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This document is for an old release of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

Source code for galaxy.config

"""
Universe configuration builder.
"""
# absolute_import needed for tool_shed package.
from __future__ import absolute_import

import logging
import logging.config
import os
import re
import signal
import socket
import string
import sys
import tempfile
import threading
import time

from datetime import timedelta

from six import string_types
from six.moves import configparser

from galaxy.containers import parse_containers_config
from galaxy.exceptions import ConfigurationError
from galaxy.util import ExecutionTimer
from galaxy.util import listify
from galaxy.util import string_as_bool
from galaxy.util.dbkeys import GenomeBuilds
from galaxy.web.formatting import expand_pretty_datetime_format
from galaxy.web.stack import register_postfork_function
from .version import VERSION_MAJOR

log = logging.getLogger( __name__ )


PATH_DEFAULTS = dict(
    auth_config_file=['config/auth_conf.xml', 'config/auth_conf.xml.sample'],
    data_manager_config_file=['config/data_manager_conf.xml', 'data_manager_conf.xml', 'config/data_manager_conf.xml.sample'],
    datatypes_config_file=['config/datatypes_conf.xml', 'datatypes_conf.xml', 'config/datatypes_conf.xml.sample'],
    build_sites_config_file=['config/build_sites.yml', 'config/build_sites.yml.sample'],
    external_service_type_config_file=['config/external_service_types_conf.xml', 'external_service_types_conf.xml', 'config/external_service_types_conf.xml.sample'],
    job_config_file=['config/job_conf.xml', 'job_conf.xml'],
    tool_destinations_config_file=['config/tool_destinations.yml', 'config/tool_destinations.yml.sample'],
    job_metrics_config_file=['config/job_metrics_conf.xml', 'job_metrics_conf.xml', 'config/job_metrics_conf.xml.sample'],
    dependency_resolvers_config_file=['config/dependency_resolvers_conf.xml', 'dependency_resolvers_conf.xml'],
    job_resource_params_file=['config/job_resource_params_conf.xml', 'job_resource_params_conf.xml'],
    migrated_tools_config=['migrated_tools_conf.xml', 'config/migrated_tools_conf.xml'],
    object_store_config_file=['config/object_store_conf.xml', 'object_store_conf.xml'],
    openid_config_file=['config/openid_conf.xml', 'openid_conf.xml', 'config/openid_conf.xml.sample'],
    shed_data_manager_config_file=['shed_data_manager_conf.xml', 'config/shed_data_manager_conf.xml'],
    shed_tool_data_table_config=['shed_tool_data_table_conf.xml', 'config/shed_tool_data_table_conf.xml'],
    tool_sheds_config_file=['config/tool_sheds_conf.xml', 'tool_sheds_conf.xml', 'config/tool_sheds_conf.xml.sample'],
    workflow_schedulers_config_file=['config/workflow_schedulers_conf.xml', 'config/workflow_schedulers_conf.xml.sample'],
    modules_mapping_files=['config/environment_modules_mapping.yml', 'config/environment_modules_mapping.yml.sample'],
    local_conda_mapping_file=['config/local_conda_mapping.yml', 'config/local_conda_mapping.yml.sample'],
    containers_config_file=['config/containers_conf.yml'],
)

PATH_LIST_DEFAULTS = dict(
    tool_data_table_config_path=['config/tool_data_table_conf.xml', 'tool_data_table_conf.xml', 'config/tool_data_table_conf.xml.sample'],
    # rationale:
    # [0]: user has explicitly created config/tool_conf.xml but did not
    #      move their existing shed_tool_conf.xml, don't use
    #      config/shed_tool_conf.xml, which is probably the empty
    #      version copied from the sample, or else their shed tools
    #      will disappear
    # [1]: user has created config/tool_conf.xml and, having passed
    #      [0], probably moved their shed_tool_conf.xml as well
    # [2]: user has done nothing, use the old files
    # [3]: fresh install
    tool_config_file=['config/tool_conf.xml,shed_tool_conf.xml',
                      'config/tool_conf.xml,config/shed_tool_conf.xml',
                      'tool_conf.xml,shed_tool_conf.xml',
                      'config/tool_conf.xml.sample,config/shed_tool_conf.xml']
)


[docs]def resolve_path( path, root ): """If 'path' is relative make absolute by prepending 'root'""" if not os.path.isabs( path ): path = os.path.join( root, path ) return path
[docs]def find_path(kwargs, var, root): """Find a configuration path that may exist at different defaults.""" defaults = PATH_DEFAULTS[var] if kwargs.get(var, None) is not None: path = kwargs.get(var) else: for default in defaults: if os.path.exists(resolve_path(default, root)): path = default break else: path = defaults[-1] return resolve_path(path, root)
[docs]def find_root(kwargs): root = kwargs.get('root_dir', '.') return root
[docs]class Configuration( object ): deprecated_options = ( 'database_file', )
[docs] def __init__( self, **kwargs ): self.config_dict = kwargs self.root = find_root(kwargs) # Resolve paths of other config files self.__parse_config_file_options( kwargs ) # Collect the umask and primary gid from the environment self.umask = os.umask( 0o77 ) # get the current umask os.umask( self.umask ) # can't get w/o set, so set it back self.gid = os.getgid() # if running under newgrp(1) we'll need to fix the group of data created on the cluster self.version_major = VERSION_MAJOR # Database related configuration self.database = resolve_path( kwargs.get( "database_file", "database/universe.sqlite" ), self.root ) self.database_connection = kwargs.get( "database_connection", False ) self.database_engine_options = get_database_engine_options( kwargs ) self.database_create_tables = string_as_bool( kwargs.get( "database_create_tables", "True" ) ) self.database_query_profiling_proxy = string_as_bool( kwargs.get( "database_query_profiling_proxy", "False" ) ) self.slow_query_log_threshold = float( kwargs.get( "slow_query_log_threshold", 0) ) # Don't set this to true for production databases, but probably should # default to True for sqlite databases. self.database_auto_migrate = string_as_bool( kwargs.get( "database_auto_migrate", "False" ) ) # Install database related configuration (if different). self.install_database_connection = kwargs.get( "install_database_connection", None ) self.install_database_engine_options = get_database_engine_options( kwargs, model_prefix="install_" ) # Where dataset files are stored self.file_path = resolve_path( kwargs.get( "file_path", "database/files" ), self.root ) self.new_file_path = resolve_path( kwargs.get( "new_file_path", "database/tmp" ), self.root ) override_tempdir = string_as_bool( kwargs.get( "override_tempdir", "True" ) ) if override_tempdir: tempfile.tempdir = self.new_file_path self.openid_consumer_cache_path = resolve_path( kwargs.get( "openid_consumer_cache_path", "database/openid_consumer_cache" ), self.root ) self.cookie_path = kwargs.get( "cookie_path", "/" ) # Galaxy OpenID settings self.enable_openid = string_as_bool( kwargs.get( 'enable_openid', False ) ) self.enable_quotas = string_as_bool( kwargs.get( 'enable_quotas', False ) ) self.enable_unique_workflow_defaults = string_as_bool( kwargs.get( 'enable_unique_workflow_defaults', False ) ) self.tool_path = resolve_path( kwargs.get( "tool_path", "tools" ), self.root ) self.tool_data_path = resolve_path( kwargs.get( "tool_data_path", "tool-data" ), os.getcwd() ) self.builds_file_path = resolve_path( kwargs.get( "builds_file_path", os.path.join( self.tool_data_path, 'shared', 'ucsc', 'builds.txt') ), self.root ) self.len_file_path = resolve_path( kwargs.get( "len_file_path", os.path.join( self.tool_data_path, 'shared', 'ucsc', 'chrom') ), self.root ) # The value of migrated_tools_config is the file reserved for containing only those tools that have been eliminated from the distribution # and moved to the tool shed. self.integrated_tool_panel_config = resolve_path( kwargs.get( 'integrated_tool_panel_config', 'integrated_tool_panel.xml' ), self.root ) integrated_tool_panel_tracking_directory = kwargs.get( 'integrated_tool_panel_tracking_directory', None ) if integrated_tool_panel_tracking_directory: self.integrated_tool_panel_tracking_directory = resolve_path( integrated_tool_panel_tracking_directory, self.root ) else: self.integrated_tool_panel_tracking_directory = None self.toolbox_filter_base_modules = listify( kwargs.get( "toolbox_filter_base_modules", "galaxy.tools.filters,galaxy.tools.toolbox.filters" ) ) self.tool_filters = listify( kwargs.get( "tool_filters", [] ), do_strip=True ) self.tool_label_filters = listify( kwargs.get( "tool_label_filters", [] ), do_strip=True ) self.tool_section_filters = listify( kwargs.get( "tool_section_filters", [] ), do_strip=True ) self.user_tool_filters = listify( kwargs.get( "user_tool_filters", [] ), do_strip=True ) self.user_tool_label_filters = listify( kwargs.get( "user_tool_label_filters", [] ), do_strip=True ) self.user_tool_section_filters = listify( kwargs.get( "user_tool_section_filters", [] ), do_strip=True ) self.has_user_tool_filters = bool( self.user_tool_filters or self.user_tool_label_filters or self.user_tool_section_filters ) self.tour_config_dir = resolve_path( kwargs.get("tour_config_dir", "config/plugins/tours"), self.root) self.webhooks_dirs = resolve_path( kwargs.get("webhooks_dir", "config/plugins/webhooks"), self.root) self.expose_user_name = kwargs.get( "expose_user_name", False ) self.expose_user_email = kwargs.get( "expose_user_email", False ) self.password_expiration_period = timedelta( days=int( kwargs.get( "password_expiration_period", 0 ) ) ) # Check for tools defined in the above non-shed tool configs (i.e., tool_conf.xml) tht have # been migrated from the Galaxy code distribution to the Tool Shed. self.check_migrate_tools = string_as_bool( kwargs.get( 'check_migrate_tools', True ) ) self.shed_tool_data_path = kwargs.get( "shed_tool_data_path", None ) self.x_frame_options = kwargs.get( "x_frame_options", "SAMEORIGIN" ) if self.shed_tool_data_path: self.shed_tool_data_path = resolve_path( self.shed_tool_data_path, self.root ) else: self.shed_tool_data_path = self.tool_data_path self.manage_dependency_relationships = string_as_bool( kwargs.get( 'manage_dependency_relationships', False ) ) self.running_functional_tests = string_as_bool( kwargs.get( 'running_functional_tests', False ) ) self.hours_between_check = kwargs.get( 'hours_between_check', 12 ) self.enable_tool_shed_check = string_as_bool( kwargs.get( 'enable_tool_shed_check', False ) ) if isinstance( self.hours_between_check, string_types ): self.hours_between_check = float( self.hours_between_check ) try: if isinstance( self.hours_between_check, int ): if self.hours_between_check < 1 or self.hours_between_check > 24: self.hours_between_check = 12 elif isinstance( self.hours_between_check, float ): # If we're running functional tests, the minimum hours between check should be reduced to 0.001, or 3.6 seconds. if self.running_functional_tests: if self.hours_between_check < 0.001 or self.hours_between_check > 24.0: self.hours_between_check = 12.0 else: if self.hours_between_check < 1.0 or self.hours_between_check > 24.0: self.hours_between_check = 12.0 else: self.hours_between_check = 12 except: self.hours_between_check = 12 self.update_integrated_tool_panel = kwargs.get( "update_integrated_tool_panel", True ) self.enable_data_manager_user_view = string_as_bool( kwargs.get( "enable_data_manager_user_view", "False" ) ) self.galaxy_data_manager_data_path = kwargs.get( 'galaxy_data_manager_data_path', self.tool_data_path ) self.tool_secret = kwargs.get( "tool_secret", "" ) self.id_secret = kwargs.get( "id_secret", "USING THE DEFAULT IS NOT SECURE!" ) self.retry_metadata_internally = string_as_bool( kwargs.get( "retry_metadata_internally", "True" ) ) self.max_metadata_value_size = int( kwargs.get( "max_metadata_value_size", 5242880 ) ) self.single_user = kwargs.get( "single_user", None ) self.use_remote_user = string_as_bool( kwargs.get( "use_remote_user", "False" ) ) or self.single_user self.normalize_remote_user_email = string_as_bool( kwargs.get( "normalize_remote_user_email", "False" ) ) self.remote_user_maildomain = kwargs.get( "remote_user_maildomain", None ) self.remote_user_header = kwargs.get( "remote_user_header", 'HTTP_REMOTE_USER' ) self.remote_user_logout_href = kwargs.get( "remote_user_logout_href", None ) self.remote_user_secret = kwargs.get( "remote_user_secret", None ) self.require_login = string_as_bool( kwargs.get( "require_login", "False" ) ) self.allow_user_creation = string_as_bool( kwargs.get( "allow_user_creation", "True" ) ) self.allow_user_deletion = string_as_bool( kwargs.get( "allow_user_deletion", "False" ) ) self.allow_user_dataset_purge = string_as_bool( kwargs.get( "allow_user_dataset_purge", "True" ) ) self.allow_user_impersonation = string_as_bool( kwargs.get( "allow_user_impersonation", "False" ) ) self.new_user_dataset_access_role_default_private = string_as_bool( kwargs.get( "new_user_dataset_access_role_default_private", "False" ) ) self.collect_outputs_from = [ x.strip() for