Fix all E722 errors and ignore E741

Introduced in flake8 3.5.0
Fix import order.

.ci/flake8_lint_include_list.txt

@@ -1,4 +1,5 @@
 client/galaxy/style/source_material/circle.py
+config/
 contrib/
 cron/
 doc/parse_gx_xsd.py
@@ -21,22 +22,13 @@ lib/galaxy/jobs/command_factory.py
 lib/galaxy/jobs/datasets.py
 lib/galaxy/jobs/deferred/
 lib/galaxy/jobs/error_level.py
+lib/galaxy/jobs/handler.py
 lib/galaxy/jobs/__init__.py
 lib/galaxy/jobs/manager.py
 lib/galaxy/jobs/metrics/
+lib/galaxy/jobs/output_checker.py
 lib/galaxy/jobs/rules/
-lib/galaxy/jobs/runners/cli.py
-lib/galaxy/jobs/runners/condor.py
-lib/galaxy/jobs/runners/drmaa.py
-lib/galaxy/jobs/runners/godocker.py
-lib/galaxy/jobs/runners/kubernetes.py
-lib/galaxy/jobs/runners/local.py
-lib/galaxy/jobs/runners/pbs.py
-lib/galaxy/jobs/runners/pulsar.py
-lib/galaxy/jobs/runners/slurm.py
-lib/galaxy/jobs/runners/state_handlers/
-lib/galaxy/jobs/runners/tasks.py
-lib/galaxy/jobs/runners/util/
+lib/galaxy/jobs/runners/
 lib/galaxy/jobs/splitters/basic.py
 lib/galaxy/jobs/splitters/__init__.py
 lib/galaxy/jobs/stock_rules.py
@@ -61,9 +53,7 @@ lib/galaxy/objectstore/s3_multipart_upload.py
 lib/galaxy/objectstore/s3.py
 lib/galaxy/openid/__init__.py
 lib/galaxy/quota/
-lib/galaxy/sample_tracking/data_transfer.py
-lib/galaxy/sample_tracking/__init__.py
-lib/galaxy/sample_tracking/sample.py
+lib/galaxy/sample_tracking/
 lib/galaxy/security/
 lib/galaxy/tags/
 lib/galaxy/tools/
@@ -71,6 +61,7 @@ lib/galaxy/util/
 lib/galaxy/version.py
 lib/galaxy/visualization/data_providers/basic.py
 lib/galaxy/visualization/data_providers/cigar.py
+lib/galaxy/visualization/data_providers/genome.py
 lib/galaxy/visualization/data_providers/__init__.py
 lib/galaxy/visualization/data_providers/phyloviz/baseparser.py
 lib/galaxy/visualization/genome/
@@ -99,14 +90,23 @@ lib/galaxy/web/framework/middleware/xforwardedhost.py
 lib/galaxy/web/framework/webapp.py
 lib/galaxy/web/__init__.py
 lib/galaxy/web/params.py
+lib/galaxy/web/stack/
+lib/galaxy/webapps/galaxy/api/authenticate.py
+lib/galaxy/webapps/galaxy/api/forms.py
 lib/galaxy/webapps/galaxy/api/genomes.py
+lib/galaxy/webapps/galaxy/api/group_roles.py
+lib/galaxy/webapps/galaxy/api/group_users.py
+lib/galaxy/webapps/galaxy/api/groups.py
 lib/galaxy/webapps/galaxy/api/histories.py
 lib/galaxy/webapps/galaxy/api/__init__.py
 lib/galaxy/webapps/galaxy/api/jobs.py
+lib/galaxy/webapps/galaxy/api/library_contents.py
 lib/galaxy/webapps/galaxy/api/library_datasets.py
 lib/galaxy/webapps/galaxy/api/requests.py
+lib/galaxy/webapps/galaxy/api/request_types.py
 lib/galaxy/webapps/galaxy/api/roles.py
 lib/galaxy/webapps/galaxy/api/samples.py
+lib/galaxy/webapps/galaxy/api/tool_data.py
 lib/galaxy/webapps/galaxy/api/tools.py
 lib/galaxy/webapps/galaxy/api/tours.py
 lib/galaxy/webapps/galaxy/api/users.py
@@ -116,6 +116,7 @@ lib/galaxy/webapps/galaxy/config_watchers.py
 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
 lib/galaxy/webapps/galaxy/controllers/async.py
 lib/galaxy/webapps/galaxy/controllers/data_manager.py
+lib/galaxy/webapps/galaxy/controllers/dataset.py
 lib/galaxy/webapps/galaxy/controllers/error.py
 lib/galaxy/webapps/galaxy/controllers/external_services.py
 lib/galaxy/webapps/galaxy/controllers/forms.py
@@ -124,21 +125,29 @@ lib/galaxy/webapps/galaxy/controllers/__init__.py
 lib/galaxy/webapps/galaxy/controllers/library_common.py
 lib/galaxy/webapps/galaxy/controllers/mobile.py
 lib/galaxy/webapps/galaxy/controllers/page.py
+lib/galaxy/webapps/galaxy/controllers/requests_admin.py
+lib/galaxy/webapps/galaxy/controllers/requests_common.py
 lib/galaxy/webapps/galaxy/controllers/requests.py
+lib/galaxy/webapps/galaxy/controllers/request_type.py
+lib/galaxy/webapps/galaxy/controllers/root.py
 lib/galaxy/webapps/galaxy/controllers/search.py
 lib/galaxy/webapps/galaxy/controllers/tool_runner.py
 lib/galaxy/webapps/galaxy/controllers/userskeys.py
 lib/galaxy/webapps/galaxy/__init__.py
 lib/galaxy/webapps/__init__.py
+lib/galaxy/webapps/reports/buildapp.py
 lib/galaxy/webapps/reports/config.py
 lib/galaxy/webapps/reports/controllers/__init__.py
 lib/galaxy/webapps/reports/controllers/query.py
+lib/galaxy/webapps/reports/controllers/system.py
 lib/galaxy/webapps/reports/controllers/tools.py
 lib/galaxy/webapps/reports/__init__.py
 lib/galaxy/webapps/tool_shed/api/__init__.py
+lib/galaxy/webapps/tool_shed/buildapp.py
 lib/galaxy/webapps/tool_shed/config.py
 lib/galaxy/webapps/tool_shed/controllers/groups.py
 lib/galaxy/webapps/tool_shed/controllers/__init__.py
+lib/galaxy/webapps/tool_shed/controllers/repository.py
 lib/galaxy/webapps/tool_shed/controllers/user.py
 lib/galaxy/webapps/tool_shed/framework/__init__.py
 lib/galaxy/webapps/tool_shed/framework/middleware/__init__.py

config/plugins/webhooks/demo/tour_generator/helper/__init__.py

@@ -1,5 +1,5 @@
-import os
 import logging
+import os
 from cgi import FieldStorage
 
 from galaxy.util import Params

cron/add_manual_builds.py

@@ -19,7 +19,7 @@ def add_manual_builds(input_file, build_file, chr_dir):
             if line.startswith("#"):
                 continue
             existing_builds.append(line.replace("\n", "").replace("\r", "").split("\t")[0])
-        except:
+        except Exception:
             continue
     build_file_out = open(build_file, 'a')
     for line in open(input_file):
@@ -31,7 +31,7 @@ def add_manual_builds(input_file, build_file, chr_dir):
             name = fields.pop(0)
             try:  # get chrom lens if included in file, otherwise still add build
                 chrs = fields.pop(0).split(",")
-            except:
+            except Exception:
                 chrs = []
             print>>build_file_out, build + "\t" + name + " (" + build + ")"
             if chrs:  # create len file if provided chrom lens
@@ -39,7 +39,7 @@ def add_manual_builds(input_file, build_file, chr_dir):
                 for chr in chrs:
                     print>>chr_len_out, chr.replace("=", "\t")
                 chr_len_out.close()
-        except:
+        except Exception:
             continue
     build_file_out.close()
 

cron/build_chrom_db.py

@@ -60,13 +60,13 @@ if __name__ == "__main__":
                 if line.startswith("#"):
                     continue
                 builds.append(line.split("\t")[0])
-        except:
+        except Exception:
             sys.exit("Bad input file.")
     else:
         try:
             for build in parse_builds.getbuilds("http://genome.cse.ucsc.edu/cgi-bin/das/dsn"):
                 builds.append(build[0])
-        except:
+        except Exception:
             sys.exit("Unable to retrieve builds.")
     for build in builds:
         if build == "?":

cron/parse_builds.py

@@ -15,14 +15,14 @@ import requests
 def getbuilds(url):
     try:
         text = requests.get(url).text
-    except:
+    except Exception:
         print("#Unable to open " + url)
         print("?\tunspecified (?)")
         sys.exit(1)
 
     try:
         tree = ElementTree.fromstring(text)
-    except:
+    except Exception:
         print("#Invalid xml passed back from " + url)
         print("?\tunspecified (?)")
         sys.exit(1)

cron/parse_builds_3_sites.py

@@ -21,13 +21,13 @@ def main():
         builds = []
         try:
             text = requests.get(site).text
-        except:
+        except Exception:
             print("#Unable to connect to " + site)
             continue
 
         try:
             tree = ElementTree.fromstring(text)
-        except:
+        except Exception:
             print("#Invalid xml passed back from " + site)
             continue
         print("#Harvested from", site)

lib/galaxy/auth/providers/ldap_ad.py

@@ -95,7 +95,7 @@ class LDAP(AuthProvider):
 
         try:
             import ldap
-        except:
+        except ImportError:
             log.debug('LDAP authenticate: could not load ldap module')
             return (failure_mode, '', '')
 

lib/galaxy/config.py

@@ -212,7 +212,7 @@ class Configuration(object):
                         self.hours_between_check = 12.0
             else:
                 self.hours_between_check = 12
-        except:
+        except Exception:
             self.hours_between_check = 12
         self.update_integrated_tool_panel = kwargs.get("update_integrated_tool_panel", True)
         self.enable_data_manager_user_view = string_as_bool(kwargs.get("enable_data_manager_user_view", "False"))
@@ -794,7 +794,7 @@ class Configuration(object):
 
         try:
             port = config.getint('server:%s' % self.server_name, 'port')
-        except:
+        except Exception:
             # uWSGI galaxy installations don't use paster and only speak uWSGI not http
             port = None
         return port

lib/galaxy/datatypes/annotation.py

@@ -23,7 +23,7 @@ class SnapHmm(Text):
     def display_peek(self, dataset):
         try:
             return dataset.peek
-        except:
+        except Exception:
             return "SNAP HMM model (%s)" % (nice_size(dataset.get_size()))
 
     def sniff(self, filename):
@@ -54,7 +54,7 @@ class Augustus(CompressedArchive):
     def display_peek(self, dataset):
         try:
             return dataset.peek
-        except:
+        except Exception:
             return "Augustus model (%s)" % (nice_size(dataset.get_size()))
 
     def sniff(self, filename):

lib/galaxy/datatypes/assembly.py

@@ -63,7 +63,7 @@ class Amos(data.Text):
                         if re.match(r'{(RED|CTG|TLE)$', line):
                             isAmos = True
             fh.close()
-        except:
+        except Exception:
             pass
         return isAmos
 
@@ -102,7 +102,7 @@ class Sequences(sequence.Fasta):
                     else:
                         break  # we found a non-empty line, but it's not a fasta header
             fh.close()
-        except:
+        except Exception:
             pass
         return False
 
@@ -138,7 +138,7 @@ class Roadmaps(data.Text):
                 else:
                     break  # we found a non-empty line, but it's not a fasta header
             fh.close()
-        except:
+        except Exception:
             pass
         return False
 
@@ -202,7 +202,7 @@ class Velvet(Html):
                 gen_msg = gen_msg + ' Long Reads'
             if len(gen_msg) > 0:
                 gen_msg = 'Uses: ' + gen_msg
-        except:
+        except Exception:
             log.debug("Velveth could not read Log file in %s" % efp)
         log.debug("Velveth log info  %s" % gen_msg)
         rval = ['<html><head><title>Velvet Galaxy Composite Dataset </title></head><p/>']

lib/galaxy/datatypes/binary.py

@@ -106,7 +106,7 @@ class Ab1(Binary):
     def display_peek(self, dataset):
         try:
             return dataset.peek
-        except:
+        except Exception:
             return "Binary ab1 sequence file (%s)" % (nice_size(dataset.get_size()))
 
 
@@ -125,7 +125,7 @@ class Idat(Binary):
             if header == b'IDAT':
                 return True
             return False
-        except:
+        except Exception:
             return False
 
 
@@ -157,7 +157,7 @@ class Cel(Binary):
             if header == b';\x01\x00\x00':
                 return True
             return False
-        except:
+        except Exception:
             return False
 
 
@@ -183,7 +183,7 @@ class CompressedArchive(Binary):
     def display_peek(self, dataset):
         try:
             return dataset.peek
-        except:
+        except Exception:
             return "Compressed binary file (%s)" % (nice_size(dataset.get_size()))
 
 
@@ -208,7 +208,7 @@ class CompressedZipArchive(CompressedArchive):
     def display_peek(self, dataset):
         try:
             return dataset.peek
-        except:
+        except Exception:
             return "Compressed zip file (%s)" % (nice_size(dataset.get_size()))
 
 
@@ -425,7 +425,7 @@ class Bam(Binary):
             dataset.metadata.read_groups = [read_group['ID'] for read_group in dataset.metadata.bam_header.get('RG', []) if 'ID' in read_group]
             dataset.metadata.sort_order = dataset.metadata.bam_header.get('HD', {}).get('SO', None)
             dataset.metadata.bam_version = dataset.metadata.bam_header.get('HD', {}).get('VN', None)
-        except:
+        except Exception:
             # Per Dan, don't log here because doing so will cause datasets that
             # fail metadata to end in the error state
             pass
@@ -438,7 +438,7 @@ class Bam(Binary):
             if header == b'BAM\1':
                 return True
             return False
-        except:
+        except Exception:
             return False
 
     def set_peek(self, dataset, is_multi_byte=False):
@@ -452,7 +452,7 @@ class Bam(Binary):
     def display_peek(self, dataset):
         try:
             return dataset.peek
-        except:
+        except Exception:
             return "Binary bam alignments file (%s)" % (nice_size(dataset.get_size()))
 
     def to_archive(self, trans, dataset, name=""):
@@ -664,7 +664,7 @@ class CRAM(Binary):
             if header == b"CRAM":
                 return True
             return False
-        except:
+        except Exception:
             return False
 
