Merge pull request #31 from DiamondLightSource/implicit-factory

Implicit factory

.gitignore

@@ -6,6 +6,7 @@ conf/config.cfg
 __pycache__/
 *.py[cod]
 *$py.class
+.pytest_cache
 
 # C extensions
 *.so

README.md

@@ -8,7 +8,7 @@
 
 This package provides a way to write acquisition and processing results into
 an ISPyB database. Currently, the only supported method is through stored
-procedures, but the package is designed to allow for other methods as well, such  
+procedures, but the package is designed to allow for other methods as well, such
 as webservices.
 
 ### Requirements
@@ -34,25 +34,25 @@ pip2.7 install --user ispyb
 
 ### Examples
 ```python
-import ispyb.factory
+import ispyb
 from datetime import datetime
 
 # Get a connection and data area objects
 with ispyb.open('config.cfg') as conn:
-  core = ispyb.factory.create_data_area(ispyb.factory.DataAreaType.CORE, conn)
-  mxacquisition = ispyb.factory.create_data_area(ispyb.factory.DataAreaType.MXACQUISITION, conn)
+  core = conn.core
+  mx_acquisition = conn.mx_acquisition
 
   # Find the id for a given visit
   sessionid = core.retrieve_visit_id('cm14451-2')
 
   # Create a new data collection group entry:
-  params = mxacquisition.get_data_collection_group_params()
+  params = mx_acquisition.get_data_collection_group_params()
   params['parentid'] = sessionid
   params['experimenttype'] = 'OSC'
   params['starttime'] = datetime.strptime('2017-09-21 13:00:00', '%Y-%m-%d %H:%M:%S')
   params['endtime'] = datetime.strptime('2017-09-21 13:00:10', '%Y-%m-%d %H:%M:%S')
   params['comments'] = 'This is a test of data collection group.'
-  dcg_id = mxacquisition.insert_data_collection_group(list(params.values()))
+  dcg_id = mx_acquisition.insert_data_collection_group(list(params.values()))
   print("dcg_id: %i" % dcg_id)
 ```
 

bin/mxdatareduction2ispyb.py

@@ -12,7 +12,7 @@
 import sys
 from datetime import datetime
 
-import ispyb.factory
+import ispyb
 from ispyb.xmltools import mx_data_reduction_to_ispyb, xml_file_to_dict
 
 if len(sys.argv) not in (3,4):
@@ -24,7 +24,7 @@
 conf_file = sys.argv[1]
 
 with ispyb.open(conf_file) as conn:
-    mxprocessing = ispyb.factory.create_data_area(ispyb.factory.DataAreaType.MXPROCESSING, conn)
+    mxprocessing = conn.mx_processing
 
     xml_file = sys.argv[2]
     xml_dir = os.path.split(xml_file)[0]

docs/pipeline2ispyb.py

@@ -10,17 +10,18 @@
 # data acquisition and processing pipeline.
 #
 
+from __future__ import absolute_import, division
 
 import sys
 from datetime import datetime
 
-import ispyb.factory
+import ispyb
 
 with ispyb.open(sys.argv[1]) as conn:
-    core = ispyb.factory.create_data_area(ispyb.factory.DataAreaType.CORE, conn)
-    mxacquisition = ispyb.factory.create_data_area(ispyb.factory.DataAreaType.MXACQUISITION, conn)
-    mxprocessing = ispyb.factory.create_data_area(ispyb.factory.DataAreaType.MXPROCESSING, conn)
-    mxscreening = ispyb.factory.create_data_area(ispyb.factory.DataAreaType.MXSCREENING, conn)
+    core = conn.core
+    mxacquisition = conn.mx_acquisition
+    mxprocessing = conn.mx_processing
+    mxscreening = conn.mx_screening
 
     # Find the id for a given visit
     sessionid = core.retrieve_visit_id('cm14451-2')

ispyb/__init__.py

@@ -6,7 +6,7 @@
   import ConfigParser as configparser
 import logging
 
-__version__ = '4.6.0'
+__version__ = '4.7.0'
 
