API: passing PrepTemplate.unique_ids

Author: wasade

qiita_db/metadata_template/prep_template.py

@@ -324,6 +324,50 @@ def delete(cls, id_):
 
             qdb.sql_connection.TRN.execute()
 
+    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}
+        """
+        sample_idx = qdb.study.Study(self.study_id).sample_template.unique_ids()
+
+        paired = []
+        for p_id in sorted(self.keys()):
+            if p_id in sample_idx:
+                paired.append([self._id, sample_idx[p_id]])
+
+        with qdb.sql_connection.TRN:
+            # insert any IDs not present
+            sql = """INSERT INTO map_prep_sample_idx (prep_idx, sample_idx)
+                     VALUES (%s, %s)
+                     ON CONFLICT (prep_idx, sample_idx)
+                     DO NOTHING"""
+            qdb.sql_connection.TRN.add(sql, paired, many=True)
+
+            # obtain the association
+            sql = """SELECT
+                         sample_name,
+                         prep_sample_idx
+                     FROM map_prep_sample_idx
+                     JOIN map_sample_idx USING (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 data_type(self, ret_id=False):
         """Returns the data_type or the data_type id
 

qiita_db/metadata_template/test/test_prep_template.py

@@ -432,7 +432,7 @@ 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

@@ -16,7 +16,7 @@ CREATE TABLE map_prep_sample_idx (
     prep_sample_idx BIGINT NOT NULL PRIMARY KEY DEFAULT NEXTVAL('sequence_prep_sample_idx'),
     prep_idx BIGINT NOT NULL,
     sample_idx BIGINT NOT NULL,
-    UNIQUE (prep_idx, prep_sample_idx),
+    CONSTRAINT uc_prep_sample UNIQUE(prep_idx, sample_idx),
     CONSTRAINT fk_prep_template FOREIGN KEY (prep_idx) REFERENCES qiita.prep_template (prep_template_id)
 );
 
@@ -25,6 +25,6 @@ CREATE TABLE map_artifact_sample_idx (
     artifact_sample_idx BIGINT NOT NULL PRIMARY KEY DEFAULT NEXTVAL('sequence_artifact_sample_idx'),
     artifact_idx BIGINT NOT NULL,
     prep_sample_idx BIGINT NOT NULL,
-    UNIQUE (artifact_idx, artifact_sample_idx),
+    CONSTRAINT uc_artifact_sample UNIQUE(artifact_idx, prep_sample_idx),
     CONSTRAINT fk_artifact FOREIGN KEY (artifact_idx) REFERENCES qiita.artifact (artifact_id)
 );