Do not log exceptions twice

`logging.exception()` already adds the the exception information after
the supplied message.

Also: the `message` attribute of `Exception` class has been dropped in
Python 3, always use `str(e)`.

xref. #1715

lib/galaxy/authnz/managers.py

@@ -65,7 +65,7 @@ def _parse_oidc_config(self, config_file):
         except ImportError:
             raise
         except ParseError as e:
-            raise ParseError("Invalid configuration at `{}`: {} -- unable to continue.".format(config_file, e.message))
+            raise ParseError("Invalid configuration at `{}`: {} -- unable to continue.".format(config_file, e))
 
     def _parse_oidc_backends_config(self, config_file):
         self.oidc_backends_config = {}
@@ -91,9 +91,7 @@ def _parse_oidc_backends_config(self, config_file):
         except ImportError:
             raise
         except ParseError as e:
-            raise ParseError("Invalid configuration at `{}`: {} -- unable to continue.".format(config_file, e.message))
-        # except Exception as e:
-        #     raise Exception("Malformed OIDC Configuration XML -- unable to continue. {}".format(e.message))
+            raise ParseError("Invalid configuration at `{}`: {} -- unable to continue.".format(config_file, e))
 
     def _parse_google_config(self, config_xml):
         rtv = {
@@ -117,7 +115,7 @@ def _get_authnz_backend(self, provider):
             try:
                 return True, "", PSAAuthnz(provider, self.oidc_config, self.oidc_backends_config[provider])
             except Exception as e:
-                log.exception('An error occurred when loading PSAAuthnz: ', str(e))
+                log.exception('An error occurred when loading PSAAuthnz')
                 return False, str(e), None
         else:
             msg = 'The requested identity provider, `{}`, is not a recognized/expected provider'.format(provider)
@@ -200,8 +198,8 @@ def authenticate(self, provider, trans):
             if success is False:
                 return False, message, None
             return True, "Redirecting to the `{}` identity provider for authentication".format(provider), backend.authenticate(trans)
-        except Exception as e:
-            msg = 'An error occurred when authenticating a user on `{}` identity provider: {}'.format(provider, str(e))
+        except Exception:
+            msg = 'An error occurred when authenticating a user on `{}` identity provider'.format(provider)
             log.exception(msg)
             return False, msg, None
 
@@ -211,8 +209,8 @@ def callback(self, provider, state_token, authz_code, trans, login_redirect_url)
             if success is False:
                 return False, message, (None, None)
             return True, message, backend.callback(state_token, authz_code, trans, login_redirect_url)
-        except Exception as e:
-            msg = 'An error occurred when handling callback from `{}` identity provider; {}'.format(provider, str(e))
+        except Exception:
+            msg = 'An error occurred when handling callback from `{}` identity provider'.format(provider)
             log.exception(msg)
             return False, msg, (None, None)
 
@@ -222,9 +220,9 @@ def disconnect(self, provider, trans, disconnect_redirect_url=None):
             if success is False:
                 return False, message, None
             return backend.disconnect(provider, trans, disconnect_redirect_url)
-        except Exception as e:
-            msg = 'An error occurred when disconnecting authentication with `{}` identity provider for user `{}`; ' \
-                  '{}'.format(provider, trans.user.username, str(e))
+        except Exception:
+            msg = 'An error occurred when disconnecting authentication with `{}` identity provider for user `{}`' \
+                  .format(provider, trans.user.username)
             log.exception(msg)
             return False, msg, None
 
@@ -265,5 +263,5 @@ def get_cloud_access_credentials(self, cloudauthz, sa_session, user_id, request=
             ca = CloudAuthz()
             return ca.authorize(cloudauthz.provider, config)
         except CloudAuthzBaseException as e:
-            log.exception(e.message)
-            raise exceptions.AuthenticationFailed(e.message)
+            log.exception("Error while requesting temporary access credentials")
+            raise exceptions.AuthenticationFailed(str(e))

lib/galaxy/jobs/runners/__init__.py

@@ -193,7 +193,7 @@ def prepare_job(self, job_wrapper, include_metadata=False, include_work_dir_outp
             )
         except Exception as e:
             log.exception("(%s) Failure preparing job" % job_id)
-            job_wrapper.fail(e.message if hasattr(e, 'message') else "Job preparation failed", exception=True)
+            job_wrapper.fail(str(e), exception=True)
             return False
 
         if not job_wrapper.runner_command_line:

lib/galaxy/jobs/runners/drmaa.py

@@ -282,9 +282,9 @@ def check_watched_items(self):
                 log.warning("(%s/%s) unable to communicate with DRM: %s", galaxy_id_tag, external_job_id, e)
                 new_watched.append(ajs)
                 continue
-            except Exception as e:
+            except Exception:
                 # so we don't kill the monitor thread
-                log.exception("(%s/%s) unable to check job status: %s" % (galaxy_id_tag, external_job_id, e))
+                log.exception("(%s/%s) unable to check job status" % (galaxy_id_tag, external_job_id))
                 log.warning("(%s/%s) job will now be errored" % (galaxy_id_tag, external_job_id))
                 ajs.fail_message = "Cluster could not complete job"
                 self.work_queue.put((self.fail_job, ajs))
@@ -329,8 +329,8 @@ def stop_job(self, job):
             log.info("(%s/%s) Removed from DRM queue at user's request" % (job.get_id(), ext_id))
         except drmaa.InvalidJobException:
             log.exception("(%s/%s) User killed running job, but it was already dead" % (job.get_id(), ext_id))
-        except Exception as e:
-            log.exception("(%s/%s) User killed running job, but error encountered removing from DRM queue: %s" % (job.get_id(), ext_id, e))
+        except Exception:
+            log.exception("(%s/%s) User killed running job, but error encountered removing from DRM queue" % (job.get_id(), ext_id))
 
     def recover(self, job, job_wrapper):
         """Recovers jobs stuck in the queued/running state when Galaxy started"""

lib/galaxy/managers/cloud.py

@@ -316,6 +316,6 @@ def download(self, trans, history_id, provider, bucket_name, credentials, datase
                     downloaded.append(object_label)
                 except Exception as e:
                     log.debug("Failed to download dataset to cloud, maybe invalid or unauthorized credentials. "
-                              "{}".format(e.message))
+                              "{}".format(e))
                     failed.append(object_label)
         return downloaded, failed

lib/galaxy/model/migrate/versions/0141_add_oidc_tables.py

@@ -69,8 +69,8 @@ def upgrade(migrate_engine):
         psa_nonce.create()
         psa_partial.create()
         oidc_user_authnz_tokens.create()
-    except Exception as e:
-        log.exception("Creating OIDC table failed: %s" % str(e))
+    except Exception:
+        log.exception("Creating OIDC table failed")
 
 
 def downgrade(migrate_engine):
@@ -83,5 +83,5 @@ def downgrade(migrate_engine):
         psa_nonce.drop()
         psa_partial.drop()
         oidc_user_authnz_tokens.drop()
-    except Exception as e:
-        log.exception("Dropping OIDC table failed: %s" % str(e))
+    except Exception:
+        log.exception("Dropping OIDC table failed")

lib/galaxy/model/migrate/versions/0142_change_numeric_metric_precision.py

@@ -21,8 +21,8 @@ def upgrade(migrate_engine):
         t.c.metric_value.alter(type=Numeric(26, 7))
         t = Table("task_metric_numeric", metadata, autoload=True)
         t.c.metric_value.alter(type=Numeric(26, 7))
-    except Exception as e:
-        log.exception("Modifying numeric column failed: %s", str(e))
+    except Exception:
+        log.exception("Modifying numeric column failed")
 
 
 def downgrade(migrate_engine):

lib/galaxy/model/migrate/versions/0143_add_cloudauthz_tables.py

@@ -32,8 +32,8 @@ def upgrade(migrate_engine):
 
     try:
         cloudauthz.create()
-    except Exception as e:
-        log.exception("Failed to create cloudauthz table: {}".format(str(e)))
+    except Exception:
+        log.exception("Failed to create cloudauthz table")
 
 
 def downgrade(migrate_engine):
@@ -42,5 +42,5 @@ def downgrade(migrate_engine):
 
     try:
         cloudauthz.drop()
-    except Exception as e:
-        log.exception("Failed to drop cloudauthz table: {}".format(str(e)))
+    except Exception:
+        log.exception("Failed to drop cloudauthz table")

lib/galaxy/objectstore/cloud.py

@@ -178,13 +178,13 @@ def _get_bucket(self, bucket_name):
                 bucket = self.conn.storage.buckets.create(bucket_name)
             log.debug("Using cloud ObjectStore with bucket '%s'", bucket.name)
             return bucket
-        except InvalidNameException as e:
-            log.exception("Invalid bucket name -- unable to continue. {}".format(e.message))
+        except InvalidNameException:
+            log.exception("Invalid bucket name -- unable to continue")
             raise
-        except Exception as e:
+        except Exception:
             # These two generic exceptions will be replaced by specific exceptions
             # once proper exceptions are exposed by CloudBridge.
-            log.exception("Could not get bucket '{}'. {}".format(bucket_name, e.message))
+            log.exception("Could not get bucket '{}'".format(bucket_name))
         raise Exception
 
