Skip to content

Commit

Permalink
Merge branch 'release_23.1' into release_23.2
Browse files Browse the repository at this point in the history
  • Loading branch information
mvdbeek committed Jun 5, 2024
2 parents 192fbde + 53b56a8 commit fed2294
Show file tree
Hide file tree
Showing 13 changed files with 95 additions and 89 deletions.
67 changes: 33 additions & 34 deletions lib/galaxy/web/framework/middleware/error.py
Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,7 @@
When an exception is thrown from the wrapper application, this logs
the exception and displays an error page.
"""
import logging
import sys
import traceback
from io import StringIO
Expand All @@ -25,6 +26,8 @@
reporter,
)

log = logging.getLogger(__name__)

__all__ = ("ErrorMiddleware", "handle_exception")


Expand Down Expand Up @@ -170,10 +173,11 @@ def __call__(self, environ, start_response):
for expect in environ.get("paste.expected_exceptions", []):
if isinstance(exc_info[1], expect):
raise
log.exception("Uncaught Exception")
start_response("500 Internal Server Error", [("content-type", "text/html")], exc_info)
# @@: it would be nice to deal with bad content types here
response = self.exception_handler(exc_info, environ)
return [response]
return [response.encode(errors="ignore")]
finally:
# clean up locals...
exc_info = None
Expand All @@ -184,7 +188,7 @@ def make_catching_iter(self, app_iter, environ, sr_checker):
return app_iter
return CatchingIter(app_iter, environ, sr_checker, self)

def exception_handler(self, exc_info, environ):
def exception_handler(self, exc_info, environ) -> str:
simple_html_error = False
if self.xmlhttp_key:
get_vars = wsgilib.parse_querystring(environ)
Expand All @@ -193,7 +197,6 @@ def exception_handler(self, exc_info, environ):
return handle_exception(
exc_info,
environ["wsgi.errors"],
html=True,
debug_mode=self.debug_mode,
error_email=self.error_email,
error_log=self.error_log,
Expand Down Expand Up @@ -344,7 +347,6 @@ def extraData(self):
def handle_exception(
exc_info,
error_stream,
html=True,
debug_mode=False,
error_email=None,
error_log=None,
Expand All @@ -358,7 +360,7 @@ def handle_exception(
error_message=None,
simple_html_error=False,
environ=None,
):
) -> str:
"""
For exception handling outside of a web context
Expand Down Expand Up @@ -389,54 +391,51 @@ def handle_exception(
smtp_use_tls=smtp_use_tls,
subject_prefix=error_subject_prefix,
)
rep_err = send_report(rep, exc_data, html=html)
rep_err = send_report(rep, exc_data, html=True)
if rep_err:
extra_data += rep_err
else:
reported = True
if error_log:
rep = reporter.LogReporter(filename=error_log)
rep_err = send_report(rep, exc_data, html=html)
rep_err = send_report(rep, exc_data, html=True)
if rep_err:
extra_data += rep_err
else:
reported = True
if show_exceptions_in_wsgi_errors:
rep = reporter.FileReporter(file=error_stream)
rep_err = send_report(rep, exc_data, html=html)
rep_err = send_report(rep, exc_data, html=True)
if rep_err:
extra_data += rep_err
else:
reported = True
else:
error_stream.write(f"Error - {exc_data.exception_type}: {exc_data.exception_value}\n")
if html:
if debug_mode and simple_html_error:
return_error = formatter.format_html(
exc_data, include_hidden_frames=False, include_reusable=False, show_extra_data=False
)
reported = True
elif debug_mode and not simple_html_error:
error_html = formatter.format_html(exc_data, include_hidden_frames=True, include_reusable=False)
head_html = formatter.error_css + formatter.hide_display_js
return_error = error_template(head_html, error_html, extra_data)
extra_data = ""
reported = True
else:
msg = (
error_message
or """
An error occurred.
"""
)
extra = "<p><b>The error has been logged to our team.</b>"
if "sentry_event_id" in environ:
extra += " If you want to contact us about this error, please reference the following<br><br>"
extra += f"<b><large>GURU MEDITATION: #{environ['sentry_event_id']}</large></b>"
extra += "</p>"
return_error = error_template("", msg, extra)
if debug_mode and simple_html_error:
return_error = formatter.format_html(
exc_data, include_hidden_frames=False, include_reusable=False, show_extra_data=False
)
reported = True
elif debug_mode and not simple_html_error:
error_html = formatter.format_html(exc_data, include_hidden_frames=True, include_reusable=False)
head_html = formatter.error_css + formatter.hide_display_js
return_error = error_template(head_html, error_html, extra_data)
extra_data = ""
reported = True
else:
return_error = None
msg = (
error_message
or """
An error occurred.
"""
)
extra = "<p><b>The error has been logged to our team.</b>"
if "sentry_event_id" in environ:
extra += " If you want to contact us about this error, please reference the following<br><br>"
extra += f"<b><large>GURU MEDITATION: #{environ['sentry_event_id']}</large></b>"
extra += "</p>"
return_error = error_template("", msg, extra)
if not reported and error_stream:
err_report = formatter.format_text(exc_data, show_hidden_frames=True)
err_report += f"\n{'-' * 60}\n"
Expand Down
2 changes: 1 addition & 1 deletion lib/tool_shed/managers/repositories.py
Original file line number Diff line number Diff line change
Expand Up @@ -468,7 +468,7 @@ def create_repository(trans: ProvidesUserContext, request: CreateRepositoryReque
type=request.type_,
description=request.synopsis,
long_description=request.description,
user_id=user.id,
user=user,
category_ids=category_ids,
remote_repository_url=request.remote_repository_url,
homepage_url=request.homepage_url,
Expand Down
3 changes: 1 addition & 2 deletions lib/tool_shed/util/hg_util.py
Original file line number Diff line number Diff line change
Expand Up @@ -71,14 +71,13 @@ def get_hgrc_path(repo_path):
return os.path.join(repo_path, ".hg", "hgrc")


