mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Merge pull request #9582 from ic4f/dev_config4
This commit is contained in:
Nicola Soranzo
@@ -340,6 +340,13 @@ class CommonConfigurationMixin(object):
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# Warning: the value of self.config_dict['foo'] may be different from self.foo
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return self.config_dict.get(key, default)
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def _ensure_directory(self, path):
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if path not in [None, False] and not os.path.isdir(path):
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try:
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os.makedirs(path)
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except Exception as e:
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raise ConfigurationError("Unable to create missing directory: %s\n%s" % (path, unicodify(e)))
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class GalaxyAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
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deprecated_options = ('database_file', 'track_jobs_in_database')
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@@ -804,26 +811,21 @@ class GalaxyAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
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def ensure_tempdir(self):
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self._ensure_directory(self.new_file_path)
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def _ensure_directory(self, path):
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if path not in [None, False] and not os.path.isdir(path):
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try:
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os.makedirs(path)
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except Exception as e:
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raise ConfigurationError("Unable to create missing directory: %s\n%s" % (path, unicodify(e)))
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def check(self):
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paths_to_check = [self.tool_data_path, self.data_dir, self.managed_config_dir]
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# Check that required directories exist
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# Check that required directories exist; attempt to create otherwise
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paths_to_check = [
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self.data_dir,
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self.ftp_upload_dir,
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self.library_import_dir,
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self.managed_config_dir,
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self.new_file_path,
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self.nginx_upload_store,
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self.object_store_cache_path,
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self.template_cache_path,
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self.tool_data_path,
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self.user_library_import_dir,
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]
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for path in paths_to_check:
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if path not in [None, False] and not os.path.isdir(path):
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try:
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os.makedirs(path)
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except Exception as e:
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raise ConfigurationError("Unable to create missing directory: %s\n%s" % (path, unicodify(e)))
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# Create the directories that it makes sense to create
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for path in (self.new_file_path, self.template_cache_path, self.ftp_upload_dir,
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self.library_import_dir, self.user_library_import_dir,
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self.nginx_upload_store, self.object_store_cache_path):
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self._ensure_directory(path)
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# Check that required files exist
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tool_configs = self.tool_configs
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@@ -246,10 +246,12 @@ tool_shed:
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#allow_user_deletion: false
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# For use by email messages sent from the Tool Shed.
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#smtp_server: smtp.your_tool_shed_server
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# (smtp.your_tool_shed_server)
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#smtp_server: null
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# For use by email messages sent from the Tool Shed.
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#email_from: your_tool_shed_email@server
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# (your_tool_shed_email@server)
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#email_from: null
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# If your SMTP server requires a username and password, you can
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# provide them here (password in cleartext here, but if your server
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@@ -377,7 +379,7 @@ tool_shed:
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# logged are grid views, tool searches, and use of "recently" used
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# tools menu. The log_events and log_actions functionality will
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# eventually be merged.
