Merge pull request #2001 from antgonza/fix-fix-1971

fix-fix-1971
qiita-spots · Nov 29, 2016 · 547319a · 547319a
2 parents d9d7f83 + 09d23db
commit 547319a
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Showing 5 changed files with 109 additions and 14 deletions.
diff --git a/qiita_pet/handlers/api_proxy/studies.py b/qiita_pet/handlers/api_proxy/studies.py
@@ -173,7 +173,9 @@ def study_prep_get_req(study_id, user_id):
                 info['start_artifact_id'] = start_artifact.id
                 info['youngest_artifact'] = '%s - %s' % (
                     youngest_artifact.name, youngest_artifact.artifact_type)
-                info['ebi_experiment'] = bool(prep.ebi_experiment_accessions)
+                info['ebi_experiment'] = bool(
+                    [v for _, v in viewitems(prep.ebi_experiment_accessions)
+                     if v is not None])
             else:
                 info['start_artifact'] = None
                 info['start_artifact_id'] = None

diff --git a/qiita_pet/handlers/api_proxy/tests/test_studies.py b/qiita_pet/handlers/api_proxy/tests/test_studies.py
@@ -7,9 +7,10 @@
 # -----------------------------------------------------------------------------
 from unittest import TestCase, main
 from datetime import datetime
-from os.path import exists, join, basename
+from os.path import exists, join, basename, isdir
 from os import remove, close
-from tempfile import mkstemp
+from shutil import rmtree
+from tempfile import mkstemp, mkdtemp
 
 import pandas as pd
 import numpy.testing as npt
@@ -29,7 +30,10 @@ def setUp(self):
     def tearDown(self):
         for fp in self._clean_up_files:
             if exists(fp):
-                remove(fp)
+                if isdir(fp):
+                    rmtree(fp)
+                else:
+                    remove(fp)
 
     def test_data_types_get_req(self):
         obs = data_types_get_req()
@@ -232,6 +236,103 @@ def test_study_prep_get_req(self):
         for i in range(4, 0, -1):
             qdb.artifact.Artifact(i).visibility = "private"
 
+    def test_study_prep_get_req_failed_EBI(self):
+        temp_dir = mkdtemp()
+        self._clean_up_files.append(temp_dir)
+        user_email = 'test@foo.bar'
+
+        # creating a (A) new study, (B) sample info, (C) prep without EBI
+        # values
+
+        # (A)
+        info = {
+            "timeseries_type_id": 1,
+            "metadata_complete": True,
+            "mixs_compliant": True,
+            "number_samples_collected": 3,
+            "number_samples_promised": 3,
+            "study_alias": "Test EBI",
+            "study_description": "Study for testing EBI",
+            "study_abstract": "Study for testing EBI",
+            "emp_person_id": qdb.study.StudyPerson(2),
+            "principal_investigator_id": qdb.study.StudyPerson(3),
+            "lab_person_id": qdb.study.StudyPerson(1)
+        }
+        study = qdb.study.Study.create(
+            qdb.user.User(user_email), "Test EBI study", [1], info)
+
+        # (B)
+        metadata_dict = {
+            'Sample1': {'collection_timestamp': datetime(2015, 6, 1, 7, 0, 0),
+                        'physical_specimen_location': 'location1',
+                        'taxon_id': 9606,
+                        'scientific_name': 'homo sapiens',
+                        'Description': 'Test Sample 1'},
+            'Sample2': {'collection_timestamp': datetime(2015, 6, 2, 7, 0, 0),
+                        'physical_specimen_location': 'location1',
+                        'taxon_id': 9606,
+                        'scientific_name': 'homo sapiens',
+                        'Description': 'Test Sample 2'},
+            'Sample3': {'collection_timestamp': datetime(2015, 6, 3, 7, 0, 0),
+                        'physical_specimen_location': 'location1',
+                        'taxon_id': 9606,
+                        'scientific_name': 'homo sapiens',
+                        'Description': 'Test Sample 3'}
+        }
+        metadata = pd.DataFrame.from_dict(metadata_dict, orient='index',
+                                          dtype=str)
+        qdb.metadata_template.sample_template.SampleTemplate.create(
+            metadata, study)
+
+        # (C)
+        metadata_dict = {
+            'Sample1': {'primer': 'GTGCCAGCMGCCGCGGTAA',
+                        'barcode': 'CGTAGAGCTCTC',
+                        'center_name': 'KnightLab',
+                        'platform': 'ILLUMINA',
+                        'instrument_model': 'Illumina MiSeq',
+                        'library_construction_protocol': 'Protocol ABC',
+                        'experiment_design_description': "Random value 1"},
+            'Sample2': {'primer': 'GTGCCAGCMGCCGCGGTAA',
+                        'barcode': 'CGTAGAGCTCTA',
+                        'center_name': 'KnightLab',
+                        'platform': 'ILLUMINA',
+                        'instrument_model': 'Illumina MiSeq',
+                        'library_construction_protocol': 'Protocol ABC',
+                        'experiment_design_description': "Random value 2"},
+            'Sample3': {'primer': 'GTGCCAGCMGCCGCGGTAA',
+                        'barcode': 'CGTAGAGCTCTT',
+                        'center_name': 'KnightLab',
+                        'platform': 'ILLUMINA',
+                        'instrument_model': 'Illumina MiSeq',
+                        'library_construction_protocol': 'Protocol ABC',
+                        'experiment_design_description': "Random value 3"},
+        }
+        metadata = pd.DataFrame.from_dict(metadata_dict, orient='index',
+                                          dtype=str)
+        pt = qdb.metadata_template.prep_template.PrepTemplate.create(
+            metadata, study, "16S", 'Metagenomics')
+
+        # making sure that the EBI values are empty
+        exp = {('%d.Sample3' % study.id): None,
+               ('%d.Sample2' % study.id): None,
+               ('%d.Sample1' % study.id): None}
+        self.assertEqual(pt.ebi_experiment_accessions, exp)
+
+        # actual test
+        obs = study_prep_get_req(study.id, user_email)
+        exp = {
+            'info': {
+                '16S': [
+                    {'status': 'sandbox', 'name': 'PREP %d NAME' % pt.id,
+                     'start_artifact': None, 'youngest_artifact': None,
+                     'ebi_experiment': False, 'id': pt.id,
+                     'start_artifact_id': None}]
+            },
+            'message': '',
+            'status': 'success'}
+        self.assertEqual(obs, exp)
+
     def test_study_prep_get_req_no_access(self):
         obs = study_prep_get_req(1, 'demo@microbio.me')
         exp = {'status': 'error',

