merge qualid

Author: stephanie

odmtools/controller/frmAddPoints.py

@@ -242,7 +242,9 @@ def parseTable(self):
                 if i.offSetType != "NULL":
                     row[6] = i.offSetType
                 if i.qualifierCode != "NULL":
-                    row[8] = i.qualifierCode
+                    code = i.qualifierCode.split(':')[0]
+                    q=self.recordService._edit_service.memDB.series_service.get_qualifier_by_code(code=code)
+                    row[8] = q.id
                 if i.labSampleCode != "NULL":
                     row[9] = i.labSampleCode
 

odmtools/controller/logicCellEdit.py

@@ -34,7 +34,7 @@ def __init__(self, parent, serviceManager, recordService):
             self.censorCodeChoices = [NULL] + [x.term for x in self.cv_service.get_censor_code_cvs()]
             self.labSampleChoices = [NULL] + labChoices.keys()
 
-            self.qualifierChoices = OrderedDict((x.code + '-' + x.description, x.id)
+            self.qualifierChoices = OrderedDict((x.code + ':' + x.description, x.id)
                                            for x in self.series_service.get_all_qualifiers() if x.code and x.description)
             self.qualifierCodeChoices = [NULL] + self.qualifierChoices.keys() + [NEW]
 
@@ -375,7 +375,7 @@ def cbHandler(event):
                 #dlg.Destroy()
 
         try:
-            self.qualifierChoices = OrderedDict((x.code + '-' + x.description, x.id)
+            self.qualifierChoices = OrderedDict((x.code + ':' + x.description, x.id)
                                                for x in self.cv_service.get_all_qualifiers() if x.code and x.description)
             self.qualifierCodeChoices = [NULL] + self.qualifierChoices.keys() + [NEW]
         except:

odmtools/odmdata/memory_database.py

@@ -90,6 +90,11 @@ def rollback(self):
         # self.mem_service._session_factory.engine.connect().connection.rollback()
         #self.updateDF()
 
+    #TODO is there a way to do a single rollback
+    def rollbacksingle(self):
+        pass
+
+
     def update(self, updates):
         '''
         updates : list of dictionary that contains 2 items, id and value

odmtools/odmservices/cv_service.py

@@ -36,8 +36,6 @@ def get_samples(self):
         result = self._edit_session.query(Sample).order_by(Sample.lab_sample_code).all()
         return result
 
-
-
     def get_site_type_cvs(self):
         result = self._edit_session.query(SiteTypeCV).order_by(SiteTypeCV.term).all()
         return result

odmtools/odmservices/series_service.py

@@ -191,6 +191,14 @@ def get_all_qualifiers(self):
         result = self._edit_session.query(Qualifier).order_by(Qualifier.code).all()
         return result
 
+    def get_qualifier_by_code(self, code):
+        """
+
+        :return: Qualifiers
+        """
+        result = self._edit_session.query(Qualifier).filter(Qualifier.code==code).first()
+        return result
+
     def get_qualifiers_by_series_id(self, series_id):
         """
 

odmtools/odmservices/service_manager.py

@@ -21,31 +21,34 @@
 logger =logging.getLogger('main')
 
 class ServiceManager():
-    def __init__(self, debug=False):
+    def __init__(self, debug=False, conn_dict = None):
         self.debug = debug
         f = self._get_file('r')
         self._conn_dicts = []
         self.version = 0
         self._connection_format = "%s+%s://%s:%s@%s/%s"
 
         # Read all lines (connections) in the connection.cfg file
-        while True:
-            line = f.readline()
-            if not line:
-                break
-            else:
-                line = line.split()
-                #logger.debug(line)
-
-                if len(line) >= 5:
-                    line_dict = {}
-
-                    line_dict['engine'] = line[0]
-                    line_dict['user'] = line[1]
-                    line_dict['password'] = line[2]
-                    line_dict['address'] = line[3]
-                    line_dict['db'] = line[4]
-                    self._conn_dicts.append(line_dict)
+        if conn_dict is None:
+            while True:
+                line = f.readline()
+                if not line:
+                    break
+                else:
+                    line = line.split()
+                    #logger.debug(line)
+
+                    if len(line) >= 5:
+                        line_dict = {}
+
+                        line_dict['engine'] = line[0]
+                        line_dict['user'] = line[1]
+                        line_dict['password'] = line[2]
+                        line_dict['address'] = line[3]
+                        line_dict['db'] = line[4]
+                        self._conn_dicts.append(line_dict)
+        else:
+            self._conn_dicts.append(conn_dict)
 