x in kwargs.get( 'collect_outputs_from', 'new_file_path,job_working_directory' ).lower().split(',') ] self.template_path = resolve_path( kwargs.get( "template_path", "templates" ), self.root ) self.template_cache = resolve_path( kwargs.get( "template_cache_path", "database/compiled_templates" ), self.root ) self.local_job_queue_workers = int( kwargs.get( "local_job_queue_workers", "5" ) ) self.cluster_job_queue_workers = int( kwargs.get( "cluster_job_queue_workers", "3" ) ) self.job_queue_cleanup_interval = int( kwargs.get("job_queue_cleanup_interval", "5") ) self.cluster_files_directory = os.path.abspath( kwargs.get( "cluster_files_directory", "database/pbs" ) ) # Fall back to legacy job_working_directory config variable if set. default_jobs_directory = kwargs.get( "job_working_directory", "database/jobs_directory" ) self.jobs_directory = resolve_path( kwargs.get( "jobs_directory", default_jobs_directory ), self.root ) self.default_job_shell = kwargs.get( "default_job_shell", "/bin/bash" ) self.cleanup_job = kwargs.get( "cleanup_job", "always" ) preserve_python_environment = kwargs.get( "preserve_python_environment", "legacy_only" ) if preserve_python_environment not in ["legacy_only", "legacy_and_local", "always"]: log.warn("preserve_python_environment set to unknown value [%s], defaulting to legacy_only") preserve_python_environment = "legacy_only" self.preserve_python_environment = preserve_python_environment self.container_image_cache_path = self.resolve_path( kwargs.get( "container_image_cache_path", "database/container_images" ) ) self.outputs_to_working_directory = string_as_bool( kwargs.get( 'outputs_to_working_directory', False ) ) self.output_size_limit = int( kwargs.get( 'output_size_limit', 0 ) ) self.retry_job_output_collection = int( kwargs.get( 'retry_job_output_collection', 0 ) ) self.check_job_script_integrity = string_as_bool( kwargs.get( "check_job_script_integrity", True ) ) self.job_walltime = kwargs.get( 'job_walltime', None ) self.job_walltime_delta = None if self.job_walltime is not None: h, m, s = [ int( v ) for v in self.job_walltime.split( ':' ) ] self.job_walltime_delta = timedelta( 0, s, 0, 0, m, h ) self.admin_users = kwargs.get( "admin_users", "" ) self.admin_users_list = [u.strip() for u in self.admin_users.split(',') if u] self.mailing_join_addr = kwargs.get('mailing_join_addr', 'galaxy-announce-join@bx.psu.edu') self.error_email_to = kwargs.get( 'error_email_to', None ) # activation_email was used until release_15.03 activation_email = kwargs.get( 'activation_email', None ) self.email_from = kwargs.get( 'email_from', activation_email ) self.user_activation_on = string_as_bool( kwargs.get( 'user_activation_on', False ) ) self.activation_grace_period = int( kwargs.get( 'activation_grace_period', 3 ) ) default_inactivity_box_content = ( "Your account has not been activated yet. Feel free to browse around and see what's available, but" " you won't be able to upload data or run jobs until you have verified your email address." ) self.inactivity_box_content = kwargs.get( 'inactivity_box_content', default_inactivity_box_content ) self.terms_url = kwargs.get( 'terms_url', None ) self.instance_resource_url = kwargs.get( 'instance_resource_url', None ) self.registration_warning_message = kwargs.get( 'registration_warning_message', None ) self.ga_code = kwargs.get( 'ga_code', None ) self.session_duration = int(kwargs.get( 'session_duration', 0 )) # Get the disposable email domains blacklist file and its contents self.blacklist_location = kwargs.get( 'blacklist_file', None ) self.blacklist_content = None if self.blacklist_location is not None: self.blacklist_file = resolve_path( kwargs.get( 'blacklist_file', None ), self.root ) try: with open( self.blacklist_file ) as blacklist: self.blacklist_content = [ line.rstrip() for line in blacklist.readlines() ] except IOError: log.error( "CONFIGURATION ERROR: Can't open supplied blacklist file from path: " + str( self.blacklist_file ) ) self.smtp_server = kwargs.get( 'smtp_server', None ) self.smtp_username = kwargs.get( 'smtp_username', None ) self.smtp_password = kwargs.get( 'smtp_password', None ) self.smtp_ssl = kwargs.get( 'smtp_ssl', None ) self.track_jobs_in_database = string_as_bool( kwargs.get( 'track_jobs_in_database', 'True') ) self.start_job_runners = listify(kwargs.get( 'start_job_runners', '' )) self.expose_dataset_path = string_as_bool( kwargs.get( 'expose_dataset_path', 'False' ) ) self.expose_potentially_sensitive_job_metrics = string_as_bool( kwargs.get( 'expose_potentially_sensitive_job_metrics', 'False' ) ) self.enable_communication_server = string_as_bool( kwargs.get( 'enable_communication_server', 'False' ) ) self.communication_server_host = kwargs.get( 'communication_server_host', 'http://localhost' ) self.communication_server_port = int( kwargs.get( 'communication_server_port', '7070' ) ) self.persistent_communication_rooms = listify( kwargs.get( "persistent_communication_rooms", [] ), do_strip=True ) self.enable_openid = string_as_bool( kwargs.get( 'enable_openid', 'False' ) ) self.enable_quotas = string_as_bool( kwargs.get( 'enable_quotas', 'False' ) ) # External Service types used in sample tracking self.external_service_type_path = resolve_path( kwargs.get( 'external_service_type_path', 'external_service_types' ), self.root ) # Tasked job runner. self.use_tasked_jobs = string_as_bool( kwargs.get( 'use_tasked_jobs', False ) ) self.local_task_queue_workers = int(kwargs.get("local_task_queue_workers", 2)) self.tool_submission_burst_threads = int( kwargs.get( 'tool_submission_burst_threads', '1' ) ) self.tool_submission_burst_at = int( kwargs.get( 'tool_submission_burst_at', '10' ) ) # Enable new interface for API installations from TS. # Admin menu will list both if enabled. self.enable_beta_ts_api_install = string_as_bool( kwargs.get( 'enable_beta_ts_api_install', 'False' ) ) # The transfer manager and deferred job queue self.enable_beta_job_managers = string_as_bool( kwargs.get( 'enable_beta_job_managers', 'False' ) ) # These workflow modules should not be considered part of Galaxy's # public API yet - the module state definitions may change and # workflows built using these modules may not function in the # future. self.enable_beta_workflow_modules = string_as_bool( kwargs.get( 'enable_beta_workflow_modules', 'False' ) ) # These are not even beta - just experiments - don't use them unless # you want yours tools to be broken in the future. self.enable_beta_tool_formats = string_as_bool( kwargs.get( 'enable_beta_tool_formats', 'False' ) ) # Beta containers interface used by GIEs self.enable_beta_containers_interface = string_as_bool( kwargs.get( 'enable_beta_containers_interface', 'False' ) ) # Certain modules such as the pause module will automatically cause # workflows to be scheduled in job handlers the way all workflows will # be someday - the following two properties can also be used to force this # behavior in under conditions - namely for workflows that have a minimum # number of steps or that consume collections. self.force_beta_workflow_scheduled_min_steps = int( kwargs.get( 'force_beta_workflow_scheduled_min_steps', '250' ) ) self.force_beta_workflow_scheduled_for_collections = string_as_bool( kwargs.get( 'force_beta_workflow_scheduled_for_collections', 'False' ) ) self.history_local_serial_workflow_scheduling = string_as_bool( kwargs.get( 'history_local_serial_workflow_scheduling', 'False' ) ) self.parallelize_workflow_scheduling_within_histories = string_as_bool( kwargs.get( 'parallelize_workflow_scheduling_within_histories', 'False' ) ) self.maximum_workflow_invocation_duration = int( kwargs.get( "maximum_workflow_invocation_duration", 2678400 ) ) # Per-user Job concurrency limitations self.cache_user_job_count = string_as_bool( kwargs.get( 'cache_user_job_count', False ) ) self.user_job_limit = int( kwargs.get( 'user_job_limit', 0 ) ) self.registered_user_job_limit = int( kwargs.get( 'registered_user_job_limit', self.user_job_limit ) ) self.anonymous_user_job_limit = int( kwargs.get( 'anonymous_user_job_limit', self.user_job_limit ) ) self.default_cluster_job_runner = kwargs.get( 'default_cluster_job_runner', 'local:///' ) self.pbs_application_server = kwargs.get('pbs_application_server', "" ) self.pbs_dataset_server = kwargs.get('pbs_dataset_server', "" ) self.pbs_dataset_path = kwargs.get('pbs_dataset_path', "" ) self.pbs_stage_path = kwargs.get('pbs_stage_path', "" ) self.drmaa_external_runjob_script = kwargs.get('drmaa_external_runjob_script', None ) self.drmaa_external_killjob_script = kwargs.get('drmaa_external_killjob_script', None) self.external_chown_script = kwargs.get('external_chown_script', None) self.environment_setup_file = kwargs.get( 'environment_setup_file', None ) self.use_heartbeat = string_as_bool( kwargs.get( 'use_heartbeat', 'False' ) ) self.heartbeat_interval = int( kwargs.get( 'heartbeat_interval', 20 ) ) self.heartbeat_log = kwargs.get( 'heartbeat_log', None ) self.log_actions = string_as_bool( kwargs.get( 'log_actions', 'False' ) ) self.log_events = string_as_bool( kwargs.get( 'log_events', 'False' ) ) self.sanitize_all_html = string_as_bool( kwargs.get( 'sanitize_all_html', True ) ) self.sanitize_whitelist_file = resolve_path( kwargs.get( 'sanitize_whitelist_file', "config/sanitize_whitelist.txt" ), self.root ) self.serve_xss_vulnerable_mimetypes = string_as_bool( kwargs.get( 'serve_xss_vulnerable_mimetypes', False ) ) self.allowed_origin_hostnames = self._parse_allowed_origin_hostnames( kwargs ) if "trust_jupyter_notebook_conversion" in kwargs: trust_jupyter_notebook_conversion = string_as_bool( kwargs.get( 'trust_jupyter_notebook_conversion', False ) ) else: trust_jupyter_notebook_conversion = string_as_bool( kwargs.get( 'trust_ipython_notebook_conversion', False ) ) self.trust_jupyter_notebook_conversion = trust_jupyter_notebook_conversion self.enable_old_display_applications = string_as_bool( kwargs.get( "enable_old_display_applications", "True" ) ) self.brand = kwargs.get( 'brand', None ) self.welcome_url = kwargs.get( 'welcome_url', '/static/welcome.html' ) self.show_welcome_with_login = string_as_bool( kwargs.get( "show_welcome_with_login", "False" ) ) # Configuration for the message box directly below the masthead. self.message_box_visible = string_as_bool( kwargs.get( 'message_box_visible', False ) ) self.message_box_content = kwargs.get( 'message_box_content', None ) self.message_box_class = kwargs.get( 'message_box_class', 'info' ) self.support_url = kwargs.get( 'support_url', 'https://galaxyproject.org/support' ) self.citation_url = kwargs.get( 'citation_url', 'https://galaxyproject.org/citing-galaxy' ) self.wiki_url = kwargs.get( 'wiki_url', 'https://galaxyproject.org/' ) self.blog_url = kwargs.get( 'blog_url', None ) self.screencasts_url = kwargs.get( 'screencasts_url', None ) self.library_import_dir = kwargs.get( 'library_import_dir', None ) self.user_library_import_dir = kwargs.get( 'user_library_import_dir', None ) self.user_library_import_symlink_whitelist = listify( kwargs.get( 'user_library_import_symlink_whitelist', []), do_strip=True ) # Searching data libraries self.enable_lucene_library_search = string_as_bool( kwargs.get( 'enable_lucene_library_search', False ) ) self.enable_whoosh_library_search = string_as_bool( kwargs.get( 'enable_whoosh_library_search', False ) ) self.whoosh_index_dir = resolve_path( kwargs.get( "whoosh_index_dir", "database/whoosh_indexes" ), self.root ) self.ftp_upload_dir = kwargs.get( 'ftp_upload_dir', None ) self.ftp_upload_dir_identifier = kwargs.get( 'ftp_upload_dir_identifier', 'email' ) # attribute on user - email, username, id, etc... self.ftp_upload_dir_template = kwargs.get( 'ftp_upload_dir_template', '${ftp_upload_dir}%s${ftp_upload_dir_identifier}' % os.path.sep ) self.ftp_upload_purge = string_as_bool( kwargs.get( 'ftp_upload_purge', 'True' ) ) self.ftp_upload_site = kwargs.get( 'ftp_upload_site', None ) self.allow_library_path_paste = kwargs.get( 'allow_library_path_paste', False ) self.disable_library_comptypes = kwargs.get( 'disable_library_comptypes', '' ).lower().split( ',' ) self.watch_tools = kwargs.get( 'watch_tools', 'false' ) self.watch_tool_data_dir = kwargs.get( 'watch_tool_data_dir', 'false' ) # On can mildly speed up Galaxy startup time by disabling index of help, # not needed on production systems but useful if running many functional tests. self.index_tool_help = string_as_bool( kwargs.get( "index_tool_help", True ) ) self.tool_name_boost = kwargs.get( "tool_name_boost", 9 ) self.tool_section_boost = kwargs.get( "tool_section_boost", 3 ) self.tool_description_boost = kwargs.get( "tool_description_boost", 2 ) self.tool_labels_boost = kwargs.get( "tool_labels_boost", 1 ) self.tool_stub_boost = kwargs.get( "tool_stub_boost", 5 ) self.tool_help_boost = kwargs.get( "tool_help_boost", 0.5 ) self.tool_search_limit = kwargs.get( "tool_search_limit", 20 ) self.tool_enable_ngram_search = kwargs.get( "tool_enable_ngram_search", False ) self.tool_ngram_minsize = kwargs.get( "tool_ngram_minsize", 3 ) self.tool_ngram_maxsize = kwargs.get( "tool_ngram_maxsize", 4 ) # Location for tool dependencies. use_tool_dependencies, tool_dependency_dir, use_cached_dependency_manager, tool_dependency_cache_dir, precache_dependencies = \ parse_dependency_options(kwargs, self.root, self.dependency_resolvers_config_file) self.use_tool_dependencies = use_tool_dependencies self.tool_dependency_dir = tool_dependency_dir self.use_cached_dependency_manager = use_cached_dependency_manager self.tool_dependency_cache_dir = tool_dependency_cache_dir self.precache_dependencies = precache_dependencies # Deployers may either specify a complete list of mapping files or get the default for free and just # specify a local mapping file to adapt and extend the default one. if "conda_mapping_files" in kwargs: self.conda_mapping_files = kwargs["conda_mapping_files"] else: self.conda_mapping_files = [ self.local_conda_mapping_file, os.path.join(self.root, "lib", "galaxy", "tools", "deps", "resolvers", "default_conda_mapping.yml"), ] self.enable_beta_mulled_containers = string_as_bool( kwargs.get( 'enable_beta_mulled_containers', 'False' ) ) containers_resolvers_config_file = kwargs.get( 'containers_resolvers_config_file', None ) if containers_resolvers_config_file: containers_resolvers_config_file = resolve_path(containers_resolvers_config_file, self.root) self.containers_resolvers_config_file = containers_resolvers_config_file involucro_path = kwargs.get('involucro_path', None) if involucro_path is None: involucro_path = os.path.join(tool_dependency_dir, "involucro") self.involucro_path = resolve_path(involucro_path, self.root) self.involucro_auto_init = string_as_bool(kwargs.get( 'involucro_auto_init', True)) default_job_resubmission_condition = kwargs.get( 'default_job_resubmission_condition', '') if not default_job_resubmission_condition.strip(): default_job_resubmission_condition = None self.default_job_resubmission_condition = default_job_resubmission_condition # Configuration options for taking advantage of nginx features self.upstream_gzip = string_as_bool( kwargs.get( 'upstream_gzip', False ) ) self.apache_xsendfile = string_as_bool( kwargs.get( 'apache_xsendfile', False ) ) self.nginx_x_accel_redirect_base = kwargs.get( 'nginx_x_accel_redirect_base', False ) self.nginx_x_archive_files_base = kwargs.get( 'nginx_x_archive_files_base', False ) self.nginx_upload_store = kwargs.get( 'nginx_upload_store', False ) self.nginx_upload_path = kwargs.get( 'nginx_upload_path', False ) self.nginx_upload_job_files_store = kwargs.get( 'nginx_upload_job_files_store', False ) self.nginx_upload_job_files_path = kwargs.get( 'nginx_upload_job_files_path', False ) if self.nginx_upload_store: self.nginx_upload_store = os.path.abspath( self.nginx_upload_store ) self.object_store = kwargs.get( 'object_store', 'disk' ) self.object_store_check_old_style = string_as_bool( kwargs.get( 'object_store_check_old_style', False ) ) self.object_store_cache_path = resolve_path( kwargs.get( "object_store_cache_path", "database/object_store_cache" ), self.root ) # Handle AWS-specific config options for backward compatibility if kwargs.get( 'aws_access_key', None) is not None: self.os_access_key = kwargs.get( 'aws_access_key', None ) self.os_secret_key = kwargs.get( 'aws_secret_key', None ) self.os_bucket_name = kwargs.get( 's3_bucket', None ) self.os_use_reduced_redundancy = kwargs.get( 'use_reduced_redundancy', False ) else: self.os_access_key = kwargs.get( 'os_access_key', None ) self.os_secret_key = kwargs.get( 'os_secret_key', None ) self.os_bucket_name = kwargs.get( 'os_bucket_name', None ) self.os_use_reduced_redundancy = kwargs.get( 'os_use_reduced_redundancy', False ) self.os_host = kwargs.get( 'os_host', None ) self.os_port = kwargs.get( 'os_port', None ) self.os_is_secure = string_as_bool( kwargs.get( 'os_is_secure', True ) ) self.os_conn_path = kwargs.get( 'os_conn_path', '/' ) self.object_store_cache_size = float(kwargs.get( 'object_store_cache_size', -1 )) self.distributed_object_store_config_file = kwargs.get( 'distributed_object_store_config_file', None ) if self.distributed_object_store_config_file is not None: self.distributed_object_store_config_file = resolve_path( self.distributed_object_store_config_file, self.root ) self.irods_root_collection_path = kwargs.get( 'irods_root_collection_path', None ) self.irods_default_resource = kwargs.get( 'irods_default_resource', None ) # Parse global_conf and save the parser global_conf = kwargs.get( 'global_conf', None ) global_conf_parser = configparser.ConfigParser() self.config_file = None self.global_conf_parser = global_conf_parser if global_conf and "__file__" in global_conf: self.config_file = global_conf['__file__'] global_conf_parser.read(global_conf['__file__']) # Heartbeat log file name override if global_conf is not None and 'heartbeat_log' in global_conf: self.heartbeat_log = global_conf['heartbeat_log'] if self.heartbeat_log is None: self.heartbeat_log = 'heartbeat_{server_name}.log' # Determine which 'server:' this is self.server_name = 'main' for arg in sys.argv: # Crummy, but PasteScript does not give you a way to determine this if arg.lower().startswith('--server-name='): self.server_name = arg.split('=', 1)[-1] # Allow explicit override of server name in confg params if "server_name" in kwargs: self.server_name = kwargs.get("server_name") # Store all configured server names self.server_names = [] for section in global_conf_parser.sections(): if section.startswith('server:'): self.server_names.append(section.replace('server:', '', 1)) # Default URL (with schema http/https) of the Galaxy instance within the # local network - used to remotely communicate with the Galaxy API. web_port = kwargs.get("galaxy_infrastructure_web_port", None) self.galaxy_infrastructure_web_port = web_port galaxy_infrastructure_url = kwargs.get( 'galaxy_infrastructure_url', None ) galaxy_infrastructure_url_set = True if galaxy_infrastructure_url is None: # Still provide a default but indicate it was not explicitly set # so dependending on the context a better default can be used ( # request url in a web thread, Docker parent in IE stuff, etc...) galaxy_infrastructure_url = "http://localhost" web_port = self.galaxy_infrastructure_web_port or self.guess_galaxy_port() if web_port: galaxy_infrastructure_url += ":%s" % (web_port) galaxy_infrastructure_url_set = False if "HOST_IP" in galaxy_infrastructure_url: galaxy_infrastructure_url = string.Template(galaxy_infrastructure_url).safe_substitute({ 'HOST_IP': socket.gethostbyname(socket.gethostname()) }) self.galaxy_infrastructure_url = galaxy_infrastructure_url self.galaxy_infrastructure_url_set = galaxy_infrastructure_url_set # Store advanced job management config self.job_manager = kwargs.get('job_manager', self.server_name).strip() self.job_handlers = [ x.strip() for x in kwargs.get('job_handlers', self.server_name).split(',') ] self.default_job_handlers = [ x.strip() for x in kwargs.get('default_job_handlers', ','.join( self.job_handlers ) ).split(',') ] # Store per-tool runner configs self.tool_handlers = self.