add ability to uncouple qtp-diversity filesystem

qtp_visualization/tests/test_data/bad_vis.qzv

@@ -0,0 +1 @@
+This is truly no qiime2 visualization!

qtp_visualization/tests/test_validate.py

@@ -26,7 +26,8 @@ def setUp(self):
         self.out_dir = mkdtemp()
         self._clean_up_files = [self.out_dir]
 
-        path_builder = partial(join, dirname(__file__), 'test_data')
+        path_builder = partial(join, self.base_data_dir,
+                               dirname(__file__), 'test_data')
         self.valid_qzv = path_builder('good_vis.qzv')
         self.invalid_qzv = path_builder('bad_vis.qzv')
 
@@ -43,19 +44,21 @@ def tearDown(self):
 
     def test_validate_q2_visualization(self):
         # Valid qzv
+        valid_qzv = self.qclient.push_file_to_central(self.valid_qzv)
         obs_succes, obs_ainfo, obs_error = _validate_q2_visualization(
-            {'qzv': [self.valid_qzv]}, self.out_dir)
+            {'qzv': [valid_qzv]}, self.out_dir)
         self.assertEqual(obs_error, "")
         self.assertTrue(obs_succes)
-        exp_files = [(self.valid_qzv, 'qzv'),
+        exp_files = [(valid_qzv, 'qzv'),
                      (join(self.out_dir, 'index.html'), 'html_summary'),
                      (join(self.out_dir, 'support_files'), 'html_summary_dir')]
         exp_ainfo = [ArtifactInfo(None, 'q2_visualization', exp_files)]
         self.assertEqual(obs_ainfo, exp_ainfo)
 
         # Invalid qzv
+        invalid_qzv = self.qclient.push_file_to_central(self.invalid_qzv)
         obs_succes, obs_ainfo, obs_error = _validate_q2_visualization(
-            {'qzv': [self.invalid_qzv]}, self.out_dir)
+            {'qzv': [invalid_qzv]}, self.out_dir)
         self.assertIn("Error loading Qiime 2 visualization:", obs_error)
         self.assertFalse(obs_succes)
         self.assertIsNone(obs_ainfo)
@@ -83,13 +86,14 @@ def test_validate(self):
         self.assertIsNone(obs_ainfo)
 
         # q2_visualization success
+        valid_qzv = self.qclient.push_file_to_central(self.valid_qzv)
         job_id, params = self._create_job('q2_visualization',
-                                          {'qzv': [self.valid_qzv]})
+                                          {'qzv': [valid_qzv]})
         obs_succes, obs_ainfo, obs_error = validate(
             self.qclient, job_id, params, self.out_dir)
         self.assertEqual(obs_error, "")
         self.assertTrue(obs_succes)
-        exp_files = [(self.valid_qzv, 'qzv'),
+        exp_files = [(valid_qzv, 'qzv'),
                      (join(self.out_dir, 'index.html'), 'html_summary'),
                      (join(self.out_dir, 'support_files'), 'html_summary_dir')]
         exp_ainfo = [ArtifactInfo(None, 'q2_visualization', exp_files)]

scripts/configure_visualization_types

@@ -17,12 +17,14 @@ from qtp_visualization import plugin
 @click.option('--env-script', prompt='Environment script',
               default='source activate qtp-visualization')
 @click.option('--server-cert', prompt='Server certificate', default='None')
-def config(env_script, server_cert):
+@click.argument('plugincoupling', required=False, default='filesystem')
+def config(env_script, server_cert, plugincoupling):
     """Generates the Qiita configuration files"""
     if server_cert == 'None':
         server_cert = None
     plugin.generate_config(env_script, 'start_visualization_types',
-                           server_cert=server_cert)
+                           server_cert=server_cert,
+                           plugin_coupling=plugincoupling)
 
 if __name__ == '__main__':
     config()