Convert old style except blocks to except Exception as variable: blocks

diff --git a/bcmagic/views.py b/bcmagic/views.py
index df860770fc26309dbfe2aa64cc8bceb63b112989..3d9206fec91e52321043f649cfb9937481f0a07e 100644 (file)
--- a/bcmagic/views.py
+++ b/bcmagic/views.py
@@ -11,7 +11,7 @@ from . import plugin
 
 try:
     import json
-except ImportError, e:
+except ImportError as e:
     import simplejson as json
 
 import re

diff --git a/encode_submission/encode_find.py b/encode_submission/encode_find.py
index 7589f5487aef5ef85a6c4ec65072aa3d025ef5bc..60e0bee9b5700f8be2a58e7e45480dddf0bd0c6f 100644 (file)
--- a/encode_submission/encode_find.py
+++ b/encode_submission/encode_find.py
@@ -566,7 +566,7 @@ def load_library_detail(model, libraryUrn):
         try:
             body = get_url_as_text(str(libraryUrn.uri), 'GET')
             rdfaParser.parse_string_into_model(model, body, libraryUrn.uri)
-        except httplib2.HttpLib2ErrorWithResponse, e:
+        except httplib2.HttpLib2ErrorWithResponse as e:
             LOGGER.error(str(e))
     elif len(results) == 1:
         pass  # Assuming that a loaded dataset has one record

diff --git a/experiments/experiments.py b/experiments/experiments.py
index a5b8436df567ee7396a46abd9697fcb5c1557f79..b8f905ecf3682d0e59e340b4597c12a17fdc084d 100644 (file)
--- a/experiments/experiments.py
+++ b/experiments/experiments.py
@@ -4,7 +4,7 @@ from __future__ import absolute_import, print_function
 from datetime import datetime, timedelta
 try:
     import json
-except ImportError, e:
+except ImportError as e:
     import simplejson as json
 
 import os
@@ -28,7 +28,7 @@ def flowcell_information(flowcell_id):
     """
     try:
         fc = FlowCell.objects.get(flowcell_id__startswith=flowcell_id)
-    except FlowCell.DoesNotExist, e:
+    except FlowCell.DoesNotExist as e:
         return None
 
     lane_set = {}
@@ -126,7 +126,7 @@ def lanes_for_json(request, username):
 
     try:
         result = lanes_for(username)
-    except ObjectDoesNotExist, e:
+    except ObjectDoesNotExist as e:
         raise Http404
 
     #convert query set to python structure

diff --git a/experiments/models.py b/experiments/models.py
index 6b92a1845dc334b2fa6a1ae3e8a68f2371186253..3377e28c38c95354d0e7aa972456fbb1070dd135 100644 (file)
--- a/experiments/models.py
+++ b/experiments/models.py
@@ -25,7 +25,7 @@ LOGGER = logging.getLogger(__name__)
 default_pM = 5
 try:
     default_pM = int(settings.DEFAULT_PM)
-except AttributeError, e:
+except AttributeError as e:
     LOGGER.error("invalid value for default_pm")
 
 # how many days to wait before trying to re-import a runfolder

diff --git a/htsworkflow/pipelines/configure_run.py b/htsworkflow/pipelines/configure_run.py
index 83c7569d2816b03e3a67a3fb4f376589ae472a5f..d0d43d25e579e62e7a7ddceb6774d187457a118b 100644 (file)
--- a/htsworkflow/pipelines/configure_run.py
+++ b/htsworkflow/pipelines/configure_run.py
@@ -377,16 +377,16 @@ def retrieve_config(conf_info, flowcell, cfg_filepath, genome_dir):
   try:
     saveConfigFile(flowcell, options.url, cfg_filepath)
     conf_info.config_filepath = cfg_filepath
-  except FlowCellNotFound, e:
+  except FlowCellNotFound as e:
     LOGGER.error(e)
     return False
-  except WebError404, e:
+  except WebError404 as e:
     LOGGER.error(e)
     return False
-  except IOError, e:
+  except IOError as e:
     LOGGER.error(e)
     return False
-  except Exception, e:
+  except Exception as e:
     LOGGER.error(e)
     return False
 

