def get_containing_tool_sections(self, tool_config):
"""
If tool_config is defined somewhere in self.proprietary_tool_panel_elems, return True and a list of ToolSections in which the
tool is displayed. If the tool is displayed outside of any sections, None is appended to the list.
"""
tool_sections = []
is_displayed = False
for proprietary_tool_panel_elem in self.proprietary_tool_panel_elems:
if proprietary_tool_panel_elem.tag == 'tool':
# The proprietary_tool_panel_elem looks something like <tool file="emboss_5/emboss_antigenic.xml" />.
proprietary_tool_config = proprietary_tool_panel_elem.get(
'file')
proprietary_name = suc.strip_path(proprietary_tool_config)
if tool_config == proprietary_name:
# The tool is loaded outside of any sections.
tool_sections.append(None)
if not is_displayed:
is_displayed = True
if proprietary_tool_panel_elem.tag == 'section':
# The proprietary_tool_panel_elem looks something like <section name="EMBOSS" id="EMBOSSLite">.
for section_elem in proprietary_tool_panel_elem:
if section_elem.tag == 'tool':
# The section_elem looks something like <tool file="emboss_5/emboss_antigenic.xml" />.
proprietary_tool_config = section_elem.get('file')
proprietary_name = suc.strip_path(
proprietary_tool_config)
if tool_config == proprietary_name:
# The tool is loaded inside of the section_elem.
tool_sections.append(
ToolSection(proprietary_tool_panel_elem))
if not is_displayed:
is_displayed = True
return is_displayed, tool_sections
def get_containing_tool_sections( self, tool_config ):
"""
If tool_config is defined somewhere in self.proprietary_tool_panel_elems, return True and a list of ToolSections in which the
tool is displayed. If the tool is displayed outside of any sections, None is appended to the list.
"""
tool_sections = []
is_displayed = False
for proprietary_tool_panel_elem in self.proprietary_tool_panel_elems:
if proprietary_tool_panel_elem.tag == 'tool':
# The proprietary_tool_panel_elem looks something like <tool file="emboss_5/emboss_antigenic.xml" />.
proprietary_tool_config = proprietary_tool_panel_elem.get( 'file' )
proprietary_name = suc.strip_path( proprietary_tool_config )
if tool_config == proprietary_name:
# The tool is loaded outside of any sections.
tool_sections.append( None )
if not is_displayed:
is_displayed = True
if proprietary_tool_panel_elem.tag == 'section':
# The proprietary_tool_panel_elem looks something like <section name="EMBOSS" id="EMBOSSLite">.
for section_elem in proprietary_tool_panel_elem:
if section_elem.tag == 'tool':
# The section_elem looks something like <tool file="emboss_5/emboss_antigenic.xml" />.
proprietary_tool_config = section_elem.get( 'file' )
proprietary_name = suc.strip_path( proprietary_tool_config )
if tool_config == proprietary_name:
# The tool is loaded inside of the section_elem.
tool_sections.append( ToolSection( proprietary_tool_panel_elem ) )
if not is_displayed:
is_displayed = True
return is_displayed, tool_sections
def get_proprietary_tool_panel_elems(self,
latest_tool_migration_script_number):
# Parse each config in self.proprietary_tool_confs (the default is tool_conf.xml) and generate a list of Elements that are
# either ToolSection elements or Tool elements. These will be used to generate new entries in the migrated_tools_conf.xml
# file for the installed tools.
tools_xml_file_path = os.path.abspath(
os.path.join(
'scripts', 'migrate_tools',
'%04d_tools.xml' % latest_tool_migration_script_number))
# Parse the XML and load the file attributes for later checking against the integrated elements from self.proprietary_tool_confs.
migrated_tool_configs = []
tree = util.parse_xml(tools_xml_file_path)
root = tree.getroot()
for elem in root:
if elem.tag == 'repository':
for tool_elem in elem:
migrated_tool_configs.append(tool_elem.get('file'))
# Parse each file in self.proprietary_tool_confs and generate the integrated list of tool panel Elements that contain them.
tool_panel_elems = []
for proprietary_tool_conf in self.proprietary_tool_confs:
tree = util.parse_xml(proprietary_tool_conf)
root = tree.getroot()
for elem in root:
if elem.tag == 'tool':
# Tools outside of sections.
file_path = elem.get('file', None)
if file_path:
name = suc.strip_path(file_path)
if name in migrated_tool_configs:
if elem not in tool_panel_elems:
tool_panel_elems.append(elem)
elif elem.tag == 'section':
# Tools contained in a section.
for section_elem in elem:
if section_elem.tag == 'tool':
file_path = section_elem.get('file', None)
if file_path:
name = suc.strip_path(file_path)
if name in migrated_tool_configs:
# Append the section, not the tool.
if elem not in tool_panel_elems:
tool_panel_elems.append(elem)
return tool_panel_elems
def get_proprietary_tool_panel_elems( self, latest_tool_migration_script_number ):
# Parse each config in self.proprietary_tool_confs (the default is tool_conf.xml) and generate a list of Elements that are
# either ToolSection elements or Tool elements. These will be used to generate new entries in the migrated_tools_conf.xml
# file for the installed tools.
tools_xml_file_path = os.path.abspath( os.path.join( 'scripts', 'migrate_tools', '%04d_tools.xml' % latest_tool_migration_script_number ) )
# Parse the XML and load the file attributes for later checking against the integrated elements from self.proprietary_tool_confs.
migrated_tool_configs = []
tree = util.parse_xml( tools_xml_file_path )
root = tree.getroot()
for elem in root:
if elem.tag == 'repository':
for tool_elem in elem:
migrated_tool_configs.append( tool_elem.get( 'file' ) )
# Parse each file in self.proprietary_tool_confs and generate the integrated list of tool panel Elements that contain them.
tool_panel_elems = []
for proprietary_tool_conf in self.proprietary_tool_confs:
tree = util.parse_xml( proprietary_tool_conf )
root = tree.getroot()
for elem in root:
if elem.tag == 'tool':
# Tools outside of sections.
file_path = elem.get( 'file', None )
if file_path:
name = suc.strip_path( file_path )
if name in migrated_tool_configs:
if elem not in tool_panel_elems:
tool_panel_elems.append( elem )
elif elem.tag == 'section':
# Tools contained in a section.
for section_elem in elem:
if section_elem.tag == 'tool':
file_path = section_elem.get( 'file', None )
if file_path:
name = suc.strip_path( file_path )
if name in migrated_tool_configs:
# Append the section, not the tool.
if elem not in tool_panel_elems:
tool_panel_elems.append( elem )
return tool_panel_elems
