From 8a43b2b492e6282a67cc7e8279cc727d5de26dc2 Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Tue, 17 May 2016 23:09:01 +0100 Subject: [PATCH] Python 3: use "as" instead of comma in except clause --- contrib/nagios/check_galaxy.py | 4 ++-- .../0018_ordered_tags_and_page_tags.py | 2 +- .../migrate/versions/0057_request_notify.py | 2 +- .../versions/0059_sample_dataset_file_path.py | 2 +- .../versions/0067_populate_sequencer_table.py | 6 ++--- ...8_rename_sequencer_to_external_services.py | 10 ++++----- scripts/api/upload_to_history.py | 2 +- scripts/check_galaxy.py | 4 ++-- scripts/cleanup_datasets/cleanup_datasets.py | 6 ++--- scripts/cleanup_datasets/pgcleanup.py | 10 ++++----- .../remove_renamed_datasets_from_disk.py | 2 +- .../rename_purged_datasets.py | 2 +- scripts/data_libraries/build_whoosh_index.py | 2 +- scripts/drmaa_external_killer.py | 2 +- scripts/drmaa_external_runner.py | 2 +- scripts/extract_dataset_part.py | 2 +- scripts/microbes/harvest_bacteria.py | 6 ++--- scripts/others/incorrect_gops_jobs.py | 2 +- scripts/others/incorrect_gops_join_jobs.py | 2 +- scripts/tool_shed/api/common.py | 14 ++++++------ scripts/tool_shed/api/create_categories.py | 2 +- scripts/tool_shed/api/create_users.py | 2 +- scripts/tool_shed/api/import_capsule.py | 2 +- .../api/reset_metadata_on_repositories.py | 4 ++-- scripts/tool_shed/check_download_urls.py | 4 ++-- ...deprecate_repositories_without_metadata.py | 2 +- scripts/tools/maf/check_loc_file.py | 2 +- scripts/transfer.py | 14 ++++++------ test/base/asserts/__init__.py | 2 +- test/base/asserts/xml.py | 2 +- test/base/driver_util.py | 2 +- test/base/twilltestcase.py | 22 +++++++++---------- test/casperjs/casperjs_runner.py | 8 +++---- test/casperjs/server_env.py | 6 ++--- test/functional/test_data_managers.py | 2 +- test/functional/test_toolbox.py | 2 +- test/shed_functional/base/twilltestcase.py | 2 +- test/unit/tools/test_execution.py | 6 ++--- test/unit/tools/test_select_parameters.py | 6 ++--- .../plugins/test_VisualizationPlugin.py | 2 +- tools/data_source/data_source.py | 6 ++--- tools/data_source/fetch.py | 2 +- tools/data_source/hbvar_filter.py | 2 +- tools/data_source/upload.py | 6 ++--- tools/evolution/add_scores.py | 4 ++-- tools/extract/extract_genomic_dna.py | 4 ++-- tools/extract/liftOver_wrapper.py | 2 +- tools/filters/gff/gff_filter_by_attribute.py | 4 ++-- tools/filters/gtf_to_bedgraph_converter.py | 4 ++-- tools/filters/join.py | 2 +- tools/filters/joinWrapper.py | 4 ++-- tools/filters/lav_to_bed.py | 2 +- tools/filters/sff_extract.py | 6 ++--- tools/filters/sorter.py | 2 +- tools/filters/wiggle_to_simple.py | 2 +- tools/genomespace/genomespace_exporter.py | 2 +- tools/maf/interval_maf_to_merged_fasta.py | 6 ++--- tools/maf/maf_split_by_species.py | 6 ++--- tools/maf/maf_thread_for_species.py | 2 +- tools/maf/maf_to_fasta_concat.py | 10 ++++----- tools/maf/maf_to_fasta_multiple_sets.py | 8 +++---- tools/metag_tools/shrimp_color_wrapper.py | 4 ++-- tools/metag_tools/shrimp_wrapper.py | 6 ++--- .../next_gen_conversion/fastq_conversions.py | 2 +- tools/next_gen_conversion/solid_to_fastq.py | 4 ++-- tools/ngs_simulation/ngs_simulation.py | 8 +++---- tools/phenotype_association/pagetag.py | 2 +- tools/phenotype_association/senatag.py | 2 +- tools/solid_tools/maq_cs_wrapper.py | 4 ++-- tools/stats/aggregate_scores_in_intervals.py | 2 +- tools/stats/filtering.py | 2 +- tools/stats/grouping.py | 2 +- tools/stats/gsummary.py | 2 +- 73 files changed, 152 insertions(+), 152 deletions(-) diff --git a/contrib/nagios/check_galaxy.py b/contrib/nagios/check_galaxy.py index 36b021f1466..7588d24cbdd 100755 --- a/contrib/nagios/check_galaxy.py +++ b/contrib/nagios/check_galaxy.py @@ -62,7 +62,7 @@ def usage(): try: opts, args = getopt.getopt( sys.argv[1:], 'n' ) -except getopt.GetoptError, e: +except getopt.GetoptError as e: print str(e) usage() if len( args ) < 1: @@ -133,7 +133,7 @@ class Browser: tc.get_browser()._browser.set_handle_redirect(True) dprint( "%s is returning redirect (302)" % url ) return(True) - except twill.errors.TwillAssertionError, e: + except twill.errors.TwillAssertionError as e: tc.get_browser()._browser.set_handle_redirect(True) dprint( "%s is not returning redirect (302): %s" % (url, e) ) code = tc.browser.get_code() diff --git a/lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py b/lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py index dc232ae37d5..bf2c144f22e 100644 --- a/lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py +++ b/lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py @@ -79,7 +79,7 @@ def upgrade(migrate_engine): try: HistoryDatasetAssociationTagAssociation_table.drop() HistoryDatasetAssociationTagAssociation_table.create() - except OperationalError, e: + except OperationalError as e: # Handle error that results from and index name that is too long; this occurs # in MySQL. if str(e).find("CREATE INDEX") != -1: diff --git a/lib/galaxy/model/migrate/versions/0057_request_notify.py b/lib/galaxy/model/migrate/versions/0057_request_notify.py index 827d176eb3c..711a352fff8 100644 --- a/lib/galaxy/model/migrate/versions/0057_request_notify.py +++ b/lib/galaxy/model/migrate/versions/0057_request_notify.py @@ -22,7 +22,7 @@ def upgrade(migrate_engine): metadata.reflect() try: Request_table = Table( "request", metadata, autoload=True ) - except NoSuchTableError, e: + except NoSuchTableError: Request_table = None log.debug( "Failed loading table 'request'" ) diff --git a/lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py b/lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py index 16df1aa883b..c03d59129f6 100644 --- a/lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py +++ b/lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py @@ -19,7 +19,7 @@ def upgrade(migrate_engine): metadata.reflect() try: SampleDataset_table = Table( "sample_dataset", metadata, autoload=True ) - except NoSuchTableError, e: + except NoSuchTableError: SampleDataset_table = None log.debug( "Failed loading table 'sample_dataset'" ) diff --git a/lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py b/lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py index 71dc1884207..88622f60262 100644 --- a/lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py +++ b/lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py @@ -193,7 +193,7 @@ def upgrade(migrate_engine): metadata.reflect() try: RequestType_table = Table( "request_type", metadata, autoload=True ) - except NoSuchTableError, e: + except NoSuchTableError: RequestType_table = None log.debug( "Failed loading table 'request_type'" ) if RequestType_table is None: @@ -201,7 +201,7 @@ def upgrade(migrate_engine): # load the sequencer table try: Sequencer_table = Table( "sequencer", metadata, autoload=True ) - except NoSuchTableError, e: + except NoSuchTableError: Sequencer_table = None log.debug( "Failed loading table 'sequencer'" ) if Sequencer_table is None: @@ -258,7 +258,7 @@ def downgrade(migrate_engine): metadata.reflect() try: RequestType_table = Table( "request_type", metadata, autoload=True ) - except NoSuchTableError, e: + except NoSuchTableError: RequestType_table = None log.debug( "Failed loading table 'request_type'" ) if RequestType_table is not None: diff --git a/lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py b/lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py index 7199dceb803..6514438dd6f 100644 --- a/lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py +++ b/lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py @@ -38,14 +38,14 @@ def upgrade(migrate_engine): # add a foreign key to the external_service table in the sample_dataset table try: SampleDataset_table = Table( "sample_dataset", metadata, autoload=True ) - except NoSuchTableError, e: + except NoSuchTableError: SampleDataset_table = None log.debug( "Failed loading table 'sample_dataset'" ) if SampleDataset_table is None: return try: Sequencer_table = Table( "sequencer", metadata, autoload=True ) - except NoSuchTableError, e: + except NoSuchTableError: Sequencer_table = None log.debug( "Failed loading table 'sequencer'" ) if Sequencer_table is None: @@ -92,7 +92,7 @@ def upgrade(migrate_engine): migrate_engine.execute( cmd ) try: ExternalServices_table = Table( "external_service", metadata, autoload=True ) - except NoSuchTableError, e: + except NoSuchTableError: ExternalServices_table = None log.debug( "Failed loading table 'external_service'" ) if ExternalServices_table is None: @@ -201,7 +201,7 @@ def downgrade(migrate_engine): return try: ExternalServices_table = Table( "external_service", metadata, autoload=True ) - except NoSuchTableError, e: + except NoSuchTableError: ExternalServices_table = None log.debug( "Failed loading table 'external_service'" ) if ExternalServices_table is None: @@ -262,7 +262,7 @@ def downgrade(migrate_engine): # drop the 'external_service_id' column in the 'sample_dataset' table try: SampleDataset_table = Table( "sample_dataset", metadata, autoload=True ) - except NoSuchTableError, e: + except NoSuchTableError: SampleDataset_table = None log.debug( "Failed loading table 'sample_dataset'" ) if SampleDataset_table is None: diff --git a/scripts/api/upload_to_history.py b/scripts/api/upload_to_history.py index 212456d0fba..7b538822e29 100755 --- a/scripts/api/upload_to_history.py +++ b/scripts/api/upload_to_history.py @@ -8,7 +8,7 @@ import sys try: import requests -except ImportError, imp_err: +except ImportError: print "Could not import the requests module. See http://docs.python-requests.org/en/latest/" + \ " or install with 'pip install requests'" raise diff --git a/scripts/check_galaxy.py b/scripts/check_galaxy.py index 5d140dbb89b..65d52ffc8d5 100755 --- a/scripts/check_galaxy.py +++ b/scripts/check_galaxy.py @@ -54,7 +54,7 @@ def usage(): try: opts, args = getopt.getopt( sys.argv[1:], 'n' ) -except getopt.GetoptError, e: +except getopt.GetoptError as e: print str(e) usage() if len( args ) < 1: @@ -151,7 +151,7 @@ class Browser: tc.get_browser()._browser.set_handle_redirect(True) dprint( "%s is returning redirect (302)" % url ) return(True) - except twill.errors.TwillAssertionError, e: + except twill.errors.TwillAssertionError as e: tc.get_browser()._browser.set_handle_redirect(True) dprint( "%s is not returning redirect (302): %s" % (url, e) ) code = tc.browser.get_code() diff --git a/scripts/cleanup_datasets/cleanup_datasets.py b/scripts/cleanup_datasets/cleanup_datasets.py index 29161541b62..36d8b5a151f 100755 --- a/scripts/cleanup_datasets/cleanup_datasets.py +++ b/scripts/cleanup_datasets/cleanup_datasets.py @@ -440,7 +440,7 @@ def _delete_dataset( dataset, app, remove_from_disk, info_only=False, is_deletab try: print "Removing disk file ", metadata_file.file_name os.unlink( metadata_file.file_name ) - except Exception, e: + except Exception as e: print "Error, exception: %s caught attempting to purge metadata file %s\n" % ( str( e ), metadata_file.file_name ) metadata_file.purged = True app.sa_session.add( metadata_file ) @@ -488,7 +488,7 @@ def _purge_dataset( app, dataset, remove_from_disk, info_only=False ): print "Dataset %i will be purged (without 'info_only' mode)" % (dataset.id) else: print "This dataset (%i) is not purgable, the file (%s) will not be removed.\n" % ( dataset.id, dataset.file_name ) - except OSError, exc: + except OSError as exc: print "Error, dataset file has already been removed: %s" % str( exc ) print "Purging dataset id", dataset.id dataset.purged = True @@ -496,7 +496,7 @@ def _purge_dataset( app, dataset, remove_from_disk, info_only=False ): app.sa_session.flush() except ObjectNotFound: print "Dataset %i cannot be found in the object store" % dataset.id - except Exception, exc: + except Exception as exc: print "Error attempting to purge data file: ", dataset.file_name, " error: ", str( exc ) else: print "Error: '%s' has not previously been deleted, so it cannot be purged\n" % dataset.file_name diff --git a/scripts/cleanup_datasets/pgcleanup.py b/scripts/cleanup_datasets/pgcleanup.py index ade7d6229b8..ab8ca7c3250 100755 --- a/scripts/cleanup_datasets/pgcleanup.py +++ b/scripts/cleanup_datasets/pgcleanup.py @@ -239,14 +239,14 @@ class Cleanup(object): try: filename = self.object_store.get_filename(metadata_file, extra_dir='_metadata_files', extra_dir_at_root=True, alt_name="metadata_%d.dat" % id) self._log('Removing from disk: %s' % filename, action_name) - except (ObjectNotFound, AttributeError), e: + except (ObjectNotFound, AttributeError) as e: log.error('Unable to get MetadataFile %s filename: %s' % (id, e)) return if not self.options.dry_run: try: os.unlink(filename) - except Exception, e: + except Exception as e: self._log('Removal of %s failed with error: %s' % (filename, e), action_name) def _update_user_disk_usage(self): @@ -739,7 +739,7 @@ class Cleanup(object): dataset = Dataset(id=tup[0], object_store_id=tup[1]) try: filename = self.object_store.get_filename(dataset) - except (ObjectNotFound, AttributeError), e: + except (ObjectNotFound, AttributeError) as e: log.error('Unable to get Dataset %s filename: %s' % (tup[0], e)) continue @@ -753,7 +753,7 @@ class Cleanup(object): if not self.options.dry_run: try: os.unlink(filename) - except Exception, e: + except Exception as e: self._log('Removal of %s failed with error: %s' % (filename, e)) # extra_files_dir is optional so it's checked first @@ -762,7 +762,7 @@ class Cleanup(object): if not self.options.dry_run: try: shutil.rmtree(extra_files_dir) - except Exception, e: + except Exception as e: self._log('Removal of %s failed with error: %s' % (extra_files_dir, e)) self._close_logfile() diff --git a/scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py b/scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py index 4a1026a3dcc..21372cbd5a9 100755 --- a/scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py +++ b/scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py @@ -40,7 +40,7 @@ def main(): os.unlink( line ) print >> out, line removed_files += 1 - except Exception, exc: + except Exception as exc: print >> out, "# Error, exception " + str( exc ) + " caught attempting to remove " + line print >> out, "# Removed " + str( removed_files ) + " files" diff --git a/scripts/cleanup_datasets/rename_purged_datasets.py b/scripts/cleanup_datasets/rename_purged_datasets.py index 6189b7fdf11..eae995bd680 100755 --- a/scripts/cleanup_datasets/rename_purged_datasets.py +++ b/scripts/cleanup_datasets/rename_purged_datasets.py @@ -42,7 +42,7 @@ def main(): os.rename( line, purged_filename ) print >> out, purged_filename renamed_files += 1 - except Exception, exc: + except Exception as exc: print >> out, "# Error, exception " + str( exc ) + " caught attempting to rename " + purged_filename print >> out, "# Renamed " + str( renamed_files ) + " files" diff --git a/scripts/data_libraries/build_whoosh_index.py b/scripts/data_libraries/build_whoosh_index.py index 8ba2cca6be0..ba80fdee813 100644 --- a/scripts/data_libraries/build_whoosh_index.py +++ b/scripts/data_libraries/build_whoosh_index.py @@ -22,7 +22,7 @@ try: schema = Schema( id=STORED, name=TEXT, info=TEXT, dbkey=TEXT, message=TEXT ) import galaxy.model.mapping from galaxy import config, model -except ImportError, e: +except ImportError: whoosh_search_enabled = False schema = None diff --git a/scripts/drmaa_external_killer.py b/scripts/drmaa_external_killer.py index 6c74a0cfaab..9aff1d60d70 100755 --- a/scripts/drmaa_external_killer.py +++ b/scripts/drmaa_external_killer.py @@ -27,7 +27,7 @@ def set_user(uid): gid = pwd.getpwuid(uid).pw_gid os.setgid(gid) os.setuid(uid) - except OSError, e: + except OSError as e: if e.errno == errno.EPERM: sys.stderr.write("error: setuid(%d) failed: permission denied. Did you setup 'sudo' correctly for this script?\n" % uid ) exit(1) diff --git a/scripts/drmaa_external_runner.py b/scripts/drmaa_external_runner.py index a1474feb418..1311348fbad 100755 --- a/scripts/drmaa_external_runner.py +++ b/scripts/drmaa_external_runner.py @@ -96,7 +96,7 @@ def set_user(uid, assign_all_groups): os.setgroups(groups) os.setuid(uid) - except OSError, e: + except OSError as e: if e.errno == errno.EPERM: sys.stderr.write( "error: setuid(%d) failed: permission denied. Did you setup 'sudo' correctly for this script?