 
@@ -700,7 +700,7 @@ class Bcf(BaseBcf):
             if header == b'BCF':
                 return True
             return False
-        except:
+        except Exception:
             return False
 
     def set_meta(self, dataset, overwrite=True, **kwd):
@@ -756,7 +756,7 @@ class BcfUncompressed(Bcf):
             if header == b'BCF':
                 return True
             return False
-        except:
+        except Exception:
             return False
 
 
@@ -789,7 +789,7 @@ class H5(Binary):
             if header == self._magic:
                 return True
             return False
-        except:
+        except Exception:
             return False
 
     def set_peek(self, dataset, is_multi_byte=False):
@@ -803,7 +803,7 @@ class H5(Binary):
     def display_peek(self, dataset):
         try:
             return dataset.peek
-        except:
+        except Exception:
             return "Binary HDF5 file (%s)" % (nice_size(dataset.get_size()))
 
 
@@ -886,7 +886,7 @@ class Biom2(H5):
     def display_peek(self, dataset):
         try:
             return dataset.peek
-        except:
+        except Exception:
             return "Biom2 (HDF5) file (%s)" % (nice_size(dataset.get_size()))
 
 
@@ -911,7 +911,7 @@ class Scf(Binary):
     def display_peek(self, dataset):
         try:
             return dataset.peek
-        except:
+        except Exception:
             return "Binary scf sequence file (%s)" % (nice_size(dataset.get_size()))
 
 
@@ -932,7 +932,7 @@ class Sff(Binary):
             if header == b'.sff':
                 return True
             return False
-        except:
+        except Exception:
             return False
 
     def set_peek(self, dataset, is_multi_byte=False):
@@ -946,7 +946,7 @@ class Sff(Binary):
     def display_peek(self, dataset):
         try:
             return dataset.peek
-        except:
+        except Exception:
             return "Binary sff file (%s)" % (nice_size(dataset.get_size()))
 
 
@@ -976,7 +976,7 @@ class BigWig(Binary):
         try:
             magic = self._unpack("I", open(filename, 'rb'))
             return magic[0] == self._magic
-        except:
+        except Exception:
             return False
 
     def set_peek(self, dataset, is_multi_byte=False):
@@ -990,7 +990,7 @@ class BigWig(Binary):
     def display_peek(self, dataset):
         try:
             return dataset.peek
-        except:
+        except Exception:
             return "Binary UCSC %s file (%s)" % (self._name, nice_size(dataset.get_size()))
 
 
@@ -1040,7 +1040,7 @@ class TwoBit(Binary):
     def display_peek(self, dataset):
         try:
             return dataset.peek
-        except:
+        except Exception:
             return "Binary TwoBit format nucleotide file (%s)" % (nice_size(dataset.get_size()))
 
 
@@ -1097,7 +1097,7 @@ class SQlite(Binary):
             if header == b'SQLite format 3\0':
                 return True
             return False
-        except:
+        except Exception:
             return False
 
     def set_peek(self, dataset, is_multi_byte=False):
@@ -1108,7 +1108,7 @@ class SQlite(Binary):
                 for table in dataset.metadata.tables:
                     try:
                         lines.append('%s [%s]' % (table, dataset.metadata.table_row_count[table]))
-                    except:
+                    except Exception:
                         continue
             dataset.peek = '\n'.join(lines)
             dataset.blurb = nice_size(dataset.get_size())
@@ -1119,7 +1119,7 @@ class SQlite(Binary):
     def display_peek(self, dataset):
         try:
             return dataset.peek
-        except:
+        except Exception:
             return "SQLite Database (%s)" % (nice_size(dataset.get_size()))
 
     @dataproviders.decorators.dataprovider_factory('sqlite', dataproviders.dataset.SQliteDataProvider.settings)
@@ -1191,7 +1191,7 @@ class GeminiSQLite(SQlite):
     def display_peek(self, dataset):
         try:
             return dataset.peek
-        except:
+        except Exception:
             return "Gemini SQLite Database, version %s" % (dataset.metadata.gemini_version or 'unknown')
 
 
@@ -1265,7 +1265,7 @@ class IdpDB(SQlite):
     def display_peek(self, dataset):
         try:
             return dataset.peek
-        except:
+        except Exception:
             return "IDPickerDB SQLite file (%s)" % (nice_size(dataset.get_size()))
 
 
@@ -1289,7 +1289,7 @@ class Xlsx(Binary):
                 if "[Content_Types].xml" in tempzip.namelist() and tempzip.read("[Content_Types].xml").find(b'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet.main+xml') != -1:
                     return True
             return False
-        except:
+        except Exception:
             return False
 
 
@@ -1320,7 +1320,7 @@ class ExcelXls(Binary):
     def display_peek(self, dataset):
         try:
             return dataset.peek
-        except:
+        except Exception:
             return "Microsoft Excel XLS file (%s)" % (data.nice_size(dataset.get_size()))
 
 
@@ -1341,7 +1341,7 @@ class Sra(Binary):
                 return True
             else:
                 return False
-        except:
+        except Exception:
             return False
 
     def set_peek(self, dataset, is_multi_byte=False):
@@ -1355,7 +1355,7 @@ class Sra(Binary):
     def display_peek(self, dataset):
         try:
             return dataset.peek
-        except:
+        except Exception:
             return 'Binary sra file (%s)' % (nice_size(dataset.get_size()))
 
 
@@ -1376,7 +1376,7 @@ class RData(Binary):
             header = gzip.open(filename).read(7)
             if header == rdata_header:
                 return True
-        except:
+        except Exception:
             return False
 
 
@@ -1612,7 +1612,7 @@ class PostgresqlArchive(CompressedArchive):
     def display_peek(self, dataset):
         try:
             return dataset.peek
-        except:
+        except Exception:
             return "PostgreSQL Archive (%s)" % (nice_size(dataset.get_size()))
 
 
@@ -1669,7 +1669,7 @@ class Fast5Archive(CompressedArchive):
     def display_peek(self, dataset):
         try:
             return dataset.peek
-        except:
+        except Exception:
             return "FAST5 Archive (%s)" % (nice_size(dataset.get_size()))
 
 
@@ -1771,7 +1771,7 @@ class SearchGuiArchive(CompressedArchive):
     def display_peek(self, dataset):
         try:
             return dataset.peek
-        except:
+        except Exception:
             return "SearchGUI Archive, version %s" % (dataset.metadata.searchgui_version or 'unknown')
 
 
@@ -1795,7 +1795,7 @@ class NetCDF(Binary):
     def display_peek(self, dataset):
         try:
             return dataset.peek
-        except:
+        except Exception:
             return "Binary netCDF file (%s)" % (nice_size(dataset.get_size()))
 
     def sniff(self, filename):
@@ -1805,7 +1805,7 @@ class NetCDF(Binary):
             if header == b'CDF':
                 return True
             return False
-        except:
+        except Exception:
             return False
 
 
@@ -1838,7 +1838,7 @@ class DMND(Binary):
             if header == self._magic:
                 return True
             return False
-        except:
+        except Exception:
             return False
 
 

lib/galaxy/datatypes/constructive_solid_geometry.py

@@ -111,7 +111,7 @@ class Ply(object):
     def display_peek(self, dataset):
         try:
             return dataset.peek
-        except:
+        except Exception:
             return "Ply file (%s)" % (nice_size(dataset.get_size()))
 
 
@@ -301,7 +301,7 @@ class Vtk(object):
                                 dataset.metadata.field_names.append(field_name)
                                 try:
                                     num_components = int(items[-1])
-                                except:
+                                except Exception:
                                     num_components = 1
                                 field_component_indexes = [str(i) for i in range(num_components)]
                                 field_components[field_name] = field_component_indexes
@@ -319,7 +319,7 @@ class Vtk(object):
                                         float(items[0])
                                         # Don't process the cell data.
                                         # 0.0123457 0.197531
-                                    except:
+                                    except Exception:
                                         # Line consists of arrayName numComponents numTuples dataType.
                                         # Example: surface_field1 1 12 double
                                         field_name = items[0]
@@ -438,7 +438,7 @@ class Vtk(object):
     def display_peek(self, dataset):
         try:
             return dataset.peek
-        except:
+        except Exception:
             return "Vtk file (%s)" % (nice_size(dataset.get_size()))
 
 

lib/galaxy/datatypes/converters/bed_to_gff_converter.py

@@ -30,21 +30,21 @@ def __main__():
                 else:
                     try:
                         feature = elems[3]
-                    except:
+                    except Exception:
                         feature = 'feature%d' % (i + 1)
                 start = int(elems[1]) + 1
                 end = int(elems[2])
                 try:
                     score = elems[4]
-                except:
+                except Exception:
                     score = '0'
                 try:
                     strand = elems[5]
-                except:
+                except Exception:
                     strand = '+'
                 try:
                     group = elems[3]
-                except:
+                except Exception:
                     group = 'group%d' % (i + 1)
                 if complete_bed:
                     out.write('%s\tbed2gff\t%s\t%d\t%d\t%s\t%s\t.\t%s %s;\n' % (chrom, feature, start, end, score, strand, feature, group))
@@ -59,7 +59,7 @@ def __main__():
                         exon_start = int(start) + int(block_starts[j])
                         exon_end = exon_start + int(block_sizes[j]) - 1
                         out.write('%s\tbed2gff\texon\t%d\t%d\t%s\t%s\t.\texon %s;\n' % (chrom, exon_start, exon_end, score, strand, group))
-            except:
+            except Exception:
                 skipped_lines += 1
                 if not first_skipped_line:
                     first_skipped_line = i + 1

lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py

@@ -68,10 +68,10 @@ def __main__():
             # peek: ascii or digits?
             val = line.split()[0]
 
+            fastq_integer = True
             try:
                 int(val)
-                fastq_integer = True
-            except:
+            except ValueError:
                 fastq_integer = False
 
             if fastq_integer:  # digits

lib/galaxy/datatypes/converters/gff_to_bed_converter.py

@@ -28,7 +28,7 @@ def __main__():
                 # Replace any spaces in the name with underscores so UCSC will not complain
                 name = elems[2].replace(" ", "_")
                 out.write("%s\t%s\t%s\t%s\t0\t%s\n" % (elems[0], start, elems[4], name, strand))
-            except:
+            except Exception:
                 skipped_lines += 1
                 if not first_skipped_line:
                     first_skipped_line = i + 1

lib/galaxy/datatypes/converters/interval_to_bed_converter.py

@@ -19,23 +19,23 @@ def __main__():
     input_name = sys.argv[2]
     try:
         chromCol = int(sys.argv[3]) - 1
-    except:
+    except Exception:
         stop_err("'%s' is an invalid chrom column, correct the column settings before attempting to convert the data format." % str(sys.argv[3]))
     try:
         startCol = int(sys.argv[4]) - 1
-    except:
+    except Exception:
         stop_err("'%s' is an invalid start column, correct the column settings before attempting to convert the data format." % str(sys.argv[4]))
     try:
         endCol = int(sys.argv[5]) - 1
-    except:
+    except Exception:
         stop_err("'%s' is an invalid end column, correct the column settings before attempting to convert the data format." % str(sys.argv[5]))
     try:
         strandCol = int(sys.argv[6]) - 1
-    except:
+    except Exception:
         strandCol = -1
     try:
         nameCol = int(sys.argv[7]) - 1
-    except:
+    except Exception:
         nameCol = -1
     skipped_lines = 0
     first_skipped_line = 0
@@ -47,12 +47,12 @@ def __main__():
                 name = region.fields[nameCol]
             else:
                 raise IndexError
-        except:
+        except Exception:
             name = "region_%i" % count
         try:
 
             out.write("%s\t%i\t%i\t%s\t%i\t%s\n" % (region.chrom, region.start, region.end, name, 0, region.strand))
-        except:
+        except Exception:
             skipped_lines += 1
             if not first_skipped_line:
                 first_skipped_line = count + 1

lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py

@@ -41,31 +41,31 @@ def __main__():
     input_name = sys.argv[2]
     try:
         chromCol = int(sys.argv[3]) - 1
-    except:
+    except Exception:
         stop_err("'%s' is an invalid chrom column, correct the column settings before attempting to convert the data format." % str(sys.argv[3]))
     try:
         startCol = int(sys.argv[4]) - 1
-    except:
+    except Exception:
         stop_err("'%s' is an invalid start column, correct the column settings before attempting to convert the data format." % str(sys.argv[4]))
     try:
         endCol = int(sys.argv[5]) - 1
-    except:
+    except Exception:
         stop_err("'%s' is an invalid end column, correct the column settings before attempting to convert the data format." % str(sys.argv[5]))
     try:
         strandCol = int(sys.argv[6]) - 1
-    except:
+    except Exception:
         strandCol = -1
     try:
         nameCol = int(sys.argv[7]) - 1
-    except:
+    except Exception:
         nameCol = -1
     try:
         extension = sys.argv[8]
-    except:
+    except IndexError:
         extension = 'interval'  # default extension
     try:
         force_num_columns = int(sys.argv[9])
-    except:
+    except Exception:
         force_num_columns = None
 
     skipped_lines = 0
@@ -116,7 +116,7 @@ def __main__():
                                                     fields2 = fields[11].rstrip(",").split(",")  # remove trailing comma and split on comma
                                                     for field in fields2:
                                                         int(field)
-            except:
+            except Exception:
                 strict_bed = False
                 break
             if force_num_columns is not None and len(fields) != force_num_columns:
@@ -137,14 +137,14 @@ def __main__():
                     name = region.fields[nameCol]
                 else:
                     raise IndexError
-            except:
+            except Exception:
                 name = "region_%i" % count
             try:
                 fields = [str(item) for item in (region.chrom, region.start, region.end, name, 0, region.strand)]
                 if force_num_columns is not None and len(fields) != force_num_columns:
                     fields = force_bed_field_count(fields, count, force_num_columns)
                 out.write("%s\n" % '\t'.join(fields))
-            except:
+            except Exception:
                 skipped_lines += 1
                 if first_skipped_line is None:
                     first_skipped_line = count + 1

lib/galaxy/datatypes/converters/interval_to_coverage.py

@@ -127,7 +127,7 @@ if __name__ == "__main__":
         chr_col_1, start_col_1, end_col_1, strand_col_1 = [int(x) - 1 for x in options.cols1.split(',')]
         chr_col_2, position_col_2, forward_col_2, reverse_col_2 = [int(x) - 1 for x in options.cols2.split(',')]
         in_fname, out_fname = args
-    except:
+    except Exception:
         doc_optparse.exception()
 
