round of code cleanup (#72)

bin/dimple2ispyb.py

@@ -3,12 +3,9 @@
 import ConfigParser
 import logging
 import os
-import pickle
-import pipes
 import re
 import sys
 import time
-import traceback
 from datetime import datetime
 from logging.handlers import RotatingFileHandler
 

bin/em_put_movie.py

@@ -14,12 +14,8 @@
 
 import datetime
 import logging
-import os
-import string
 import sys
-import time
 from datetime import datetime
-from logging.handlers import RotatingFileHandler
 
 from ispyb.core import core
 from ispyb.dbconnection import DBConnection
@@ -93,7 +89,7 @@ def exit(code, message=None):
 
     result = None
     if visitid is not None or opts.movieid is not None:
-	# EMMovieId, blsessionId,blsampleId,movieFile,p_NOImages,frameLength,totalExposure,magnification,samplePixSize,dosePerFrame,totalDose,runStatus,comments,runDirectory,binning,particleDiameter,pixelSize,boxSize,minResolution,maxResolution, minDefocus, maxDefocus, defocusStepSize, amountAstigmatism, extractSize, starttime, endtime
+        # EMMovieId, blsessionId,blsampleId,movieFile,p_NOImages,frameLength,totalExposure,magnification,samplePixSize,dosePerFrame,totalDose,runStatus,comments,runDirectory,binning,particleDiameter,pixelSize,boxSize,minResolution,maxResolution, minDefocus, maxDefocus, defocusStepSize, amountAstigmatism, extractSize, starttime, endtime
 
         # Store a movie data collection ...
         params = mxacquisition.get_data_collection_params()

bin/legacy/em_put_particle.py

@@ -8,31 +8,21 @@
 # python em_put_particle.py --movieid=1 --x=123.4 --y=50.02
 
 import logging
-import os
-import string
 import sys
-import time
-from logging.handlers import RotatingFileHandler
-
-import cx_Oracle
 
 if __name__ == '__main__' :
 
     from ispyb_api.dbconnection import dbconnection
-    from ispyb_api.core import core
-    from ispyb_api.mxacquisition import mxacquisition
     from ispyb_api.em import em
 
-    from datetime import datetime
-
     def exit(code, message=None):
         dbconnection.disconnect()
         if not message is None:
             print(message)
         sys.exit(code)
-    
+
     logging.info("test")
-    
+
     import optparse
     parser = optparse.OptionParser()
     parser.add_option("--particleid", dest="particleid", help="Id for particle", metavar="INTEGER")
@@ -44,17 +34,17 @@ def exit(code, message=None):
     (opts, args) = parser.parse_args()
 
     cursor = None
-    if opts.db is None or opts.db == "prod": 
+    if opts.db is None or opts.db == "prod":
         cursor = dbconnection.connect_to_prod()
     elif opts.db == "dev":
         cursor = dbconnection.connect_to_dev()
     elif opts.db == "test":
         cursor = dbconnection.connect_to_test()
     else:
         exit(1, "ERROR: Invalid database")
-    
+
     if opts.particleid is None and opts.dcid is None:
         exit(1, "ERROR: Both movieid and particleid are None.")
-        
+
     p_id = em.put_particle(cursor, opts.particleid, opts.dcid, opts.x, opts.y)
     exit(0, "--particleid=%d" % p_id)

bin/legacy/em_put_sample.py

@@ -8,30 +8,21 @@
 # python em_put_sample.py --proposal=em1234 --x=123.4 --y=50.02
 
 import logging
-import os
-import string
 import sys
-import time
-from logging.handlers import RotatingFileHandler
-
-import cx_Oracle
 
 if __name__ == '__main__' :
 
     from ispyb_api.dbconnection import dbconnection
     from ispyb_api.core import core
-    from ispyb_api.mxacquisition import mxacquisition
 
