Merge pull request #3029 from antgonza/fix-2839

fix #2839

Author: wasade

qiita_db/metadata_template/base_metadata_template.py

@@ -1158,8 +1158,8 @@ def to_file(self, fp, samples=None):
             df.to_csv(fp, index_label='sample_name', na_rep="", sep='\t',
                       encoding='utf-8')
 
-    def to_dataframe(self):
-        """Returns the metadata template as a dataframe
+    def _common_to_dataframe_steps(self):
+        """Perform the common to_dataframe steps
 
         Returns
         -------

qiita_db/metadata_template/prep_template.py

@@ -767,3 +767,20 @@ def name(self, value):
                      WHERE prep_template_id = %s"""
             qdb.sql_connection.TRN.add(sql, [value, self.id])
             qdb.sql_connection.TRN.execute()
+
+    def to_dataframe(self, add_ebi_accessions=False):
+        """Returns the metadata template as a dataframe
+
+        Parameters
+        ----------
+        add_ebi_accessions : bool, optional
+            If this should add the ebi accessions
+        """
+        df = self._common_to_dataframe_steps()
+
+        if add_ebi_accessions:
+            accessions = self.ebi_experiment_accessions
+            df['qiita_ebi_experiment_accessions'] = df.index.map(
+                lambda sid: accessions[sid])
+
+        return df

qiita_db/metadata_template/sample_template.py

@@ -332,3 +332,20 @@ def biosample_accessions(self, value):
             If a sample in `value` already has an accession number
         """
         self._update_accession_numbers('biosample_accession', value)
+
+    def to_dataframe(self, add_ebi_accessions=False):
+        """Returns the metadata template as a dataframe
+
+        Parameters
+        ----------
+        add_ebi_accessions : bool, optional
+            If this should add the ebi accessions
+        """
+        df = self._common_to_dataframe_steps()
+
+        if add_ebi_accessions:
+            accessions = self.ebi_sample_accessions
+            df['qiita_ebi_sample_accessions'] = df.index.map(
+                lambda sid: accessions[sid])
+
+        return df

qiita_db/metadata_template/test/test_prep_template.py

@@ -685,6 +685,12 @@ def test_to_dataframe(self):
             u'illumina_technology', u'sample_center', u'pcr_primers',
             u'study_center', 'qiita_prep_id'})
 
+        # test with add_ebi_accessions as True
+        obs = self.tester.to_dataframe(True)
+        self.assertEqual(
+            self.tester.ebi_experiment_accessions,
+            obs.qiita_ebi_experiment_accessions.to_dict())
+
     def test_clean_validate_template_error_bad_chars(self):
         """Raises an error if there are invalid characters in the sample names
         """

qiita_db/metadata_template/test/test_sample_template.py

@@ -1975,6 +1975,12 @@ def test_to_dataframe(self):
             'anonymized_name', 'tot_org_carb', 'description_duplicate',
             'env_feature', 'scientific_name', 'qiita_study_id'})
 
+        # test with add_ebi_accessions as True
+        obs = self.tester.to_dataframe(True)
+        self.assertEqual(
+            self.tester.ebi_sample_accessions,
+            obs.qiita_ebi_sample_accessions.to_dict())
+
     def test_check_restrictions(self):
         obs = self.tester.check_restrictions(
             [STC['EBI']])