     # Sort through a tempfile first

lib/galaxy/datatypes/converters/interval_to_fli.py

@@ -48,7 +48,7 @@ def main():
                 try:
                     float(val)
                     continue
-                except:
+                except ValueError:
                     convert_gff_coords_to_bed(feature)
                     # Value is not a number, so it can be indexed.
                     if val not in name_loc_dict:

lib/galaxy/datatypes/converters/lped_to_fped_converter.py

@@ -41,17 +41,17 @@ def rgConv(inpedfilepath, outhtmlname, outfilepath):
     outfpath = os.path.join(outfilepath, outf)  # where to write the fbat format file to
     try:
         mf = open(inmap, 'r')
-    except:
+    except Exception:
         sys.stderr.write('%s cannot open inmap file %s - do you have permission?\n' % (prog, inmap))
         sys.exit(1)
     try:
         rsl = [x.split()[1] for x in mf]
-    except:
+    except Exception:
         sys.stderr.write('## cannot parse %s' % inmap)
         sys.exit(1)
     try:
         os.makedirs(outfilepath)
-    except:
+    except Exception:
         pass  # already exists
     head = ' '.join(rsl)  # list of rs numbers
     # TODO add anno to rs but fbat will prolly barf?
@@ -64,7 +64,7 @@ def rgConv(inpedfilepath, outhtmlname, outfilepath):
             lrow = row.split()
             try:
                 [int(x) for x in lrow[10:50]]  # look for non numeric codes
-            except:
+            except Exception:
                 dorecode = 1
         if dorecode:
             lrow = row.strip().split()
@@ -94,7 +94,7 @@ def main():
     outfilepath = sys.argv[3]
     try:
         os.makedirs(outfilepath)
-    except:
+    except Exception:
         pass
     rgConv(inpedfilepath, outhtmlname, outfilepath)
     flist = os.listdir(outfilepath)

lib/galaxy/datatypes/converters/lped_to_pbed_converter.py

@@ -42,13 +42,13 @@ def getMissval(inped=''):
     commonmissvals = {'N': 'N', '0': '0', 'n': 'n', '9': '9', '-': '-', '.': '.'}
     try:
         f = open(inped, 'r')
-    except:
+    except Exception:
         return None  # signal no in file
     missval = None
     while missval is None:  # doggedly continue until we solve the mystery
         try:
             l = f.readline()
-        except:
+        except Exception:
             break
         ll = l.split()[6:]  # ignore pedigree stuff
         for c in ll:
@@ -94,7 +94,7 @@ def main():
     outfilepath = sys.argv[3]
     try:
         os.makedirs(outfilepath)
-    except:
+    except Exception:
         pass
     plink = sys.argv[4]
     rgConv(inpedfilepath, outhtmlname, outfilepath, plink)

lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py

@@ -48,7 +48,7 @@ def pruneLD(plinktasks=[], cd='./', vclbase=[]):
             alog += lplog
             alog.append('\n')
             os.unlink(plog)  # no longer needed
-        except:
+        except Exception:
             alog.append('### %s Strange - no std out from plink when running command line\n%s\n' % (timenow(), ' '.join(vcl)))
     return alog
 
@@ -92,7 +92,7 @@ def main():
     outfilepath = sys.argv[6]
     try:
         os.makedirs(outfilepath)
-    except:
+    except Exception:
         pass
     plink = sys.argv[7]
     makeLDreduced(base_name, infpath=inpedfilepath, outfpath=outfilepath, plinke=plink, forcerebuild=False, returnFname=False,

lib/galaxy/datatypes/converters/pbed_to_lped_converter.py

@@ -60,7 +60,7 @@ def main():
     outfilepath = sys.argv[3]
     try:
         os.makedirs(outfilepath)
-    except:
+    except Exception:
         pass
     plink = sys.argv[4]
     rgConv(inpedfilepath, outhtmlname, outfilepath, plink)

lib/galaxy/datatypes/data.py

@@ -179,7 +179,7 @@ class Data(object):
     def set_max_optional_metadata_filesize(self, max_value):
         try:
             max_value = int(max_value)
-        except:
+        except (TypeError, ValueError):
             return
         self.__class__._max_optional_metadata_filesize = max_value
 
@@ -394,7 +394,7 @@ class Data(object):
                 if not mime:
                     try:
                         mime = trans.app.datatypes_registry.get_mimetype_by_extension(".".split(file_path)[-1])
-                    except:
+                    except Exception:
                         mime = "text/plain"
                 self._clean_and_set_mime_type(trans, mime)
                 return self._yield_user_file_content(trans, data, file_path)
@@ -490,7 +490,7 @@ class Data(object):
             info = unicodify(info, 'utf-8')
 
             return info
-        except:
+        except Exception:
             return "info unavailable"
 
     def validate(self, dataset):
@@ -521,7 +521,7 @@ class Data(object):
         self.supported_display_apps = self.supported_display_apps.copy()
         try:
             del self.supported_display_apps[app_id]
-        except:
+        except Exception:
             log.exception('Tried to remove display app %s from datatype %s, but this display app is not declared.', type, self.__class__.__name__)
 
     def clear_display_apps(self):
@@ -551,7 +551,7 @@ class Data(object):
         """Returns primary label for display app"""
         try:
             return self.supported_display_apps[type]['label']
-        except:
+        except Exception:
             return 'unknown'
 
     def as_display_type(self, dataset, type, **kwd):
@@ -559,7 +559,7 @@ class Data(object):
         try:
             if type in self.get_display_types():
                 return getattr(self, self.supported_display_apps[type]['file_function'])(dataset, **kwd)
-        except:
+        except Exception:
             log.exception('Function %s is referred to in datatype %s for displaying as type %s, but is not accessible', self.supported_display_apps[type]['file_function'], self.__class__.__name__, type)
         return "This display type (%s) is not implemented for this datatype (%s)." % (type, dataset.ext)
 
@@ -573,7 +573,7 @@ class Data(object):
         try:
             if app.config.enable_old_display_applications and type in self.get_display_types():
                 return target_frame, getattr(self, self.supported_display_apps[type]['links_function'])(dataset, type, app, base_url, **kwd)
-        except:
+        except Exception:
             log.exception('Function %s is referred to in datatype %s for generating links for type %s, but is not accessible',
                           self.supported_display_apps[type]['links_function'], self.__class__.__name__, type)
         return target_frame, []

lib/galaxy/datatypes/display_applications/application.py

@@ -122,7 +122,7 @@ class DynamicDisplayApplicationBuilder(object):
         id_col = elem.get('id', None)
         try:
             id_col = int(id_col)
-        except:
+        except (TypeError, ValueError):
             if data_table:
                 if id_col is None:
                     id_col = data_table.columns.get('id', None)
@@ -130,14 +130,14 @@ class DynamicDisplayApplicationBuilder(object):
                     id_col = data_table.columns.get('value', None)
                 try:
                     id_col = int(id_col)
-                except:
+                except (TypeError, ValueError):
                     # id is set to a string or None, use column by that name if available
                     id_col = data_table.columns.get(id_col, None)
                     id_col = int(id_col)
         name_col = elem.get('name', None)
         try:
             name_col = int(name_col)
-        except:
+        except (TypeError, ValueError):
             if data_table:
                 if name_col is None:
                     name_col = data_table.columns.get('name', None)

lib/galaxy/datatypes/genetics.py

@@ -126,7 +126,7 @@ class GenomeGraphs(Tabular):
             hasheader = 0
             try:
                 ['%f' % x for x in d[0][1:]]  # first is name - see if starts all numerics
-            except:
+            except Exception:
                 hasheader = 1
             # Generate column header
             out.append('<tr>')
@@ -158,7 +158,7 @@ class GenomeGraphs(Tabular):
                 for j, x in enumerate(ll):
                     try:
                         x = float(x)
-                    except:
+                    except Exception:
                         badvals.append('col%d:%s' % (j + 1, x))
         if len(badvals) > 0:
             errors.append('row %d, %s' % (' '.join(badvals)))
@@ -331,13 +331,13 @@ class Rgenetics(Html):
             return True
         try:
             efp = dataset.extra_files_path
-        except:
+        except Exception:
             if verbose:
                 gal_Log.debug('@@@rgenetics set_meta failed %s - dataset %s has no efp ?' % (sys.exc_info()[0], dataset.name))
             return False
         try:
             flist = os.listdir(efp)
-        except:
+        except Exception:
             if verbose:
                 gal_Log.debug('@@@rgenetics set_meta failed %s - dataset %s has no efp ?' % (sys.exc_info()[0], dataset.name))
             return False
@@ -655,7 +655,7 @@ class RexpBase(Html):
             pp = os.path.join(dataset.extra_files_path, '%s.pheno' % dataset.metadata.base_name)
             try:
                 p = open(pp, 'r').readlines()
-            except:
+            except Exception:
                 p = ['##failed to find %s' % pp, ]
             dataset.peek = ''.join(p[:5])
             dataset.blurb = 'Galaxy Rexpression composite file'
@@ -670,7 +670,7 @@ class RexpBase(Html):
         pp = os.path.join(dataset.extra_files_path, '%s.pheno' % dataset.metadata.base_name)
         try:
             p = open(pp, 'r').readlines()
-        except:
+        except Exception:
             p = ['##failed to find %s' % pp]
         return ''.join(p[:5])
 
@@ -681,7 +681,7 @@ class RexpBase(Html):
         h = '## rexpression get_file_peek: no file found'
         try:
             h = open(filename, 'r').readlines()
-        except:
+        except Exception:
             pass
         return ''.join(h[:5])
 
@@ -713,7 +713,7 @@ class RexpBase(Html):
         Html.set_meta(self, dataset, **kwd)
         try:
             flist = os.listdir(dataset.extra_files_path)
-        except:
+        except Exception:
             if verbose:
                 gal_Log.debug('@@@rexpression set_meta failed - no dataset?')
             return False
@@ -731,7 +731,7 @@ class RexpBase(Html):
         dataset.metadata.pheno_path = pp
         try:
             pf = open(pp, 'r').readlines()  # read the basename.phenodata in the extra_files_path
-        except:
+        except Exception:
             pf = None
         if pf:
             h = pf[0].strip()

lib/galaxy/datatypes/images.py

@@ -225,7 +225,7 @@ class Gmaj(data.Data):
     def display_peek(self, dataset):
         try:
             return dataset.peek
-        except:
+        except Exception:
             return "peek unavailable"
 
     def get_mime(self):
@@ -285,5 +285,5 @@ class Laj(data.Text):
     def display_peek(self, dataset):
         try:
             return dataset.peek
-        except:
+        except Exception:
             return "peek unavailable"

lib/galaxy/datatypes/interval.py

@@ -111,20 +111,20 @@ class Interval(Tabular):
                                         int(elems[1])
                                         if overwrite or not dataset.metadata.element_is_set('startCol'):
                                             dataset.metadata.startCol = 2
-                                    except:
+                                    except Exception:
                                         pass  # Metadata default will be used
                                     try:
                                         int(elems[2])
                                         if overwrite or not dataset.metadata.element_is_set('endCol'):
                                             dataset.metadata.endCol = 3
-                                    except:
+                                    except Exception:
                                         pass  # Metadata default will be used
                                     # we no longer want to guess that this column is the 'name', name must now be set manually for interval files
                                     # we will still guess at the strand, as we can make a more educated guess
                                     # if len( elems ) > 3:
                                     #    try:
                                     #        int( elems[3] )
-                                    #    except:
+                                    #    except Exception:
                                     #        if overwrite or not dataset.metadata.element_is_set( 'nameCol' ):
                                     #            dataset.metadata.nameCol = 4
                                     if len(elems) < 6 or elems[5] not in data.valid_strand:
@@ -149,7 +149,7 @@ class Interval(Tabular):
                 and dataset.metadata.chromCol \
                 and dataset.metadata.startCol \
                 and dataset.metadata.endCol
-        except:
+        except Exception:
             return False
 
     def get_estimated_display_viewport(self, dataset, chrom_col=None, start_col=None, end_col=None):
@@ -331,10 +331,10 @@ class Interval(Tabular):
                         # respectively ( for 0 based columns )
                         int(hdr[1])
                         int(hdr[2])
-                    except:
+                    except Exception:
                         return False
             return True
-        except:
+        except Exception:
             return False
 
     def get_track_resolution(self, dataset, start, end):
@@ -458,14 +458,14 @@ class Bed(Interval):
                                         fields2 = fields[11].rstrip(",").split(",")  # remove trailing comma and split on comma
                                         for field in fields2:
                                             int(field)
-            except:
+            except Exception:
                 return Interval.as_ucsc_display_file(self, dataset)
             # only check first line for proper form
             break
 
         try:
             return open(dataset.file_name)
-        except:
+        except Exception:
             return "This item contains no content"
 