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#log_actions: true
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#log_actions: false
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# Password expiration period (in days). Users are required to change
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# their password every x days. Users will be redirected to the change
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+88
-109
@@ -14,6 +14,7 @@ from galaxy.config import (
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get_database_engine_options,
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)
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from galaxy.config.schema import AppSchema
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from galaxy.exceptions import ConfigurationError
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from galaxy.util import string_as_bool
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from galaxy.version import VERSION, VERSION_MAJOR
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from galaxy.web.formatting import expand_pretty_datetime_format
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@@ -21,16 +22,12 @@ from galaxy.web.formatting import expand_pretty_datetime_format
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log = logging.getLogger(__name__)
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ts_webapp_path = os.path.abspath(os.path.dirname(__file__))
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templates_path = os.path.join(ts_webapp_path, "templates")
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templates_path = os.path.join(ts_webapp_path, 'templates')
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TOOLSHED_APP_NAME = 'tool_shed'
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TOOLSHED_CONFIG_SCHEMA_PATH = 'lib/tool_shed/webapp/config_schema.yml'
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class ConfigurationError(Exception):
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pass
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class ToolShedAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
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default_config_file_name = 'tool_shed.yml'
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@@ -39,91 +36,7 @@ class ToolShedAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
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def __init__(self, **kwargs):
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super(ToolShedAppConfiguration, self).__init__(**kwargs)
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# Resolve paths of other config files
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self.parse_config_file_options(kwargs)
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# Collect the umask and primary gid from the environment
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self.umask = os.umask(0o77) # get the current umask
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os.umask(self.umask) # can't get w/o set, so set it back
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self.gid = os.getgid() # if running under newgrp(1) we'll need to fix the group of data created on the cluster
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self.version_major = VERSION_MAJOR
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self.version = VERSION
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# Database related configuration
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if not self.database_connection: # Provide default if not supplied by user
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self.database_connection = 'sqlite:///%s?isolation_level=IMMEDIATE' % self._in_data_dir('community.sqlite')
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self.database_engine_options = get_database_engine_options(kwargs)
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self.database_create_tables = string_as_bool(kwargs.get("database_create_tables", "True"))
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# Where dataset files are stored
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self.file_path = self._in_root_dir(self.file_path)
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self.new_file_path = self._in_root_dir(self.new_file_path)
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self.cookie_path = kwargs.get("cookie_path", None)
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self.cookie_domain = kwargs.get("cookie_domain", None)
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self.enable_quotas = string_as_bool(kwargs.get('enable_quotas', False))
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# Tool stuff
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self.tool_path = self._in_root_dir(kwargs.get("tool_path", "tools"))
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self.tool_secret = kwargs.get("tool_secret", "")
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self.tool_data_path = os.path.join(os.getcwd(), kwargs.get("tool_data_path", "shed-tool-data"))
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self.tool_data_table_config_path = None
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self.integrated_tool_panel_config = self._in_root_dir(kwargs.get('integrated_tool_panel_config', 'integrated_tool_panel.xml'))
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self.builds_file_path = self._in_root_dir(kwargs.get("builds_file_path", os.path.join(self.tool_data_path, 'shared', 'ucsc', 'builds.txt')))
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self.len_file_path = self._in_root_dir(kwargs.get("len_file_path", os.path.join(self.tool_data_path, 'shared', 'ucsc', 'chrom')))
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self.ftp_upload_dir = kwargs.get('ftp_upload_dir', None)
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self.update_integrated_tool_panel = False
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# Galaxy flavor Docker Image
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self.user_activation_on = None
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self.registration_warning_message = kwargs.get('registration_warning_message', None)
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self.blacklist_location = kwargs.get('blacklist_file', None)
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self.blacklist_content = None
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self.whitelist_location = kwargs.get('whitelist_file', None)
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self.whitelist_content = None
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self.remote_user_maildomain = kwargs.get("remote_user_maildomain", None)
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self.remote_user_header = kwargs.get("remote_user_header", 'HTTP_REMOTE_USER')
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self.remote_user_logout_href = kwargs.get("remote_user_logout_href", None)
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self.remote_user_secret = kwargs.get("remote_user_secret", None)
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self.template_path = templates_path
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self.template_cache_path = self._in_root_dir(kwargs.get("template_cache_path", "database/compiled_templates/community"))
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self.error_email_to = kwargs.get('error_email_to', None)
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self.smtp_server = kwargs.get('smtp_server', None)
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self.smtp_ssl = kwargs.get('smtp_ssl', None)
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self.email_from = kwargs.get('email_from', None)
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self.nginx_upload_path = kwargs.get('nginx_upload_path', False)
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self.log_actions = string_as_bool(kwargs.get('log_actions', 'False'))
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self.pretty_datetime_format = expand_pretty_datetime_format(self.pretty_datetime_format)
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# Configuration for the message box directly below the masthead.
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self.wiki_url = kwargs.get('wiki_url', 'https://galaxyproject.org/')
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self.blog_url = kwargs.get('blog_url', None)
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self.screencasts_url = kwargs.get('screencasts_url', None)
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self.log_events = False
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self.cloud_controller_instance = False
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self.server_name = ''
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# Where the tool shed hgweb.config file is stored - the default is the Galaxy installation directory.
