Fixing study.py and tests. Removing add_raw_data as it is no longer needed

Author: josenavas

qiita_db/study.py

@@ -642,10 +642,11 @@ def data_types(self):
         list of str
         """
         conn_handler = SQLConnectionHandler()
-        sql = ("SELECT DISTINCT DT.data_type FROM qiita.study_raw_data SRD "
-               "JOIN qiita.prep_template PT ON SRD.raw_data_id = "
-               "PT.raw_data_id JOIN qiita.data_type DT ON PT.data_type_id = "
-               "DT.data_type_id WHERE SRD.study_id = %s")
+        sql = """SELECT DISTINCT data_type
+                 FROM qiita.study_prep_template
+                    JOIN qiita.prep_template USING (prep_template_id)
+                    JOIN qiita.data_type USING (data_type_id)
+                 WHERE study_id = %s"""
         return [x[0] for x in conn_handler.execute_fetchall(sql, (self._id,))]
 
     @property
@@ -759,36 +760,30 @@ def raw_data(self, data_type=None):
 
         return [x[0] for x in conn_handler.execute_fetchall(sql, (self._id,))]
 
-    def add_raw_data(self, raw_data):
-        """ Adds raw_data to the current study
+    def prep_templates(self, data_type=None):
+        """Return list of prep template ids
 
         Parameters
         ----------
-        raw_data : list of RawData
-            The RawData objects to be added to the study
+        data_type : str, optional
+            If given, retrieve only prep templates for given datatype.
+            Default None.
 
-        Raises
-        ------
-        QiitaDBError
-            If the raw_data is already linked to the current study
+        Returns
+        -------
+        list of PrepTemplate ids
         """
-        conn_handler = SQLConnectionHandler()
-        self._lock_non_sandbox(conn_handler)
-        queue = "%d_add_raw_data" % self.id
-        sql = ("SELECT EXISTS(SELECT * FROM qiita.study_raw_data WHERE "
-               "study_id=%s AND raw_data_id=%s)")
-        conn_handler.create_queue(queue)
-        sql_args = [(self.id, rd.id) for rd in raw_data]
-        conn_handler.add_to_queue(queue, sql, sql_args, many=True)
-        linked = conn_handler.execute_queue(queue)
-
-        if any(linked):
-            raise QiitaDBError("Some of the passed raw datas have been already"
-                               " linked to the study %s" % self.id)
+        spec_data = ""
+        if data_type:
+            spec_data = " AND data_type_id = %s" % convert_to_id(data_type,
+                                                                 "data_type")
 
-        conn_handler.executemany(
-            "INSERT INTO qiita.study_raw_data (study_id, raw_data_id) "
-            "VALUES (%s, %s)", sql_args)
+        conn_handler = SQLConnectionHandler()
+        sql = """SELECT prep_template_id
+                 FROM qiita.study_prep_template
+                    JOIN qiita.prep_template USING (prep_template_id)
+                 WHERE study_id = %s{0}""".format(spec_data)
+        return [x[0] for x in conn_handler.execute_fetchall(sql, (self._id,))]
 
     def preprocessed_data(self, data_type=None):
         """ Returns list of data ids for preprocessed data info

qiita_db/test/test_study.py

@@ -2,6 +2,7 @@
 from datetime import datetime
 
 from future.utils import viewitems
+import pandas as pd
 
 from qiita_core.exceptions import IncompetentQiitaDeveloperError
 from qiita_core.util import qiita_test_checker
@@ -11,6 +12,7 @@
 from qiita_db.user import User
 from qiita_db.data import RawData
 from qiita_db.util import convert_to_id
+from qiita_db.metadata_template import PrepTemplate
 from qiita_db.exceptions import (
     QiitaDBColumnError, QiitaDBStatusError, QiitaDBError,
     QiitaDBUnknownIDError)
@@ -586,26 +588,20 @@ def test_retrieve_data_types_none(self):
         self.assertEqual(new.data_types, [])
 
     def test_retrieve_raw_data(self):
-        self.assertEqual(self.study.raw_data(), [1, 2, 3, 4])
+        self.assertEqual(self.study.raw_data(), [1])
 
     def test_retrieve_raw_data_none(self):
         new = Study.create(User('test@foo.bar'), 'NOT Identification of the '
                            'Microbiomes for Cannabis Soils', [1], self.info)
         self.assertEqual(new.raw_data(), [])
 
-    def test_add_raw_data(self):
-        self._change_processed_data_status('awaiting_approval')
+    def test_retrieve_prep_templates(self):
+        self.assertEqual(self.study.prep_templates(), [1])
+
+    def test_retrieve_prep_templates_none(self):
         new = Study.create(User('test@foo.bar'), 'NOT Identification of the '
                            'Microbiomes for Cannabis Soils', [1], self.info)
-        new.add_raw_data([RawData(1), RawData(2)])
-        obs = self.conn_handler.execute_fetchall(
-            "SELECT * FROM qiita.study_raw_data WHERE study_id=%s",
-            (new.id,))
-        self.assertEqual(obs, [[new.id, 1], [new.id, 2]])
-
-    def test_add_raw_data_private(self):
-        with self.assertRaises(QiitaDBStatusError):
-            self.study.add_raw_data([RawData(2)])
+        self.assertEqual(new.prep_templates(), [])
 
     def test_retrieve_preprocessed_data(self):
         self.assertEqual(self.study.preprocessed_data(), [1, 2])