     def sniff(self, filename):
@@ -510,7 +510,7 @@ class Bed(Interval):
                     try:
                         int(hdr[1])
                         int(hdr[2])
-                    except:
+                    except Exception:
                         return False
                     if len(hdr) > 4:
                         # hdr[3] is a string, 'name', which defines the name of the BED line - difficult to test for this.
@@ -518,7 +518,7 @@ class Bed(Interval):
                         try:
                             if int(hdr[4]) < 0 or int(hdr[4]) > 1000:
                                 return False
-                        except:
+                        except Exception:
                             return False
                     if len(hdr) > 5:
                         # hdr[5] is strand
@@ -528,48 +528,48 @@ class Bed(Interval):
                         # hdr[6] is thickStart, the starting position at which the feature is drawn thickly.
                         try:
                             int(hdr[6])
-                        except:
+                        except Exception:
                             return False
                     if len(hdr) > 7:
                         # hdr[7] is thickEnd, the ending position at which the feature is drawn thickly
                         try:
                             int(hdr[7])
-                        except:
+                        except Exception:
                             return False
                     if len(hdr) > 8:
                         # hdr[8] is itemRgb, an RGB value of the form R,G,B (e.g. 255,0,0).  However, this could also be an int (e.g., 0)
                         try:
                             int(hdr[8])
-                        except:
+                        except Exception:
                             try:
                                 hdr[8].split(',')
-                            except:
+                            except Exception:
                                 return False
                     if len(hdr) > 9:
                         # hdr[9] is blockCount, the number of blocks (exons) in the BED line.
                         try:
                             block_count = int(hdr[9])
-                        except:
+                        except Exception:
                             return False
                     if len(hdr) > 10:
                         # hdr[10] is blockSizes - A comma-separated list of the block sizes.
                         # Sometimes the blosck_sizes and block_starts lists end in extra commas
                         try:
                             block_sizes = hdr[10].rstrip(',').split(',')
-                        except:
+                        except Exception:
                             return False
                     if len(hdr) > 11:
                         # hdr[11] is blockStarts - A comma-separated list of block starts.
                         try:
                             block_starts = hdr[11].rstrip(',').split(',')
-                        except:
+                        except Exception:
                             return False
                         if len(block_sizes) != block_count or len(block_starts) != block_count:
                             return False
                 else:
                     return False
             return True
-        except:
+        except Exception:
             return False
 
 
@@ -678,15 +678,15 @@ class Gff(Tabular, _RemoteCallMixin):
                                 # Try int.
                                 int(value)
                                 value_type = "int"
-                            except:
+                            except ValueError:
                                 try:
                                     # Try float.
                                     float(value)
                                     value_type = "float"
-                                except:
+                                except ValueError:
                                     pass
                             attribute_types[name] = value_type
-                    except:
+                    except Exception:
                         pass
                 if i + 1 == num_lines:
                     break
@@ -708,7 +708,7 @@ class Gff(Tabular, _RemoteCallMixin):
                         int(elems[3])
                         int(elems[4])
                         break
-                    except:
+                    except Exception:
                         pass
         Tabular.set_meta(self, dataset, overwrite=overwrite, skip=i)
 
@@ -771,7 +771,7 @@ class Gff(Tabular, _RemoteCallMixin):
                                     # Make sure we have not spanned chromosomes
                                     start = min(start, int(elems[3]))
                                     stop = max(stop, int(elems[4]))
-                    except:
+                    except Exception:
                         # most likely start/stop is not an int or not enough fields
                         pass
                     # make sure we are at the next new line
@@ -848,19 +848,19 @@ class Gff(Tabular, _RemoteCallMixin):
                     try:
                         int(hdr[3])
                         int(hdr[4])
-                    except:
+                    except Exception:
                         return False
                     if hdr[5] != '.':
                         try:
                             float(hdr[5])
-                        except:
+                        except Exception:
                             return False
                     if hdr[6] not in data.valid_strand:
                         return False
                     if hdr[7] not in self.valid_gff_frame:
                         return False
             return True
-        except:
+        except Exception:
             return False
 
     # ------------- Dataproviders
@@ -919,13 +919,13 @@ class Gff3(Gff):
                     try:
                         start = int(elems[3])
                         valid_start = True
-                    except:
+                    except Exception:
                         if elems[3] == '.':
                             valid_start = True
                     try:
                         end = int(elems[4])
                         valid_end = True
-                    except:
+                    except Exception:
                         if elems[4] == '.':
                             valid_end = True
                     strand = elems[6]
@@ -982,18 +982,18 @@ class Gff3(Gff):
                         return False
                     try:
                         int(hdr[3])
-                    except:
+                    except Exception:
                         if hdr[3] != '.':
                             return False
                     try:
                         int(hdr[4])
-                    except:
+                    except Exception:
                         if hdr[4] != '.':
                             return False
                     if hdr[5] != '.':
                         try:
                             float(hdr[5])
-                        except:
+                        except Exception:
                             return False
                     if hdr[6] not in self.valid_gff3_strand:
                         return False
@@ -1001,7 +1001,7 @@ class Gff3(Gff):
                         return False
                     parse_gff3_attributes(hdr[8])
             return True
-        except:
+        except Exception:
             return False
 
 
@@ -1055,12 +1055,12 @@ class Gtf(Gff):
                     try:
                         int(hdr[3])
                         int(hdr[4])
-                    except:
+                    except Exception:
                         return False
                     if hdr[5] != '.':
                         try:
                             float(hdr[5])
-                        except:
+                        except Exception:
                             return False
                     if hdr[6] not in data.valid_strand:
                         return False
@@ -1077,7 +1077,7 @@ class Gtf(Gff):
                     else:
                         return False
             return True
-        except:
+        except Exception:
             return False
 
 
@@ -1140,7 +1140,7 @@ class Wiggle(Tabular, _RemoteCallMixin):
                                     start = min(int(fields[0]), start)
                                     end = max(end, int(fields[0]) + span)
                                 viewport_feature_count -= 1
-                    except:
+                    except Exception:
                         pass
                     # make sure we are at the next new line
                     readline_count = VIEWPORT_MAX_READS_PER_LINE
@@ -1199,7 +1199,7 @@ class Wiggle(Tabular, _RemoteCallMixin):
                 try:
                     float(elems[0])  # "Wiggle track data values can be integer or real, positive or negative values"
                     break
-                except:
+                except Exception:
                     do_break = False
                     for col_startswith in data.col1_startswith:
                         if elems[0].lower().startswith(col_startswith):
@@ -1244,7 +1244,7 @@ class Wiggle(Tabular, _RemoteCallMixin):
                 if len(hdr) > 1 and hdr[0] == 'track' and hdr[1].startswith('type=wiggle'):
                     return True
             return False
-        except:
+        except Exception:
             return False
 
     def get_track_resolution(self, dataset, start, end):
@@ -1394,7 +1394,7 @@ class CustomTrack (Tabular):
                             return False
                     else:
                         return False
-                except:
+                except Exception:
                     return False
             else:
                 try:
@@ -1404,9 +1404,9 @@ class CustomTrack (Tabular):
                         try:
                             int(hdr[1])
                             int(hdr[2])
-                        except:
+                        except Exception:
                             return False
-                except:
+                except Exception:
                     return False
         return True
 
@@ -1539,7 +1539,7 @@ class ScIdx(Tabular):
                 count += 1
             if count < 100 and count > 0:
                 return True
-        except:
+        except Exception:
             return False
         finally:
             fh.close()

lib/galaxy/datatypes/molecules.py

@@ -33,7 +33,7 @@ def count_special_lines(word, filename, invert=False):
         cmd.extend([word, filename])
         out = subprocess.Popen(cmd, stdout=subprocess.PIPE)
         return int(out.communicate()[0].split()[0])
-    except:
+    except Exception:
         pass
     return 0
 
@@ -48,7 +48,7 @@ def count_lines(filename, non_empty=False):
         else:
             out = subprocess.Popen(['wc', '-l', filename], stdout=subprocess.PIPE)
         return int(out.communicate()[0].split()[0])
-    except:
+    except Exception:
         pass
     return 0
 
@@ -427,7 +427,7 @@ class OBFS(Binary):
         """Create HTML content, used for displaying peek."""
         try:
             return dataset.peek
-        except:
+        except Exception:
             return "OpenBabel Fastsearch Index"
 
     def display_data(self, trans, data, preview=False, filename=None,
@@ -702,7 +702,7 @@ class SMILES(Tabular):
                     # if we have atoms, we have a molecule
                     if not len(pybel.readstring('smi', smiles).atoms) > 0:
                         return False
-                except:
+                except Exception:
                     # if convert fails its not a smiles string
                     return False
             return True

lib/galaxy/datatypes/msa.py

@@ -26,7 +26,7 @@ class Hmmer(Text):
     def display_peek(self, dataset):
         try:
             return dataset.peek
-        except:
+        except Exception:
             return "HMMER database (%s)" % (nice_size(dataset.get_size()))
 
     @abc.abstractmethod
@@ -77,7 +77,7 @@ class HmmerPress(Binary):
         """Create HTML content, used for displaying peek."""
         try:
             return dataset.peek
-        except:
+        except Exception:
             return "HMMER3 database (multiple files)"
 
     def __init__(self, **kwd):

lib/galaxy/datatypes/ngsindex.py

@@ -55,7 +55,7 @@ class BowtieIndex(Html):
     def display_peek(self, dataset):
         try:
             return dataset.peek
-        except:
+        except Exception:
             return "Bowtie index file"
 
 

lib/galaxy/datatypes/plant_tribes.py

@@ -18,7 +18,7 @@ class Smat(Text):
     def display_peek(self, dataset):
         try:
             return dataset.peek
-        except:
+        except Exception:
             return "ESTScan scores matrices (%s)" % (nice_size(dataset.get_size()))
 
     def set_peek(self, dataset, is_multi_byte=False):
@@ -98,7 +98,7 @@ class PlantTribesKsComponents(Tabular):
     def display_peek(self, dataset):
         try:
             return dataset.peek
-        except:
+        except Exception:
             return "Significant components in the Ks distribution (%s)" % (nice_size(dataset.get_size()))
 
     def set_meta(self, dataset, **kwd):

lib/galaxy/datatypes/proteomics.py

@@ -285,7 +285,7 @@ class ThermoRAW(Binary):
             if header.find(finnigan) != -1:
                 return True
             return False
-        except:
+        except Exception:
             return False
 
     def set_peek(self, dataset, is_multi_byte=False):
@@ -299,7 +299,7 @@ class ThermoRAW(Binary):
     def display_peek(self, dataset):
         try:
             return dataset.peek
-        except:
+        except Exception:
             return "Thermo Finnigan RAW file (%s)" % (nice_size(dataset.get_size()))
 
 

lib/galaxy/datatypes/qualityscore.py

@@ -56,7 +56,7 @@ class QualityScoreSOLiD (QualityScore):
                             if not(readlen):
                                 readlen = len(line.split())
                             assert len(line.split()) == readlen  # SOLiD reads should be of the same length
-                        except:
+                        except Exception:
                             break
                         goodblock += 1
                         if goodblock > 10:
@@ -64,7 +64,7 @@ class QualityScoreSOLiD (QualityScore):
                     else:
                         break  # we found a non-empty line, but it's not a header
             fh.close()
-        except:
+        except Exception:
             pass
         return False
 
@@ -106,13 +106,13 @@ class QualityScore454 (QualityScore):
                             break
                         try:
                             [int(x) for x in line.split()]
-                        except:
+                        except Exception:
                             break
                         return True
                     else:
                         break  # we found a non-empty line, but it's not a header
             fh.close()
-        except:
+        except Exception:
             pass
         return False
 

lib/galaxy/datatypes/sequence.py

@@ -81,7 +81,7 @@ class SequenceSplitLocations(data.Text):
                     if 'start' not in section or 'end' not in section or 'sequences' not in section:
                         return False
                 return True
-            except:
+            except Exception:
                 pass
         return False
 
@@ -376,7 +376,7 @@ class Fasta(Sequence):
                     else:
                         break  # we found a non-empty line, but it's not a fasta header
             fh.close()
-        except:
+        except Exception:
             pass
         return False
 
@@ -543,7 +543,7 @@ class csFasta(Sequence):
                     else:
                         break  # we found a non-empty line, but it's not a header
             fh.close()
-        except:
+        except Exception:
             pass
         return False
 
@@ -634,7 +634,7 @@ class BaseFastq (Sequence):
                     return False
                 return True
             return False
-        except:
+        except Exception:
             return False
 
     def display_data(self, trans, dataset, preview=False, filename=None, to_ext=None, **kwd):
@@ -930,7 +930,7 @@ class Maf(Alignment):
                 return True
             else:
                 return False
-        except:
+        except Exception:
             return False
 
 
@@ -968,7 +968,7 @@ class MafCustomTrack(data.Text):
                 dataset.metadata.vp_chromosome = chrom
                 dataset.metadata.vp_start = forward_strand_start
                 dataset.metadata.vp_end = forward_strand_end
-        except:
+        except Exception:
             pass
 
 
@@ -1019,7 +1019,7 @@ class Axt(data.Text):
                     return False
                 try:
                     map(int, [hdr[0], hdr[2], hdr[3], hdr[5], hdr[6], hdr[8]])
-                except:
+                except Exception:
                     return False
                 if hdr[7] not in data.valid_strand:
                     return False
@@ -1060,7 +1060,7 @@ class Lav(data.Text):
                 return True
             else:
                 return False
-        except:
+        except Exception:
             return False
 
