1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/changeset/25db1453bb2e/ changeset: 25db1453bb2e user: greg date: 2012-03-30 20:19:44 summary: Enhance odict to enable insertion into a specified location in it's keys, and enhance integrated_tool_panel generation to take advantage of this. New tool panel items will now be inserted into an existing integrated_tool_panel.xml file in the location in whatever tool panel configuration file the new item has been added. affected #: 2 files

diff -r 0626ddb49084b94248e9621d584409d398fd546d -r 25db1453bb2e55d7d58d407364ce71001bd24096 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -114,17 +114,17 @@ tool_path = self.tool_root_dir # Only load the panel_dict under certain conditions. load_panel_dict = not self.integrated_tool_panel_config_has_contents - for elem in root: + for index, elem in enumerate( root ): if parsing_shed_tool_conf: config_elems.append( elem ) if elem.tag == 'tool': - self.load_tool_tag_set( elem, self.tool_panel, self.integrated_tool_panel, tool_path, load_panel_dict, guid=elem.get( 'guid' ) ) + self.load_tool_tag_set( elem, self.tool_panel, self.integrated_tool_panel, tool_path, load_panel_dict, guid=elem.get( 'guid' ), index=index ) elif elem.tag == 'workflow': - self.load_workflow_tag_set( elem, self.tool_panel, self.integrated_tool_panel, load_panel_dict ) + self.load_workflow_tag_set( elem, self.tool_panel, self.integrated_tool_panel, load_panel_dict, index=index ) elif elem.tag == 'section': - self.load_section_tag_set( elem, tool_path, load_panel_dict ) + self.load_section_tag_set( elem, tool_path, load_panel_dict, index=index ) elif elem.tag == 'label': - self.load_label_tag_set( elem, self.tool_panel, self.integrated_tool_panel, load_panel_dict ) + self.load_label_tag_set( elem, self.tool_panel, self.integrated_tool_panel, load_panel_dict, index=index ) if parsing_shed_tool_conf: shed_tool_conf_dict = dict( config_filename=config_filename, tool_path=tool_path, @@ -286,7 +286,7 @@ self.app.model.ToolShedRepository.table.c.owner == owner, self.app.model.ToolShedRepository.table.c.installed_changeset_revision == installed_changeset_revision ) ) \ .first() - def load_tool_tag_set( self, elem, panel_dict, integrated_panel_dict, tool_path, load_panel_dict, guid=None ): + def load_tool_tag_set( self, elem, panel_dict, integrated_panel_dict, tool_path, load_panel_dict, guid=None, index=None ): try: path = elem.get( "file" ) if guid is None: @@ -354,10 +354,13 @@ if load_panel_dict: panel_dict[ key ] = tool # Always load the tool into the integrated_panel_dict, or it will not be included in the integrated_tool_panel.xml file. - integrated_panel_dict[ key ] = tool + if key in integrated_panel_dict or index is None: + integrated_panel_dict[ key ] = tool + else: + integrated_panel_dict.insert( index, key, tool ) except: log.exception( "Error reading tool from path: %s" % path ) - def load_workflow_tag_set( self, elem, panel_dict, integrated_panel_dict, load_panel_dict ): + def load_workflow_tag_set( self, elem, panel_dict, integrated_panel_dict, load_panel_dict, index=None ): try: # TODO: should id be encoded? workflow_id = elem.get( 'id' ) @@ -367,16 +370,22 @@ if load_panel_dict: panel_dict[ key ] = workflow # Always load workflows into the integrated_panel_dict. - integrated_panel_dict[ key ] = workflow + if key in integrated_panel_dict or index is None: + integrated_panel_dict[ key ] = workflow + else: + integrated_panel_dict.insert( index, key, workflow ) except: log.exception( "Error loading workflow: %s" % workflow_id ) - def load_label_tag_set( self, elem, panel_dict, integrated_panel_dict, load_panel_dict ): + def load_label_tag_set( self, elem, panel_dict, integrated_panel_dict, load_panel_dict, index=None ): label = ToolSectionLabel( elem ) key = 'label_' + label.id if load_panel_dict: panel_dict[ key ] = label - integrated_panel_dict[ key ] = label - def load_section_tag_set( self, elem, tool_path, load_panel_dict ): + if key in integrated_panel_dict or index is None: + integrated_panel_dict[ key ] = label + else: + integrated_panel_dict.insert( index, key, label ) + def load_section_tag_set( self, elem, tool_path, load_panel_dict, index=None ): key = 'section_' + elem.get( "id" ) if key in self.tool_panel: section = self.tool_panel[ key ] @@ -390,17 +399,20 @@ else: integrated_section = ToolSection( elem ) integrated_elems = integrated_section.elems - for sub_elem in elem: + for sub_index, sub_elem in enumerate( elem ): if sub_elem.tag == 'tool': - self.load_tool_tag_set( sub_elem, elems, integrated_elems, tool_path, load_panel_dict, guid=sub_elem.get( 'guid' ) ) + self.load_tool_tag_set( sub_elem, elems, integrated_elems, tool_path, load_panel_dict, guid=sub_elem.get( 'guid' ), index=sub_index ) elif sub_elem.tag == 'workflow': - self.load_workflow_tag_set( sub_elem, elems, integrated_elems, load_panel_dict ) + self.load_workflow_tag_set( sub_elem, elems, integrated_elems, load_panel_dict, index=sub_index ) elif sub_elem.tag == 'label': - self.load_label_tag_set( sub_elem, elems, integrated_elems, load_panel_dict ) + self.load_label_tag_set( sub_elem, elems, integrated_elems, load_panel_dict, index=sub_index ) if load_panel_dict: self.tool_panel[ key ] = section # Always load sections into the integrated_tool_panel. - self.integrated_tool_panel[ key ] = integrated_section + if key in self.integrated_tool_panel or index is None: + 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 ): """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

