diff --git a/datatypes_conf.xml.sample b/datatypes_conf.xml.sample index 57122d0d8c3..ecb3554d075 100644 --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -59,7 +59,6 @@ - diff --git a/lib/galaxy/app.py b/lib/galaxy/app.py index 040cd472d47..e3ca063ced7 100644 --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -18,7 +18,6 @@ from galaxy.tools.imp_exp import load_history_imp_exp_tools from galaxy.tools.genome_index import load_genome_index_tools from galaxy.sample_tracking import external_service_types from galaxy.openid.providers import OpenIDProviders -from galaxy.tools.data_manager.manager import DataManagers class UniverseApplication( object ): """Encapsulates the state of a Universe application""" @@ -94,8 +93,6 @@ class UniverseApplication( object ): self.toolbox = tools.ToolBox( tool_configs, self.config.tool_path, self ) # Search support for tools self.toolbox_search = galaxy.tools.search.ToolBoxSearch( self.toolbox ) - #datamanager - self.data_managers = DataManagers( self ) # If enabled, poll respective tool sheds to see if updates are available for any installed tool shed repositories. if self.config.get_bool( 'enable_tool_shed_check', False ): from tool_shed import update_manager diff --git a/lib/galaxy/config.py b/lib/galaxy/config.py index 66c476fce25..823003fe38b 100644 --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -75,10 +75,6 @@ class Configuration( object ): except: 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" ) ) - self.data_manager_config_file = resolve_path( kwargs.get(' data_manager_config_file', 'data_manager_conf.xml' ), self.root ) - self.data_manager_move_files = string_as_bool( kwargs.get( "data_manager_move_files", "False" ) ) - self.galaxy_data_manager_data_path = kwargs.get( 'galaxy_data_manager_data_dir', self.tool_data_path ) self.tool_secret = kwargs.get( "tool_secret", "" ) self.id_secret = kwargs.get( "id_secret", "USING THE DEFAULT IS NOT SECURE!" ) self.set_metadata_externally = string_as_bool( kwargs.get( "set_metadata_externally", "False" ) ) diff --git a/lib/galaxy/jobs/runners/local.py b/lib/galaxy/jobs/runners/local.py index b2323286fa2..acd748528b9 100644 --- a/lib/galaxy/jobs/runners/local.py +++ b/lib/galaxy/jobs/runners/local.py @@ -44,7 +44,7 @@ class LocalJobRunner( BaseJobRunner ): log.debug( "%d workers ready", nworkers ) def run_next( self ): - """Run the next job, waiting until one is available if necessary""" + """Run the next job, waiting until one is available if neccesary""" while 1: job_wrapper = self.queue.get() if job_wrapper is self.STOP_SIGNAL: diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py index b53e3655e9b..ff316dba983 100644 --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -2996,20 +2996,6 @@ class VisualizationRatingAssociation( ItemRatingAssociation ): def set_item( self, visualization ): self.visualization = visualization -#Data Manager Classes -class DataManagerHistoryAssociation( object ): - def __init__( self, id=None, history=None, user=None ): - self.id = id - self.history = history - self.user = user - -class DataManagerJobAssociation( object ): - def __init__( self, id=None, job=None, data_manager_id=None ): - self.id = id - self.job = job - self.data_manager_id = data_manager_id -#end of Data Manager Classes - class UserPreference ( object ): def __init__( self, name=None, value=None ): self.name = name diff --git a/lib/galaxy/model/mapping.py b/lib/galaxy/model/mapping.py index ca10ee35c47..ff58bf7e37d 100644 --- a/lib/galaxy/model/mapping.py +++ b/lib/galaxy/model/mapping.py @@ -930,23 +930,6 @@ VisualizationUserShareAssociation.table = Table( "visualization_user_share_assoc Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ) ) -#Data Manager tables -DataManagerHistoryAssociation.table = Table( "data_manager_history_association", metadata, - Column( "id", Integer, primary_key=True), - Column( "create_time", DateTime, default=now ), - Column( "update_time", DateTime, index=True, default=now, onupdate=now ), - Column( "history_id", Integer, ForeignKey( "history.id" ), index=True ), - Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ) - ) - -DataManagerJobAssociation.table = Table( "data_manager_job_association", metadata, - Column( "id", Integer, primary_key=True), - Column( "create_time", DateTime, default=now ), - Column( "update_time", DateTime, index=True, default=now, onupdate=now ), - Column( "job_id", Integer, ForeignKey( "job.id" ), index=True ), - Column( "data_manager_id", TEXT, index=True ) - ) - # Tagging tables. Tag.table = Table( "tag", metadata, @@ -1916,17 +1899,6 @@ assign_mapper( context, VisualizationRatingAssociation, VisualizationRatingAssoc properties=dict( visualization=relation( Visualization ), user=relation( User ) ) ) -#Data Manager tables -assign_mapper( context, DataManagerHistoryAssociation, DataManagerHistoryAssociation.table, - properties=dict( history=relation( History ), - user=relation( User, backref='data_manager_histories' ) - ) - ) - -assign_mapper( context, DataManagerJobAssociation, DataManagerJobAssociation.table, - properties=dict( job=relation( Job, backref=backref('data_manager_association', uselist=False ), uselist=False ) ) - ) - # User tables. assign_mapper( context, UserPreference, UserPreference.table, diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py index 0d291aefbf8..4a57a1c321f 100755 --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -6,7 +6,7 @@ import pkg_resources pkg_resources.require( "simplejson" ) pkg_resources.require( "Mako" ) -import logging, os, string, sys, tempfile, glob, shutil, types, urllib, subprocess, random, math, traceback, re, pipes +import logging, os, string, sys, tempfile, glob, shutil, types, urllib, subprocess, random, math, traceback, re import simplejson import binascii from mako.template import Template @@ -25,7 +25,6 @@ from parameters.input_translation import ToolInputTranslator from galaxy.util.expressions import ExpressionContext from galaxy.tools.test import ToolTestBuilder from galaxy.tools.actions import DefaultToolAction -from galaxy.tools.actions.data_manager import DataManagerToolAction from galaxy.tools.deps import DependencyManager from galaxy.model import directory_hash_id from galaxy.model.orm import * @@ -80,7 +79,6 @@ class ToolBox( object ): # In-memory dictionary that defines the layout of the tool panel. self.tool_panel = odict() self.index = 0 - self.data_manager_tools = odict() # File that contains the XML section and tool tags from all tool panel config files integrated into a # single file that defines the tool panel layout. This file can be changed by the Galaxy administrator # (in a way similar to the single tool_conf.xml file in the past) to alter the layout of the tool panel. @@ -510,7 +508,7 @@ class ToolBox( object ): self.integrated_tool_panel[ key ] = integrated_section else: self.integrated_tool_panel.insert( index, key, integrated_section ) - def load_tool( self, config_file, guid=None, **kwds ): + def load_tool( self, config_file, guid=None ): """Load a single tool from the file named by `config_file` and return an instance of `Tool`.""" # Parse XML configuration file and get the root element tree = util.parse_xml( config_file ) @@ -526,7 +524,7 @@ class ToolBox( object ): ToolClass = tool_types.get( root.get( 'tool_type' ) ) else: ToolClass = Tool - return ToolClass( config_file, root, self.app, guid=guid, **kwds ) + return ToolClass( config_file, root, self.app, guid=guid ) def reload_tool_by_id( self, tool_id ): """ Attempt to reload the tool identified by 'tool_id', if successful @@ -813,7 +811,6 @@ class Tool( object ): """ tool_type = 'default' - default_tool_action = DefaultToolAction