fix #2751 (#3062)

Author: antgonza

qiita_db/meta_util.py

@@ -412,7 +412,7 @@ def generate_biom_and_metadata_release(study_status='public'):
                     continue
                 fp = relpath(x['fp'], bdir)
                 for pt in a.prep_templates:
-                    categories = pt.categories()
+                    categories = pt.categories
                     platform = ''
                     target_gene = ''
                     if 'platform' in categories:

qiita_db/metadata_template/base_metadata_template.py

@@ -55,6 +55,19 @@
 QIITA_COLUMN_NAME = 'qiita_sample_column_names'
 
 
+def _helper_get_categories(table):
+    """This is a helper function to avoid duplication of code"""
+    with qdb.sql_connection.TRN:
+        sql = """SELECT sample_values->>'columns'
+                 FROM qiita.{0}
+                 WHERE sample_id = '{1}'""".format(table, QIITA_COLUMN_NAME)
+        qdb.sql_connection.TRN.add(sql)
+        results = qdb.sql_connection.TRN.execute_fetchflatten()
+        if results:
+            results = sorted(loads(results[0]))
+        return results
+
+
 class BaseSample(qdb.base.QiitaObject):
     r"""Sample object that accesses the db to get the information of a sample
     belonging to a PrepTemplate or a SampleTemplate.
@@ -184,17 +197,7 @@ def _get_categories(self):
         set of str
             The set of all available metadata categories
         """
-        with qdb.sql_connection.TRN:
-            sql = """SELECT sample_values->>'columns'
-                     FROM qiita.{0}
-                     WHERE sample_id = '{1}'""".format(
-                        self._dynamic_table, QIITA_COLUMN_NAME)
-            qdb.sql_connection.TRN.add(sql)
-            results = qdb.sql_connection.TRN.execute_fetchflatten()
-            if results:
-                results = loads(results[0])
-
-            return set(results)
+        return set(_helper_get_categories(self._dynamic_table))
 
     def _to_dict(self):
         r"""Returns the categories and their values in a dictionary
@@ -729,7 +732,7 @@ def delete_column(self, column_name):
             If the column_name is selected as a specimen_id_column in the
             study.
         """
-        if column_name not in self.categories():
+        if column_name not in self.categories:
             raise qdb.exceptions.QiitaDBColumnError(
                 "'%s' not in info file %d" % (column_name, self._id))
         if not self.can_be_updated(columns={column_name}):
@@ -754,7 +757,7 @@ def delete_column(self, column_name):
             qdb.sql_connection.TRN.add(sql, [column_name, QIITA_COLUMN_NAME])
 
             # deleting from QIITA_COLUMN_NAME
-            columns = self.categories()
+            columns = self.categories
             columns.remove(column_name)
             values = '{"columns": %s}' % dumps(columns)
             sql = """UPDATE {0}
@@ -834,7 +837,7 @@ def _common_extend_steps(self, md_template):
 
             # Check if we are adding new columns
             headers = md_template.keys().tolist()
-            new_cols = set(headers).difference(self.categories())
+            new_cols = set(headers).difference(self.categories)
 
             if not new_cols and not new_samples:
                 return None, None
@@ -855,7 +858,7 @@ def _common_extend_steps(self, md_template):
                 # code). Sorting the new columns to enforce an order
                 new_cols = sorted(new_cols)
 
-                cols = self.categories()
+                cols = self.categories
                 cols.extend(new_cols)
 
                 values = dumps({"columns": cols})
@@ -1167,7 +1170,7 @@ def _common_to_dataframe_steps(self):
         """
         with qdb.sql_connection.TRN:
             # Retrieve all the information from the database
-            cols = self.categories()
+            cols = self.categories
             sql = """SELECT sample_id, sample_values
                      FROM qiita.{0}
                      WHERE sample_id != '{1}'""".format(
@@ -1237,6 +1240,7 @@ def get_filepaths(self):
                         self._filepath_table, self._id_column, self.id,
                         sort='descending')]
 
+    @property
     def categories(self):
         """Identifies the metadata columns present in an info file
 
