def _configure_models( self, check_migrate_databases=False, check_migrate_tools=False, config_file=None ):
"""
Preconditions: object_store must be set on self.
"""
if self.config.database_connection:
db_url = self.config.database_connection
else:
db_url = "sqlite:///%s?isolation_level=IMMEDIATE" % self.config.database
install_db_url = self.config.install_database_connection
# TODO: Consider more aggressive check here that this is not the same
# database file under the hood.
combined_install_database = not( install_db_url and install_db_url != db_url )
install_db_url = install_db_url or db_url
if check_migrate_databases:
# Initialize database / check for appropriate schema version. # If this
# is a new installation, we'll restrict the tool migration messaging.
from galaxy.model.migrate.check import create_or_verify_database
create_or_verify_database( db_url, config_file, self.config.database_engine_options, app=self )
if not combined_install_database:
from galaxy.model.tool_shed_install.migrate.check import create_or_verify_database as tsi_create_or_verify_database
tsi_create_or_verify_database( install_db_url, self.config.install_database_engine_options, app=self )
if check_migrate_tools:
# Alert the Galaxy admin to tools that have been moved from the distribution to the tool shed.
from tool_shed.galaxy_install.migrate.check import verify_tools
if combined_install_database:
install_database_options = self.config.database_engine_options
else:
install_database_options = self.config.install_database_engine_options
verify_tools( self, install_db_url, config_file, install_database_options )
from galaxy.model import mapping
self.model = mapping.init( self.config.file_path,
db_url,
self.config.database_engine_options,
map_install_models=combined_install_database,
database_query_profiling_proxy=self.config.database_query_profiling_proxy,
object_store=self.object_store,
trace_logger=getattr(self, "trace_logger", None),
use_pbkdf2=self.config.get_bool( 'use_pbkdf2', True ) )
if combined_install_database:
log.info("Install database targetting Galaxy's database configuration.")
self.install_model = self.model
else:
from galaxy.model.tool_shed_install import mapping as install_mapping
install_db_url = self.config.install_database_connection
log.info("Install database using its own connection %s" % install_db_url)
install_db_engine_options = self.config.install_database_engine_options
self.install_model = install_mapping.init( install_db_url,
install_db_engine_options )
def __init__(self, **kwargs):
print >>sys.stderr, "python path is: " + ", ".join(sys.path)
self.name = "galaxy"
self.new_installation = False
# Read config file and check for errors
self.config = config.Configuration(**kwargs)
self.config.check()
config.configure_logging(self.config)
self.configure_fluent_log()
# Determine the database url
if self.config.database_connection:
db_url = self.config.database_connection
else:
db_url = "sqlite:///%s?isolation_level=IMMEDIATE" % self.config.database
# Set up the tool sheds registry
if os.path.isfile(self.config.tool_sheds_config):
self.tool_shed_registry = tool_shed.tool_shed_registry.Registry(
self.config.root, self.config.tool_sheds_config
)
else:
self.tool_shed_registry = None
# Initialize database / check for appropriate schema version. # If this
# is a new installation, we'll restrict the tool migration messaging.
from galaxy.model.migrate.check import create_or_verify_database
create_or_verify_database(
db_url, kwargs.get("global_conf", {}).get("__file__", None), self.config.database_engine_options, app=self
)
# Alert the Galaxy admin to tools that have been moved from the distribution to the tool shed.
from tool_shed.galaxy_install.migrate.check import verify_tools
verify_tools(
self, db_url, kwargs.get("global_conf", {}).get("__file__", None), self.config.database_engine_options
)
# Object store manager
self.object_store = build_object_store_from_config(self.config, fsmon=True)
# Setup the database engine and ORM
from galaxy.model import mapping
self.model = mapping.init(
self.config.file_path,
db_url,
self.config.database_engine_options,
database_query_profiling_proxy=self.config.database_query_profiling_proxy,
object_store=self.object_store,
trace_logger=self.trace_logger,
use_pbkdf2=self.config.get_bool("use_pbkdf2", True),
)
# Manage installed tool shed repositories.
self.installed_repository_manager = tool_shed.galaxy_install.InstalledRepositoryManager(self)
# Create an empty datatypes registry.
self.datatypes_registry = galaxy.datatypes.registry.Registry()
