def __init__(self, **kwargs):
for key in os.environ:
if key.startswith(CONFIG_OVERRIDE_PREFIX):
config_key = key[len(CONFIG_OVERRIDE_PREFIX):].lower()
kwargs[config_key] = os.environ[key]
elif key.startswith(CONFIG_DEFAULT_PREFIX):
config_key = key[len(CONFIG_DEFAULT_PREFIX):].lower()
if config_key not in kwargs:
kwargs[config_key] = os.environ[key]
self.config_dict = kwargs
self.root = kwargs.get('root_dir', '.')
# 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(077) # 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
# 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"))
# 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)
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)
self.test_conf = resolve_path(kwargs.get("test_conf", ""), 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)
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_label_filters = listify(kwargs.get("user_tool_label_filters",
[]),
do_strip=True)
self.user_section_filters = listify(kwargs.get(
"user_tool_section_filters", []),
do_strip=True)
# 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)
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)
if isinstance(self.hours_between_check, basestring):
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.use_remote_user = string_as_bool(
kwargs.get("use_remote_user", "False"))
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.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", "False"))
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"))
self.job_working_directory = resolve_path(
kwargs.get("job_working_directory",
"database/job_working_directory"), self.root)
self.cleanup_job = kwargs.get("cleanup_job", "always")
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.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.reset_password_length = int(
kwargs.get('reset_password_length', '15'))
self.mailing_join_addr = kwargs.get('mailing_join_addr',
'*****@*****.**')
self.error_email_to = kwargs.get('error_email_to', None)
self.activation_email = kwargs.get('activation_email', None)
self.user_activation_on = string_as_bool(
kwargs.get('user_activation_on', False))
self.activation_grace_period = kwargs.get('activation_grace_period',
None)
self.inactivity_box_content = kwargs.get('inactivity_box_content',
None)
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)
# 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:
print(
"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 = kwargs.get('track_jobs_in_database',
'None')
self.start_job_runners = listify(kwargs.get('start_job_runners', ''))
self.expose_dataset_path = string_as_bool(
kwargs.get('expose_dataset_path', '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))
# The transfer manager and deferred job queue
self.enable_beta_job_managers = string_as_bool(
kwargs.get('enable_beta_job_managers', 'False'))
# 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.use_memdump = string_as_bool(kwargs.get('use_memdump', 'False'))
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.serve_xss_vulnerable_mimetypes = string_as_bool(
kwargs.get('serve_xss_vulnerable_mimetypes', False))
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')
# Configuration for the message box directly below the masthead.
self.message_box_visible = 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://wiki.galaxyproject.org/Support')
self.wiki_url = kwargs.get('wiki_url',
'http://wiki.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)
# 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_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(',')
# Location for tool dependencies.
if 'tool_dependency_dir' in kwargs:
self.tool_dependency_dir = resolve_path(
kwargs.get("tool_dependency_dir"), self.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.
self.use_tool_dependencies = True
else:
self.tool_dependency_dir = None
self.use_tool_dependencies = False
# 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)
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:
self.heartbeat_log = global_conf.get('heartbeat_log',
'heartbeat.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]
# 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))
# 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(',')
]
# Use database for job running IPC unless this is a standalone server or explicitly set in the config
if self.track_jobs_in_database == 'None':
self.track_jobs_in_database = False
if len(self.server_names) > 1:
self.track_jobs_in_database = True
else:
self.track_jobs_in_database = string_as_bool(
self.track_jobs_in_database)
# 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')
# Cloud configuration options
self.enable_cloud_launch = string_as_bool(
kwargs.get('enable_cloud_launch', False))
self.cloudlaunch_default_ami = kwargs.get('cloudlaunch_default_ami',
'ami-a7dbf6ce')
# 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 Exception(
"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)
# 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')
# 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"))
def __init__(self, **kwargs):
self.config_dict = kwargs
self.root = kwargs.get('root_dir', '.')