diff -r 0626ddb49084b94248e9621d584409d398fd546d -r 25db1453bb2e55d7d58d407364ce71001bd24096 lib/galaxy/util/odict.py --- a/lib/galaxy/util/odict.py +++ b/lib/galaxy/util/odict.py @@ -11,23 +11,22 @@ This dictionary class extends UserDict to record the order in which items are added. Calling keys(), values(), items(), etc. will return results in this order. + """ + def __init__( self, dict = None ): + self._keys = [] + UserDict.__init__( self, dict )

- I've added iterkeys, itervalues, iteritems - """ - def __init__(self, dict = None): - self._keys = [] - UserDict.__init__(self, dict) + def __delitem__( self, key ): + UserDict.__delitem__( self, key ) + self._keys.remove( key )

- def __delitem__(self, key): - UserDict.__delitem__(self, key) - self._keys.remove(key) + def __setitem__( self, key, item ): + UserDict.__setitem__( self, key, item ) + if key not in self._keys: + self._keys.append( key )

- def __setitem__(self, key, item): - UserDict.__setitem__(self, key, item) - if key not in self._keys: self._keys.append(key) - - def clear(self): - UserDict.clear(self) + def clear( self ): + UserDict.clear( self ) self._keys = []

def copy(self): @@ -35,49 +34,43 @@ new.update( self ) return new

- def items(self): - return zip(self._keys, self.values()) + def items( self ): + return zip( self._keys, self.values() )

- def keys(self): + def keys( self ): return self._keys[:]

- def popitem(self): + def popitem( self ): try: key = self._keys[-1] except IndexError: - raise KeyError('dictionary is empty') + raise KeyError( 'dictionary is empty' ) + val = self[ key ] + del self[ key ] + return ( key, val )

- val = self[key] - del self[key] + def setdefault( self, key, failobj=None ): + if key not in self._keys: + self._keys.append( key ) + return UserDict.setdefault( self, key, failobj )

- return (key, val) + def update( self, dict ): + for ( key, val ) in dict.items(): + self.__setitem__( key, val )

- def setdefault(self, key, failobj = None): - if key not in self._keys: self._keys.append(key) - return UserDict.setdefault(self, key, failobj) + def values( self ): + return map( self.get, self._keys )

- def update(self, dict): - UserDict.update(self, dict) - for key in dict.keys(): - if key not in self._keys: self._keys.append(key) - - def update(self, dict): - for (key,val) in dict.items(): - self.__setitem__(key,val) - - def values(self): - return map(self.get, self._keys) - - def iterkeys(self): + def iterkeys( self ): return iter( self._keys )

- def itervalues(self): + def itervalues( self ): for key in self._keys: - yield self.get(key) + yield self.get( key )

- def iteritems(self): + def iteritems( self ): for key in self._keys: - yield key, self.get(key) + yield key, self.get( key )

def __iter__( self ): for key in self._keys: @@ -86,3 +79,7 @@ def reverse( self ): self._keys.reverse()

+ def insert( self, index, key, item ): + if key not in self._keys: + self._keys.insert( index, key ) + UserDict.__setitem__( self, key, item )

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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