 
@@ -1205,7 +1205,7 @@ class Genbank(data.Text):
         try:
             with open(filename, 'r') as handle:
                 return 'LOCUS ' == handle.read(6)
-        except:
+        except Exception:
             pass
 
         return False
@@ -1236,7 +1236,7 @@ class MemePsp(Sequence):
             for item in l.split():
                 try:
                     float(item)
-                except:
+                except ValueError:
                     return False
             return True
         try:
@@ -1269,7 +1269,7 @@ class MemePsp(Sequence):
                         # We found a non-empty line,
                         # but it's not a psp id width.
                         return False
-        except:
+        except Exception:
             return False
         # We've reached EOF in less than 100 lines.
         return True

lib/galaxy/datatypes/sniff.py

@@ -54,7 +54,7 @@ def stream_to_open_named_file(stream, fd, filename, source_encoding=None, source
     is_multi_byte = False
     try:
         codecs.lookup(target_encoding)
-    except:
+    except Exception:
         target_encoding = util.DEFAULT_ENCODING  # utf-8
     if not source_encoding:
         source_encoding = util.DEFAULT_ENCODING  # sys.getdefaultencoding() would mimic old behavior (defaults to ascii)
@@ -70,7 +70,7 @@ def stream_to_open_named_file(stream, fd, filename, source_encoding=None, source
                 try:
                     if text_type(chunk[:2]) == text_type(util.gzip_magic):
                         is_compressed = True
-                except:
+                except Exception:
                     pass
             if not is_compressed:
                 # See if we have a multi-byte character file
@@ -408,7 +408,7 @@ def guess_ext(fname, sniff_order, is_multi_byte=False):
             if datatype.sniff(fname):
                 file_ext = datatype.file_ext
                 break
-        except:
+        except Exception:
             pass
     # Ugly hack for tsv vs tabular sniffing, we want to prefer tabular
     # to tsv but it doesn't have a sniffer - is TSV was sniffed just check

lib/galaxy/datatypes/tabular.py

@@ -62,7 +62,7 @@ class TabularData(data.Text):
                 and dataset.state == dataset.states.OK \
                 and dataset.metadata.columns > 0 \
                 and dataset.metadata.data_lines != 0
-        except:
+        except Exception:
             return False
 
     def get_chunk(self, trans, dataset, offset=0, ck_size=None):
@@ -156,7 +156,7 @@ class TabularData(data.Text):
                 if isinstance(spec.param, metadata.ColumnParameter):
                     try:
                         i = int(getattr(dataset.metadata, name)) - 1
-                    except:
+                    except Exception:
                         i = -1
                     if 0 <= i < columns and column_headers[i] is None:
                         column_headers[i] = column_parameter_alias.get(name, name)
@@ -294,14 +294,14 @@ class Tabular(TabularData):
             try:
                 int(column_text)
                 return True
-            except:
+            except ValueError:
                 return False
 
         def is_float(column_text):
             try:
                 float(column_text)
                 return True
-            except:
+            except ValueError:
                 if column_text.strip().lower() == 'na':
                     return True  # na is special cased to be a float
                 return False
@@ -488,7 +488,7 @@ class Sam(Tabular):
             fh.close()
             if count < 5 and count > 0:
                 return True
-        except:
+        except Exception:
             pass
         return False
 
@@ -650,10 +650,10 @@ class Pileup(Tabular):
                         chrom = int(hdr[1])
                         assert chrom >= 0
                         assert hdr[2] in ['A', 'C', 'G', 'T', 'N', 'a', 'c', 'g', 't', 'n']
-                    except:
+                    except Exception:
                         return False
             return True
-        except:
+        except Exception:
             return False
 
     # Dataproviders
@@ -919,14 +919,14 @@ class BaseCSV(TabularData):
         try:
             int(column_text)
             return True
-        except:
+        except ValueError:
             return False
 
     def is_float(self, column_text):
         try:
             float(column_text)
             return True
-        except:
+        except ValueError:
             if column_text.strip().lower() == 'na':
                 return True  # na is special cased to be a float
             return False
@@ -990,7 +990,7 @@ class BaseCSV(TabularData):
             if not csv.Sniffer().has_header(open(filename, 'r').read(self.big_peek_size)):
                 return False
             return True
-        except:
+        except Exception:
             # Not readable by Python's csv using this dialect
             return False
 
@@ -1137,7 +1137,7 @@ class ConnectivityTable(Tabular):
                                     j += 1
                         i += 1
             return False
-        except:
+        except Exception:
             return False
 
     def get_chunk(self, trans, dataset, chunk):

lib/galaxy/datatypes/text.py

@@ -55,7 +55,7 @@ class Html(Text):
                 if hdr and hdr[0].lower().find('<html>') >= 0:
                     return True
             return False
-        except:
+        except Exception:
             return True
 
 
@@ -104,7 +104,7 @@ class Json(Text):
     def display_peek(self, dataset):
         try:
             return dataset.peek
-        except:
+        except Exception:
             return "JSON file (%s)" % (nice_size(dataset.get_size()))
 
 
@@ -130,7 +130,7 @@ class Ipynb(Json):
                     return True
                 else:
                     return False
-            except:
+            except Exception:
                 return False
 
     def display_data(self, trans, dataset, preview=False, filename=None, to_ext=None, **kwd):
@@ -420,7 +420,7 @@ class SnpEffDb(Text):
             if m:
                 snpeff_version = m.groups()[0] + m.groups()[1]
             fh.close()
-        except:
+        except Exception:
             pass
         return snpeff_version
 
@@ -465,7 +465,7 @@ class SnpEffDb(Text):
                         fh.write("annotations: %s\n" % ','.join(annotations))
                     if regulations:
                         fh.write("regulations: %s\n" % ','.join(regulations))
-            except:
+            except Exception:
                 pass
 
 

lib/galaxy/datatypes/tracks.py

@@ -78,7 +78,7 @@ class UCSCTrackHub(Html):
     def display_peek(self, dataset):
         try:
             return dataset.peek
-        except:
+        except Exception:
             return "Track Hub structure: Visualization in UCSC Track Hub"
 
     def sniff(self, filename):

lib/galaxy/datatypes/util/generic_util.py

@@ -14,6 +14,6 @@ def count_special_lines(word, filename, invert=False):
         cmd.extend([word, filename])
         out = subprocess.Popen(cmd, stdout=subprocess.PIPE)
         return int(out.communicate()[0].split()[0])
-    except:
+    except Exception:
         pass
     return 0

lib/galaxy/dependencies/__init__.py

@@ -63,7 +63,7 @@ class ConditionalDependencies(object):
         try:
             name = name.replace('-', '_').replace('.', '_')
             return getattr(self, 'check_' + name)()
-        except:
+        except Exception:
             return False
 
     def check_psycopg2(self):

lib/galaxy/jobs/__init__.py

@@ -1166,7 +1166,7 @@ class JobWrapper(object, HasResourceParameters):
         # TODO: After failing here, consider returning from the function.
         try:
             self.reclaim_ownership()
-        except:
+        except Exception:
             log.exception('(%s) Failed to change ownership of %s, failing' % (job.id, self.working_directory))
             return self.fail(job.info, stdout=stdout, stderr=stderr, exit_code=tool_exit_code)
 
@@ -1316,7 +1316,7 @@ class JobWrapper(object, HasResourceParameters):
                             dataset.set_peek(line_count=context['line_count'], is_multi_byte=True)
                         else:
                             dataset.set_peek(line_count=context['line_count'])
-                    except:
+                    except Exception:
                         if (not dataset.datatype.composite_type and dataset.dataset.is_multi_byte()) or self.tool.is_multi_byte:
                             dataset.set_peek(is_multi_byte=True)
                         else:
@@ -1467,7 +1467,7 @@ class JobWrapper(object, HasResourceParameters):
             galaxy.tools.imp_exp.JobImportHistoryArchiveWrapper(self.app, self.job_id).cleanup_after_job()
             if delete_files:
                 self.app.object_store.delete(self.get_job(), base_dir='job_work', entire_dir=True, dir_only=True, obj_dir=True)
-        except:
+        except Exception:
             log.exception("Unable to cleanup job %d", self.job_id)
 
     def _collect_extra_files(self, dataset, job_working_directory):
@@ -1765,7 +1765,7 @@ class JobWrapper(object, HasResourceParameters):
         if external_chown_script and job.user is not None:
             try:
                 self._change_ownership(self.user_system_pwent[0], str(self.user_system_pwent[3]))
-            except:
+            except Exception:
                 log.exception('(%s) Failed to change ownership of %s, making world-writable instead' % (job.id, self.working_directory))
                 os.chmod(self.working_directory, 0o777)
 

lib/galaxy/jobs/deferred/__init__.py

@@ -39,7 +39,7 @@ class DeferredJobQueue(object):
                 module_name = 'galaxy.jobs.deferred.' + name
                 try:
                     module = __import__(module_name)
-                except:
+                except ImportError:
                     log.exception('Deferred job plugin appears to exist but is not loadable: %s', module_name)
                     continue
                 for comp in module_name.split(".")[1:]:
@@ -76,7 +76,7 @@ class DeferredJobQueue(object):
         while self.running:
             try:
                 self.__monitor_step()
-            except:
+            except Exception:
                 log.exception('Exception in monitor_step')
             self.sleeper.sleep(1)
         log.info('job queue stopped')
@@ -100,7 +100,7 @@ class DeferredJobQueue(object):
                 # Recovered jobs are passed in by ID
                 assert type(job) is int
                 job = self.sa_session.query(model.DeferredJob).get(job)
-            except:
+            except Exception:
                 pass
             if job.is_check_time:
                 try:

lib/galaxy/jobs/handler.py

@@ -1,20 +1,33 @@
 """
 Galaxy job handler, prepares, runs, tracks, and finishes Galaxy jobs
 """
-
 import datetime
-import os
-import time
 import logging
+import os
 import threading
-from Queue import Queue, Empty
+import time
+from Queue import (
+    Empty,
+    Queue
+)
 
-from sqlalchemy.sql.expression import and_, or_, select, func, true, null
+from sqlalchemy.sql.expression import (
+    and_,
+    func,
+    null,
+    or_,
+    select,
+    true
+)
 
 from galaxy import model
-from galaxy.util.sleeper import Sleeper
-from galaxy.jobs import JobWrapper, TaskWrapper, JobDestination
+from galaxy.jobs import (
+    JobDestination,
+    JobWrapper,
+    TaskWrapper
+)
 from galaxy.jobs.mapper import JobNotReadyException
+from galaxy.util.sleeper import Sleeper
 
 log = logging.getLogger(__name__)
 
@@ -196,7 +209,7 @@ class JobHandlerQueue(object):
                 # to the sleep.
                 if not self.app.job_manager.job_lock:
                     self.__monitor_step()
-            except:
+            except Exception:
                 log.exception("Exception in monitor_step")
             # Sleep
             self.sleeper.sleep(1)
@@ -703,7 +716,7 @@ class JobHandlerStopQueue(object):
         while self.running:
             try:
                 self.monitor_step()
-            except:
+            except Exception:
                 log.exception("Exception in monitor_step")
             # Sleep
             self.sleeper.sleep(1)

lib/galaxy/jobs/output_checker.py

@@ -1,9 +1,9 @@
 import re
-from .error_level import StdioErrorLevel
 import traceback
-
 from logging import getLogger
 
+from .error_level import StdioErrorLevel
+
 log = getLogger(__name__)
 
 
@@ -126,7 +126,7 @@ def check_output(tool, stdout, stderr, tool_exit_code, job):
                 success = True
 
     # On any exception, return True.
-    except:
+    except Exception:
         tb = traceback.format_exc()
         log.warning("Tool check encountered unexpected exception; " +
                     "assuming tool was successful: " + tb)

lib/galaxy/jobs/runners/__init__.py

@@ -1,28 +1,34 @@
 """
 Base classes for job runner plugins.
 """
-
-import os
-import time
-import string
-import logging
 import datetime
-import threading
+import logging
+import os
+import string
 import subprocess
-
-from Queue import Queue, Empty
+import threading
+import time
+from Queue import (
+    Empty,
+    Queue
+)
 
 import galaxy.jobs
-from galaxy.jobs.command_factory import build_command
 from galaxy import model
-from galaxy.util import DATABASE_MAX_STRING_SIZE, shrink_stream_by_size
-from galaxy.util import in_directory
-from galaxy.util import ParamsWithSpecs
-from galaxy.util import ExecutionTimer
-from galaxy.util.bunch import Bunch
-from galaxy.jobs.runners.util.job_script import write_script
-from galaxy.jobs.runners.util.job_script import job_script
+from galaxy.jobs.command_factory import build_command
 from galaxy.jobs.runners.util.env import env_to_statement
+from galaxy.jobs.runners.util.job_script import (
+    job_script,
+    write_script
+)
+from galaxy.util import (
+    DATABASE_MAX_STRING_SIZE,
+    ExecutionTimer,
+    in_directory,
+    ParamsWithSpecs,
+    shrink_stream_by_size
+)
+from galaxy.util.bunch import Bunch
 
 from .state_handler_factory import build_state_handlers
 
@@ -94,15 +100,15 @@ class BaseJobRunner(object):
                 else:
                     # arg should be a JobWrapper/TaskWrapper
                     job_id = arg.get_id_tag()
-            except:
+            except Exception:
                 job_id = 'unknown'
             try:
                 name = method.__name__
-            except:
+            except Exception:
                 name = 'unknown'
             try:
                 method(arg)
-            except:
+            except Exception:
                 log.exception("(%s) Unhandled exception calling %s" % (job_id, name))
 
     # Causes a runner's `queue_job` method to be called from a worker thread
@@ -366,7 +372,7 @@ class BaseJobRunner(object):
                 handler(self.app, self, job_state)
                 if job_state.runner_state_handled:
                     break
-        except:
+        except Exception:
             log.exception('Caught exception in runner state handler')
 
     def fail_job(self, job_state, exception=False):
@@ -610,14 +616,14 @@ class AsynchronousJobRunner(BaseJobRunner):
         try:
             # This should be an 8-bit exit code, but read ahead anyway:
             exit_code_str = open(job_state.exit_code_file, "r").read(32)
-        except:
+        except Exception:
             # By default, the exit code is 0, which typically indicates success.
             exit_code_str = "0"
 
         try:
             # Decode the exit code. If it's bogus, then just use 0.
             exit_code = int(exit_code_str)
-        except:
+        except ValueError:
             log.warning("(%s/%s) Exit code '%s' invalid. Using 0." % (galaxy_id_tag, external_job_id, exit_code_str))
             exit_code = 0
 