diff --git a/qiita_ware/test/test_commands.py b/qiita_ware/test/test_commands.py
@@ -9,7 +9,6 @@
 # -----------------------------------------------------------------------------
 from unittest import TestCase, main
 from os.path import join
-from warnings import simplefilter
 from tempfile import mkdtemp
 import pandas as pd
 from datetime import datetime
@@ -62,8 +61,6 @@ def write_demux_files(self, prep_template, generate_hdf5=True):
 
     def generate_new_study_with_preprocessed_data(self):
         """Creates a new study up to the processed data for testing"""
-        # ignoring warnings generated when adding templates
-        simplefilter("ignore")
         info = {
             "timeseries_type_id": 1,
             "metadata_complete": True,

diff --git a/qiita_ware/test/test_dispatchable.py b/qiita_ware/test/test_dispatchable.py
@@ -96,9 +96,9 @@ def test_update_sample_template(self):
                            "existing template: new_col\nThere are no "
                            "differences between the data stored in the DB and "
                            "the new data provided")}
-        self.assertEqual(obs['status'], exp['status'])
         self.assertItemsEqual(obs['message'].split('\n'),
                               exp['message'].split('\n'))
+        self.assertEqual(obs['status'], exp['status'])
 
     def test_delete_sample_template(self):
         obs = delete_sample_template(1)
@@ -115,9 +115,9 @@ def test_update_prep_template(self):
                           'existing template: new_col\nThere are no '
                           'differences between the data stored in the DB and '
                           'the new data provided'}
-        self.assertEqual(obs['status'], exp['status'])
         self.assertItemsEqual(obs['message'].split('\n'),
                               exp['message'].split('\n'))
+        self.assertEqual(obs['status'], exp['status'])
 
     def test_delete_sample_or_column(self):
         st = SampleTemplate(1)

diff --git a/qiita_ware/test/test_ebi.py b/qiita_ware/test/test_ebi.py
@@ -8,7 +8,6 @@
 # The full license is in the file LICENSE, distributed with this software.
 # -----------------------------------------------------------------------------
 
-from warnings import simplefilter
 from os import remove
 from os.path import join, isdir, exists
 from shutil import rmtree
@@ -299,8 +298,6 @@ def generate_new_prep_template_and_write_demux_files(self,
                                                          valid_metadata=False):
         """Creates new prep-template/demux-file to avoid duplication of code"""
 
-        # ignoring warnings generated when adding templates
-        simplefilter("ignore")
         # creating prep template without required EBI submission columns
         if not valid_metadata:
             metadata_dict = {
@@ -364,8 +361,6 @@ def generate_new_prep_template_and_write_demux_files(self,
 
     def generate_new_study_with_preprocessed_data(self):
         """Creates a new study up to the processed data for testing"""
-        # ignoring warnings generated when adding templates
-        simplefilter("ignore")
         info = {
             "timeseries_type_id": 1,
             "metadata_complete": True,