\n" % uid ) exit(1) diff --git a/scripts/extract_dataset_part.py b/scripts/extract_dataset_part.py index 6cf43a33999..470205b60aa 100644 --- a/scripts/extract_dataset_part.py +++ b/scripts/extract_dataset_part.py @@ -40,7 +40,7 @@ def __main__(): if not cls.process_split_file(data): sys.stderr.write('Writing split file failed\n') sys.exit(1) - except Exception, e: + except Exception as e: sys.stderr.write(str(e)) sys.exit(1) diff --git a/scripts/microbes/harvest_bacteria.py b/scripts/microbes/harvest_bacteria.py index 09fd6f6a17c..5566f25c160 100644 --- a/scripts/microbes/harvest_bacteria.py +++ b/scripts/microbes/harvest_bacteria.py @@ -170,7 +170,7 @@ def process_Genbank( filename, org_num, refseq ): def process_Glimmer3( filename, org_num, refseq ): try: glimmer3_bed = get_bed_from_glimmer3( filename, refseq ) - except Exception, e: + except Exception as e: print "Converting Glimmer3 to bed FAILED! For chrom:", refseq, "file:", filename, e glimmer3_bed = [] glimmer3_bed_file = open( os.path.join( os.path.split( filename )[0], "%s.Glimmer3.bed" % refseq ), 'wb+' ) @@ -181,7 +181,7 @@ def process_Glimmer3( filename, org_num, refseq ): def process_GeneMarkHMM( filename, org_num, refseq ): try: geneMarkHMM_bed = get_bed_from_GeneMarkHMM( filename, refseq ) - except Exception, e: + except Exception as e: print "Converting GeneMarkHMM to bed FAILED! For chrom:", refseq, "file:", filename, e geneMarkHMM_bed = [] geneMarkHMM_bed_bed_file = open( os.path.join( os.path.split( filename )[0], "%s.GeneMarkHMM.bed" % refseq ), 'wb+' ) @@ -192,7 +192,7 @@ def process_GeneMarkHMM( filename, org_num, refseq ): def process_GeneMark( filename, org_num, refseq ): try: geneMark_bed = get_bed_from_GeneMark( filename, refseq ) - except Exception, e: + except Exception as e: print "Converting GeneMark to bed FAILED! For chrom:", refseq, "file:", filename, e geneMark_bed = [] geneMark_bed_bed_file = open( os.path.join( os.path.split( filename )[0], "%s.GeneMark.bed" % refseq ), 'wb+' ) diff --git a/scripts/others/incorrect_gops_jobs.py b/scripts/others/incorrect_gops_jobs.py index a96d136ec28..fc22ac5e71a 100755 --- a/scripts/others/incorrect_gops_jobs.py +++ b/scripts/others/incorrect_gops_jobs.py @@ -87,7 +87,7 @@ def main(): jobs[ job.id ][ 'history_name' ] = history.name jobs[ job.id ][ 'history_update_time' ] = history.update_time jobs[ job.id ][ 'user_email' ] = user.email - except Exception, e: + except Exception as e: print "# caught exception: %s" % str( e ) print "\n\n# Number of incorrect Jobs: %d\n\n" % ( len( jobs ) ) diff --git a/scripts/others/incorrect_gops_join_jobs.py b/scripts/others/incorrect_gops_join_jobs.py index bcefdb6f4c7..e8de640614d 100644 --- a/scripts/others/incorrect_gops_join_jobs.py +++ b/scripts/others/incorrect_gops_join_jobs.py @@ -77,7 +77,7 @@ def main(): jobs[ job.id ][ 'history_name' ] = history.name jobs[ job.id ][ 'history_update_time' ] = history.update_time jobs[ job.id ][ 'user_email' ] = user.email - except Exception, e: + except Exception as e: print "# caught exception: %s" % str( e ) print "\n\n# Number of incorrect Jobs: %d\n\n" % ( len( jobs ) ) diff --git a/scripts/tool_shed/api/common.py b/scripts/tool_shed/api/common.py index 1b249149eff..21d73f81cbd 100644 --- a/scripts/tool_shed/api/common.py +++ b/scripts/tool_shed/api/common.py @@ -60,7 +60,7 @@ def delete( api_key, url, data, return_formatted=True ): opener, request = build_request_with_data( url, data, api_key, 'DELETE' ) delete_request = opener.open( request ) response = json.loads( delete_request.read() ) - except urllib2.HTTPError, e: + except urllib2.HTTPError as e: if return_formatted: print e print e.read( 1024 ) @@ -79,7 +79,7 @@ def display( url, api_key=None, return_formatted=True ): """Sends an API GET request and acts as a generic formatter for the JSON response.""" try: r = get( url, api_key=api_key ) - except urllib2.HTTPError, e: + except urllib2.HTTPError as e: print e # Only return the first 1K of errors. print e.read( 1024 ) @@ -193,7 +193,7 @@ def json_from_url( url ): url_contents = url_handle.read() try: parsed_json = json.loads( url_contents ) - except Exception, e: + except Exception as e: error_message = str( url_contents ) print 'Error parsing JSON data in json_from_url(): ', str( e ) return None, error_message @@ -219,7 +219,7 @@ def post( url, data, api_key=None ): opener, request = build_request_with_data( url, data, api_key, 'POST' ) post_request = opener.open( request ) return json.loads( post_request.read() ) - except urllib2.HTTPError, e: + except urllib2.HTTPError as e: return dict( status='error', message=str( e.read( 1024 ) ) ) @@ -229,7 +229,7 @@ def put( url, data, api_key=None ): opener, request = build_request_with_data( url, data, api_key, 'PUT' ) put_request = opener.open( request ) return json.loads( put_request.read() ) - except urllib2.HTTPError, e: + except urllib2.HTTPError as e: return dict( status='error', message=str( e.read( 1024 ) ) ) @@ -240,7 +240,7 @@ def submit( url, data, api_key=None, return_formatted=True ): """ try: response = post( url, data, api_key=api_key ) - except urllib2.HTTPError, e: + except urllib2.HTTPError as e: if return_formatted: print e print e.read( 1024 ) @@ -277,7 +277,7 @@ def update( api_key, url, data, return_formatted=True ): """ try: response = put( url, data, api_key=api_key ) - except urllib2.HTTPError, e: + except urllib2.HTTPError as e: if return_formatted: print e print e.read( 1024 ) diff --git a/scripts/tool_shed/api/create_categories.py b/scripts/tool_shed/api/create_categories.py index 871cb69e3a8..f2cf778b8b5 100644 --- a/scripts/tool_shed/api/create_categories.py +++ b/scripts/tool_shed/api/create_categories.py @@ -40,7 +40,7 @@ def main( options ): url = '%s/api/categories' % to_tool_shed try: response = submit( url, data, api_key ) - except Exception, e: + except Exception as e: response = str( e ) print "Error attempting to create category using URL: ", url, " exception: ", str( e ) create_response_dict = dict( response=response ) diff --git a/scripts/tool_shed/api/create_users.py b/scripts/tool_shed/api/create_users.py index 6bb8b206a34..f2d45317751 100644 --- a/scripts/tool_shed/api/create_users.py +++ b/scripts/tool_shed/api/create_users.py @@ -43,7 +43,7 @@ def main( options ): url = '%s/api/users' % to_tool_shed try: response = submit( url, data, api_key ) - except Exception, e: + except Exception as e: response = str( e ) print "Error attempting to create user using URL: ", url, " exception: ", str( e ) create_response_dict = dict( response=response ) diff --git a/scripts/tool_shed/api/import_capsule.py b/scripts/tool_shed/api/import_capsule.py index 5c41a336fab..97fef3fa617 100644 --- a/scripts/tool_shed/api/import_capsule.py +++ b/scripts/tool_shed/api/import_capsule.py @@ -32,7 +32,7 @@ def main( options ): url = '%s/api/repositories/new/import_capsule' % base_tool_shed_url try: submit( url, data, api_key ) - except Exception, e: + except Exception as e: log.exception( str( e ) ) sys.exit( 1 ) diff --git a/scripts/tool_shed/api/reset_metadata_on_repositories.py b/scripts/tool_shed/api/reset_metadata_on_repositories.py index 824d3d67d97..2098977ed3d 100644 --- a/scripts/tool_shed/api/reset_metadata_on_repositories.py +++ b/scripts/tool_shed/api/reset_metadata_on_repositories.py @@ -64,7 +64,7 @@ def main( options ): url = '%s/api/repositories/reset_metadata_on_repository' % base_tool_shed_url try: submit( url, data, options.api ) - except Exception, e: + except Exception as e: log.exception( ">>>>>>>>>>>>>>>Blew up on data: %s, exception: %s" % ( str( data ), str( e ) ) ) # An nginx timeout undoubtedly occurred. sys.exit( 1 ) @@ -74,7 +74,7 @@ def main( options ): url = '%s/api/repositories/reset_metadata_on_repositories' % base_tool_shed_url try: submit( url, data, options.api ) - except Exception, e: + except Exception as e: log.exception( str( e ) ) # An nginx timeout undoubtedly occurred. sys.exit( 1 ) diff --git a/scripts/tool_shed/check_download_urls.py b/scripts/tool_shed/check_download_urls.py index 4698eb404c3..de8409aeee5 100644 --- a/scripts/tool_shed/check_download_urls.py +++ b/scripts/tool_shed/check_download_urls.py @@ -29,9 +29,9 @@ def main(): url = element.text.strip() try: urllib2.urlopen( urllib2.Request( url ) ) - except Exception, e: + except Exception as e: print "Bad URL '%s' in file '%s': %s" % ( url, path, e ) - except Exception, e: + except Exception as e: print "Unable to check XML file '%s': %s" % ( path, e ) if __name__ == "__main__": diff --git a/scripts/tool_shed/deprecate_repositories_without_metadata.py b/scripts/tool_shed/deprecate_repositories_without_metadata.py index 164db8f197c..e0caea75238 100644 --- a/scripts/tool_shed/deprecate_repositories_without_metadata.py +++ b/scripts/tool_shed/deprecate_repositories_without_metadata.py @@ -91,7 +91,7 @@ def send_mail_to_owner( app, name, owner, email, repositories_deprecated, days=1 galaxy_send_mail( from_address, repository.user.email, subject, body, app.config ) print "# An email has been sent to %s, the owner of %s." % ( repository.user.username, ', '.join( [ repository.name for repository in repositories_deprecated ] ) ) return True - except Exception, e: + except Exception as e: print "# An error occurred attempting to send email: %s" % str( e ) return False diff --git a/scripts/tools/maf/check_loc_file.py b/scripts/tools/maf/check_loc_file.py index efd95320ce6..3e61dc713e9 100644 --- a/scripts/tools/maf/check_loc_file.py +++ b/scripts/tools/maf/check_loc_file.py @@ -48,7 +48,7 @@ def __main__(): for spec in species_found_in_maf: if spec not in species_exist: print "Line %i, %s contains %s, but is not listed in loc file." % ( i, uid, spec ) - except Exception, e: + except Exception as e: print "Line %i is invalid: %s" % ( i, e ) if __name__ == "__main__": diff --git a/scripts/transfer.py b/scripts/transfer.py index 38215edb363..84f0c446fed 100644 --- a/scripts/transfer.py +++ b/scripts/transfer.py @@ -121,7 +121,7 @@ class ListenerServer( SocketServer.ThreadingTCPServer ): SocketServer.ThreadingTCPServer.__init__( self, ( 'localhost', random_port ), RequestHandlerClass ) log.info( 'Listening on port %s' % random_port ) break - except Exception, e: + except Exception as e: log.warning( 'Tried binding port %s: %s' % ( random_port, str( e ) ) ) transfer_job.socket = random_port app.sa_session.add( transfer_job ) @@ -162,7 +162,7 @@ def transfer( app, transfer_job_id ): port_range = app.config.get( 'app:main', 'transfer_worker_port_range' ) try: port_range = [ int( p ) for p in port_range.split( '-' ) ] - except Exception, e: + except Exception as e: log.error( 'Invalid port range set in transfer_worker_port_range: %s: %s' % ( port_range, str( e ) ) ) return False protocol = transfer_job.params[ 'protocol' ] @@ -217,7 +217,7 @@ def http_transfer( transfer_job ): url = transfer_job.params['url'] try: f = urllib2.urlopen( url ) - except urllib2.URLError, e: + except urllib2.URLError as e: yield dict( state=transfer_job.states.ERROR, info='Unable to open URL: %s' % str( e ) ) return size = f.info().getheader( 'Content-Length' ) @@ -230,7 +230,7 @@ def http_transfer( transfer_job ): last = 0 try: fh, fn = tempfile.mkstemp() - except Exception, e: + except Exception as e: yield dict( state=transfer_job.states.ERROR, info='Unable to create temporary file for transfer: %s' % str( e ) ) return log.debug( 'Writing %s to %s, size is %s' % ( url, fn, size or 'unknown' ) ) @@ -252,7 +252,7 @@ def http_transfer( transfer_job ): time.sleep( 1 ) os.close( fh ) yield dict( state=transfer_job.states.DONE, path=fn ) - except Exception, e: + except Exception as e: yield dict( state=transfer_job.states.ERROR, info='Error during file transfer: %s' % str( e ) ) return return @@ -270,7 +270,7 @@ def scp_transfer( transfer_job ): return dict( state=transfer_job.states.ERROR, info=PEXPECT_IMPORT_MESSAGE ) try: fh, fn = tempfile.mkstemp() - except Exception, e: + except Exception as e: return dict( state=transfer_job.states.ERROR, info='Unable to create temporary file for transfer: %s' % str( e ) ) try: # TODO: add the ability to determine progress of the copy here like we do in the http_transfer above. @@ -282,7 +282,7 @@ def scp_transfer( transfer_job ): pexpect.TIMEOUT: print_ticks }, timeout=10 ) return dict( state=transfer_job.states.DONE, path=fn ) - except Exception, e: + except Exception as e: return dict( state=transfer_job.states.ERROR, info='Error during file transfer: %s' % str( e ) ) if __name__ == '__main__': diff --git a/test/base/asserts/__init__.py b/test/base/asserts/__init__.py index 04a18e08733..da33da35eeb 100644 --- a/test/base/asserts/__init__.py +++ b/test/base/asserts/__init__.py @@ -19,7 +19,7 @@ for assertion_module_name in assertion_module_names: __import__(full_assertion_module_name) assertion_module = sys.modules[full_assertion_module_name] assertion_modules.append(assertion_module) - except Exception, e: + except Exception as e: log.exception('Failed to load assertion module: %s %s' % (assertion_module_name, str(e))) diff --git a/test/base/asserts/xml.py b/test/base/asserts/xml.py index a141333e0ef..d9af28512b1 100644 --- a/test/base/asserts/xml.py +++ b/test/base/asserts/xml.py @@ -24,7 +24,7 @@ def assert_is_valid_xml(output): is valid XML.""" try: to_xml(output) - except Exception, e: + except Exception as e: # TODO: Narrow caught exception to just parsing failure raise AssertionError("Expected valid XML, but could not parse output. %s" % str(e)) diff --git a/test/base/driver_util.py b/test/base/driver_util.py index aafd9d289df..231a7201efa 100644 --- a/test/base/driver_util.py +++ b/test/base/driver_util.py @@ -384,7 +384,7 @@ def serve_webapp(webapp, port=None, host=None): port = str( random.randint( 8000, 10000 ) ) server = httpserver.serve( webapp, host=host, port=port, start_loop=False ) break - except socket.error, e: + except socket.error as e: if e[0] == 98: continue raise diff --git a/test/base/twilltestcase.py b/test/base/twilltestcase.py index b39ea5472bb..df34d958336 100644 --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -334,7 +334,7 @@ class TwillTestCase( unittest.TestCase ): assert os.path.exists( downloaded_file ) try: self.files_diff( orig_file, downloaded_file ) - except AssertionError, err: + except AssertionError as err: errmsg = 'Library item %s different than expected, difference:\n' % ldda.name errmsg += str( err ) errmsg += 'Unpacked archive remains in: %s\n' % tmpd @@ -421,7 +421,7 @@ class TwillTestCase( unittest.TestCase ): json_data = self.get_history_from_api( show_deleted=show_deleted, show_details=True ) check_result = check_fn( json_data ) assert check_result, 'failed check_fn: %s (got %s)' % ( check_fn.func_name, str( check_result ) ) - except Exception, e: + except Exception as e: log.exception( e ) log.debug( 'json_data: %s', ( '\n' + pprint.pformat( json_data ) if json_data else '(no match)' ) ) fname = self.write_temp_file( tc.browser.get_html() ) @@ -1935,7 +1935,7 @@ class TwillTestCase( unittest.TestCase ): try: checkbox = control.get() checkbox.selected = is_checked( control_value ) - except Exception, e1: + except Exception as e1: print "Attempting to set checkbox selected value threw exception: ", e1 # if there's more than one checkbox, probably should use the behaviour for # ClientForm.ListControl ( see twill code ), but this works for now... @@ -1972,7 +1972,7 @@ class TwillTestCase( unittest.TestCase ): log.debug( formcontrol ) log.exception( "Attempting to set control '%s' to value '%s' (also tried '%s') threw exception.", control.name, elem, elem_name ) pass - except Exception, exc: + except Exception as exc: for formcontrol in formcontrols: log.debug( formcontrol ) errmsg = "Attempting to set field '%s' to value '%s' in form '%s' threw exception: %s\n" % ( control_name, str( control_value ), f.name, str( exc ) ) @@ -2131,7 +2131,7 @@ class TwillTestCase( unittest.TestCase ): tc.config("readonly_controls_writeable", 1) tc.fv( "tool_form", "NAME", name ) tc.submit( "runtool_btn" ) - except AssertionError, err: + except AssertionError as err: errmsg = "Uploading file resulted in the following exception. Make sure the file (%s) exists. " % filename errmsg += str( err ) raise AssertionError( errmsg ) @@ -2155,7 +2155,7 @@ class TwillTestCase( unittest.TestCase ): tc.fv( "tool_form", "dbkey", dbkey ) tc.fv( "tool_form", "url_paste", url_paste ) tc.submit( "runtool_btn" ) - except Exception, e: + except Exception as e: errmsg = "Problem executing upload utility using url_paste: %s" % str( e ) raise AssertionError( errmsg ) # Make sure every