Merge 389830f into 145b707

ispyb/__init__.py

@@ -38,3 +38,18 @@ def open(configuration_file):
     raise AttributeError('No supported connection type found in %s' % configuration_file)
 
   return conn
+
+
+class ISPyBException(Exception):
+  '''Base class for all exceptions'''
+
+class ConnectionError(ISPyBException):
+  '''Unable to connect or connection has been closed.'''
+
+class NoResult(ISPyBException):
+  '''Query returned no result.'''
+
+class ReadWriteError(ISPyBException):
+  '''Record could not be read, inserted, updated or deleted. This could be due to
+  illegal values, the wrong number of parameters, a violation of table or
+  index constraints, or a database failure.'''

ispyb/connector/mysqlsp/main.py

@@ -7,8 +7,7 @@
 
 import ispyb.interface.connection
 import mysql.connector
-from ispyb.exception import (ISPyBConnectionException, ISPyBNoResultException,
-                                ISPyBRetrieveFailed, ISPyBWriteFailed)
+from ispyb import (ConnectionError, NoResult, ReadWriteError)
 from mysql.connector.errors import DatabaseError, DataError, Error, InterfaceError
 
 class ISPyBMySQLSPConnector(ispyb.interface.connection.IF):
@@ -23,7 +22,7 @@ def __enter__(self):
     if hasattr(self, 'conn') and self.conn is not None:
         return self
     else:
-        raise ISPyBConnectionException
+        raise ConnectionError
 
   def __exit__(self, type, value, traceback):
     self.disconnect()
@@ -37,7 +36,7 @@ def connect(self, user=None, pw=None, host='localhost', db=None, port=3306, conn
         database=db,
         port=int(port))
     if not self.conn:
-      raise ISPyBConnectionException('Could not connect to database')
+      raise ConnectionError('Could not connect to database')
     self.conn.autocommit = True
     self.reconn_attempts = reconn_attempts
     self.reconn_delay = reconn_delay
@@ -56,14 +55,14 @@ def get_data_area_package(self):
 
   def create_cursor(self, dictionary=False):
     if not self.conn:
-      raise ISPyBConnectionException('Not connected to database')
+      raise ConnectionError('Not connected to database')
     try:
       self.conn.ping(reconnect=True, attempts=self.reconn_attempts, delay=self.reconn_delay)
     except InterfaceError:
-      raise ISPyBConnectionException('Failed to ping connection')
+      raise ConnectionError('Failed to ping connection')
     cursor = self.conn.cursor(dictionary=dictionary)
     if not cursor:
-      raise ISPyBConnectionException('Could not create database cursor')
+      raise ConnectionError('Could not create database cursor')
     return cursor
 
   def call_sp_write(self, procname, args):
@@ -72,7 +71,7 @@ def call_sp_write(self, procname, args):
         try:
             result_args = cursor.callproc(procname=procname, args=args)
         except DataError as e:
-            raise ISPyBWriteFailed("DataError({0}): {1}".format(e.errno, traceback.format_exc()))
+            raise ReadWriteError("DataError({0}): {1}".format(e.errno, traceback.format_exc()))
         finally:
             cursor.close()
     if result_args is not None and len(result_args) > 0:
@@ -84,7 +83,7 @@ def call_sp_retrieve(self, procname, args):
         try:
             cursor.callproc(procname=procname, args=args)
         except DataError as e:
-            raise ISPyBRetrieveFailed("DataError({0}): {1}".format(e.errno, traceback.format_exc()))
+            raise ReadWriteError("DataError({0}): {1}".format(e.errno, traceback.format_exc()))
 
         result = []
         for recordset in cursor.stored_results():
@@ -96,7 +95,7 @@ def call_sp_retrieve(self, procname, args):
 
         cursor.close()
     if result == []:
-        raise ISPyBNoResultException
+        raise NoResult
     return result
 