 _log = logging.getLogger('ispyb')
 

ispyb/factory.py

@@ -26,6 +26,8 @@ def create_connection(conf_file):
 def create_data_area(data_area_type, conn):
   '''Factory function. Given a DataArea type and a Connection object imports the relevant data area module and
      returns the correct type of Data Area object with its connection as the Connection object.'''
+  import warnings
+  warnings.warn("deprecated, use the data area properties on the connection object", DeprecationWarning)
   if not hasattr(data_area_type, 'module') or not hasattr(data_area_type, 'classname'):
       raise AttributeError('DataArea type %s does not exist' % data_area_type)
   da_mod = importlib.import_module('%s.%s' % (conn.get_data_area_package(), data_area_type.module))

ispyb/interface/connection.py

@@ -1,8 +1,9 @@
 import abc
+import ispyb.interface.factory
 
 ABC = abc.ABCMeta('ABC', (object,), {'__slots__': ()}) # compatible with Python 2 *and* 3
 
-class IF(ABC):
+class IF(ABC, ispyb.interface.factory.factory_mixin):
   '''ISPyB connection interface definition object.'''
 
   @abc.abstractmethod

ispyb/interface/factory.py

@@ -0,0 +1,45 @@
+from __future__ import absolute_import, division, print_function
+
+import importlib
+
+class factory_mixin():
+  def _get_data_area(self, module, classname):
+    '''Helper function to instantiate a data area or return a cached instance.'''
+    if hasattr(self, '_cache_' + module):
+      return getattr(self, '_cache_' + module)
+    da_mod = importlib.import_module('%s.%s' % (self.get_data_area_package(), module))
+    DAClass = getattr(da_mod, classname)
+    da = DAClass()
+    da.set_connection(self)
+    setattr(self, '_cache_' + module, da)
+    return da
+
+  @property
+  def core(self):
+    '''Core part of the database schema'''
+    return self._get_data_area('core', 'Core')
+
+  @property
+  def mx_acquisition(self):
+    '''MX acquisition tables'''
+    return self._get_data_area('mxacquisition', 'MXAcquisition')
+
+  @property
+  def em_acquisition(self):
+    '''EM acquisition tables'''
+    return self._get_data_area('emacquisition', 'EMAcquisition')
+
+  @property
+  def mx_processing(self):
+    '''MX processing tables'''
+    return self._get_data_area('mxprocessing', 'MXProcessing')
+
+  @property
+  def mx_screening(self):
+    '''MX screening tables'''
+    return self._get_data_area('mxscreening', 'MXScreening')
+
+  @property
+  def shipping(self):
+    '''Shipping tables'''
+    return self._get_data_area('shipping', 'Shipping')

tests/test_core.py

@@ -1,12 +1,12 @@
-from __future__ import division, print_function
+from __future__ import absolute_import, division, print_function
 
 import context
-import ispyb.factory
+import ispyb
 import time
 
 def test_insert_session_for_proposal_code_number(testconfig):
   with ispyb.open(testconfig) as conn:
-        core = ispyb.factory.create_data_area(ispyb.factory.DataAreaType.CORE, conn)
+        core = conn.core
 
         # Test upsert_person:
         params = core.get_person_params()
@@ -72,7 +72,7 @@ def test_insert_session_for_proposal_code_number(testconfig):
 
 def test_upsert_sample(testconfig):
   with ispyb.open(testconfig) as conn:
-        core = ispyb.factory.create_data_area(ispyb.factory.DataAreaType.CORE, conn)
+        core = conn.core
         params = core.get_sample_params()
         params['containerid'] = 1326
         params['crystalid'] = 3918
@@ -89,50 +89,42 @@ def test_upsert_sample(testconfig):
 
 def test_retrieve_visit_id(testconfig):
   with ispyb.open(testconfig) as conn:
-        core = ispyb.factory.create_data_area(ispyb.factory.DataAreaType.CORE, conn)
-        id = core.retrieve_visit_id('cm14451-2')
+        id = conn.core.retrieve_visit_id('cm14451-2')
         assert id == 55168
 
 def test_retrieve_current_sessions(testconfig):
   with ispyb.open(testconfig) as conn:
-        core = ispyb.factory.create_data_area(ispyb.factory.DataAreaType.CORE, conn)
-        rs = core.retrieve_current_sessions('i03', 24*60*30000)
+        rs = conn.core.retrieve_current_sessions('i03', 24*60*30000)
         assert len(rs) > 0
 
