def get_or_create_tool_shed_repository( self, tool_shed, name, owner, changeset_revision ):
"""
Return a tool shed repository database record defined by the combination of
tool shed, repository name, repository owner and changeset_revision or
installed_changeset_revision. A new tool shed repository record will be
created if one is not located.
"""
install_model = self.app.install_model
# We store the port in the database.
tool_shed = common_util.remove_protocol_from_tool_shed_url( tool_shed )
# This method is used only in Galaxy, not the tool shed.
repository = suc.get_repository_for_dependency_relationship( self.app, tool_shed, name, owner, changeset_revision )
if not repository:
tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( self.app, tool_shed )
repository_clone_url = os.path.join( tool_shed_url, 'repos', owner, name )
ctx_rev = suc.get_ctx_rev( self.app, tool_shed_url, name, owner, changeset_revision )
repository = suc.create_or_update_tool_shed_repository( app=self.app,
name=name,
description=None,
installed_changeset_revision=changeset_revision,
ctx_rev=ctx_rev,
repository_clone_url=repository_clone_url,
metadata_dict={},
status=install_model.ToolShedRepository.installation_status.NEW,
current_changeset_revision=None,
owner=owner,
dist_to_shed=False )
return repository
def get_or_create_tool_shed_repository( self, tool_shed, name, owner, changeset_revision ):
"""
Return a tool shed repository database record defined by the combination of
tool shed, repository name, repository owner and changeset_revision or
installed_changeset_revision. A new tool shed repository record will be
created if one is not located.
"""
install_model = self.app.install_model
# We store the port in the database.
tool_shed = common_util.remove_protocol_from_tool_shed_url( tool_shed )
# This method is used only in Galaxy, not the tool shed.
repository = suc.get_repository_for_dependency_relationship( self.app, tool_shed, name, owner, changeset_revision )
if not repository:
tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( self.app, tool_shed )
repository_clone_url = os.path.join( tool_shed_url, 'repos', owner, name )
ctx_rev = suc.get_ctx_rev( self.app, tool_shed_url, name, owner, changeset_revision )
repository = suc.create_or_update_tool_shed_repository( app=self.app,
name=name,
description=None,
installed_changeset_revision=changeset_revision,
ctx_rev=ctx_rev,
repository_clone_url=repository_clone_url,
metadata_dict={},
status=install_model.ToolShedRepository.installation_status.NEW,
current_changeset_revision=None,
owner=owner,
dist_to_shed=False )
return repository
def get_env_shell_file_paths( app, elem ):
# Currently only the following tag set is supported.
# <repository toolshed="http://localhost:9009/" name="package_numpy_1_7" owner="test" changeset_revision="c84c6a8be056">
# <package name="numpy" version="1.7.1" />
# </repository>
env_shell_file_paths = []
toolshed = elem.get( 'toolshed', None )
repository_name = elem.get( 'name', None )
repository_owner = elem.get( 'owner', None )
changeset_revision = elem.get( 'changeset_revision', None )
if toolshed and repository_name and repository_owner and changeset_revision:
toolshed = clean_tool_shed_url( toolshed )
repository = suc.get_repository_for_dependency_relationship( app, toolshed, repository_name, repository_owner, changeset_revision )
if repository:
for sub_elem in elem:
tool_dependency_type = sub_elem.tag
tool_dependency_name = sub_elem.get( 'name' )
tool_dependency_version = sub_elem.get( 'version' )
if tool_dependency_type and tool_dependency_name and tool_dependency_version:
