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Source code for galaxy.tools.cache
import logging
import os
from threading import (
local,
Lock,
)
from sqlalchemy import inspect
from sqlalchemy.orm.exc import DetachedInstanceError
from galaxy.util import unicodify
from galaxy.util.hash_util import md5_hash_file
log = logging.getLogger(__name__)
[docs]class ToolCache(object):
"""
Cache tool definitions to allow quickly reloading the whole
toolbox.
"""
[docs] def __init__(self):
self._lock = Lock()
self._hash_by_tool_paths = {}
self._tools_by_path = {}
self._tool_paths_by_id = {}
self._macro_paths_by_id = {}
self._mod_time_by_path = {}
self._new_tool_ids = set()
self._removed_tool_ids = set()
self._removed_tools_by_path = {}
[docs] def cleanup(self):
"""
Remove uninstalled tools from tool cache if they are not on disk anymore or if their content has changed.
Returns list of tool_ids that have been removed.
"""
removed_tool_ids = []
try:
with self._lock:
paths_to_cleanup = {path: tool.all_ids for path, tool in self._tools_by_path.items() if self._should_cleanup(path)}
for config_filename, tool_ids in paths_to_cleanup.items():
del self._hash_by_tool_paths[config_filename]
if os.path.exists(config_filename):
# This tool has probably been broken while editing on disk
# We record it here, so that we can recover it
self._removed_tools_by_path[config_filename] = self._tools_by_path[config_filename]
del self._tools_by_path[config_filename]
for tool_id in tool_ids:
if tool_id in self._tool_paths_by_id:
del self._tool_paths_by_id[tool_id]
removed_tool_ids.extend(tool_ids)
for tool_id in removed_tool_ids:
self._removed_tool_ids.add(tool_id)
if tool_id in self._new_tool_ids:
self._new_tool_ids.remove(tool_id)
except Exception as e:
log.debug("Exception while checking tools to remove from cache: %s", unicodify(e))
# If by chance the file is being removed while calculating the hash or modtime
# we don't want the thread to die.
pass
if removed_tool_ids:
log.debug("Removed the following tools from cache: %s" % removed_tool_ids)
return removed_tool_ids
def _should_cleanup(self, config_filename):
"""Return True if `config_filename` does not exist or if modtime and hash have changes, else return False."""
if not os.path.exists(config_filename):
return True
new_mtime = os.path.getmtime(config_filename)
if self._mod_time_by_path.get(config_filename) < new_mtime:
if md5_hash_file(config_filename) != self._hash_by_tool_paths.get(config_filename):
return True
tool = self._tools_by_path[config_filename]
for macro_path in tool._macro_paths:
new_mtime = os.path.getmtime(macro_path)
if self._mod_time_by_path.get(macro_path) < new_mtime:
return True
return False
[docs] def get_tool(self, config_filename):
"""Get the tool at `config_filename` from the cache if the tool is up to date."""
return self._tools_by_path.get(config_filename, None)
[docs] def get_removed_tool(self, config_filename):
return self._removed_tools_by_path.get(config_filename)
[docs] def get_tool_by_id(self, tool_id):
"""Get the tool with the id `tool_id` from the cache if the tool is up to date. """
return self.get_tool(self._tool_paths_by_id.get(tool_id))
[docs] def expire_tool(self, tool_id):
with self._lock:
if tool_id in self._tool_paths_by_id:
config_filename = self._tool_paths_by_id[tool_id]
del self._hash_by_tool_paths[config_filename]
del self._tool_paths_by_id[tool_id]
del self._tools_by_path[config_filename]
del self._mod_time_by_path[config_filename]
if tool_id in self._new_tool_ids:
self._new_tool_ids.remove(tool_id)
[docs] def cache_tool(self, config_filename, tool):
tool_hash = md5_hash_file(config_filename)
if tool_hash is None:
return
tool_id = str(tool.id)
with self._lock:
self._hash_by_tool_paths[config_filename] = tool_hash
self._mod_time_by_path[config_filename] = os.path.getmtime(config_filename)
self._tool_paths_by_id[tool_id] = config_filename
self._tools_by_path[config_filename] = tool
self._new_tool_ids.add(tool_id)
for macro_path in tool._macro_paths:
self._mod_time_by_path[macro_path] = os.path.getmtime(macro_path)
if tool_id not in self._macro_paths_by_id:
self._macro_paths_by_id[tool_id] = {macro_path}
else:
self._macro_paths_by_id[tool_id].add(macro_path)
[docs] def reset_status(self):
"""
Reset tracking of new and newly disabled tools.
"""
with self._lock:
self._new_tool_ids = set()
self._removed_tool_ids = set()
self._removed_tools_by_path = {}
[docs]class ToolShedRepositoryCache(object):
"""
Cache installed ToolShedRepository objects.
"""
@property
def tool_shed_repositories(self):
try:
repositories = self.cache.repositories
except AttributeError:
self.rebuild()
repositories = self.cache.repositories
tool_shed_repositories = [repo for repo in repositories if isinstance(repo, self.app.install_model.ToolShedRepository)]
if tool_shed_repositories and inspect(tool_shed_repositories[0]).detached:
self.rebuild()
repositories = self.cache.repositories
return repositories
[docs] def rebuild(self):
self.cache.repositories = self.app.install_model.context.current.query(self.app.install_model.ToolShedRepository).all()
[docs] def get_installed_repository(self, tool_shed=None, name=None, owner=None, installed_changeset_revision=None, changeset_revision=None, repository_id=None):
try:
return self._get_installed_repository(tool_shed=tool_shed,
name=name,
owner=owner,
installed_changeset_revision=installed_changeset_revision,
changeset_revision=changeset_revision,
repository_id=repository_id)
except DetachedInstanceError:
self.rebuild()
return self._get_installed_repository(tool_shed=tool_shed,
name=name,
owner=owner,
installed_changeset_revision=installed_changeset_revision,
changeset_revision=changeset_revision,
repository_id=repository_id)
def _get_installed_repository(self, tool_shed=None, name=None, owner=None, installed_changeset_revision=None, changeset_revision=None, repository_id=None):
if repository_id:
repos = [repo for repo in self.tool_shed_repositories if repo.id == repository_id]
if repos:
return repos[0]
else:
return None
repos = [repo for repo in self.tool_shed_repositories if repo.tool_shed == tool_shed and repo.owner == owner and repo.name == name]
if installed_changeset_revision:
repos = [repo for repo in repos if repo.installed_changeset_revision == installed_changeset_revision]
if changeset_revision:
repos = [repo for repo in repos if repo.changeset_revision == changeset_revision]
if repos:
return repos[0]
else:
return None