P3.6 items equal

.travis.yml

@@ -26,13 +26,13 @@ install:
     pyzmq networkx pyparsing natsort mock future libgfortran seaborn nltk pandas
     matplotlib scipy numpy h5py
   - source activate qiita
+  - 'echo "backend: Agg" > ~/matplotlibrc'
   - pip install sphinx sphinx-bootstrap-theme nose-timer codecov Click
   - git clone https://github.com/nicolasff/webdis
   - pushd webdis
   - make
   - ./webdis &
   - popd
-  # export PATH="$PATH:/Applications/Postgres.app/Contents/Versions/9.5/bin/"
   - travis_retry pip install . --process-dependency-links
   # loading redbiom with Qiita's test set
   # but first let's make sure redis is empty

qiita_core/configuration_manager.py

@@ -136,7 +136,7 @@ def __init__(self):
 
         # Parse the configuration file
         config = ConfigParser()
-        with open(conf_fp, 'U') as conf_file:
+        with open(conf_fp, newline=None) as conf_file:
             config.readfp(conf_file)
 
         _required_sections = {'main', 'redis', 'postgres', 'smtp', 'ebi',

qiita_core/tests/test_configuration_manager.py

@@ -30,7 +30,7 @@ def setUp(self):
         environ['QIITA_CONFIG_FP'] = self.conf_fp
 
         self.conf = ConfigParser()
-        with open(self.conf_fp, 'U') as f:
+        with open(self.conf_fp, newline=None) as f:
             self.conf.readfp(f)
 
     def tearDown(self):
@@ -136,9 +136,9 @@ def test_get_main(self):
         with warnings.catch_warnings(record=True) as warns:
             obs._get_main(self.conf)
 
-            obs_warns = [str(w.message) for w in warns]
+            obs_warns = [str(w) for w in warns]
             exp_warns = ['Random cookie secret generated.']
-            self.assertItemsEqual(obs_warns, exp_warns)
+            self.assertCountEqual(obs_warns, exp_warns)
 
         self.assertNotEqual(obs.cookie_secret, "SECRET")
         # Test default base_data_dir

qiita_core/tests/test_util.py

@@ -76,7 +76,7 @@ def test_get_release_info(self):
         # and then we will test that at least the 2nd element is correct
         self.assertNotEqual(biom_metadata_release, ('', '', ''))
         self.assertEqual(biom_metadata_release[1],
-                         'releases/QIITA-private.tgz')
+                         b'releases/QIITA-private.tgz')
         self.assertEqual(archive_release, ('', '', ''))
 
         generate_plugin_releases()

qiita_db/environment_manager.py

@@ -65,14 +65,14 @@ def create_layout(test=False, verbose=False):
         if verbose:
             print('Building SQL layout')
         # Create the schema
-        with open(LAYOUT_FP, 'U') as f:
+        with open(LAYOUT_FP, newline=None) as f:
             qdb.sql_connection.TRN.add(f.read())
         qdb.sql_connection.TRN.execute()
 
 
 def _populate_test_db():
     with qdb.sql_connection.TRN:
-        with open(POPULATE_FP, 'U') as f:
+        with open(POPULATE_FP, newline=None) as f:
             qdb.sql_connection.TRN.add(f.read())
         qdb.sql_connection.TRN.execute()
 
@@ -194,7 +194,7 @@ def make_environment(load_ontologies, download_reference, add_demo_user):
     except ValueError as error:
         # if database exists ignore
         msg = 'database "%s" already exists' % qiita_config.database
-        if msg in error.message:
+        if msg in str(error):
             print("Database exits, let's make sure it's test")
             with qdb.sql_connection.TRN:
                 # Insert the settings values to the database
@@ -218,7 +218,7 @@ def make_environment(load_ontologies, download_reference, add_demo_user):
         verbose = True
         if create_settings_table:
             # Build the SQL layout into the database
-            with open(SETTINGS_FP, 'U') as f:
+            with open(SETTINGS_FP, newline=None) as f:
                 qdb.sql_connection.TRN.add(f.read())
             qdb.sql_connection.TRN.execute()
 