__read_tool_job_config( global_conf_parser, 'galaxy:tool_handlers', 'name' ) self.tool_runners = self.__read_tool_job_config( global_conf_parser, 'galaxy:tool_runners', 'url' ) # Galaxy messaging (AMQP) configuration options self.amqp = {} try: amqp_config = global_conf_parser.items("galaxy_amqp") except configparser.NoSectionError: amqp_config = {} for k, v in amqp_config: self.amqp[k] = v # Galaxy internal control queue configuration. # If specified in universe, use it, otherwise we use whatever 'real' # database is specified. Lastly, we create and use new sqlite database # (to minimize locking) as a final option. if 'amqp_internal_connection' in kwargs: self.amqp_internal_connection = kwargs.get('amqp_internal_connection') # TODO Get extra amqp args as necessary for ssl elif 'database_connection' in kwargs: self.amqp_internal_connection = "sqlalchemy+" + self.database_connection else: self.amqp_internal_connection = "sqlalchemy+sqlite:///%s?isolation_level=IMMEDIATE" % resolve_path( "database/control.sqlite", self.root ) self.biostar_url = kwargs.get( 'biostar_url', None ) self.biostar_key_name = kwargs.get( 'biostar_key_name', None ) self.biostar_key = kwargs.get( 'biostar_key', None ) self.biostar_enable_bug_reports = string_as_bool( kwargs.get( 'biostar_enable_bug_reports', True ) ) self.biostar_never_authenticate = string_as_bool( kwargs.get( 'biostar_never_authenticate', False ) ) self.pretty_datetime_format = expand_pretty_datetime_format( kwargs.get( 'pretty_datetime_format', '$locale (UTC)' ) ) self.master_api_key = kwargs.get( 'master_api_key', None ) if self.master_api_key == "changethis": # default in sample config file raise ConfigurationError("Insecure configuration, please change master_api_key to something other than default (changethis)") # Experimental: This will not be enabled by default and will hide # nonproduction code. # The api_folders refers to whether the API exposes the /folders section. self.api_folders = string_as_bool( kwargs.get( 'api_folders', False ) ) # This is for testing new library browsing capabilities. self.new_lib_browse = string_as_bool( kwargs.get( 'new_lib_browse', False ) ) # Error logging with sentry self.sentry_dsn = kwargs.get( 'sentry_dsn', None ) # Statistics and profiling with statsd self.statsd_host = kwargs.get( 'statsd_host', '') self.statsd_port = int( kwargs.get( 'statsd_port', 8125 ) ) self.statsd_prefix = kwargs.get( 'statsd_prefix', 'galaxy' ) # Statistics and profiling with graphite self.graphite_host = kwargs.get( 'graphite_host', '') self.graphite_port = int( kwargs.get( 'graphite_port', 2003 ) ) self.graphite_prefix = kwargs.get( 'graphite_prefix', 'galaxy' ) # Logging with fluentd self.fluent_log = string_as_bool( kwargs.get( 'fluent_log', False ) ) self.fluent_host = kwargs.get( 'fluent_host', 'localhost' ) self.fluent_port = int( kwargs.get( 'fluent_port', 24224 ) ) # directory where the visualization registry searches for plugins self.visualization_plugins_directory = kwargs.get( 'visualization_plugins_directory', 'config/plugins/visualizations' ) ie_dirs = kwargs.get( 'interactive_environment_plugins_directory', None ) self.gie_dirs = [d.strip() for d in (ie_dirs.split(",") if ie_dirs else [])] if ie_dirs and not self.visualization_plugins_directory: self.visualization_plugins_directory = ie_dirs elif ie_dirs: self.visualization_plugins_directory += ",%s" % ie_dirs self.gie_swarm_mode = string_as_bool( kwargs.get( 'interactive_environment_swarm_mode', False ) ) self.proxy_session_map = self.resolve_path( kwargs.get( "dynamic_proxy_session_map", "database/session_map.sqlite" ) ) self.manage_dynamic_proxy = string_as_bool( kwargs.get( "dynamic_proxy_manage", "True" ) ) # Set to false if being launched externally self.dynamic_proxy_debug = string_as_bool( kwargs.get( "dynamic_proxy_debug", "False" ) ) self.dynamic_proxy_bind_port = int( kwargs.get( "dynamic_proxy_bind_port", "8800" ) ) self.dynamic_proxy_bind_ip = kwargs.get( "dynamic_proxy_bind_ip", "0.0.0.0" ) self.dynamic_proxy_external_proxy = string_as_bool( kwargs.get( "dynamic_proxy_external_proxy", "False" ) ) self.dynamic_proxy_prefix = kwargs.get( "dynamic_proxy_prefix", "gie_proxy" ) self.dynamic_proxy = kwargs.get( "dynamic_proxy", "node" ) self.dynamic_proxy_golang_noaccess = kwargs.get( "dynamic_proxy_golang_noaccess", 60 ) self.dynamic_proxy_golang_clean_interval = kwargs.get( "dynamic_proxy_golang_clean_interval", 10 ) self.dynamic_proxy_golang_docker_address = kwargs.get( "dynamic_proxy_golang_docker_address", "unix:///var/run/docker.sock" ) self.dynamic_proxy_golang_api_key = kwargs.get( "dynamic_proxy_golang_api_key", None ) # Default chunk size for chunkable datatypes -- 64k self.display_chunk_size = int( kwargs.get( 'display_chunk_size', 65536) ) self.citation_cache_type = kwargs.get( "citation_cache_type", "file" ) self.citation_cache_data_dir = self.resolve_path( kwargs.get( "citation_cache_data_dir", "database/citations/data" ) ) self.citation_cache_lock_dir = self.resolve_path( kwargs.get( "citation_cache_lock_dir", "database/citations/locks" ) ) self.containers_conf = parse_containers_config(self.containers_config_file)
@property def sentry_dsn_public( self ): """ Sentry URL with private key removed for use in client side scripts, sentry server will need to be configured to accept events """ if self.sentry_dsn: return re.sub( r"^([^:/?#]+:)?//(\w+):(\w+)", r"\1//\2", self.sentry_dsn ) else: return None
[docs] def reload_sanitize_whitelist( self, explicit=True ): self.sanitize_whitelist = [] try: with open(self.sanitize_whitelist_file, 'rt') as f: for line in f.readlines(): if not line.startswith("#"): self.sanitize_whitelist.append(line.strip()) except IOError: if explicit: log.warning("Sanitize log file explicitly specified as '%s' but does not exist, continuing with no tools whitelisted.", self.sanitize_whitelist_file)