# Load proprietary datatypes defined in datatypes_conf.xml files in all installed tool shed repositories. We
# load proprietary datatypes before datatypes in the distribution because Galaxy's default sniffers include some
# generic sniffers (eg text,xml) which catch anything, so it's impossible for proprietary sniffers to be used.
# However, if there is a conflict (2 datatypes with the same extension) between a proprietary datatype and a datatype
# in the Galaxy distribution, the datatype in the Galaxy distribution will take precedence. If there is a conflict
# between 2 proprietary datatypes, the datatype from the repository that was installed earliest will take precedence.
self.installed_repository_manager.load_proprietary_datatypes()
# Load the data types in the Galaxy distribution, which are defined in self.config.datatypes_config.
self.datatypes_registry.load_datatypes(self.config.root, self.config.datatypes_config)
galaxy.model.set_datatypes_registry(self.datatypes_registry)
# Security helper
self.security = security.SecurityHelper(id_secret=self.config.id_secret)
# Tag handler
self.tag_handler = GalaxyTagHandler()
# Genomes
self.genomes = Genomes(self)
# Data providers registry.
self.data_provider_registry = DataProviderRegistry()
# Initialize tool data tables using the config defined by self.config.tool_data_table_config_path.
self.tool_data_tables = galaxy.tools.data.ToolDataTableManager(
tool_data_path=self.config.tool_data_path, config_filename=self.config.tool_data_table_config_path
)
# Load additional entries defined by self.config.shed_tool_data_table_config into tool data tables.
self.tool_data_tables.load_from_config_file(
config_filename=self.config.shed_tool_data_table_config,
tool_data_path=self.tool_data_tables.tool_data_path,
from_shed_config=False,
)
# Initialize the job management configuration
self.job_config = jobs.JobConfiguration(self)
# Initialize the tools, making sure the list of tool configs includes the reserved migrated_tools_conf.xml file.
tool_configs = self.config.tool_configs
if self.config.migrated_tools_config not in tool_configs:
tool_configs.append(self.config.migrated_tools_config)
self.toolbox = tools.ToolBox(tool_configs, self.config.tool_path, self)
# Search support for tools
self.toolbox_search = galaxy.tools.search.ToolBoxSearch(self.toolbox)
# Load Data Manager
self.data_managers = DataManagers(self)
# If enabled, poll respective tool sheds to see if updates are available for any installed tool shed repositories.
if self.config.get_bool("enable_tool_shed_check", False):
from tool_shed.galaxy_install import update_manager
self.update_manager = update_manager.UpdateManager(self)
else:
self.update_manager = None
# Load proprietary datatype converters and display applications.
self.installed_repository_manager.load_proprietary_converters_and_display_applications()
# Load datatype display applications defined in local datatypes_conf.xml
self.datatypes_registry.load_display_applications()
# Load datatype converters defined in local datatypes_conf.xml
self.datatypes_registry.load_datatype_converters(self.toolbox)
# Load external metadata tool
self.datatypes_registry.load_external_metadata_tool(self.toolbox)
# Load history import/export tools.
load_history_imp_exp_tools(self.toolbox)
# Load genome indexer tool.
load_genome_index_tools(self.toolbox)
# visualizations registry: associates resources with visualizations, controls how to render
self.visualizations_registry = None
if self.config.visualizations_config_directory:
self.visualizations_registry = VisualizationsRegistry(
self.config.root, self.config.visualizations_config_directory
)
# Load security policy.
self.security_agent = self.model.security_agent
self.host_security_agent = galaxy.security.HostAgent(
model=self.security_agent.model, permitted_actions=self.security_agent.permitted_actions
)