# Get the tool_dependency so we can get it's installation directory.
tool_dependency = None
for tool_dependency in repository.tool_dependencies:
if tool_dependency.type == tool_dependency_type and tool_dependency.name == tool_dependency_name and tool_dependency.version == tool_dependency_version:
break
if tool_dependency:
tool_dependency_key = '%s/%s' % ( tool_dependency_name, tool_dependency_version )
installation_directory = tool_dependency.installation_directory( app )
env_shell_file_path = get_env_shell_file_path( installation_directory )
if env_shell_file_path:
env_shell_file_paths.append( env_shell_file_path )
else:
error_message = "Skipping tool dependency definition because unable to locate env.sh file for tool dependency "
error_message += "type %s, name %s, version %s for repository %s" % \
( str( tool_dependency_type ), str( tool_dependency_name ), str( tool_dependency_version ), str( repository.name ) )
log.debug( error_message )
continue
else:
error_message = "Skipping tool dependency definition because unable to locate tool dependency "
error_message += "type %s, name %s, version %s for repository %s" % \
( str( tool_dependency_type ), str( tool_dependency_name ), str( tool_dependency_version ), str( repository.name ) )
log.debug( error_message )
continue
else:
error_message = "Skipping invalid tool dependency definition: type %s, name %s, version %s." % \
( str( tool_dependency_type ), str( tool_dependency_name ), str( tool_dependency_version ) )
log.debug( error_message )
continue
else:
error_message = "Skipping set_environment_for_install definition because unable to locate required installed tool shed repository: "
error_message += "toolshed %s, name %s, owner %s, changeset_revision %s." % \
( str( toolshed ), str( repository_name ), str( repository_owner ), str( changeset_revision ) )
log.debug( error_message )
else:
error_message = "Skipping invalid set_environment_for_install definition: toolshed %s, name %s, owner %s, changeset_revision %s." % \
( str( toolshed ), str( repository_name ), str( repository_owner ), str( changeset_revision ) )
log.debug( error_message )
return env_shell_file_paths
def handle_complex_repository_dependency_for_package(
self,
elem,
package_name,
package_version,
tool_shed_repository,
from_tool_migration_manager=False):
"""
Inspect the repository defined by a complex repository dependency definition and take certain steps to
enable installation of the received package name and version to proceed. The received elem is the
<repository> tag set which defines the complex repository dependency. The received tool_shed_repository
is the installed tool shed repository for which the tool dependency defined by the received package_name
and package_version is being installed.
"""
handled_tool_dependencies = []
tool_shed_url = elem.attrib['toolshed']
required_repository_name = elem.attrib['name']
required_repository_owner = elem.attrib['owner']
default_required_repository_changeset_revision = elem.attrib[
'changeset_revision']
required_repository = suc.get_repository_for_dependency_relationship(
self.app, tool_shed_url, required_repository_name,
required_repository_owner,
default_required_repository_changeset_revision)
tool_shed = common_util.remove_protocol_from_tool_shed_url(
tool_shed_url)
tmp_filename = None
if required_repository:
required_repository_changeset_revision = required_repository.installed_changeset_revision
# Define the installation directory for the required tool dependency package in the required repository.
required_repository_package_install_dir = \
tool_dependency_util.get_tool_dependency_install_dir( app=self.app,
repository_name=required_repository_name,
repository_owner=required_repository_owner,
repository_changeset_revision=required_repository_changeset_revision,
tool_dependency_type='package',
tool_dependency_name=package_name,
tool_dependency_version=package_version )
# Define this dependent repository's tool dependency installation directory that will contain
# the env.sh file with a path to the required repository's installed tool dependency package.
dependent_install_dir = \
tool_dependency_util.get_tool_dependency_install_dir( app=self.app,
repository_name=tool_shed_repository.name,
repository_owner=tool_shed_repository.owner,
repository_changeset_revision=tool_shed_repository.installed_changeset_revision,
tool_dependency_type='package',
tool_dependency_name=package_name,
tool_dependency_version=package_version )
if os.path.exists(dependent_install_dir):
# The install manager handles tool migration stages and the sync_database_with_file_system()
# method handles two scenarios: (1) where a Galaxy file system environment related to installed
# Tool Shed repositories and tool dependencies has somehow gotten out of sync with the Galaxy
# database tables associated with these installed items, and (2) the Tool Shed's install and test
# framework which installs repositories in 2 stages, those of type tool_dependency_definition
# followed by those containing valid tools and tool functional test components. Neither of these
# scenarios apply when the install manager is running.
if from_tool_migration_manager:
can_install_tool_dependency = True
else:
# Notice that we'll throw away the following tool_dependency if it can be installed.
tool_dependency, can_install_tool_dependency = self.sync_database_with_file_system(
self.app,
tool_shed_repository,
package_name,
package_version,
dependent_install_dir,
tool_dependency_type='package')
if not can_install_tool_dependency:
log.debug(
"Tool dependency %s version %s cannot be installed (it was probably previously installed), "
"so appending it to the list of handled tool dependencies.",
str(tool_dependency.name),
str(tool_dependency.version))
handled_tool_dependencies.append(tool_dependency)
else:
can_install_tool_dependency = True
if can_install_tool_dependency:
# Set this dependent repository's tool dependency env.sh file with a path to the required repository's
# installed tool dependency package. We can get everything we need from the discovered installed
# required_repository.
if required_repository.is_deactivated_or_installed:
if not os.path.exists(
required_repository_package_install_dir):
log.error(
'Missing required tool dependency directory %s' %
str(required_repository_package_install_dir))
repo_files_dir = required_repository.repo_files_directory(
self.app)
if not repo_files_dir:
message = "Unable to locate the repository directory for revision %s of installed repository %s owned by %s." % \
( str( required_repository.changeset_revision ), str( required_repository.name ), str( required_repository.owner ) )
raise Exception(message)
tool_dependencies_config = suc.get_absolute_path_to_file_in_repository(
repo_files_dir, 'tool_dependencies.xml')
if tool_dependencies_config:
config_to_use = tool_dependencies_config
else:
message = "Unable to locate required tool_dependencies.xml file for revision %s of installed repository %s owned by %s." % \
( str( required_repository.changeset_revision ), str( required_repository.name ), str( required_repository.owner ) )
raise Exception(message)
else:
# Make a call to the tool shed to get the changeset revision to which the current value of required_repository_changeset_revision
# should be updated if it's not current.
text = suc.get_updated_changeset_revisions_from_tool_shed(
app=self.app,
tool_shed_url=tool_shed,
name=required_repository_name,
owner=required_repository_owner,
changeset_revision=
required_repository_changeset_revision)
if text:
updated_changeset_revisions = listify(text)
# The list of changeset revisions is in reverse order, so the newest will be first.
required_repository_changeset_revision = updated_changeset_revisions[
0]
# Make a call to the tool shed to get the required repository's tool_dependencies.xml file.
tmp_filename = self.create_temporary_tool_dependencies_config(
tool_shed, required_repository_name,
required_repository_owner,
required_repository_changeset_revision)
config_to_use = tmp_filename
handled_tool_dependencies = \
self.create_tool_dependency_with_initialized_env_sh_file( dependent_install_dir=dependent_install_dir,
tool_shed_repository=tool_shed_repository,
required_repository=required_repository,
package_name=package_name,
package_version=package_version,
tool_dependencies_config=config_to_use )
self.remove_file(tmp_filename)
else:
message = "Unable to locate required tool shed repository named %s owned by %s with revision %s." % \
( str( required_repository_name ), str( required_repository_owner ), str( default_required_repository_changeset_revision ) )
raise Exception(message)
return handled_tool_dependencies
def get_dependencies_for_repository( trans, tool_shed_url, repo_info_dict, includes_tool_dependencies ):
"""
Return dictionaries containing the sets of installed and missing tool dependencies and repository dependencies associated with the repository defined
by the received repo_info_dict.
"""
name = repo_info_dict.keys()[ 0 ]
repo_info_tuple = repo_info_dict[ name ]
description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, installed_td = \
suc.get_repo_info_tuple_contents( repo_info_tuple )
if repository_dependencies:
# We have a repository with one or more defined repository dependencies.
missing_td = {}
# Handle the scenario where a repository was installed, then uninstalled and an error occurred during the re-installation process.
# In this case, a record for the repository will exist in the database with the status of 'New'.
repository = suc.get_repository_for_dependency_relationship( trans.app, tool_shed_url, name, repository_owner, changeset_revision )
if repository and repository.metadata:
installed_rd, missing_rd = get_installed_and_missing_repository_dependencies( trans, repository )
else:
installed_rd, missing_rd = get_installed_and_missing_repository_dependencies_for_new_install( trans, repo_info_tuple )