def __parse_config_file_options( self, kwargs ): """ Backwards compatibility for config files moved to the config/ dir. """ for var in PATH_DEFAULTS: setattr( self, var, find_path( kwargs, var, self.root ) ) for var, defaults in PATH_LIST_DEFAULTS.items(): paths = [] if kwargs.get( var, None ) is not None: paths = listify( kwargs.get( var ) ) else: for default in defaults: for path in listify( default ): if not os.path.exists( resolve_path( path, self.root ) ): break else: paths = listify( default ) break else: paths = listify( defaults[-1] ) setattr( self, var, [ resolve_path( x, self.root ) for x in paths ] ) # Backwards compatibility for names used in too many places to fix self.datatypes_config = self.datatypes_config_file self.tool_configs = self.tool_config_file def __read_tool_job_config( self, global_conf_parser, section, key ): try: tool_runners_config = global_conf_parser.items( section ) # Process config to group multiple configs for the same tool. rval = {} for entry in tool_runners_config: tool_config, val = entry tool = None runner_dict = {} if tool_config.find("[") != -1: # Found tool with additional params; put params in dict. tool, params = tool_config[:-1].split( "[" ) param_dict = {} for param in params.split( "," ): name, value = param.split( "@" ) param_dict[ name ] = value runner_dict[ 'params' ] = param_dict else: tool = tool_config # Add runner URL. runner_dict[ key ] = val # Create tool entry if necessary. if tool not in rval: rval[ tool ] = [] # Add entry to runners. rval[ tool ].append( runner_dict ) return rval except configparser.NoSectionError: return {}
[docs] def get( self, key, default ): return self.config_dict.get( key, default )
[docs] def get_bool( self, key, default ): if key in self.config_dict: return string_as_bool( self.config_dict[key] ) else: return default
[docs] def ensure_tempdir( self ): self._ensure_directory( self.new_file_path )
def _ensure_directory( self, path ): if path not in [ None, False ] and not os.path.isdir( path ): try: os.makedirs( path ) except Exception as e: raise ConfigurationError( "Unable to create missing directory: %s\n%s" % ( path, e ) )
[docs] def check( self ): paths_to_check = [ self.root, self.tool_path, self.tool_data_path, self.template_path ] # Check that required directories exist for path in paths_to_check: if path not in [ None, False ] and not os.path.isdir( path ): try: os.makedirs( path ) except Exception as e: raise ConfigurationError( "Unable to create missing directory: %s\n%s" % ( path, e ) ) # Create the directories that it makes sense to create for path in (self.new_file_path, self.template_cache, self.ftp_upload_dir, self.library_import_dir, self.user_library_import_dir, self.nginx_upload_store, self.whoosh_index_dir, self.object_store_cache_path): self._ensure_directory( path ) # Check that required files exist tool_configs = self.tool_configs if self.migrated_tools_config not in tool_configs: tool_configs.append( self.migrated_tools_config ) for path in tool_configs: if not os.path.exists( path ): raise ConfigurationError("Tool config file not found: %s" % path ) for datatypes_config in listify( self.datatypes_config ): if not os.path.isfile( datatypes_config ): raise ConfigurationError("Datatypes config file not found: %s" % datatypes_config ) # Check for deprecated options. for key in self.config_dict.keys(): if key in self.deprecated_options: log.warning( "Config option '%s' is deprecated and will be removed in a future release. Please consult the latest version of the sample configuration file." % key )
[docs] def is_admin_user( self, user ): """ Determine if the provided user is listed in `admin_users`. NOTE: This is temporary, admin users will likely be specified in the database in the future. """ admin_users = [ x.strip() for x in self.get( "admin_users", "" ).split( "," ) ] return user is not None and user.email in admin_users
[docs] def resolve_path( self, path ): """ Resolve a path relative to Galaxy's root. """ return resolve_path( path, self.root )
[docs] def guess_galaxy_port(self): # Code derived from Jupyter work ie.mako config = configparser.SafeConfigParser({'port': '8080'}) if self.config_file: config.read( self.config_file ) try: port = config.getint('server:%s' % self.server_name, 'port') except: # uWSGI galaxy installations don't use paster and only speak uWSGI not http port = None return port
def _parse_allowed_origin_hostnames( self, kwargs ): """ Parse a CSV list of strings/regexp of hostnames that should be allowed to use CORS and will be sent the Access-Control-Allow-Origin header. """ allowed_origin_hostnames = listify( kwargs.get( 'allowed_origin_hostnames', None ) ) if not allowed_origin_hostnames: return None def parse( string ): # a string enclosed in fwd slashes will be parsed as a regexp: e.g. /<some val>/ if string[0] == '/' and string[-1] == '/': string = string[1:-1] return re.compile( string, flags=( re.UNICODE | re.LOCALE ) ) return string return [ parse( v ) for v in allowed_origin_hostnames if v ]
[docs]def parse_dependency_options(kwargs, root, dependency_resolvers_config_file): # Location for tool dependencies. tool_dependency_dir = kwargs.get("tool_dependency_dir", "database/dependencies") if tool_dependency_dir.lower() == "none": tool_dependency_dir = None if tool_dependency_dir is not None: tool_dependency_dir = resolve_path(tool_dependency_dir, root) # Setting the following flag to true will ultimately cause tool dependencies # to be located in the shell environment and used by the job that is executing # the tool. use_tool_dependencies = True tool_dependency_cache_dir = kwargs.get('tool_dependency_cache_dir', os.path.join(tool_dependency_dir, '_cache')) use_cached_dependency_manager = string_as_bool(kwargs.get("use_cached_dependency_manager", 'False')) precache_dependencies = string_as_bool(kwargs.get("precache_dependencies", 'True')) else: tool_dependency_dir = None use_tool_dependencies = os.path.exists(dependency_resolvers_config_file) tool_dependency_cache_dir = None precache_dependencies = False use_cached_dependency_manager = False return use_tool_dependencies, tool_dependency_dir, use_cached_dependency_manager, tool_dependency_cache_dir, precache_dependencies