diff --git a/htsworkflow/pipelines/genome_mapper.py b/htsworkflow/pipelines/genome_mapper.py
index fb16d7ffc60ed70ce11c10b4a204316de9e3f37e..35830a2dc0a615f917a0a4dac2c3f9b1ea962874 100644 (file)
--- a/htsworkflow/pipelines/genome_mapper.py
+++ b/htsworkflow/pipelines/genome_mapper.py
@@ -103,7 +103,7 @@ class constructMapperDict(object):
     def get(self, key, default=None):
       try:
         return self[key]
-      except KeyError, e:
+      except KeyError as e:
         return default
 
     def keys(self):

diff --git a/htsworkflow/pipelines/gerald.py b/htsworkflow/pipelines/gerald.py
index 2eaff677e6d90c75848a24a43f4b28fad8d2beff..dd70fe262bbed816e0d0ed38c9ab793dca79281e 100644 (file)
--- a/htsworkflow/pipelines/gerald.py
+++ b/htsworkflow/pipelines/gerald.py
@@ -283,7 +283,7 @@ class LaneParametersGA(LaneParameters):
         lanes = [x.tag.split('_')[1] for x in container.getchildren()]
         try:
             index = lanes.index(self._lane_id)
-        except ValueError, e:
+        except ValueError as e:
             return None
         element = container[index]
         return element.text

diff --git a/htsworkflow/pipelines/retrieve_config.py b/htsworkflow/pipelines/retrieve_config.py
index 7951752318aebe7d2443c010e64ac24149023167..1d442145ae07f0bd17ac694bd9fd472e45337c04 100644 (file)
--- a/htsworkflow/pipelines/retrieve_config.py
+++ b/htsworkflow/pipelines/retrieve_config.py
@@ -49,7 +49,7 @@ def retrieve_flowcell_info(base_host_url, flowcell):
     try:
         apipayload = urllib.urlencode(apidata)
         web = urllib2.urlopen(url, apipayload)
-    except urllib2.URLError, e:
+    except urllib2.URLError as e:
         errmsg = 'URLError: %d %s' % (e.code, e.msg)
         LOGGER.error(errmsg)
         LOGGER.error('opened %s' % (url,))

diff --git a/htsworkflow/pipelines/runfolder.py b/htsworkflow/pipelines/runfolder.py
index 669c5f03363dfc8c647730133af71678319d0336..dfc75f4b0f44492338458df766a6f6c4039fe301 100644 (file)
--- a/htsworkflow/pipelines/runfolder.py
+++ b/htsworkflow/pipelines/runfolder.py
@@ -336,7 +336,7 @@ def build_gerald_runs(runs, b, image_analysis, bustard_pathname, datadir, pathna
             p.bustard = b
             p.gerald = g
             runs.append(p)
-        except IOError, e:
+        except IOError as e:
             LOGGER.error("Ignoring " + str(e))
     return len(runs) - start
 

diff --git a/htsworkflow/pipelines/summary.py b/htsworkflow/pipelines/summary.py
index 8f47670d99521f37fc8afe75ab8edf292b4c5396..100b2c0edcf7fd8cae1f48f679b7f673cc8a1c75 100644 (file)
--- a/htsworkflow/pipelines/summary.py
+++ b/htsworkflow/pipelines/summary.py
@@ -311,7 +311,7 @@ class LaneResultSummary(object):
                 variable_name = tags[element.tag]
                 setattr(self, variable_name,
                         parse_summary_element(element))
-            except KeyError, e:
+            except KeyError as e:
                 LOGGER.warn('Unrecognized tag %s' % (element.tag,))
 
