1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/changeset/886d8ada4a22/ changeset: 886d8ada4a22 user: dannon date: 2012-11-19 18:54:46 summary: Refactor imports to remove 'import *s', remove unused variables/dead code, strip whitespace. affected #: 1 file

diff -r 950544a9b858d86bd1f3ff51c7433a90d2e89bfb -r 886d8ada4a2215aa4b69244908cb4859352a2f03 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -4,24 +4,22 @@ Naming: try to use class names that have a distinct plural form so that the relationship cardinalities are obvious (e.g. prefer Dataset to Data) """ -import pkg_resources + +import pkg_resources, os, errno, codecs, operator, socket, pexpect, logging, time pkg_resources.require( "simplejson" ) import simplejson +from sqlalchemy.orm import object_session +from sqlalchemy.sql.expression import func import galaxy.datatypes -from galaxy.util.bunch import Bunch -from galaxy import util import galaxy.datatypes.registry from galaxy.datatypes.metadata import MetadataCollection -from galaxy.security import RBACAgent, get_permitted_actions -from galaxy.util.hash_util import * -from galaxy.web.form_builder import * +from galaxy.security import get_permitted_actions +from galaxy import util +from galaxy.util.bunch import Bunch +from galaxy.util.hash_util import new_secure_hash +from galaxy.web.form_builder import (AddressField, CheckboxField, PasswordField, SelectField, TextArea, TextField, + WorkflowField, WorkflowMappingField, HistoryField) from galaxy.model.item_attrs import UsesAnnotations, APIItem -from sqlalchemy.orm import object_session -from sqlalchemy.sql.expression import func -import os.path, os, errno, codecs, operator, socket, pexpect, logging, time, shutil - -if sys.version_info[:2] < ( 2, 5 ): - from sets import Set as set

log = logging.getLogger( __name__ )

@@ -138,13 +136,13 @@ self.exit_code = None

# TODO: Add accessors for members defined in SQL Alchemy for the Job table and - # for the mapper defined to the Job table. + # for the mapper defined to the Job table. def get_external_output_metadata( self ): """ - The external_output_metadata is currently a reference from Job to + The external_output_metadata is currently a reference from Job to JobExternalOutputMetadata. It exists for a job but not a task. """ - return self.external_output_metadata + return self.external_output_metadata def get_session_id( self ): return self.session_id def get_user_id( self ): @@ -177,7 +175,7 @@ # runner_name is not the same thing. return self.job_runner_name def get_job_runner_external_id( self ): - # This is different from the Task just in the member accessed: + # This is different from the Task just in the member accessed: return self.job_runner_external_id def get_post_job_actions( self ): return self.post_job_actions @@ -197,10 +195,10 @@ # The tasks member is pert of a reference in the SQL Alchemy schema: return self.tasks def get_id_tag( self ): - """ - Return a tag that can be useful in identifying a Job. + """ + Return a tag that can be useful in identifying a Job. This returns the Job's get_id - """ + """ return "%s" % self.id;

def set_session_id( self, session_id ): @@ -324,8 +322,8 @@ self.task_runner_name = None self.task_runner_external_id = None self.job = job - self.stdout = "" - self.stderr = "" + self.stdout = "" + self.stderr = "" self.exit_code = None self.prepare_input_files_cmd = prepare_files_cmd

@@ -340,8 +338,8 @@ return param_dict

def get_id( self ): - # This is defined in the SQL Alchemy schema: - return self.id + # This is defined in the SQL Alchemy schema: + return self.id def get_id_tag( self ): """ Return an id tag suitable for identifying the task. @@ -378,7 +376,7 @@ # metdata). These can be filled in as needed. def get_external_output_metadata( self ): """ - The external_output_metadata is currently a backref to + The external_output_metadata is currently a backref to JobExternalOutputMetadata. It exists for a job but not a task, and when a task is cancelled its corresponding parent Job will be cancelled. So None is returned now, but that could be changed @@ -395,13 +393,13 @@ """ Runners will use the same methods to get information about the Task class as they will about the Job class, so this method just returns - the task's external id. + the task's external id. """ # TODO: Merge into get_runner_external_id. return self.task_runner_external_id def get_session_id( self ): # The Job's galaxy session is equal to the Job's session, so the - # Job's session is the same as the Task's session. + # Job's session is the same as the Task's session. return self.get_job().get_session_id()

