1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/changeset/b36526f8edbc/ changeset: b36526f8edbc user: greg date: 2012-01-16 16:43:33 summary: Fix for reloading a tool in the tool panel - make sure to keep the tool's tool shed related attributes when the tool is reloaded. Also make sure to send the guid attribute when loading a tool into the tool panel if the tool is contained in an installed tool shed repository. affected #: 3 files

diff -r e2ac92093afda6743ea68766be96c9c7a454568d -r b36526f8edbc2776225b5b9a8da7657771186025 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -163,6 +163,7 @@ tool.repository_name = repository_name tool.repository_owner = repository_owner tool.installed_changeset_revision = installed_changeset_revision + tool.guid = guid tool.old_id = elem.find( "id" ).text tool.version = elem.find( "version" ).text if self.app.config.get_bool( 'enable_tool_tags', False ): @@ -261,6 +262,15 @@ else: old_tool = self.tools_by_id[ tool_id ] new_tool = self.load_tool( old_tool.config_file ) + # The tool may have been installed from a tool shed, so set the tool shed attributes. + # Since the tool version may have changed, we don't override it here. + new_tool.id = old_tool.id + new_tool.guid = old_tool.guid + new_tool.tool_shed = old_tool.tool_shed + new_tool.repository_name = old_tool.repository_name + new_tool.repository_owner = old_tool.repository_owner + new_tool.installed_changeset_revision = old_tool.installed_changeset_revision + new_tool.old_id = old_tool.old_id # Replace old_tool with new_tool in self.tool_panel tool_key = 'tool_' + tool_id for key, val in self.tool_panel.items(): @@ -268,11 +278,9 @@ self.tool_panel[ key ] = new_tool break elif key.startswith( 'section' ): - section = val - for section_key, section_val in section.elems.items(): - if section_key == tool_key: - self.tool_panel[ key ].elems[ section_key ] = new_tool - break + if tool_key in val.elems: + self.tool_panel[ key ].elems[ tool_key ] = new_tool + break self.tools_by_id[ tool_id ] = new_tool message = "Reloaded the tool:<br/>" message += "<b>name:</b> %s<br/>" % old_tool.name @@ -462,18 +470,19 @@ self.repository_name = None self.repository_owner = None self.installed_changeset_revision = None + # The tool.id value will be the value of guid, but we'll keep the + # guid attribute since it is useful to have. + self.guid = guid self.old_id = None self.version = None # Parse XML element containing configuration self.parse( root, guid=guid ) - @property def sa_session( self ): """ Returns a SQLAlchemy session """ return self.app.model.context - def parse( self, root, guid=None ): """ Read tool configuration from the element `root` and fill in `self`. @@ -625,7 +634,6 @@ self.trackster_conf = TracksterConfig.parse( trackster_conf ) else: self.trackster_conf = None - def parse_inputs( self, root ): """ Parse the "<inputs>" element and create appropriate `ToolParameter`s. @@ -683,7 +691,6 @@ if not isinstance( param, ( HiddenToolParameter, BaseURLToolParameter ) ): self.input_required = True break - def parse_help( self, root ): """ Parse the help text for the tool. Formatted in reStructuredText. @@ -715,7 +722,6 @@ # 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 ) - def parse_outputs( self, root ): """ Parse <outputs> elements and fill in self.outputs (keyed by name) @@ -739,7 +745,6 @@ output.tool = self output.actions = ToolOutputActionGroup( output, data_elem.find( 'actions' ) ) self.outputs[ output.name ] = output - def parse_tests( self, tests_elem ): """ Parse any "<test>" elements, create a `ToolTestBuilder` for each and @@ -853,7 +858,6 @@ test.error = True test.exception = e self.tests.append( test ) - def parse_input_page( self, input_elem, enctypes ): """ Parse a page of inputs. This basically just calls 'parse_input_elem', @@ -868,7 +872,6 @@ else: display = None return display, inputs - def parse_input_elem( self, parent_elem, enctypes, context=None ): """ Parse a parent element whose children are inputs -- these could be @@ -960,7 +963,6 @@ param.ref_input = context[ param.data_ref ] self.input_params.append( param ) return rval - def