Mercurial > repos > gga > apollo_export
view webapollo.py @ 15:b503fe85f261 draft
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 7f742b16e6e4c33b9abdb633405298e05760c84b"
author | gga |
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date | Tue, 08 Jun 2021 09:16:01 +0000 |
parents | c3b5bc8b4080 |
children | f6e09a37bc8b |
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from __future__ import print_function import argparse import collections import json import logging import os import time from abc import abstractmethod import requests from six.moves.builtins import next from six.moves.builtins import object import yaml logging.getLogger("requests").setLevel(logging.CRITICAL) log = logging.getLogger() ############################################# # 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 5 * 60 # 5 minute cache life ) userCache = TTLCache( 2, # Up to 2 items 60 # 1 minute cache life ) class UnknownUserException(Exception): pass def WAAuth(parser): parser.add_argument('apollo', help='Complete Apollo URL') parser.add_argument('username', help='WA Username') parser.add_argument('password', help='WA Password') def OrgOrGuess(parser): parser.add_argument('--org_json', type=argparse.FileType("r"), help='Apollo JSON output, source for common name') parser.add_argument('--org_raw', help='Common Name') parser.add_argument('--org_id', help='Organism ID') def CnOrGuess(parser): OrgOrGuess(parser) parser.add_argument('--seq_fasta', type=argparse.FileType("r"), help='Fasta file, IDs used as sequence sources') parser.add_argument('--seq_raw', nargs='*', help='Sequence Names') def AssertUser(user_list): if len(user_list) == 0: raise UnknownUserException() elif len(user_list) == 1: return user_list[0] else: raise Exception("Too many users!") class WebApolloInstance(object): def __init__(self): if 'ARROW_GLOBAL_CONFIG_PATH' in os.environ: with open(os.environ['ARROW_GLOBAL_CONFIG_PATH'], 'r') as config: conf = yaml.safe_load(config) try: instance_name = conf['__default'] except KeyError: raise Exception("Unknown Apollo instance and no __default provided") self.apollo_url = conf[instance_name]['url'] self.username = conf[instance_name]['username'] self.password = conf[instance_name]['password'] else: self.apollo_url = os.environ['GALAXY_WEBAPOLLO_URL'] self.username = os.environ['GALAXY_WEBAPOLLO_USER'] self.password = os.environ['GALAXY_WEBAPOLLO_PASSWORD'] self.groups = GroupsClient(self) self.organisms = OrganismsClient(self) self.users = UsersClient(self) def __str__(self): return '<WebApolloInstance at %s>' % self.apollo_url def requireUser(self, email): cacheKey = 'user-list' try: # Get the cached value data = userCache[cacheKey] except KeyError: # If we hit a key error above, indicating that # we couldn't find the key, we'll simply re-request # the data data = self.users.loadUsers() userCache[cacheKey] = data return AssertUser([x for x in data if x.username == email]) class GroupObj(object): def __init__(self, **kwargs): self.name = kwargs['name'] if 'id' in kwargs: self.groupId = kwargs['id'] class UserObj(object): ROLE_USER = 'USER' ROLE_ADMIN = 'ADMIN' def __init__(self, **kwargs): # Generally expect 'userId', 'firstName', 'lastName', 'username' (email) for attr in kwargs.keys(): setattr(self, attr, kwargs[attr]) if 'groups' in kwargs: groups = [] for groupData in kwargs['groups']: groups.append(GroupObj(**groupData)) self.groups = groups self.__props = kwargs.keys() def __str__(self): return '<User %s: %s %s <%s>>' % (self.userId, self.firstName, self.lastName, self.username) class Client(object): def __init__(self, webapolloinstance, **requestArgs): self._wa = webapolloinstance self.__verify = requestArgs.get('verify', True) self._requestArgs = requestArgs if 'verify' in self._requestArgs: del self._requestArgs['verify'] def request(self, clientMethod, data, post_params={}, isJson=True): url = self._wa.apollo_url + self.CLIENT_BASE + clientMethod headers = { 'Content-Type': 'application/json' } data.update({ 'username': self._wa.username, 'password': self._wa.password, }) r = requests.post(url, data=json.dumps(data), headers=headers, verify=self.