@@ -628,7 +634,7 @@ class AsynchronousJobRunner(BaseJobRunner):
 
         try:
             job_state.job_wrapper.finish(stdout, stderr, exit_code)
-        except:
+        except Exception:
             log.exception("(%s/%s) Job wrapper finish method failed" % (galaxy_id_tag, external_job_id))
             job_state.job_wrapper.fail("Unable to finish job", exception=True)
 

lib/galaxy/jobs/runners/cli.py

@@ -82,7 +82,7 @@ class ShellJobRunner(AsynchronousJobRunner):
 
         try:
             self.write_executable_script(ajs.job_file, script)
-        except:
+        except Exception:
             log.exception("(%s) failure writing job script" % galaxy_id_tag)
             job_wrapper.fail("failure preparing job script", exception=True)
             return

lib/galaxy/jobs/runners/condor.py

@@ -105,7 +105,7 @@ class CondorJobRunner(AsynchronousJobRunner):
         )
         try:
             self.write_executable_script(executable, script)
-        except:
+        except Exception:
             job_wrapper.fail("failure preparing job script", exception=True)
             log.exception("(%s) failure preparing job script" % galaxy_id_tag)
             return

lib/galaxy/jobs/runners/drmaa.py

@@ -110,7 +110,7 @@ class DRMAAJobRunner(AsynchronousJobRunner):
         """Get any native DRM arguments specified by the site configuration"""
         try:
             return url.split('/')[2] or None
-        except:
+        except Exception:
             return None
 
     def queue_job(self, job_wrapper):
@@ -151,7 +151,7 @@ class DRMAAJobRunner(AsynchronousJobRunner):
         script = self.get_job_file(job_wrapper, exit_code_path=ajs.exit_code_file)
         try:
             self.write_executable_script(ajs.job_file, script)
-        except:
+        except Exception:
             job_wrapper.fail("failure preparing job script", exception=True)
             log.exception("(%s) failure writing job script" % galaxy_id_tag)
             return
@@ -183,7 +183,7 @@ class DRMAAJobRunner(AsynchronousJobRunner):
                     log.warning('(%s) drmaa.Session.runJob() failed, will retry: %s', galaxy_id_tag, e)
                     fail_msg = "Unable to run this job due to a cluster error, please retry it later"
                     time.sleep(5)
-                except:
+                except Exception:
                     log.exception('(%s) drmaa.Session.runJob() failed unconditionally', galaxy_id_tag)
                     trynum = 5
             else:

lib/galaxy/jobs/runners/godocker.py

@@ -336,16 +336,16 @@ class GodockerJobRunner(AsynchronousJobRunner):
             job_destination = job_wrapper.job_destination
             try:
                 docker_cpu = int(job_destination.params["docker_cpu"])
-            except:
+            except Exception:
                 docker_cpu = 1
             try:
                 docker_ram = int(job_destination.params["docker_memory"])
-            except:
+            except Exception:
                 docker_ram = 1
             try:
                 docker_image = self._find_container(job_wrapper).container_id
                 log.debug("GoDocker runner using container %s.", docker_image)
-            except:
+            except Exception:
                 log.error("Unable to find docker_image for job %s, failing." % job_wrapper.job_id)
                 return False
 
@@ -367,7 +367,7 @@ class GodockerJobRunner(AsynchronousJobRunner):
                 for i in volume:
                     temp = dict({"name": i})
                     volumes.append(temp)
-            except:
+            except Exception:
                 log.debug("godocker_volume not set, using default.")
 
             dt = datetime.now()
@@ -379,7 +379,7 @@ class GodockerJobRunner(AsynchronousJobRunner):
                     command = "#!/bin/bash\n" + "cd " + job_wrapper.working_directory + "\n" + venv + "\n" + job_wrapper.runner_command_line
                 else:
                     command = "#!/bin/bash\n" + "cd " + job_wrapper.working_directory + "\n" + job_wrapper.runner_command_line
-            except:
+            except Exception:
                 command = "#!/bin/bash\n" + "cd " + job_wrapper.working_directory + "\n" + job_wrapper.runner_command_line
 
             # GoDocker Job model schema

lib/galaxy/jobs/runners/kubernetes.py

@@ -131,7 +131,7 @@ class KubernetesJobRunner(AsynchronousJobRunner):
         if "k8s_supplemental_group_id" in self.runner_params:
             try:
                 return int(self.runner_params["k8s_supplemental_group_id"])
-            except:
+            except Exception:
                 log.warning("Supplemental group passed for Kubernetes runner needs to be an integer, value "
                          + self.runner_params["k8s_supplemental_group_id"] + " passed is invalid")
                 return None
@@ -141,7 +141,7 @@ class KubernetesJobRunner(AsynchronousJobRunner):
         if "k8s_fs_group_id" in self.runner_params:
             try:
                 return int(self.runner_params["k8s_fs_group_id"])
-            except:
+            except Exception:
                 log.warning("FS group passed for Kubernetes runner needs to be an integer, value "
                          + self.runner_params["k8s_fs_group_id"] + " passed is invalid")
                 return None

lib/galaxy/jobs/runners/local.py

@@ -128,7 +128,7 @@ class LocalJobRunner(BaseJobRunner):
         # Finish the job!
         try:
             job_wrapper.finish(stdout, stderr, exit_code)
-        except:
+        except Exception:
             log.exception("Job wrapper finish method failed")
             self._fail_job_local(job_wrapper, "Unable to finish job")
 

lib/galaxy/jobs/runners/pbs.py

@@ -143,7 +143,7 @@ class PBSJobRunner(AsynchronousJobRunner):
             # stripping the - comes later (in parse_destination_params)
             for i, opt in enumerate(opts):
                 opts[i] = '-' + opt
-        except:
+        except Exception:
             opts = []
         for opt in opts:
             param, value = opt.split(None, 1)
@@ -168,7 +168,7 @@ class PBSJobRunner(AsynchronousJobRunner):
                     arg = PBS_ARGMAP[arg]
                 arg = arg.lstrip('-')
                 args[arg] = value
-            except:
+            except Exception:
                 log.warning('Unrecognized long argument in destination params: %s' % arg)
         return self.__args_to_attrs(args)
 
@@ -371,7 +371,7 @@ class PBSJobRunner(AsynchronousJobRunner):
                     self.check_single_job(pbs_server_name, job_id)
                     log.warning("(%s/%s) PBS job was not in state check list, but was found with individual state check" % (galaxy_job_id, job_id))
                     new_watched.append(pbs_job_state)
-                except:
+                except Exception:
                     errno, text = pbs.error()
                     if errno == 15001:
                         # 15001 == job not in queue
@@ -525,7 +525,7 @@ class PBSJobRunner(AsynchronousJobRunner):
             pbs.pbs_deljob(c, job_id, '')
             log.debug("%s Removed from PBS queue before job completion"
                       % job_tag)
-        except:
+        except Exception:
             e = traceback.format_exc()
             log.debug("%s Unable to stop job: %s" % (job_tag, e))
         finally:

lib/galaxy/jobs/runners/slurm.py

@@ -104,7 +104,7 @@ class SlurmJobRunner(DRMAAJobRunner):
                     try:
                         self.queue_job(ajs.job_wrapper)
                         return
-                    except:
+                    except Exception:
                         ajs.fail_message = "This job failed due to a cluster node failure, and an attempt to resubmit the job failed."
                 elif slurm_state == 'CANCELLED':
                     # Check to see if the job was killed for exceeding memory consumption
@@ -164,7 +164,7 @@ class SlurmJobRunner(DRMAAJobRunner):
                         return 'This job was terminated because it used more memory than it was allocated.'
                     elif any(_ in stripped_line for _ in SLURM_MEMORY_LIMIT_EXCEEDED_PARTIAL_WARNINGS):
                         return 'This job was cancelled probably because it used more memory than it was allocated.'
-        except:
+        except Exception:
             log.exception('Error reading end of %s:', efile_path)
 
         return False

lib/galaxy/jobs/runners/state_handler_factory.py

@@ -1,9 +1,7 @@
 import logging
 
-from galaxy.util.submodules import submodules
-
 import galaxy.jobs.runners.state_handlers
-
+from galaxy.util.submodules import submodules
 
 log = logging.getLogger(__name__)
 

lib/galaxy/jobs/runners/tasks.py

@@ -52,7 +52,7 @@ class TaskedJobRunner(BaseJobRunner):
             parallelism = job_wrapper.get_parallelism()
             try:
                 splitter = getattr(__import__('galaxy.jobs.splitters', globals(), locals(), [parallelism.method]), parallelism.method)
-            except:
+            except Exception:
                 job_wrapper.change_state(model.Job.states.ERROR)
                 job_wrapper.fail("Job Splitting Failed, no match for '%s'" % parallelism)
                 return
@@ -125,7 +125,7 @@ class TaskedJobRunner(BaseJobRunner):
         # Finish the job
         try:
             job_wrapper.finish(stdout, stderr, job_exit_code)
-        except:
+        except Exception:
             log.exception("Job wrapper finish method failed")
             job_wrapper.fail("Unable to finish job", exception=True)
 

lib/galaxy/jobs/runners/util/cli/job/slurm.py

@@ -41,7 +41,7 @@ class Slurm(BaseJobExec):
                 if not k.startswith('-'):
                     k = argmap[k]
                 scriptargs[k] = v
-            except:
+            except Exception:
                 log.warning('Unrecognized long argument passed to Slurm CLI plugin: %s' % k)
 
         # Generated template.

lib/galaxy/jobs/runners/util/cli/job/torque.py

@@ -1,7 +1,7 @@
 from logging import getLogger
 try:
     import xml.etree.cElementTree as et
-except:
+except ImportError:
     import xml.etree.ElementTree as et
 
 try:

lib/galaxy/jobs/transfer_manager.py

@@ -147,7 +147,7 @@ class TransferManager(object):
                 # restart the transfer if socket communication fails repeatedly.
                 try:
                     os.kill(tj.pid, 0)
-                except:
+                except Exception:
                     self.sa_session.refresh(tj)
                     if tj.state == tj.states.RUNNING:
                         log.error('Transfer job %s is marked as running but pid %s appears to be dead.' % (tj.id, tj.pid))

lib/galaxy/managers/context.py

@@ -27,11 +27,11 @@ class ProvidesAppContext(object):
                     action.user = user
                 else:
                     action.user = self.user
-            except:
+            except Exception:
                 action.user = None
             try:
                 action.session_id = self.galaxy_session.id
-            except:
+            except Exception:
                 action.session_id = None
             self.sa_session.add(action)
             self.sa_session.flush()
@@ -46,23 +46,23 @@ class ProvidesAppContext(object):
             event.tool_id = tool_id
             try:
                 event.message = message % kwargs
-            except:
+            except Exception:
                 event.message = message
             try:
                 event.history = self.get_history()
-            except:
+            except Exception:
                 event.history = None
             try:
                 event.history_id = self.history.id
-            except:
+            except Exception:
                 event.history_id = None
             try:
                 event.user = self.user
-            except:
+            except Exception:
                 event.user = None
             try:
                 event.session_id = self.galaxy_session.id
-            except:
+            except Exception:
                 event.session_id = None
             self.sa_session.add(event)
             self.sa_session.flush()

lib/galaxy/model/__init__.py

@@ -1172,7 +1172,7 @@ class DeferredJob(object):
     def set_last_check(self, seconds):
         try:
             self._last_check = int(seconds)
-        except:
+        except ValueError:
             self._last_check = time.time()
     last_check = property(get_last_check, set_last_check)
 
@@ -4324,7 +4324,7 @@ class FormDefinition(object, Dictifiable):
                 try:
                     # This field has a saved value.
                     value = str(contents[field['name']])
-                except:
+                except Exception:
                     # If there was an error getting the saved value, we'll still
                     # display the widget, but it will be empty.
                     if field_type == 'AddressField':

lib/galaxy/model/custom_types.py

@@ -291,10 +291,10 @@ class MetadataType(JSONType):
             ret = metadata_pickler.loads(str(value))
             if ret:
                 ret = dict(ret.__dict__)
-        except:
+        except Exception:
             try:
                 ret = json_decoder.decode(str(_sniffnfix_pg9_hex(value)))
-            except:
+            except Exception:
                 ret = None
         return ret
 

lib/galaxy/model/mapping.py

@@ -2534,7 +2534,7 @@ def db_next_hid(self, n=1):
         table.update(table.c.id == self.id).execute(hid_counter=(next_hid + n))
         trans.commit()
         return next_hid
-    except:
+    except Exception:
         trans.rollback()
         raise
 

lib/galaxy/model/metadata.py

@@ -91,7 +91,7 @@ class MetadataCollection(object):
     def get(self, key, default=None):
         try:
             return self.__getattr__(key) or default
-        except:
+        except Exception:
             return default
 
     def items(self):

lib/galaxy/model/migrate/check.py

@@ -36,7 +36,7 @@ def create_or_verify_database(url, galaxy_config_file, engine_options={}, app=No
         try:
             # Declare the database to be under a repository's version control
             db_schema = schema.ControlledSchema.create(engine, migrate_repository)
-        except:
+        except Exception:
             # The database is already under version control
             db_schema = schema.ControlledSchema(engine, migrate_repository)
         # Apply all scripts to get to current version

lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py

@@ -692,7 +692,7 @@ def __guess_dataset_by_filename(filename):
         if fields:
             if fields[-1].startswith('dataset_') and fields[-1].endswith('.dat'):  # dataset_%d.dat
                 return Dataset.get(int(fields[-1][len('dataset_'): -len('.dat')]))
-    except:
+    except Exception:
         pass  # some parsing error, we can't guess Dataset
     return None
 

lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py

@@ -29,7 +29,7 @@ def upgrade(migrate_engine):
         i = Index("ix_page_slug", Page_table.c.slug, unique=False)
         i.create()
 