@@ -1245,19 +1249,7 @@ def categories(self):
         cols : list
             The category fields
         """
-        with qdb.sql_connection.TRN:
-            sql = """SELECT sample_values->>'columns'
-                     FROM qiita.{0}
-                     WHERE sample_id = '{1}'""".format(
-                        self._table_name(self._id), QIITA_COLUMN_NAME)
-
-            qdb.sql_connection.TRN.add(sql)
-
-            results = qdb.sql_connection.TRN.execute_fetchflatten()
-            if results:
-                results = sorted(loads(results[0]))
-
-            return results
+        return _helper_get_categories(self._table_name(self._id))
 
     def extend(self, md_template):
         """Adds the given template to the current one
@@ -1269,7 +1261,7 @@ def extend(self, md_template):
         """
         with qdb.sql_connection.TRN:
             md_template = self._clean_validate_template(
-                md_template, self.study_id, current_columns=self.categories())
+                md_template, self.study_id, current_columns=self.categories)
             new_samples, new_columns = self._common_extend_steps(md_template)
             if new_samples or new_columns:
                 self.validate(self.columns_restrictions)
@@ -1396,7 +1388,7 @@ def _update(self, md_template):
                             self._table_name(self._id))
                 qdb.sql_connection.TRN.add(sql, [dumps(values), sid])
 
-            nc = list(set(new_columns).union(set(self.categories())))
+            nc = list(set(new_columns).union(set(self.categories)))
             table_name = self._table_name(self.id)
             values = dumps({"columns": nc})
             sql = """UPDATE qiita.{0}
@@ -1430,7 +1422,7 @@ def update(self, md_template):
         with qdb.sql_connection.TRN:
             # Clean and validate the metadata template given
             new_map = self._clean_validate_template(
-                md_template, self.study_id, current_columns=self.categories())
+                md_template, self.study_id, current_columns=self.categories)
             samples, columns = self._update(new_map)
             self.validate(self.columns_restrictions)
             self.generate_files(samples, columns)
@@ -1450,7 +1442,7 @@ def extend_and_update(self, md_template):
         """
         with qdb.sql_connection.TRN:
             md_template = self._clean_validate_template(
-                md_template, self.study_id, current_columns=self.categories())
+                md_template, self.study_id, current_columns=self.categories)
             new_samples, new_columns = self._common_extend_steps(md_template)
             samples, columns = self._update(md_template)
             if samples is None:
@@ -1516,7 +1508,7 @@ def get_category(self, category):
             If category is not part of the template
         """
         with qdb.sql_connection.TRN:
-            if category not in self.categories():
+            if category not in self.categories:
                 raise qdb.exceptions.QiitaDBColumnError(category)
             sql = """SELECT sample_id,
                         COALESCE(sample_values->>'{0}', 'None') AS {0}
@@ -1542,7 +1534,7 @@ def check_restrictions(self, restrictions):
         cols = {col for restriction in restrictions
                 for col in restriction.columns}
 
-        return cols.difference(self.categories())
+        return cols.difference(self.categories)
 
     def _get_accession_numbers(self, column):
         """Return the accession numbers stored in `column`
@@ -1639,7 +1631,7 @@ def validate(self, restriction_dict):
             If the values aren't castable
         """
         warning_msg = []
-        columns = self.categories()
+        columns = self.categories
         wrong_msg = 'Sample "%s", column "%s", wrong value "%s"'
         for label, restriction in restriction_dict.items():
             missing = set(restriction.columns).difference(columns)
@@ -1796,7 +1788,7 @@ def validate_restrictions(self):
             success = True
             message = []
             restrictions = self.restrictions
-            categories = self.categories()
+            categories = self.categories
 
             difference = sorted(set(restrictions.keys()) - set(categories))
             if difference:

qiita_db/metadata_template/prep_template.py

@@ -142,7 +142,7 @@ def create(cls, md_template, study, data_type, investigation_type=None,
 
             md_template = cls._clean_validate_template(md_template, study.id)
             _check_duplicated_columns(list(md_template.columns),
-                                      study.sample_template.categories())
+                                      study.sample_template.categories)
 
             # Insert the metadata template
             sql = """INSERT INTO qiita.prep_template
@@ -394,7 +394,7 @@ def can_be_extended(self, new_samples, new_columns):
                                        "prep template")
 
