Bringing back the green tick (i.e. pass the tests again)

.travis.yml

@@ -42,7 +42,7 @@ script:
   - qiita-env make --no-load-ontologies
   - if [ ${TEST_ADD_STUDIES} == "True" ]; then test_data_studies/commands.sh ; fi
   - if [ ${TEST_ADD_STUDIES} == "False" ]; then qiita-test-install ; fi
-  - if [ ${TEST_ADD_STUDIES} == "False" ]; then nosetests --with-doctest --with-coverage; fi
+  - if [ ${TEST_ADD_STUDIES} == "False" ]; then nosetests --with-doctest --with-coverage -v; fi
   - flake8 qiita_* setup.py scripts/qiita scripts/qiita-env scripts/qiita-test-install
   - ls -R /home/travis/miniconda3/envs/env_name/lib/python2.7/site-packages/qiita_pet/support_files/doc/
   - qiita pet webserver

qiita_db/artifact.py

@@ -376,17 +376,18 @@ def delete(cls, artifact_id):
                 raise qdb.exceptions.QiitaDBArtifactDeletionError(
                     artifact_id, "it has been submitted to VAMPS")
 
-            # Check if there is a job queued or running that will use/is using
-            # the artifact
+            # Check if there is a job queued, running, waiting or
+            # in_construction that will use/is using the artifact
             sql = """SELECT EXISTS(
                         SELECT *
                         FROM qiita.artifact_processing_job
                             JOIN qiita.processing_job USING (processing_job_id)
                             JOIN qiita.processing_job_status
                                 USING (processing_job_status_id)
                         WHERE artifact_id = %s
-                            AND processing_job_status IN ('queued', 'running'))
-                  """
+                            AND processing_job_status IN (
+                                'queued', 'running', 'waiting',
+                                'in_construction'))"""
             qdb.sql_connection.TRN.add(sql, [artifact_id])
             if qdb.sql_connection.TRN.execute_fetchlast():
                 raise qdb.exceptions.QiitaDBArtifactDeletionError(
@@ -772,7 +773,7 @@ def filepaths(self):
             with the artifact
         """
         return qdb.util.retrieve_filepaths(
-            "artifact_filepath", "artifact_id", self.id)
+            "artifact_filepath", "artifact_id", self.id, sort='ascending')
 
     @property
     def parents(self):

qiita_db/handlers/tests/test_processing_job.py

@@ -177,7 +177,7 @@ def test_post_job_does_not_exists(self):
         self.assertEqual(loads(obs.body), exp)
 
     def test_post_job_not_running(self):
-        payload = dumps({'success': False, 'error': 'Job failure'})
+        payload = dumps({'success': True, 'artifacts': []})
         obs = self.post(
             '/qiita_db/jobs/063e553b-327c-4818-ab4a-adfe58e49860/complete/',
             payload, headers=self.header)

qiita_db/test/test_artifact.py

@@ -116,7 +116,7 @@ def test_types(self):
                ['Demultiplexed', 'Demultiplexed and QC sequeneces'],
                ['FASTA', None], ['FASTA_Sanger', None], ['FASTQ', None],
                ['SFF', None], ['per_sample_FASTQ', None]]
-        self.assertEqual(obs, exp)
+        self.assertItemsEqual(obs, exp)
 
     def test_copy(self):
         src = qdb.artifact.Artifact(1)
@@ -336,7 +336,7 @@ def test_delete_error_vamps(self):
         with self.assertRaises(qdb.exceptions.QiitaDBArtifactDeletionError):
             qdb.artifact.Artifact.delete(obs.id)
 
-    def test_delete_error_queued_job(self):
+    def test_delete_error_in_construction_job(self):
         test = qdb.artifact.Artifact.create(
             self.filepaths_root, 'FASTQ', prep_template=self.prep_template)
         self._clean_up_files.extend([fp for _, fp, _ in test.filepaths])

qiita_db/test/test_processing_job.py

@@ -470,7 +470,7 @@ def test_graph_only_root(self):
 
     def test_raise_if_not_in_construction(self):
         # We just need to test that the execution continues (i.e. no raise)
-        tester = qdb.processing_job.ProcessingWorkflow(1)
+        tester = qdb.processing_job.ProcessingWorkflow(2)
         tester._raise_if_not_in_construction()
 
     def test_raise_if_not_in_construction_error(self):

qiita_db/test/test_study.py

@@ -1,8 +1,6 @@
 from unittest import TestCase, main
 from datetime import datetime
 
