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.tools.error_reports

"""This module defines the error reporting framework for Galaxy jobs.
import collections
import logging
import os

from galaxy.util import plugin_config

log = logging.getLogger(__name__)

        'type': 'email',
        'verbose': True,
        'user_submission': True,
DEFAULT_PLUGINS_SOURCE = plugin_config.PluginConfigSource('dict', DEFAULT_CONFIG)

[docs]class ErrorReports: """Load and store a collection of :class:`ErrorPlugin` objects."""
[docs] def __init__(self, conf_file=None, **kwargs): """Load :class:`ErrorPlugin` objects from specified configuration file.""" self.plugin_classes = self.__plugins_dict() self.default_error_plugin = ErrorPlugin.from_file(self.plugin_classes, conf_file, **kwargs) self.error_plugin = collections.defaultdict(lambda: self.default_error_plugin)
def __plugins_dict(self): import galaxy.tools.error_reports.plugins return plugin_config.plugins_dict(galaxy.tools.error_reports.plugins, 'plugin_type')
[docs]class NullErrorPlugin:
[docs] def submit_report(self, dataset, job, tool, **kwargs): log.warning("Bug report for dataset %s, job %s submitted to NullErrorPlugin", dataset, job) return [("Error reporting is not configured for this Galaxy instance", "danger")]
NULL_ERROR_PLUGIN = NullErrorPlugin()
[docs]class ErrorPlugin:
[docs] def __init__(self, plugin_classes, plugins_source, **kwargs): self.extra_kwargs = kwargs self.app = kwargs['app'] self.plugin_classes = plugin_classes self.plugins = self.__plugins_from_source(plugins_source)
def _can_access_dataset(self, dataset, user): if user: roles = user.all_roles() else: roles = [] return self.app.security_agent.can_access_dataset(roles, dataset.dataset)
[docs] def submit_report(self, dataset, job, tool, user=None, user_submission=False, **kwargs): if user_submission: assert self._can_access_dataset(dataset, user), Exception("You are not allowed to access this dataset.") responses = [] for plugin in self.plugins: if user_submission == plugin.user_submission: try: response = plugin.submit_report(dataset, job, tool, **kwargs) log.debug("Bug report plugin %s generated response %s", plugin, response) if plugin.verbose and response: responses.append(response) except Exception: log.exception("Failed to generate submit_report commands for plugin %s", plugin) return responses
def __plugins_from_source(self, plugins_source): return plugin_config.load_plugins(self.plugin_classes, plugins_source, self.extra_kwargs)
[docs] @staticmethod def from_file(plugin_classes, conf_file, **kwargs): plugins_source = DEFAULT_PLUGINS_SOURCE if conf_file and os.path.exists(conf_file): plugins_source = plugin_config.plugin_source_from_path(conf_file) if not plugins_source.source: return NULL_ERROR_PLUGIN return ErrorPlugin(plugin_classes, plugins_source, **kwargs)