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self.hgweb_config_dir = self._in_root_dir(self.hgweb_config_dir) or self.root
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# Proxy features
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self.nginx_x_accel_redirect_base = kwargs.get('nginx_x_accel_redirect_base', False)
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self.drmaa_external_runjob_script = kwargs.get('drmaa_external_runjob_script', None)
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# Parse global_conf and save the parser
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global_conf = kwargs.get('global_conf', None)
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global_conf_parser = configparser.ConfigParser()
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self.global_conf_parser = global_conf_parser
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if global_conf and "__file__" in global_conf and ".yml" not in global_conf["__file__"]:
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global_conf_parser.read(global_conf['__file__'])
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self.running_functional_tests = string_as_bool(kwargs.get('running_functional_tests', False))
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self.citation_cache_type = kwargs.get("citation_cache_type", "file")
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self.citation_cache_data_dir = self._in_root_dir(kwargs.get("citation_cache_data_dir", "database/tool_shed_citations/data"))
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self.citation_cache_lock_dir = self._in_root_dir(kwargs.get("citation_cache_lock_dir", "database/tool_shed_citations/locks"))
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self.password_expiration_period = timedelta(days=int(kwargs.get("password_expiration_period", 0)))
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# Security/Policy Compliance
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self.redact_username_during_deletion = False
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self.redact_email_during_deletion = False
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self.redact_username_in_logs = False
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self.enable_beta_gdpr = string_as_bool(kwargs.get("enable_beta_gdpr", False))
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if self.enable_beta_gdpr:
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self.redact_username_during_deletion = True
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self.redact_email_during_deletion = True
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self.redact_username_in_logs = True
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self.allow_user_deletion = True
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self._process_config(kwargs)
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@property
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def shed_tool_data_path(self):
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@@ -135,33 +48,99 @@ class ToolShedAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
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datatypes_config_file=[self._in_config_dir('datatypes_conf.xml'), self._in_sample_dir('datatypes_conf.xml.sample')],
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shed_tool_data_table_config=[self._in_managed_config_dir('shed_tool_data_table_conf.xml')],
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)
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self._parse_config_file_options(defaults, dict(), kwargs)
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# Backwards compatibility for names used in too many places to fix
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self.datatypes_config = self.datatypes_config_file
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def check(self):
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# Check that required directories exist.
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paths_to_check = [self.file_path, self.hgweb_config_dir, self.tool_data_path, self.template_path]
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# Check that required directories exist; attempt to create otherwise
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paths_to_check = [
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self.file_path,
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self.hgweb_config_dir,
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self.template_path,
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self.tool_data_path,
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self.template_cache_path,
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os.path.join(self.tool_data_path, 'shared', 'jars'),
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]
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for path in paths_to_check:
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if path not in [None, False] and not os.path.isdir(path):
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try:
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os.makedirs(path)
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except Exception as e:
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raise ConfigurationError("Unable to create missing directory: %s\n%s" % (path, e))
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# Create the directories that it makes sense to create.
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for path in self.file_path, \
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self.template_cache_path, \
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os.path.join(self.tool_data_path, 'shared', 'jars'):
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if path not in [None, False] and not os.path.isdir(path):
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try:
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os.makedirs(path)
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except Exception as e:
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raise ConfigurationError("Unable to create missing directory: %s\n%s" % (path, e))
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self._ensure_directory(path)
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# Check that required files exist.