history item has a valid hid @@ -2214,7 +2214,7 @@ class TwillTestCase( unittest.TestCase ): raise Exception( 'Files %s=%db but %s=%db - compare (delta=%s) failed' % (temp_name, s1, local_name, s2, delta) ) else: raise Exception( 'Unimplemented Compare type: %s' % compare ) - except AssertionError, err: + except AssertionError as err: errmsg = 'Composite file (%s) of History item %s different than expected, difference (using %s):\n' % ( base_name, hda_id, compare ) errmsg += str( err ) raise AssertionError( errmsg ) @@ -2273,7 +2273,7 @@ class TwillTestCase( unittest.TestCase ): if attributes is not None and attributes.get( "assert_list", None ) is not None: try: verify_assertions(data, attributes["assert_list"]) - except AssertionError, err: + except AssertionError as err: errmsg = 'History item %s different than expected\n' % (hid) errmsg += str( err ) raise AssertionError( errmsg ) @@ -2281,7 +2281,7 @@ class TwillTestCase( unittest.TestCase ): md5 = attributes.get("md5") try: self._verify_md5(data, md5) - except AssertionError, err: + except AssertionError as err: errmsg = 'History item %s different than expected\n' % (hid) errmsg += str( err ) raise AssertionError( errmsg ) @@ -2296,7 +2296,7 @@ class TwillTestCase( unittest.TestCase ): log.debug( 'keepoutdir: %s, ofn: %s', self.keepOutdir, ofn ) try: shutil.copy( temp_name, ofn ) - except Exception, exc: + except Exception as exc: error_log_msg = ( 'TwillTestCase could not save output file %s to %s: ' % ( temp_name, ofn ) ) error_log_msg += str( exc ) log.error( error_log_msg, exc_info=True ) @@ -2328,7 +2328,7 @@ class TwillTestCase( unittest.TestCase ): raise Exception( 'Unimplemented Compare type: %s' % compare ) if extra_files: self.verify_extra_files_content( extra_files, hda_id, shed_tool_id=shed_tool_id, dataset_fetcher=dataset_fetcher ) - except AssertionError, err: + except AssertionError as err: errmsg = 'History item %s different than expected, difference (using %s):\n' % ( hid, compare ) errmsg += "( %s v. %s )\n" % ( local_name, temp_name ) errmsg += str( err ) diff --git a/test/casperjs/casperjs_runner.py b/test/casperjs/casperjs_runner.py index 82db1838aa7..1b643cd6f73 100644 --- a/test/casperjs/casperjs_runner.py +++ b/test/casperjs/casperjs_runner.py @@ -54,7 +54,7 @@ if minor < 6: # if nose is installed do a skip test from nose.plugins.skip import SkipTest raise SkipTest( msg ) - except ImportError, i_err: + except ImportError as i_err: raise AssertionError( msg ) # -------------------------------------------------------------------- @@ -145,7 +145,7 @@ class CasperJSTestCase( unittest.TestCase ): # couldn't find the headless browser, # provide information (as it won't be included by default with galaxy) - except OSError, os_err: + except OSError as os_err: if os_err.errno == errno.ENOENT: log.error( 'No path to headless browser executable: %s\n' + 'These tests were designed to use the following headless browser:\n%s', @@ -208,7 +208,7 @@ class CasperJSTestCase( unittest.TestCase ): self.browser_backtrace_to_string( last_error['backtrace'] ) ) ) # if we couldn't parse json from what's returned on the error, dump stdout - except ValueError, val_err: + except ValueError as val_err: if str( val_err ) == 'No JSON object could be decoded': log.debug( '(error parsing returned JSON from casperjs, dumping stdout...)\n:%s', stdout_output ) return HeadlessJSJavascriptError( 'see log for details' ) @@ -216,7 +216,7 @@ class CasperJSTestCase( unittest.TestCase ): raise # otherwise, raise a vanilla exc - except Exception, exc: + except Exception as exc: log.debug( '(failed to parse error returned from %s: %s)', _PATH_TO_HEADLESS, str( exc ) ) return HeadlessJSJavascriptError( "ERROR in headless browser script %s" % ( script_path ) ) diff --git a/test/casperjs/server_env.py b/test/casperjs/server_env.py index 5b779cc9675..739b89f9f17 100644 --- a/test/casperjs/server_env.py +++ b/test/casperjs/server_env.py @@ -104,7 +104,7 @@ class TestEnvironment( object ): text = f.read() f.close() shed_tools_dict = loads( text ) - except Exception, exc: + except Exception as exc: log.error( 'Error reading tool shed test file "%s": %s', self.tool_shed_test_file, exc, exc_info=True ) return shed_tools_dict @@ -116,7 +116,7 @@ class TestEnvironment( object ): try: if not os.path.exists( self.saved_output_dir ): os.makedirs( self.saved_output_dir ) - except Exception, exc: + except Exception as exc: log.error( 'unable to create saved files directory "%s": %s', self.saved_output_dir, exc, exc_info=True ) self.saved_output_dir = None @@ -128,7 +128,7 @@ class TestEnvironment( object ): if self.debug_these_tests: try: debug_list = self.debug_these_tests.split( delim ) - except Exception, exc: + except Exception as exc: log.error( 'unable to parse debug_these_tests "%s": %s', self.debug_these_tests, exc, exc_info=True ) self.debug_these_tests = debug_list diff --git a/test/functional/test_data_managers.py b/test/functional/test_data_managers.py index 332fd7feae0..2843ad070c3 100644 --- a/test/functional/test_data_managers.py +++ b/test/functional/test_data_managers.py @@ -73,7 +73,7 @@ def build_tests( tmp_dir=None, testing_shed_tools=False, master_api_key=None, us new_filename = tempfile.NamedTemporaryFile( prefix=os.path.basename( filename ), dir=tmp_dir ).name try: shutil.copy( filename, new_filename ) - except IOError, e: + except IOError as e: log.warning( "Failed to copy '%s' to '%s', will create empty file at '%s': %s", filename, new_filename, new_filename, e ) open( new_filename, 'wb' ).close() if 'filename' in value: diff --git a/test/functional/test_toolbox.py b/test/functional/test_toolbox.py index 4b50e2f0300..18c3bf578a4 100644 --- a/test/functional/test_toolbox.py +++ b/test/functional/test_toolbox.py @@ -180,7 +180,7 @@ class ToolTestCase( TwillTestCase ): try: data = job_stdio[what] verify_assertions( data, getattr( testdef, what ) ) - except AssertionError, err: + except AssertionError as err: errmsg = '%s different than expected\n' % description errmsg += str( err ) register_exception( AssertionError( errmsg ) ) diff --git a/test/shed_functional/base/twilltestcase.py b/test/shed_functional/base/twilltestcase.py index b4a5cc9e114..e03e252a958 100644 --- a/test/shed_functional/base/twilltestcase.py +++ b/test/shed_functional/base/twilltestcase.py @@ -1320,7 +1320,7 @@ class ShedTwillTestCase( TwillTestCase ): # try: # self.check_for_strings( strings_displayed, strings_not_displayed ) # break - # except Exception, e: + # except Exception as e: # if i == 4: # raise e # else: diff --git a/test/unit/tools/test_execution.py b/test/unit/tools/test_execution.py index dea955f6a3c..de066083cf9 100644 --- a/test/unit/tools/test_execution.py +++ b/test/unit/tools/test_execution.py @@ -60,7 +60,7 @@ class ToolExecutionTestCase( TestCase, tools_support.UsesApp, tools_support.Uses self.tool_action.raise_exception( ) try: self.__handle_with_incoming( param1="moo" ) - except Exception, e: + except Exception as e: assert 'Error executing tool' in str( e ) def test_execute_errors( self ): @@ -68,7 +68,7 @@ class ToolExecutionTestCase( TestCase, tools_support.UsesApp, tools_support.Uses self.tool_action.return_error( ) try: self.__handle_with_incoming( param1="moo" ) - except Exception, e: + except Exception as e: assert 'Test Error Message' in str( e ) def test_redirect( self ): @@ -91,7 +91,7 @@ class ToolExecutionTestCase( TestCase, tools_support.UsesApp, tools_support.Uses self._init_tool( tools_support.SIMPLE_TOOL_CONTENTS ) try: self.