# Load quota management.
if self.config.enable_quotas:
self.quota_agent = galaxy.quota.QuotaAgent(self.model)
else:
self.quota_agent = galaxy.quota.NoQuotaAgent(self.model)
# Heartbeat and memdump for thread / heap profiling
self.heartbeat = None
self.memdump = None
self.memory_usage = None
# Container for OpenID authentication routines
if self.config.enable_openid:
from galaxy.web.framework import openid_manager
self.openid_manager = openid_manager.OpenIDManager(self.config.openid_consumer_cache_path)
self.openid_providers = OpenIDProviders.from_file(self.config.openid_config)
else:
self.openid_providers = OpenIDProviders()
# Start the heartbeat process if configured and available
if self.config.use_heartbeat:
from galaxy.util import heartbeat
if heartbeat.Heartbeat:
self.heartbeat = heartbeat.Heartbeat(fname=self.config.heartbeat_log)
self.heartbeat.start()
# Enable the memdump signal catcher if configured and available
if self.config.use_memdump:
from galaxy.util import memdump
if memdump.Memdump:
self.memdump = memdump.Memdump()
# Transfer manager client
if self.config.get_bool("enable_beta_job_managers", False):
from galaxy.jobs import transfer_manager
self.transfer_manager = transfer_manager.TransferManager(self)
# Start the job manager
from galaxy.jobs import manager
self.job_manager = manager.JobManager(self)
# FIXME: These are exposed directly for backward compatibility
self.job_queue = self.job_manager.job_queue
self.job_stop_queue = self.job_manager.job_stop_queue
# Initialize the external service types
self.external_service_types = external_service_types.ExternalServiceTypesCollection(
self.config.external_service_type_config_file, self.config.external_service_type_path, self
)
def __init__(self, **kwargs):
print >> sys.stderr, "python path is: " + ", ".join(sys.path)
self.name = 'galaxy'
self.new_installation = False
# Read config file and check for errors
self.config = config.Configuration(**kwargs)
self.config.check()
config.configure_logging(self.config)
self.configure_fluent_log()
# Determine the database url
if self.config.database_connection:
db_url = self.config.database_connection
else:
db_url = "sqlite:///%s?isolation_level=IMMEDIATE" % self.config.database
# Set up the tool sheds registry
if os.path.isfile(self.config.tool_sheds_config):
self.tool_shed_registry = tool_shed.tool_shed_registry.Registry(
self.config.root, self.config.tool_sheds_config)
else:
self.tool_shed_registry = None
# Initialize database / check for appropriate schema version. # If this
# is a new installation, we'll restrict the tool migration messaging.
from galaxy.model.migrate.check import create_or_verify_database
create_or_verify_database(db_url,
kwargs.get('global_conf',
{}).get('__file__', None),
self.config.database_engine_options,
app=self)
# Alert the Galaxy admin to tools that have been moved from the distribution to the tool shed.
from tool_shed.galaxy_install.migrate.check import verify_tools
verify_tools(self, db_url,
kwargs.get('global_conf', {}).get('__file__', None),
self.config.database_engine_options)
# Object store manager
self.object_store = build_object_store_from_config(self.config,
fsmon=True)
# Setup the database engine and ORM
from galaxy.model import mapping
self.model = mapping.init(self.config.file_path,
db_url,
self.config.database_engine_options,
database_query_profiling_proxy=self.config.
database_query_profiling_proxy,
object_store=self.object_store,
trace_logger=self.trace_logger,
use_pbkdf2=self.config.get_bool(
'use_pbkdf2', True))
# Manage installed tool shed repositories.
self.installed_repository_manager = tool_shed.galaxy_install.InstalledRepositoryManager(
self)
# Create an empty datatypes registry.
self.datatypes_registry = galaxy.datatypes.registry.Registry()
# Load proprietary datatypes defined in datatypes_conf.xml files in all installed tool shed repositories. We
# load proprietary datatypes before datatypes in the distribution because Galaxy's default sniffers include some
# generic sniffers (eg text,xml) which catch anything, so it's impossible for proprietary sniffers to be used.
# However, if there is a conflict (2 datatypes with the same extension) between a proprietary datatype and a datatype
# in the Galaxy distribution, the datatype in the Galaxy distribution will take precedence. If there is a conflict
# between 2 proprietary datatypes, the datatype from the repository that was installed earliest will take precedence.
self.installed_repository_manager.load_proprietary_datatypes()
# Load the data types in the Galaxy distribution, which are defined in self.config.datatypes_config.
self.datatypes_registry.load_datatypes(self.config.root,
self.config.datatypes_config)
galaxy.model.set_datatypes_registry(self.datatypes_registry)
# Security helper
self.security = security.SecurityHelper(
id_secret=self.config.id_secret)
# Tag handler
self.tag_handler = GalaxyTagHandler()
# Genomes
self.genomes = Genomes(self)
