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Cleanup update_repository_manager in Galaxy repository install code.

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This commit is contained in:
John Chilton
2022-09-15 13:39:25 -04:00
parent 2ee253cbbd
commit c04dd77de0
3 changed files with 27 additions and 71 deletions
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lib/galaxy/tool_shed/galaxy_install/install_manager.py
+3 -3
View File
@@ -579,11 +579,11 @@ class InstallRepositoryManager:
if reinstalling:
# Since we're reinstalling the repository we need to find the latest changeset revision to
# which it can be updated.
changeset_revision_dict = self.app.update_repository_manager.get_update_to_changeset_revision_and_ctx_rev(
update_to_changeset = self.app.update_repository_manager.get_update_to_changeset_revision_and_ctx_rev(
tool_shed_repository
)
current_changeset_revision = changeset_revision_dict.get("changeset_revision", None)
current_ctx_rev = changeset_revision_dict.get("ctx_rev", None)
current_changeset_revision = update_to_changeset.changeset_revision
current_ctx_rev = update_to_changeset.ctx_rev
if current_ctx_rev != ctx_rev:
repo_path = os.path.abspath(install_dir)
hg_util.pull_repository(repo_path, repository_clone_url, current_changeset_revision)
lib/galaxy/tool_shed/galaxy_install/update_repository_manager.py
+21 -65
View File
@@ -3,18 +3,26 @@ Determine if installed tool shed repositories have updates available in their re
"""
import logging
import threading
from typing import NamedTuple
from sqlalchemy import false
from galaxy import util
from galaxy.model.tool_shed_install import ToolShedRepository
from galaxy.tool_shed.util.repository_util import get_tool_shed_status_for_installed_repository
from galaxy.tool_shed.util.shed_util_common import clean_dependency_relationships
from galaxy.util.sleeper import Sleeper
from galaxy.util.tool_shed.common_util import get_tool_shed_url_from_tool_shed_registry
from galaxy.util.tool_shed.encoding_util import tool_shed_decode
log = logging.getLogger(__name__)
class UpdateToChangeset(NamedTuple):
changeset_revision: str
ctx_rev: str
class UpdateRepositoryManager:
def __init__(self, app):
self.app = app
@@ -28,9 +36,8 @@ class UpdateRepositoryManager:
self.app.application_stack.register_postfork_function(self.restarter.start)
self.seconds_to_sleep = int(app.config.hours_between_check * 3600)
def get_update_to_changeset_revision_and_ctx_rev(self, repository):
def get_update_to_changeset_revision_and_ctx_rev(self, repository: ToolShedRepository) -> UpdateToChangeset:
"""Return the changeset revision hash to which the repository can be updated."""
changeset_revision_dict = {}
tool_shed_url = get_tool_shed_url_from_tool_shed_registry(self.app, str(repository.tool_shed))
params = dict(
name=str(repository.name),
@@ -45,52 +52,19 @@ class UpdateRepositoryManager:
pathspec=pathspec,
params=params,
)
if encoded_update_dict:
update_dict = tool_shed_decode(encoded_update_dict)
includes_data_managers = update_dict.get("includes_data_managers", False)
includes_tools = update_dict.get("includes_tools", False)
includes_tools_for_display_in_tool_panel = update_dict.get(
"includes_tools_for_display_in_tool_panel", False
)
includes_tool_dependencies = update_dict.get("includes_tool_dependencies", False)
includes_workflows = update_dict.get("includes_workflows", False)
has_repository_dependencies = update_dict.get("has_repository_dependencies", False)
has_repository_dependencies_only_if_compiling_contained_td = update_dict.get(
"has_repository_dependencies_only_if_compiling_contained_td", False
)
changeset_revision = update_dict.get("changeset_revision", None)
ctx_rev = update_dict.get("ctx_rev", None)
changeset_revision_dict["includes_data_managers"] = includes_data_managers
changeset_revision_dict["includes_datatypes"] = False
changeset_revision_dict["includes_tools"] = includes_tools
changeset_revision_dict[
"includes_tools_for_display_in_tool_panel"
] = includes_tools_for_display_in_tool_panel