[docs]def get_database_engine_options( kwargs, model_prefix='' ): """ Allow options for the SQLAlchemy database engine to be passed by using the prefix "database_engine_option". """ conversions = { 'convert_unicode': string_as_bool, 'pool_timeout': int, 'echo': string_as_bool, 'echo_pool': string_as_bool, 'pool_recycle': int, 'pool_size': int, 'max_overflow': int, 'pool_threadlocal': string_as_bool, 'server_side_cursors': string_as_bool } prefix = "%sdatabase_engine_option_" % model_prefix prefix_len = len( prefix ) rval = {} for key, value in kwargs.items(): if key.startswith( prefix ): key = key[prefix_len:] if key in conversions: value = conversions[key](value) rval[ key ] = value return rval
[docs]def configure_logging( config ): """Allow some basic logging configuration to be read from ini file. This should be able to consume either a galaxy.config.Configuration object or a simple dictionary of configuration variables. """ # Get root logger root = logging.getLogger() # PasteScript will have already configured the logger if the # 'loggers' section was found in the config file, otherwise we do # some simple setup using the 'log_*' values from the config. parser = getattr(config, "global_conf_parser", None) if parser: paste_configures_logging = config.global_conf_parser.has_section( "loggers" ) else: paste_configures_logging = False auto_configure_logging = not paste_configures_logging and string_as_bool( config.get( "auto_configure_logging", "True" ) ) if auto_configure_logging: format = config.get( "log_format", "%(name)s %(levelname)s %(asctime)s %(message)s" ) level = logging._levelNames[ config.get( "log_level", "DEBUG" ) ] destination = config.get( "log_destination", "stdout" ) log.info( "Logging at '%s' level to '%s'" % ( level, destination ) ) # Set level root.setLevel( level ) disable_chatty_loggers = string_as_bool( config.get( "auto_configure_logging_disable_chatty", "True" ) ) if disable_chatty_loggers: # Turn down paste httpserver logging if level <= logging.DEBUG: for chatty_logger in ["paste.httpserver.ThreadPool", "routes.middleware"]: logging.getLogger( chatty_logger ).setLevel( logging.WARN ) # Remove old handlers for h in root.handlers[:]: root.removeHandler(h) # Create handler if destination == "stdout": handler = logging.StreamHandler( sys.stdout ) else: handler = logging.FileHandler( destination ) # Create formatter formatter = logging.Formatter( format ) # Hook everything up handler.setFormatter( formatter ) root.addHandler( handler ) # If sentry is configured, also log to it if getattr(config, "sentry_dsn", None): from raven.handlers.logging import SentryHandler sentry_handler = SentryHandler( config.sentry_dsn ) sentry_handler.setLevel( logging.WARN ) register_postfork_function(root.addHandler, sentry_handler)
[docs]class ConfiguresGalaxyMixin: """ Shared code for configuring Galaxy-like app objects. """ def _configure_genome_builds( self, data_table_name="__dbkeys__", load_old_style=True ): self.genome_builds = GenomeBuilds( self, data_table_name=data_table_name, load_old_style=load_old_style )
[docs] def wait_for_toolbox_reload(self, old_toolbox): timer = ExecutionTimer() while True: # Wait till toolbox reload has been triggered # (or more than 60 seconds have passed) if self.toolbox.has_reloaded(old_toolbox) or timer.elapsed > 60: break time.sleep(0.1)
def _configure_toolbox( self ): from galaxy import tools from galaxy.managers.citations import CitationsManager from galaxy.tools.deps import containers from galaxy.tools.toolbox.lineages.tool_shed import ToolVersionCache import galaxy.tools.search self.citations_manager = CitationsManager( self ) self.tool_version_cache = ToolVersionCache(self) self._toolbox_lock = threading.RLock() # 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 ) galaxy_root_dir = os.path.abspath(self.config.root) file_path = os.path.abspath(getattr(self.config, "file_path")) app_info = containers.AppInfo( galaxy_root_dir=galaxy_root_dir, default_file_path=file_path, outputs_to_working_directory=self.config.outputs_to_working_directory, container_image_cache_path=self.config.container_image_cache_path, library_import_dir=self.config.library_import_dir, enable_beta_mulled_containers=self.config.enable_beta_mulled_containers, containers_resolvers_config_file=self.config.containers_resolvers_config_file, involucro_path=self.config.involucro_path, involucro_auto_init=self.config.involucro_auto_init, ) self.container_finder = containers.ContainerFinder(app_info) index_help = getattr(self.config, "index_tool_help", True) self.toolbox_search = galaxy.tools.search.ToolBoxSearch(self.toolbox, index_help) self.reindex_tool_search() def _configure_tool_data_tables( self, from_shed_config ): from galaxy.tools.data import ToolDataTableManager # Initialize tool data tables using the config defined by self.config.tool_data_table_config_path. self.tool_data_tables = 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=from_shed_config ) def _configure_datatypes_registry( self, installed_repository_manager=None ): from galaxy.datatypes import registry # Create an empty datatypes registry. self.datatypes_registry = registry.Registry( self.config ) if installed_repository_manager: # 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. installed_repository_manager.load_proprietary_datatypes() # Load the data types in the Galaxy distribution, which are defined in self.config.datatypes_config. datatypes_configs = self.config.datatypes_config for datatypes_config in listify( datatypes_configs ): # Setting override=False would make earlier files would take # precedence - but then they wouldn't override tool shed # datatypes. self.datatypes_registry.load_datatypes( self.config.root, datatypes_config, override=True ) def _configure_object_store( self, **kwds ): from galaxy.objectstore import build_object_store_from_config self.object_store = build_object_store_from_config( self.config, **kwds ) def _configure_security( self ): from galaxy.web import security self.security = security.SecurityHelper( id_secret=self.config.id_secret ) def _configure_tool_shed_registry( self ): import tool_shed.tool_shed_registry # Set up the tool sheds registry if os.path.isfile( self.config.tool_sheds_config_file ): self.tool_shed_registry = tool_shed.tool_shed_registry.Registry( self.config.root, self.config.tool_sheds_config_file ) else: self.tool_shed_registry = None 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 ), slow_query_log_threshold=self.config.slow_query_log_threshold ) 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 _configure_signal_handlers( self, handlers ): for sig, handler in handlers.items(): signal.signal( sig, handler )