def generate_tool_panel_elem_list( self, repository_name, repository_clone_url, changeset_revision,
tool_panel_dict, repository_tools_tups, owner='' ):
"""Generate a list of ElementTree Element objects for each section or tool."""
elem_list = []
tool_elem = None
cleaned_repository_clone_url = common_util.remove_protocol_and_user_from_clone_url( repository_clone_url )
if not owner:
owner = suc.get_repository_owner( cleaned_repository_clone_url )
tool_shed = cleaned_repository_clone_url.split( '/repos/' )[ 0 ].rstrip( '/' )
for guid, tool_section_dicts in tool_panel_dict.items():
for tool_section_dict in tool_section_dicts:
tool_section = None
inside_section = False
section_in_elem_list = False
if tool_section_dict[ 'id' ]:
inside_section = True
# Create a new section element only if we haven't already created it.
for index, elem in enumerate( elem_list ):
if elem.tag == 'section':
section_id = elem.get( 'id', None )
if section_id == tool_section_dict[ 'id' ]:
section_in_elem_list = True
tool_section = elem
break
if tool_section is None:
tool_section = self.generate_tool_section_element_from_dict( tool_section_dict )
# Find the tuple containing the current guid from the list of repository_tools_tups.
for repository_tool_tup in repository_tools_tups:
tool_file_path, tup_guid, tool = repository_tool_tup
if tup_guid == guid:
break
if inside_section:
tool_elem = self.generate_tool_elem( tool_shed,
repository_name,
changeset_revision,
owner,
tool_file_path,
tool,
tool_section )
else:
tool_elem = self.generate_tool_elem( tool_shed,
repository_name,
changeset_revision,
owner,
tool_file_path,
tool,
None )
if inside_section:
if section_in_elem_list:
elem_list[ index ] = tool_section
else:
elem_list.append( tool_section )
else:
elem_list.append( tool_elem )
return elem_list
def generate_tool_panel_elem_list(self,
repository_name,
repository_clone_url,
changeset_revision,
tool_panel_dict,
repository_tools_tups,
owner=''):
"""Generate a list of ElementTree Element objects for each section or tool."""
elem_list = []
tool_elem = None
cleaned_repository_clone_url = common_util.remove_protocol_and_user_from_clone_url(
repository_clone_url)
if not owner:
owner = suc.get_repository_owner(cleaned_repository_clone_url)
tool_shed = cleaned_repository_clone_url.split('/repos/')[0].rstrip(
'/')
for guid, tool_section_dicts in tool_panel_dict.items():
for tool_section_dict in tool_section_dicts:
tool_section = None
inside_section = False
section_in_elem_list = False
if tool_section_dict['id']:
inside_section = True
# Create a new section element only if we haven't already created it.
for index, elem in enumerate(elem_list):
if elem.tag == 'section':
section_id = elem.get('id', None)
if section_id == tool_section_dict['id']:
section_in_elem_list = True
tool_section = elem
break
if tool_section is None:
tool_section = self.generate_tool_section_element_from_dict(
tool_section_dict)
# Find the tuple containing the current guid from the list of repository_tools_tups.
for repository_tool_tup in repository_tools_tups:
tool_file_path, tup_guid, tool = repository_tool_tup
if tup_guid == guid:
break
if inside_section:
tool_elem = self.generate_tool_elem(
tool_shed, repository_name, changeset_revision, owner,
tool_file_path, tool, tool_section)
else:
tool_elem = self.generate_tool_elem(
tool_shed, repository_name, changeset_revision, owner,
tool_file_path, tool, None)
if inside_section:
if section_in_elem_list:
elem_list[index] = tool_section
else:
elem_list.append(tool_section)
else:
elem_list.append(tool_elem)
return elem_list
def update_in_shed_tool_config(self):
"""
A tool shed repository is being updated so change the shed_tool_conf file. Parse the config
file to generate the entire list of config_elems instead of using the in-memory list.
"""
shed_conf_dict = self.repository.get_shed_config_dict(self.app)
shed_tool_conf = shed_conf_dict['config_filename']
tool_path = shed_conf_dict['tool_path']
tool_panel_dict = self.tpm.generate_tool_panel_dict_from_shed_tool_conf_entries(
self.repository)
repository_tools_tups = self.get_repository_tools_tups()
clone_url = common_util.generate_clone_url_for_installed_repository(
self.app, self.repository)
tool_shed = self.tool_shed_from_repository_clone_url()
owner = self.repository.owner
if not owner:
cleaned_repository_clone_url = common_util.remove_protocol_and_user_from_clone_url(
clone_url)
owner = suc.get_repository_owner(cleaned_repository_clone_url)
guid_to_tool_elem_dict = {}
for tool_config_filename, guid, tool in repository_tools_tups:
guid_to_tool_elem_dict[guid] = self.tpm.generate_tool_elem(
tool_shed, self.repository.name,
self.repository.changeset_revision, self.repository.owner
or '', tool_config_filename, tool, None)
config_elems = []
tree, error_message = xml_util.parse_xml(shed_tool_conf)
if tree:
root = tree.getroot()
for elem in root:
if elem.tag == 'section':
for i, tool_elem in enumerate(elem):
guid = tool_elem.attrib.get('guid')
if guid in guid_to_tool_elem_dict:
elem[i] = guid_to_tool_elem_dict[guid]
elif elem.tag == 'tool':
guid = elem.attrib.get('guid')
if guid in guid_to_tool_elem_dict:
elem = guid_to_tool_elem_dict[guid]
config_elems.append(elem)
self.tpm.config_elems_to_xml_file(config_elems, shed_tool_conf,
tool_path)
def update_in_shed_tool_config( self ):
"""
A tool shed repository is being updated so change the shed_tool_conf file. Parse the config
file to generate the entire list of config_elems instead of using the in-memory list.
"""
shed_conf_dict = self.repository.get_shed_config_dict( self.app )
shed_tool_conf = shed_conf_dict[ 'config_filename' ]
tool_path = shed_conf_dict[ 'tool_path' ]
self.tpm.generate_tool_panel_dict_from_shed_tool_conf_entries( self.repository )
repository_tools_tups = self.get_repository_tools_tups()
clone_url = common_util.generate_clone_url_for_installed_repository( self.app, self.repository )
tool_shed = self.tool_shed_from_repository_clone_url()
owner = self.repository.owner
if not owner:
cleaned_repository_clone_url = common_util.remove_protocol_and_user_from_clone_url( clone_url )
owner = suc.get_repository_owner( cleaned_repository_clone_url )
guid_to_tool_elem_dict = {}
for tool_config_filename, guid, tool in repository_tools_tups:
guid_to_tool_elem_dict[ guid ] = self.tpm.generate_tool_elem( tool_shed,
self.repository.name,
self.repository.changeset_revision,
self.repository.owner or '',
tool_config_filename,
tool,
None )
config_elems = []
tree, error_message = xml_util.parse_xml( shed_tool_conf )
if tree:
root = tree.getroot()
for elem in root:
if elem.tag == 'section':
for i, tool_elem in enumerate( elem ):
guid = tool_elem.attrib.get( 'guid' )
if guid in guid_to_tool_elem_dict:
elem[i] = guid_to_tool_elem_dict[ guid ]
elif elem.tag == 'tool':
guid = elem.attrib.get( 'guid' )
if guid in guid_to_tool_elem_dict:
elem = guid_to_tool_elem_dict[ guid ]
config_elems.append( elem )
self.tpm.config_elems_to_xml_file( config_elems, shed_tool_conf, tool_path )