changeset_revision_dict["includes_tool_dependencies"] = includes_tool_dependencies
changeset_revision_dict["includes_workflows"] = includes_workflows
changeset_revision_dict["has_repository_dependencies"] = has_repository_dependencies
changeset_revision_dict[
"has_repository_dependencies_only_if_compiling_contained_td"
] = has_repository_dependencies_only_if_compiling_contained_td
changeset_revision_dict["changeset_revision"] = changeset_revision
changeset_revision_dict["ctx_rev"] = ctx_rev
update_dict = tool_shed_decode(encoded_update_dict)
changeset_revision = update_dict.get("changeset_revision", None)
ctx_rev = update_dict.get("ctx_rev", None)
except Exception as e:
log.debug(
f"Error getting change set revision for update from the tool shed for repository '{repository.name}': {str(e)}"
)
changeset_revision_dict["includes_data_managers"] = False
changeset_revision_dict["includes_datatypes"] = False
changeset_revision_dict["includes_tools"] = False
changeset_revision_dict["includes_tools_for_display_in_tool_panel"] = False
changeset_revision_dict["includes_tool_dependencies"] = False
changeset_revision_dict["includes_workflows"] = False
changeset_revision_dict["has_repository_dependencies"] = False
changeset_revision_dict["has_repository_dependencies_only_if_compiling_contained_td"] = False
changeset_revision_dict["changeset_revision"] = None
changeset_revision_dict["ctx_rev"] = None
return changeset_revision_dict
changeset_revision = None
ctx_rev = None
# restore_repository uses changeset_revision, ctx_rev
return UpdateToChangeset(changeset_revision, ctx_rev)
def __restarter(self):
def __restarter(self) -> None:
log.info("Update repository manager restarter starting up...")
while self.running:
# Make a call to the Tool Shed for each installed repository to get the latest
@@ -115,12 +89,14 @@ class UpdateRepositoryManager:
self.sleeper.sleep(self.seconds_to_sleep)
log.info("Update repository manager restarter shutting down...")
def shutdown(self):
def shutdown(self) -> None:
if self.app.config.enable_tool_shed_check:
self.running = False
self.sleeper.wake()
def update_repository_record(self, repository, updated_metadata_dict, updated_changeset_revision, updated_ctx_rev):
def update_repository_record(
self, repository: ToolShedRepository, updated_metadata_dict, updated_changeset_revision, updated_ctx_rev
) -> ToolShedRepository:
"""
Update a tool_shed_repository database record with new information retrieved from the
Tool Shed. This happens when updating an installed repository to a new changeset revision.
@@ -141,23 +117,3 @@ class UpdateRepositoryManager:
self.app.install_model.context.flush()
self.app.install_model.context.refresh(repository)
return repository
class Sleeper:
"""
Provides a 'sleep' method that sleeps for a number of seconds *unless* the notify method
is called (from a different thread).
"""
def __init__(self):
self.condition = threading.Condition()
def sleep(self, seconds):
self.condition.acquire()
self.condition.wait(seconds)
self.condition.release()
def wake(self):
self.condition.acquire()
self.condition.notify()
self.condition.release()
lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+3 -3
View File
@@ -113,11 +113,11 @@ class AdminToolshed(AdminGalaxy):
# repository dependencies and tool dependencies will be current. Only allow selecting a different section
# in the tool panel if the repository was uninstalled and it contained tools that should be displayed in
# the tool panel.
changeset_revision_dict = trans.app.update_repository_manager.get_update_to_changeset_revision_and_ctx_rev(
update_to_changeset = trans.app.update_repository_manager.get_update_to_changeset_revision_and_ctx_rev(
repository
)
current_changeset_revision = changeset_revision_dict.get("changeset_revision", None)
current_ctx_rev = changeset_revision_dict.get("ctx_rev", None)
current_changeset_revision = update_to_changeset.changeset_revision
current_ctx_rev = update_to_changeset.ctx_rev
if current_changeset_revision and current_ctx_rev:
if current_ctx_rev == repository.ctx_rev:
# The uninstalled repository is current.