-    except:
+    except Exception:
 
         # Mysql doesn't have a named index, but alter should work
 

lib/galaxy/model/migrate/versions/0032_stored_workflow_slug_column.py

@@ -30,7 +30,7 @@ def upgrade(migrate_engine):
         try:
             i = Index("ix_stored_workflow_slug", StoredWorkflow_table.c.slug, mysql_length=200)
             i.create()
-        except:
+        except Exception:
             # Mysql doesn't have a named index, but alter should work
             StoredWorkflow_table.c.slug.alter(unique=False)
 

lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py

@@ -31,7 +31,7 @@ def upgrade(migrate_engine):
         try:
             i = Index("ix_history_published", History_table.c.published)
             i.create()
-        except:
+        except Exception:
             # Mysql doesn't have a named index, but alter should work
             History_table.c.published.alter(unique=False)
 
@@ -49,7 +49,7 @@ def upgrade(migrate_engine):
         try:
             i = Index("ix_stored_workflow_published", StoredWorkflow_table.c.published)
             i.create()
-        except:
+        except Exception:
             # Mysql doesn't have a named index, but alter should work
             StoredWorkflow_table.c.published.alter(unique=False)
 
@@ -67,7 +67,7 @@ def upgrade(migrate_engine):
         try:
             i = Index("ix_page_importable", Page_table.c.importable)
             i.create()
-        except:
+        except Exception:
             # Mysql doesn't have a named index, but alter should work
             Page_table.c.importable.alter(unique=False)
 

lib/galaxy/model/migrate/versions/0041_workflow_invocation.py

@@ -38,7 +38,7 @@ def upgrade(migrate_engine):
     for table in tables:
         try:
             table.create()
-        except:
+        except Exception:
             log.warning("Failed to create table '%s', ignoring (might result in wrong schema)" % table.name)
 
 

lib/galaxy/model/migrate/versions/0042_workflow_invocation_fix.py

@@ -25,7 +25,7 @@ def upgrade(migrate_engine):
             t = Table(table_name, metadata, autoload=True)
             t.drop()
             metadata.remove(t)
-        except:
+        except Exception:
             log.exception("Failed to drop table '%s', ignoring (might result in wrong schema)" % table_name)
 
     # 2) Readd
@@ -46,7 +46,7 @@ def upgrade(migrate_engine):
     for table in [WorkflowInvocation_table, WorkflowInvocationStep_table]:
         try:
             table.create()
-        except:
+        except Exception:
             log.exception("Failed to create table '%s', ignoring (might result in wrong schema)" % table.name)
 
 

lib/galaxy/model/migrate/versions/0056_workflow_outputs.py

@@ -27,7 +27,7 @@ def upgrade(migrate_engine):
     for table in tables:
         try:
             table.create()
-        except:
+        except Exception:
             log.warning("Failed to create table '%s', ignoring (might result in wrong schema)" % table.name)
 
 

lib/galaxy/model/migrate/versions/0061_tasks.py

@@ -39,7 +39,7 @@ def upgrade(migrate_engine):
     for table in tables:
         try:
             table.create()
-        except:
+        except Exception:
             log.warning("Failed to create table '%s', ignoring (might result in wrong schema)" % table.name)
 
 

lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py

@@ -39,7 +39,7 @@ def upgrade(migrate_engine):
                 # Encoding errors?  Just to be safe.
                 print("Attempting to fix row %s" % row['id'])
                 print("Prior to replacement: %s" % field_values_str)
-            except:
+            except Exception:
                 pass
             field_values_dict = {}
             # look for each field name in the values and extract its value (string)
@@ -77,7 +77,7 @@ def upgrade(migrate_engine):
             migrate_engine.execute(cmd)
             try:
                 print("Post replacement: %s" % json_values)
-            except:
+            except Exception:
                 pass
     if corrupted_rows:
         print('Fixed %i corrupted rows.' % corrupted_rows)

lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py

@@ -13,7 +13,7 @@ def upgrade(migrate_engine):
     user = Table('galaxy_user', meta, autoload=True)
     try:
         user.c.password.alter(type=String(255))
-    except:
+    except Exception:
         log.exception("Altering password column failed")
 
 

lib/galaxy/model/tool_shed_install/migrate/check.py

@@ -30,7 +30,7 @@ def create_or_verify_database(url, engine_options={}, app=None):
         try:
             # Declare the database to be under a repository's version control
             db_schema = schema.ControlledSchema.create(engine, migrate_repository)
-        except:
+        except Exception:
             # The database is already under version control
             db_schema = schema.ControlledSchema(engine, migrate_repository)
         # Apply all scripts to get to current version

lib/galaxy/sample_tracking/external_service_types.py

@@ -1,10 +1,15 @@
-import os
 import logging
-from galaxy.util.odict import odict
-from galaxy import util, model
-from galaxy.forms.forms import form_factory
+import os
+
+from galaxy import (
+    model,
+    util
+)
 from galaxy.external_services.service import ExternalServiceActionsGroup
+from galaxy.forms.forms import form_factory
 from galaxy.sample_tracking.data_transfer import data_transfer_factories
+from galaxy.util.odict import odict
+
 log = logging.getLogger(__name__)
 
 
@@ -20,7 +25,7 @@ class ExternalServiceTypesCollection(object):
         self.app = app
         try:
             self.load_all(config_filename)
-        except:
+        except Exception:
             log.exception("ExternalServiceTypesCollection error reading %s", config_filename)
 
     def load_all(self, config_filename):
@@ -37,7 +42,7 @@ class ExternalServiceTypesCollection(object):
                     log.debug("Loaded external_service_type: %s %s" % (external_service_type.name, external_service_type.config_version))
                     if visible:
                         self.visible_external_service_types.append(external_service_type.id)
-            except:
+            except Exception:
                 log.exception("error reading external_service_type from path: %s", file_path)
 
     def load_external_service_type(self, config_file, visible=True):

lib/galaxy/sample_tracking/request_types.py

@@ -2,7 +2,8 @@
 RequestType
 """
 from galaxy.model import RequestType
-from sample import sample_state_factory
+
+from .sample import sample_state_factory
 
 RENAME_DATASET_OPTIONS = dict([(f_type.lower(), f_descript) for f_type, f_descript in RequestType.rename_dataset_options.items()])
 

lib/galaxy/tools/__init__.py

@@ -794,7 +794,7 @@ class Tool(object, Dictifiable):
             if tests_source:
                 try:
                     self.__tests = parse_tests(self, tests_source)
-                except:
+                except Exception:
                     self.__tests = None
                     log.exception("Failed to parse tool tests")
             else:
@@ -1011,7 +1011,7 @@ class Tool(object, Dictifiable):
                         group.cases.append(case)
                         try:
                             possible_cases.remove(case.value)
-                        except:
+                        except Exception:
                             log.warning("Tool %s: a when tag has been defined for '%s (%s) --> %s', but does not appear to be selectable." %
                                         (self.id, group.name, group.test_param.name, case.value))
                     for unspecified_case in possible_cases:
@@ -1131,8 +1131,8 @@ class Tool(object, Dictifiable):
                 self.__help = Template(rst_to_html(help_text), input_encoding='utf-8',
                                        output_encoding='utf-8', default_filters=['decode.utf8'],
                                        encoding_errors='replace')
-            except:
-                log.exception("error in help for tool %s", self.name)
+            except Exception:
+                log.exception("Exception while parsing help for tool with id '%s'", self.id)
 
             # Handle deprecated multi-page help text in XML case.
             if hasattr(tool_source, "root"):
@@ -1151,8 +1151,8 @@ class Tool(object, Dictifiable):
                                                     default_filters=['decode.utf8'],
                                                     encoding_errors='replace')
                                            for x in self.__help_by_page]
-                except:
-                    log.exception("error in multi-page help for tool %s", self.name)
+                except Exception:
+                    log.exception("Exception while parsing multi-page help for tool with id '%s'", self.id)
         # Pad out help pages to match npages ... could this be done better?
         while len(self.__help_by_page) < self.npages:
             self.__help_by_page.append(self.__help)
@@ -1422,7 +1422,7 @@ class Tool(object, Dictifiable):
                         if not prefixed_name.startswith('__'):
                             messages[prefixed_name] = error if previous_value == value else '%s Using default: \'%s\'.' % (error, value)
                         parent[input.name] = value
-                    except:
+                    except Exception:
                         messages[prefixed_name] = 'Attempt to replace invalid value for \'%s\' failed.' % (prefixed_label)
                 else:
                     messages[prefixed_name] = error

lib/galaxy/tools/actions/__init__.py

@@ -542,7 +542,7 @@ class DefaultToolAction(object):
         try:
             # For backward compatibility, some tools may not have versions yet.
             job.tool_version = tool.version
-        except:
+        except AttributeError:
             job.tool_version = "1.0.0"
         return job, galaxy_session
 
@@ -837,7 +837,7 @@ def determine_output_format(output, parameter_context, input_datasets, input_dat
                             check = '${%s}' % check
                         if str(fill_template(check, context=parameter_context)) == when_elem.get('value', None):
                             ext = when_elem.get('format', ext)
-                    except:  # bad tag input value; possibly referencing a param within a different conditional when block or other nonexistent grouping construct
+                    except Exception:  # bad tag input value; possibly referencing a param within a different conditional when block or other nonexistent grouping construct
                         continue
                 else:
                     check = when_elem.get('input_dataset', None)

lib/galaxy/tools/actions/metadata.py

@@ -60,7 +60,7 @@ class SetMetadataToolAction(ToolAction):
         try:
             # For backward compatibility, some tools may not have versions yet.
             job.tool_version = tool.version
-        except:
+        except AttributeError:
             job.tool_version = "1.0.1"
         job.state = job.states.WAITING  # we need to set job state to something other than NEW, or else when tracking jobs in db it will be picked up before we have added input / output parameters
         job.set_handler(tool.get_job_handler(job_params))

lib/galaxy/tools/actions/upload_common.py

@@ -176,7 +176,7 @@ def get_precreated_datasets(trans, params, data_obj, controller='root'):
     for id in async_datasets:
         try:
             data = trans.sa_session.query(data_obj).get(int(id))
-        except:
+        except Exception:
             log.exception('Unable to load precreated dataset (%s) sent in upload form' % id)
             continue
         if data_obj is trans.app.model.HistoryDatasetAssociation:

lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py

@@ -54,7 +54,7 @@ class UnlinkedToolShedPackageDependencyResolver(BaseGalaxyPackageDependencyResol
             else:
                 # Pick the preferred one
                 return self._select_preferred_dependency(possibles).dependency
-        except:
+        except Exception:
             log.exception("Unexpected error hunting for dependency '%s' '%s''%s'", name, version, type)
             return NullDependency(version=version, name=name)
 
@@ -126,7 +126,7 @@ class UnlinkedToolShedPackageDependencyResolver(BaseGalaxyPackageDependencyResol
             else:
                 #Pick the preferred one
                 return self._select_preferred_dependency(possibles, by_owner=False).dependency
-        except:
+        except Exception:
             log.exception("Unexpected error hunting for dependency '%s' default '%s'", name, type)
             return NullDependency(version=None, name=name)
     """

lib/galaxy/tools/imp_exp/__init__.py

@@ -244,7 +244,7 @@ class JobImportHistoryArchiveWrapper(object, UsesAnnotations):
                     try:
                         imported_job.create_time = datetime.datetime.strptime(job_attrs["create_time"], "%Y-%m-%dT%H:%M:%S.%f")
                         imported_job.update_time = datetime.datetime.strptime(job_attrs["update_time"], "%Y-%m-%dT%H:%M:%S.%f")
-                    except:
+                    except Exception:
                         pass
                     self.sa_session.add(imported_job)
                     self.sa_session.flush()
@@ -485,7 +485,7 @@ class JobExportHistoryArchiveWrapper(object, UsesAnnotations):
             # Get the job's parameters
             try:
                 params_objects = job.get_param_values(trans.app)
-            except:
+            except Exception:
                 # Could not get job params.
                 continue
 

lib/galaxy/tools/parameters/__init__.py

@@ -100,7 +100,7 @@ def visit_input_values(inputs, input_values, callback, name_prefix='', label_pre
             case_error = None
             try:
                 input.get_current_case(values[input.test_param.name])
-            except:
+            except Exception:
                 case_error = 'The selected case is unavailable/invalid.'
                 pass
             callback_helper(input.test_param, values, new_name_prefix, label_prefix, parent_prefix=name_prefix, context=context, error=case_error)

lib/galaxy/tools/parameters/basic.py

@@ -153,7 +153,7 @@ class ToolParameter(object, Dictifiable):
         if ignore_errors:
             try:
                 return self.to_python(value, app)
-            except:
+            except Exception:
                 return value
         else:
             return self.to_python(value, app)
@@ -313,7 +313,7 @@ class IntegerToolParameter(TextToolParameter):
         if self.value:
             try:
                 int(self.value)
-            except:
+            except ValueError:
                 raise ValueError("An integer is required")
         elif self.value is None and not self.optional:
             raise ValueError("The settings for the field named '%s' require a 'value' setting and optionally a default value which must be an integer" % self.name)
@@ -322,12 +322,12 @@ class IntegerToolParameter(TextToolParameter):
         if self.min:
             try:
                 self.min = int(self.min)
-            except:
+            except ValueError:
                 raise ValueError("An integer is required")
         if self.max:
             try:
                 self.max = int(self.max)
-            except:
+            except ValueError:
                 raise ValueError("An integer is required")
         if self.min is not None or self.max is not None:
             self.validators.append(validation.InRangeValidator(None, self.min, self.max))
@@ -335,7 +335,7 @@ class IntegerToolParameter(TextToolParameter):
     def from_json(self, value, trans, other_values={}):
         try:
             return int(value)
-        except:
+        except (TypeError, ValueError):
             if contains_workflow_parameter(value) and trans.workflow_building_mode is workflow_building_modes.ENABLED:
                 return value
             if not value and self.optional:
@@ -348,7 +348,7 @@ class IntegerToolParameter(TextToolParameter):
     def to_python(self, value, app):
         try:
             return int(value)
-        except Exception as err:
+        except (TypeError, ValueError) as err:
             if contains_workflow_parameter(value):
                 return value
             if not value and self.optional:
@@ -391,19 +391,19 @@ class FloatToolParameter(TextToolParameter):
         if self.value:
             try:
                 float(self.value)
-            except:
+            except ValueError:
                 raise ValueError("A real number is required")
         elif self.value is None and not self.optional:
             raise ValueError("The settings for this field require a 'value' setting and optionally a default value which must be a real number")
         if self.min:
             try:
                 self.min = float(self.min)
-            except:
+            except ValueError:
                 raise ValueError("A real number is required")
         if self.max:
             try:
                 self.max = float(self.max)
-            except:
+            except ValueError:
                 raise ValueError("A real number is required")
         if self.min is not None or self.max is not None:
             self.validators.append(validation.InRangeValidator(None, self.min, self.max))
@@ -411,7 +411,7 @@ class FloatToolParameter(TextToolParameter):
     def from_json(self, value, trans, other_values={}):
         try:
             return float(value)
-        except:
+        except (TypeError, ValueError):
             if contains_workflow_parameter(value) and trans.workflow_building_mode is workflow_building_modes.ENABLED:
                 return value
             if not value and self.optional:
@@ -424,7 +424,7 @@ class FloatToolParameter(TextToolParameter):
     def to_python(self, value, app):
         try:
             return float(value)
-        except Exception as err:
+        except (TypeError, ValueError) as err:
             if contains_workflow_parameter(value):
                 return value
             if not value and self.optional:
@@ -434,7 +434,7 @@ class FloatToolParameter(TextToolParameter):
     def get_initial_value(self, trans, other_values):
         try:
             return float(self.value)
-        except:
+        except Exception:
             return None
 