def create_hgrc_file(app, repository):
def create_hgrc_file(app, repository, repo_path):
# Since we support both http and https, we set `push_ssl` to False to
# override the default (which is True) in the Mercurial API.
# The hg purge extension purges all files and directories not being tracked
# by Mercurial in the current repository. It will remove unknown files and
# empty directories. This is not currently used because it is not supported
# in the Mercurial API.
repo_path = repository.repo_path(app)
hgrc_path = get_hgrc_path(repo_path)
with open(hgrc_path, "w") as fp:
fp.write("[paths]\n")
Expand Down
11 changes: 5 additions & 6 deletions lib/tool_shed/util/hgweb_config.py
Original file line number Diff line number Diff line change
Expand Up @@ -5,8 +5,6 @@
import threading
from datetime import date

from galaxy.util import unicodify

log = logging.getLogger(__name__)

new_hgweb_config_template = """
Expand All @@ -20,6 +18,7 @@ def __init__(self):
self.hgweb_config_dir = None
self.in_memory_config = None
self.lock = threading.Lock()
self.hgweb_repo_prefix = None

def add_entry(self, lhs, rhs):
"""Add an entry in the hgweb.config file for a new repository."""
Expand All @@ -35,8 +34,8 @@ def add_entry(self, lhs, rhs):
self.in_memory_config.set("paths", lhs, rhs)
# Persist our in-memory configuration.
self.write_config()
except Exception as e:
log.debug("Exception in HgWebConfigManager.add_entry(): %s", unicodify(e))
except Exception:
log.exception("Exception in HgWebConfigManager.add_entry()")
finally:
self.lock.release()

Expand All @@ -51,8 +50,8 @@ def change_entry(self, old_lhs, new_lhs, new_rhs):
self.in_memory_config.set("paths", new_lhs, new_rhs)
# Persist our in-memory configuration.
self.write_config()
except Exception as e:
log.debug("Exception in HgWebConfigManager.change_entry(): %s", unicodify(e))
except Exception:
log.exception("Exception in HgWebConfigManager.change_entry()")
finally:
self.lock.release()