# 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(077) # 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
self.version = VERSION
# Database related configuration
self.database = resolve_path(
kwargs.get("database_file", "database/community.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"))
# Repository and Tool search API
self.toolshed_search_on = string_as_bool(
kwargs.get("toolshed_search_on", True))
self.whoosh_index_dir = kwargs.get("whoosh_index_dir",
'database/toolshed_whoosh_indexes')
self.repo_name_boost = kwargs.get("repo_name_boost", 0.9)
self.repo_description_boost = kwargs.get("repo_description_boost", 0.6)
self.repo_long_description_boost = kwargs.get(
"repo_long_description_boost", 0.5)
self.repo_homepage_url_boost = kwargs.get("repo_homepage_url_boost",
0.3)
self.repo_remote_repository_url_boost = kwargs.get(
"repo_remote_repository_url_boost", 0.2)
self.repo_owner_username_boost = kwargs.get(
"repo_owner_username_boost", 0.3)
self.tool_name_boost = kwargs.get("tool_name_boost", 1.2)
self.tool_description_boost = kwargs.get("tool_description_boost", 0.6)
self.tool_help_boost = kwargs.get("tool_help_boost", 0.4)
self.tool_repo_owner_username = kwargs.get("tool_repo_owner_username",
0.3)
# Analytics
self.ga_code = kwargs.get("ga_code", None)
self.session_duration = int(kwargs.get('session_duration', 0))
# Where dataset files are stored
self.file_path = resolve_path(
kwargs.get("file_path", "database/community_files"), self.root)
self.new_file_path = resolve_path(
kwargs.get("new_file_path", "database/tmp"), self.root)
self.cookie_path = kwargs.get("cookie_path", "/")
self.enable_quotas = string_as_bool(kwargs.get('enable_quotas', False))
self.id_secret = kwargs.get("id_secret",
"USING THE DEFAULT IS NOT SECURE!")
# Tool stuff
self.tool_path = resolve_path(kwargs.get("tool_path", "tools"),
self.root)
self.tool_secret = kwargs.get("tool_secret", "")
self.tool_data_path = resolve_path(
kwargs.get("tool_data_path", "shed-tool-data"), os.getcwd())
self.tool_data_table_config_path = None
self.integrated_tool_panel_config = resolve_path(
kwargs.get('integrated_tool_panel_config',
'integrated_tool_panel.xml'), self.root)
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)
self.ftp_upload_dir = kwargs.get('ftp_upload_dir', None)
# Install and test framework for testing tools contained in repositories.
self.display_legacy_test_results = string_as_bool(
kwargs.get('display_legacy_test_results', True))
self.num_tool_test_results_saved = kwargs.get(
'num_tool_test_results_saved', 5)
self.update_integrated_tool_panel = False
# Galaxy flavor Docker Image
self.enable_galaxy_flavor_docker_image = string_as_bool(
kwargs.get("enable_galaxy_flavor_docker_image", "False"))
self.use_remote_user = string_as_bool(
kwargs.get("use_remote_user", "False"))
self.user_activation_on = kwargs.get('user_activation_on', None)
self.activation_grace_period = kwargs.get('activation_grace_period',
None)
self.inactivity_box_content = kwargs.get('inactivity_box_content',
None)
self.registration_warning_message = kwargs.get(
'registration_warning_message', None)
self.terms_url = kwargs.get('terms_url', None)
self.blacklist_location = kwargs.get('blacklist_file', None)
self.blacklist_content = None
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.enable_openid = string_as_bool(kwargs.get('enable_openid', False))
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/community"), self.root)
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',
"*****@*****.**")
self.error_email_to = kwargs.get('error_email_to', None)
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.start_job_runners = kwargs.get('start_job_runners', None)
self.email_from = kwargs.get('email_from', None)
self.nginx_upload_path = kwargs.get('nginx_upload_path', False)
self.log_actions = string_as_bool(kwargs.get('log_actions', 'False'))
self.brand = kwargs.get('brand', None)
self.pretty_datetime_format = expand_pretty_datetime_format(
kwargs.get('pretty_datetime_format', '$locale (UTC)'))
