '1.SKD9.640182',
-                        '1.SKM1.640183', '1.SKM2.640199', '1.SKM3.640197',
-                        '1.SKM4.640180', '1.SKM5.640177', '1.SKM6.640187',
-                        '1.SKM7.640188', '1.SKM8.640201', '1.SKM9.640192'],
-            'data_type': '16S'}])
-
+        exp_info[0]['proc_data_info'] = [
+            {'data_type': '18S',
+             'algorithm': 'QIIME (Pick closed-reference OTUs)', 'pid': 4,
+             'processed_date': '2012-10-02 17:30:00',
+             'params': {'similarity': 0.97, 'reference_name': 'Greengenes',
+                        'sortmerna_e_value': 1, u'sortmerna_max_pos': 10000,
+                        'threads': 1, 'sortmerna_coverage': 0.97,
+                        'reference_version': '13_8'},
+             'samples': ['1.SKB1.640202', '1.SKB2.640194', '1.SKB3.640195',
+                         '1.SKB4.640189', '1.SKB5.640181', '1.SKB6.640176',
+                         '1.SKB7.640196', '1.SKB8.640193', '1.SKB9.640200',
+                         '1.SKD1.640179', '1.SKD2.640178', '1.SKD3.640198',
+                         '1.SKD4.640185', '1.SKD5.640186', '1.SKD6.640190',
+                         '1.SKD7.640191', '1.SKD8.640184', '1.SKD9.640182',
+                         '1.SKM1.640183', '1.SKM2.640199', '1.SKM3.640197',
+                         '1.SKM4.640180', '1.SKM5.640177', '1.SKM6.640187',
+                         '1.SKM7.640188', '1.SKM8.640201', '1.SKM9.640192']},
+            {'data_type': '18S',
+             'algorithm': 'QIIME (Pick closed-reference OTUs)', 'pid': 5,
+             'processed_date': '2012-10-02 17:30:00',
+             'params': {'similarity': 0.97, 'reference_name': 'Greengenes',
+                        'sortmerna_e_value': 1, u'sortmerna_max_pos': 10000,
+                        'threads': 1, 'sortmerna_coverage': 0.97,
+                        'reference_version': '13_8'},
+             'samples': ['1.SKB1.640202', '1.SKB2.640194', '1.SKB3.640195',
+                         '1.SKB4.640189', '1.SKB5.640181', '1.SKB6.640176',
+                         '1.SKB7.640196', '1.SKB8.640193', '1.SKB9.640200',
+                         '1.SKD1.640179', '1.SKD2.640178', '1.SKD3.640198',
+                         '1.SKD4.640185', '1.SKD5.640186', '1.SKD6.640190',
+                         '1.SKD7.640191', '1.SKD8.640184', '1.SKD9.640182',
+                         '1.SKM1.640183', '1.SKM2.640199', '1.SKM3.640197',
+                         '1.SKM4.640180', '1.SKM5.640177', '1.SKM6.640187',
+                         '1.SKM7.640188', '1.SKM8.640201', '1.SKM9.640192']},
+            {'data_type': '16S',
+             'algorithm': 'QIIME (Pick closed-reference OTUs)', 'pid': 6,
+             'processed_date': '2012-10-02 17:30:00',
+             'params': {'similarity': 0.97, 'reference_name': 'Silva',
+                        'sortmerna_e_value': 1, u'sortmerna_max_pos': 10000,
+                        'threads': 1, 'sortmerna_coverage': 0.97,
+                        'reference_version': 'test'},
+             'samples': ['1.SKB1.640202', '1.SKB2.640194', '1.SKB3.640195',
+                         '1.SKB4.640189', '1.SKB5.640181', '1.SKB6.640176',
+                         '1.SKB7.640196', '1.SKB8.640193', '1.SKB9.640200',
+                         '1.SKD1.640179', '1.SKD2.640178', '1.SKD3.640198',
+                         '1.SKD4.640185', '1.SKD5.640186', '1.SKD6.640190',
+                         '1.SKD7.640191', '1.SKD8.640184', '1.SKD9.640182',
+                         '1.SKM1.640183', '1.SKM2.640199', '1.SKM3.640197',
+                         '1.SKM4.640180', '1.SKM5.640177', '1.SKM6.640187',
+                         '1.SKM7.640188', '1.SKM8.640201', '1.SKM9.640192']},