 
@@ -414,7 +414,7 @@ def tonumber(v):
     """
     try:
         v = int(v)
-    except ValueError, e:
+    except ValueError as e:
         v = float(v)
     return v
 

diff --git a/htsworkflow/pipelines/test/test_retrieve_config.py b/htsworkflow/pipelines/test/test_retrieve_config.py
index 1a24c633b82314ac40ed933a7bfb2698d27d8510..7ca87905d623e0ff6ce0c5c880851a283490176f 100644 (file)
--- a/htsworkflow/pipelines/test/test_retrieve_config.py
+++ b/htsworkflow/pipelines/test/test_retrieve_config.py
@@ -5,7 +5,7 @@ from StringIO import StringIO
 
 try:
     import json
-except ImportError, e:
+except ImportError as e:
     import simplejson as json
 
 from django.test import TestCase

diff --git a/htsworkflow/submission/daf.py b/htsworkflow/submission/daf.py
index f04ac8fe5328e738a012738a5d256b9307e11504..30edcdc54ba3ca60fc231334c5de2b3a38909568 100644 (file)
--- a/htsworkflow/submission/daf.py
+++ b/htsworkflow/submission/daf.py
@@ -300,7 +300,7 @@ class UCSCSubmission(object):
             LOGGER.info("Importing %s from %s" % (lib_id, result_dir))
             try:
                 self.import_submission_dir(result_dir, lib_id)
-            except MetadataLookupException, e:
+            except MetadataLookupException as e:
                 LOGGER.error("Skipping %s: %s" % (lib_id, str(e)))
 
     def import_submission_dir(self, submission_dir, library_id):
@@ -531,7 +531,7 @@ class UCSCSubmission(object):
             LOGGER.debug("Found: %s" % (literal_re,))
             try:
                 filename_re = re.compile(literal_re)
-            except re.error, e:
+            except re.error as e:
                 LOGGER.error("Unable to compile: %s" % (literal_re,))
             patterns[literal_re] = view_name
         return patterns

diff --git a/htsworkflow/submission/submission.py b/htsworkflow/submission/submission.py
index 897053fbc148477c108d232635958db45488dfc5..cb204557cecf8a74dbd230e9475ad55f76b05e66 100644 (file)
--- a/htsworkflow/submission/submission.py
+++ b/htsworkflow/submission/submission.py
@@ -44,7 +44,7 @@ class Submission(object):
             LOGGER.info("Importing %s from %s" % (lib_id, result_dir))
             try:
                 self.import_analysis_dir(result_dir, lib_id)
-            except MetadataLookupException, e:
+            except MetadataLookupException as e:
                 LOGGER.error("Skipping %s: %s" % (lib_id, str(e)))
 
     def import_analysis_dir(self, analysis_dir, library_id):
@@ -245,7 +245,7 @@ class Submission(object):
             LOGGER.debug("Importing %s" % (lane.uri,))
             try:
                 parser.parse_into_model(self.model, lane.uri)
-            except RDF.RedlandError, e:
+            except RDF.RedlandError as e:
                 LOGGER.error("Error accessing %s" % (lane.uri,))
                 raise e
 
@@ -286,7 +286,7 @@ class Submission(object):
             LOGGER.debug("Found: %s" % (literal_re,))
             try:
                 filename_re = re.compile(literal_re)
-            except re.error, e:
+            except re.error as e:
                 LOGGER.error("Unable to compile: %s" % (literal_re,))
             patterns[literal_re] = view_name
         return patterns

diff --git a/htsworkflow/submission/ucsc.py b/htsworkflow/submission/ucsc.py
index f7734adbd972b26db9150b155a7cdeb39818e0c1..ff717366f2066b14e8f48213834d1ec27001f3e8 100644 (file)
--- a/htsworkflow/submission/ucsc.py
+++ b/htsworkflow/submission/ucsc.py
@@ -61,7 +61,7 @@ def get_encodedcc_file_index(genome, composite):
             request = urllib2.urlopen(request_url)
             file_index = parse_ucsc_file_index(request, base_url)
             return file_index
-        except urllib2.HTTPError, e:
+        except urllib2.HTTPError as e:
             err = e
             pass
 