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if not os.path.isfile(self.datatypes_config):
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raise ConfigurationError("File not found: %s" % self.datatypes_config)
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raise ConfigurationError('File not found: %s' % self.datatypes_config)
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def _process_config(self, kwargs):
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# Resolve paths of other config files
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self.parse_config_file_options(kwargs)
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# Collect the umask and primary gid from the environment
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self.umask = os.umask(0o77) # get the current umask
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os.umask(self.umask) # can't get w/o set, so set it back
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self.gid = os.getgid() # if running under newgrp(1) we'll need to fix the group of data created on the cluster
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self.version_major = VERSION_MAJOR
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self.version = VERSION
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# Database related configuration
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if not self.database_connection: # Provide default if not supplied by user
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self.database_connection = 'sqlite:///%s?isolation_level=IMMEDIATE' % self._in_data_dir('community.sqlite')
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self.database_engine_options = get_database_engine_options(kwargs)
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self.database_create_tables = string_as_bool(kwargs.get('database_create_tables', 'True'))
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# Where dataset files are stored
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self.file_path = self._in_root_dir(self.file_path)
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self.new_file_path = self._in_root_dir(self.new_file_path)
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self.cookie_path = kwargs.get('cookie_path')
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self.cookie_domain = kwargs.get('cookie_domain')
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self.enable_quotas = string_as_bool(kwargs.get('enable_quotas', False))
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# Tool stuff
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self.tool_path = self._in_root_dir(kwargs.get('tool_path', 'tools'))
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self.tool_secret = kwargs.get('tool_secret', '')
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self.tool_data_path = os.path.join(os.getcwd(), kwargs.get('tool_data_path', 'shed-tool-data'))
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self.tool_data_table_config_path = None
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self.integrated_tool_panel_config = self._in_root_dir(kwargs.get('integrated_tool_panel_config', 'integrated_tool_panel.xml'))
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self.builds_file_path = self._in_root_dir(kwargs.get('builds_file_path', os.path.join(self.tool_data_path, 'shared', 'ucsc', 'builds.txt')))
|
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self.len_file_path = self._in_root_dir(kwargs.get('len_file_path', os.path.join(self.tool_data_path, 'shared', 'ucsc', 'chrom')))
|
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self.ftp_upload_dir = kwargs.get('ftp_upload_dir')
|
||||
self.update_integrated_tool_panel = False
|
||||
# Galaxy flavor Docker Image
|
||||
self.user_activation_on = None
|
||||
self.registration_warning_message = kwargs.get('registration_warning_message')
|
||||
self.blacklist_location = kwargs.get('blacklist_file')
|
||||
self.blacklist_content = None
|
||||
self.whitelist_location = kwargs.get('whitelist_file')
|
||||
self.whitelist_content = None
|
||||
self.template_path = templates_path
|
||||
self.template_cache_path = self._in_root_dir(kwargs.get('template_cache_path', 'database/compiled_templates/community'))
|
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self.error_email_to = kwargs.get('error_email_to')
|
||||
self.pretty_datetime_format = expand_pretty_datetime_format(self.pretty_datetime_format)
|
||||
# Configuration for the message box directly below the masthead.
|
||||
self.wiki_url = kwargs.get('wiki_url', 'https://galaxyproject.org/')
|
||||
self.blog_url = kwargs.get('blog_url')
|
||||
self.screencasts_url = kwargs.get('screencasts_url')
|
||||
self.log_events = False
|
||||
self.cloud_controller_instance = False
|
||||
self.server_name = ''
