Mercurial > repos > gga > chado_expression_add_biomaterial
view chado.py @ 2:ecf81582c5cc draft
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit f5c5d81fc9781371e12b91c0d609b9201587cda5
author | gga |
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date | Fri, 23 Nov 2018 11:14:54 -0500 |
parents | 676c49ac9cb5 |
children | 04bdb1e66a27 |
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import collections import os import time from abc import abstractmethod import chado ############################################# # BEGIN IMPORT OF CACHING LIBRARY # ############################################# # This code is licensed under the MIT # # License and is a copy of code publicly # # available in rev. # # e27332bc82f4e327aedaec17c9b656ae719322ed # # of https://github.com/tkem/cachetools/ # ############################################# class DefaultMapping(collections.MutableMapping): __slots__ = () @abstractmethod def __contains__(self, key): # pragma: nocover return False @abstractmethod def __getitem__(self, key): # pragma: nocover if hasattr(self.__class__, '__missing__'): return self.__class__.__missing__(self, key) else: raise KeyError(key) def get(self, key, default=None): if key in self: return self[key] else: return default __marker = object() def pop(self, key, default=__marker): if key in self: value = self[key] del self[key] elif default is self.__marker: raise KeyError(key) else: value = default return value def setdefault(self, key, default=None): if key in self: value = self[key] else: self[key] = value = default return value DefaultMapping.register(dict) class _DefaultSize(object): def __getitem__(self, _): return 1 def __setitem__(self, _, value): assert value == 1 def pop(self, _): return 1 class Cache(DefaultMapping): """Mutable mapping to serve as a simple cache or cache base class.""" __size = _DefaultSize() def __init__(self, maxsize, missing=None, getsizeof=None): if missing: self.__missing = missing if getsizeof: self.__getsizeof = getsizeof self.__size = dict() self.__data = dict() self.__currsize = 0 self.__maxsize = maxsize def __repr__(self): return '%s(%r, maxsize=%r, currsize=%r)' % ( self.__class__.__name__, list(self.__data.items()), self.__maxsize, self.__currsize, ) def __getitem__(self, key): try: return self.__data[key] except KeyError: return self.__missing__(key) def __setitem__(self, key, value): maxsize = self.__maxsize size = self.getsizeof(value) if size > maxsize: raise ValueError('value too large') if key not in self.__data or self.__size[key] < size: while self.__currsize + size > maxsize: self.popitem() if key in self.__data: diffsize = size - self.__size[key] else: diffsize = size self.__data[key] = value self.__size[key] = size self.__currsize += diffsize def __delitem__(self, key): size = self.__size.pop(key) del self.__data[key] self.__currsize -= size def __contains__(self, key): return key in self.__data def __missing__(self, key): value = self.__missing(key) try: self.__setitem__(key, value) except ValueError: pass # value too large return value def __iter__(self): return iter(self.__data) def __len__(self): return len(self.__data) @staticmethod def __getsizeof(value): return 1 @staticmethod def __missing(key): raise KeyError(key) @property def maxsize(self): """The maximum size of the cache.""" return self.__maxsize @property def currsize(self): """The current size of the cache.""" return self.__currsize def getsizeof(self, value): """Return the size of a cache element's value.""" return self.__getsizeof(value) class _Link(object): __slots__ = ('key', 'expire', 'next', 'prev') def __init__(self, key=None, expire=None): self.key = key self.expire = expire def __reduce__(self): return _Link, (self.key, self.expire) def unlink(self): next = self.next prev = self.prev prev.next = next next.prev = prev class _Timer(object): def __init__(self, timer): self.__timer = timer self.__nesting = 0 def __call__(self): if self.__nesting == 0: return self.__timer() else: return self.__time def __enter__(self): if self.__nesting == 0: self.__time = time = self.__timer() else: time = self.__time self.__nesting += 1 return time def __exit__(self, *exc): self.__nesting -= 1 def __reduce__(self): return _Timer, (self.__timer,) def __getattr__(self, name): return getattr(self.__timer, name) class TTLCache(Cache): """LRU Cache implementation with per-item time-to-live (TTL) value.""" def __init__(self, maxsize, ttl, timer=time.time, missing=None, getsizeof=None): Cache.__init__(self, maxsize, missing, getsizeof) self.__root = root = _Link() root.prev = root.next = root self.__links = collections.OrderedDict() self.__timer = _Timer(timer) self.__ttl = ttl def __contains__(self, key): try: link = self.__links[key] # no reordering except KeyError: return False else: return not (link.expire < self.__timer()) def __getitem__(self, key, cache_getitem=Cache.__getitem__): try: link = self.__getlink(key) except KeyError: expired = False else: expired = link.expire < self.__timer() if expired: return self.__missing__(key) else: return cache_getitem(self, key) def __setitem__(self, key, value, cache_setitem=Cache.__setitem__): with self.__timer as time: self.expire(time) cache_setitem(self, key, value) try: link = self.__getlink(key) except KeyError: self.__links[key] = link = _Link(key) else: link.unlink() link.expire = time + self.__ttl link.next = root = self.