def update_repository_record(self, repository, updated_metadata_dict,
updated_changeset_revision, updated_ctx_rev):
"""
Update a tool_shed_repository database record with new information retrieved from the
Tool Shed. This happens when updating an installed repository to a new changeset revision.
"""
repository.metadata = updated_metadata_dict
tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(
self.app, repository.tool_shed)
suc.clean_dependency_relationships(self.app, updated_metadata_dict,
repository, tool_shed_url)
# Update the repository.changeset_revision column in the database.
repository.changeset_revision = updated_changeset_revision
repository.ctx_rev = updated_ctx_rev
# Update the repository.tool_shed_status column in the database.
tool_shed_status_dict = repository_util.get_tool_shed_status_for_installed_repository(
self.app, repository)
if tool_shed_status_dict:
repository.tool_shed_status = tool_shed_status_dict
else:
repository.tool_shed_status = None
self.app.install_model.context.add(repository)
self.app.install_model.context.flush()
self.app.install_model.context.refresh(repository)
return repository
def update_repository_record( self, repository, updated_metadata_dict, updated_changeset_revision, updated_ctx_rev ):
"""
Update a tool_shed_repository database record with new information retrieved from the
Tool Shed. This happens when updating an installed repository to a new changeset revision.
"""
repository.metadata = updated_metadata_dict
tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( self.app, repository.tool_shed )
suc.clean_dependency_relationships(self.app, updated_metadata_dict, repository, tool_shed_url)
# Update the repository.changeset_revision column in the database.
repository.changeset_revision = updated_changeset_revision
repository.ctx_rev = updated_ctx_rev
# Update the repository.tool_shed_status column in the database.
tool_shed_status_dict = suc.get_tool_shed_status_for_installed_repository( self.app, repository )
if tool_shed_status_dict:
repository.tool_shed_status = tool_shed_status_dict
else:
repository.tool_shed_status = None
self.app.install_model.context.add( repository )
self.app.install_model.context.flush()
self.app.install_model.context.refresh( repository )
return repository
def repair_tool_shed_repository( self, repository, repo_info_dict ):
def add_repair_dict_entry( repository_name, error_message ):
if repository_name in repair_dict:
repair_dict[ repository_name ].append( error_message )
else:
repair_dict[ repository_name ] = [ error_message ]
return repair_dict
tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( self.app, repository.tool_shed )
metadata = repository.metadata
# The repository.metadata contains dependency information that corresponds to the current changeset revision,
# which may be different from what is stored in the database
# If any of these repository-repository dependency associations is obsolete, clean_dependency_relationships removes them.
suc.clean_dependency_relationships(self.app, metadata, repository, tool_shed_url)
repair_dict = {}
tpm = tool_panel_manager.ToolPanelManager( self.app )
if repository.status in [ self.app.install_model.ToolShedRepository.installation_status.DEACTIVATED ]:
try:
self.app.installed_repository_manager.activate_repository( repository )
except Exception, e:
error_message = "Error activating repository %s: %s" % ( repository.name, str( e ) )
log.debug( error_message )
repair_dict[ repository.name ] = error_message
def repair_tool_shed_repository(self, repository, repo_info_dict):
def add_repair_dict_entry(repository_name, error_message):
if repository_name in repair_dict:
repair_dict[repository_name].append(error_message)
else:
repair_dict[repository_name] = [error_message]
return repair_dict
tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(
self.app, repository.tool_shed)
metadata = repository.metadata
# The repository.metadata contains dependency information that corresponds to the current changeset revision,
# which may be different from what is stored in the database
# If any of these repository-repository dependency associations is obsolete, clean_dependency_relationships removes them.
suc.clean_dependency_relationships(self.app, metadata, repository,
tool_shed_url)
repair_dict = {}
tpm = tool_panel_manager.ToolPanelManager(self.app)
if repository.status in [
self.app.install_model.ToolShedRepository.installation_status.