# Data providers registry.
self.data_provider_registry = DataProviderRegistry()
# Initialize tool data tables using the config defined by self.config.tool_data_table_config_path.
self.tool_data_tables = galaxy.tools.data.ToolDataTableManager(
tool_data_path=self.config.tool_data_path,
config_filename=self.config.tool_data_table_config_path)
# Load additional entries defined by self.config.shed_tool_data_table_config into tool data tables.
self.tool_data_tables.load_from_config_file(
config_filename=self.config.shed_tool_data_table_config,
tool_data_path=self.tool_data_tables.tool_data_path,
from_shed_config=False)
# Initialize the job management configuration
self.job_config = jobs.JobConfiguration(self)
# Initialize the tools, making sure the list of tool configs includes the reserved migrated_tools_conf.xml file.
tool_configs = self.config.tool_configs
if self.config.migrated_tools_config not in tool_configs:
tool_configs.append(self.config.migrated_tools_config)
self.toolbox = tools.ToolBox(tool_configs, self.config.tool_path, self)
# Search support for tools
self.toolbox_search = galaxy.tools.search.ToolBoxSearch(self.toolbox)
# Load Data Manager
self.data_managers = DataManagers(self)
# If enabled, poll respective tool sheds to see if updates are available for any installed tool shed repositories.
if self.config.get_bool('enable_tool_shed_check', False):
from tool_shed.galaxy_install import update_manager
self.update_manager = update_manager.UpdateManager(self)
else:
self.update_manager = None
# Load proprietary datatype converters and display applications.
self.installed_repository_manager.load_proprietary_converters_and_display_applications(
)
# Load datatype display applications defined in local datatypes_conf.xml
self.datatypes_registry.load_display_applications()
# Load datatype converters defined in local datatypes_conf.xml
self.datatypes_registry.load_datatype_converters(self.toolbox)
# Load external metadata tool
self.datatypes_registry.load_external_metadata_tool(self.toolbox)
# Load history import/export tools.
load_history_imp_exp_tools(self.toolbox)
# Load genome indexer tool.
load_genome_index_tools(self.toolbox)
# visualizations registry: associates resources with visualizations, controls how to render
self.visualizations_registry = None
if self.config.visualizations_config_directory:
self.visualizations_registry = VisualizationsRegistry(
self.config.root, self.config.visualizations_config_directory)
# Load security policy.
self.security_agent = self.model.security_agent
self.host_security_agent = galaxy.security.HostAgent(
model=self.security_agent.model,
permitted_actions=self.security_agent.permitted_actions)
# Load quota management.
if self.config.enable_quotas:
self.quota_agent = galaxy.quota.QuotaAgent(self.model)
else:
self.quota_agent = galaxy.quota.NoQuotaAgent(self.model)
# Heartbeat and memdump for thread / heap profiling
self.heartbeat = None
self.memdump = None
self.memory_usage = None
# Container for OpenID authentication routines
if self.config.enable_openid:
from galaxy.web.framework import openid_manager
self.openid_manager = openid_manager.OpenIDManager(
self.config.openid_consumer_cache_path)
self.openid_providers = OpenIDProviders.from_file(
self.config.openid_config)
else:
self.openid_providers = OpenIDProviders()
# Start the heartbeat process if configured and available
if self.config.use_heartbeat:
from galaxy.util import heartbeat
if heartbeat.Heartbeat:
self.heartbeat = heartbeat.Heartbeat(
fname=self.config.heartbeat_log)
self.heartbeat.start()
# Enable the memdump signal catcher if configured and available
if self.config.use_memdump:
from galaxy.util import memdump
if memdump.Memdump:
self.memdump = memdump.Memdump()
# Transfer manager client
if self.config.get_bool('enable_beta_job_managers', False):
from galaxy.jobs import transfer_manager
self.transfer_manager = transfer_manager.TransferManager(self)
# Start the job manager
from galaxy.jobs import manager
self.job_manager = manager.JobManager(self)
# FIXME: These are exposed directly for backward compatibility
self.job_queue = self.job_manager.job_queue
self.job_stop_queue = self.job_manager.job_stop_queue
# Initialize the external service types
self.external_service_types = external_service_types.ExternalServiceTypesCollection(
self.config.external_service_type_config_file,
self.config.external_service_type_path, self)