def __init__( self, config_file, root, app, guid=None ): """Load a tool from the config named by `config_file`""" @@ -1054,7 +1051,7 @@ class Tool( object ): # Action action_elem = root.find( "action" ) if action_elem is None: - self.tool_action = self.default_tool_action() + self.tool_action = DefaultToolAction() else: module = action_elem.get( 'module' ) cls = action_elem.get( 'class' ) @@ -2573,24 +2570,18 @@ class Tool( object ): temp_file_path = os.path.join( job_working_directory, "dataset_%s_files" % ( hda.dataset.id ) ) try: a_files = os.listdir( temp_file_path ) - print 'a_files',a_files if len( a_files ) > 0: for f in a_files: - print 'f', f self.app.object_store.update_from_file(hda.dataset, extra_dir="dataset_%d_files" % hda.dataset.id, alt_name = f, file_name = os.path.join(temp_file_path, f), - create = True, - preserve_symlinks = True ) + create = True) # Clean up after being handled by object store. # FIXME: If the object (e.g., S3) becomes async, this will # cause issues so add it to the object store functionality? - print 'before rmtree' shutil.rmtree(temp_file_path) - print 'after rm tree' - except Exception, e: - log.debug( "Error in collect_associated_files: %s" % ( e ) ) + except: continue def collect_child_datasets( self, output, job_working_directory ): """ @@ -2815,64 +2806,7 @@ class Tool( object ): return tool_dict - def get_default_history_by_trans( self, trans, create=False ): - return trans.get_history( create=create ) - - -class OutputParameterJSONTool( Tool ): - """ - Alternate implementation of Tool that provides parameters and other values - JSONified within the contents of an output dataset - """ - tool_type = 'output_parameter_json' - def _prepare_json_list( self, param_list ): - rval = [] - for value in param_list: - if isinstance( value, dict ): - rval.append( self._prepare_json_param_dict( value ) ) - elif isinstance( value, list ): - rval.append( self._prepare_json_list( value ) ) - else: - rval.append( str( value ) ) - return rval - def _prepare_json_param_dict( self, param_dict ): - rval = {} - for key, value in param_dict.iteritems(): - if isinstance( value, dict ): - rval[ key ] = self._prepare_json_param_dict( value ) - elif isinstance( value, list ): - rval[ key ] = self._prepare_json_list( value ) - else: - rval[ key ] = str( value ) - return rval - def exec_before_job( self, app, inp_data, out_data, param_dict=None ): - if param_dict is None: - param_dict = {} - json_params = {} - json_params[ 'param_dict' ] = self._prepare_json_param_dict( param_dict ) #it would probably be better to store the original incoming parameters here, instead of the Galaxy modified ones? - json_params[ 'output_data' ] = [] - json_params[ 'job_config' ] = dict( GALAXY_DATATYPES_CONF_FILE=param_dict.get( 'GALAXY_DATATYPES_CONF_FILE' ), GALAXY_ROOT_DIR=param_dict.get( 'GALAXY_ROOT_DIR' ), TOOL_PROVIDED_JOB_METADATA_FILE=jobs.TOOL_PROVIDED_JOB_METADATA_FILE ) - json_filename = None - for i, ( out_name, data ) in enumerate( out_data.iteritems() ): - #use wrapped dataset to access certain values - wrapped_data = param_dict.get( out_name ) - #allow multiple files to be created - file_name = str( wrapped_data ) - extra_files_path = str( wrapped_data.files_path ) - data_dict = dict( out_data_name = out_name, - ext = data.ext, - dataset_id = data.dataset.id, - hda_id = data.id, - file_name = file_name, - extra_files_path = extra_files_path ) - json_params[ 'output_data' ].append( data_dict ) - if json_filename is None: - json_filename = file_name - out = open( json_filename, 'w' ) - out.write( simplejson.dumps( json_params ) ) - out.close() - -class DataSourceTool( OutputParameterJSONTool ): +class DataSourceTool( Tool ): """ Alternate implementation of Tool for data_source tools -- those that allow the user to query and extract data from another web site. @@ -2882,10 +2816,29 @@ class DataSourceTool( OutputParameterJSONTool ): def _build_GALAXY_URL_parameter( self ): return ToolParameter.build( self, ElementTree.XML( '' % self.id ) ) def parse_inputs( self, root ): - super( DataSourceTool, self ).parse_inputs( root ) + Tool.parse_inputs( self, root ) if 'GALAXY_URL' not in self.inputs: self.inputs[ 'GALAXY_URL' ] = self._build_GALAXY_URL_parameter() - self.inputs_by_page[0][ 'GALAXY_URL' ] = self.inputs[ 'GALAXY_URL' ] + def _prepare_datasource_json_list( self, param_list ): + rval = [] + for value in param_list: + if isinstance( value, dict ): + rval.append( self._prepare_datasource_json_param_dict( value ) ) + elif isinstance( value, list ): + rval.append( self._prepare_datasource_json_list( value ) ) + else: + rval.append( str( value ) ) + return rval + def _prepare_datasource_json_param_dict( self, param_dict ): + rval = {} + for key, value in param_dict.iteritems(): + if isinstance( value, dict ): + rval[ key ] = self._prepare_datasource_json_param_dict( value ) + elif isinstance( value, list ): + rval[ key ] = self._prepare_datasource_json_list( value ) + else: + rval[ key ] = str( value ) + return rval def exec_before_job( self, app, inp_data, out_data, param_dict=None ): if param_dict is None: param_dict = {} @@ -2895,7 +2848,7 @@ class DataSourceTool( OutputParameterJSONTool ): name = param_dict.get( 'name' ) json_params = {} - json_params[ 'param_dict' ] = self._prepare_json_param_dict( param_dict ) #it would probably be better to store the original incoming parameters here, instead of the Galaxy modified ones? + json_params[ 'param_dict' ] = self._prepare_datasource_json_param_dict( param_dict ) #it would probably be better to store the original incoming parameters here, instead of the Galaxy modified ones? json_params[ 'output_data' ] = [] json_params[ 'job_config' ] = dict( GALAXY_DATATYPES_CONF_FILE=param_dict.get( 'GALAXY_DATATYPES_CONF_FILE' ), GALAXY_ROOT_DIR=param_dict.get( 'GALAXY_ROOT_DIR' ), TOOL_PROVIDED_JOB_METADATA_FILE=jobs.TOOL_PROVIDED_JOB_METADATA_FILE ) json_filename = None @@ -2986,186 +2939,9 @@ class ImportHistoryTool( Tool ): class GenomeIndexTool( Tool ): tool_type = 'index_genome' -class DataManagerTool( OutputParameterJSONTool ): - tool_type = 'manage_data' - default_tool_action = DataManagerToolAction - - def __init__( self, config_file, root, app, guid=None, data_manager_id=None, **kwds ): - self.data_manager_id = data_manager_id - super( DataManagerTool, self ).__init__( config_file, root, app, guid=guid, **kwds ) - if self.data_manager_id is None: - self.data_manager_id = self.id - - #def parse_inputs( self, root ): - # super( DataManagerTool, self ).parse_inputs( root ) - # ''' - # if '__GALAXY_MOVE_OUTPUT_FILES__' not in self.inputs: - # self.inputs[ '__GALAXY_MOVE_OUTPUT_FILES__' ] = ToolParameter.build( self, ElementTree.XML( '' % self.app.config.data_manager_move_files ) ) - # print 'self.inputs_by_page',self.inputs_by_page - # self.inputs_by_page[0][ '__GALAXY_MOVE_OUTPUT_FILES__' ] = self.inputs[ '__GALAXY_MOVE_OUTPUT_FILES__' ] - # print 'self.inputs', self.inputs - # ''' - # #self.inputs[ '__DATA_MANAGER_ID__' ] = ToolParameter.build( self, ElementTree.XML( '' % ( self.data_manager_id ) ) ) - # #self.inputs_by_page[0][ '__DATA_MANAGER_ID__' ] = self.inputs[ '__DATA_MANAGER_ID__' ] - - def exec_after_process( self, app, inp_data, out_data, param_dict, job = None, **kwds ): - #run original exec_after_process - super( DataManagerTool, self ).exec_after_process( app, inp_data, out_data, param_dict, job = job, **kwds ) - #process results of tool - print 'exect after', self.id - print 'inp_data', inp_data - print 'out_data', out_data - print 'param_dict', param_dict - print 'job', job, job.state - if job and job.state == job.states.ERROR: - return - #print 'data_manager.output_ref',data_manager.output_ref - #data_manager = self.app.data_managers.get( self.id, None ) #fix me to not only use tool ID! - data_manager_id = job.data_manager_association.data_manager_id - data_manager = self.app.data_managers.get( data_manager_id, None ) - #TODO: need to be able to handle using a data manager tool for more than one manager - #manager id is currently same as tool id - assert data_manager is not None, "Invalid data manager (%s) requested. It may have been removed before the job completed." % ( data_manager_id ) - data_manager_dicts = {} - data_manager_dict = {} - #TODO: fix this merging below - for output_name, output_dataset in out_data.iteritems(): - try: - output_dict = simplejson.loads( open( output_dataset.file_name ).read() ) - except Exception, e: - log.warning( 'Error reading DataManagerTool json for "%s": %s' % ( output_name, e ) ) - continue - data_manager_dicts[ output_name ] = output_dict - print 'data_manager_dicts', data_manager_dicts - for key, value in output_dict.iteritems(): - if key not in data_manager_dict: - data_manager_dict[ key ] = {} - print 'key', key - print ' data_manager_dict[ key ]', data_manager_dict[ key ] - print 'value', value - data_manager_dict[ key ].update( value ) - data_manager_dict.update( output_dict ) - - print 'data_manager_dicts',data_manager_dicts - print 'data_manager_dict', data_manager_dict - data_tables_dict = data_manager_dict.get( 'data_tables', {} ) - #for data_table_name, data_table_values in data_tables_dict.iteritems(): - for data_table_name, data_table_columns in data_manager.data_tables.iteritems(): - print 'data_table_name', data_table_name - data_table_values = data_tables_dict.pop( data_table_name, None ) #data_tables_dict.get( data_table_name, [] ) - if not data_table_values: - log.warning( 'No values for data table "%s" were returned by the data manager "%s".' % ( data_table_name, data_manager.id ) ) - continue #next data table - data_table = app.tool_data_tables.get( data_table_name, None ) - if data_table is None: - log.error( 'The data manager "%s" returned an unknown data table "%s" with new entries "%s". These entries will not be created. Please confirm that an entry for "%s" exists in your "%s" file.' % ( data_manager.id, data_table_name, data_table_values, data_table_name, 'tool_data_table_conf.xml' ) ) - continue #next table name - output_ref_values = {} - if data_table_name in data_manager.output_ref_by_data_table: - for data_table_column, output_ref in data_manager.output_ref_by_data_table[ data_table_name ].iteritems(): - output_ref_dataset = out_data.get( output_ref, None ) - assert output_ref_dataset is not None, "Referenced output was not found." - output_ref_values[ data_table_column ] = output_ref_dataset - print 'output_ref_values', output_ref_values - - final_data_table_values = [] - if not isinstance( data_table_values, list ): - data_table_values = [ data_table_values ] - columns = data_table.get_column_name_list() - - try: - data_table_fh = open( data_table.filename, 'r+b' ) - except IOError, e: - log.warning( 'Error opening data table file (%s) with r+b, assuming file does not exist and will open as wb: %s' % ( data_table.filename, e ) ) - data_table_fh = open( data_table.filename, 'wb' ) - if os.stat( data_table.filename )[6] != 0: - # ensure last existing line ends with new line - data_table_fh.seek( -1, 2 ) #last char in file - last_char = data_table_fh.read() - if last_char not in [ '\n', '\r' ]: - data_table_fh.write( '\n' ) - for data_table_row in data_table_values: - data_table_value = dict( **data_table_row ) #keep original values here - for name, value in data_table_row.iteritems(): #FIXME: need to loop through here based upon order listed in data_manager config - if name in output_ref_values: - #TODO: Allow moving! - #if param_dict[ '__GALAXY_MOVE_OUTPUT_FILES__' ]: - # #FIXME: allow moving - # log.error( "\n\nShould be moving output files directory, but not implemented yet.