 def test_retrieve_current_sessions_for_person(testconfig):
   with ispyb.open(testconfig) as conn:
-        core = ispyb.factory.create_data_area(ispyb.factory.DataAreaType.CORE, conn)
-        rs = core.retrieve_current_sessions_for_person('i03', 'boaty', tolerance_mins=24*60*30000)
+        rs = conn.core.retrieve_current_sessions_for_person('i03', 'boaty', tolerance_mins=24*60*30000)
         assert len(rs) > 0
 
 def test_retrieve_most_recent_session(testconfig):
   with ispyb.open(testconfig) as conn:
-        core = ispyb.factory.create_data_area(ispyb.factory.DataAreaType.CORE, conn)
-        rs = core.retrieve_most_recent_session('i03', 'cm')
+        rs = conn.core.retrieve_most_recent_session('i03', 'cm')
         assert len(rs) == 1
 
 def test_retrieve_persons_for_proposal(testconfig):
   with ispyb.open(testconfig) as conn:
-        core = ispyb.factory.create_data_area(ispyb.factory.DataAreaType.CORE, conn)
-        rs = core.retrieve_persons_for_proposal('cm', 14451)
+        rs = conn.core.retrieve_persons_for_proposal('cm', 14451)
         assert len(rs) == 1
         login = rs[0]['login']
         assert login is not None
 
 def test_retrieve_current_cm_sessions(testconfig):
   with ispyb.open(testconfig) as conn:
-        core = ispyb.factory.create_data_area(ispyb.factory.DataAreaType.CORE, conn)
-        rs = core.retrieve_current_cm_sessions('i03')
+        rs = conn.core.retrieve_current_cm_sessions('i03')
         assert len(rs) > 0
 
 def test_retrieve_active_plates(testconfig):
   with ispyb.open(testconfig) as conn:
-        core = ispyb.factory.create_data_area(ispyb.factory.DataAreaType.CORE, conn)
-        rs = core.retrieve_active_plates('i02-2')
+        rs = conn.core.retrieve_active_plates('i02-2')
         assert len(rs) >= 0
 
 def test_retrieve_proposal_title(testconfig):
   with ispyb.open(testconfig) as conn:
-        core = ispyb.factory.create_data_area(ispyb.factory.DataAreaType.CORE, conn)
-        title = core.retrieve_proposal_title('cm', 14451)
+        title = conn.core.retrieve_proposal_title('cm', 14451)
         assert title.strip() == 'I03 Commissioning Directory 2016'

tests/test_em_structures.py

@@ -1,11 +1,11 @@
-from __future__ import division, print_function
+from __future__ import absolute_import, division, print_function
 
 import context
-import ispyb.factory
+import ispyb
 
 def test_insert_movie(testconfig):
   with ispyb.open(testconfig) as conn:
-        emacquisition = ispyb.factory.create_data_area(ispyb.factory.DataAreaType.EMACQUISITION, conn)
+        emacquisition = conn.em_acquisition
         group_params = emacquisition.get_data_collection_group_params()
         group_params['parentid'] = 55168
         group_id = emacquisition.insert_data_collection_group(list(group_params.values()))
@@ -25,7 +25,7 @@ def test_insert_movie(testconfig):
 
 def test_insert_motion_correction(testconfig):
   with ispyb.open(testconfig) as conn:
-        emacquisition = ispyb.factory.create_data_area(ispyb.factory.DataAreaType.EMACQUISITION, conn)
+        emacquisition = conn.em_acquisition
         group_params = emacquisition.get_data_collection_group_params()
         group_params['parentid'] = 55168
         group_id = emacquisition.insert_data_collection_group(list(group_params.values()))
@@ -48,7 +48,7 @@ def test_insert_motion_correction(testconfig):
 
 def test_insert_ctf(testconfig):
   with ispyb.open(testconfig) as conn:
-        emacquisition = ispyb.factory.create_data_area(ispyb.factory.DataAreaType.EMACQUISITION, conn)
+        emacquisition = conn.em_acquisition
         group_params = emacquisition.get_data_collection_group_params()
         group_params['parentid'] = 55168
         group_id = emacquisition.insert_data_collection_group(list(group_params.values()))
@@ -75,7 +75,7 @@ def test_insert_ctf(testconfig):
 
 def test_insert_drift(testconfig):
   with ispyb.open(testconfig) as conn:
-        emacquisition = ispyb.factory.create_data_area(ispyb.factory.DataAreaType.EMACQUISITION, conn)
+        emacquisition = conn.em_acquisition
         group_params = emacquisition.get_data_collection_group_params()
         group_params['parentid'] = 55168
         group_id = emacquisition.insert_data_collection_group(list(group_params.values()))

