This document is for an old release of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

Source code for galaxy.tools.cache

import json
import logging
import os
import shutil
import sqlite3
import tempfile
import zlib
from threading import Lock
from typing import (

from sqlitedict import SqliteDict

from galaxy.util import unicodify
from galaxy.util.hash_util import md5_hash_file

log = logging.getLogger(__name__)


[docs]def encoder(obj): return sqlite3.Binary(zlib.compress(json.dumps(obj).encode("utf-8")))
[docs]def decoder(obj): return json.loads(zlib.decompress(bytes(obj)).decode("utf-8"))
[docs]class ToolDocumentCache:
[docs] def __init__(self, cache_dir): self.cache_dir = cache_dir if not os.path.exists(self.cache_dir): os.makedirs(self.cache_dir) self.cache_file = os.path.join(self.cache_dir, "cache.sqlite") self.writeable_cache_file = None self._cache = None self.disabled = False self._get_cache(create_if_necessary=True)
[docs] def close(self): self._cache and self._cache.close()
def _get_cache(self, flag="r", create_if_necessary=False): try: if create_if_necessary and not os.path.exists(self.cache_file): # Create database if necessary using 'c' flag self._cache = SqliteDict(self.cache_file, flag="c", encode=encoder, decode=decoder, autocommit=False) if flag == "r": self._cache.flag = flag else: cache_file = self.writeable_cache_file.name if self.writeable_cache_file else self.cache_file self._cache = SqliteDict(cache_file, flag=flag, encode=encoder, decode=decoder, autocommit=False) except (sqlite3.OperationalError, RuntimeError): log.warning("Tool document cache unavailable") self._cache = None self.disabled = True @property def cache_file_is_writeable(self): return os.access(self.cache_file, os.W_OK)
[docs] def reopen_ro(self): self._get_cache(flag="r") self.writeable_cache_file = None
[docs] def get(self, config_file): try: tool_document = self._cache.get(config_file) except sqlite3.OperationalError: log.debug("Tool document cache unavailable") return None if not tool_document: return None if tool_document.get("tool_cache_version") != CURRENT_TOOL_CACHE_VERSION: return None if self.cache_file_is_writeable: for path, modtime in tool_document["paths_and_modtimes"].items(): if os.path.getmtime(path) != modtime: return None return tool_document
def _make_writable(self): if not self.writeable_cache_file: self.writeable_cache_file = tempfile.NamedTemporaryFile( dir=self.cache_dir, suffix="cache.sqlite.tmp", delete=False ) if os.path.exists(self.cache_file): shutil.copy(self.cache_file, self.writeable_cache_file.name) self._get_cache(flag="c")
[docs] def persist(self): if self.writeable_cache_file: self._cache.commit() os.rename(self.writeable_cache_file.name, self.cache_file) self.reopen_ro()
[docs] def set(self, config_file, tool_source): try: if self.cache_file_is_writeable: self._make_writable() to_persist = { "document": tool_source.to_string(), "macro_paths": tool_source.macro_paths, "paths_and_modtimes": tool_source.paths_and_modtimes(), "tool_cache_version": CURRENT_TOOL_CACHE_VERSION, } try: self._cache[config_file] = to_persist except RuntimeError: log.debug("Tool document cache not writeable") except sqlite3.OperationalError: log.debug("Tool document cache unavailable")
[docs] def delete(self, config_file): if self.cache_file_is_writeable: self._make_writable() try: del self._cache[config_file] except (KeyError, RuntimeError): pass
def __del__(self): if self.writeable_cache_file: try: os.unlink(self.writeable_cache_file.name) except Exception: pass
[docs]class ToolCache: """ Cache tool definitions to allow quickly reloading the whole toolbox. """
[docs] def __init__(self): self._lock = Lock() self._hash_by_tool_paths: Dict[str, ToolHash] = {} self._tools_by_path = {} self._tool_paths_by_id = {} self._macro_paths_by_id = {} self._new_tool_ids = set() self._removed_tool_ids = set() self._removed_tools_by_path = {} self._hashes_initialized = False
[docs] def assert_hashes_initialized(self): if not self._hashes_initialized: for tool_hash in self._hash_by_tool_paths.values(): tool_hash.hash # noqa: B018 self._hashes_initialized = True
[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: persist_tool_document_cache = False paths_to_cleanup = { (path, tool) for path, tool in self._tools_by_path.items() if self._should_cleanup(path) } for config_filename, tool in paths_to_cleanup: tool.remove_from_cache() persist_tool_document_cache = True 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] tool_ids = tool.all_ids 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) if persist_tool_document_cache: tool.app.toolbox.persist_cache() 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. if removed_tool_ids: log.debug(f"Removed the following tools from cache: {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.""" try: new_mtime = os.path.getmtime(config_filename) tool_hash = self._hash_by_tool_paths.get(config_filename) if tool_hash and tool_hash.modtime_less_than(new_mtime): if not tool_hash.hash_equals(md5_hash_file(config_filename)): return True else: # No change of content, so not necessary to calculate the md5 checksum every time tool_hash.modtime = new_mtime tool = self._tools_by_path[config_filename] for macro_path in tool._macro_paths: new_mtime = os.path.getmtime(macro_path) if self._hash_by_tool_paths.get(macro_path).modtime < new_mtime: return True except FileNotFoundError: 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] if tool_id in self._new_tool_ids: self._new_tool_ids.remove(tool_id)
[docs] def cache_tool(self, config_filename, tool): tool_id = str(tool.id) # We defer hashing of the config file if we haven't called assert_hashes_initialized. # This allows startup to occur without having to read in and hash all tool and macro files lazy_hash = not self._hashes_initialized with self._lock: self._hash_by_tool_paths[config_filename] = ToolHash(config_filename, lazy_hash=lazy_hash) 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._hash_by_tool_paths[macro_path] = ToolHash(macro_path, lazy_hash=lazy_hash) 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 ToolHash:
[docs] def __init__(self, path: str, modtime: Optional[float] = None, lazy_hash: bool = False): self.path = path self._modtime = modtime or os.path.getmtime(path) self._tool_hash = None if not lazy_hash: self.hash # noqa: B018
[docs] def modtime_less_than(self, other_modtime: float): if self._modtime is None: # For the purposes of the tool cache, # if we haven't seen the modtime we consider it not equal return True return self._modtime < other_modtime
[docs] def hash_equals(self, other_hash: Optional[str]): if self._tool_hash is None or other_hash is None: # For the purposes of the tool cache, # if we haven't seen the hash yet we consider it not equal return False return self.hash == other_hash
@property def modtime(self) -> float: if self._modtime is None: self._modtime = os.path.getmtime(self.path) return self._modtime @modtime.setter def modtime(self, new_value: float): self._modtime = new_value @property def hash(self): if self._tool_hash is None: self._tool_hash = md5_hash_file(self.path) return self._tool_hash