Merge pull request #1050 from josenavas/unify-update-category

Unify update category

Author: squirrelo

qiita_db/metadata_template/base_metadata_template.py

@@ -1083,3 +1083,30 @@ def categories(self):
                 cols[idx] = self.translate_cols_dict[c]
 
         return cols
+
+    def update_category(self, category, samples_and_values):
+        """Update an existing column
+
+        Parameters
+        ----------
+        category : str
+            The category to update
+        samples_and_values : dict
+            A mapping of {sample_id: value}
+
+        Raises
+        ------
+        QiitaDBUnknownIDError
+            If a sample_id is included in values that is not in the template
+        QiitaDBColumnError
+            If the column does not exist in the table. This is implicit, and
+            can be thrown by the contained Samples.
+        """
+        if not set(self.keys()).issuperset(samples_and_values):
+            missing = set(self.keys()) - set(samples_and_values)
+            table_name = self._table_name(self.study_id)
+            raise QiitaDBUnknownIDError(missing, table_name)
+
+        for k, v in viewitems(samples_and_values):
+            sample = self[k]
+            sample[category] = v

qiita_db/metadata_template/sample_template.py

@@ -8,7 +8,6 @@
 
 from __future__ import division
 from future.builtins import zip
-from future.utils import viewitems
 from copy import deepcopy
 from os.path import join
 from time import strftime
@@ -20,7 +19,6 @@
 
 from qiita_core.exceptions import IncompetentQiitaDeveloperError
 from qiita_db.exceptions import (QiitaDBDuplicateError, QiitaDBColumnError,
-                                 QiitaDBUnknownIDError,
                                  QiitaDBDuplicateHeaderError, QiitaDBError,
                                  QiitaDBWarning)
 from qiita_db.sql_connection import SQLConnectionHandler
@@ -407,33 +405,6 @@ def update(self, md_template):
                     if '_qiime_' not in basename(fp):
                         pt.create_qiime_mapping_file(fp)
 
-    def update_category(self, category, samples_and_values):
-        """Update an existing column
-
-        Parameters
-        ----------
-        category : str
-            The category to update
-        samples_and_values : dict
-            A mapping of {sample_id: value}
-
-        Raises
-        ------
-        QiitaDBUnknownIDError
-            If a sample_id is included in values that is not in the template
-        QiitaDBColumnError
-            If the column does not exist in the table. This is implicit, and
-            can be thrown by the contained Samples.
-        """
-        if not set(self.keys()).issuperset(samples_and_values):
-            missing = set(self.keys()) - set(samples_and_values)
-            table_name = self._table_name(self.study_id)
-            raise QiitaDBUnknownIDError(missing, table_name)
-
-        for k, v in viewitems(samples_and_values):
-            sample = self[k]
-            sample[category] = v
-
     def add_category(self, category, samples_and_values, dtype, default):
         """Add a metadata category
 

qiita_db/metadata_template/test/test_prep_template.py

@@ -1167,6 +1167,37 @@ def test_status(self):
                                  self.test_study, self.data_type_id)
         self.assertEqual(pt.status, 'sandbox')
 
+    def test_update_category(self):
+        with self.assertRaises(QiitaDBUnknownIDError):
+            self.tester.update_category('barcodesequence', {"foo": "bar"})
+
+        with self.assertRaises(QiitaDBColumnError):
+            self.tester.update_category('missing column',
+                                        {'1.SKB7.640196': 'bar'})
+
+        neg_test = self.tester['1.SKB7.640196']['barcodesequence']
+        mapping = {'1.SKB8.640193': 'AAAAAAAAAAAA',
+                   '1.SKD8.640184': 'CCCCCCCCCCCC'}
+
+        self.tester.update_category('barcodesequence', mapping)
+
+        self.assertEqual(self.tester['1.SKB7.640196']['barcodesequence'],
+                         neg_test)
+        self.assertEqual(self.tester['1.SKB8.640193']['barcodesequence'],
+                         'AAAAAAAAAAAA')
+        self.assertEqual(self.tester['1.SKD8.640184']['barcodesequence'],
+                         'CCCCCCCCCCCC')
+
+        neg_test = self.tester['1.SKB7.640196']['center_name']
+        mapping = {'1.SKB8.640193': 'FOO',
+                   '1.SKD8.640184': 'BAR'}
+
+        self.tester.update_category('center_name', mapping)
+
+        self.assertEqual(self.tester['1.SKB7.640196']['center_name'], neg_test)
+        self.assertEqual(self.tester['1.SKB8.640193']['center_name'], 'FOO')
+        self.assertEqual(self.tester['1.SKD8.640184']['center_name'], 'BAR')
+
 
 EXP_PREP_TEMPLATE = (
     'sample_name\tbarcodesequence\tcenter_name\tcenter_project_name\t'