diff --git a/htsworkflow/util/api.py b/htsworkflow/util/api.py
index 76ee84dc318005fea7281d6b838244fb869b811f..7abfa2a2266594147946c875a87c85213d3975d0 100644 (file)
--- a/htsworkflow/util/api.py
+++ b/htsworkflow/util/api.py
@@ -131,7 +131,7 @@ def retrieve_info(url, apidata):
     try:
         apipayload = urllib.urlencode(apidata)
         web = urllib2.urlopen(url, apipayload)
-    except urllib2.URLError, e:
+    except urllib2.URLError as e:
         if hasattr(e, 'code') and e.code == 404:
             LOGGER.info("%s was not found" % (url,))
             return None
@@ -168,7 +168,7 @@ def make_django_secret_key(size=216):
     """return key suitable for use as secret key"""
     try:
         source = random.SystemRandom()
-    except AttributeError, e:
+    except AttributeError as e:
         source = random.random()
     bits = source.getrandbits(size)
     chars = []

diff --git a/htsworkflow/util/config_helper.py b/htsworkflow/util/config_helper.py
index 162580f2765d4cd72a27f16bd7911b4dbf3082ac..4b86da4541de29d3c9430eeb9acd92ca9cbf7b46 100644 (file)
--- a/htsworkflow/util/config_helper.py
+++ b/htsworkflow/util/config_helper.py
@@ -39,5 +39,5 @@ class HTSWConfig(ConfigParser.SafeConfigParser):
             ini_stream = open(self.filename, 'w')
             self.write(ini_stream)
             ini_stream.close()
-        except IOError, e:
+        except IOError as e:
             LOGGER.info("Error saving setting: %s" % (str(e)))

diff --git a/htsworkflow/util/hdquery.py b/htsworkflow/util/hdquery.py
index 57c05e6025bf847e31e32875f44b34ea49c6adc6..37fd555d3fd6c0f55c2aba2676ceaf62425f309d 100644 (file)
--- a/htsworkflow/util/hdquery.py
+++ b/htsworkflow/util/hdquery.py
@@ -23,7 +23,7 @@ try:
         #  the 2nd of which is the serial number
         return data.strip('\x00').split()[1]
     
-except ImportError, e:
+except ImportError as e:
     print >>sys.stderr, "hdquery requires py_sg"
 
     def get_hd_serial_num(device):

diff --git a/htsworkflow/util/rdfhelp.py b/htsworkflow/util/rdfhelp.py
index 48294416abf1def5a9bc1c3d77b0a4eaa1a607b0..cc16f794ffa9392924880f566a7cbc243c444471 100644 (file)
--- a/htsworkflow/util/rdfhelp.py
+++ b/htsworkflow/util/rdfhelp.py
@@ -147,7 +147,7 @@ def fromTypedNode(node):
     elif value_type in ('dateTime'):
         try:
             return datetime.strptime(literal, ISOFORMAT_MS)
-        except ValueError, _:
+        except ValueError:
             return datetime.strptime(literal, ISOFORMAT_SHORT)
     return literal
 
@@ -280,7 +280,7 @@ def load_into_model(model, parser_name, path, ns=None):
             statements = rdf_parser.parse_as_stream(url, ns)
             retries = 0
             succeeded = True
-        except RDF.RedlandError, e:
+        except RDF.RedlandError as e:
             errmsg = "RDF.RedlandError: {0} {1} tries remaining"
             logger.error(errmsg.format(str(e), retries))
 

diff --git a/htsworkflow/util/test/test_ethelp.py b/htsworkflow/util/test/test_ethelp.py
index 379dd9e1e525e45bc81e414a60d21b07694d9333..5d982e8a29c200fe49b8393900a13bd600862c9f 100644 (file)
--- a/htsworkflow/util/test/test_ethelp.py
+++ b/htsworkflow/util/test/test_ethelp.py
@@ -3,7 +3,7 @@ from unittest import TestCase
 