__handle_with_incoming( param1="moo", rerun_remap_job_id='123' ) - except Exception, e: + except Exception as e: assert 'invalid job' in str( e ) def test_data_param_execute( self ): diff --git a/test/unit/tools/test_select_parameters.py b/test/unit/tools/test_select_parameters.py index 226cd088a63..7eca591a0fa 100644 --- a/test/unit/tools/test_select_parameters.py +++ b/test/unit/tools/test_select_parameters.py @@ -11,7 +11,7 @@ class SelectToolParameterTestCase( BaseParameterTestCase ): self.options_xml = '''''' try: self.param.from_json("42", self.trans, { "input_bam": model.HistoryDatasetAssociation() }) - except ValueError, err: + except ValueError as err: assert str(err) == "An invalid option was selected for my_name, '42', please verify." return assert False @@ -20,7 +20,7 @@ class SelectToolParameterTestCase( BaseParameterTestCase ): self.options_xml = '''''' try: self.param.from_json("42", self.trans) - except AssertionError, err: + except AssertionError as err: assert str(err) == "Required dependency 'input_bam' not found in incoming values" return assert False @@ -34,7 +34,7 @@ class SelectToolParameterTestCase( BaseParameterTestCase ): self.options_xml = '''''' try: self.param.from_json( model.HistoryDatasetAssociation(), self.trans, { "input_bam": basic.RuntimeValue() } ) - except ValueError, err: + except ValueError as err: assert str(err) == "Parameter my_name requires a value, but has no legal values defined." return assert False diff --git a/test/unit/visualizations/plugins/test_VisualizationPlugin.py b/test/unit/visualizations/plugins/test_VisualizationPlugin.py index c696f15ec6e..5cf2facce1e 100644 --- a/test/unit/visualizations/plugins/test_VisualizationPlugin.py +++ b/test/unit/visualizations/plugins/test_VisualizationPlugin.py @@ -165,7 +165,7 @@ class VisualizationsPlugin_TestCase( test_utils.unittest.TestCase ): for var in should_have: try: var = str( var ) - except NameError, name_err: + except NameError as name_err: found_all = False break %> diff --git a/tools/data_source/data_source.py b/tools/data_source/data_source.py index 2d3dbcb9e5c..319c6bf11c2 100644 --- a/tools/data_source/data_source.py +++ b/tools/data_source/data_source.py @@ -88,7 +88,7 @@ def __main__(): page = urllib.urlopen( cur_URL ) elif URL_method == 'post': page = urllib.urlopen( cur_URL, urllib.urlencode( params ) ) - except Exception, e: + except Exception as e: stop_err( 'The remote data source application may be off line, please try again later. Error: %s' % str( e ) ) if max_file_size: file_size = int( page.info().get( 'Content-Length', 0 ) ) @@ -97,14 +97,14 @@ def __main__(): # do sniff stream for multi_byte try: cur_filename, is_multi_byte = sniff.stream_to_open_named_file( page, os.open( cur_filename, os.O_WRONLY | os.O_CREAT ), cur_filename, source_encoding=get_charset_from_http_headers( page.headers ) ) - except Exception, e: + except Exception as e: stop_err( 'Unable to fetch %s:\n%s' % ( cur_URL, e ) ) # here import checks that upload tool performs if enhanced_handling: try: ext = sniff.handle_uploaded_dataset_file( filename, datatypes_registry, ext=data_dict[ 'ext' ], is_multi_byte=is_multi_byte ) - except Exception, e: + except Exception as e: stop_err( str( e ) ) info = dict( type='dataset', dataset_id=data_dict[ 'dataset_id' ], diff --git a/tools/data_source/fetch.py b/tools/data_source/fetch.py index 12f7140a665..2b8de91e268 100644 --- a/tools/data_source/fetch.py +++ b/tools/data_source/fetch.py @@ -20,6 +20,6 @@ try: if not data: break out.write(data) -except Exception, e: +except Exception as e: print 'Error getting the data -> %s' % e out.close() diff --git a/tools/data_source/hbvar_filter.py b/tools/data_source/hbvar_filter.py index c7a6ac0c2d9..688c69f59c0 100644 --- a/tools/data_source/hbvar_filter.py +++ b/tools/data_source/hbvar_filter.py @@ -31,7 +31,7 @@ def exec_after_process(app, inp_data, out_data, param_dict, tool=None, stdout=No try: page = urllib.urlopen(URL) - except Exception, exc: + except Exception as exc: raise Exception('Problems connecting to %s (%s)' % (URL, exc) ) name, data = out_data.items()[0] diff --git a/tools/data_source/upload.py b/tools/data_source/upload.py index 008b2da0ee2..0450538f9fc 100644 --- a/tools/data_source/upload.py +++ b/tools/data_source/upload.py @@ -96,7 +96,7 @@ def add_file( dataset, registry, json_file, output_path ): try: page = urllib.urlopen( dataset.path ) # page will be .close()ed by sniff methods temp_name, dataset.is_multi_byte = sniff.stream_to_file( page, prefix='url_paste', source_encoding=util.get_charset_from_http_headers( page.headers ) ) - except Exception, e: + except Exception as e: file_err( 'Unable to fetch %s\n%s' % ( dataset.path, str( e ) ), dataset, json_file ) return dataset.path = temp_name @@ -111,7 +111,7 @@ def add_file( dataset, registry, json_file, output_path ): # Already set is_multi_byte above if type == 'url' try: dataset.is_multi_byte = multi_byte.is_multi_byte( codecs.open( dataset.path, 'r', 'utf-8' ).read( 100 ) ) - except UnicodeDecodeError, e: + except UnicodeDecodeError as e: dataset.is_multi_byte = False # Is dataset an image? image = check_image( dataset.path ) @@ -364,7 +364,7 @@ def add_composite_file( dataset, json_file, output_path, files_path ): if isurl: try: temp_name, dataset.is_multi_byte = sniff.stream_to_file( urllib.urlopen( dp ), prefix='url_paste' ) - except Exception, e: + except Exception as e: file_err( 'Unable to fetch %s\n%s' % ( dp, str( e ) ), dataset, json_file ) return dataset.path = temp_name diff --git a/tools/evolution/add_scores.py b/tools/evolution/add_scores.py index 212d5fcb7d3..0763648e000 100755 --- a/tools/evolution/add_scores.py +++ b/tools/evolution/add_scores.py @@ -16,7 +16,7 @@ def open_or_die( filename, mode='r', message=None ): message = 'Error opening %s' % filename try: fh = open( filename, mode ) - except IOError, err: + except IOError as err: die( '%s: %s' % ( message, err.strerror ) ) return fh @@ -51,7 +51,7 @@ class LocationFile( object ): die( 'Location file %s line %d: duplicate key "%s"' % ( self.filename, line_number, key ) ) else: self._map[key] = elems - except IOError, err: + except IOError as err: die( 'Error opening location file %s: %s' % ( self.filename, err.strerror ) ) def get_values( self, key ): diff --git a/tools/extract/extract_genomic_dna.py b/tools/extract/extract_genomic_dna.py index dcd49af5df0..359d530209d 100755 --- a/tools/extract/extract_genomic_dna.py +++ b/tools/extract/extract_genomic_dna.py @@ -119,7 +119,7 @@ def __main__(): # Error checking. if returncode != 0: raise Exception(stderr) - except Exception, e: + except Exception as e: stop_err( 'Error running faToTwoBit. ' + str( e ) ) else: seq_path = check_seq_file( dbkey, GALAXY_DATA_INDEX_DIR ) @@ -210,7 +210,7 @@ def __main__(): nibs[chrom] = nib = bx.seq.nib.NibFile( open( "%s/%s.nib" % ( seq_path, chrom ) ) ) try: sequence = nib.get( start, end - start ) - except Exception, e: + except Exception as e: warning = "Unable to fetch the sequence from '%d' to '%d' for build '%s'. " % ( start, end - start, dbkey ) warnings.append( warning ) if not invalid_lines: diff --git a/tools/extract/liftOver_wrapper.py b/tools/extract/liftOver_wrapper.py index f321dd5a0e0..83fe6ea9110 100644 --- a/tools/extract/liftOver_wrapper.py +++ b/tools/extract/liftOver_wrapper.py @@ -79,7 +79,7 @@ try: stderr = proc.stderr.read() if returncode != 0: raise Exception(stderr) - except Exception, e: + except Exception as e: raise Exception('Exception caught attempting conversion: ' + str( e )) finally: os.remove(safe_infile) diff --git a/tools/filters/gff/gff_filter_by_attribute.py b/tools/filters/gff/gff_filter_by_attribute.py index e8975206764..6125df5381b 100644 --- a/tools/filters/gff/gff_filter_by_attribute.py +++ b/tools/filters/gff/gff_filter_by_attribute.py @@ -126,7 +126,7 @@ for i, line in enumerate( open( in_fname ) ): if %s: lines_kept += 1 print >> out, line - except Exception, e: + except Exception as e: print e skipped_lines += 1 if not invalid_line: @@ -137,7 +137,7 @@ for i, line in enumerate( open( in_fname ) ): valid_filter = True try: exec code -except Exception, e: +except Exception as e: out.close() if str( e ).startswith( 'invalid syntax' ): valid_filter = False diff --git a/tools/filters/gtf_to_bedgraph_converter.py b/tools/filters/gtf_to_bedgraph_converter.py index abfcd1a3e03..df2dd056b19 100644 --- a/tools/filters/gtf_to_bedgraph_converter.py +++ b/tools/filters/gtf_to_bedgraph_converter.py @@ -62,7 +62,7 @@ def __main__(): try: os.system(cmd) os.remove(tmp_name1) - except Exception, ex: + except Exception as ex: sys.stderr.write( "%s\n" % ex ) sys.exit(1) @@ -71,7 +71,7 @@ def __main__(): try: os.system(cmd) os.remove(tmp_name2) - except Exception, ex: + except Exception as ex: sys.stderr.write( "%s\n" % ex ) sys.exit(1) diff --git a/tools/filters/join.py b/tools/filters/join.py index 7177f59440e..81a8fbe59da 