# Discover all repository dependencies and retrieve information for installing them.
all_repo_info_dict = get_required_repo_info_dicts( trans, tool_shed_url, util.listify( repo_info_dict ) )
has_repository_dependencies = all_repo_info_dict.get( 'has_repository_dependencies', False )
includes_tools_for_display_in_tool_panel = all_repo_info_dict.get( 'includes_tools_for_display_in_tool_panel', False )
includes_tool_dependencies = all_repo_info_dict.get( 'includes_tool_dependencies', False )
includes_tools = all_repo_info_dict.get( 'includes_tools', False )
required_repo_info_dicts = all_repo_info_dict.get( 'all_repo_info_dicts', [] )
# Display tool dependencies defined for each of the repository dependencies.
if required_repo_info_dicts:
all_tool_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, rid_installed_td = \
suc.get_repo_info_tuple_contents( repo_info_tuple )
if rid_installed_td:
for td_key, td_dict in rid_installed_td.items():
if td_key not in all_tool_dependencies:
all_tool_dependencies[ td_key ] = td_dict
if all_tool_dependencies:
if installed_td is None:
installed_td = {}
else:
# Move all tool dependencies to the missing_tool_dependencies container.
for td_key, td_dict in installed_td.items():
if td_key not in missing_td:
missing_td[ td_key ] = td_dict
installed_td = {}
# Discover and categorize all tool dependencies defined for this repository's repository dependencies.
required_tool_dependencies, required_missing_tool_dependencies = \
get_installed_and_missing_tool_dependencies_for_new_install( trans, all_tool_dependencies )
if required_tool_dependencies:
if not includes_tool_dependencies:
includes_tool_dependencies = True
for td_key, td_dict in required_tool_dependencies.items():
if td_key not in installed_td:
installed_td[ td_key ] = td_dict
if required_missing_tool_dependencies:
if not includes_tool_dependencies:
includes_tool_dependencies = True
for td_key, td_dict in required_missing_tool_dependencies.items():
if td_key not in missing_td:
missing_td[ td_key ] = td_dict
else:
# We have a single repository with no defined repository dependencies.
all_repo_info_dict = get_required_repo_info_dicts( trans, tool_shed_url, util.listify( repo_info_dict ) )
has_repository_dependencies = all_repo_info_dict.get( 'has_repository_dependencies', False )
includes_tools_for_display_in_tool_panel = all_repo_info_dict.get( 'includes_tools_for_display_in_tool_panel', False )
includes_tool_dependencies = all_repo_info_dict.get( 'includes_tool_dependencies', False )
includes_tools = all_repo_info_dict.get( 'includes_tools', False )
required_repo_info_dicts = all_repo_info_dict.get( 'all_repo_info_dicts', [] )
installed_rd = None
missing_rd = None
missing_td = None
dependencies_for_repository_dict = dict( changeset_revision=changeset_revision,
has_repository_dependencies=has_repository_dependencies,
includes_tool_dependencies=includes_tool_dependencies,
includes_tools=includes_tools,
includes_tools_for_display_in_tool_panel=includes_tools_for_display_in_tool_panel,
installed_repository_dependencies=installed_rd,
installed_tool_dependencies=installed_td,
missing_repository_dependencies=missing_rd,
missing_tool_dependencies=missing_td,
name=name,
repository_owner=repository_owner )
return dependencies_for_repository_dict
def handle_complex_repository_dependency_for_package( self, elem, package_name, package_version, tool_shed_repository,
from_tool_migration_manager=False ):
"""
Inspect the repository defined by a complex repository dependency definition and take certain steps to
enable installation of the received package name and version to proceed. The received elem is the
<repository> tag set which defines the complex repository dependency. The received tool_shed_repository
is the installed tool shed repository for which the tool dependency defined by the received package_name
and package_version is being installed.
"""
handled_tool_dependencies = []
tool_shed_url = elem.attrib[ 'toolshed' ]
required_repository_name = elem.attrib[ 'name' ]
required_repository_owner = elem.attrib[ 'owner' ]
default_required_repository_changeset_revision = elem.attrib[ 'changeset_revision' ]
required_repository = suc.get_repository_for_dependency_relationship( self.app, tool_shed_url,
required_repository_name,
required_repository_owner,
default_required_repository_changeset_revision )
tool_shed = common_util.remove_protocol_from_tool_shed_url( tool_shed_url )
tmp_filename = None
if required_repository:
required_repository_changeset_revision = required_repository.installed_changeset_revision