     def _fix_permissions(self, rel_path):

lib/galaxy/tools/__init__.py

@@ -1968,9 +1968,9 @@ def populate_model(self, request_context, inputs, state_inputs, group_inputs, ot
                     tool_dict['value'] = input.value_to_basic(state_inputs.get(input.name, initial_value), self.app, use_security=True)
                     tool_dict['default_value'] = input.value_to_basic(initial_value, self.app, use_security=True)
                     tool_dict['text_value'] = input.value_to_display_text(tool_dict['value'])
-                except Exception as e:
+                except Exception:
                     tool_dict = input.to_dict(request_context)
-                    log.exception('tools::to_json() - Skipping parameter expansion \'%s\': %s.' % (input.name, e))
+                    log.exception("tools::to_json() - Skipping parameter expansion '%s'", input.name)
                     pass
             if input_index >= len(group_inputs):
                 group_inputs.append(tool_dict)

lib/galaxy/util/pastescript/serve.py

@@ -1060,6 +1060,6 @@ def invoke(command, command_name, options, args):
         runner = command(command_name)
         exit_code = runner.run(args)
     except BadCommand as e:
-        print(e.message)
+        print(e)
         exit_code = e.exit_code
     sys.exit(exit_code)

lib/galaxy/webapps/galaxy/api/cloudauthz.py

@@ -123,7 +123,7 @@ def create(self, trans, payload, **kwargs):
             raise e
 
         # No two authorization configuration with
-        # exact same key/value should not exist.
+        # exact same key/value should exist.
         for ca in trans.user.cloudauthzs:
             if ca.equals(trans.user.id, provider, authn_id, config):
                 log.debug("Rejected user `{}`'s request to create cloud authorization because a similar config "
@@ -142,8 +142,7 @@ def create(self, trans, payload, **kwargs):
             log.debug('Created a new cloudauthz record for the user id `{}` '.format(str(trans.user.id)))
             trans.response.status = '200'
             return view
-
         except Exception as e:
-            log.exception(msg_template.format(e.message))
+            log.exception(msg_template.format("exception while creating the new cloudauthz record"))
             raise InternalServerError('An unexpected error has occurred while responding to the create request of the '
                                       'cloudauthz API.' + str(e))

lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py

@@ -577,7 +577,7 @@ def install_repositories(self, trans, **kwd):
             tsr_ids_for_monitoring = [trans.security.encode_id(tsr.id) for tsr in tool_shed_repositories]
             return json.dumps(tsr_ids_for_monitoring)
         except install_manager.RepositoriesInstalledException as e:
-            return self.message_exception(trans, e.message)
+            return self.message_exception(trans, str(e))
 
     @web.expose
     @web.require_admin

lib/galaxy/webapps/galaxy/controllers/dataset.py

@@ -872,9 +872,9 @@ def _delete(self, trans, dataset_id):
             trans.log_event("Dataset id %s marked as deleted" % str(id))
             self.hda_manager.stop_creating_job(hda)
             trans.sa_session.flush()
-        except Exception as e:
+        except Exception:
             msg = 'HDA deletion failed (encoded: %s, decoded: %s)' % (dataset_id, id)
-            log.exception(msg + ': ' + str(e))
+            log.exception(msg)
             trans.log_event(msg)
             message = 'Dataset deletion failed'
             status = 'error'
@@ -966,8 +966,8 @@ def _purge(self, trans, dataset_id):
                 except Exception:
                     log.exception('Unable to purge dataset (%s) on purge of HDA (%s):' % (hda.dataset.id, hda.id))
             trans.sa_session.flush()
-        except Exception as exc:
-            msg = 'HDA purge failed (encoded: %s, decoded: %s): %s' % (dataset_id, id, exc)
+        except Exception:
+            msg = 'HDA purge failed (encoded: %s, decoded: %s)' % (dataset_id, id)
             log.exception(msg)
             trans.log_event(msg)
             message = 'Dataset removal from disk failed'

