Merge pull request #70 from squirrelo/addstudy

Study and StudyPerson object

qiita_db/base.py

@@ -199,7 +199,7 @@ def status(self):
             "{0}_id = %s)".format(self._table),
             (self._id, ))[0]
 
-    def _status_setter_checks(self):
+    def _status_setter_checks(self, conn_handler):
         r"""Perform any extra checks that needed to be done before setting the
         object status on the database. Should be overwritten by the subclasses
         """
@@ -218,10 +218,10 @@ def status(self, status):
         self._check_subclass()
 
         # Perform any extra checks needed before we update the status in the DB
-        self._status_setter_checks()
+        conn_handler = SQLConnectionHandler()
+        self._status_setter_checks(conn_handler)
 
         # Update the status of the object
-        conn_handler = SQLConnectionHandler()
         conn_handler.execute(
             "UPDATE qiita.{0} SET {0}_status_id = "
             "(SELECT {0}_status_id FROM qiita.{0}_status WHERE status = %s) "

qiita_db/exceptions.py

@@ -30,13 +30,18 @@ class QiitaDBConnectionError(QiitaDBError):
     pass
 
 
+class QiitaDBColumnError(QiitaDBError):
+    """Exception when missing table information or excess information passed"""
+    pass
+
+
 class QiitaDBDuplicateError(QiitaDBError):
     """Exception when duplicating something in the database"""
     pass
 
 
-class QiitaDBColumnError(QiitaDBError):
-    """Exception when database column info missing or incorrect"""
+class QiitaDBStatusError(QiitaDBError):
+    """Exception when editing is done with an unallowed status"""
     pass
 
 
@@ -45,4 +50,4 @@ class QiitaDBUnknownIDError(QiitaDBError):
     def __init__(self, missing_id, table):
         super(QiitaDBUnknownIDError, self).__init__()
         self.args = ("The object with ID '%s' does not exists in table '%s"
-                     % (missing_id, table))
+                     % (missing_id, table),)

qiita_db/metadata_template.py

@@ -66,6 +66,18 @@ class MetadataTemplate(QiitaStatusObject):
     # instantiate this base class
     _table_prefix = None
     _column_table = None
+    _id_column = None
+
+    def _check_id(self, id_, conn_handler=None):
+        # PLACEHOLDER SO TESTS PASS. Jose will rewrite for metadata pr
+        r""""""
+        self._check_subclass()
+        conn_handler = (conn_handler if conn_handler is not None
+                        else SQLConnectionHandler())
+        return conn_handler.execute_fetchone(
+            "SELECT EXISTS(SELECT * FROM qiita.{0} WHERE "
+            "{1}=%s)".format(self._table, self._id_column),
+            (id_, ))[0]
 
     @classmethod
     def _get_table_name(cls, study_id):
@@ -262,8 +274,10 @@ def has_single_category_values(self, category):
 
 class SampleTemplate(MetadataTemplate):
     """"""
+    _table = "required_sample_info"
     _table_prefix = "sample_"
     _column_table = "study_sample_columns"
+    _id_column = "study_id"
 
 
 class PrepTemplate(MetadataTemplate):