100644 --- a/tools/filters/join.py +++ b/tools/filters/join.py @@ -359,7 +359,7 @@ def main(): if options.fill_options_file is not None: try: fill_options = Bunch( **stringify_dictionary_keys( json.load( open( options.fill_options_file ) ) ) ) # json.load( open( options.fill_options_file ) ) - except Exception, e: + except Exception as e: print "Warning: Ignoring fill options due to json error (%s)." % e if fill_options is None: fill_options = Bunch() diff --git a/tools/filters/joinWrapper.py b/tools/filters/joinWrapper.py index b08e08c9fb5..e2a9820d418 100644 --- a/tools/filters/joinWrapper.py +++ b/tools/filters/joinWrapper.py @@ -29,7 +29,7 @@ def main(): # Sort the two files based on specified fields os.system("sort -t ' ' -k %d,%d -o %s %s" % (field1, field1, tmpfile1.name, infile1)) os.system("sort -t ' ' -k %d,%d -o %s %s" % (field2, field2, tmpfile2.name, infile2)) - except Exception, exc: + except Exception as exc: stop_err( 'Initialization error -> %s' % str(exc) ) option = "" @@ -69,7 +69,7 @@ def main(): try: os.system(cmdline) - except Exception, exj: + except Exception as exj: stop_err('Error joining the two datasets -> %s' % str(exj)) if __name__ == "__main__": diff --git a/tools/filters/lav_to_bed.py b/tools/filters/lav_to_bed.py index 79322c116aa..0aa2689936d 100644 --- a/tools/filters/lav_to_bed.py +++ b/tools/filters/lav_to_bed.py @@ -15,7 +15,7 @@ def main(): lav_file = open(sys.argv[1], 'r') bed_file1 = open(sys.argv[2], 'w') bed_file2 = open(sys.argv[3], 'w') - except Exception, e: + except Exception as e: stop_err( str( e ) ) lavsRead = 0 diff --git a/tools/filters/sff_extract.py b/tools/filters/sff_extract.py index 06158434f19..7711a5e7f57 100644 --- a/tools/filters/sff_extract.py +++ b/tools/filters/sff_extract.py @@ -859,7 +859,7 @@ def extract_reads_from_sff(config, sff_files): qual_fh = None try: os.remove(config['qual_fname']) - except : + except: pass else: qual_fh = open(config['qual_fname'], openmode) @@ -1100,7 +1100,7 @@ def tests_for_ssaha(): subprocess.call(["ssaha2"], stdout=fh) fh.close() print "ok." - except : + except: print "nope? Uh oh ...\n\n" raise RuntimeError('Could not launch ssaha2. Have you installed it? Is it in your path?') @@ -1325,7 +1325,7 @@ def main(): if len(args) == 0: raise RuntimeError("No SFF file given?") extract_reads_from_sff(config, args) - except (OSError, IOError, RuntimeError), errval: + except (OSError, IOError, RuntimeError) as errval: print errval return 1 diff --git a/tools/filters/sorter.py b/tools/filters/sorter.py index 9d41101397f..d9619bce5e2 100644 --- a/tools/filters/sorter.py +++ b/tools/filters/sorter.py @@ -47,7 +47,7 @@ def main(): os.system(grep_comments) os.system(sort_columns) - except Exception, ex: + except Exception as ex: stop_err('Error running sorter.py\n' + str(ex)) # exit diff --git a/tools/filters/wiggle_to_simple.py b/tools/filters/wiggle_to_simple.py index ca18084a1ea..bfb1a6dfcc9 100755 --- a/tools/filters/wiggle_to_simple.py +++ b/tools/filters/wiggle_to_simple.py @@ -34,7 +34,7 @@ def main(): except UCSCLimitException: # Wiggle data was truncated, at the very least need to warn the user. print 'Encountered message from UCSC: "Reached output limit of 100000 data values", so be aware your data was truncated.' - except ValueError, e: + except ValueError as e: in_file.close() out_file.close() stop_err( str( e ) ) diff --git a/tools/genomespace/genomespace_exporter.py b/tools/genomespace/genomespace_exporter.py index 925ccf67f3b..a146bff7eb0 100644 --- a/tools/genomespace/genomespace_exporter.py +++ b/tools/genomespace/genomespace_exporter.py @@ -165,7 +165,7 @@ def galaxy_code_get_genomespace_folders( genomespace_site='prod', trans=None, va # get url to upload to try: cur_directory = url_opener.open( cur_directory ).read() - except urllib2.HTTPError, e: + except urllib2.HTTPError as e: log.debug( 'GenomeSpace export tool failed reading a directory "%s": %s' % ( url, e ) ) return # bad url, go to next cur_directory = json.loads( cur_directory ) diff --git a/tools/maf/interval_maf_to_merged_fasta.py b/tools/maf/interval_maf_to_merged_fasta.py index 079cc443baf..d51c2572cfb 100644 --- a/tools/maf/interval_maf_to_merged_fasta.py +++ b/tools/maf/interval_maf_to_merged_fasta.py @@ -141,7 +141,7 @@ def __main__(): overwrite_with_gaps=overwrite_with_gaps ) primary_name = secondary_name = fields[3] alignment_strand = fields[5] - except Exception, e: + except Exception as e: print "Error loading exon positions from input line %i: %s" % ( line_count, e ) continue else: # Process as standard intervals @@ -154,7 +154,7 @@ def __main__(): primary_name = "%s(%s):%s-%s" % ( line.chrom, line.strand, line.start, line.end ) secondary_name = "" alignment_strand = line.strand - except Exception, e: + except Exception as e: print "Error loading region positions from input line %i: %s" % ( line_count, e ) continue @@ -181,7 +181,7 @@ def __main__(): output.write( "\n" ) regions_extracted += 1 - except Exception, e: + except Exception as e: print "Unexpected error from input line %i: %s" % ( line_count, e ) continue diff --git a/tools/maf/maf_split_by_species.py b/tools/maf/maf_split_by_species.py index 85ee936a0c6..470b356cfa2 100644 --- a/tools/maf/maf_split_by_species.py +++ b/tools/maf/maf_split_by_species.py @@ -13,15 +13,15 @@ from galaxy.util import string_as_bool def __main__(): try: maf_reader = maf.Reader( open( sys.argv[1] ) ) - except Exception, e: + except Exception as e: maf_utilities.tool_fail( "Error opening MAF: %s" % e ) try: out = maf.Writer( open( sys.argv[2], "w") ) - except Exception, e: + except Exception as e: maf_utilities.tool_fail( "Error opening file for output: %s" % e ) try: collapse_columns = string_as_bool( sys.argv[3] ) - except Exception, e: + except Exception as e: maf_utilities.tool_fail( "Error determining collapse columns value: %s" % e ) start_count = 0 diff --git a/tools/maf/maf_thread_for_species.py b/tools/maf/maf_thread_for_species.py index 253cb68061d..2aca2e10bfd 100644 --- a/tools/maf/maf_thread_for_species.py +++ b/tools/maf/maf_thread_for_species.py @@ -41,7 +41,7 @@ def main(): m.components = new_components m.score = 0.0 maf_writer.write( m ) - except Exception, e: + except Exception as e: print >> sys.stderr, "Error steping through MAF File: %s" % e sys.exit() maf_reader.close() diff --git a/tools/maf/maf_to_fasta_concat.py b/tools/maf/maf_to_fasta_concat.py index e2fec94b520..d1b52295ac0 100755 --- a/tools/maf/maf_to_fasta_concat.py +++ b/tools/maf/maf_to_fasta_concat.py @@ -15,15 +15,15 @@ from galaxy.tools.util import maf_utilities def __main__(): try: species = maf_utilities.parse_species_option( sys.argv[1] ) - except Exception, e: + except Exception as e: maf_utilities.tool_fail( "Error determining species value: %s" % e ) try: input_filename = sys.argv[2] - except Exception, e: + except Exception as e: maf_utilities.tool_fail( "Error reading MAF filename: %s" % e ) try: file_out = open( sys.argv[3], 'w' ) - except Exception, e: + except Exception as e: maf_utilities.tool_fail( "Error opening file for output: %s" % e ) if species: @@ -34,7 +34,7 @@ def __main__(): if not species: try: species = maf_utilities.get_species_in_maf( input_filename ) - except Exception, e: + except Exception as e: maf_utilities.tool_fail( "Error determining species in input MAF: %s" % e ) for spec in species: @@ -48,7 +48,7 @@ def __main__(): file_out.write( component.text ) else: file_out.write( "-" * block.text_size ) - except Exception, e: + except Exception as e: maf_utilities.tool_fail( "Your MAF file appears to be malformed: %s" % e ) file_out.write( "\n" ) file_out.close() diff --git a/tools/maf/maf_to_fasta_multiple_sets.py b/tools/maf/maf_to_fasta_multiple_sets.py index e1a5ee6ebd4..38d6170350f 100755 --- a/tools/maf/maf_to_fasta_multiple_sets.py +++ b/tools/maf/maf_to_fasta_multiple_sets.py @@ -14,11 +14,11 @@ from galaxy.tools.util import maf_utilities def __main__(): try: maf_reader = maf.Reader( open( sys.argv[1] ) ) - except Exception, e: + except Exception as e: maf_utilities.tool_fail( "Error opening input MAF: %s" % e ) try: file_out = open( sys.argv[2], 'w' ) - except Exception, e: + except Exception as e: maf_utilities.tool_fail( "Error