Merge pull request #3191 from antgonza/rm-specimen_id

rm specimen_id

Author: charles-cowart

qiita_db/metadata_template/base_metadata_template.py

@@ -726,8 +726,6 @@ def delete_column(self, column_name):
             If the `column_name` doesn't exist
         QiitaDBOperationNotPermittedError
             If a the info file can't be updated
-            If the column_name is selected as a specimen_id_column in the
-            study.
         """
         if column_name not in self.categories:
             raise qdb.exceptions.QiitaDBColumnError(
@@ -736,14 +734,6 @@ def delete_column(self, column_name):
             raise qdb.exceptions.QiitaDBOperationNotPermittedError(
                 '%s cannot be deleted' % column_name)
 
-        # if a tube identifier column is selected disallow its deletion
-        specimen_id_column = qdb.study.Study(self.study_id).specimen_id_column
-        if specimen_id_column == column_name:
-            raise qdb.exceptions.QiitaDBOperationNotPermittedError(
-                    '"%s" cannot be deleted, this column is currently selected'
-                    ' as the tube identifier (specimen_id_column)' %
-                    column_name)
-
         with qdb.sql_connection.TRN:
             table_name = 'qiita.{0}{1}'.format(self._table_prefix, self._id)
             # deleting from all samples; note that (-) in pgsql jsonb means

qiita_db/metadata_template/test/test_sample_template.py

@@ -2256,19 +2256,6 @@ def test_delete_column(self):
         st.delete_column('dna_extracted')
         self.assertNotIn('dna_extracted', st.categories)
 
-    def test_delete_column_specimen_id(self):
-        st = qdb.metadata_template.sample_template.SampleTemplate.create(
-            self.metadata, self.new_study)
-        self.new_study.specimen_id_column = 'latitude'
-
-        with self.assertRaisesRegex(
-                qdb.exceptions.QiitaDBOperationNotPermittedError,
-                '"latitude" cannot be deleted, this column is currently '
-                r'selected as the tube identifier \(specimen_id_column\)'):
-            st.delete_column('latitude')
-
-        self.new_study.specimen_id_column = None
-
     def test_delete_samples(self):
         QE = qdb.exceptions
         st = qdb.metadata_template.sample_template.SampleTemplate(1)

qiita_db/study.py

@@ -56,7 +56,6 @@ class Study(qdb.base.QiitaObject):
     status
     title
     owner
-    specimen_id_column
     autoloaded
 
     Methods
@@ -778,62 +777,6 @@ def publications(self, values):
             qdb.sql_connection.TRN.add(sql, sql_args, many=True)
             qdb.sql_connection.TRN.execute()
 
-    @property
-    def specimen_id_column(self):
-        """Returns the specimen identifier column
-
-        Returns
-        -------
-        str
-            The name of the specimen id column
-        """
-        with qdb.sql_connection.TRN:
-            sql = """SELECT specimen_id_column
-                     FROM qiita.study
-                     WHERE study_id = %s"""
-            qdb.sql_connection.TRN.add(sql, [self._id])
-            return qdb.sql_connection.TRN.execute_fetchlast()
-
-    @specimen_id_column.setter
-    def specimen_id_column(self, value):
-        """Sets the specimen identifier column
-
-        Parameters
-        ----------
-        value : str
-            The name of the column with the specimen identifiers.
-
-        Raises
-        ------
-        QiitaDBLookupError
-            If value is not in the sample information for this study.
-            If the study does not have sample information.
-        QiitaDBColumnError
-            Category is not unique.
-        """
-        st = self.sample_template
-        if st is None:
-            raise qdb.exceptions.QiitaDBLookupError("Study does not have a "
-                                                    "sample information.")
-
-        if value is not None:
-            if value not in st.categories:
-                raise qdb.exceptions.QiitaDBLookupError("Category '%s' is not "
-                                                        "present in the sample"
-                                                        " information."
-                                                        % value)
-
-            observed_values = st.get_category(value)
-            if len(observed_values) != len(set(observed_values.values())):
-                raise qdb.exceptions.QiitaDBColumnError("The category does not"
-                                                        " contain unique "
-                                                        "values.")
-
-        sql = """UPDATE qiita.study SET
-                 specimen_id_column = %s
-                 WHERE study_id = %s"""
-        qdb.sql_connection.perform_as_transaction(sql, [value, self._id])
-
     @property
     def investigation(self):
         """ Returns Investigation this study is part of