   def call_sf_retrieve(self, funcname, args):
@@ -105,14 +104,14 @@ def call_sf_retrieve(self, funcname, args):
         try:
             cursor.execute(('select %s' % funcname) + ' (%s)' % ','.join(['%s'] * len(args)), args)
         except DataError as e:
-            raise ISPyBRetrieveFailed("DataError({0}): {1}".format(e.errno, traceback.format_exc()))
+            raise ReadWriteError("DataError({0}): {1}".format(e.errno, traceback.format_exc()))
         result = None
         rs = cursor.fetchone()
         if len(rs) > 0:
             result = next(iter(rs.items()))[1]  #iter(rs.items()).next()[1]
         cursor.close()
     if result is None:
-        raise ISPyBNoResultException
+        raise NoResult
     return result
 
   def call_sf_write(self, funcname, args):
@@ -121,7 +120,7 @@ def call_sf_write(self, funcname, args):
         try:
             cursor.execute(('select %s' % funcname) + ' (%s)' % ','.join(['%s'] * len(args)), args)
         except DataError as e:
-            raise ISPyBWriteFailed("DataError({0}): {1}".format(e.errno, traceback.format_exc()))
+            raise ReadWriteError("DataError({0}): {1}".format(e.errno, traceback.format_exc()))
         result = None
         rs = cursor.fetchone()
         if len(rs) > 0:

ispyb/exception.py

@@ -1,20 +1,14 @@
-class ISPyBException(Exception):
-  '''Base class for all exceptions'''
+from __future__ import absolute_import, division, print_function
 
-class ISPyBConnectionException(ISPyBException):
-  '''Unable to connect or connection has been closed.'''
+import warnings
 
-class ISPyBNoResultException(ISPyBException):
-  '''Query returned no result.'''
+import ispyb
 
-class ISPyBWriteFailed(ISPyBException):
-  '''Record could not be inserted, updated or deleted. This could be due to
-  illegal values, the wrong number of parameters, a violation of table or
-  index constraints, or a database failure.'''
+warnings.warn("ispyb.exceptions is deprecated and will be removed in the next release. Use the exceptions underneath ispyb. instead.", DeprecationWarning)
 
-class ISPyBRetrieveFailed(ISPyBException):
-  '''Record(s) could not be retrieved. This could be due to invalid argument
-  values, or a database failure. '''
-
-class ISPyBKeyProblem(ISPyBException):
-  '''A mandatory key is missing or its value is None.'''
+ISPyBException = ispyb.ISPyBException
+ISPyBConnectionException = ispyb.ConnectionError
+ISPyBNoResultException = ispyb.NoResult
+ISPyBWriteFailed = ispyb.ReadWriteError
+ISPyBRetrieveFailed = ispyb.ReadWriteError
+ISPyBKeyProblem = KeyError

ispyb/model/gridinfo.py

@@ -1,6 +1,6 @@
 from __future__ import absolute_import, division, print_function
 
-import ispyb.exception
+import ispyb
 import ispyb.model
 
 class GridInfo(ispyb.model.DBCache):
@@ -27,7 +27,7 @@ def reload(self):
     '''Load/update information from the database.'''
     try:
       self._data = self._db.mx_acquisition.retrieve_dcg_grid(self._dcgid)[0]
-    except ispyb.exception.ISPyBNoResultException:
+    except ispyb.NoResult:
       self._data = None
 
   @property

ispyb/model/processingjob.py

@@ -164,7 +164,7 @@ def reload(self):
                p['parameterKey'], p['parameterValue'], p['parameterId']))
           for p in self._db.retrieve_job_parameters(self._jobid)
       ]
-    except ispyb.exception.ISPyBNoResultException:
+    except ispyb.NoResult:
       self._data = []
     self._data_dict = collections.OrderedDict(self._data)
 
