def activate_repository( trans, repository ):
"""Activate an installed tool shed repository that has been marked as deactivated."""
repository_clone_url = suc.generate_clone_url_for_installed_repository( trans.app, repository )
shed_tool_conf, tool_path, relative_install_dir = suc.get_tool_panel_config_tool_path_install_dir( trans.app, repository )
repository.deleted = False
repository.status = trans.install_model.ToolShedRepository.installation_status.INSTALLED
if repository.includes_tools_for_display_in_tool_panel:
metadata = repository.metadata
repository_tools_tups = suc.get_repository_tools_tups( trans.app, metadata )
# Reload tools into the appropriate tool panel section.
tool_panel_dict = repository.metadata[ 'tool_panel_section' ]
tool_util.add_to_tool_panel( trans.app,
repository.name,
repository_clone_url,
repository.installed_changeset_revision,
repository_tools_tups,
repository.owner,
shed_tool_conf,
tool_panel_dict,
new_install=False )
if repository.includes_data_managers:
tp, data_manager_relative_install_dir = repository.get_tool_relative_path( trans.app )
# Hack to add repository.name here, which is actually the root of the installed repository
data_manager_relative_install_dir = os.path.join( data_manager_relative_install_dir, repository.name )
new_data_managers = data_manager_util.install_data_managers( trans.app,
trans.app.config.shed_data_manager_config_file,
metadata,
repository.get_shed_config_dict( trans.app ),
data_manager_relative_install_dir,
repository,
repository_tools_tups )
trans.install_model.context.add( repository )
trans.install_model.context.flush()
if repository.includes_datatypes:
if tool_path:
repository_install_dir = os.path.abspath( os.path.join( tool_path, relative_install_dir ) )
else:
repository_install_dir = os.path.abspath( relative_install_dir )
# Activate proprietary datatypes.
installed_repository_dict = datatype_util.load_installed_datatypes( trans.app, repository, repository_install_dir, deactivate=False )
if installed_repository_dict:
converter_path = installed_repository_dict.get( 'converter_path' )
if converter_path is not None:
datatype_util.load_installed_datatype_converters( trans.app, installed_repository_dict, deactivate=False )
display_path = installed_repository_dict.get( 'display_path' )
if display_path is not None:
datatype_util.load_installed_display_applications( trans.app, installed_repository_dict, deactivate=False )
def activate_repository( trans, repository ):
"""Activate an installed tool shed repository that has been marked as deactivated."""
repository_clone_url = suc.generate_clone_url_for_installed_repository( trans.app, repository )
shed_tool_conf, tool_path, relative_install_dir = suc.get_tool_panel_config_tool_path_install_dir( trans.app, repository )
repository.deleted = False
repository.status = trans.model.ToolShedRepository.installation_status.INSTALLED
if repository.includes_tools_for_display_in_tool_panel:
metadata = repository.metadata
repository_tools_tups = suc.get_repository_tools_tups( trans.app, metadata )
# Reload tools into the appropriate tool panel section.
tool_panel_dict = repository.metadata[ 'tool_panel_section' ]
tool_util.add_to_tool_panel( trans.app,
repository.name,
repository_clone_url,
repository.installed_changeset_revision,
repository_tools_tups,
repository.owner,
shed_tool_conf,
tool_panel_dict,
new_install=False )
if repository.includes_data_managers:
tp, data_manager_relative_install_dir = repository.get_tool_relative_path( trans.app )
# Hack to add repository.name here, which is actually the root of the installed repository
data_manager_relative_install_dir = os.path.join( data_manager_relative_install_dir, repository.name )
new_data_managers = data_manager_util.install_data_managers( trans.app,
trans.app.config.shed_data_manager_config_file,
metadata,
repository.get_shed_config_dict( trans.app ),
data_manager_relative_install_dir,
repository,
repository_tools_tups )
trans.sa_session.add( repository )
trans.sa_session.flush()
if repository.includes_datatypes:
if tool_path:
repository_install_dir = os.path.abspath( os.path.join( tool_path, relative_install_dir ) )
else:
repository_install_dir = os.path.abspath( relative_install_dir )