# Configuration for the message box directly below the masthead.
self.message_box_visible = 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://wiki.galaxyproject.org/Support')
self.wiki_url = kwargs.get('wiki_url',
'https://wiki.galaxyproject.org/')
self.blog_url = kwargs.get('blog_url', None)
self.biostar_url = kwargs.get('biostar_url', None)
self.screencasts_url = kwargs.get('screencasts_url', None)
self.log_events = False
self.cloud_controller_instance = False
self.server_name = ''
self.job_manager = ''
self.default_job_handlers = []
self.default_cluster_job_runner = 'local:///'
self.job_handlers = []
self.tool_handlers = []
self.tool_runners = []
# Error logging with sentry
self.sentry_dsn = kwargs.get('sentry_dsn', None)
# Where the tool shed hgweb.config file is stored - the default is the Galaxy installation directory.
self.hgweb_config_dir = resolve_path(
kwargs.get('hgweb_config_dir', ''), self.root)
self.disable_push = string_as_bool(kwargs.get("disable_push", "True"))
# Proxy features
self.apache_xsendfile = kwargs.get('apache_xsendfile', False)
self.nginx_x_accel_redirect_base = kwargs.get(
'nginx_x_accel_redirect_base', False)
self.drmaa_external_runjob_script = kwargs.get(
'drmaa_external_runjob_script', None)
# Parse global_conf and save the parser
global_conf = kwargs.get('global_conf', None)
global_conf_parser = ConfigParser.ConfigParser()
self.global_conf_parser = global_conf_parser
if global_conf and "__file__" in global_conf:
global_conf_parser.read(global_conf['__file__'])
self.running_functional_tests = string_as_bool(
kwargs.get('running_functional_tests', False))
self.citation_cache_type = kwargs.get("citation_cache_type", "file")
self.citation_cache_data_dir = resolve_path(
kwargs.get("citation_cache_data_dir",
"database/tool_shed_citations/data"), self.root)
self.citation_cache_lock_dir = resolve_path(
kwargs.get("citation_cache_lock_dir",
"database/tool_shed_citations/locks"), self.root)
def __init__( self, **kwargs ):
self.config_dict = kwargs
self.root = kwargs.get( 'root_dir', '.' )
# 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( 077 ) # 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
# 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" ) )
# 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 )
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 )
self.test_conf = resolve_path( kwargs.get( "test_conf", "" ), 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 )
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_label_filters = listify( kwargs.get( "user_tool_label_filters", [] ), do_strip=True )
self.user_section_filters = listify( kwargs.get( "user_tool_section_filters", [] ), do_strip=True )
# 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 )
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 )
if isinstance( self.hours_between_check, basestring ):
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.use_remote_user = string_as_bool( kwargs.get( "use_remote_user", "False" ) )
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.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", "False" ) )
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" ) )
self.job_working_directory = resolve_path( kwargs.get( "job_working_directory", "database/job_working_directory" ), self.root )
self.cleanup_job = kwargs.get( "cleanup_job", "always" )
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.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.reset_password_length = int( kwargs.get('reset_password_length', '15') )
self.mailing_join_addr = kwargs.get('mailing_join_addr', '*****@*****.**')
self.error_email_to = kwargs.get( 'error_email_to', None )
self.activation_email = kwargs.get( 'activation_email', None )
self.user_activation_on = string_as_bool( kwargs.get( 'user_activation_on', False ) )
self.activation_grace_period = kwargs.get( 'activation_grace_period', None )
self.inactivity_box_content = kwargs.get( 'inactivity_box_content', None )
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 )
# 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:
print ( "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 = kwargs.get( 'track_jobs_in_database', 'None' )
self.start_job_runners = listify(kwargs.get( 'start_job_runners', '' ))
self.expose_dataset_path = string_as_bool( kwargs.get( 'expose_dataset_path', '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))
# The transfer manager and deferred job queue
self.enable_beta_job_managers = string_as_bool( kwargs.get( 'enable_beta_job_managers', 'False' ) )
# 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.use_memdump = string_as_bool( kwargs.get( 'use_memdump', 'False' ) )
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.serve_xss_vulnerable_mimetypes = string_as_bool( kwargs.get( 'serve_xss_vulnerable_mimetypes', False ) )
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' )