# Define the installation directory for the required tool dependency package in the required repository.
required_repository_package_install_dir = \
tool_dependency_util.get_tool_dependency_install_dir( app=self.app,
repository_name=required_repository_name,
repository_owner=required_repository_owner,
repository_changeset_revision=required_repository_changeset_revision,
tool_dependency_type='package',
tool_dependency_name=package_name,
tool_dependency_version=package_version )
# Define this dependent repository's tool dependency installation directory that will contain
# the env.sh file with a path to the required repository's installed tool dependency package.
dependent_install_dir = \
tool_dependency_util.get_tool_dependency_install_dir( app=self.app,
repository_name=tool_shed_repository.name,
repository_owner=tool_shed_repository.owner,
repository_changeset_revision=tool_shed_repository.installed_changeset_revision,
tool_dependency_type='package',
tool_dependency_name=package_name,
tool_dependency_version=package_version )
if os.path.exists( dependent_install_dir ):
# The install manager handles tool migration stages and the sync_database_with_file_system()
# method handles two scenarios: (1) where a Galaxy file system environment related to installed
# Tool Shed repositories and tool dependencies has somehow gotten out of sync with the Galaxy
# database tables associated with these installed items, and (2) the Tool Shed's install and test
# framework which installs repositories in 2 stages, those of type tool_dependency_definition
# followed by those containing valid tools and tool functional test components. Neither of these
# scenarios apply when the install manager is running.
if from_tool_migration_manager:
can_install_tool_dependency = True
else:
# Notice that we'll throw away the following tool_dependency if it can be installed.
tool_dependency, can_install_tool_dependency = self.sync_database_with_file_system( self.app,
tool_shed_repository,
package_name,
package_version,
dependent_install_dir,
tool_dependency_type='package' )
if not can_install_tool_dependency:
log.debug( "Tool dependency %s version %s cannot be installed (it was probably previously installed), " %
( str( tool_dependency.name, str( tool_dependency.version ) ) ) )
log.debug( "so appending it to the list of handled tool dependencies." )
handled_tool_dependencies.append( tool_dependency )
else:
can_install_tool_dependency = True
if can_install_tool_dependency:
# Set this dependent repository's tool dependency env.sh file with a path to the required repository's
# installed tool dependency package. We can get everything we need from the discovered installed
# required_repository.
if required_repository.is_deactivated_or_installed:
if not os.path.exists( required_repository_package_install_dir ):
log.error( 'Missing required tool dependency directory %s' % str( required_repository_package_install_dir ) )
repo_files_dir = required_repository.repo_files_directory( self.app )
if not repo_files_dir:
message = "Unable to locate the repository directory for revision %s of installed repository %s owned by %s." % \
( str( required_repository.changeset_revision ), str( required_repository.name ), str( required_repository.owner ) )
raise Exception( message )
tool_dependencies_config = suc.get_absolute_path_to_file_in_repository( repo_files_dir, 'tool_dependencies.xml' )
if tool_dependencies_config:
config_to_use = tool_dependencies_config
else:
message = "Unable to locate required tool_dependencies.xml file for revision %s of installed repository %s owned by %s." % \
( str( required_repository.changeset_revision ), str( required_repository.name ), str( required_repository.owner ) )
raise Exception( message )
else:
# Make a call to the tool shed to get the changeset revision to which the current value of required_repository_changeset_revision
# should be updated if it's not current.
text = suc.get_updated_changeset_revisions_from_tool_shed( app=self.app,
tool_shed_url=tool_shed,
name=required_repository_name,
owner=required_repository_owner,
changeset_revision=required_repository_changeset_revision )
if text:
updated_changeset_revisions = listify( text )
# The list of changeset revisions is in reverse order, so the newest will be first.
required_repository_changeset_revision = updated_changeset_revisions[ 0 ]
# Make a call to the tool shed to get the required repository's tool_dependencies.xml file.
tmp_filename = self.create_temporary_tool_dependencies_config( tool_shed,
required_repository_name,
required_repository_owner,
required_repository_changeset_revision )
config_to_use = tmp_filename
handled_tool_dependencies = \
self.create_tool_dependency_with_initialized_env_sh_file( dependent_install_dir=dependent_install_dir,
tool_shed_repository=tool_shed_repository,
required_repository=required_repository,
package_name=package_name,
package_version=package_version,
tool_dependencies_config=config_to_use )
self.remove_file( tmp_filename )
else:
message = "Unable to locate required tool shed repository named %s owned by %s with revision %s." % \
( str( required_repository_name ), str( required_repository_owner ), str( default_required_repository_changeset_revision ) )
raise Exception( message )
return handled_tool_dependencies
def get_env_shell_file_paths(self, elem):