parse_param_elem( self, input_elem, enctypes, context ): """ Parse a single "<param>" element and return a ToolParameter instance. @@ -976,7 +978,6 @@ for name in param.get_dependencies(): context[ name ].refresh_on_change = True return param - def parse_requirements( self, requirements_elem ): """ Parse each requirement from the <requirements> element and add to @@ -999,7 +1000,6 @@ method = None requirement = ToolRequirement( name=name, type=type, version=version, fabfile=fabfile, method=method ) self.requirements.append( requirement ) - def check_workflow_compatible( self ): """ Determine if a tool can be used in workflows. External tools and the @@ -1020,7 +1020,6 @@ # TODO: Anyway to capture tools that dynamically change their own # outputs? return True - def new_state( self, trans, all_pages=False ): """ Create a new `DefaultToolState` for this tool. It will be initialized @@ -1037,7 +1036,6 @@ inputs = self.inputs_by_page[ 0 ] self.fill_in_new_state( trans, inputs, state.inputs ) return state - def fill_in_new_state( self, trans, inputs, state, context=None ): """ Fill in a tool state dictionary with default values for all parameters @@ -1046,7 +1044,6 @@ context = ExpressionContext( state, context ) for input in inputs.itervalues(): state[ input.name ] = input.get_initial_value( trans, context ) - def get_param_html_map( self, trans, page=0, other_values={} ): """ Return a dictionary containing the HTML representation of each @@ -1062,14 +1059,12 @@ raise Exception( "'get_param_html_map' only supported for simple paramters" ) rval[key] = param.get_html( trans, other_values=other_values ) return rval - def get_param( self, key ): """ Returns the parameter named `key` or None if there is no such parameter. """ return self.inputs.get( key, None ) - def get_hook(self, name): """ Returns an object from the code file referenced by `code_namespace` @@ -1082,7 +1077,6 @@ elif name in self.code_namespace: return self.code_namespace[name] return None - def visit_inputs( self, value, callback ): """ Call the function `callback` on each parameter of this tool. Visits @@ -1099,7 +1093,6 @@ callback( "", input, value[input.name] ) else: input.visit_inputs( "", value[input.name], callback ) - def handle_input( self, trans, incoming, history=None ): """ Process incoming parameters for this tool from the dict `incoming`, @@ -1177,7 +1170,6 @@ pass # Just a refresh, render the form with updated state and errors. return 'tool_form.mako', dict( errors=errors, tool_state=state ) - def find_fieldstorage( self, x ): if isinstance( x, FieldStorage ): raise InterruptedUpload( None ) @@ -1185,7 +1177,6 @@ [ self.find_fieldstorage( y ) for y in x.values() ] elif type( x ) is types.ListType: [ self.find_fieldstorage( y ) for y in x ] - def handle_interrupted( self, trans, inputs ): """ Upon handling inputs, if it appears that we have received an incomplete @@ -1216,7 +1207,6 @@ return 'message.mako', dict( status='error', message='Your upload was interrupted. If this was uninentional, please retry it.', refresh_frames=[], cont=None ) - def update_state( self, trans, inputs, state, incoming, prefix="", context=None, update_only=False, old_errors={}, item_callback=None ): """ @@ -1458,7 +1448,6 @@ else: raise Exception( "Unexpected parameter type" ) return args - def execute( self, trans, incoming={}, set_output_hid=True, history=None, **kwargs ): """ Execute the tool using parameter values in `incoming`. This just @@ -1467,13 +1456,10 @@ when run will build the tool's outputs, e.g. `DefaultToolAction`. """ return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs ) - def params_to_strings( self, params, app ): return params_to_strings( self.inputs, params, app ) - def params_from_strings( self, params, app, ignore_errors=False ): return params_from_strings( self.inputs, params, app, ignore_errors ) - def check_and_update_param_values( self, values, trans ): """ Check that all parameters have values, and fill in with default @@ -1483,7 +1469,6 @@ messages = {} self.check_and_update_param_values_helper( self.inputs, values, trans, messages ) return messages - def