@@ -425,7 +425,7 @@ def patch(patches_dir=PATCHES_DIR, verbose=False, test=False):
                 _populate_test_db()
 
         with qdb.sql_connection.TRN:
-            with open(sql_patch_fp, 'U') as patch_file:
+            with open(sql_patch_fp, newline=None) as patch_file:
                 if verbose:
                     print('\tApplying patch %s...' % sql_patch_filename)
                 qdb.sql_connection.TRN.add(patch_file.read())

qiita_db/handlers/oauth2.py

@@ -149,7 +149,7 @@ def write_error(self, status_code, **kwargs):
                 'ERROR:\n%s\nTRACE:\n%s\nHTTP INFO:\n%s\n' %
                 (error, trace_info, request_info))
 
-        message = exc_info[1].message
+        message = str(exc_info[1])
         if hasattr(exc_info[1], 'log_message'):
             message = exc_info[1].log_message
 

qiita_db/handlers/processing_job.py

@@ -142,7 +142,8 @@ def post(self, job_id):
             cmd = qiita_plugin.get_command('complete_job')
             params = qdb.software.Parameters.load(
                 cmd, values_dict={'job_id': job_id,
-                                  'payload': self.request.body})
+                                  'payload': self.request.body.decode(
+                                      'ascii')})
             job = qdb.processing_job.ProcessingJob.create(job.user, params)
             job.submit()
 

qiita_db/handlers/tests/test_analysis.py

@@ -43,7 +43,7 @@ def test_get(self):
         obs = loads(obs.body)
         exp = ['1.SKM4.640180', '1.SKB8.640193', '1.SKD8.640184',
                '1.SKM9.640192', '1.SKB7.640196']
-        self.assertItemsEqual(obs, exp)
+        self.assertCountEqual(obs, exp)
 
         exp = {'platform': 'Illumina', 'longitude': '95.5088566087',
                'experiment_center': 'ANL', 'center_name': 'ANL',

qiita_db/handlers/tests/test_prep_template.py

@@ -87,7 +87,7 @@ def test_get(self):
                '1.SKD3.640198', '1.SKB5.640181', '1.SKB4.640189',
                '1.SKB9.640200', '1.SKM9.640192', '1.SKD8.640184',
                '1.SKM5.640177', '1.SKM7.640188', '1.SKD7.640191']
-        self.assertItemsEqual(obs.keys(), exp)
+        self.assertCountEqual(obs.keys(), exp)
 
         obs = obs['1.SKB1.640202']
         exp = {
@@ -152,7 +152,7 @@ def test_post(self):
         self.assertEqual(obs.keys(), ['prep'])
 
         pt = qdb.metadata_template.prep_template.PrepTemplate(obs['prep'])
-        self.assertItemsEqual(pt.keys(), ['1.SKB8.640193', '1.SKD8.640184'])
+        self.assertCountEqual(pt.keys(), ['1.SKB8.640193', '1.SKD8.640184'])
 
         # testing that a new prep doesn't break the call due to empty artifact
         obs = self.get('/qiita_db/prep_template/%d/' % pt.id,

qiita_db/handlers/tests/test_processing_job.py

@@ -161,7 +161,7 @@ def test_post_job_not_running(self):
             '/qiita_db/jobs/063e553b-327c-4818-ab4a-adfe58e49860/complete/',
             payload, headers=self.header)
         self.assertEqual(obs.code, 403)
-        self.assertEqual(obs.body,
+        self.assertEqual(obs.body.decode('ascii'),
                          "Can't complete job: not in a running state")
 
     def test_post_job_failure(self):
@@ -280,7 +280,7 @@ def test_post_processing_job(self):
         self.assertEqual(obs.code, 200)
 
         obs = loads(obs.body)
-        self.assertEqual(obs.keys(), ['job'])
+        self.assertEqual(list(obs.keys()), ['job'])
         self.assertIsNotNone(obs['job'])
 
     def test_post_processing_job_status(self):
@@ -302,7 +302,7 @@ def test_post_processing_job_status(self):
         self.assertEqual(obs.code, 200)
 
         obs = loads(obs.body)
-        self.assertEqual(obs.keys(), ['job'])
+        self.assertEqual(list(obs.keys()), ['job'])
         job_id = obs['job']
         self.assertTrue(qdb.processing_job.ProcessingJob.exists(job_id))
         self.assertEqual(qdb.processing_job.ProcessingJob(job_id).status,