|
||||
# Where the tool shed hgweb.config file is stored - the default is the Galaxy installation directory.
|
||||
self.hgweb_config_dir = self._in_root_dir(self.hgweb_config_dir) or self.root
|
||||
# Proxy features
|
||||
self.drmaa_external_runjob_script = kwargs.get('drmaa_external_runjob_script')
|
||||
# Parse global_conf and save the parser
|
||||
global_conf = kwargs.get('global_conf')
|
||||
global_conf_parser = configparser.ConfigParser()
|
||||
self.global_conf_parser = global_conf_parser
|
||||
if global_conf and '__file__' in global_conf and '.yml' not in global_conf['__file__']:
|
||||
global_conf_parser.read(global_conf['__file__'])
|
||||
self.running_functional_tests = string_as_bool(kwargs.get('running_functional_tests', False))
|
||||
self.citation_cache_data_dir = self._in_root_dir(kwargs.get('citation_cache_data_dir', 'database/tool_shed_citations/data'))
|
||||
self.citation_cache_lock_dir = self._in_root_dir(kwargs.get('citation_cache_lock_dir', 'database/tool_shed_citations/locks'))
|
||||
self.password_expiration_period = timedelta(days=int(self.password_expiration_period))
|
||||
|
||||
# Security/Policy Compliance
|
||||
self.redact_username_during_deletion = False
|
||||
self.redact_email_during_deletion = False
|
||||
self.redact_username_in_logs = False
|
||||
self.enable_beta_gdpr = string_as_bool(kwargs.get('enable_beta_gdpr', False))
|
||||
if self.enable_beta_gdpr:
|
||||
self.redact_username_during_deletion = True
|
||||
self.redact_email_during_deletion = True
|
||||
self.redact_username_in_logs = True
|
||||
self.allow_user_deletion = True
|
||||
|
||||
|
||||
Configuration = ToolShedAppConfiguration
|
||||
|
||||
@@ -208,7 +208,6 @@ mapping:
|
||||
|
||||
remote_user_maildomain:
|
||||
type: str
|
||||
default: null
|
||||
required: false
|
||||
desc: |
|
||||
If use_remote_user is enabled and your external authentication
|
||||
@@ -228,7 +227,6 @@ mapping:
|
||||
|
||||
remote_user_logout_href:
|
||||
type: str
|
||||
default: null
|
||||
required: false
|
||||
desc: |
|
||||
If use_remote_user is enabled, you can set this to a URL that will log your
|
||||
@@ -289,17 +287,17 @@ mapping:
|
||||
|
||||
smtp_server:
|
||||
type: str
|
||||
default: smtp.your_tool_shed_server
|
||||
required: false
|
||||
desc: |
|
||||
For use by email messages sent from the Tool Shed.
|
||||
(smtp.your_tool_shed_server)
|
||||
|
||||
email_from:
|
||||
type: str
|
||||
default: your_tool_shed_email@server
|
||||
required: false
|
||||
desc: |
|
||||
For use by email messages sent from the Tool Shed.
|
||||
(your_tool_shed_email@server)
|
||||
|
||||
smtp_username:
|
||||
type: str
|
||||
@@ -457,7 +455,6 @@ mapping:
|
||||
|
||||
nginx_x_accel_redirect_base:
|
||||
type: str
|
||||
default: null
|
||||
required: false
|
||||
desc: |
|
||||
The same download handling can be done by nginx using X-Accel-Redirect. This
|
||||
@@ -466,7 +463,6 @@ mapping:
|
||||
|
||||
nginx_upload_path:
|
||||
type: str
|
||||
default: null
|
||||
required: false
|
||||
desc: |
|
||||
This value overrides the action set on the file upload form, e.g. the web
|
||||
@@ -496,7 +492,6 @@ mapping:
|
||||
|
||||
brand:
|
||||
type: str
|
||||
default: null
|
||||
required: false
|
||||
desc: |
|
||||
Append "/{brand}" to the "Galaxy" text in the masthead.
|
||||
@@ -530,7 +525,7 @@ mapping:
|
||||
|
||||
log_actions:
|
||||
type: bool
|
||||
default: true
|
||||
default: false
|
||||
required: false
|
||||
desc: |
|
||||
Turn on logging of user actions to the database. Actions currently logged
|
||||
@@ -549,7 +544,6 @@ mapping:
|
||||
|
||||
sentry_dsn:
|
||||
type: str
|
||||
default: null
|
||||
required: false
|
||||
desc: |
|
||||
Log to Sentry
|
||||
@@ -569,7 +563,6 @@ mapping:
|
||||
|
||||
terms_url:
|
||||
type: str
|
||||
default: null
|
||||
required: false
|
||||
desc: |
|
||||
The URL linked by the "Terms and Conditions" link in the "Help" menu, as well
|
||||
|
||||
Reference in New Issue
Block a user