check_and_update_param_values_helper( self, inputs, values, trans, messages, context=None, prefix="" ): """ Recursive helper for `check_and_update_param_values_helper` @@ -1529,7 +1514,6 @@ else: # Regular tool parameter, no recursion needed pass - def handle_unvalidated_param_values( self, input_values, app ): """ Find any instances of `UnvalidatedValue` within input_values and @@ -1540,7 +1524,6 @@ if not self.check_values: return self.handle_unvalidated_param_values_helper( self.inputs, input_values, app ) - def handle_unvalidated_param_values_helper( self, inputs, input_values, app, context=None, prefix="" ): """ Recursive helper for `handle_unvalidated_param_values` @@ -1582,7 +1565,6 @@ % ( prefix, input.label, e ) raise LateValidationError( message ) input_values[ input.name ] = value - def handle_job_failure_exception( self, e ): """ Called by job.fail when an exception is generated to allow generation @@ -1594,7 +1576,6 @@ if isinstance( e, LateValidationError ): message = e.message return message - def build_param_dict( self, incoming, input_datasets, output_datasets, output_paths, job_working_directory ): """ Build the dictionary of parameters for substituting into the command @@ -1734,7 +1715,6 @@ param_dict['__datatypes_config__'] = param_dict['GALAXY_DATATYPES_CONF_FILE'] = self.app.datatypes_registry.integrated_datatypes_configs # Return the dictionary of parameters return param_dict - def build_param_file( self, param_dict, directory=None ): """ Build temporary file for file based parameter transfer if needed @@ -1754,7 +1734,6 @@ return param_filename else: return None - def build_config_files( self, param_dict, directory=None ): """ Build temporary file for file based parameter transfer if needed @@ -1775,7 +1754,6 @@ param_dict[name] = config_filename config_filenames.append( config_filename ) return config_filenames - def build_command_line( self, param_dict ): """ Build command line to invoke this tool given a populated param_dict @@ -1799,7 +1777,6 @@ command_line = command_line.replace(executable, abs_executable, 1) command_line = self.interpreter + " " + command_line return command_line - def build_dependency_shell_commands( self ): """ Return a list of commands to be run to populate the current @@ -1820,7 +1797,6 @@ else: commands.append( 'PACKAGE_BASE=%s; export PACKAGE_BASE; . %s' % ( base_path, script_file ) ) return commands - def build_redirect_url_params( self, param_dict ): """ Substitute parameter values into self.redirect_url_params @@ -1833,7 +1809,6 @@ # Remove newlines redirect_url_params = redirect_url_params.replace( "\n", " " ).replace( "\r", " " ) return redirect_url_params - def parse_redirect_url( self, data, param_dict ): """ Parse the REDIRECT_URL tool param. Tools that send data to an external @@ -1873,7 +1848,6 @@ USERNAME = 'Anonymous' redirect_url += "&USERNAME=%s" % USERNAME return redirect_url - def call_hook( self, hook_name, *args, **kwargs ): """ Call the custom code hook function identified by 'hook_name' if any, @@ -1886,19 +1860,15 @@ except Exception, e: e.args = ( "Error in '%s' hook '%s', original message: %s" % ( self.name, hook_name, e.args[0] ) ) raise - def exec_before_job( self, app, inp_data, out_data, param_dict={} ): pass - def exec_after_process( self, app, inp_data, out_data, param_dict, job = None ): pass - def job_failed( self, job_wrapper, message, exception = False ): """ Called when a job has failed """ pass - def collect_associated_files( self, output, job_working_directory ): """ Find extra files in the job working directory and move them into @@ -1922,7 +1892,6 @@ shutil.rmtree(temp_file_path) except: continue - def collect_child_datasets( self, output): """ Look for child dataset files, create HDA and attach to parent. @@ -1983,7 +1952,6 @@ self.sa_session.add( child_dataset ) self.sa_session.flush() return children - def collect_primary_datasets( self, output): """ Find any additional datasets generated by a tool and attach (for @@ -2062,12 +2030,10 @@