DEACTIVATED
]:
try:
self.app.installed_repository_manager.activate_repository(
repository)
except Exception as e:
error_message = "Error activating repository %s: %s" % (
repository.name, str(e))
log.debug(error_message)
repair_dict[repository.name] = error_message
elif repository.status not in [
self.app.install_model.ToolShedRepository.installation_status.
INSTALLED
]:
shed_tool_conf, tool_path, relative_install_dir = \
suc.get_tool_panel_config_tool_path_install_dir( self.app, repository )
# Reset the repository attributes to the New state for installation.
if metadata:
_, tool_panel_section_key = \
tpm.handle_tool_panel_selection( self.app.toolbox,
metadata,
no_changes_checked=True,
tool_panel_section_id=None,
new_tool_panel_section_label=None )
else:
# The tools will be loaded outside of any sections in the tool panel.
tool_panel_section_key = None
repository_util.set_repository_attributes(
self.app,
repository,
status=self.app.install_model.ToolShedRepository.
installation_status.NEW,
error_message=None,
deleted=False,
uninstalled=False,
remove_from_disk=True)
irm = install_manager.InstallRepositoryManager(self.app, tpm)
irm.install_tool_shed_repository(
repository,
repo_info_dict,
tool_panel_section_key,
shed_tool_conf,
tool_path,
install_tool_dependencies=True,
install_resolver_dependencies=
False, # Assuming repairs are only necessary toolshed packages
reinstalling=True)
if repository.status in [
self.app.install_model.ToolShedRepository.
installation_status.ERROR
]:
repair_dict = add_repair_dict_entry(repository.name,
repository.error_message)
else:
irm = install_manager.InstallRepositoryManager(self.app, tpm)
# We have an installed tool shed repository, so handle tool dependencies if necessary.
if repository.missing_tool_dependencies and metadata and 'tool_dependencies' in metadata:
work_dir = tempfile.mkdtemp(prefix="tmp-toolshed-itdep")
# Reset missing tool dependencies.
for tool_dependency in repository.missing_tool_dependencies:
if tool_dependency.status in [
self.app.install_model.ToolDependency.
installation_status.ERROR, self.app.install_model.
ToolDependency.installation_status.INSTALLING
]:
tool_dependency = \
tool_dependency_util.set_tool_dependency_attributes( self.app,
tool_dependency=tool_dependency,
status=self.app.install_model.ToolDependency.installation_status.UNINSTALLED )
# Install tool dependencies.
irm.update_tool_shed_repository_status(
repository, self.app.install_model.ToolShedRepository.
installation_status.INSTALLING_TOOL_DEPENDENCIES)
# Get the tool_dependencies.xml file from the repository.
tool_dependencies_config = hg_util.get_config_from_disk(
'tool_dependencies.xml', repository.repo_path(self.app))
itdm = install_manager.InstallToolDependencyManager(self.app)
installed_tool_dependencies = itdm.install_specified_tool_dependencies(
tool_shed_repository=repository,
tool_dependencies_config=tool_dependencies_config,
tool_dependencies=repository.tool_dependencies,
from_tool_migration_manager=False)
for installed_tool_dependency in installed_tool_dependencies:
if installed_tool_dependency.status in [
self.app.install_model.ToolDependency.
installation_status.ERROR
]:
repair_dict = add_repair_dict_entry(
repository.name,
installed_tool_dependency.error_message)
basic_util.remove_dir(work_dir)
irm.update_tool_shed_repository_status(
repository, self.app.install_model.ToolShedRepository.
installation_status.INSTALLED)
return repair_dict
def repair_tool_shed_repository( self, repository, repo_info_dict ):
def add_repair_dict_entry( repository_name, error_message ):
if repository_name in repair_dict:
repair_dict[ repository_name ].append( error_message )
else:
repair_dict[ repository_name ] = [ error_message ]
return repair_dict
tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( self.app, repository.tool_shed )
metadata = repository.metadata
# The repository.metadata contains dependency information that corresponds to the current changeset revision,
# which may be different from what is stored in the database
# If any of these repository-repository dependency associations is obsolete, clean_dependency_relationships removes them.