\n" ) - # base_path = output_ref_values[ name ].extra_files_path - #else: - # base_path = output_ref_values[ name ].extra_files_path - moved = data_manager.process_move( data_table_name, name, output_ref_values[ name ].extra_files_path, **data_table_value ) - print 'moved', moved #should we always move? - data_table_value[ name ] = data_manager.process_value_translation( data_table_name, name, **data_table_value ) - final_data_table_values.append( data_table_value ) - fields = [] - for column_name in columns: - if column_name is None or column_name not in data_table_value: - fields.append( data_table.get_empty_field_by_name( column_name ) ) - else: - fields.append( data_table_value[ column_name ] ) - print 'fields', fields - #should we add a comment to file about automatically generated value here? - data_table_fh.write( "%s\n" % ( data_table.separator.join( self._replace_field_separators( fields, separator=data_table.separator ) ) ) ) #write out fields to disk - data_table.data.append( fields ) #add fields to loaded data table - print 'final_data_table_values', final_data_table_values - print 'data_table.data', data_table.data - data_table_fh.close() - for data_table_name, data_table_values in data_tables_dict.iteritems(): - #tool returned extra data table entries, but data table was not declared in data manager - #do not add these values, but do provide messages - log.warning( 'The data manager "%s" returned an undeclared data table "%s" with new entries "%s". These entries will not be created. Please confirm that an entry for "%s" exists in your "%s" file.' % ( data_manager.id, data_table_name, data_table_values, data_table_name, self.app.data_managers.filename ) ) - - def _replace_field_separators( self, fields, separator="\t", replace=None, comment_char=None ): - #make sure none of the fields contain separator - #make sure separator replace is different from comment_char, - #due to possible leading replace - if replace is None: - if separator == " ": - if comment_char == "\t": - replace = "_" - else: - replace = "\t" - else: - if comment_char == " ": - replace = "_" - else: - replace = " " - return map( lambda x: x.replace( separator, replace ), fields ) - - def get_default_history_by_trans( self, trans, create=False ): - def _create_data_manager_history( user ): - history = trans.app.model.History( name='Data Manager History (automatically created)', user=user ) - data_manager_association = trans.app.model.DataManagerHistoryAssociation( user=user, history=history ) - trans.sa_session.add_all( ( history, data_manager_association ) ) - trans.sa_session.flush() - return history - user = trans.user - assert user, 'You must be logged in to use this tool.' - history = user.data_manager_histories - if not history: - #create - if create: - history = _create_data_manager_history( user ) - else: - history = None - else: - for history in reversed( history ): - history = history.history - if not history.deleted: - break - if history.deleted: - if create: - history = _create_data_manager_history( user ) - else: - history = None - return history - - # Populate tool_type to ToolClass mappings tool_types = {} -for tool_class in [ Tool, DataDestinationTool, SetMetadataTool, DataSourceTool, AsyncDataSourceTool, DataManagerTool ]: +for tool_class in [ Tool, DataDestinationTool, SetMetadataTool, DataSourceTool, AsyncDataSourceTool ]: tool_types[ tool_class.tool_type ] = tool_class # ---- Utility classes to be factored out ----------------------------------- @@ -3207,12 +2983,6 @@ class ToolParameterValueWrapper( object ): """ def __nonzero__( self ): return bool( self.value ) - def get_display_text( self, quote=True ): - print 'self.input',self.input - print 'self.input.tool.app', self.input.tool.app - print 'self.value', self.value - print 'self.input.value_to_display_text( self.value, self.input.tool.app )', self.input.value_to_display_text( self.value, self.input.tool.app ) - return pipes.quote( self.input.value_to_display_text( self.value, self.input.tool.app ) ) class RawObjectWrapper( ToolParameterValueWrapper ): """ diff --git a/lib/galaxy/tools/actions/__init__.py b/lib/galaxy/tools/actions/__init__.py index 5e6315ec5ec..3f4fa6a7dad 100644 --- a/lib/galaxy/tools/actions/__init__.py +++ b/lib/galaxy/tools/actions/__init__.py @@ -168,7 +168,7 @@ class DefaultToolAction( object ): # Set history. if not history: - history = tool.get_default_history_by_trans( trans, create=True ) #trans..history + history = trans.history out_data = odict() # Collect any input datasets from the incoming parameters diff --git a/lib/galaxy/tools/data/__init__.py b/lib/galaxy/tools/data/__init__.py index f3df0c4371d..0d4643f5c8c 100644 --- a/lib/galaxy/tools/data/__init__.py +++ b/lib/galaxy/tools/data/__init__.py @@ -28,11 +28,6 @@ class ToolDataTableManager( object ): return self.data_tables.__getitem__( key ) def __contains__( self, key ): return self.data_tables.__contains__( key ) - def get( self, name, default=None ): - try: - return self[ name ] - except KeyError: - return default def load_from_config_file( self, config_filename, tool_data_path, from_shed_config=False ): """ This method is called under 3 conditions: @@ -130,8 +125,6 @@ class ToolDataTable( object ): def __init__( self, config_element, tool_data_path ): self.name = config_element.get( 'name' ) self.comment_char = config_element.get( 'comment_char' ) - self.empty_field_value = config_element.get( 'empty_field_value', '' ) - self.empty_field_values = {} for file_elem in config_element.findall( 'file' ): # There should only be one file_elem. if 'path' in file_elem.attrib: @@ -141,8 +134,6 @@ class ToolDataTable( object ): self.tool_data_file = None self.tool_data_path = tool_data_path self.missing_index_file = None - def get_empty_field_by_name( self, name ): - return self.empty_field_values.get( name, self.empty_field_value ) class TabularToolDataTable( ToolDataTable ): """ @@ -185,7 +176,6 @@ class TabularToolDataTable( ToolDataTable ): if os.path.exists( filename ): found = True all_rows.extend( self.parse_file_fields( open( filename ) ) ) - self.filename = filename else: # Since the path attribute can include a hard-coded path to a specific directory # (e.g., ) which may not be the same value @@ -197,7 +187,6 @@ class TabularToolDataTable( ToolDataTable ): if os.path.exists( corrected_filename ): found = True all_rows.extend( self.parse_file_fields( open( corrected_filename ) ) ) - self.filename = corrected_filename if not found: self.missing_index_file = filename log.warn( "Cannot find index file '%s' for tool data table '%s'" % ( filename, self.name ) ) @@ -233,9 +222,6 @@ class TabularToolDataTable( ToolDataTable ): self.columns[name] = index if index > self.largest_index: self.largest_index = index - empty_field_value = column_elem.get( 'empty_field_value', None ) - if empty_field_value is not None: - self.empty_field_values[ name ] = empty_field_value assert 'value' in self.columns, "Required 'value' column missing from column def" if 'name' not in self.columns: self.columns['name'] = self.columns['value'] @@ -254,19 +240,7 @@ class TabularToolDataTable( ToolDataTable ): fields = line.split( self.separator ) if self.largest_index < len( fields ): rval.append( fields ) - return rval - def get_column_name_list( self ): - rval = [] - for i in range( self.largest_index + 1 ): - found_column = False - for name, index in self.columns.iteritems(): - if index == i: - rval.append( name ) - found_column = True - break - if not found_column: - rval.append( None ) - return rval + return rval # Registry of tool data types by type_key tool_data_table_types = dict( [ ( cls.type_key, cls ) for cls in [ TabularToolDataTable ] ] ) diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py index 778beddb80b..8eb77ff50bd 100644 --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -880,9 +880,6 @@ class GenomeBuildParameter( SelectToolParameter ): >>> print p.filter_value( "hg17" ) hg17 """ - def __init__( self, *args, **kwds ): - super( GenomeBuildParameter, self ).