Python DefaultToolState.decode方法代码示例

# 需要导入模块: from galaxy.tools import DefaultToolState [as 别名]
# 或者: from galaxy.tools.DefaultToolState import decode [as 别名]
 def upload_async_create( self, trans, tool_id=None, **kwd ):
     """
     Precreate datasets for asynchronous uploading.
     """
     cntrller = kwd.get( 'cntrller', '' )
     roles = kwd.get( 'roles', False )
     if roles:
         # The user associated the DATASET_ACCESS permission on the uploaded datasets with 1 or more roles.
         # We need to ensure that the roles are legitimately derived from the roles associated with the LIBRARY_ACCESS
         # permission if the library is not public ( this should always be the case since any ill-legitimate roles
         # were filtered out of the roles displayed on the upload form.  In addition, we need to ensure that the user
         # did not associated roles that would make the dataset in-accessible by everyone.
         library_id = trans.app.security.decode_id( kwd.get( 'library_id', '' ) )
         vars = dict( DATASET_ACCESS_in=roles )
         permissions, in_roles, error, msg = trans.app.security_agent.derive_roles_from_access( trans, library_id, cntrller, library=True, **vars )
         if error:
             return [ 'error', msg ]
     def create_dataset( name ):
         ud = Bunch( name=name, file_type=None, dbkey=None )
         if nonfile_params.get( 'folder_id', False ):
             replace_id = nonfile_params.get( 'replace_id', None )
             if replace_id not in [ None, 'None' ]:
                 replace_dataset = trans.sa_session.query( trans.app.model.LibraryDataset ).get( trans.security.decode_id( replace_id ) )
             else:
                 replace_dataset = None
             # FIXME: instead of passing params here ( chiech have been process by util.Params(), the original kwd
             # should be passed so that complex objects that may have been included in the initial request remain.
             library_bunch = upload_common.handle_library_params( trans, nonfile_params, nonfile_params.folder_id, replace_dataset )
         else:
             library_bunch = None
         return upload_common.new_upload( trans, cntrller, ud, library_bunch=library_bunch, state=trans.app.model.HistoryDatasetAssociation.states.UPLOAD )
     tool = self.get_toolbox().get_tool( tool_id )
     if not tool:
         return False # bad tool_id
     nonfile_params = galaxy.util.Params( kwd, sanitize=False )
     if kwd.get( 'tool_state', None ) not in ( None, 'None' ):
         encoded_state = galaxy.util.string_to_object( kwd["tool_state"] )
         tool_state = DefaultToolState()
         tool_state.decode( encoded_state, tool, trans.app )
     else:
         tool_state = tool.new_state( trans )
     tool.update_state( trans, tool.inputs, tool_state.inputs, kwd, update_only = True )
     datasets = []
     dataset_upload_inputs = []
     for input_name, input in tool.inputs.iteritems():
         if input.type == "upload_dataset":
             dataset_upload_inputs.append( input )
     assert dataset_upload_inputs, Exception( "No dataset upload groups were found." )
     for dataset_upload_input in dataset_upload_inputs:
         d_type = dataset_upload_input.get_datatype( trans, kwd )
         if d_type.composite_type is not None:
             datasets.append( create_dataset( dataset_upload_input.get_composite_dataset_name( kwd ) ) )
         else:
             params = Bunch( ** tool_state.inputs[dataset_upload_input.name][0] )
             if params.file_data not in [ None, "" ]:
                 name = params.file_data
                 if name.count('/'):
                     name = name.rsplit('/',1)[1]
                 if name.count('\\'):
                     name = name.rsplit('\\',1)[1]
                 datasets.append( create_dataset( name ) )
             if params.url_paste not in [ None, "" ]:
                 url_paste = params.url_paste.replace( '\r', '' ).split( '\n' )
                 url = False
                 for line in url_paste:
                     line = line.rstrip( '\r\n' ).strip()
                     if not line:
                         continue
                     elif line.lower().startswith( 'http://' ) or line.lower().startswith( 'ftp://' ) or line.lower().startswith( 'https://' ):
                         url = True
                         datasets.append( create_dataset( line ) )
                     else:
                         if url:
                             continue # non-url when we've already processed some urls
                         else:
                             # pasted data
                             datasets.append( create_dataset( 'Pasted Entry' ) )
                             break
     return [ d.id for d in datasets ]

# 需要导入模块: from galaxy.tools import DefaultToolState [as 别名]
# 或者: from galaxy.tools.DefaultToolState import decode [as 别名]
 def decode_runtime_state( self, trans, string ):
     fake_tool = Bunch( inputs = self.get_runtime_inputs() )
     state = DefaultToolState()
     state.decode( string, fake_tool, trans.app )
     return state