@@ -261,7 +261,7 @@ def reload(self):
           ProcessingJobImageSweep(p['dataCollectionId'], p['startImage'], p['endImage'], p['sweepId'], self._db)
           for p in self._db.retrieve_job_image_sweeps(self._jobid)
       ]
-    except ispyb.exception.ISPyBNoResultException:
+    except ispyb.NoResult:
       self._data = []
 
   def __getitem__(self, item):
@@ -307,7 +307,7 @@ def reload(self):
           ispyb.model.processingprogram.ProcessingProgram(p['id'], self._db, preload=p)
           for p in self._db.retrieve_programs_for_job_id(self._jobid)
       ]
-    except ispyb.exception.ISPyBNoResultException:
+    except ispyb.NoResult:
       self._data = []
 
   def __getitem__(self, item):

ispyb/xmltools.py

@@ -1,10 +1,10 @@
+from __future__ import absolute_import, division, print_function
+
 # XML-to-dict code from here:
 # http://code.activestate.com/recipes/410469-xml-as-dictionary/
 
 from xml.etree import ElementTree
 
-from ispyb.exception import ISPyBKeyProblem
-
 class XmlListConfig(list):
     def __init__(self, aList):
         for element in aList:
@@ -100,11 +100,11 @@ def mx_data_reduction_to_ispyb(xmldict, dc_id = None, mxprocessing = None):
     scaling = xmldict['AutoProcScalingContainer']['AutoProcScaling']
 
     if proc == None:
-        raise ISPyBKeyProblem("Missing key 'AutoProc'")
+        raise KeyError("Missing key 'AutoProc'")
     if scaling == None:
-        raise ISPyBKeyProblem("Missing key 'AutoProcScaling'")
+        raise KeyError("Missing key 'AutoProcScaling'")
     if int_containers == None:
-        raise ISPyBKeyProblem("Missing key 'AutoProcIntegrationContainer'")
+        raise KeyError("Missing key 'AutoProcIntegrationContainer'")
 
     s = [None, None, None]
     for i in range(0,3):
@@ -117,15 +117,15 @@ def mx_data_reduction_to_ispyb(xmldict, dc_id = None, mxprocessing = None):
             s[2] = stats
 
     if s[0] == None or s[1] == None or s[2] == None:
-        raise ISPyBKeyProblem("Need 3 'AutoProcScalingStatistics' keys in 'AutoProcScalingContainer'")
+        raise KeyError("Need 3 'AutoProcScalingStatistics' keys in 'AutoProcScalingContainer'")
 
     for int_container in int_containers:
         integration = int_container['AutoProcIntegration']
         if 'dataCollectionId' not in integration:
             if dc_id is not None:
     	        integration['dataCollectionId'] = dc_id
             else:
-                raise ISPyBKeyProblem("Missing key 'dataCollectionId'")
+                raise KeyError("Missing key 'dataCollectionId'")
 
     # Store results from MX data reduction pipelines
     # ...first the program info

tests/test_misc.py

@@ -2,7 +2,7 @@
 
 import threading
 
-import ispyb.exception
+import ispyb
 import ispyb.model.__future__
 import mysql.connector.errors
 import pytest
@@ -39,7 +39,7 @@ def test_multi_threads_upsert(testdb):
             worker.join()
 
 def test_retrieve_failure(testdb):
-    with pytest.raises(ispyb.exception.ISPyBNoResultException):
+    with pytest.raises(ispyb.NoResult):
       rs = testdb.mx_acquisition.retrieve_data_collection_main(0)
 
 def test_database_reconnects_on_connection_failure(testconfig, testdb):

tests/test_mxacquisition.py

@@ -2,7 +2,7 @@
 
 from datetime import datetime
 
-import ispyb.exception
+import ispyb
 import pytest
 
 def test_mxacquisition_methods(testdb):
@@ -54,7 +54,7 @@ def test_mxacquisition_methods(testdb):
         params['comments'] = 'Forgot to comment!'
         iid = mxacquisition.upsert_image(list(params.values()))
 
-        with pytest.raises(ispyb.exception.ISPyBNoResultException):
+        with pytest.raises(ispyb.NoResult):
           gridinfo = mxacquisition.retrieve_dcg_grid(dcgid)
 
         params = mxacquisition.get_dcg_grid_params()