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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__)

DEFAULT_CONFIG = [
    {
        '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)