# Currently only the following tag set is supported.
# <repository toolshed="http://localhost:9009/" name="package_numpy_1_7" owner="test" changeset_revision="c84c6a8be056">
# <package name="numpy" version="1.7.1" />
# </repository>
env_shell_file_paths = []
toolshed = elem.get('toolshed', None)
repository_name = elem.get('name', None)
repository_owner = elem.get('owner', None)
changeset_revision = elem.get('changeset_revision', None)
if toolshed and repository_name and repository_owner and changeset_revision:
# The protocol is not stored, but the port is if it exists.
toolshed = common_util.remove_protocol_from_tool_shed_url(toolshed)
repository = suc.get_repository_for_dependency_relationship(
self.app, toolshed, repository_name, repository_owner,
changeset_revision)
if repository:
for sub_elem in elem:
tool_dependency_type = sub_elem.tag
tool_dependency_name = sub_elem.get('name')
tool_dependency_version = sub_elem.get('version')
if tool_dependency_type and tool_dependency_name and tool_dependency_version:
# Get the tool_dependency so we can get its installation directory.
tool_dependency = None
for tool_dependency in repository.tool_dependencies:
if tool_dependency.type == tool_dependency_type and \
tool_dependency.name == tool_dependency_name and \
tool_dependency.version == tool_dependency_version:
break
if tool_dependency:
tool_dependency_key = '%s/%s' % (
tool_dependency_name, tool_dependency_version)
installation_directory = tool_dependency.installation_directory(
self.app)
env_shell_file_path = self.get_env_shell_file_path(
installation_directory)
if env_shell_file_path:
env_shell_file_paths.append(
env_shell_file_path)
else:
error_message = "Skipping tool dependency definition because unable to locate env.sh file for tool dependency "
error_message += "type %s, name %s, version %s for repository %s" % \
( str( tool_dependency_type ), str( tool_dependency_name ), str( tool_dependency_version ), str( repository.name ) )
log.debug(error_message)
continue
else:
error_message = "Skipping tool dependency definition because unable to locate tool dependency "
error_message += "type %s, name %s, version %s for repository %s" % \
( str( tool_dependency_type ), str( tool_dependency_name ), str( tool_dependency_version ), str( repository.name ) )
log.debug(error_message)
continue
else:
error_message = "Skipping invalid tool dependency definition: type %s, name %s, version %s." % \
( str( tool_dependency_type ), str( tool_dependency_name ), str( tool_dependency_version ) )
log.debug(error_message)
continue
else:
error_message = "Skipping set_environment_for_install definition because unable to locate required installed tool shed repository: "
error_message += "toolshed %s, name %s, owner %s, changeset_revision %s." % \
( str( toolshed ), str( repository_name ), str( repository_owner ), str( changeset_revision ) )
log.debug(error_message)
else:
error_message = "Skipping invalid set_environment_for_install definition: toolshed %s, name %s, owner %s, changeset_revision %s." % \
( str( toolshed ), str( repository_name ), str( repository_owner ), str( changeset_revision ) )
log.debug(error_message)
return env_shell_file_paths
def get_dependencies_for_repository( trans, tool_shed_url, repo_info_dict, includes_tool_dependencies ):
"""
Return dictionaries containing the sets of installed and missing tool dependencies and repository dependencies associated
with the repository defined by the received repo_info_dict.