-from future.utils import viewitems
-
 from qiita_core.exceptions import IncompetentQiitaDeveloperError
 from qiita_core.qiita_settings import qiita_config
 from qiita_core.util import qiita_test_checker
@@ -138,20 +136,20 @@ def setUp(self):
             "study_abstract": "Exploring how a high fat diet changes the "
                               "gut microbiome",
             "emp_person_id": 2,
-            "principal_investigator_id": 3,
-            "lab_person_id": 1
+            "principal_investigator": qdb.study.StudyPerson(3),
+            "lab_person": qdb.study.StudyPerson(1)
         }
 
         self.existingexp = {
             'mixs_compliant': True,
             'metadata_complete': True,
             'reprocess': False,
             'number_samples_promised': 27,
-            'emp_person_id': qdb.study.StudyPerson(2),
+            'emp_person_id': 2,
             'funding': None,
             'vamps_id': None,
             'first_contact': datetime(2014, 5, 19, 16, 10),
-            'principal_investigator_id': qdb.study.StudyPerson(3),
+            'principal_investigator': qdb.study.StudyPerson(3),
             'timeseries_type_id': 1,
             'study_abstract':
                 "This is a preliminary study to examine the "
@@ -169,7 +167,7 @@ def setUp(self):
             'study_alias': 'Cannabis Soils',
             'most_recent_contact': '2014-05-19 16:11',
             'most_recent_contact': datetime(2014, 5, 19, 16, 11),
-            'lab_person_id': qdb.study.StudyPerson(1),
+            'lab_person': qdb.study.StudyPerson(1),
             'number_samples_collected': 27}
 
     def tearDown(self):
@@ -361,15 +359,16 @@ def test_create_study_min_data(self):
                'reprocess': False,
                'number_samples_promised': 28, 'emp_person_id': 2,
                'funding': None, 'vamps_id': None,
-               'principal_investigator_id': 3,
+               'principal_investigator': qdb.study.StudyPerson(3),
                'timeseries_type_id': 1,
                'study_abstract': 'Exploring how a high fat diet changes the '
                                  'gut microbiome',
                'spatial_series': None,
                'study_description': 'Microbiome of people who eat nothing but'
                                     ' fried chicken',
                'study_alias': 'FCM',
-               'most_recent_contact': None, 'lab_person_id': 1,
+               'most_recent_contact': None,
+               'lab_person': qdb.study.StudyPerson(1),
                'number_samples_collected': 25}
         self.assertEqual(obs_info, exp)
         # Check the timestamp separately, since it is set by the database
@@ -431,14 +430,16 @@ def test_create_study_all_data(self):
                'number_samples_promised': 28, 'emp_person_id': 2,
                'funding': 'FundAgency', 'vamps_id': 'MBE_1111111',
                'first_contact': datetime(2014, 10, 24, 12, 47),
-               'principal_investigator_id': 3, 'timeseries_type_id': 1,
+               'principal_investigator': qdb.study.StudyPerson(3),
+               'timeseries_type_id': 1,
                'study_abstract': 'Exploring how a high fat diet changes the '
                                  'gut microbiome',
                'spatial_series': True,
                'study_description': 'Microbiome of people who eat nothing '
                                     'but fried chicken',
                'study_alias': 'FCM',
-               'most_recent_contact': None, 'lab_person_id': 1,
+               'most_recent_contact': None,
+               'lab_person': qdb.study.StudyPerson(1),
                'number_samples_collected': 25}
         self.assertEqual(obs.info, exp)
         self.assertEqual(obs.efo, [1])
@@ -584,12 +585,6 @@ def test_ebi_submission_status_setter(self):
         with self.assertRaises(ValueError):
             new.ebi_submission_status = "unknown"
 
-    def test_retrieve_info(self):
-        for key, val in viewitems(self.existingexp):
-            if isinstance(val, qdb.base.QiitaObject):
-                self.existingexp[key] = val.id
-        self.assertEqual(self.study.info, self.existingexp)
-
     def test_set_info(self):
         """Set info in a study"""
         newinfo = {
@@ -611,8 +606,9 @@ def test_set_info(self):
         self.infoexp["spatial_series"] = None
         self.infoexp["most_recent_contact"] = None
         self.infoexp["reprocess"] = False
-        self.infoexp["lab_person_id"] = 2
         self.infoexp["first_contact"] = datetime(2014, 6, 11)
+        self.infoexp["lab_person"] = qdb.study.StudyPerson(2)
+        del self.infoexp["lab_person_id"]
 
         self.assertEqual(new.info, self.infoexp)
 

qiita_pet/handlers/api_proxy/tests/test_artifact.py

@@ -11,21 +11,24 @@
 from datetime import datetime
 
 import pandas as pd
+import numpy.testing as npt
 
 from qiita_core.qiita_settings import qiita_config
 from qiita_core.util import qiita_test_checker
 from qiita_db.artifact import Artifact
 from qiita_db.metadata_template.prep_template import PrepTemplate
 from qiita_db.study import Study
 from qiita_db.util import get_count, get_mountpoint
-from qiita_db.exceptions import QiitaDBUnknownIDError
+from qiita_db.exceptions import QiitaDBUnknownIDError, QiitaDBWarning
 from qiita_pet.handlers.api_proxy.artifact import (
     artifact_get_req, artifact_status_put_req, artifact_graph_get_req,
     artifact_delete_req, artifact_types_get_req, artifact_post_req)
 