# 需要导入模块: from galaxy.tools import DefaultToolState [as 别名]
# 或者: from galaxy.tools.DefaultToolState import decode [as 别名]
class WorkflowModule(object):

    def __init__(self, trans, content_id=None, **kwds):
        self.trans = trans
        self.content_id = content_id
        self.state = DefaultToolState()

    # ---- Creating modules from various representations ---------------------

    @classmethod
    def from_dict(Class, trans, d, **kwds):
        module = Class(trans, **kwds)
        module.recover_state(d.get("tool_state"))
        module.label = d.get("label")
        return module

    @classmethod
    def from_workflow_step(Class, trans, step, **kwds):
        module = Class(trans, **kwds)
        module.recover_state(step.tool_inputs)
        module.label = step.label
        return module

    # ---- Saving in various forms ------------------------------------------

    def save_to_step(self, step):
        step.type = self.type
        step.tool_inputs = self.get_state()

    # ---- General attributes -----------------------------------------------

    def get_type(self):
        return self.type

    def get_name(self):
        return self.name

    def get_version(self):
        return None

    def get_content_id(self):
        """ If this component has an identifier external to the step (such
        as a tool or another workflow) return the identifier for that content.
        """
        return None

    def get_tooltip(self, static_path=''):
        return None

    # ---- Configuration time -----------------------------------------------

    def get_state(self, nested=True):
        """ Return a serializable representation of the persistable state of
        the step.
        """
        inputs = self.get_inputs()
        if inputs:
            return self.state.encode(Bunch(inputs=inputs), self.trans.app, nested=nested)
        else:
            return self.state.inputs

    def recover_state(self, state, **kwds):
        """ Recover state `dict` from simple dictionary describing configuration
        state (potentially from persisted step state).

        Sub-classes should supply a `default_state` method which contains the
        initial state `dict` with key, value pairs for all available attributes.
        """
        self.state = DefaultToolState()
        inputs = self.get_inputs()
        if inputs:
            self.state.decode(state, Bunch(inputs=inputs), self.trans.app)
        else:
            self.state.inputs = safe_loads(state) or {}

    def get_errors(self):
        """ This returns a step related error message as string or None """
        return None

    def get_inputs(self):
        """ This returns inputs displayed in the workflow editor """
        return {}

    def get_data_inputs(self):
        """ Get configure time data input descriptions. """
        return []

    def get_data_outputs(self):
        return []

    def get_post_job_actions(self, incoming):
        return []

    def check_and_update_state(self):
        """
        If the state is not in sync with the current implementation of the
        module, try to update. Returns a list of messages to be displayed
        """
        pass

#.........这里部分代码省略.........

# 需要导入模块: from galaxy.tools import DefaultToolState [as 别名]
# 或者: from galaxy.tools.DefaultToolState import decode [as 别名]
 def decode_runtime_state(self, runtime_state):
     """ Takes the serialized runtime state and decodes it when running the workflow. """
     state = DefaultToolState()
     state.decode(runtime_state, Bunch(inputs=self.get_runtime_inputs()), self.trans.app)
     return state

# 需要导入模块: from galaxy.tools import DefaultToolState [as 别名]
# 或者: from galaxy.tools.DefaultToolState import decode [as 别名]
 def __string_to_state( self, state_string ):
     encoded_state = string_to_object( state_string )
     state = DefaultToolState()
     state.decode( encoded_state, self.tool, self.app )
     return state

# 需要导入模块: from galaxy.tools import DefaultToolState [as 别名]
# 或者: from galaxy.tools.DefaultToolState import decode [as 别名]
 def upload_async_create( self, trans, tool_id=None, **kwd ):
     """
     Precreate datasets for asynchronous uploading.
     """
     def create_dataset( name, history ):
         data = trans.app.model.HistoryDatasetAssociation( create_dataset = True )
         data.name = name
         data.state = data.states.UPLOAD
         data.history = history
         data.flush()
         history.add_dataset( data )
         return data
     tool = self.get_toolbox().tools_by_id.get( tool_id, None )
     if not tool:
         return False # bad tool_id
     #params = util.Params( kwd, sanitize=tool.options.sanitize, tool=tool )
     if "tool_state" in kwd:
         encoded_state = util.string_to_object( kwd["tool_state"] )
         tool_state = DefaultToolState()
         tool_state.decode( encoded_state, tool, trans.app )
     else:
         tool_state = tool.new_state( trans )
     errors = tool.update_state( trans, tool.inputs, tool_state.inputs, kwd, update_only = True )
     datasets = []
     dataset_upload_inputs = []
     for input_name, input in tool.inputs.iteritems():
         if input.type == "upload_dataset":
             dataset_upload_inputs.append( input )
     assert dataset_upload_inputs, Exception( "No dataset upload groups were found." )
     for dataset_upload_input in dataset_upload_inputs:
         d_type = dataset_upload_input.get_datatype( trans, kwd )
         
