def create_repository_dependency_objects(self, tool_path, tool_shed_url, repo_info_dicts, install_repository_dependencies=False,
no_changes_checked=False, tool_panel_section_id=None, new_tool_panel_section_label=None):
"""
Discover all repository dependencies and make sure all tool_shed_repository and
associated repository_dependency records exist as well as the dependency relationships
between installed repositories. This method is called when uninstalled repositories
are being reinstalled. If the user elected to install repository dependencies, all
items in the all_repo_info_dicts list will be processed. However, if repository
dependencies are not to be installed, only those items contained in the received
repo_info_dicts list will be processed.
"""
install_model = self.app.install_model
log.debug("Creating repository dependency objects...")
# The following list will be maintained within this method to contain all created
# or updated tool shed repositories, including repository dependencies that may not
# be installed.
all_created_or_updated_tool_shed_repositories = []
# There will be a one-to-one mapping between items in 3 lists:
# created_or_updated_tool_shed_repositories, tool_panel_section_keys
# and filtered_repo_info_dicts. The 3 lists will filter out repository
# dependencies that are not to be installed.
created_or_updated_tool_shed_repositories = []
tool_panel_section_keys = []
# Repositories will be filtered (e.g., if already installed, if elected
# to not be installed, etc), so filter the associated repo_info_dicts accordingly.
filtered_repo_info_dicts = []
# Discover all repository dependencies and retrieve information for installing
# them. Even if the user elected to not install repository dependencies we have
# to make sure all repository dependency objects exist so that the appropriate
# repository dependency relationships can be built.
all_required_repo_info_dict = self.get_required_repo_info_dicts(tool_shed_url, repo_info_dicts)
all_repo_info_dicts = all_required_repo_info_dict.get('all_repo_info_dicts', [])
if not all_repo_info_dicts:
# No repository dependencies were discovered so process the received repositories.
all_repo_info_dicts = [rid for rid in repo_info_dicts]
for repo_info_dict in all_repo_info_dicts:
# If the user elected to install repository dependencies, all items in the
# all_repo_info_dicts list will be processed. However, if repository dependencies
# are not to be installed, only those items contained in the received repo_info_dicts
# list will be processed but the all_repo_info_dicts list will be used to create all
# defined repository dependency relationships.
if self.is_in_repo_info_dicts(repo_info_dict, repo_info_dicts) or install_repository_dependencies:
for name, repo_info_tuple in repo_info_dict.items():
can_update_db_record = False
description, \
repository_clone_url, \
changeset_revision, \
ctx_rev, \
repository_owner, \
repository_dependencies, \
tool_dependencies = \
repository_util.get_repo_info_tuple_contents(repo_info_tuple)
# See if the repository has an existing record in the database.
repository_db_record, installed_changeset_revision = \
repository_util.repository_was_previously_installed(self.app, tool_shed_url, name, repo_info_tuple, from_tip=False)
if repository_db_record:
if repository_db_record.status in [install_model.ToolShedRepository.installation_status.INSTALLED,
install_model.ToolShedRepository.installation_status.CLONING,
install_model.ToolShedRepository.installation_status.SETTING_TOOL_VERSIONS,
install_model.ToolShedRepository.installation_status.INSTALLING_REPOSITORY_DEPENDENCIES,
install_model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES,
install_model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES]:
debug_msg = "Skipping installation of revision %s of repository '%s' because it was installed " % \
(str(changeset_revision), str(repository_db_record.name))
debug_msg += "with the (possibly updated) revision %s and its current installation status is '%s'." % \
(str(installed_changeset_revision), str(repository_db_record.status))
log.debug(debug_msg)
can_update_db_record = False
else:
if repository_db_record.status in [install_model.ToolShedRepository.installation_status.ERROR,
install_model.ToolShedRepository.installation_status.NEW,
install_model.ToolShedRepository.installation_status.UNINSTALLED]:
# The current tool shed repository is not currently installed, so we can update its
# record in the database.
name = repository_db_record.name
installed_changeset_revision = repository_db_record.installed_changeset_revision
can_update_db_record = True
elif repository_db_record.status in [install_model.ToolShedRepository.installation_status.DEACTIVATED]:
# The current tool shed repository is deactivated, so updating its database record
# is not necessary - just activate it.
log.debug("Reactivating deactivated tool_shed_repository '%s'." % str(repository_db_record.name))
self.app.installed_repository_manager.activate_repository(repository_db_record)
# No additional updates to the database record are necessary.
can_update_db_record = False
elif repository_db_record.status not in [install_model.ToolShedRepository.installation_status.NEW]:
# Set changeset_revision here so repository_util.create_or_update_tool_shed_repository will find
# the previously installed and uninstalled repository instead of creating a new record.
changeset_revision = repository_db_record.installed_changeset_revision
self.reset_previously_installed_repository(repository_db_record)
can_update_db_record = True
else:
# No record exists in the database for the repository currently being processed.
installed_changeset_revision = changeset_revision
can_update_db_record = True
if can_update_db_record:
# The database record for the tool shed repository currently being processed can be updated.
# Get the repository metadata to see where it was previously located in the tool panel.
tpm = tool_panel_manager.ToolPanelManager(self.app)
if repository_db_record and repository_db_record.metadata:
_, tool_panel_section_key = \
tpm.handle_tool_panel_selection(toolbox=self.app.toolbox,
metadata=repository_db_record.metadata,
no_changes_checked=no_changes_checked,
tool_panel_section_id=tool_panel_section_id,
new_tool_panel_section_label=new_tool_panel_section_label)
else:
# We're installing a new tool shed repository that does not yet have a database record.
tool_panel_section_key, _ = \
tpm.handle_tool_panel_section(self.app.toolbox,
tool_panel_section_id=tool_panel_section_id,
new_tool_panel_section_label=new_tool_panel_section_label)
tool_shed_repository = \
repository_util.create_or_update_tool_shed_repository(app=self.app,
name=name,
description=description,
installed_changeset_revision=installed_changeset_revision,
ctx_rev=ctx_rev,
repository_clone_url=repository_clone_url,
metadata_dict={},
status=install_model.ToolShedRepository.installation_status.NEW,
current_changeset_revision=changeset_revision,
owner=repository_owner,
dist_to_shed=False)
if tool_shed_repository not in all_created_or_updated_tool_shed_repositories:
all_created_or_updated_tool_shed_repositories.append(tool_shed_repository)
# Only append the tool shed repository to the list of created_or_updated_tool_shed_repositories if
# it is supposed to be installed.
if install_repository_dependencies or self.is_in_repo_info_dicts(repo_info_dict, repo_info_dicts):
if tool_shed_repository not in created_or_updated_tool_shed_repositories:
# Keep the one-to-one mapping between items in 3 lists.
created_or_updated_tool_shed_repositories.append(tool_shed_repository)
tool_panel_section_keys.append(tool_panel_section_key)
filtered_repo_info_dicts.append(repo_info_dict)
# Build repository dependency relationships even if the user chose to not install repository dependencies.
self.build_repository_dependency_relationships(all_repo_info_dicts, all_created_or_updated_tool_shed_repositories)
return created_or_updated_tool_shed_repositories, tool_panel_section_keys, all_repo_info_dicts, filtered_repo_info_dicts
def populate_tool_dependencies_dicts( self, tool_shed_url, tool_path, repository_installed_tool_dependencies,
repository_missing_tool_dependencies, required_repo_info_dicts ):
"""
Return the populated installed_tool_dependencies and missing_tool_dependencies dictionaries
for all repositories defined by entries in the received required_repo_info_dicts.
"""
installed_tool_dependencies = None
missing_tool_dependencies = None
if repository_installed_tool_dependencies is None:
repository_installed_tool_dependencies = {}
else:
# Add the install_dir attribute to the tool_dependencies.
repository_installed_tool_dependencies = \
self.add_installation_directories_to_tool_dependencies( repository_installed_tool_dependencies )
if repository_missing_tool_dependencies is None:
repository_missing_tool_dependencies = {}
else:
# Add the install_dir attribute to the tool_dependencies.
repository_missing_tool_dependencies = \
self.add_installation_directories_to_tool_dependencies( repository_missing_tool_dependencies )
if required_repo_info_dicts:
# Handle the tool dependencies defined for each of the repository's repository dependencies.
for rid in required_repo_info_dicts:
for name, repo_info_tuple in rid.items():
description, repository_clone_url, changeset_revision, \
ctx_rev, repository_owner, repository_dependencies, \
tool_dependencies = \
repository_util.get_repo_info_tuple_contents( repo_info_tuple )
if tool_dependencies:
# Add the install_dir attribute to the tool_dependencies.
tool_dependencies = self.add_installation_directories_to_tool_dependencies( tool_dependencies )
# The required_repository may have been installed with a different changeset revision.
required_repository, installed_changeset_revision = \
repository_util.repository_was_previously_installed( self.app,
tool_shed_url,
name,
repo_info_tuple,
from_tip=False )
if required_repository:
required_repository_installed_tool_dependencies, required_repository_missing_tool_dependencies = \
self.get_installed_and_missing_tool_dependencies_for_installed_repository( required_repository,
tool_dependencies )
if required_repository_installed_tool_dependencies:
# Add the install_dir attribute to the tool_dependencies.
required_repository_installed_tool_dependencies = \
self.add_installation_directories_to_tool_dependencies( required_repository_installed_tool_dependencies )
for td_key, td_dict in required_repository_installed_tool_dependencies.items():
if td_key not in repository_installed_tool_dependencies:
repository_installed_tool_dependencies[ td_key ] = td_dict
if required_repository_missing_tool_dependencies:
# Add the install_dir attribute to the tool_dependencies.
required_repository_missing_tool_dependencies = \
self.add_installation_directories_to_tool_dependencies( required_repository_missing_tool_dependencies )
for td_key, td_dict in required_repository_missing_tool_dependencies.items():
if td_key not in repository_missing_tool_dependencies:
repository_missing_tool_dependencies[ td_key ] = td_dict
if repository_installed_tool_dependencies:
installed_tool_dependencies = repository_installed_tool_dependencies
if repository_missing_tool_dependencies:
missing_tool_dependencies = repository_missing_tool_dependencies
return installed_tool_dependencies, missing_tool_dependencies
def populate_tool_dependencies_dicts(
self, tool_shed_url, tool_path,
repository_installed_tool_dependencies,
repository_missing_tool_dependencies, required_repo_info_dicts):
"""
Return the populated installed_tool_dependencies and missing_tool_dependencies dictionaries
for all repositories defined by entries in the received required_repo_info_dicts.
"""
installed_tool_dependencies = None
missing_tool_dependencies = None
if repository_installed_tool_dependencies is None:
repository_installed_tool_dependencies = {}
else:
# Add the install_dir attribute to the tool_dependencies.
repository_installed_tool_dependencies = \
self.add_installation_directories_to_tool_dependencies( repository_installed_tool_dependencies )
if repository_missing_tool_dependencies is None:
repository_missing_tool_dependencies = {}
else:
# Add the install_dir attribute to the tool_dependencies.
repository_missing_tool_dependencies = \
self.add_installation_directories_to_tool_dependencies( repository_missing_tool_dependencies )
if required_repo_info_dicts:
# Handle the tool dependencies defined for each of the repository's repository dependencies.
for rid in required_repo_info_dicts:
for name, repo_info_tuple in rid.items():
description, repository_clone_url, changeset_revision, \
ctx_rev, repository_owner, repository_dependencies, \
tool_dependencies = \
repository_util.get_repo_info_tuple_contents( repo_info_tuple )
if tool_dependencies:
# Add the install_dir attribute to the tool_dependencies.
tool_dependencies = self.add_installation_directories_to_tool_dependencies(
tool_dependencies)
# The required_repository may have been installed with a different changeset revision.
required_repository, installed_changeset_revision = \
repository_util.repository_was_previously_installed( self.app,
tool_shed_url,
name,
repo_info_tuple,
from_tip=False )
if required_repository:
required_repository_installed_tool_dependencies, required_repository_missing_tool_dependencies = \
self.get_installed_and_missing_tool_dependencies_for_installed_repository( required_repository,
tool_dependencies )
if required_repository_installed_tool_dependencies:
# Add the install_dir attribute to the tool_dependencies.
required_repository_installed_tool_dependencies = \
self.add_installation_directories_to_tool_dependencies( required_repository_installed_tool_dependencies )
for td_key, td_dict in required_repository_installed_tool_dependencies.items(
):
if td_key not in repository_installed_tool_dependencies:
repository_installed_tool_dependencies[
td_key] = td_dict
if required_repository_missing_tool_dependencies:
# Add the install_dir attribute to the tool_dependencies.
required_repository_missing_tool_dependencies = \
self.add_installation_directories_to_tool_dependencies( required_repository_missing_tool_dependencies )
for td_key, td_dict in required_repository_missing_tool_dependencies.items(
):
if td_key not in repository_missing_tool_dependencies:
repository_missing_tool_dependencies[
td_key] = td_dict
if repository_installed_tool_dependencies:
installed_tool_dependencies = repository_installed_tool_dependencies
if repository_missing_tool_dependencies:
missing_tool_dependencies = repository_missing_tool_dependencies
return installed_tool_dependencies, missing_tool_dependencies
def create_repository_dependency_objects( self, tool_path, tool_shed_url, repo_info_dicts, install_repository_dependencies=False,
no_changes_checked=False, tool_panel_section_id=None, new_tool_panel_section_label=None ):
"""
Discover all repository dependencies and make sure all tool_shed_repository and
associated repository_dependency records exist as well as the dependency relationships
between installed repositories. This method is called when uninstalled repositories
are being reinstalled. If the user elected to install repository dependencies, all
items in the all_repo_info_dicts list will be processed. However, if repository
dependencies are not to be installed, only those items contained in the received
repo_info_dicts list will be processed.
"""
install_model = self.app.install_model
log.debug( "Creating repository dependency objects..." )
# The following list will be maintained within this method to contain all created
# or updated tool shed repositories, including repository dependencies that may not
# be installed.
all_created_or_updated_tool_shed_repositories = []
# There will be a one-to-one mapping between items in 3 lists:
# created_or_updated_tool_shed_repositories, tool_panel_section_keys
# and filtered_repo_info_dicts. The 3 lists will filter out repository
# dependencies that are not to be installed.
created_or_updated_tool_shed_repositories = []
tool_panel_section_keys = []
# Repositories will be filtered (e.g., if already installed, if elected
# to not be installed, etc), so filter the associated repo_info_dicts accordingly.
filtered_repo_info_dicts = []
# Discover all repository dependencies and retrieve information for installing
# them. Even if the user elected to not install repository dependencies we have
# to make sure all repository dependency objects exist so that the appropriate
# repository dependency relationships can be built.
all_required_repo_info_dict = self.get_required_repo_info_dicts( tool_shed_url, repo_info_dicts )
all_repo_info_dicts = all_required_repo_info_dict.get( 'all_repo_info_dicts', [] )
if not all_repo_info_dicts:
# No repository dependencies were discovered so process the received repositories.
all_repo_info_dicts = [ rid for rid in repo_info_dicts ]
for repo_info_dict in all_repo_info_dicts:
# If the user elected to install repository dependencies, all items in the
# all_repo_info_dicts list will be processed. However, if repository dependencies
# are not to be installed, only those items contained in the received repo_info_dicts
# list will be processed but the all_repo_info_dicts list will be used to create all
# defined repository dependency relationships.
if self.is_in_repo_info_dicts( repo_info_dict, repo_info_dicts ) or install_repository_dependencies:
for name, repo_info_tuple in repo_info_dict.items():
can_update_db_record = False
description, \
repository_clone_url, \
changeset_revision, \
ctx_rev, \
repository_owner, \
repository_dependencies, \
tool_dependencies = \
repository_util.get_repo_info_tuple_contents( repo_info_tuple )