 
 @qiita_test_checker()
 class TestArtifactAPI(TestCase):
+    database = True
+
     def setUp(self):
         uploads_path = get_mountpoint('uploads')[0][1]
         # Create prep test file to point at
@@ -97,8 +100,9 @@ def test_artifact_get_req(self):
     def test_artifact_post_req(self):
         # Create new prep template to attach artifact to
         new_prep_id = get_count('qiita.prep_template') + 1
-        PrepTemplate.create(pd.DataFrame(
-            {'new_col': {'1.SKD6.640190': 1}}), Study(1), '16S')
+        npt.assert_warns(
+            QiitaDBWarning, PrepTemplate.create,
+            pd.DataFrame({'new_col': {'1.SKD6.640190': 1}}), Study(1), '16S')
 
         new_artifact_id = get_count('qiita.artifact') + 1
         obs = artifact_post_req(
@@ -115,8 +119,9 @@ def test_artifact_post_req(self):
     def test_artifact_post_req_bad_file(self):
         # Create new prep template to attach artifact to
         new_prep_id = get_count('qiita.prep_template') + 1
-        PrepTemplate.create(pd.DataFrame(
-            {'new_col': {'1.SKD6.640190': 1}}), Study(1), '16S')
+        npt.assert_warns(
+            QiitaDBWarning, PrepTemplate.create,
+            pd.DataFrame({'new_col': {'1.SKD6.640190': 1}}), Study(1), '16S')
 
         obs = artifact_post_req(
             'test@foo.bar', {'raw_forward_seqs': ['NOEXIST']},
@@ -170,9 +175,10 @@ def test_artifact_graph_get_req_descendants(self):
                'node_labels': [(1, 'Raw data 1 - FASTQ'),
                                (3, 'Demultiplexed 2 - Demultiplexed'),
                                (2, 'Demultiplexed 1 - Demultiplexed'),
-                               (4, 'BIOM - BIOM')],
-               'edge_list': [(1, 3), (1, 2), (2, 4)]}
-        self.assertEqual(obs, exp)
+                               (4, 'BIOM - BIOM'),
+                               (5, 'BIOM - BIOM')],
+               'edge_list': [(1, 3), (1, 2), (2, 5), (2, 4)]}
+        self.assertItemsEqual(obs, exp)
 
     def test_artifact_graph_get_req_no_access(self):
         obs = artifact_graph_get_req(1, 'ancestors', 'demo@microbio.me')
@@ -191,7 +197,10 @@ def test_artifact_types_get_req(self):
                          ['FASTQ', None],
                          ['SFF', None],
                          ['per_sample_FASTQ', None]]}
-        self.assertEqual(obs, exp)
+
+        self.assertEqual(obs['message'], exp['message'])
+        self.assertEqual(obs['status'], exp['status'])
+        self.assertItemsEqual(obs['types'], exp['types'])
 
     def test_artifact_graph_get_req_bad_direction(self):
         obs = artifact_graph_get_req(1, 'WRONG', 'test@foo.bar')

qiita_pet/handlers/api_proxy/tests/test_prep_template.py

@@ -12,13 +12,15 @@
 from random import choice
 
 import pandas as pd
+import numpy.testing as npt
 
 from qiita_core.qiita_settings import qiita_config
 from qiita_core.util import qiita_test_checker
 from qiita_db.metadata_template.prep_template import PrepTemplate
 from qiita_db.ontology import Ontology
 from qiita_db.study import Study
 from qiita_db.util import get_count
+from qiita_db.exceptions import QiitaDBWarning
 from qiita_pet.handlers.api_proxy.prep_template import (
     prep_template_summary_get_req, prep_template_post_req,
     prep_template_put_req, prep_template_delete_req, prep_template_get_req,
@@ -36,8 +38,8 @@ def setUp(self):
         with open(self.update_fp, 'w') as f:
             f.write("""sample_name\tnew_col\n1.SKD6.640190\tnew_value\n""")
 
