API: passing SampleTemplate.unique_ids

Author: wasade

qiita_db/metadata_template/base_metadata_template.py

@@ -470,8 +470,6 @@ class MetadataTemplate(qdb.base.QiitaObject):
     # forbidden_words not defined for base class. Please redefine for
     # sub-classes.
     _forbidden_words = {}
-    # qiita-unique integer identifier mapping table
-    _id_map_table = None
 
     @classmethod
     def _check_id(cls, id_):

qiita_db/metadata_template/sample_template.py

@@ -172,6 +172,43 @@ def columns_restrictions(self):
         """
         return qdb.metadata_template.constants.SAMPLE_TEMPLATE_COLUMNS
 
+    def unique_ids(self):
+        r"""Return a stable mapping of sample_name to integers
+
+        Obtain a map from a sample_name to an integer. The association is
+        unique Qiita-wide and 1-1.
+
+        This method is idempotent.
+
+        Returns
+        ------
+        dict
+            {sample_name: integer_index}
+        """
+        samples = [[self._id, s_id] for s_id in sorted(self.keys())]
+        with qdb.sql_connection.TRN:
+            # insert any IDs not present
+            sql = """INSERT INTO map_sample_idx (study_idx, sample_name)
+                     VALUES (%s, %s)
+                     ON CONFLICT (sample_name)
+                     DO NOTHING"""
+            qdb.sql_connection.TRN.add(sql, samples, many=True)
+
+            # obtain the association
+            sql = """SELECT
+                         sample_name,
+                         sample_idx
+                     FROM map_sample_idx"""
+            qdb.sql_connection.TRN.add(sql)
+
+            # form into a dict
+            mapping = {r[0]: r[1] for r in qdb.sql_connection.TRN.execute_fetchindex()}
+
+            # commit in the event changes were made
+            qdb.sql_connection.TRN.commit()
+
+        return mapping
+
     def delete_samples(self, sample_names):
         """Delete `sample_names` from sample information file
 

qiita_db/metadata_template/test/test_sample_template.py

@@ -500,7 +500,7 @@ def test_init(self):
 
     def test_unique_ids(self):
         obs = self.tester.unique_ids()
-        exp = {name: idx for idx, name in enumerate(sorted(self.tester.keys()))}
+        exp = {name: idx for idx, name in enumerate(sorted(self.tester.keys()), 1)}
         self.assertEqual(obs, exp)
 
         # verify a repeat call is unchanged

qiita_db/support_files/patches/95.sql

@@ -7,7 +7,6 @@ CREATE TABLE map_sample_idx (
     sample_name VARCHAR NOT NULL PRIMARY KEY,
     study_idx BIGINT NOT NULL,
     sample_idx BIGINT DEFAULT NEXTVAL('sequence_sample_idx') NOT NULL,
-    UNIQUE (study_idx, sample_idx),
     UNIQUE (sample_idx),
     CONSTRAINT fk_study FOREIGN KEY (study_idx) REFERENCES qiita.study (study_id)
 );