# Activate proprietary datatypes.
installed_repository_dict = datatype_util.load_installed_datatypes( trans.app, repository, repository_install_dir, deactivate=False )
if installed_repository_dict and 'converter_path' in installed_repository_dict:
datatype_util.load_installed_datatype_converters( trans.app, installed_repository_dict, deactivate=False )
if installed_repository_dict and 'display_path' in installed_repository_dict:
datatype_util.load_installed_display_applications( trans.app, installed_repository_dict, deactivate=False )
# Handle missing data table entries for tool parameters that are dynamically generated select lists.
repository_tools_tups = tool_util.handle_missing_data_table_entry( self.app, relative_install_dir, self.tool_path, repository_tools_tups )
# Handle missing index files for tool parameters that are dynamically generated select lists.
repository_tools_tups, sample_files_copied = tool_util.handle_missing_index_file( self.app,
self.tool_path,
sample_files,
repository_tools_tups,
sample_files_copied )
# Copy remaining sample files included in the repository to the ~/tool-data directory of the local Galaxy instance.
tool_util.copy_sample_files( self.app, sample_files, tool_path=self.tool_path, sample_files_copied=sample_files_copied )
if not is_repository_dependency:
tool_util.add_to_tool_panel( self.app,
tool_shed_repository.name,
repository_clone_url,
tool_shed_repository.installed_changeset_revision,
repository_tools_tups,
self.repository_owner,
self.migrated_tools_config,
tool_panel_dict=tool_panel_dict_for_display,
new_install=True )
if install_dependencies and tool_dependencies and has_tool_dependencies:
# Install tool dependencies.
suc.update_tool_shed_repository_status( self.app,
tool_shed_repository,
self.app.install_model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES )
# Get the tool_dependencies.xml file from disk.
tool_dependencies_config = suc.get_config_from_disk( 'tool_dependencies.xml', repo_install_dir )
installed_tool_dependencies = common_install_util.handle_tool_dependencies( app=self.app,
tool_shed_repository=tool_shed_repository,
tool_dependencies_config=tool_dependencies_config,
tool_dependencies=tool_dependencies,
def handle_repository_contents( self, tool_shed_repository, repository_clone_url, relative_install_dir, repository_elem, install_dependencies ):
"""Generate the metadata for the installed tool shed repository, among other things."""
tool_panel_dict_for_display = odict()
if self.tool_path:
repo_install_dir = os.path.join( self.tool_path, relative_install_dir )
else:
repo_install_dir = relative_install_dir
for tool_elem in repository_elem:
# The tool_elem looks something like this: <tool id="EMBOSS: antigenic1" version="5.0.0" file="emboss_antigenic.xml" />
tool_config = tool_elem.get( 'file' )
guid = self.get_guid( repository_clone_url, relative_install_dir, tool_config )
# See if tool_config is defined inside of a section in self.proprietary_tool_panel_elems.
is_displayed, tool_sections = self.get_containing_tool_sections( tool_config )
if is_displayed:
tool_panel_dict_for_tool_config = tool_util.generate_tool_panel_dict_for_tool_config( guid, tool_config, tool_sections=tool_sections )
for k, v in tool_panel_dict_for_tool_config.items():
tool_panel_dict_for_display[ k ] = v
else:
print 'The tool "%s" (%s) has not been enabled because it is not defined in a proprietary tool config (%s).' \
% ( guid, tool_config, ", ".join( self.proprietary_tool_confs or [] ) )
metadata_dict, invalid_file_tups = metadata_util.generate_metadata_for_changeset_revision( app=self.app,
repository=tool_shed_repository,
changeset_revision=tool_shed_repository.changeset_revision,
repository_clone_url=repository_clone_url,
shed_config_dict = self.shed_config_dict,
relative_install_dir=relative_install_dir,
repository_files_dir=None,
resetting_all_metadata_on_repository=False,
updating_installed_repository=False,
persist=True )
tool_shed_repository.metadata = metadata_dict
self.app.sa_session.add( tool_shed_repository )
self.app.sa_session.flush()
if 'tool_dependencies' in metadata_dict:
# All tool_dependency objects must be created before the tools are processed even if no tool dependencies will be installed.