qiita_db/support_files/patches/85.sql

@@ -21,3 +21,8 @@ ALTER TABLE qiita.default_workflow
     FOREIGN KEY (artifact_type_id)
     REFERENCES qiita.artifact_type(artifact_type_id)
     ON UPDATE CASCADE;
+
+-- Mar 17, 2022
+-- deleting specimen_id_column from qiita.study
+
+ALTER TABLE qiita.study DROP COLUMN specimen_id_column;

qiita_db/test/test_study.py

@@ -150,8 +150,7 @@ def setUp(self):
             "study_abstract": "Exploring how a high fat diet changes the "
                               "gut microbiome",
             "principal_investigator_id": qdb.study.StudyPerson(3),
-            "lab_person_id": qdb.study.StudyPerson(1),
-            'specimen_id_column': None
+            "lab_person_id": qdb.study.StudyPerson(1)
         }
 
         self.infoexp = {
@@ -165,7 +164,6 @@ def setUp(self):
                               "gut microbiome",
             "principal_investigator": qdb.study.StudyPerson(3),
             "lab_person": qdb.study.StudyPerson(1),
-            'specimen_id_column': None,
             'public_raw_download': False
         }
 
@@ -193,8 +191,7 @@ def setUp(self):
             'study_description': 'Analysis of the Cannabis Plant Microbiome',
             'study_alias': 'Cannabis Soils',
             'most_recent_contact': datetime(2014, 5, 19, 16, 11),
-            'lab_person': qdb.study.StudyPerson(1),
-            'specimen_id_column': None}
+            'lab_person': qdb.study.StudyPerson(1)}
 
     def tearDown(self):
         qiita_config.portal = self.portal
@@ -251,8 +248,7 @@ def test_get_info(self):
             'Soils',
             'ebi_submission_status': 'submitted',
             'ebi_study_accession': 'EBI123456-BB',
-            'autoloaded': False,
-            'specimen_id_column': None}
+            'autoloaded': False}
         self.assertDictEqual(obs, exp)
 
         # Test get specific keys for single study
@@ -446,8 +442,7 @@ def test_create_study_min_data(self):
                'study_alias': 'FCM',
                'most_recent_contact': None,
                'lab_person': qdb.study.StudyPerson(1),
-               'notes': '',
-               'specimen_id_column': None}
+               'notes': ''}
         self.assertEqual(obs_info, exp)
         # Check the timestamp separately, since it is set by the database
         # to the microsecond, and we can't predict it a priori
@@ -529,8 +524,7 @@ def test_create_study_all_data(self):
                'study_alias': 'FCM',
                'most_recent_contact': None,
                'lab_person': qdb.study.StudyPerson(1),
-               'notes': 'an analysis was performed \n here and \n here',
-               'specimen_id_column': None}
+               'notes': 'an analysis was performed \n here and \n here'}
         self.assertEqual(obs.info, exp)
         self.assertEqual(obs.shared_with, [])
         self.assertEqual(obs.publications, [])
@@ -912,31 +906,6 @@ def test_study_tags(self):
         self.assertEqual(study.tags, [])
         self.assertEqual(message, '')
 