-    from datetime import datetime
-
     def exit(code, message=None):
         dbconnection.disconnect()
         if not message is None:
             print(message)
         sys.exit(code)
-    
+
     logging.info("test")
-    
+
     import optparse
     parser = optparse.OptionParser()
     parser.add_option("--sampleid", dest="sampleid", help="Id for sample", metavar="INTEGER")
@@ -43,22 +34,22 @@ def exit(code, message=None):
     (opts, args) = parser.parse_args()
 
     cursor = None
-    if opts.db is None or opts.db == "prod": 
+    if opts.db is None or opts.db == "prod":
         cursor = dbconnection.connect_to_prod()
     elif opts.db == "dev":
         cursor = dbconnection.connect_to_dev()
     elif opts.db == "test":
         cursor = dbconnection.connect_to_test()
     else:
         exit(1, "ERROR: Invalid database")
-    
-        
+
+
     params = core.get_sample_params()
     if not opts.sampleid is None:
         params['id'] = int(opts.sampleid)
     params['name'] = opts.longname
     params['code'] = opts.shortname
     params['comments'] = opts.comments
-        
+
     s_id = core.put_sample(cursor, params.values())
     exit(0, "--sampleid=%d" % s_id)

bin/legacy/put_dcgroup.py

@@ -8,13 +8,7 @@
 # python put_dcgroup.py --movieid=1 --x=123.4 --y=50.02
 
 import logging
-import os
-import string
 import sys
-import time
-from logging.handlers import RotatingFileHandler
-
-import cx_Oracle
 
 if __name__ == '__main__' :
 
@@ -29,9 +23,9 @@ def exit(code, message=None):
         if not message is None:
             print(message)
         sys.exit(code)
-    
+
     logging.info("test")
-    
+
     import optparse
     parser = optparse.OptionParser()
     parser.add_option("--id", dest="id", help="Id for d.c.group", metavar="INTEGER")
@@ -49,15 +43,15 @@ def exit(code, message=None):
     (opts, args) = parser.parse_args()
 
     cursor = None
-    if opts.db is None or opts.db == "prod": 
+    if opts.db is None or opts.db == "prod":
         cursor = dbconnection.connect_to_prod()
     elif opts.db == "dev":
         cursor = dbconnection.connect_to_dev()
     elif opts.db == "test":
         cursor = dbconnection.connect_to_test()
     else:
         exit(1, "ERROR: Invalid database")
-    
+
     # Find the id for a given visit
     visitid = core.retrieve_visit_id(cursor, opts.visit)
     if visitid is None:
@@ -81,7 +75,7 @@ def exit(code, message=None):
     params['actual_sample_barcode'] = opts.actual_sample_barcode
     params['comments'] = opts.comments
     dcg_id = mxacquisition.put_data_collection_group(cursor, params.values())
-    
+
     if dcg_id is None:
         exit(1, "ERROR: dc_group is None.") # exit code 1 - indicates error
     exit(0, "--dcg_id=%d" % dcg_id)

bin/legacy/put_program.py

@@ -8,15 +8,9 @@
 # python put_program.py --....
 
 import logging
-import os
-import string
 import sys
-import time
-from logging.handlers import RotatingFileHandler
 
-import cx_Oracle
-
-# AutoProcProgram.processingStatus: 
+# AutoProcProgram.processingStatus:
 # no row = didn't run
 # NULL (None) = running
 # 0 = failed
@@ -25,7 +19,6 @@
 if __name__ == '__main__' :
 
     from ispyb_api.dbconnection import dbconnection
-    from ispyb_api.core import core
     from ispyb_api.mxdatareduction import mxdatareduction
 
     from datetime import datetime
@@ -35,9 +28,9 @@ def exit(code, message=None):
         if not message is None:
             print(message)
         sys.exit(code)
-    
+
     logging.info("test")
-    
+
     import optparse
     parser = optparse.OptionParser()
     parser.add_option("--id", dest="id", help="Id for program run", metavar="INTEGER")
@@ -53,7 +46,7 @@ def exit(code, message=None):
     (opts, args) = parser.parse_args()
 