Expand Down
69 changes: 31 additions & 38 deletions lib/tool_shed/util/repository_util.py
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@
import logging
import os
import re
import tempfile
from typing import (
List,
Optional,
Expand Down Expand Up @@ -164,23 +165,18 @@ def create_repo_info_dict(
def create_repository_admin_role(app: "ToolShedApp", repository: "Repository"):
"""
Create a new role with name-spaced name based on the repository name and its owner's public user
name. This will ensure that the tole name is unique.
name. This will ensure that the role name is unique.
"""
sa_session = app.model.session
name = get_repository_admin_role_name(str(repository.name), str(repository.user.username))
description = "A user or group member with this role can administer this repository."
role = app.model.Role(name=name, description=description, type=app.model.Role.types.SYSTEM)
sa_session.add(role)
session = sa_session()
with transaction(session):
session.commit()
# Associate the role with the repository owner.
app.model.UserRoleAssociation(repository.user, role)
# Associate the role with the repository.
rra = app.model.RepositoryRoleAssociation(repository, role)
sa_session.add(rra)
with transaction(session):
session.commit()
return role


Expand All @@ -190,7 +186,7 @@ def create_repository(
type: str,
description,
long_description,
user_id,
user,
category_ids: Optional[List[str]] = None,
remote_repository_url=None,
homepage_url=None,
Expand All @@ -206,43 +202,40 @@ def create_repository(
homepage_url=homepage_url,
description=description,
long_description=long_description,
user_id=user_id,
user=user,
)
# Flush to get the id.
sa_session.add(repository)
session = sa_session()
with transaction(session):
session.commit()
# Create an admin role for the repository.
create_repository_admin_role(app, repository)
# Determine the repository's repo_path on disk.
dir = os.path.join(app.config.file_path, *util.directory_hash_id(repository.id))
# Create directory if it does not exist.
if not os.path.exists(dir):
os.makedirs(dir)
# Define repo name inside hashed directory.
repository_path = os.path.join(dir, "repo_%d" % repository.id)
# Create local repository directory.
if not os.path.exists(repository_path):
os.makedirs(repository_path)
# Create the local repository.
init_repository(repo_path=repository_path)
# Add an entry in the hgweb.config file for the local repository.
lhs = f"{app.config.hgweb_repo_prefix}{repository.user.username}/{repository.name}"
app.hgweb_config_manager.add_entry(lhs, repository_path)
# Create a .hg/hgrc file for the local repository.
create_hgrc_file(app, repository)
flush_needed = False
if category_ids:
# Create category associations
for category_id in category_ids:
category = sa_session.get(app.model.Category, app.security.decode_id(category_id))
rca = app.model.RepositoryCategoryAssociation(repository, category)
sa_session.add(rca)
flush_needed = True
if flush_needed:
with transaction(session):
session.commit()
# Create an admin role for the repository.
create_repository_admin_role(app, repository)
# Create a temporary repo_path on disk.
repository_path = tempfile.mkdtemp(
dir=app.config.file_path,
prefix=f"{repository.user.username}-{repository.name}",
)
# Create the local repository.
init_repository(repo_path=repository_path)
# Create a .hg/hgrc file for the local repository.
create_hgrc_file(app, repository, repo_path=repository_path)
# Add an entry in the hgweb.config file for the local repository.
lhs = f"{app.config.hgweb_repo_prefix}{repository.user.username}/{repository.name}"
# Flush to get the id.
session = sa_session()
with transaction(session):
session.commit()
dir = os.path.join(app.config.file_path, *util.directory_hash_id(repository.id))
# Define repo name inside hashed directory.
final_repository_path = os.path.join(dir, "repo_%d" % repository.id)
# Create final repository directory.
if not os.path.exists(final_repository_path):
os.makedirs(final_repository_path)
os.rename(repository_path, final_repository_path)
app.hgweb_config_manager.add_entry(lhs, final_repository_path)
# Update the repository registry.
app.repository_registry.add_entry(repository)
message = f"Repository <b>{escape(str(repository.name))}</b> has been created."
Expand Down Expand Up @@ -486,8 +479,8 @@ def update_repository(trans: "ProvidesUserContext", id: str, **kwds) -> Tuple[Op

repo_dir = repository.repo_path(app)
# Change the entry in the hgweb.config file for the repository.
old_lhs = f"repos/{repository.user.username}/{repository.name}"
new_lhs = f"repos/{repository.user.username}/{kwds['name']}"
old_lhs = f"{trans.app.config.hgweb_repo_prefix}{repository.user.username}/{repository.name}"
new_lhs = f"{trans.app.config.hgweb_repo_prefix}{repository.user.username}/{kwds['name']}"
trans.app.hgweb_config_manager.change_entry(old_lhs, new_lhs, repo_dir)