__root link.prev = prev = root.prev prev.next = root.prev = link def __delitem__(self, key, cache_delitem=Cache.__delitem__): cache_delitem(self, key) link = self.__links.pop(key) link.unlink() if link.expire < self.__timer(): raise KeyError(key) def __iter__(self): root = self.__root curr = root.next while curr is not root: # "freeze" time for iterator access with self.__timer as time: if not (curr.expire < time): yield curr.key curr = curr.next def __len__(self): root = self.__root curr = root.next time = self.__timer() count = len(self.__links) while curr is not root and curr.expire < time: count -= 1 curr = curr.next return count def __setstate__(self, state): self.__dict__.update(state) root = self.__root root.prev = root.next = root for link in sorted(self.__links.values(), key=lambda obj: obj.expire): link.next = root link.prev = prev = root.prev prev.next = root.prev = link self.expire(self.__timer()) def __repr__(self, cache_repr=Cache.__repr__): with self.__timer as time: self.expire(time) return cache_repr(self) @property def currsize(self): with self.__timer as time: self.expire(time) return super(TTLCache, self).currsize @property def timer(self): """The timer function used by the cache.""" return self.__timer @property def ttl(self): """The time-to-live value of the cache's items.""" return self.__ttl def expire(self, time=None): """Remove expired items from the cache.""" if time is None: time = self.__timer() root = self.__root curr = root.next links = self.__links cache_delitem = Cache.__delitem__ while curr is not root and curr.expire < time: cache_delitem(self, curr.key) del links[curr.key] next = curr.next curr.unlink() curr = next def clear(self): with self.__timer as time: self.expire(time) Cache.clear(self) def get(self, *args, **kwargs): with self.__timer: return Cache.get(self, *args, **kwargs) def pop(self, *args, **kwargs): with self.__timer: return Cache.pop(self, *args, **kwargs) def setdefault(self, *args, **kwargs): with self.__timer: return Cache.setdefault(self, *args, **kwargs) def popitem(self): """Remove and return the `(key, value)` pair least recently used that has not already expired. """ with self.__timer as time: self.expire(time) try: key = next(iter(self.__links)) except StopIteration: raise KeyError('%s is empty' % self.__class__.__name__) else: return (key, self.pop(key)) if hasattr(collections.OrderedDict, 'move_to_end'): def __getlink(self, key): value = self.__links[key] self.__links.move_to_end(key) return value else: def __getlink(self, key): value = self.__links.pop(key) self.__links[key] = value return value ############################################# # END IMPORT OF CACHING LIBRARY # ############################################# cache = TTLCache( 100, # Up to 100 items 1 * 60 # 5 minute cache life ) def _get_instance(): return chado.ChadoInstance( os.environ['GALAXY_CHADO_DBHOST'], os.environ['GALAXY_CHADO_DBNAME'], os.environ['GALAXY_CHADO_DBUSER'], os.environ['GALAXY_CHADO_DBPASS'], os.environ['GALAXY_CHADO_DBSCHEMA'], os.environ['GALAXY_CHADO_DBPORT'], no_reflect=True ) def list_organisms(*args, **kwargs): ci = _get_instance() # Key for cached data cacheKey = 'orgs' # We don't want to trust "if key in cache" because between asking and fetch # it might through key error. if cacheKey not in cache: # However if it ISN'T there, we know we're safe to fetch + put in # there. data = _list_organisms(ci, *args, **kwargs) cache[cacheKey] = data ci.session.close() return data try: # The cache key may or may not be in the cache at this point, it # /likely/ is. However we take no chances that it wasn't evicted between # when we checked above and now, so we reference the object from the # cache in preparation to return. data = cache[cacheKey] ci.session.close() return data except KeyError: # If access fails due to eviction, we will fail over and can ensure that # data is inserted. data = _list_organisms(ci, *args, **kwargs) cache[cacheKey] = data ci.session.close() return data def _list_organisms(ci, *args, **kwargs): # Fetch the orgs. orgs_data = [] for org in ci.organism.get_organisms(): clean_name = '%s %s' % (org['genus'], org['species']) if 'infraspecific_name' in org and org['infraspecific_name']: clean_name += ' (%s)' % (org['infraspecific_name']) orgs_data.append((clean_name, str(org['organism_id']), False)) return orgs_data def list_analyses(*args, **kwargs): ci = _get_instance() # Key for cached data cacheKey = 'analyses' # We don't want to trust "if key in cache" because between asking and fetch # it might through key error. if cacheKey not in cache: # However if it ISN'T there, we know we're safe to fetch + put in # there.<?xml version="1.0"?> data = _list_analyses(ci, *args, **kwargs) cache[cacheKey] = data ci.session.close() return data try: # The cache key may or may not be in the cache at this point, it # /likely/ is. However we take no chances that it wasn't evicted between # when we checked above and now, so we reference the object from the # cache in preparation to return. data = cache[cacheKey] ci.session.close() return data except KeyError: # If access fails due to eviction, we will fail over and can ensure that # data is inserted. data = _list_analyses(ci, *args, **kwargs) cache[cacheKey] = data ci.session.close() return data def _list_analyses(ci, *args, **kwargs): ans_data = [] for an in ci.analysis.get_analyses(): ans_data.append((an['name'], str(an['analysis_id']), False)) return ans_data