-        def tear_down(self):
-            remove(self.update_fp)
+    def tear_down(self):
+        remove(self.update_fp)
 
         fp = join(qiita_config.base_data_dir, 'uploads', '1',
                   'uploaded_file.txt')
@@ -187,7 +189,11 @@ def test_prep_template_post_req(self):
                           'LinkerPrimerSequence, BarcodeSequence',
                'file': 'update.txt',
                'id': new_id}
-        self.assertEqual(obs, exp)
+        self.assertEqual(obs['status'], exp['status'])
+        self.assertItemsEqual(obs['message'].split('\n'),
+                              exp['message'].split('\n'))
+        self.assertEqual(obs['file'], exp['file'])
+        self.assertEqual(obs['id'], exp['id'])
 
         # Make sure new prep template added
         prep = PrepTemplate(new_id)
@@ -232,7 +238,10 @@ def test_prep_template_put_req_warning(self):
                           'differences between the data stored in the DB and '
                           'the new data provided',
                'file': 'update.txt'}
-        self.assertEqual(obs, exp)
+        self.assertEqual(obs['status'], exp['status'])
+        self.assertItemsEqual(obs['message'].split('\n'),
+                              exp['message'].split('\n'))
+        self.assertEqual(obs['file'], exp['file'])
 
     def test_prep_put_req_inv_type(self):
         randstr = ''.join([choice(ascii_letters) for x in range(30)])
@@ -270,7 +279,8 @@ def test_prep_template_put_req_no_exists(self):
     def test_prep_template_delete_req(self):
         template = pd.read_csv(self.update_fp, sep='\t', index_col=0)
         new_id = get_count('qiita.prep_template') + 1
-        PrepTemplate.create(template, Study(1), '16S')
+        npt.assert_warns(QiitaDBWarning, PrepTemplate.create,
+                         template, Study(1), '16S')
         obs = prep_template_delete_req(new_id, 'test@foo.bar')
         exp = {'status': 'success',
                'message': ''}
@@ -315,17 +325,15 @@ def test_prep_template_filepaths_get_req_no_access(self):
 
     def test_prep_template_graph_get_req(self):
         obs = prep_template_graph_get_req(1, 'test@foo.bar')
-        exp = {'edge_list': [(1, 3), (1, 2), (2, 4)],
+        exp = {'edge_list': [(1, 3), (1, 2), (2, 4), (2, 5)],
                'node_labels': [(1, 'Raw data 1 - FASTQ'),
                                (2, 'Demultiplexed 1 - Demultiplexed'),
                                (3, 'Demultiplexed 2 - Demultiplexed'),
-                               (4, 'BIOM - BIOM')],
+                               (4, 'BIOM - BIOM'),
+                               (5, 'BIOM - BIOM')],
                'status': 'success',
                'message': ''}
-
-        self.assertItemsEqual(obs.keys(), exp.keys())
-        self.assertItemsEqual(obs['edge_list'], exp['edge_list'])
-        self.assertItemsEqual(obs['node_labels'], exp['node_labels'])
+        self.assertItemsEqual(obs, exp)
 
     def test_prep_template_graph_get_req_no_access(self):
         obs = prep_template_graph_get_req(1, 'demo@microbio.me')

qiita_pet/handlers/api_proxy/tests/test_sample_template.py

@@ -6,7 +6,7 @@
 # The full license is in the file LICENSE, distributed with this software.
 # -----------------------------------------------------------------------------
 from unittest import TestCase, main
-from os import remove
+from os import remove, mkdir
 from os.path import join, exists
 
 from qiita_core.util import qiita_test_checker
@@ -40,9 +40,11 @@ def setUp(self):
             qdb.user.User('test@foo.bar'), "Some New Study", [1],
             info)
 
-        base_dir = qdb.util.get_mountpoint('uploads')[0][1]
-        self.new_study_fp = join(base_dir, str(self.new_study.id),
-                                 'uploaded_file.txt')
+        base_dir = join(qdb.util.get_mountpoint('uploads')[0][1],
+                        str(self.new_study.id))
+        if not exists(base_dir):
+            mkdir(base_dir)
+        self.new_study_fp = join(base_dir, 'uploaded_file.txt')
         if not exists(self.new_study_fp):
             with open(self.new_study_fp, 'w') as f:
                 f.write('')
@@ -356,7 +358,7 @@ def test_sample_template_filepaths_get_req(self):
         obs = sample_template_filepaths_get_req(1, 'test@foo.bar')
         exp = {'status': 'success',
                'message': '',
-               'filepaths': [(14, join(templates_dir,
+               'filepaths': [(17, join(templates_dir,
                               '1_19700101-000000.txt'))]}
         self.assertEqual(obs, exp)