__init__( *args, **kwds ) - self.static_options = [ ( value, key, False ) for key, value in util.dbnames ] def get_options( self, trans, other_values ): if not trans.history: yield 'unspecified', '?', False diff --git a/lib/galaxy/util/__init__.py b/lib/galaxy/util/__init__.py index e0ea0fc19f0..4e36d6b665a 100644 --- a/lib/galaxy/util/__init__.py +++ b/lib/galaxy/util/__init__.py @@ -567,22 +567,6 @@ def relpath( path, start = None ): return curdir return join( *rel_list ) -def relativize_symlinks( path, start=None, followlinks=False): - for root, dirs, files in os.walk( path, followlinks=followlinks ): - rel_start = None - for file_name in files: - symlink_file_name = os.path.join( root, file_name ) - if os.path.islink( symlink_file_name ): - symlink_target = os.readlink( symlink_file_name ) - if rel_start is None: - if start is None: - rel_start = root - else: - rel_start = start - rel_path = relpath( symlink_target, rel_start ) - os.remove( symlink_file_name ) - os.symlink( rel_path, symlink_file_name ) - def stringify_dictionary_keys( in_dict ): #returns a new dictionary #changes unicode keys into strings, only works on top level (does not recurse) diff --git a/lib/galaxy/webapps/community/config.py b/lib/galaxy/webapps/community/config.py index eb1f06c8711..ae7bebe9893 100644 --- a/lib/galaxy/webapps/community/config.py +++ b/lib/galaxy/webapps/community/config.py @@ -92,8 +92,6 @@ class Configuration( object ): self.job_handlers = [] self.tool_handlers = [] self.tool_runners = [] - # Error logging with sentry - self.sentry_dsn = kwargs.get( 'sentry_dsn', None ) # Where the tool shed hgweb.config file is stored - the default is the Galaxy installation directory. self.hgweb_config_dir = resolve_path( kwargs.get( 'hgweb_config_dir', '' ), self.root ) # Proxy features diff --git a/lib/galaxy/webapps/galaxy/controllers/tool_runner.py b/lib/galaxy/webapps/galaxy/controllers/tool_runner.py index e42a31c06d7..b99b8c82832 100644 --- a/lib/galaxy/webapps/galaxy/controllers/tool_runner.py +++ b/lib/galaxy/webapps/galaxy/controllers/tool_runner.py @@ -89,8 +89,7 @@ class ToolRunner( BaseUIController ): tool.input_translator.translate( params ) # We may be visiting Galaxy for the first time ( e.g., sending data from UCSC ), # so make sure to create a new history if we've never had one before. - #history = trans.get_history( create=True ) - history = tool.get_default_history_by_trans( trans, create=True ) + history = trans.get_history( create=True ) template, vars = tool.handle_input( trans, params.__dict__ ) if len( params ) > 0: trans.log_event( "Tool params: %s" % ( str( params ) ), tool_id=tool_id ) diff --git a/templates/webapps/galaxy/admin/index.mako b/templates/webapps/galaxy/admin/index.mako index 4bab8634280..e5a21911764 100644 --- a/templates/webapps/galaxy/admin/index.mako +++ b/templates/webapps/galaxy/admin/index.mako @@ -57,10 +57,8 @@
Manage quotas
Manage data libraries
%if trans.app.config.enable_beta_job_managers: -
Manage old local data
+
Manage local data
%endif - ##how to name this? -
Manage local (cached) data (beta)
diff --git a/tools/data_source/upload.xml b/tools/data_source/upload.xml index ab6e86deec0..a5fbfe147c5 100644 --- a/tools/data_source/upload.xml +++ b/tools/data_source/upload.xml @@ -33,7 +33,7 @@ - + not ( ( isinstance( value, unicode ) or isinstance( value, str ) ) and value != "" )