"""This module defines the common functions for error reporting for Galaxy jobs towards Git applications (e.g. Github/GitLab).
"""
import logging
from abc import (
ABCMeta,
abstractmethod,
)
from typing import Dict
import requests
from galaxy.tools.errors import EmailErrorReporter
from galaxy.util import (
DEFAULT_SOCKET_TIMEOUT,
unicodify,
)
from . import ErrorPlugin
log = logging.getLogger(__name__)
[docs]class BaseGitPlugin(ErrorPlugin, metaclass=ABCMeta):
"""Base definition to send error reports to a Git repository provider"""
issue_cache: Dict[str, Dict] = {}
ts_urls: Dict[str, str] = {}
ts_repo_cache: Dict[str, Dict] = {}
git_project_cache: Dict[str, Dict] = {}
label_cache: Dict[str, Dict] = {}
git_username_id_cache: Dict[str, str] = {}
# Git variables
git_default_repo_owner = False
git_default_repo_name = False
git_default_repo_only = True
def _determine_ts_url(self, tool):
if not tool.tool_shed or self.git_default_repo_only:
return None
try:
if tool.tool_shed not in self.ts_urls:
ts_url_request = requests.get(f"http://{tool.tool_shed}", timeout=DEFAULT_SOCKET_TIMEOUT)
self.ts_urls[tool.tool_shed] = ts_url_request.url
return self.ts_urls[tool.tool_shed]
except Exception:
return None
def _get_gitrepo_from_ts(self, job, ts_url):
if not ts_url or self.git_default_repo_only:
return None
try:
if job.tool_id not in self.ts_repo_cache:
ts_repo_request_data = requests.get(
f"{ts_url}/api/repositories?tool_ids={str(job.tool_id)}", timeout=DEFAULT_SOCKET_TIMEOUT
).json()
for repoinfo in ts_repo_request_data.values():
if isinstance(repoinfo, dict):
self.ts_repo_cache[job.tool_id] = repoinfo.get("repository", {}).get(
"remote_repository_url", None
)
return self.ts_repo_cache[job.tool_id]
except Exception:
return None
def _get_issue_cache_key(self, job, ts_repourl):
return job.tool_id if ts_repourl else "default"
def _generate_error_message(self, dataset, job, kwargs):
# We'll re-use the email error reporter's template since most Git providers supports HTML
error_reporter = EmailErrorReporter(dataset.id, self.app)
error_reporter.create_report(
job.get_user(),
email=kwargs.get("email", None),
message=kwargs.get("message", None),
redact_user_details_in_bugreport=self.redact_user_details_in_bugreport,
)
# Return the HTML report
return error_reporter.html_report
def _generate_error_title(self, job):
tool_kw = {"tool_id": unicodify(job.tool_id), "tool_version": unicodify(job.tool_version)}
return """Galaxy Job Error: {tool_id} v{tool_version}""".format(**tool_kw)
@abstractmethod
def _create_issue(self, issue_cache_key, error_title, error_mesage, project, **kwargs):
raise NotImplementedError("Method _create_issue is required")
@abstractmethod
def _append_issue(self, issue_cache_key, error_title, error_message, **kwargs):
raise NotImplementedError("Method _append_issue is required")
@abstractmethod
def _fill_issue_cache(self, git_project, issue_cache_key):
raise NotImplementedError("Method _fill_issue_cache is required")