qiita_db/handlers/tests/test_sample_information.py

@@ -42,7 +42,7 @@ def test_get(self):
                '1.SKD3.640198', '1.SKB5.640181', '1.SKB4.640189',
                '1.SKB9.640200', '1.SKM9.640192', '1.SKD8.640184',
                '1.SKM5.640177', '1.SKM7.640188', '1.SKD7.640191']
-        self.assertItemsEqual(obs.keys(), exp)
+        self.assertCountEqual(obs.keys(), exp)
 
         obs = obs['1.SKB1.640202']
         exp = {'qiita_study_id': '1', 'physical_specimen_location': 'ANL',

qiita_db/meta_util.py

@@ -455,7 +455,6 @@ def generate_biom_and_metadata_release(study_status='public'):
 
         txt_hd.seek(0)
         info = TarInfo(name='%s-%s-%s.txt' % (portal, study_status, ts))
-        info.size = len(txt_hd.buf)
         tgz.addfile(tarinfo=info, fileobj=txt_hd)
 
     with open(tgz_name, "rb") as f:

qiita_db/metadata_template/test/test_base_metadata_template.py

@@ -73,7 +73,7 @@ def test_identify_pgsql_reserved_words(self):
             'select',
             'column',
             'just_fine1'])
-        self.assertItemsEqual(set(results), {'column', 'select'})
+        self.assertCountEqual(set(results), {'column', 'select'})
 
     def test_identify_invalid_characters(self):
         MT = qdb.metadata_template.base_metadata_template.MetadataTemplate
@@ -87,7 +87,7 @@ def test_identify_invalid_characters(self):
             'this|is',
             '4column',
             'just_fine2'])
-        self.assertItemsEqual(set(results), {'tax on',
+        self.assertCountEqual(set(results), {'tax on',
                                              'bla.',
                                              '.',
                                              '{',

qiita_db/metadata_template/test/test_prep_template.py

@@ -258,7 +258,7 @@ def test_metadata_headers(self):
                'primer', 'run_center', 'run_date', 'run_prefix', 'samp_size',
                'sample_center', 'sequencing_meth', 'study_center',
                'target_gene', 'target_subfragment']
-        self.assertItemsEqual(obs, exp)
+        self.assertCountEqual(obs, exp)
 
     def test_setitem(self):
         with self.assertRaises(qdb.exceptions.QiitaDBColumnError):
@@ -877,7 +877,7 @@ def _common_creation_checks(self, pt, fp_count, name):
                           'instrument_model', 'experiment_design_description',
                           'library_construction_protocol', 'center_name',
                           'center_project_name', 'emp_status'}
-        self.assertItemsEqual(pt.categories(), exp_categories)
+        self.assertCountEqual(pt.categories(), exp_categories)
         exp_dict = {
             '%s.SKB7.640196' % self.test_study.id: {
                 'barcode': 'CCTCTGAGAGCT',
@@ -1010,7 +1010,7 @@ def test_create_warning(self):
                           'instrument_model', 'experiment_design_description',
                           'library_construction_protocol', 'center_name',
                           'center_project_name', 'emp_status'}
-        self.assertItemsEqual(pt.categories(), exp_categories)
+        self.assertCountEqual(pt.categories(), exp_categories)
         exp_dict = {
             '%s.SKB7.640196' % self.test_study.id: {
                 'ebi_submission_accession': None,
@@ -1134,7 +1134,7 @@ def test_to_file(self):
             self.metadata, self.test_study, self.data_type)
         pt.to_file(fp)
         self._clean_up_files.append(fp)
-        with open(fp, 'U') as f:
+        with open(fp, newline=None) as f:
             obs = f.read()
         self.assertEqual(obs, EXP_PREP_TEMPLATE.format(pt.id))
 
@@ -1329,7 +1329,7 @@ def test_extend_add_cols(self):
                 'center_project_name': 'Test Project',
                 'emp_status': 'EMP',
                 'new_col': 'val3'}}
-        self.assertItemsEqual(obs, exp)
+        self.assertCountEqual(obs, exp)
 
     def test_extend_update(self):
         pt = qdb.metadata_template.prep_template.PrepTemplate.create(
@@ -1388,7 +1388,7 @@ def test_extend_update(self):
                 'emp_status': 'EMP',
                 'new_col': 'val3'}}
 
-        self.assertItemsEqual(obs, exp)
+        self.assertCountEqual(obs, exp)
 
     def test_ebi_experiment_accessions(self):
         obs = self.tester.ebi_experiment_accessions