Merge pull request #1141 from josenavas/add-check-restriction

Adding check_restrictions functionality

Author: wasade

qiita_db/metadata_template/base_metadata_template.py

@@ -1157,3 +1157,21 @@ def update_category(self, category, samples_and_values):
                     % (category, value_str, value_types_str, column_type))
 
             raise e
+
+    def check_restrictions(self, restrictions):
+        """Checks if the template fulfills the restrictions
+
+        Parameters
+        ----------
+        restrictions : list of Restriction
+            The restrictions to test if the template fulfills
+
+        Returns
+        -------
+        set of str
+            The missing columns
+        """
+        cols = {col for restriction in restrictions
+                for col in restriction.columns}
+
+        return cols.difference(self.categories())

qiita_db/metadata_template/test/test_prep_template.py

@@ -32,7 +32,8 @@
                            get_count)
 from qiita_db.metadata_template.prep_template import PrepTemplate, PrepSample
 from qiita_db.metadata_template.sample_template import SampleTemplate, Sample
-from qiita_db.metadata_template.constants import PREP_TEMPLATE_COLUMNS
+from qiita_db.metadata_template.constants import (
+    PREP_TEMPLATE_COLUMNS, PREP_TEMPLATE_COLUMNS_TARGET_GENE)
 
 
 class BaseTestPrepSample(TestCase):
@@ -1299,6 +1300,20 @@ def test_qiime_map_fp(self):
                    '1_prep_1_qiime_19700101-000000.txt')
         self.assertEqual(pt.qiime_map_fp, exp)
 
+    def test_check_restrictions(self):
+        obs = self.tester.check_restrictions([PREP_TEMPLATE_COLUMNS['EBI']])
+        self.assertEqual(obs, set())
+
+        del self.metadata['primer']
+        pt = npt.assert_warns(QiitaDBWarning, PrepTemplate.create,
+                              self.metadata, self.new_raw_data,
+                              self.test_study, self.data_type)
+
+        obs = pt.check_restrictions(
+            [PREP_TEMPLATE_COLUMNS['EBI'],
+             PREP_TEMPLATE_COLUMNS_TARGET_GENE['demultiplex']])
+        self.assertEqual(obs, {'primer'})
+
 
 EXP_PREP_TEMPLATE = (
     'sample_name\tbarcode\tcenter_name\tcenter_project_name\t'

qiita_db/metadata_template/test/test_sample_template.py

@@ -1955,6 +1955,16 @@ def test_to_dataframe(self):
             'anonymized_name', 'tot_org_carb', 'description_duplicate',
             'env_feature'})
 
+    def test_check_restrictions(self):
+        obs = self.tester.check_restrictions([SAMPLE_TEMPLATE_COLUMNS['EBI']])
+        self.assertEqual(obs, set())
+
+        del self.metadata['collection_timestamp']
+        st = npt.assert_warns(QiitaDBWarning, SampleTemplate.create,
+                              self.metadata, self.new_study)
+        obs = st.check_restrictions([SAMPLE_TEMPLATE_COLUMNS['EBI']])
+        self.assertEqual(obs, {'collection_timestamp'})
+
 EXP_SAMPLE_TEMPLATE = (
     "sample_name\tcollection_timestamp\tdescription\tdna_extracted"
     "\thost_subject_id\tint_column\tlatitude\tlongitude"