# Configuration for the message box directly below the masthead.
self.message_box_visible = 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://wiki.galaxyproject.org/Support' )
self.wiki_url = kwargs.get( 'wiki_url', 'http://wiki.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 )
# 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_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( ',' )
# Location for tool dependencies.
if 'tool_dependency_dir' in kwargs:
self.tool_dependency_dir = resolve_path( kwargs.get( "tool_dependency_dir" ), self.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.
self.use_tool_dependencies = True
else:
self.tool_dependency_dir = None
self.use_tool_dependencies = False
# 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 )
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:
self.heartbeat_log = global_conf.get( 'heartbeat_log', 'heartbeat.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]
# 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))
# 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(',') ]
# Use database for job running IPC unless this is a standalone server or explicitly set in the config
if self.track_jobs_in_database == 'None':
self.track_jobs_in_database = False
if len(self.server_names) > 1:
self.track_jobs_in_database = True
else:
self.track_jobs_in_database = string_as_bool( self.track_jobs_in_database )
# 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' )
# Cloud configuration options
self.enable_cloud_launch = string_as_bool( kwargs.get( 'enable_cloud_launch', False ) )
self.cloudlaunch_default_ami = kwargs.get( 'cloudlaunch_default_ami', 'ami-a7dbf6ce' )
# 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 Exception("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 )
# 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' )
# 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" ) )
def __init__( self, **kwargs ):
self.config_dict = kwargs
self.root = kwargs.get( 'root_dir', '.' )
# 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( 077 ) # 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
self.version = VERSION
# Database related configuration
self.database = resolve_path( kwargs.get( "database_file", "database/community.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" ) )
# Repository and Tool search API
self.toolshed_search_on = string_as_bool( kwargs.get( "toolshed_search_on", True ) )
self.whoosh_index_dir = kwargs.get( "whoosh_index_dir", 'database/toolshed_whoosh_indexes' )
self.repo_name_boost = kwargs.get( "repo_name_boost", 0.9 )
self.repo_description_boost = kwargs.get( "repo_description_boost", 0.6 )
self.repo_long_description_boost = kwargs.get( "repo_long_description_boost", 0.5 )
self.repo_homepage_url_boost = kwargs.get( "repo_homepage_url_boost", 0.3 )
self.repo_remote_repository_url_boost = kwargs.get( "repo_remote_repository_url_boost", 0.2 )
self.repo_owner_username_boost = kwargs.get( "repo_owner_username_boost", 0.3 )
self.tool_name_boost = kwargs.get( "tool_name_boost", 1.2 )
self.tool_description_boost = kwargs.get( "tool_description_boost", 0.6 )
self.tool_help_boost = kwargs.get( "tool_help_boost", 0.4 )
self.tool_repo_owner_username = kwargs.get( "tool_repo_owner_username", 0.3 )
# Analytics
self.ga_code = kwargs.get( "ga_code", None )
self.session_duration = int(kwargs.get( 'session_duration', 0 ))
# Where dataset files are stored
self.file_path = resolve_path( kwargs.get( "file_path", "database/community_files" ), self.root )
self.new_file_path = resolve_path( kwargs.get( "new_file_path", "database/tmp" ), self.root )
self.cookie_path = kwargs.get( "cookie_path", "/" )
self.enable_quotas = string_as_bool( kwargs.get( 'enable_quotas', False ) )
self.id_secret = kwargs.get( "id_secret", "USING THE DEFAULT IS NOT SECURE!" )
# Tool stuff
self.tool_path = resolve_path( kwargs.get( "tool_path", "tools" ), self.root )