 try:
   from xml.etree import ElementTree
-except ImportError, e:
+except ImportError as e:
   from elementtree import ElementTree
 
 from htsworkflow.util.ethelp import indent, flatten

diff --git a/htsworkflow/util/test/test_rdfhelp.py b/htsworkflow/util/test/test_rdfhelp.py
index 9694c37e244658b274735603c8723fc9986f3e32..d11d98bb2642ed539f6da544c7057e40e0cfa935 100644 (file)
--- a/htsworkflow/util/test/test_rdfhelp.py
+++ b/htsworkflow/util/test/test_rdfhelp.py
@@ -261,7 +261,7 @@ _:a owl:imports "{loc}extra.turtle" .
             self.assertTrue(model.contains_statement(s))
 
 
-except ImportError, e:
+except ImportError as e:
     print "Unable to test rdfhelp"
 
 def suite():

diff --git a/htsworkflow/util/version.py b/htsworkflow/util/version.py
index 8097edbedb8d95acddad2c9626d47050c4d92817..56a1b113513345e0fe4fcf84115d70e86c774379 100644 (file)
--- a/htsworkflow/util/version.py
+++ b/htsworkflow/util/version.py
@@ -8,13 +8,13 @@ def version():
     version = None
     try:
         import pkg_resources
-    except ImportError, e:
+    except ImportError as e:
         LOGGER.error("Can't find version number, please install setuptools")
         raise e
 
     try:
         version = pkg_resources.get_distribution("htsworkflow")
-    except pkg_resources.DistributionNotFound, e:
+    except pkg_resources.DistributionNotFound as e:
         LOGGER.error("Package not installed")
 
     return version

diff --git a/inventory/models.py b/inventory/models.py
index deefeedb64e50c37c0855d4c66fb0b24eaf214c9..d41025ad2732953a2bd6091b536c1405791efdf4 100644 (file)
--- a/inventory/models.py
+++ b/inventory/models.py
@@ -13,7 +13,7 @@ LOGGER = logging.getLogger(__name__)
 
 try:
     import uuid
-except ImportError, e:
+except ImportError as e:
     # Some systems are using python 2.4, which doesn't have uuid
     # this is a stub
     LOGGER.warning('Real uuid is not available, initializing fake uuid module')

diff --git a/inventory/views.py b/inventory/views.py
index 05f300a08fdde5d4329f26f3d896ea8c2092e5d6..149710ff22466df20da3905a2ccb12180113f434 100644 (file)
--- a/inventory/views.py
+++ b/inventory/views.py
@@ -21,7 +21,7 @@ register_search_plugin('Inventory Item', item_search)
 
 try:
     import json
-except ImportError, e:
+except ImportError as e:
     import simplejson as json
 
 INVENTORY_CONTEXT_DEFAULTS = {
@@ -216,7 +216,7 @@ def item_summary_by_barcode(request, barcode_id, msg=''):
     """
     try:
         item = Item.objects.get(barcode_id=barcode_id)
-    except ObjectDoesNotExist, e:
+    except ObjectDoesNotExist as e:
         item = None
 
     return item_summary_by_uuid(request, None, msg, item)
@@ -231,7 +231,7 @@ def item_summary_by_uuid(request, uuid, msg='', item=None):
     if item is None:
         try:
             item = Item.objects.get(uuid=uuid)
-        except ObjectDoesNotExist, e:
+        except ObjectDoesNotExist as e:
             item = None
 
     context_dict = {
@@ -291,7 +291,7 @@ def item_print(request, uuid):
     """
     try:
         item = Item.objects.get(uuid=uuid)
-    except ObjectDoesNotExist, e:
+    except ObjectDoesNotExist as e:
         item = None
         msg = "Item with UUID %s does not exist" % (uuid)
 