# Change the entry in the repository's hgrc file.
Expand Down
8 changes: 4 additions & 4 deletions lib/tool_shed/util/shed_index.py
Original file line number Diff line number Diff line change
Expand Up @@ -37,7 +37,7 @@ def _get_or_create_index(whoosh_index_dir):
return get_or_create_index(whoosh_index_dir, repo_schema), get_or_create_index(tool_index_dir, tool_schema)


def build_index(whoosh_index_dir, file_path, hgweb_config_dir, dburi, **kwargs):
def build_index(whoosh_index_dir, file_path, hgweb_config_dir, hgweb_repo_prefix, dburi, **kwargs):
"""
Build two search indexes simultaneously
One is for repositories and the other for tools.
Expand All @@ -55,7 +55,7 @@ def build_index(whoosh_index_dir, file_path, hgweb_config_dir, dburi, **kwargs):

execution_timer = ExecutionTimer()
with repo_index.searcher() as searcher:
for repo in get_repos(sa_session, file_path, hgweb_config_dir, **kwargs):
for repo in get_repos(sa_session, file_path, hgweb_config_dir, hgweb_repo_prefix, **kwargs):
tools_list = repo.pop("tools_list")
repo_id = repo["id"]
indexed_document = searcher.document(id=repo_id)
Expand Down Expand Up @@ -89,7 +89,7 @@ def build_index(whoosh_index_dir, file_path, hgweb_config_dir, dburi, **kwargs):
return repos_indexed, tools_indexed


def get_repos(sa_session, file_path, hgweb_config_dir, **kwargs):
def get_repos(sa_session, file_path, hgweb_config_dir, hgweb_repo_prefix, **kwargs):
"""
Load repos from DB and included tools from .xml configs.
"""
Expand Down Expand Up @@ -120,7 +120,7 @@ def get_repos(sa_session, file_path, hgweb_config_dir, **kwargs):

# Load all changesets of the repo for lineage.
repo_path = os.path.join(
hgweb_config_dir, hgwcm.get_entry(os.path.join("repos", repo.user.username, repo.name))
hgweb_config_dir, hgwcm.get_entry(os.path.join(hgweb_repo_prefix, repo.user.username, repo.name))
)
hg_repo = hg.repository(ui.ui(), repo_path.encode("utf-8"))
lineage = []
Expand Down
1 change: 1 addition & 0 deletions lib/tool_shed/webapp/api/tools.py
Original file line number Diff line number Diff line change
Expand Up @@ -33,6 +33,7 @@ def build_search_index(self, trans, **kwd):
trans.app.config.whoosh_index_dir,
trans.app.config.file_path,
trans.app.config.hgweb_config_dir,
trans.app.config.hgweb_repo_prefix,
trans.app.config.database_connection,
)
return {
Expand Down
1 change: 1 addition & 0 deletions lib/tool_shed/webapp/api2/tools.py
Original file line number Diff line number Diff line change
Expand Up @@ -74,6 +74,7 @@ def build_search_index(self) -> BuildSearchIndexResponse:
config.whoosh_index_dir,
config.file_path,
config.hgweb_config_dir,
config.hgweb_repo_prefix,
config.database_connection,
)
return BuildSearchIndexResponse(
Expand Down
1 change: 1 addition & 0 deletions lib/tool_shed/webapp/app.py
Original file line number Diff line number Diff line change
Expand Up @@ -104,6 +104,7 @@ def __init__(self, **kwd) -> None:
# Let the Tool Shed's HgwebConfigManager know where the hgweb.config file is located.
self.hgweb_config_manager = hgweb_config_manager
self.hgweb_config_manager.hgweb_config_dir = self.config.hgweb_config_dir
self.hgweb_config_manager.hgweb_repo_prefix = self.config.hgweb_repo_prefix
# Initialize the repository registry.
self.repository_registry = tool_shed.repository_registry.Registry(self)
# Configure Sentry client if configured
Expand Down
Loading

0 comments on commit fed2294

Please sign in to comment.