Source code for galaxy.tool_shed.galaxy_install.update_repository_manager

"""
Determine if installed tool shed repositories have updates available in their respective tool sheds.
"""
import logging
import threading

from sqlalchemy import false

from galaxy import util
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.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__)


[docs]class UpdateRepositoryManager:
[docs]    def __init__(self, app):
        self.app = app
        self.context = self.app.install_model.context
        # Ideally only one Galaxy server process should be able to check for repository updates.
        if self.app.config.enable_tool_shed_check:
            self.running = True
            self.sleeper = Sleeper()
            self.restarter = threading.Thread(target=self.__restarter)
            self.restarter.daemon = True
            self.app.application_stack.register_postfork_function(self.restarter.start)
            self.seconds_to_sleep = int(app.config.hours_between_check * 3600)

[docs]    def get_update_to_changeset_revision_and_ctx_rev(self, repository):
        """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),
            owner=str(repository.owner),
            changeset_revision=str(repository.installed_changeset_revision),
        )
        pathspec = ["repository", "get_changeset_revision_and_ctx_rev"]
        try:
            encoded_update_dict = util.url_get(
                tool_shed_url,
                auth=self.app.tool_shed_registry.url_auth(tool_shed_url),
                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_datatypes = update_dict.get("includes_datatypes", 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"] = includes_datatypes
            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
        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

    def __restarter(self):
        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
            # status information in the Tool Shed for the repository.  This information includes
            # items like newer installable repository revisions, current revision updates, whether
            # the repository revision is the latest installable revision, and whether the repository
            # has been deprecated in the Tool Shed.
            for repository in self.context.query(self.app.install_model.ToolShedRepository).filter(
                self.app.install_model.ToolShedRepository.table.c.deleted == false()
            ):
                tool_shed_status_dict = get_tool_shed_status_for_installed_repository(self.app, repository)
                if tool_shed_status_dict:
                    if tool_shed_status_dict != repository.tool_shed_status:
                        repository.tool_shed_status = tool_shed_status_dict
                        self.context.flush()
                else:
                    # The received tool_shed_status_dict is an empty dictionary, so coerce to None.
                    tool_shed_status_dict = None
                    if tool_shed_status_dict != repository.tool_shed_status:
                        repository.tool_shed_status = tool_shed_status_dict
                        self.context.flush()
            self.sleeper.sleep(self.seconds_to_sleep)
        log.info("Update repository manager restarter shutting down...")

[docs]    def shutdown(self):
        if self.app.config.enable_tool_shed_check:
            self.running = False
            self.sleeper.wake()

[docs]    def update_repository_record(self, repository, updated_metadata_dict, updated_changeset_revision, updated_ctx_rev):
        """
        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.
        """
        repository.metadata_ = updated_metadata_dict
        tool_shed_url = get_tool_shed_url_from_tool_shed_registry(self.app, repository.tool_shed)
        clean_dependency_relationships(self.app, updated_metadata_dict, repository, tool_shed_url)
        # Update the repository.changeset_revision column in the database.
        repository.changeset_revision = updated_changeset_revision
        repository.ctx_rev = updated_ctx_rev
        # Update the repository.tool_shed_status column in the database.
        tool_shed_status_dict = get_tool_shed_status_for_installed_repository(self.app, repository)
        if tool_shed_status_dict:
            repository.tool_shed_status = tool_shed_status_dict
        else:
            repository.tool_shed_status = None
        self.app.install_model.context.add(repository)
        self.app.install_model.context.flush()
        self.app.install_model.context.refresh(repository)
        return repository


[docs]class Sleeper:
    """
    Provides a 'sleep' method that sleeps for a number of seconds *unless* the notify method
    is called (from a different thread).
    """

[docs]    def __init__(self):
        self.condition = threading.Condition()

[docs]    def sleep(self, seconds):
        self.condition.acquire()
        self.condition.wait(seconds)
        self.condition.release()

[docs]    def wake(self):
        self.condition.acquire()
        self.condition.notify()
        self.condition.release()