def _build_GALAXY_URL_parameter( self ): return ToolParameter.build( self, ElementTree.XML( '<param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=%s" />' % self.id ) ) - def parse_inputs( self, root ): Tool.parse_inputs( self, root ) if 'GALAXY_URL' not in self.inputs: self.inputs[ 'GALAXY_URL' ] = self._build_GALAXY_URL_parameter() - def _prepare_datasource_json_list( self, param_list ): rval = [] for value in param_list: @@ -2088,7 +2054,6 @@ 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 = {} @@ -2111,7 +2076,6 @@ cur_dbkey = param_dict.get( cur_base_param_name + 'dkey', dbkey ) cur_info = param_dict.get( cur_base_param_name + 'info', info ) cur_data_type = param_dict.get( cur_base_param_name + 'data_type', data_type ) - if cur_name: data.name = cur_name if not data.info and cur_info: @@ -2122,16 +2086,13 @@ data.extension = cur_data_type 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' ) @@ -2176,7 +2137,6 @@ dataset.set_peek() self.sa_session.add( dataset ) self.sa_session.flush() - def job_failed( self, job_wrapper, message, exception = False ): job = job_wrapper.sa_session.query( model.Job ).get( job_wrapper.job_id ) if job: @@ -2334,19 +2294,16 @@ self.dataset = dataset self.metadata = self.MetadataWrapper( dataset.metadata ) self.false_path = false_path - def __str__( self ): if self.false_path is not None: return self.false_path else: return self.dataset.file_name - def __getattr__( self, key ): if self.false_path is not None and key == 'file_name': return self.false_path else: return getattr( self.dataset, key ) - def __nonzero__( self ): return bool( self.dataset )

diff -r e2ac92093afda6743ea68766be96c9c7a454568d -r b36526f8edbc2776225b5b9a8da7657771186025 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -347,7 +347,7 @@ for tool_dict in metadata_dict[ 'tools' ]: relative_path = tool_dict[ 'tool_config' ] guid = tool_dict[ 'guid' ] - tool = app.toolbox.load_tool( os.path.abspath( relative_path ) ) + tool = app.toolbox.load_tool( os.path.abspath( relative_path ), guid=guid ) repository_tools_tups.append( ( relative_path, guid, tool ) ) return repository_tools_tups def get_tool_id_guid_map( app, tool_id, version, tool_shed, repository_owner, repository_name ): @@ -398,7 +398,7 @@ # TODO: Do more here than logging an exception. log.debug( exception_msg ) # Reload the tool into the local list of repository_tools_tups. - repository_tool = app.toolbox.load_tool( os.path.join( tool_path, tup_path ) ) + repository_tool = app.toolbox.load_tool( os.path.join( tool_path, tup_path ), guid=guid ) repository_tools_tups[ index ] = ( tup_path, repository_tool ) return repository_tools_tups def handle_missing_index_file( app, tool_path, sample_files, repository_tools_tups ): @@ -425,7 +425,7 @@ missing_files_handled.append( missing_tail ) break # Reload the tool into the local list of repository_tools_tups. - repository_tool = app.toolbox.load_tool( os.path.join( tool_path, tup_path ) ) + repository_tool = app.toolbox.load_tool( os.path.join( tool_path, tup_path ), guid=guid ) repository_tools_tups[ index ] = ( tup_path, guid, repository_tool ) return repository_tools_tups def handle_tool_dependencies( current_working_dir, repo_files_dir, repository_tools_tups ):

diff -r e2ac92093afda6743ea68766be96c9c7a454568d -r b36526f8edbc2776225b5b9a8da7657771186025 lib/galaxy/web/controllers/admin_toolshed.py --- a/lib/galaxy/web/controllers/admin_toolshed.py +++ b/lib/galaxy/web/controllers/admin_toolshed.py @@ -467,6 +467,7 @@ tool.repository_name = repository.name tool.repository_owner = repository.owner tool.installed_changeset_revision = repository.installed_changeset_revision + tool.guid = guid # Set the tool's old_id to the id used before the tool shed existed. tool.old_id = tool.id # Set the tool's id to the tool shed guid. @@ -610,7 +611,7 @@ for tool_metadata_dict in repository.metadata[ 'tools' ]: if tool_metadata_dict[ 'id' ] == tool_id: metadata = tool_metadata_dict - tool = trans.app.toolbox.load_tool( os.path.abspath( metadata[ 'tool_config' ] ) ) + tool = trans.app.toolbox.load_tool( os.path.abspath( metadata[ 'tool_config' ] ), guid=metadata[ 'guid' ] ) break return trans.fill_template( "/admin/tool_shed_repository/view_tool_metadata.mako", repository=repository,

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