self.tool_secret = kwargs.get( "tool_secret", "" )
self.tool_data_path = resolve_path( kwargs.get( "tool_data_path", "shed-tool-data" ), os.getcwd() )
self.tool_data_table_config_path = None
self.integrated_tool_panel_config = resolve_path( kwargs.get( 'integrated_tool_panel_config', 'integrated_tool_panel.xml' ), self.root )
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 )
self.ftp_upload_dir = kwargs.get( 'ftp_upload_dir', None )
self.update_integrated_tool_panel = False
# Galaxy flavor Docker Image
self.enable_galaxy_flavor_docker_image = string_as_bool( kwargs.get( "enable_galaxy_flavor_docker_image", "False" ) )
self.use_remote_user = string_as_bool( kwargs.get( "use_remote_user", "False" ) )
self.user_activation_on = None
self.registration_warning_message = kwargs.get( 'registration_warning_message', None )
self.terms_url = kwargs.get( 'terms_url', None )
self.blacklist_location = kwargs.get( 'blacklist_file', None )
self.blacklist_content = None
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.enable_openid = string_as_bool( kwargs.get( 'enable_openid', False ) )
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/community" ), self.root )
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', "*****@*****.**")
self.error_email_to = kwargs.get( 'error_email_to', None )
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.start_job_runners = kwargs.get( 'start_job_runners', None )
self.email_from = kwargs.get( 'email_from', None )
self.nginx_upload_path = kwargs.get( 'nginx_upload_path', False )
self.log_actions = string_as_bool( kwargs.get( 'log_actions', 'False' ) )
self.brand = kwargs.get( 'brand', None )
self.pretty_datetime_format = expand_pretty_datetime_format( kwargs.get( 'pretty_datetime_format', '$locale (UTC)' ) )
# Configuration for the message box directly below the masthead.
self.message_box_visible = 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://wiki.galaxyproject.org/Support' )
self.wiki_url = kwargs.get( 'wiki_url', 'https://wiki.galaxyproject.org/' )
self.blog_url = kwargs.get( 'blog_url', None )
self.biostar_url = kwargs.get( 'biostar_url', None )
self.screencasts_url = kwargs.get( 'screencasts_url', None )
self.log_events = False
self.cloud_controller_instance = False
self.server_name = ''
self.job_manager = ''
self.default_job_handlers = []
self.default_cluster_job_runner = 'local:///'
self.job_handlers = []
self.tool_handlers = []
self.tool_runners = []
# Error logging with sentry
self.sentry_dsn = kwargs.get( 'sentry_dsn', None )
# Where the tool shed hgweb.config file is stored - the default is the Galaxy installation directory.
self.hgweb_config_dir = resolve_path( kwargs.get( 'hgweb_config_dir', '' ), self.root )
self.disable_push = string_as_bool( kwargs.get( "disable_push", "True" ) )
# Proxy features
self.apache_xsendfile = kwargs.get( 'apache_xsendfile', False )
self.nginx_x_accel_redirect_base = kwargs.get( 'nginx_x_accel_redirect_base', False )
self.drmaa_external_runjob_script = kwargs.get('drmaa_external_runjob_script', None )
# Parse global_conf and save the parser
global_conf = kwargs.get( 'global_conf', None )
global_conf_parser = ConfigParser.ConfigParser()
self.global_conf_parser = global_conf_parser
if global_conf and "__file__" in global_conf:
global_conf_parser.read(global_conf['__file__'])
self.running_functional_tests = string_as_bool( kwargs.get( 'running_functional_tests', False ) )
self.citation_cache_type = kwargs.get( "citation_cache_type", "file" )
self.citation_cache_data_dir = resolve_path( kwargs.get( "citation_cache_data_dir", "database/tool_shed_citations/data" ), self.root )
self.citation_cache_lock_dir = resolve_path( kwargs.get( "citation_cache_lock_dir", "database/tool_shed_citations/locks" ), self.root )
self.password_expiration_period = timedelta(days=int(kwargs.get("password_expiration_period", 0)))