         if d_type.composite_type is not None:
             datasets.append( create_dataset( 'Uploaded Composite Dataset (%s)' % dataset_upload_input.get_datatype_ext( trans, kwd ), trans.history ) )
         else:
             params = Bunch( ** tool_state.inputs[dataset_upload_input.name][0] )
             if params.file_data not in [ None, "" ]:
                 name = params.file_data
                 if name.count('/'):
                     name = name.rsplit('/',1)[1]
                 if name.count('\\'):
                     name = name.rsplit('\\',1)[1]
                 datasets.append( create_dataset( name, trans.history ) )
             if params.url_paste not in [ None, "" ]:
                 url_paste = params.url_paste.replace( '\r', '' ).split( '\n' )
                 url = False
                 for line in url_paste:
                     line = line.rstrip( '\r\n' ).strip()
                     if not line:
                         continue
                     elif line.lower().startswith( 'http://' ) or line.lower().startswith( 'ftp://' ):
                         url = True
                         datasets.append( create_dataset( line, trans.history ) )
                     else:
                         if url:
                             continue # non-url when we've already processed some urls
                         else:
                             # pasted data
                             datasets.append( create_dataset( 'Pasted Entry', trans.history ) )
                             break
     if datasets:
         trans.model.flush()
     return [ d.id for d in datasets ]

# 需要导入模块: from galaxy.tools import DefaultToolState [as 别名]
# 或者: from galaxy.tools.DefaultToolState import decode [as 别名]
 def upload_async_create( self, trans, tool_id=None, **kwd ):
     """
     Precreate datasets for asynchronous uploading.
     """
     permissions = trans.app.security_agent.history_get_default_permissions( trans.history )
     def create_dataset( name ):
         ud = Bunch( name=name, file_type=None, dbkey=None )
         if nonfile_params.get( 'folder_id', False ):
             replace_id = nonfile_params.get( 'replace_id', None )
             if replace_id not in [ None, 'None' ]:
                 replace_dataset = trans.sa_session.query( l.LibraryDataset ).get( int( replace_id ) )
             else:
                 replace_dataset = None
             library_bunch = upload_common.handle_library_params( trans, nonfile_params, nonfile_params.folder_id, replace_dataset )
         else:
             library_bunch = None
         return upload_common.new_upload( trans, ud, library_bunch=library_bunch, state=trans.app.model.HistoryDatasetAssociation.states.UPLOAD )
     tool = self.get_toolbox().tools_by_id.get( tool_id, None )
     if not tool:
         return False # bad tool_id
     nonfile_params = util.Params( kwd, sanitize=False )
     if kwd.get( 'tool_state', None ) not in ( None, 'None' ):
         encoded_state = util.string_to_object( kwd["tool_state"] )
         tool_state = DefaultToolState()
         tool_state.decode( encoded_state, tool, trans.app )
     else:
         tool_state = tool.new_state( trans )
     errors = tool.update_state( trans, tool.inputs, tool_state.inputs, kwd, update_only = True )
     datasets = []
     dataset_upload_inputs = []
     for input_name, input in tool.inputs.iteritems():
         if input.type == "upload_dataset":
             dataset_upload_inputs.append( input )
     assert dataset_upload_inputs, Exception( "No dataset upload groups were found." )
     for dataset_upload_input in dataset_upload_inputs:
         d_type = dataset_upload_input.get_datatype( trans, kwd )
         
         if d_type.composite_type is not None:
             datasets.append( create_dataset( 'Uploaded Composite Dataset (%s)' % dataset_upload_input.get_datatype_ext( trans, kwd ) ) )
         else:
             params = Bunch( ** tool_state.inputs[dataset_upload_input.name][0] )
             if params.file_data not in [ None, "" ]:
                 name = params.file_data
                 if name.count('/'):
                     name = name.rsplit('/',1)[1]
                 if name.count('\\'):
                     name = name.rsplit('\\',1)[1]
                 datasets.append( create_dataset( name ) )
             if params.url_paste not in [ None, "" ]:
                 url_paste = params.url_paste.replace( '\r', '' ).split( '\n' )
                 url = False
                 for line in url_paste:
                     line = line.rstrip( '\r\n' ).strip()
                     if not line:
                         continue
                     elif line.lower().startswith( 'http://' ) or line.lower().startswith( 'ftp://' ):
                         url = True
                         datasets.append( create_dataset( line ) )
                     else:
                         if url:
                             continue # non-url when we've already processed some urls
                         else:
                             # pasted data
                             datasets.append( create_dataset( 'Pasted Entry' ) )
                             break
     return [ d.id for d in datasets ]