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_guid( self, repository_clone_url, relative_install_dir, tool_config ):
if self.shed_config_dict.get( 'tool_path' ):
relative_install_dir = os.path.join( self.shed_config_dict[ 'tool_path' ], relative_install_dir )
tool_config_filename = suc.strip_path( tool_config )
for root, dirs, files in os.walk( relative_install_dir ):
if root.find( '.hg' ) < 0 and root.find( 'hgrc' ) < 0:
if '.hg' in dirs:
dirs.remove( '.hg' )
for name in files:
filename = suc.strip_path( name )
if filename == tool_config_filename:
full_path = str( os.path.abspath( os.path.join( root, name ) ) )
tool = self.toolbox.load_tool( full_path )
return suc.generate_tool_guid( repository_clone_url, tool )
# Not quite sure what should happen here, throw an exception or what?
return None
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, error_message = xml_util.parse_xml( tools_xml_file_path )
if tree is None:
return []
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, error_message = xml_util.parse_xml( proprietary_tool_conf )
if tree is None:
return []
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, error_message = xml_util.parse_xml( tools_xml_file_path )
if tree is None:
return []
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, error_message = xml_util.parse_xml( proprietary_tool_conf )
if tree is None:
return []
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_converter_and_display_paths(registration_elem, relative_install_dir):
"""Find the relative path to data type converters and display applications included in installed tool shed repositories."""
converter_path = None
display_path = None
for elem in registration_elem.findall('datatype'):
if not converter_path:
# If any of the <datatype> tag sets contain <converter> tags, set the converter_path
# if it is not already set. This requires developers to place all converters in the
# same subdirectory within the repository hierarchy.
for converter in elem.findall('converter'):
converter_config = converter.get('file', None)
if converter_config:
converter_config_file_name = suc.strip_path(
converter_config)
for root, dirs, files in os.walk(relative_install_dir):
if root.find('.hg') < 0:
for name in files:
if name == converter_config_file_name:
# The value of converter_path must be absolute due to job_working_directory.
converter_path = os.path.abspath(root)
break
if converter_path:
break
if not display_path:
# If any of the <datatype> tag sets contain <display> tags, set the display_path
# if it is not already set. This requires developers to place all display acpplications
# in the same subdirectory within the repository hierarchy.
for display_app in elem.findall('display'):
display_config = display_app.get('file', None)
if display_config:
display_config_file_name = suc.strip_path(display_config)
for root, dirs, files in os.walk(relative_install_dir):
if root.find('.hg') < 0:
for name in files:
if name == display_config_file_name:
# The value of display_path must be absolute due to job_working_directory.
display_path = os.path.abspath(root)
break
if display_path:
break
if converter_path and display_path:
break
return converter_path, display_path
def get_converter_and_display_paths( registration_elem, relative_install_dir ):
"""Find the relative path to data type converters and display applications included in installed tool shed repositories."""
converter_path = None
display_path = None
for elem in registration_elem.findall( 'datatype' ):
if not converter_path:
# If any of the <datatype> tag sets contain <converter> tags, set the converter_path
# if it is not already set. This requires developers to place all converters in the
# same subdirectory within the repository hierarchy.
for converter in elem.findall( 'converter' ):
converter_config = converter.get( 'file', None )
if converter_config:
converter_config_file_name = suc.strip_path( converter_config )
for root, dirs, files in os.walk( relative_install_dir ):
if root.find( '.hg' ) < 0:
for name in files:
if name == converter_config_file_name:
# The value of converter_path must be absolute due to job_working_directory.
converter_path = os.path.abspath( root )
break
if converter_path:
break
if not display_path:
# If any of the <datatype> tag sets contain <display> tags, set the display_path
# if it is not already set. This requires developers to place all display acpplications
# in the same subdirectory within the repository hierarchy.
for display_app in elem.findall( 'display' ):
display_config = display_app.get( 'file', None )
if display_config:
display_config_file_name = suc.strip_path( display_config )
for root, dirs, files in os.walk( relative_install_dir ):
if root.find( '.hg' ) < 0:
for name in files:
if name == display_config_file_name:
# The value of display_path must be absolute due to job_working_directory.
display_path = os.path.abspath( root )
break
if display_path:
break
if converter_path and display_path:
break
return converter_path, display_path
def filter_and_persist_proprietary_tool_panel_configs( self, tool_configs_to_filter ):
"""Eliminate all entries in all non-shed-related tool panel configs for all tool config file names in the received tool_configs_to_filter."""
for proprietary_tool_conf in self.proprietary_tool_confs:
persist_required = False
tree, error_message = xml_util.parse_xml( proprietary_tool_conf )
if tree:
root = tree.getroot()
for elem in root:
if elem.tag == 'tool':
# Tools outside of sections.
file_path = elem.get( 'file', None )
if file_path:
file_name = suc.strip_path( file_path )
if file_name in tool_configs_to_filter:
root.remove( elem )
persist_required = True
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:
file_name = suc.strip_path( file_path )
if file_name in tool_configs_to_filter:
elem.remove( section_elem )
persist_required = True
if persist_required:
fh = tempfile.NamedTemporaryFile( 'wb', prefix="tmp-toolshed-fapptpc" )
tmp_filename = fh.name
fh.close()
fh = open( tmp_filename, 'wb' )
tree.write( tmp_filename, encoding='utf-8', xml_declaration=True )
fh.close()
shutil.move( tmp_filename, os.path.abspath( proprietary_tool_conf ) )
os.chmod( proprietary_tool_conf, 0644 )
def is_valid_for_type( self, app, repository, revisions_to_check=None ):
"""
Inspect the received repository's contents to determine if they abide by the rules defined for the contents of this type.
If the received revisions_to_check is a list of changeset revisions, then inspection will be restricted to the revisions
in the list.
"""
repo = hg.repository( ui.ui(), repository.repo_path( app ) )
if revisions_to_check:
changeset_revisions = revisions_to_check
else:
changeset_revisions = repo.changelog
for changeset in changeset_revisions:
changeset_revision = str( repo.changectx( changeset ) )
ctx = repo.changectx( changeset )
# Inspect all files in the changeset (in sorted order) to make sure there is only one and it is named tool_dependencies.xml.
files_changed_in_changeset = ctx.files()
for file_path in files_changed_in_changeset:
file_name = suc.strip_path( file_path )
if file_name not in self.valid_file_names:
return False
return True
def is_valid_for_type(self, app, repository, revisions_to_check=None):
"""
Inspect the received repository's contents to determine if they abide by the rules defined for the contents of this type.
If the received revisions_to_check is a list of changeset revisions, then inspection will be restricted to the revisions
in the list.
"""
repo = hg.repository(ui.ui(), repository.repo_path(app))
if revisions_to_check:
changeset_revisions = revisions_to_check
else:
changeset_revisions = repo.changelog
for changeset in changeset_revisions:
changeset_revision = str(repo.changectx(changeset))
ctx = repo.changectx(changeset)
# Inspect all files in the changeset (in sorted order) to make sure there is only one and it is named tool_dependencies.xml.
files_changed_in_changeset = ctx.files()
for file_path in files_changed_in_changeset:
file_name = suc.strip_path(file_path)
if file_name not in self.valid_file_names:
return False
return True