__verify, params=post_params, allow_redirects=False, **self._requestArgs) if r.status_code == 200 or r.status_code == 302: if isJson: d = r.json() if 'username' in d: del d['username'] if 'password' in d: del d['password'] return d else: return r.text # @see self.body for HTTP response body raise Exception("Unexpected response from apollo %s: %s" % (r.status_code, r.text)) def get(self, clientMethod, get_params): url = self._wa.apollo_url + self.CLIENT_BASE + clientMethod headers = {} r = requests.get(url, headers=headers, verify=self.__verify, params=get_params, **self._requestArgs) if r.status_code == 200: d = r.json() if 'username' in d: del d['username'] if 'password' in d: del d['password'] return d # @see self.body for HTTP response body raise Exception("Unexpected response from apollo %s: %s" % (r.status_code, r.text)) class GroupsClient(Client): CLIENT_BASE = '/group/' def loadGroups(self, group=None): res = self.request('loadGroups', {}) data = [GroupObj(**x) for x in res] if group is not None: data = [x for x in data if x.name == group] return data class OrganismsClient(Client): CLIENT_BASE = '/organism/' def findAllOrganisms(self): orgs = self.request('findAllOrganisms', {}) if not isinstance(orgs, (list,)): orgs = [] return orgs class UsersClient(Client): CLIENT_BASE = '/user/' def loadUsers(self): res = self.request('loadUsers', {}) data = [UserObj(**x) for x in res] return data def handle_credentials(user): if hasattr(user, 'new_password'): f = open("Apollo_credentials.txt", "w") f.write('Username:\t%s\nPassword:\t%s' % (user.username, user.new_password)) def accessible_organisms(user, orgs): permissionMap = { x['organism']: x['permissions'] for x in user.organismPermissions if 'WRITE' in x['permissions'] or 'READ' in x['permissions'] or 'ADMINISTRATE' in x['permissions'] or user.role == 'ADMIN' } if 'error' in orgs: raise Exception("Error received from Apollo server: \"%s\"" % orgs['error']) return [ (org['commonName'], org['id'], False) for org in sorted(orgs, key=lambda x: x['commonName']) if org['commonName'] in permissionMap ] def galaxy_list_groups(trans, *args, **kwargs): email = trans.get_user().email wa = WebApolloInstance() # Key for cached data cacheKey = 'groups-' + email # 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 = _galaxy_list_groups(wa, *args, **kwargs) cache[cacheKey] = data 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] return data except KeyError: # If access fails due to eviction, we will fail over and can ensure that # data is inserted. data = _galaxy_list_groups(wa, *args, **kwargs) cache[cacheKey] = data return data def _galaxy_list_groups(wa, *args, **kwargs): # Fetch the groups. group_data = [] for group in wa.groups.loadGroups(): # Reformat group_data.append((group.name, group.name, False)) return group_data def galaxy_list_orgs(trans, *args, **kwargs): email = trans.get_user().email wa = WebApolloInstance() try: gx_user = wa.requireUser(email) except UnknownUserException: return [] # Key for cached data cacheKey = 'orgs-' + email if cacheKey not in cache: data = _galaxy_list_orgs(wa, gx_user, *args, **kwargs) cache[cacheKey] = data return data try: data = cache[cacheKey] return data except KeyError: data = _galaxy_list_orgs(wa, gx_user, *args, **kwargs) cache[cacheKey] = data return data def _galaxy_list_orgs(wa, gx_user, *args, **kwargs): # Fetch all organisms all_orgs = wa.organisms.findAllOrganisms() # Figure out which are accessible to the user orgs = accessible_organisms(gx_user, all_orgs) # Return org list return orgs # This is all for implementing the command line interface for testing. class obj(object): pass class fakeTrans(object): def __init__(self, username): self.un = username def get_user(self): o = obj() o.email = self.un return o if __name__ == '__main__': parser = argparse.ArgumentParser(description='Test access to apollo server') parser.add_argument('email', help='Email of user to test') parser.add_argument('--action', choices=['org', 'group'], default='org', help='Data set to test, fetch a list of groups or orgs known to the requesting user.') args = parser.parse_args() trans = fakeTrans(args.email) if args.action == 'org': print(galaxy_list_orgs(trans)) elif args.action == 'group': print(galaxy_list_groups(trans))