def set_id( self, id ): @@ -424,7 +422,7 @@ # This method is available for runners that do not want/need to # differentiate between the kinds of Runnable things (Jobs and Tasks) # that they're using. - log.debug( "Task %d: Set external id to %s" + log.debug( "Task %d: Set external id to %s" % ( self.id, task_runner_external_id ) ) self.task_runner_external_id = task_runner_external_id def set_task_runner_external_id( self, task_runner_external_id ): @@ -954,7 +952,7 @@ return False try: return util.is_multi_byte( codecs.open( self.file_name, 'r', 'utf-8' ).read( 100 ) ) - except UnicodeDecodeError, e: + except UnicodeDecodeError: return False # FIXME: sqlalchemy will replace this def _delete(self): @@ -1136,7 +1134,6 @@ """ Returns dict of { "dependency" => HDA } """ - converted_dataset = self.get_converted_files_by_type( target_ext ) # List of string of dependencies try: depends_list = trans.app.datatypes_registry.converter_deps[self.extension][target_ext] @@ -1307,7 +1304,7 @@ """ Returns datasources for dataset; if datasources are not available due to indexing, indexing is started. Return value is a dictionary - with entries of type + with entries of type (<datasource_type> : {<datasource_name>, <indexing_message>}). """ track_type, data_sources = self.datatype.get_track_type() @@ -1320,17 +1317,17 @@ else: # Convert. msg = self.convert_dataset( trans, data_source ) - + # Store msg. data_sources_dict[ source_type ] = { "name" : data_source, "message": msg } - + return data_sources_dict

def convert_dataset( self, trans, target_type ): """ - Converts a dataset to the target_type and returns a message indicating + Converts a dataset to the target_type and returns a message indicating status of the conversion. None is returned to indicate that dataset - was converted successfully. + was converted successfully. """

# FIXME: copied from controller.py @@ -1402,7 +1399,7 @@ hda.metadata = self.metadata if copy_children: for child in self.children: - child_copy = child.copy( copy_children = copy_children, parent_id = hda.id ) + child.copy( copy_children = copy_children, parent_id = hda.id ) if not self.datatype.copy_safe_peek: # In some instances peek relies on dataset_id, i.e. gmaj.zip for viewing MAFs hda.set_peek() @@ -1454,11 +1451,11 @@ object_session( self ).add( library_dataset ) object_session( self ).flush() for child in self.children: - child_copy = child.to_library_dataset_dataset_association( trans, - target_folder=target_folder, - replace_dataset=replace_dataset, - parent_id=ldda.id, - user=ldda.user ) + child.to_library_dataset_dataset_association( trans, + target_folder=target_folder, + replace_dataset=replace_dataset, + parent_id=ldda.id, + user=ldda.user ) if not self.datatype.copy_safe_peek: # In some instances peek relies on dataset_id, i.e. gmaj.zip for viewing MAFs ldda.set_peek() @@ -1808,7 +1805,7 @@ if add_to_history and target_history: target_history.add_dataset( hda ) for child in self.children: - child_copy = child.to_history_dataset_association( target_history = target_history, parent_id = hda.id, add_to_history = False ) + child.to_history_dataset_association( target_history = target_history, parent_id = hda.id, add_to_history = False ) if not self.datatype.copy_safe_peek: hda.set_peek() #in some instances peek relies on dataset_id, i.e. gmaj.zip for viewing MAFs object_session( self ).flush() @@ -1833,7 +1830,7 @@ ldda.metadata = self.metadata if copy_children: for child in self.children: - child_copy = child.copy( copy_children = copy_children, parent_id = ldda.id ) + child.copy( copy_children = copy_children, parent_id = ldda.id ) if not self.datatype.copy_safe_peek: # In some instances peek relies on dataset_id, i.e. gmaj.zip for viewing MAFs ldda.set_peek() @@ -2640,7 +2637,7 @@ events={ '.ssword:*': scp_configs['password']+'\r\n', pexpect.TIMEOUT:print_ticks}, timeout=10 ) - except Exception, e: + except Exception: return error_msg # cleanup the output to get just the file size return output.replace( filepath, '' )\ @@ -3280,7 +3277,6 @@ .first() return None def get_versions( self, app ): - sa_session = app.model.context.current tool_versions = [] # Prepend ancestors. def __ancestors( app, tool_version ):

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