opening file for output: %s" % e ) try: species = maf_utilities.parse_species_option( sys.argv[3] ) @@ -26,11 +26,11 @@ def __main__(): num_species = len( species ) else: num_species = 0 - except Exception, e: + except Exception as e: maf_utilities.tool_fail( "Error determining species value: %s" % e ) try: partial = sys.argv[4] - except Exception, e: + except Exception as e: maf_utilities.tool_fail( "Error determining keep partial value: %s" % e ) if species: diff --git a/tools/metag_tools/shrimp_color_wrapper.py b/tools/metag_tools/shrimp_color_wrapper.py index 1e5d2dcc561..9faa2523ff0 100644 --- a/tools/metag_tools/shrimp_color_wrapper.py +++ b/tools/metag_tools/shrimp_color_wrapper.py @@ -80,7 +80,7 @@ def __main__(): try: os.system(command) - except Exception, e: + except Exception as e: stop_err(str(e)) # check SHRiMP output: count number of lines @@ -93,7 +93,7 @@ def __main__(): try: line.split() num_hits += 1 - except Exception, e: + except Exception as e: stop_err(str(e)) if num_hits == 0: # no hits generated diff --git a/tools/metag_tools/shrimp_wrapper.py b/tools/metag_tools/shrimp_wrapper.py index 0a2eed33285..1083af7cc64 100644 --- a/tools/metag_tools/shrimp_wrapper.py +++ b/tools/metag_tools/shrimp_wrapper.py @@ -564,7 +564,7 @@ def __main__(): try: os.system(command) - except Exception, e: + except Exception as e: if os.path.exists(query_fasta): os.remove(query_fasta) if os.path.exists(query_qual): @@ -578,7 +578,7 @@ def __main__(): try: os.system(command_end1) os.system(command_end2) - except Exception, e: + except Exception as e: if os.path.exists(query_fasta_end1): os.remove(query_fasta_end1) if os.path.exists(query_fasta_end2): @@ -599,7 +599,7 @@ def __main__(): try: line.split() num_hits += 1 - except Exception, e: + except Exception as e: stop_err(str(e)) if num_hits == 0: # no hits generated diff --git a/tools/next_gen_conversion/fastq_conversions.py b/tools/next_gen_conversion/fastq_conversions.py index 6e52e8c5d7e..7b7a84af775 100644 --- a/tools/next_gen_conversion/fastq_conversions.py +++ b/tools/next_gen_conversion/fastq_conversions.py @@ -37,7 +37,7 @@ def __main__(): cmd = cmd % (options.command, options.input, options.outputFasta) try: os.system(cmd) - except Exception, eq: + except Exception as eq: stop_err("Error converting data format.\n" + str(eq)) if __name__ == "__main__": diff --git a/tools/next_gen_conversion/solid_to_fastq.py b/tools/next_gen_conversion/solid_to_fastq.py index 34c9a56cbff..642f478f41f 100644 --- a/tools/next_gen_conversion/solid_to_fastq.py +++ b/tools/next_gen_conversion/solid_to_fastq.py @@ -53,7 +53,7 @@ def __main__(): os.system(cmd1) os.system('gunzip -c %s >> %s' % (tmpf.name, options.output1)) os.system('gunzip -c %s >> %s' % (tmpr.name, options.output2)) - except Exception, eq: + except Exception as eq: stop_err("Error converting data to fastq format.\n" + str(eq)) tmpr.close() tmpqr.close() @@ -63,7 +63,7 @@ def __main__(): try: os.system(cmd1) os.system('gunzip -c %s >> %s' % (tmpf.name, options.output1)) - except Exception, eq: + except Exception as eq: stop_err("Error converting data to fastq format.\n" + str(eq)) tmpqf.close() tmpf.close() diff --git a/tools/ngs_simulation/ngs_simulation.py b/tools/ngs_simulation/ngs_simulation.py index 17ce765f726..5d2b5dbfa15 100644 --- a/tools/ngs_simulation/ngs_simulation.py +++ b/tools/ngs_simulation/ngs_simulation.py @@ -42,7 +42,7 @@ def __main__(): read_len = int( options.read_len ) if read_len <= 0: raise Exception(' greater than 0') - except TypeError, e: + except TypeError as e: error = ': %s' % str( e ) if error: stop_err( 'Make sure your number of reads is an integer value%s' % error ) @@ -51,7 +51,7 @@ def __main__(): avg_coverage = int( options.avg_coverage ) if avg_coverage <= 0: raise Exception(' greater than 0') - except Exception, e: + except Exception as e: error = ': %s' % str( e ) if error: stop_err( 'Make sure your average coverage is an integer value%s' % error ) @@ -62,13 +62,13 @@ def __main__(): error_rate = 10 ** ( -error_rate / 10.0 ) elif error_rate < 0: raise Exception(' between 0 and 1') - except Exception, e: + except Exception as e: error = ': %s' % str( e ) if error: stop_err( 'Make sure the error rate is a decimal value%s or the quality score is at least 1' % error ) try: num_sims = int( options.num_sims ) - except TypeError, e: + except TypeError as e: stop_err( 'Make sure the number of simulations is an integer value: %s' % str( e ) ) if options.polymorphism != 'None': polymorphisms = [ float( p ) for p in options.polymorphism.split( ',' ) ] diff --git a/tools/phenotype_association/pagetag.py b/tools/phenotype_association/pagetag.py index 130fa305330..fe19062c10e 100755 --- a/tools/phenotype_association/pagetag.py +++ b/tools/phenotype_association/pagetag.py @@ -272,7 +272,7 @@ if __name__ == "__main__": try: opts, args = getopt(argv[1:], "hds:r:f:", ["help", "debug", "rsquare=", "freq=", "sample="]) - except GetoptError, err: + except GetoptError as err: print str(err) usage() exit(2) diff --git a/tools/phenotype_association/senatag.py b/tools/phenotype_association/senatag.py index c8127b6e199..fd648c56d4f 100755 --- a/tools/phenotype_association/senatag.py +++ b/tools/phenotype_association/senatag.py @@ -225,7 +225,7 @@ if __name__ == "__main__": try: opts, args = getopt(argv[1:], "hdr:e:", ["help", "debug", "required=", "excluded="]) - except GetoptError, err: + except GetoptError as err: print str(err) usage() exit(2) diff --git a/tools/solid_tools/maq_cs_wrapper.py b/tools/solid_tools/maq_cs_wrapper.py index 04144a2c0fb..f29f1fd7f44 100644 --- a/tools/solid_tools/maq_cs_wrapper.py +++ b/tools/solid_tools/maq_cs_wrapper.py @@ -56,7 +56,7 @@ def __main__(): os.system('gunzip -c %s >> %s' % (tmpr.name, tmprfastq.name)) os.system('gunzip -c %s >> %s' % (tmps.name, tmpsfastq.name)) - except Exception, eq: + except Exception as eq: stop_err("Error converting data to fastq format." + str(eq)) # Make a temp directory where the split fastq files will be stored @@ -129,7 +129,7 @@ def __main__(): except ValueError as we: print >>sys.stderr, we print >> out_f2, "%s\t%s\t%s\t%s\t%s\t%s" % ("\t".join(elems[:4]), coverage - ref_nt_count, a, t, g, c) - except Exception, er2: + except Exception as er2: stop_err("Encountered error while mapping: %s" % (str(er2))) else: # single end reads diff --git a/tools/stats/aggregate_scores_in_intervals.py b/tools/stats/aggregate_scores_in_intervals.py index f527f37e339..77e8ca7c227 100755 --- a/tools/stats/aggregate_scores_in_intervals.py +++ b/tools/stats/aggregate_scores_in_intervals.py @@ -42,7 +42,7 @@ class PositionalScoresOnDisk: try: self.file.seek( i * self.fmt_size ) return struct.unpack( self.fmt, self.file.read( self.fmt_size ) )[0] - except Exception, e: + except Exception as e: raise IndexError(e) def __setitem__( self, i, value ): diff --git a/tools/stats/filtering.py b/tools/stats/filtering.py index fd479fa56ff..fefbceda180 100644 --- a/tools/stats/filtering.py +++ b/tools/stats/filtering.py @@ -241,7 +241,7 @@ for i, line in enumerate( open( in_fname ) ): valid_filter = True try: exec code -except Exception, e: +except Exception as e: out.close() if str( e ).startswith( 'invalid syntax' ): valid_filter = False diff --git a/tools/stats/grouping.py b/tools/stats/grouping.py index c65992b466a..f7f8031de97 100644 --- a/tools/stats/grouping.py +++ b/tools/stats/grouping.py @@ -85,7 +85,7 @@ def main(): if ignorecase == 1: case = '-f' command_line = "sort -t ' ' %s -k%s,%s -o %s %s" % (case, group_col + 1, group_col + 1, tmpfile.name, inputfile) - except Exception, exc: + except Exception as exc: stop_err( 'Initialization error -> %s' % str(exc) ) error_code, stdout = commands.getstatusoutput(command_line) diff --git a/tools/stats/gsummary.py b/tools/stats/gsummary.py index 09c9019f18e..a2a6290e986 100755 --- a/tools/stats/gsummary.py +++ b/tools/stats/gsummary.py @@ -102,7 +102,7 @@ def main(): r.assign( col, r[ "$" ]( r_data_frame, col ) ) try: summary = summary_func( r( expression ) ) - except RException, s: + except RException as s: outfile.close() stop_err( "Computation resulted in the following error: %s" % str( s ) ) summary = summary.as_py( BASIC_CONVERSION )