     cursor = None
-    if opts.db is None or opts.db == "prod": 
+    if opts.db is None or opts.db == "prod":
         cursor = dbconnection.connect_to_prod()
     elif opts.db == "dev":
         cursor = dbconnection.connect_to_dev()
@@ -84,9 +77,9 @@ def exit(code, message=None):
 #    params['filename3'] = ''
 #    params['filepath3'] = ''
 #    params['filetype3'] = ''
-    
+
     p_id = mxdatareduction.put_program(cursor, params.values())
-    
+
     if p_id is None:
         exit(1, "ERROR: p_id is None.") # exit code 1 - indicates error
     exit(0, "--p_id=%d" % p_id)

bin/legacy/tomo2ispyb.py

@@ -1,13 +1,6 @@
 #!/usr/bin/env python
 
-import logging
-import os
-import pipes
-import re
-import sys
-import time
-import traceback
-from datetime import datetime
+# from datetime import datetime
 
 from ispyb_api.core import core
 from ispyb_api.dbconnection import dbconnection
@@ -36,7 +29,7 @@ def store_dc(cursor, parentid):
     #params['frames'] = parentid
     #params['comments'] = parentid
     return tomo.insert_dc(cursor, params.values())
-    
+
 def store_recon(cursor, parentid):
     '''Populate dict and store tomography reconstruction'''
     params = tomo.get_recon_params()
@@ -50,7 +43,7 @@ def store_recon(cursor, parentid):
     #params['histogram'] = parentid
     #params['report'] = parentid
     return tomo.insert_recon(cursor, params.values())
-    
+
 
 cursor = dbconnection.connect_to_prod()
 

bin/mxdatareduction2ispyb.py

@@ -10,7 +10,6 @@
 
 import os
 import sys
-from datetime import datetime
 
 import ispyb
 from ispyb.xmltools import mx_data_reduction_to_ispyb, xml_file_to_dict

ispyb/connector/mysqlsp/main.py

@@ -1,7 +1,5 @@
 from __future__ import absolute_import, division, print_function
 
-import os
-import sys
 import threading
 import traceback
 
@@ -47,7 +45,7 @@ def __del__(self):
   def disconnect(self):
     '''Release the connection previously created.'''
     if hasattr(self, 'conn') and self.conn is not None:
-    	self.conn.close()
+        self.conn.close()
     self.conn = None
 
   def get_data_area_package(self):

ispyb/interface/shipping.py

@@ -1,4 +1,4 @@
-import abc
+from __future__ import absolute_import, division, print_function
 
 from ispyb.interface.dataarea import DataArea
 

ispyb/model/integration.py

@@ -1,7 +1,5 @@
 from __future__ import absolute_import, division, print_function
 
-import collections
-
 import ispyb.model
 import ispyb.model.processingprogram
 

ispyb/sp/core.py

@@ -8,11 +8,6 @@
 #
 
 import copy
-import datetime
-import os
-import string
-import sys
-import time
 
 import ispyb.interface.core
 from ispyb.strictordereddict import StrictOrderedDict

ispyb/sp/mxscreening.py

@@ -8,10 +8,6 @@
 #
 
 import copy
-import datetime
-import os
-import sys
-import time
 
 import ispyb.interface.screening
 from ispyb.strictordereddict import StrictOrderedDict

ispyb/sp/shipping.py

@@ -8,10 +8,6 @@
 #
 
 import copy
-import datetime
-import os
-import sys
-import time
 
 import ispyb.interface.shipping
 from ispyb.strictordereddict import StrictOrderedDict
@@ -49,6 +45,6 @@ def upsert_dewar(self, values):
   def retrieve_dewars_for_proposal_code_number(self, proposal_code, proposal_number, auth_login=None):
     '''Get a result-set with the dewars associated with shipments in a given proposal specified by proposal code, proposal_number'''
     return self.get_connection().call_sp_retrieve(
-      procname='retrieve_dewars_for_proposal_code_number_v2', 
+      procname='retrieve_dewars_for_proposal_code_number_v2',
       args=(proposal_code, proposal_number, auth_login)
     )