-    def test_specimen_id_column_get_set(self):
-        self.assertEqual(self.study.specimen_id_column, None)
-        self.study.specimen_id_column = 'anonymized_name'
-        self.assertEqual(self.study.specimen_id_column, 'anonymized_name')
-        self.study.specimen_id_column = None
-        self.assertEqual(self.study.specimen_id_column, None)
-
-    def test_specimen_id_column_not_unique(self):
-        with self.assertRaises(qdb.exceptions.QiitaDBColumnError):
-            self.study.specimen_id_column = 'dna_extracted'
-
-    def test_specimen_id_column_doesnt_exist(self):
-        with self.assertRaises(qdb.exceptions.QiitaDBLookupError):
-            self.study.specimen_id_column = 'foo'
-
-    def test_specimen_id_column_no_sample_information(self):
-        empty = qdb.study.Study.create(
-            qdb.user.User('[email protected]'), "Fried duck microbiome",
-            self.info)
-        with self.assertRaises(qdb.exceptions.QiitaDBLookupError):
-            empty.specimen_id_column = 'foo'
-
-        # cleaning up the created study
-        qdb.study.Study.delete(empty._id)
-
 
 if __name__ == "__main__":
     main()

qiita_pet/handlers/api_proxy/studies.py

@@ -455,14 +455,6 @@ def study_patch_request(user_id, study_id,
             message = study.update_tags(User(user_id), req_value)
             return {'status': 'success',
                     'message': message}
-        elif attribute == 'specimen_id_column':
-            try:
-                study.specimen_id_column = req_value
-                return {'status': 'success',
-                        'message': 'Successfully updated specimen id column'}
-            except (QiitaDBLookupError, QiitaDBColumnError) as e:
-                return {'status': 'error',
-                        'message': str(e)}
         elif attribute == 'toggle_public_raw_download':
             try:
                 study.public_raw_download = not study.public_raw_download

qiita_pet/handlers/api_proxy/tests/test_studies.py

@@ -73,7 +73,7 @@ def test_study_get_req(self):
                     'rhizospheres from the same location at different time '
                     'points in the plant lifecycle.'),
                 'status': 'private', 'spatial_series': False,
-                'specimen_id_column': None, 'public_raw_download': False,
+                'public_raw_download': False,
                 'study_description': (
                     'Analysis of the Cannabis Plant Microbiome'),
                 'shared_with': ['[email protected]'], 'publication_doi': [
@@ -127,7 +127,7 @@ def test_study_get_req(self):
                 'email': '[email protected]'}, 'study_alias': 'FCM',
             'study_id': new_study.id, 'notes': '',
             'most_recent_contact': datetime(2015, 5, 19, 16, 11),
-            'ebi_study_accession': None, 'specimen_id_column': None,
+            'ebi_study_accession': None,
             'study_title': 'Some New Study for test'}, 'message': '',
             'editable': True}
         self.assertCountEqual(obs, exp)
@@ -465,38 +465,6 @@ def test_study_patch_request_errors(self):
                            'path parameter'), 'status': 'error'}
         self.assertEqual(obs, exp)
 
-    def test_study_patch_request_specimen_id(self):
-        obs = study_patch_request('[email protected]', 1,
-                                  'replace', '/specimen_id_column',
-                                  'anonymized_name')
-        exp = {'status': 'success', 'message': 'Successfully updated '
-                                               'specimen id column'}
-        self.assertEqual(obs, exp)
-
-        obs = study_patch_request('[email protected]', 1,
-                                  'replace', '/specimen_id_column',
-                                  'host_subject_id')
-        exp = {'status': 'success', 'message': 'Successfully updated '
-                                               'specimen id column'}
-        self.assertEqual(obs, exp)
-
-        qdb.study.Study(1).specimen_id_column = None
-
-    def test_study_patch_request_specimen_id_errors(self):
-        obs = study_patch_request('[email protected]', 1,
-                                  'replace', '/specimen_id_column',
-                                  'taxon_id')
-        exp = {'status': 'error', 'message': 'The category does not contain'
-               ' unique values.'}
-        self.assertEqual(obs, exp)
-
-        obs = study_patch_request('[email protected]', 1,
-                                  'replace', '/specimen_id_column',
-                                  'bleep_bloop')
-        exp = {'status': 'error', 'message': "Category 'bleep_bloop' is not"
-               " present in the sample information."}
-        self.assertEqual(obs, exp)
-
     def test_study_patch_request_toggle_public_raw_download(self):
         study_id = 1
         study = qdb.study.Study(study_id)
@@ -508,14 +476,6 @@ def test_study_patch_request_toggle_public_raw_download(self):
         self.assertEqual(obs, exp)
         self.assertTrue(study.public_raw_download)
 