tool_dependencies = tool_dependency_util.create_tool_dependency_objects( self.app, tool_shed_repository, relative_install_dir, set_status=True )
else:
tool_dependencies = None
if 'tools' in metadata_dict:
sample_files = metadata_dict.get( 'sample_files', [] )
sample_files = [ str( s ) for s in sample_files ]
tool_index_sample_files = tool_util.get_tool_index_sample_files( sample_files )
tool_util.copy_sample_files( self.app, tool_index_sample_files, tool_path=self.tool_path )
sample_files_copied = [ s for s in tool_index_sample_files ]
repository_tools_tups = suc.get_repository_tools_tups( self.app, metadata_dict )
if repository_tools_tups:
# Handle missing data table entries for tool parameters that are dynamically generated select lists.
repository_tools_tups = tool_util.handle_missing_data_table_entry( self.app, relative_install_dir, self.tool_path, repository_tools_tups )
# Handle missing index files for tool parameters that are dynamically generated select lists.
repository_tools_tups, sample_files_copied = tool_util.handle_missing_index_file( self.app,
self.tool_path,
sample_files,
repository_tools_tups,
sample_files_copied )
# Copy remaining sample files included in the repository to the ~/tool-data directory of the local Galaxy instance.
tool_util.copy_sample_files( self.app, sample_files, tool_path=self.tool_path, sample_files_copied=sample_files_copied )
if install_dependencies and tool_dependencies and 'tool_dependencies' in metadata_dict:
# Install tool dependencies.
suc.update_tool_shed_repository_status( self.app,
tool_shed_repository,
self.app.model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES )
# Get the tool_dependencies.xml file from disk.
tool_dependencies_config = suc.get_config_from_disk( 'tool_dependencies.xml', repo_install_dir )
installed_tool_dependencies = common_install_util.handle_tool_dependencies( app=self.app,
tool_shed_repository=tool_shed_repository,
tool_dependencies_config=tool_dependencies_config,
tool_dependencies=tool_dependencies )
for installed_tool_dependency in installed_tool_dependencies:
if installed_tool_dependency.status == self.app.model.ToolDependency.installation_status.ERROR:
print '\nThe following error occurred from the InstallManager while installing tool dependency ', installed_tool_dependency.name, ':'
print installed_tool_dependency.error_message, '\n\n'
tool_util.add_to_tool_panel( self.app,
tool_shed_repository.name,
repository_clone_url,
tool_shed_repository.installed_changeset_revision,
repository_tools_tups,
self.repository_owner,
self.migrated_tools_config,
tool_panel_dict=tool_panel_dict_for_display,
new_install=True )
if 'datatypes' in metadata_dict:
tool_shed_repository.status = self.app.model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES
if not tool_shed_repository.includes_datatypes:
tool_shed_repository.includes_datatypes = True
self.app.sa_session.add( tool_shed_repository )
self.app.sa_session.flush()
work_dir = tempfile.mkdtemp( prefix="tmp-toolshed-hrc" )
datatypes_config = suc.get_config_from_disk( suc.DATATYPES_CONFIG_FILENAME, repo_install_dir )
# Load proprietary data types required by tools. The value of override is not important here since the Galaxy server will be started
# after this installation completes.
converter_path, display_path = datatype_util.alter_config_and_load_prorietary_datatypes( self.app, datatypes_config, repo_install_dir, override=False ) #repo_install_dir was relative_install_dir
if converter_path or display_path:
# Create a dictionary of tool shed repository related information.
repository_dict = datatype_util.create_repository_dict_for_proprietary_datatypes( tool_shed=self.tool_shed,
name=tool_shed_repository.name,
owner=self.repository_owner,
installed_changeset_revision=tool_shed_repository.installed_changeset_revision,
tool_dicts=metadata_dict.get( 'tools', [] ),
converter_path=converter_path,
display_path=display_path )
if converter_path:
# Load proprietary datatype converters
self.app.datatypes_registry.load_datatype_converters( self.toolbox, installed_repository_dict=repository_dict )
if display_path:
# Load proprietary datatype display applications
self.app.datatypes_registry.load_display_applications( installed_repository_dict=repository_dict )
try:
shutil.rmtree( work_dir )
except:
pass