"""
repository = None
installed_rd = {}
installed_td = {}
missing_rd = {}
missing_td = {}
name = repo_info_dict.keys()[ 0 ]
repo_info_tuple = repo_info_dict[ name ]
description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = \
suc.get_repo_info_tuple_contents( repo_info_tuple )
if tool_dependencies:
if not includes_tool_dependencies:
includes_tool_dependencies = True
# Inspect the tool_dependencies dictionary to separate the installed and missing tool dependencies. We don't add to installed_td
# and missing_td here because at this point they are empty.
installed_td, missing_td = get_installed_and_missing_tool_dependencies_for_installing_repository( trans, tool_shed_url, tool_dependencies )
# In cases where a repository dependency is required only for compiling a dependent repository's tool dependency, the value of
# repository_dependencies will be an empty dictionary here.
if repository_dependencies:
# We have a repository with one or more defined repository dependencies.
if not repository:
repository = suc.get_repository_for_dependency_relationship( trans.app, tool_shed_url, name, repository_owner, changeset_revision )
if repository and repository.metadata:
installed_rd, missing_rd = get_installed_and_missing_repository_dependencies( trans, repository )
else:
installed_rd, missing_rd = get_installed_and_missing_repository_dependencies_for_new_install( trans, repo_info_tuple )
# Discover all repository dependencies and retrieve information for installing them.
all_repo_info_dict = get_required_repo_info_dicts( trans, tool_shed_url, util.listify( repo_info_dict ) )
has_repository_dependencies = all_repo_info_dict.get( 'has_repository_dependencies', False )
has_repository_dependencies_only_if_compiling_contained_td = \
all_repo_info_dict.get( 'has_repository_dependencies_only_if_compiling_contained_td', False )
includes_tools_for_display_in_tool_panel = all_repo_info_dict.get( 'includes_tools_for_display_in_tool_panel', False )
includes_tool_dependencies = all_repo_info_dict.get( 'includes_tool_dependencies', False )
includes_tools = all_repo_info_dict.get( 'includes_tools', False )
required_repo_info_dicts = all_repo_info_dict.get( 'all_repo_info_dicts', [] )
# Display tool dependencies defined for each of the repository dependencies.
if required_repo_info_dicts:
required_tool_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, rid_repository_dependencies, rid_tool_dependencies = \
suc.get_repo_info_tuple_contents( repo_info_tuple )
if rid_tool_dependencies:
for td_key, td_dict in rid_tool_dependencies.items():
if td_key not in required_tool_dependencies:
required_tool_dependencies[ td_key ] = td_dict
if required_tool_dependencies:
# Discover and categorize all tool dependencies defined for this repository's repository dependencies.
required_installed_td, required_missing_td = \
get_installed_and_missing_tool_dependencies_for_installing_repository( trans, tool_shed_url, required_tool_dependencies )
if required_installed_td:
if not includes_tool_dependencies:
includes_tool_dependencies = True
for td_key, td_dict in required_installed_td.items():
if td_key not in installed_td:
installed_td[ td_key ] = td_dict
if required_missing_td:
if not includes_tool_dependencies:
includes_tool_dependencies = True
for td_key, td_dict in required_missing_td.items():
if td_key not in missing_td:
missing_td[ td_key ] = td_dict
else:
# We have a single repository with (possibly) no defined repository dependencies.
all_repo_info_dict = get_required_repo_info_dicts( trans, tool_shed_url, util.listify( repo_info_dict ) )
has_repository_dependencies = all_repo_info_dict.get( 'has_repository_dependencies', False )
has_repository_dependencies_only_if_compiling_contained_td = \
all_repo_info_dict.get( 'has_repository_dependencies_only_if_compiling_contained_td', False )
includes_tools_for_display_in_tool_panel = all_repo_info_dict.get( 'includes_tools_for_display_in_tool_panel', False )
includes_tool_dependencies = all_repo_info_dict.get( 'includes_tool_dependencies', False )
includes_tools = all_repo_info_dict.get( 'includes_tools', False )
required_repo_info_dicts = all_repo_info_dict.get( 'all_repo_info_dicts', [] )
dependencies_for_repository_dict = \
dict( changeset_revision=changeset_revision,
has_repository_dependencies=has_repository_dependencies,
has_repository_dependencies_only_if_compiling_contained_td=has_repository_dependencies_only_if_compiling_contained_td,
includes_tool_dependencies=includes_tool_dependencies,
includes_tools=includes_tools,
includes_tools_for_display_in_tool_panel=includes_tools_for_display_in_tool_panel,
installed_repository_dependencies=installed_rd,
installed_tool_dependencies=installed_td,
missing_repository_dependencies=missing_rd,
missing_tool_dependencies=missing_td,
name=name,
repository_owner=repository_owner )
return dependencies_for_repository_dict