-        obs = study_patch_request('[email protected]', study_id,
-                                  'replace', '/specimen_id_column',
-                                  'host_subject_id')
-        exp = {'status': 'error',
-               'message': 'User does not have access to study'}
-        self.assertEqual(obs, exp)
-        self.assertTrue(study.public_raw_download)
-
         # returning to default status
         study.public_raw_download = False
 

qiita_pet/handlers/study_handlers/sample_template.py

@@ -359,7 +359,6 @@ def sample_template_overview_handler_get_request(study_id, user):
     num_samples = 0
     num_cols = 0
     columns = []
-    specimen_id_column = None
     sample_restrictions = ''
     if exists:
         # If it exists we need to provide:
@@ -379,7 +378,6 @@ def sample_template_overview_handler_get_request(study_id, user):
         columns = st.categories
         # The number of columns
         num_cols = len(columns)
-        specimen_id_column = Study(study_id).specimen_id_column
         _, sample_restrictions = st.validate_restrictions()
     else:
         # It doesn't exist, we also need to provide the data_types in case
@@ -396,8 +394,7 @@ def sample_template_overview_handler_get_request(study_id, user):
             'num_samples': num_samples,
             'num_columns': num_cols,
             'columns': columns,
-            'sample_restrictions': sample_restrictions,
-            'specimen_id_column': specimen_id_column}
+            'sample_restrictions': sample_restrictions}
 
 
 class SampleTemplateOverviewHandler(BaseHandler):

qiita_pet/handlers/study_handlers/tests/test_base.py

@@ -104,15 +104,6 @@ def test_patch_not_allowed(self):
                          data=arguments, asjson=True)
         self.assertEqual(obs.code, 405)
 
-    def test_patch_specimen_id_column(self):
-        data = {'op': 'replace', 'path': '/specimen_id_column',
-                'value': "anonymized_name"}
-        obs = self.patch('/study/1', headers=self.header,
-                         data=data, asjson=True)
-        self.assertEqual(obs.code, 200)
-        self.assertEqual(json_decode(obs.body), {"status": "success",
-                         "message": "Successfully updated specimen id column"})
-
 
 if __name__ == "__main__":
     main()

qiita_pet/handlers/study_handlers/tests/test_sample_template.py

@@ -296,8 +296,7 @@ def test_sample_template_overview_handler_get_request(self):
                            'sample_type', 'collection_timestamp',
                            'host_subject_id', 'description', 'latitude',
                            'longitude', 'scientific_name', 'env_package']),
-               'sample_restrictions': '',
-               'specimen_id_column': None}
+               'sample_restrictions': ''}
         self.assertEqual(obs, exp)
 
         # Test sample template doesn't exist
@@ -317,8 +316,7 @@ def test_sample_template_overview_handler_get_request(self):
                'num_samples': 0,
                'num_columns': 0,
                'columns': [],
-               'sample_restrictions': '',
-               'specimen_id_column': None}
+               'sample_restrictions': ''}
         self.assertEqual(obs, exp)
 
     def test_sample_template_columns_get_req(self):
@@ -511,8 +509,7 @@ def test_get(self):
                            'sample_type', 'collection_timestamp',
                            'host_subject_id', 'description', 'latitude',
                            'longitude', 'scientific_name', 'env_package']),
-               'sample_restrictions': '',
-               'specimen_id_column': None}
+               'sample_restrictions': ''}
         self.assertDictEqual(obs, exp)