@@ -316,7 +316,7 @@ def link_flowcell_and_device(request, flowcell, serial):
     # Retrieve Storage Device
     try:
         sd = Item.objects.get(barcode_id=serial)
-    except ObjectDoesNotExist, e:
+    except ObjectDoesNotExist as e:
         msg = "Item with barcode_id of %s not found." % (serial)
         raise ObjectDoesNotExist(msg)
 
@@ -324,7 +324,7 @@ def link_flowcell_and_device(request, flowcell, serial):
     # Retrieve FlowCell
     try:
         fc = FlowCell.objects.get(flowcell_id__startswith=flowcell)
-    except ObjectDoesNotExist, e:
+    except ObjectDoesNotExist as e:
         msg = "FlowCell with flowcell_id of %s not found." % (flowcell)
         raise ObjectDoesNotExist(msg)
 

diff --git a/samples/auth_backend.py b/samples/auth_backend.py
index d3f4330bc49385ca4449d1eb75b0496524aab5d5..aacf43b3d3a7b52b5af36983117a0995554ac6e1 100644 (file)
--- a/samples/auth_backend.py
+++ b/samples/auth_backend.py
@@ -17,7 +17,7 @@ class HTSUserModelBackend(ModelBackend):
             if user.check_password(password):
                 return user
         #except self.user_class.DoesNotExist:
-        except Exception, e:
+        except Exception as e:
             logger.error(str(e))
             return None
 
@@ -25,7 +25,7 @@ class HTSUserModelBackend(ModelBackend):
         try:
             return self.user_class.objects.get(pk=user_id)
         #except self.user_class.DoesNotExist:
-        except Exception, e:
+        except Exception as e:
             logger.error(str(e))
             return None
 

diff --git a/samples/models.py b/samples/models.py
index 5c5c27c951efd831efabaa3e5495e8287dbe20c7..21b6f40f25d71495433bf6c3a3eeeae5f4fa51c0 100644 (file)
--- a/samples/models.py
+++ b/samples/models.py
@@ -272,7 +272,7 @@ class Library(models.Model):
               adapter_type = self.library_type.id,
               multiplex_id = multiplex_id)
           return multiplex.sequence
-      except MultiplexIndex.DoesNotExist, e:
+      except MultiplexIndex.DoesNotExist as e:
           return None
 
   def index_sequence_text(self, seperator=' '):

diff --git a/samples/test_samples.py b/samples/test_samples.py
index c339619eb0309ce9dfed96142010309891a7971f..61fc9305cb938382b3fa2205eead9e701cc1d817 100644 (file)
--- a/samples/test_samples.py
+++ b/samples/test_samples.py
@@ -276,7 +276,7 @@ try:
     libNS = RDF.NS("http://jumpgate.caltech.edu/wiki/LibraryOntology#")
 
     from htsworkflow.util.rdfhelp import dump_model
-except ImportError,e:
+except ImportError as e:
     HAVE_RDF = False
 
 

diff --git a/samples/views.py b/samples/views.py
index 79e7856f1041db732a1d3c5020fe8652cc9c82c4..e506c7d68789783e118ca6132d44a7e5e044c549 100644 (file)
--- a/samples/views.py
+++ b/samples/views.py
@@ -8,7 +8,7 @@ import sys
 
 try:
     import json
-except ImportError, e:
+except ImportError as e:
     import simplejson as json
 
 from django.views.decorators.csrf import csrf_exempt
@@ -338,7 +338,7 @@ def _summary_stats(flowcell_id, lane_id, library_id):
 
             summary_list.append(eland_summary)
 
-        #except Exception, e:
+        #except Exception as e:
         #    summary_list.append("Summary report needs to be updated.")
         #    LOGGER.error("Exception: " + str(e))
 
@@ -471,7 +471,7 @@ def library_dict(library_id):
     """
     try:
         lib = Library.objects.get(id=library_id)
-    except Library.DoesNotExist, e:
+    except Library.DoesNotExist as e:
         return None
 
     #lane_info = lane_information(lib.lane_set)