tests/test_misc.py

@@ -1,4 +1,4 @@
-from __future__ import division, print_function
+from __future__ import absolute_import, division, print_function
 
 import threading
 
@@ -8,7 +8,7 @@
 
 def test_multi_threads_upsert(testconfig):
   with ispyb.open(testconfig) as conn:
-        mxprocessing = ispyb.factory.create_data_area(ispyb.factory.DataAreaType.MXPROCESSING, conn)
+        mxprocessing = conn.mx_processing
 
         params = mxprocessing.get_program_params()
         params['cmd_line'] = 'dials -xia2 /path/to/files'
@@ -40,7 +40,5 @@ def test_multi_threads_upsert(testconfig):
 
 def test_retrieve_failure(testconfig):
   with ispyb.open(testconfig) as conn:
-    mxacquisition = ispyb.factory.create_data_area(ispyb.factory.DataAreaType.MXACQUISITION, conn)
-
     with pytest.raises(ispyb.exception.ISPyBNoResultException):
-      rs = mxacquisition.retrieve_data_collection_main(0)
+      rs = conn.mx_acquisition.retrieve_data_collection_main(0)

tests/test_mxacquisition.py

@@ -1,12 +1,12 @@
-from __future__ import division, print_function
+from __future__ import absolute_import, division, print_function
 
 import context
 from datetime import datetime
-import ispyb.factory
+import ispyb
 
 def test_mxacquisition_methods(testconfig):
   with ispyb.open(testconfig) as conn:
-        mxacquisition = ispyb.factory.create_data_area(ispyb.factory.DataAreaType.MXACQUISITION, conn)
+        mxacquisition = conn.mx_acquisition
 
         params = mxacquisition.get_data_collection_group_params()
         params['parentid'] = 55168 # sessionId

tests/test_mxprocessing.py

@@ -1,11 +1,11 @@
-from __future__ import division, print_function
+from __future__ import absolute_import, division, print_function
 
 import context
-import ispyb.factory
+import ispyb
 
 def test_processing_jobs(testconfig):
   with ispyb.open(testconfig) as conn:
-        mxprocessing = ispyb.factory.create_data_area(ispyb.factory.DataAreaType.MXPROCESSING, conn)
+        mxprocessing = conn.mx_processing
 
         params = mxprocessing.get_job_params()
         params['datacollectionid'] = 993677
@@ -52,7 +52,7 @@ def test_processing_jobs(testconfig):
 
 def test_processing(testconfig):
   with ispyb.open(testconfig) as conn:
-        mxprocessing = ispyb.factory.create_data_area(ispyb.factory.DataAreaType.MXPROCESSING, conn)
+        mxprocessing = conn.mx_processing
 
         params = mxprocessing.get_program_params()
         params['cmd_line'] = 'ls -ltr'
@@ -153,7 +153,7 @@ def test_processing(testconfig):
 
 def test_post_processing(testconfig):
   with ispyb.open(testconfig) as conn:
-        mxprocessing = ispyb.factory.create_data_area(ispyb.factory.DataAreaType.MXPROCESSING, conn)
+        mxprocessing = conn.mx_processing
 
         params = mxprocessing.get_run_params()
         params['parentid'] = 596133 # some autoProcScalingId

tests/test_mxscreening.py

@@ -1,15 +1,15 @@
-from __future__ import division, print_function
+from __future__ import absolute_import, division, print_function
 
 from datetime import datetime
 
 import context
-import ispyb.factory
+import ispyb
 
 def test_insert_all_screening(testconfig):
   with ispyb.open(testconfig) as conn:
-        core = ispyb.factory.create_data_area(ispyb.factory.DataAreaType.CORE, conn)
-        mxscreening = ispyb.factory.create_data_area(ispyb.factory.DataAreaType.MXSCREENING, conn)
-        mxacquisition = ispyb.factory.create_data_area(ispyb.factory.DataAreaType.MXACQUISITION, conn)
+        core = conn.core
+        mxscreening = conn.mx_screening
+        mxacquisition = conn.mx_acquisition
 
         test_session = 'cm14451-2'
         session_id = core.retrieve_visit_id(test_session)