         _check_duplicated_columns(list(new_columns), qdb.study.Study(
-            self.study_id).sample_template.categories())
+            self.study_id).sample_template.categories)
 
         return True, ""
 

qiita_db/metadata_template/test/test_prep_template.py

@@ -909,7 +909,7 @@ 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.assertCountEqual(pt.categories(), exp_categories)
+        self.assertCountEqual(pt.categories, exp_categories)
         exp_dict = {
             '%s.SKB7.640196' % self.test_study.id: {
                 'barcode': 'CCTCTGAGAGCT',
@@ -1058,7 +1058,7 @@ def test_create_warning(self):
                           'instrument_model', 'experiment_design_description',
                           'library_construction_protocol', 'center_name',
                           'center_project_name', 'emp_status'}
-        self.assertCountEqual(pt.categories(), exp_categories)
+        self.assertCountEqual(pt.categories, exp_categories)
         exp_dict = {
             '%s.SKB7.640196' % self.test_study.id: {
                 'ebi_submission_accession': None,
@@ -1628,7 +1628,7 @@ def test_delete_column(self):
         pt = qdb.metadata_template.prep_template.PrepTemplate.create(
             self.metadata, self.test_study, self.data_type)
         pt.delete_column('str_column')
-        self.assertNotIn('str_column', pt.categories())
+        self.assertNotIn('str_column', pt.categories)
 
         # testing errors
         pt = qdb.metadata_template.prep_template.PrepTemplate(1)

qiita_db/metadata_template/test/test_sample_template.py

@@ -542,7 +542,7 @@ def test_categories(self):
                'physical_specimen_remaining', 'dna_extracted',
                'sample_type', 'collection_timestamp', 'host_subject_id',
                'description', 'latitude', 'longitude', 'scientific_name'}
-        obs = set(self.tester.categories())
+        obs = set(self.tester.categories)
         self.assertCountEqual(obs, exp)
 
     def test_iter(self):
@@ -974,7 +974,7 @@ def test_create(self):
                           'longitude', 'physical_specimen_location',
                           'physical_specimen_remaining', 'sample_type',
                           'scientific_name', 'taxon_id'}
-        self.assertCountEqual(st.categories(), exp_categories)
+        self.assertCountEqual(st.categories, exp_categories)
         exp_dict = {
             "%s.Sample1" % new_id: {
                 'collection_timestamp': '2014-05-29 12:24:15',
@@ -1040,7 +1040,7 @@ def test_create_int_prefix(self):
                           'longitude', 'physical_specimen_location',
                           'physical_specimen_remaining', 'sample_type',
                           'scientific_name', 'taxon_id'}
-        self.assertCountEqual(st.categories(), exp_categories)
+        self.assertCountEqual(st.categories, exp_categories)
         exp_dict = {
             "%s.12.Sample1" % new_id: {
                 'collection_timestamp': '2014-05-29 12:24:15',
@@ -1106,7 +1106,7 @@ def test_create_str_prefixes(self):
                           'longitude', 'physical_specimen_location',
                           'physical_specimen_remaining', 'sample_type',
                           'scientific_name', 'taxon_id'}
-        self.assertCountEqual(st.categories(), exp_categories)
+        self.assertCountEqual(st.categories, exp_categories)
         exp_dict = {
             "%s.foo.Sample1" % new_id: {
                 'collection_timestamp': '2014-05-29 12:24:15',
@@ -1172,7 +1172,7 @@ def test_create_already_prefixed_samples(self):
                           'longitude', 'physical_specimen_location',
                           'physical_specimen_remaining', 'sample_type',
                           'scientific_name', 'taxon_id'}
-        self.assertCountEqual(st.categories(), exp_categories)
+        self.assertCountEqual(st.categories, exp_categories)
         exp_dict = {
             "%s.Sample1" % new_id: {
                 'collection_timestamp': '2014-05-29 12:24:15',
@@ -1463,7 +1463,7 @@ def test_extend_add_samples(self):
                           'longitude', 'physical_specimen_location',
                           'physical_specimen_remaining', 'sample_type',
                           'scientific_name', 'taxon_id'}
-        self.assertCountEqual(st.categories(), exp_categories)
+        self.assertCountEqual(st.categories, exp_categories)
         exp_dict = {
             "%s.Sample1" % st.id: {
                 'collection_timestamp': '2014-05-29 12:24:15',
@@ -1568,7 +1568,7 @@ def test_extend_add_duplicate_samples(self):
                           'longitude', 'physical_specimen_location',
                           'physical_specimen_remaining', 'sample_type',
                           'scientific_name', 'taxon_id'}
-        self.assertCountEqual(st.categories(), exp_categories)
+        self.assertCountEqual(st.categories, exp_categories)
         exp_dict = {
             "%s.Sample1" % st.id: {
                 'collection_timestamp': '2014-05-29 12:24:15',
@@ -1650,7 +1650,7 @@ def test_extend_new_columns(self):
                           'physical_specimen_remaining', 'sample_type',
                           'scientific_name', 'taxon_id',
                           'texture', 'tot_nitro'}
-        self.assertCountEqual(st.categories(), exp_categories)
+        self.assertCountEqual(st.categories, exp_categories)
         exp_dict = {
             "%s.Sample1" % st.id: {
                 'collection_timestamp': '2014-05-29 12:24:15',
@@ -1736,7 +1736,7 @@ def test_extend_new_samples_and_columns(self):
                           'longitude', 'physical_specimen_location',
                           'physical_specimen_remaining', 'sample_type',
                           'scientific_name', 'taxon_id', 'tot_nitro'}
-        self.assertCountEqual(st.categories(), exp_categories)
+        self.assertCountEqual(st.categories, exp_categories)
         exp_dict = {
             "%s.Sample1" % st.id: {
                 'collection_timestamp': '2014-05-29 12:24:15',
@@ -1835,7 +1835,7 @@ def test_extend_update(self):
                           'longitude', 'physical_specimen_location',
                           'physical_specimen_remaining', 'sample_type',
                           'scientific_name', 'taxon_id', 'tot_nitro'}
-        self.assertCountEqual(st.categories(), exp_categories)
+        self.assertCountEqual(st.categories, exp_categories)
         exp_dict = {
             "%s.Sample1" % st.id: {
                 'collection_timestamp': '2014-05-29 12:24:15',
@@ -2247,7 +2247,7 @@ def test_delete_column(self):
         st = qdb.metadata_template.sample_template.SampleTemplate.create(
             self.metadata, self.new_study)
         st.delete_column('dna_extracted')
-        self.assertNotIn('dna_extracted', st.categories())
+        self.assertNotIn('dna_extracted', st.categories)
 
