def reset_all_metadata_on_installed_repository( self, id ):
"""Reset all metadata on a single tool shed repository installed into a Galaxy instance."""
invalid_file_tups = []
metadata_dict = {}
repository = repository_util.get_installed_tool_shed_repository( self.app, id )
repository_clone_url = common_util.generate_clone_url_for_installed_repository( self.app, repository )
tool_path, relative_install_dir = repository.get_tool_relative_path( self.app )
if relative_install_dir:
original_metadata_dict = repository.metadata
metadata_dict, invalid_file_tups = \
self.generate_metadata_for_changeset_revision( repository=repository,
changeset_revision=repository.changeset_revision,
repository_clone_url=repository_clone_url,
shed_config_dict = repository.get_shed_config_dict( self.app ),
relative_install_dir=relative_install_dir,
repository_files_dir=None,
resetting_all_metadata_on_repository=False,
updating_installed_repository=False,
persist=False )
repository.metadata = metadata_dict
if metadata_dict != original_metadata_dict:
self.update_in_shed_tool_config( repository )
self.app.install_model.context.add( repository )
self.app.install_model.context.flush()
log.debug( 'Metadata has been reset on repository %s.' % repository.name )
else:
log.debug( 'Metadata did not need to be reset on repository %s.' % repository.name )
else:
log.debug( 'Error locating installation directory for repository %s.' % repository.name )
return invalid_file_tups, metadata_dict
def get_repo_info_dict_for_repair(self, rdim, repository):
tool_panel_section_key = None
repository_clone_url = common_util.generate_clone_url_for_installed_repository(
self.app, repository)
repository_dependencies = rdim.get_repository_dependencies_for_installed_tool_shed_repository(
self.app, repository)
metadata = repository.metadata
if metadata:
tool_dependencies = metadata.get('tool_dependencies', None)
tool_panel_section_dict = metadata.get('tool_panel_section', None)
if tool_panel_section_dict:
# The repository must be in the uninstalled state. The structure of tool_panel_section_dict is:
# {<tool guid> :
# [{ 'id':<section id>, 'name':<section name>, 'version':<section version>, 'tool_config':<tool config file name> }]}
# Here is an example:
# {"localhost:9009/repos/test/filter/Filter1/1.1.0":
# [{"id": "filter_and_sort", "name": "Filter and Sort", "tool_config": "filtering.xml", "version": ""}]}
# Currently all tools contained within an installed tool shed repository must be loaded into the same
# section in the tool panel, so we can get the section id of the first guid in the tool_panel_section_dict.
# In the future, we'll have to handle different sections per guid.
guid = tool_panel_section_dict.keys()[0]
section_dicts = tool_panel_section_dict[guid]
section_dict = section_dicts[0]
tool_panel_section_id = section_dict['id']
tool_panel_section_name = section_dict['name']
if tool_panel_section_id:
tpm = tool_panel_manager.ToolPanelManager(self.app)
tool_panel_section_key, _ = \
tpm.get_or_create_tool_section( self.app.toolbox,
tool_panel_section_id=tool_panel_section_id,
new_tool_panel_section_label=tool_panel_section_name )
else:
tool_dependencies = None
repo_info_dict = repository_util.create_repo_info_dict(
app=self.app,
repository_clone_url=repository_clone_url,
changeset_revision=repository.changeset_revision,
ctx_rev=repository.ctx_rev,
repository_owner=repository.owner,
repository_name=repository.name,
repository=None,
repository_metadata=None,
tool_dependencies=tool_dependencies,
repository_dependencies=repository_dependencies)
return repo_info_dict, tool_panel_section_key
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.shed_config_dict or 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 = repository_util.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 get_repo_info_dict_for_repair( self, rdim, repository ):
tool_panel_section_key = None
repository_clone_url = common_util.generate_clone_url_for_installed_repository( self.app, repository )
repository_dependencies = rdim.get_repository_dependencies_for_installed_tool_shed_repository( self.app,
repository )
metadata = repository.metadata
if metadata:
tool_dependencies = metadata.get( 'tool_dependencies', None )
tool_panel_section_dict = metadata.get( 'tool_panel_section', None )
if tool_panel_section_dict:
# The repository must be in the uninstalled state. The structure of tool_panel_section_dict is:
# {<tool guid> :
# [{ 'id':<section id>, 'name':<section name>, 'version':<section version>, 'tool_config':<tool config file name> }]}
# Here is an example:
# {"localhost:9009/repos/test/filter/Filter1/1.1.0":
# [{"id": "filter_and_sort", "name": "Filter and Sort", "tool_config": "filtering.xml", "version": ""}]}
# Currently all tools contained within an installed tool shed repository must be loaded into the same
# section in the tool panel, so we can get the section id of the first guid in the tool_panel_section_dict.
# In the future, we'll have to handle different sections per guid.
guid = tool_panel_section_dict.keys()[ 0 ]
section_dicts = tool_panel_section_dict[ guid ]
section_dict = section_dicts[ 0 ]
tool_panel_section_id = section_dict[ 'id' ]
tool_panel_section_name = section_dict[ 'name' ]
if tool_panel_section_id:
tpm = tool_panel_manager.ToolPanelManager( self.app )
tool_panel_section_key, _ = \
tpm.get_or_create_tool_section( self.app.toolbox,
tool_panel_section_id=tool_panel_section_id,
new_tool_panel_section_label=tool_panel_section_name )
else:
tool_dependencies = None
repo_info_dict = repository_util.create_repo_info_dict( app=self.app,
repository_clone_url=repository_clone_url,
changeset_revision=repository.changeset_revision,
ctx_rev=repository.ctx_rev,
repository_owner=repository.owner,
repository_name=repository.name,
repository=None,
repository_metadata=None,
tool_dependencies=tool_dependencies,
repository_dependencies=repository_dependencies )
return repo_info_dict, tool_panel_section_key
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 = repository_util.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 set_repository(self, repository):
super(InstalledRepositoryMetadataManager,
self).set_repository(repository)
self.repository_clone_url = common_util.generate_clone_url_for_installed_repository(
self.app, repository)
def set_repository( self, repository ):
super( InstalledRepositoryMetadataManager, self ).set_repository( repository )
self.repository_clone_url = common_util.generate_clone_url_for_installed_repository( self.app, repository )