+            {'processed_date': '2012-10-02 17:30:00', 'pid': 7,
+             'samples': ['1.SKB1.640202', '1.SKB2.640194', '1.SKB3.640195',
+                         '1.SKB4.640189', '1.SKB5.640181', '1.SKB6.640176',
+                         '1.SKB7.640196', '1.SKB8.640193', '1.SKB9.640200',
+                         '1.SKD1.640179', '1.SKD2.640178', '1.SKD3.640198',
+                         '1.SKD4.640185', '1.SKD5.640186', '1.SKD6.640190',
+                         '1.SKD7.640191', '1.SKD8.640184', '1.SKD9.640182',
+                         '1.SKM1.640183', '1.SKM2.640199', '1.SKM3.640197',
+                         '1.SKM4.640180', '1.SKM5.640177', '1.SKM6.640187',
+                         '1.SKM7.640188', '1.SKM8.640201', '1.SKM9.640192'],
+             'data_type': '16S'}]
         obs_info = qdb.util.generate_study_list([1, 2, 3, 4], True)
         self.assertEqual(obs_info, exp_info)
 

diff --git a/qiita_pet/handlers/api_proxy/tests/test_artifact.py b/qiita_pet/handlers/api_proxy/tests/test_artifact.py
@@ -302,7 +302,7 @@ def test_artifact_summary_get_request(self):
                'files': exp_files,
                'errored_jobs': [],
                'editable': True,
-               'visibility': 'private',
+               'visibility': 'sandbox',
                'job': None,
                'message': '',
                'name': 'Demultiplexed 1',
@@ -316,17 +316,14 @@ def test_artifact_summary_get_request(self):
                    'min_per_read_length_fraction': 0.75,
                    'barcode_type': u'golay_12'},
                'summary': None,
-               'buttons': ('<button onclick="if (confirm(\'Are you sure you '
-                           'want to make public artifact id: 2?\')) { '
-                           'set_artifact_visibility(\'public\', 2) }" '
-                           'class="btn btn-primary btn-sm">Make public'
-                           '</button> <button onclick="if (confirm(\'Are you '
-                           'sure you want to revert to sandbox artifact id: '
-                           '2?\')) { set_artifact_visibility(\'sandbox\', 2) '
-                           '}" class="btn btn-primary btn-sm">Revert to '
-                           'sandbox</button> <a class="btn btn-primary '
-                           'btn-sm" href="/vamps/2"><span class="glyphicon '
-                           'glyphicon-export"></span> Submit to VAMPS</a>'),
+               'buttons': (
+                   '<button onclick="if (confirm(\'Are you sure you want to '
+                   'request approval for artifact id: 2?\')) { '
+                   'set_artifact_visibility(\'awaiting_approval\', 2) }" '
+                   'class="btn btn-primary btn-sm">Request approval</button> '
+                   '<a class="btn btn-primary btn-sm" href="/vamps/2"><span '
+                   'class="glyphicon glyphicon-export"></span> Submit to '
+                   'VAMPS</a>'),
                'study_id': 1,
                'prep_id': 1}
         self.assertEqual(obs, exp)

diff --git a/qiita_pet/handlers/api_proxy/tests/test_prep_template.py b/qiita_pet/handlers/api_proxy/tests/test_prep_template.py
@@ -332,7 +332,7 @@ def test_prep_template_graph_get_req(self):
         obs = prep_template_graph_get_req(1, 'demo@microbio.me')
         self.assertEqual(obs['message'], '')
         self.assertEqual(obs['status'], 'success')
-        self.assertEqual(8, len(obs['node_labels']))
+        self.assertEqual(11, len(obs['node_labels']))
         self.assertIn(('artifact', 1, 'Raw data 1 - FASTQ'),
                       obs['node_labels'])
         self.assertIn(('artifact', 2, 'Demultiplexed 1 - Demultiplexed'),