suc.clean_dependency_relationships(self.app, metadata, repository, tool_shed_url)
repair_dict = {}
tpm = tool_panel_manager.ToolPanelManager( self.app )
if repository.status in [ self.app.install_model.ToolShedRepository.installation_status.DEACTIVATED ]:
try:
self.app.installed_repository_manager.activate_repository( repository )
except Exception as e:
error_message = "Error activating repository %s: %s" % ( repository.name, str( e ) )
log.debug( error_message )
repair_dict[ repository.name ] = error_message
elif repository.status not in [ self.app.install_model.ToolShedRepository.installation_status.INSTALLED ]:
shed_tool_conf, tool_path, relative_install_dir = \
suc.get_tool_panel_config_tool_path_install_dir( self.app, repository )
# Reset the repository attributes to the New state for installation.
if metadata:
_, tool_panel_section_key = \
tpm.handle_tool_panel_selection( self.app.toolbox,
metadata,
no_changes_checked=True,
tool_panel_section_id=None,
new_tool_panel_section_label=None )
else:
# The tools will be loaded outside of any sections in the tool panel.
tool_panel_section_key = None
repository_util.set_repository_attributes( self.app,
repository,
status=self.app.install_model.ToolShedRepository.installation_status.NEW,
error_message=None,
deleted=False,
uninstalled=False,
remove_from_disk=True )
irm = install_manager.InstallRepositoryManager( self.app, tpm )
irm.install_tool_shed_repository( repository,
repo_info_dict,
tool_panel_section_key,
shed_tool_conf,
tool_path,
install_tool_dependencies=True,
install_resolver_dependencies=False, # Assuming repairs are only necessary toolshed packages
reinstalling=True )
if repository.status in [ self.app.install_model.ToolShedRepository.installation_status.ERROR ]:
repair_dict = add_repair_dict_entry( repository.name, repository.error_message )
else:
irm = install_manager.InstallRepositoryManager( self.app, tpm )
# We have an installed tool shed repository, so handle tool dependencies if necessary.
if repository.missing_tool_dependencies and metadata and 'tool_dependencies' in metadata:
work_dir = tempfile.mkdtemp( prefix="tmp-toolshed-itdep" )
# Reset missing tool dependencies.
for tool_dependency in repository.missing_tool_dependencies:
if tool_dependency.status in [ self.app.install_model.ToolDependency.installation_status.ERROR,
self.app.install_model.ToolDependency.installation_status.INSTALLING ]:
tool_dependency = \
tool_dependency_util.set_tool_dependency_attributes( self.app,
tool_dependency=tool_dependency,
status=self.app.install_model.ToolDependency.installation_status.UNINSTALLED )
# Install tool dependencies.
irm.update_tool_shed_repository_status( repository,
self.app.install_model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES )
# Get the tool_dependencies.xml file from the repository.
tool_dependencies_config = hg_util.get_config_from_disk( 'tool_dependencies.xml', repository.repo_path( self.app ) )
itdm = install_manager.InstallToolDependencyManager( self.app )
installed_tool_dependencies = itdm.install_specified_tool_dependencies( tool_shed_repository=repository,
tool_dependencies_config=tool_dependencies_config,
tool_dependencies=repository.tool_dependencies,
from_tool_migration_manager=False )
for installed_tool_dependency in installed_tool_dependencies:
if installed_tool_dependency.status in [ self.app.install_model.ToolDependency.installation_status.ERROR ]:
repair_dict = add_repair_dict_entry( repository.name, installed_tool_dependency.error_message )
basic_util.remove_dir( work_dir )
irm.update_tool_shed_repository_status( repository,
self.app.install_model.ToolShedRepository.installation_status.INSTALLED )
return repair_dict