         if len(self._conn_dicts) is not 0:
             # The current connection defaults to the most recent (i.e. the last written to the file)
@@ -152,7 +155,7 @@ def get_cv_service(self):
         return CVService(conn_string, self.debug)
 
     def get_edit_service(self, series_id, connection):
-        
+
         return EditService(series_id, connection=connection,  debug=self.debug)
 
     def get_record_service(self, script, series_id, connection):
@@ -197,6 +200,10 @@ def _build_connection_string(self, conn_dict):
             #                            (conn_dict['address'], conn_dict['user'], conn_dict['password'],conn_dict['db'],
             #                             ))
             conn_string = 'mssql+pyodbc:///?odbc_connect={}'.format(quoted)
+
+        elif conn_dict['engine']=='sqlite':
+            connformat = "%s:///%s"
+            conn_string = connformat%(conn_dict['engine'], conn_dict['address'])
         else:
             if conn_dict['engine'] == 'mssql':
                 driver = "pyodbc"
@@ -217,12 +224,19 @@ def _build_connection_string(self, conn_dict):
                 driver = "None"
                 conn_string = self.constringBuilder(conn_dict, driver)
 <<<<<<< HEAD
+<<<<<<< HEAD
 
 =======
 >>>>>>> logging
 
         # print "******", conn_string
         return conn_string
+=======
+
+        # print "******", conn_string
+        return conn_string
+
+>>>>>>> qualid
 
     def constringBuilder(self, conn_dict, driver):
         if conn_dict['password'] is None or not conn_dict['password']:

tests/test_odmdata/test_FreeTDS.py

@@ -11,7 +11,7 @@
 
 class TestFreeTDS:
     def setup(self):
-<<<<<<< HEAD
+
 
         #run this setup if the current os is mac or linux
         if  sys.platform != 'win32':
@@ -40,38 +40,6 @@ def setup(self):
     #
     # def test_connection(self):
     #     pass
-=======
-        # connection string
-        
-        # create engine
-        #quoted = urllib.quote_plus('DRIVER={FreeTDS};Server=iutahqc.uwrl.usu.edu;Database=iUTAH_Logan_OD;UID=qc;PWD=iUTAH123!!;TDS_Version=8.0;Port=1433;')
-        quoted = urllib.quote_plus('DRIVER={FreeTDS};DSN=iutahqc;UID=qc;PWD=iUTAH123!!;')
-        engine = sqlalchemy.create_engine('mssql+pyodbc:///?odbc_connect={}'.format(quoted))
-        # conn = engine.connect()
-        # q = conn.execute("select * from variables")
-        print "engine:", engine
-        assert engine 
-        Session = sessionmaker(bind=engine)
-        assert Session
-        session = Session()
-        assert session
-        q= session.query(variable.Variable).all()
-        print "q:", type(q), dir(q)
-        for i in q:
-            print i
-        #conn.close()
-        q= session.query(series.Series).all()
-        for i in q[:10]:
-            print i
-        assert q
-        print engine
 
-    
-<<<<<<< HEAD
-    # def test_connection(self):
-    #     pass
-=======
-    def test_connection(self):
-        pass
->>>>>>> Beta_1.2.4
->>>>>>> logging
+
+

tests/test_odmservices/test_series_service.py

@@ -70,6 +70,15 @@ def test_create_qualifier(self):
 
         assert qual.id is not None
 
+    def test_get_qualifier_by_code(self):
+        assert self.series_service.get_all_qualifiers() == []
+
+        qual= self.series_service.create_qualifier("ABC123","This is a test")
+
+        db_qual = self.series_service.get_qualifier_by_code("ABC123")
+
+        assert qual.id == db_qual.id
+
     def test_get_qualifiers(self):
         assert self.series_service.get_all_qualifiers() == []
 
@@ -393,4 +402,5 @@ def test_variable_exists(self):
         assert self.series_service.variable_exists(variable)
         variable.code = "00000"
         variable.name = "A new name"
-        assert not self.series_service.variable_exists(variable)
+        assert not self.series_service.variable_exists(variable)
+