     def test_delete_column_specimen_id(self):
         st = qdb.metadata_template.sample_template.SampleTemplate.create(

qiita_db/processing_job.py

@@ -1815,7 +1815,7 @@ def shape(self):
                 pass
             else:
                 samples = len(st)
-                columns = len(st.categories())
+                columns = len(st.categories)
         elif analysis_id is not None:
             try:
                 analysis = qdb.analysis.Analysis(analysis_id)

qiita_db/study.py

@@ -784,7 +784,7 @@ def specimen_id_column(self, value):
                                                     "sample information.")
 
         if value is not None:
-            if value not in st.categories():
+            if value not in st.categories:
                 raise qdb.exceptions.QiitaDBLookupError("Category '%s' is not "
                                                         "present in the sample"
                                                         " information."

qiita_db/util.py

@@ -1790,7 +1790,7 @@ def get_artifacts_information(artifact_ids, only_biom=True):
             if prep_template_id is not None:
                 if prep_template_id not in ps:
                     pt = PT(prep_template_id)
-                    categories = pt.categories()
+                    categories = pt.categories
                     if 'platform' in categories:
                         platform = ', '.join(
                             set(pt.get_category('platform').values()))

qiita_pet/handlers/api_proxy/prep_template.py

@@ -137,7 +137,7 @@ def prep_template_ajax_get_req(user_id, prep_id):
 
     # The call to list is needed because keys is an iterator
     num_samples = len(list(pt.keys()))
-    num_columns = len(pt.categories())
+    num_columns = len(pt.categories)
     investigation_type = pt.investigation_type
 
     download_prep_id = None

qiita_pet/handlers/api_proxy/sample_template.py

@@ -139,7 +139,7 @@ def sample_template_meta_cats_get_req(samp_id, user_id):
 
     return {'status': 'success',
             'message': '',
-            'categories': sorted(SampleTemplate(int(samp_id)).categories())
+            'categories': sorted(SampleTemplate(int(samp_id)).categories)
             }