 
@@ -542,7 +542,7 @@ class FileToolParameter(ToolParameter):
             # or should we jsonify?
             try:
                 return value['local_filename']
-            except:
+            except KeyError:
                 return None
         raise Exception("FileToolParameter cannot be persisted")
 
@@ -1147,7 +1147,7 @@ class ColumnListParameter(SelectToolParameter):
                         if len(dataset.metadata.column_types) >= len(cnames):
                             numerics = [i for i, x in enumerate(dataset.metadata.column_types) if x in ['int', 'float']]
                             column_list = [column_list[i] for i in numerics]
-            except:
+            except Exception:
                 column_list = self.get_column_list(trans, other_values)
         else:
             column_list = self.get_column_list(trans, other_values)
@@ -1582,12 +1582,12 @@ class DataToolParameter(BaseDataToolParameter):
         if self.min:
             try:
                 self.min = int(self.min)
-            except:
+            except ValueError:
                 raise ValueError("An integer is required for min property.")
         if self.max:
             try:
                 self.max = int(self.max)
-            except:
+            except ValueError:
                 raise ValueError("An integer is required for max property.")
         if not self.multiple and (self.min is not None):
             raise ValueError("Cannot specify min property on single data parameter '%s'. Set multiple=\"true\" to enable this option." % self.name)
@@ -1696,7 +1696,7 @@ class DataToolParameter(BaseDataToolParameter):
         if value:
             try:
                 return ", ".join(["%s: %s" % (item.hid, item.name) for item in value])
-            except:
+            except Exception:
                 pass
         return "No dataset."
 

lib/galaxy/tools/parameters/dynamic_options.py

@@ -72,7 +72,7 @@ class StaticValueFilter(Filter):
         filter_value = self.value
         try:
             filter_value = User.expand_user_properties(trans.user, filter_value)
-        except:
+        except Exception:
             pass
         for fields in options:
             if (self.keep and fields[self.column] == filter_value) or (not self.keep and fields[self.column] != filter_value):

lib/galaxy/tools/parameters/grouping.py

@@ -322,7 +322,7 @@ class UploadDataset(Group):
                 if not dataset_name and 'filename' in data_file:
                     dataset_name = get_file_name(data_file['filename'])
                 return Bunch(type='file', path=data_file['local_filename'], name=dataset_name, purge_source=purge)
-            except:
+            except Exception:
                 # The uploaded file should've been persisted by the upload tool action
                 return Bunch(type=None, path=None, name=None)
 

lib/galaxy/tools/parameters/validation.py

@@ -410,7 +410,7 @@ class MetadataInDataTableColumnValidator(Validator):
         metadata_column = elem.get("metadata_column", 0)
         try:
             metadata_column = int(metadata_column)
-        except:
+        except ValueError:
             pass
         message = elem.get("message", "Value for metadata %s was not found in %s." % (metadata_name, table_name))
         line_startswith = elem.get("line_startswith", None)

lib/galaxy/tools/parser/output_actions.py

@@ -544,7 +544,7 @@ class BooleanFilter(ToolOutputActionOptionFilter):
             try:
                 value = fields[self.column]
                 value = self.cast(value)
-            except:
+            except Exception:
                 value = False  # unable to cast or access value; treat as false
             if self.keep == bool(value):
                 rval.append(fields)

lib/galaxy/tools/parser/xml.py

@@ -726,7 +726,7 @@ class StdioParser(object):
                 else:
                     try:
                         exit_code.range_start = int(code_range)
-                    except:
+                    except Exception:
                         log.error(code_range)
                         log.warning("Invalid range start for tool's exit_code %s: exit_code ignored" % code_range)
                         continue

lib/galaxy/tools/toolbox/base.py

@@ -655,7 +655,7 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin, object):
                 panel_dict[key] = workflow
             # Always load workflows into the integrated_panel_dict.
             integrated_panel_dict.update_or_append(index, key, workflow)
-        except:
+        except Exception:
             log.exception("Error loading workflow: %s", workflow_id)
 
     def _load_label_tag_set(self, item, panel_dict, integrated_panel_dict, load_panel_dict, index=None):

lib/galaxy/tools/util/maf_utilities.py

@@ -168,7 +168,7 @@ class RegionAlignment(object):
         for name in skip:
             try:
                 names.remove(name)
-            except:
+            except ValueError:
                 pass
         return names
 
@@ -295,7 +295,7 @@ def maf_index_by_uid(maf_uid, index_location_file):
                     return bx.align.maf.MultiIndexed(maf_files, keep_open=True, parse_e_rows=False)
                 except Exception as e:
                     raise Exception('MAF UID (%s) found, but configuration appears to be malformed: %s' % (maf_uid, e))
-        except:
+        except Exception:
             pass
     return None
 
@@ -304,7 +304,7 @@ def maf_index_by_uid(maf_uid, index_location_file):
 def open_or_build_maf_index(maf_file, index_filename, species=None):
     try:
         return (bx.align.maf.Indexed(maf_file, index_filename=index_filename, keep_open=True, parse_e_rows=False), None)
-    except:
+    except Exception:
         return build_maf_index(maf_file, species=species)
 
 
@@ -675,7 +675,7 @@ def parse_species_option(species):
 def remove_temp_index_file(index_filename):
     try:
         os.unlink(index_filename)
-    except:
+    except Exception:
         pass
 
 # Below are methods to deal with FASTA files
@@ -713,7 +713,7 @@ def get_attributes_from_fasta_header(header):
         region = region[1].lstrip(':').split('-')
         attributes['start'] = int(region[0])
         attributes['end'] = int(region[1])
-    except:
+    except Exception:
         # fields 0 is not a region coordinate
         pass
     if len(fields) > 2:

lib/galaxy/tools/wrappers.py

@@ -60,7 +60,7 @@ class RawObjectWrapper(ToolParameterValueWrapper):
     def __str__(self):
         try:
             return "%s:%s" % (self.obj.__module__, self.obj.__class__.__name__)
-        except:
+        except Exception:
             # Most likely None, which lacks __module__.
             return str(self.obj)
 
@@ -212,7 +212,7 @@ class DatasetFilenameWrapper(ToolParameterValueWrapper):
         def get(self, key, default=None):
             try:
                 return getattr(self, key)
-            except:
+            except Exception:
                 return default
 
         def items(self):
@@ -223,7 +223,7 @@ class DatasetFilenameWrapper(ToolParameterValueWrapper):
             try:
                 # TODO: allow this to work when working with grouping
                 ext = tool.inputs[name].extensions[0]
-            except:
+            except Exception:
                 ext = 'data'
             self.dataset = wrap_with_safe_string(NoneDataset(datatypes_registry=datatypes_registry, ext=ext), no_wrap_classes=ToolParameterValueWrapper)
         else:

lib/galaxy/util/__init__.py

@@ -311,11 +311,11 @@ def get_file_size(value, default=None):
     try:
         # try built-in
         return os.path.getsize(value)
-    except:
+    except Exception:
         try:
             # try built-in one name attribute
             return os.path.getsize(value.name)
-        except:
+        except Exception:
             try:
                 # try tell() of end of object
                 offset = value.tell()
@@ -323,7 +323,7 @@ def get_file_size(value, default=None):
                 rval = value.tell()
                 value.seek(offset)
                 return rval
-            except:
+            except Exception:
                 # return default value
                 return default
 
@@ -1029,7 +1029,7 @@ def read_dbnames(filename):
                 try:  # manual build (i.e. microbes)
                     int(fields[0])
                     man_builds.append((fields[1], fields[0]))
-                except:  # UCSC build
+                except Exception:  # UCSC build
                     db_base = fields[0].rstrip('0123456789')
                     if db_base not in ucsc_builds:
                         ucsc_builds[db_base] = []
@@ -1038,10 +1038,10 @@ def read_dbnames(filename):
                     build_rev = re.compile(r'\d+$')
                     try:
                         build_rev = int(build_rev.findall(fields[0])[0])
-                    except:
+                    except Exception:
                         build_rev = 0
                     ucsc_builds[db_base].append((build_rev, fields[0], fields[1]))
-            except:
+            except Exception:
                 continue
         sort_names = sorted(name_to_db_base.keys())
         for name in sort_names:
@@ -1079,9 +1079,9 @@ def read_build_sites(filename, check_builds=True):
                 else:
                     site_dict = {'name': site_name, 'url': site}
                 build_sites.append(site_dict)
-            except:
+            except Exception:
                 continue
-    except:
+    except Exception:
         log.error("ERROR: Unable to read builds for site file %s", filename)
     return build_sites
 
@@ -1171,7 +1171,7 @@ def umask_fix_perms(path, umask, unmasked_perms, gid=None):
             try:
                 desired_group = grp.getgrgid(gid)
                 current_group = grp.getgrgid(st.st_gid)
-            except:
+            except Exception:
                 desired_group = gid
                 current_group = st.st_gid
             log.warning('Unable to honor primary group (%s) for %s, group remains %s, error was: %s' % (desired_group,
@@ -1227,7 +1227,7 @@ def nice_size(size):
         if size < 0:
             size = abs(size)
             prefix = '-'
-    except:
+    except Exception:
         return '??? bytes'
     for ind, word in enumerate(words):
         step = 1024 ** (ind + 1)
@@ -1246,7 +1246,7 @@ def size_to_bytes(size):
     # Assume input in bytes if we can convert directly to an int
     try:
         return int(size)
-    except:
+    except ValueError:
         pass
     # Otherwise it must have non-numeric characters
     size_re = re.compile('([\d\.]+)\s*([tgmk]b?|b|bytes?)$')

lib/galaxy/util/checkers.py

@@ -71,7 +71,7 @@ def check_gzip(file_path, check_content=True):
         temp.close()
         if magic_check != util.gzip_magic:
             return (False, False)
-    except:
+    except Exception:
         return (False, False)
     # We support some binary data types, so check if the compressed binary file is valid
     # If the file is Bam, it should already have been detected as such, so we'll just check
@@ -80,7 +80,7 @@ def check_gzip(file_path, check_content=True):
         header = gzip.open(file_path).read(4)
         if header == b'.sff':
             return (True, True)
-    except:
+    except Exception:
         return(False, False)
 
     if not check_content:
@@ -103,7 +103,7 @@ def check_bz2(file_path, check_content=True):
         temp.close()
         if magic_check != util.bz2_magic:
             return (False, False)
-    except:
+    except Exception:
         return(False, False)
 
     if not check_content:

lib/galaxy/util/dictifiable.py

@@ -23,7 +23,7 @@ class Dictifiable:
             # first and then default to to_dict?
             try:
                 return item.to_dict(view=view, value_mapper=value_mapper)
-            except:
+            except Exception:
                 if key in value_mapper:
                     return value_mapper.get(key)(item)
                 if type(item) == datetime.datetime:

lib/galaxy/util/hash_util.py

@@ -44,7 +44,7 @@ def hmac_new(key, value):
 def is_hashable(value):
     try:
         hash(value)
-    except:
+    except Exception:
         return False
     return True
 

lib/galaxy/util/heartbeat.py

@@ -96,7 +96,7 @@ class Heartbeat(threading.Thread):
             self.file.write("End dump\n\n")
             self.file.flush()
             self.print_nonsleeping(threads)
-        except:
+        except Exception:
             self.file.write("Caught exception attempting to dump thread states:")
             traceback.print_exc(None, self.file)
             self.file.write("\n")

lib/galaxy/util/image_util.py

@@ -9,7 +9,7 @@ try:
 except ImportError:
     try:
         from PIL import Image as PIL
-    except:
+    except ImportError:
         PIL = None
 
 log = logging.getLogger(__name__)
@@ -22,7 +22,7 @@ def image_type(filename):
             im = PIL.open(filename)
             fmt = im.format
             im.close()
-        except:
+        except Exception:
             # We continue to try with imghdr, so this is a rare case of an
             # exception we expect to happen frequently, so we're not logging
             pass