# See if the repository has an existing record in the database.
repository_db_record, installed_changeset_revision = \
repository_util.repository_was_previously_installed( self.app, tool_shed_url, name, repo_info_tuple, from_tip=False )
if repository_db_record:
if repository_db_record.status in [ install_model.ToolShedRepository.installation_status.INSTALLED,
install_model.ToolShedRepository.installation_status.CLONING,
install_model.ToolShedRepository.installation_status.SETTING_TOOL_VERSIONS,
install_model.ToolShedRepository.installation_status.INSTALLING_REPOSITORY_DEPENDENCIES,
install_model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES,
install_model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES ]:
debug_msg = "Skipping installation of revision %s of repository '%s' because it was installed " % \
( str( changeset_revision ), str( repository_db_record.name ) )
debug_msg += "with the (possibly updated) revision %s and its current installation status is '%s'." % \
( str( installed_changeset_revision ), str( repository_db_record.status ) )
log.debug( debug_msg )
can_update_db_record = False
else:
if repository_db_record.status in [ install_model.ToolShedRepository.installation_status.ERROR,
install_model.ToolShedRepository.installation_status.NEW,
install_model.ToolShedRepository.installation_status.UNINSTALLED ]:
# The current tool shed repository is not currently installed, so we can update its
# record in the database.
name = repository_db_record.name
installed_changeset_revision = repository_db_record.installed_changeset_revision
can_update_db_record = True
elif repository_db_record.status in [ install_model.ToolShedRepository.installation_status.DEACTIVATED ]:
# The current tool shed repository is deactivated, so updating its database record
# is not necessary - just activate it.
log.debug( "Reactivating deactivated tool_shed_repository '%s'." % str( repository_db_record.name ) )
self.app.installed_repository_manager.activate_repository( repository_db_record )
# No additional updates to the database record are necessary.
can_update_db_record = False
elif repository_db_record.status not in [ install_model.ToolShedRepository.installation_status.NEW ]:
# Set changeset_revision here so repository_util.create_or_update_tool_shed_repository will find
# the previously installed and uninstalled repository instead of creating a new record.
changeset_revision = repository_db_record.installed_changeset_revision
self.reset_previously_installed_repository( repository_db_record )
can_update_db_record = True
else:
# No record exists in the database for the repository currently being processed.
installed_changeset_revision = changeset_revision
can_update_db_record = True
if can_update_db_record:
# The database record for the tool shed repository currently being processed can be updated.
# Get the repository metadata to see where it was previously located in the tool panel.
tpm = tool_panel_manager.ToolPanelManager( self.app )
if repository_db_record and repository_db_record.metadata:
_, tool_panel_section_key = \
tpm.handle_tool_panel_selection( toolbox=self.app.toolbox,
metadata=repository_db_record.metadata,
no_changes_checked=no_changes_checked,
tool_panel_section_id=tool_panel_section_id,
new_tool_panel_section_label=new_tool_panel_section_label )
else:
# We're installing a new tool shed repository that does not yet have a database record.
tool_panel_section_key, _ = \
tpm.handle_tool_panel_section( self.app.toolbox,
tool_panel_section_id=tool_panel_section_id,
new_tool_panel_section_label=new_tool_panel_section_label )
tool_shed_repository = \
repository_util.create_or_update_tool_shed_repository( app=self.app,
name=name,
description=description,
installed_changeset_revision=installed_changeset_revision,
ctx_rev=ctx_rev,
repository_clone_url=repository_clone_url,
metadata_dict={},
status=install_model.ToolShedRepository.installation_status.NEW,
current_changeset_revision=changeset_revision,
owner=repository_owner,
dist_to_shed=False )
if tool_shed_repository not in all_created_or_updated_tool_shed_repositories:
all_created_or_updated_tool_shed_repositories.append( tool_shed_repository )
# Only append the tool shed repository to the list of created_or_updated_tool_shed_repositories if
# it is supposed to be installed.
if install_repository_dependencies or self.is_in_repo_info_dicts( repo_info_dict, repo_info_dicts ):
if tool_shed_repository not in created_or_updated_tool_shed_repositories:
# Keep the one-to-one mapping between items in 3 lists.
created_or_updated_tool_shed_repositories.append( tool_shed_repository )
tool_panel_section_keys.append( tool_panel_section_key )
filtered_repo_info_dicts.append( repo_info_dict )
# Build repository dependency relationships even if the user chose to not install repository dependencies.
self.build_repository_dependency_relationships( all_repo_info_dicts, all_created_or_updated_tool_shed_repositories )
return created_or_updated_tool_shed_repositories, tool_panel_section_keys, all_repo_info_dicts, filtered_repo_info_dicts