lib/tool_shed/galaxy_install/tools/tool_panel_manager.py

@@ -86,8 +86,8 @@ def config_elems_to_xml_file(self, config_elems, config_filename, tool_path):
                 root.append(elem)
             with RenamedTemporaryFile(config_filename, mode='w') as fh:
                 fh.write(xml_to_string(root, pretty=True))
-        except Exception as e:
-            log.exception("Exception in ToolPanelManager.config_elems_to_xml_file: \n %s", str(e))
+        except Exception:
+            log.exception("Exception in ToolPanelManager.config_elems_to_xml_file")
 
     def generate_tool_elem(self, tool_shed, repository_name, changeset_revision, owner, tool_file_path,
                            tool, tool_section):

lib/tool_shed/util/readme_util.py

@@ -43,8 +43,8 @@ def build_readme_files_dict(app, repository, changeset_revision, metadata, tool_
                         f = open(full_path_to_readme_file, 'r')
                         text = unicodify(f.read())
                         f.close()
-                    except Exception as e:
-                        log.exception("Error reading README file '%s' from disk", str(relative_path_to_readme_file))
+                    except Exception:
+                        log.exception("Error reading README file '%s' from disk", relative_path_to_readme_file)
                         text = None
                     if text:
                         text_of_reasonable_length = basic_util.size_string(text)
@@ -56,7 +56,7 @@ def build_readme_files_dict(app, repository, changeset_revision, metadata, tool_
                                 text_of_reasonable_length = suc.set_image_paths(app,
                                                                                 app.security.encode_id(repository.id),
                                                                                 text_of_reasonable_length)
-                            except Exception as e:
+                            except Exception:
                                 log.exception("Exception in build_readme_files_dict, so images may not be properly displayed")
                             finally:
                                 lock.release()
@@ -81,9 +81,8 @@ def build_readme_files_dict(app, repository, changeset_revision, metadata, tool_
                             try:
                                 text = unicodify(fctx.data())
                                 readme_files_dict[readme_file_name] = basic_util.size_string(text)
-                            except Exception as e:
-                                log.exception("Error reading README file '%s' from repository manifest: %s" %
-                                              (str(relative_path_to_readme_file), str(e)))
+                            except Exception:
+                                log.exception("Error reading README file '%s' from repository manifest", relative_path_to_readme_file)
     return readme_files_dict
 
 

scripts/tool_shed/api/reset_metadata_on_repositories.py

@@ -66,8 +66,8 @@ def main(options):
                 url = '%s/api/repositories/reset_metadata_on_repository' % base_tool_shed_url
                 try:
                     submit(url, data, options.api)
-                except Exception as e:
-                    log.exception(">>>>>>>>>>>>>>>Blew up on data: %s, exception: %s" % (str(data), str(e)))
+                except Exception:
+                    log.exception(">>>>>>>>>>>>>>>Blew up on data: %s", data)
                     # An nginx timeout undoubtedly occurred.
                     sys.exit(1)
     else:
@@ -76,8 +76,8 @@ def main(options):
         url = '%s/api/repositories/reset_metadata_on_repositories' % base_tool_shed_url
         try:
             submit(url, data, options.api)
-        except Exception as e:
-            log.exception(str(e))
+        except Exception:
+            log.exception(">>>>>>>>>>>>>>>Blew up on data: %s", data)
             # An nginx timeout undoubtedly occurred.
             sys.exit(1)
 

test/base/populators.py

@@ -223,7 +223,7 @@ def has_active_jobs():
             wait_on(has_active_jobs, "active jobs", timeout=timeout)
         except TimeoutAssertionError as e:
             jobs = self.history_jobs(history_id)
-            message = "Failed waiting on active jobs to complete, current jobs are [%s]. %s" % (jobs, e.message)
+            message = "Failed waiting on active jobs to complete, current jobs are [%s]. %s" % (jobs, e)
             raise TimeoutAssertionError(message)
 
         if assert_ok:
@@ -1152,7 +1152,7 @@ def get_state():
         return wait_on(get_state, desc=desc, timeout=timeout)
     except TimeoutAssertionError as e:
         response = state_func()
-        raise TimeoutAssertionError("%s Current response containing state [%s]." % (str(e), response.json()))
+        raise TimeoutAssertionError("%s Current response containing state [%s]." % (e, response.json()))
 
 
 class GiPostGetMixin(object):

tools/data_source/upload.py

@@ -283,7 +283,7 @@ def __main__():
             else:
                 metadata.append(add_file(dataset, registry, output_path))
         except UploadProblemException as e:
-            metadata.append(file_err(e.message, dataset))
+            metadata.append(file_err(str(e), dataset))
     __write_job_metadata(metadata)