Module arvados.keep
Classes
class Counter (v=0)-
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class Counter(object): def __init__(self, v=0): self._lk = threading.Lock() self._val = v def add(self, v): with self._lk: self._val += v def get(self): with self._lk: return self._valMethods
def add(self, v)def get(self)
class Keep-
Simple interface to a global KeepClient object.
THIS CLASS IS DEPRECATED. Please instantiate your own KeepClient with your own API client. The global KeepClient will build an API client from the current Arvados configuration, which may not match the one you built.
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class Keep(object): """Simple interface to a global KeepClient object. THIS CLASS IS DEPRECATED. Please instantiate your own KeepClient with your own API client. The global KeepClient will build an API client from the current Arvados configuration, which may not match the one you built. """ _last_key = None @classmethod def global_client_object(cls): global global_client_object # Previously, KeepClient would change its behavior at runtime based # on these configuration settings. We simulate that behavior here # by checking the values and returning a new KeepClient if any of # them have changed. key = (config.get('ARVADOS_API_HOST'), config.get('ARVADOS_API_TOKEN'), config.flag_is_true('ARVADOS_API_HOST_INSECURE'), config.get('ARVADOS_KEEP_PROXY'), os.environ.get('KEEP_LOCAL_STORE')) if (global_client_object is None) or (cls._last_key != key): global_client_object = KeepClient() cls._last_key = key return global_client_object @staticmethod def get(locator, **kwargs): return Keep.global_client_object().get(locator, **kwargs) @staticmethod def put(data, **kwargs): return Keep.global_client_object().put(data, **kwargs)Static methods
def get(locator, **kwargs)def global_client_object()def put(data, **kwargs)
class KeepBlockCache (cache_max=0, max_slots=0, disk_cache=False, disk_cache_dir=None)-
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class KeepBlockCache(object): def __init__(self, cache_max=0, max_slots=0, disk_cache=False, disk_cache_dir=None): self.cache_max = cache_max self._cache = [] self._cache_lock = threading.Lock() self._max_slots = max_slots self._disk_cache = disk_cache self._disk_cache_dir = disk_cache_dir self._cache_updating = threading.Condition(self._cache_lock) if self._disk_cache and self._disk_cache_dir is None: self._disk_cache_dir = os.path.join(os.path.expanduser("~"), ".cache", "arvados", "keep") os.makedirs(self._disk_cache_dir, mode=0o700, exist_ok=True) if self._max_slots == 0: if self._disk_cache: # Each block uses two file descriptors, one used to # open it initially and hold the flock(), and a second # hidden one used by mmap(). # # Set max slots to 1/8 of maximum file handles. This # means we'll use at most 1/4 of total file handles. # # NOFILE typically defaults to 1024 on Linux so this # is 128 slots (256 file handles), which means we can # cache up to 8 GiB of 64 MiB blocks. This leaves # 768 file handles for sockets and other stuff. # # When we want the ability to have more cache (e.g. in # arv-mount) we'll increase rlimit before calling # this. self._max_slots = int(resource.getrlimit(resource.RLIMIT_NOFILE)[0] / 8) else: # RAM cache slots self._max_slots = 512 if self.cache_max == 0: if self._disk_cache: fs = os.statvfs(self._disk_cache_dir) # Calculation of available space incorporates existing cache usage existing_usage = arvados.diskcache.DiskCacheSlot.cache_usage(self._disk_cache_dir) avail = (fs.f_bavail * fs.f_bsize + existing_usage) / 4 maxdisk = int((fs.f_blocks * fs.f_bsize) * 0.10) # pick smallest of: # 10% of total disk size # 25% of available space # max_slots * 64 MiB self.cache_max = min(min(maxdisk, avail), (self._max_slots * 64 * 1024 * 1024)) else: # 256 MiB in RAM self.cache_max = (256 * 1024 * 1024) self.cache_max = max(self.cache_max, 64 * 1024 * 1024) if self._disk_cache: self._cache = arvados.diskcache.DiskCacheSlot.init_cache(self._disk_cache_dir, self._max_slots) self.cap_cache() class CacheSlot(object): __slots__ = ("locator", "ready", "content") def __init__(self, locator): self.locator = locator self.ready = threading.Event() self.content = None def get(self): self.ready.wait() return self.content def set(self, value): self.content = value self.ready.set() def size(self): if self.content is None: return 0 else: return len(self.content) def evict(self): self.content = None return self.gone() def gone(self): return (self.content is None) def _resize_cache(self, cache_max, max_slots): # Try and make sure the contents of the cache do not exceed # the supplied maximums. # Select all slots except those where ready.is_set() and content is # None (that means there was an error reading the block). self._cache = [c for c in self._cache if not (c.ready.is_set() and c.content is None)] sm = sum([slot.size() for slot in self._cache]) while len(self._cache) > 0 and (sm > cache_max or len(self._cache) > max_slots): for i in range(len(self._cache)-1, -1, -1): # start from the back, find a slot that is a candidate to evict if self._cache[i].ready.is_set(): sz = self._cache[i].size() # If evict returns false it means the # underlying disk cache couldn't lock the file # for deletion because another process was using # it. Don't count it as reducing the amount # of data in the cache, find something else to # throw out. if self._cache[i].evict(): sm -= sz # check to make sure the underlying data is gone if self._cache[i].gone(): # either way we forget about it. either the # other process will delete it, or if we need # it again and it is still there, we'll find # it on disk. del self._cache[i] break def cap_cache(self): '''Cap the cache size to self.cache_max''' with self._cache_updating: self._resize_cache(self.cache_max, self._max_slots) self._cache_updating.notify_all() def _get(self, locator): # Test if the locator is already in the cache for i in range(0, len(self._cache)): if self._cache[i].locator == locator: n = self._cache[i] if i != 0: # move it to the front del self._cache[i] self._cache.insert(0, n) return n if self._disk_cache: # see if it exists on disk n = arvados.diskcache.DiskCacheSlot.get_from_disk(locator, self._disk_cache_dir) if n is not None: self._cache.insert(0, n) return n return None def get(self, locator): with self._cache_lock: return self._get(locator) def reserve_cache(self, locator): '''Reserve a cache slot for the specified locator, or return the existing slot.''' with self._cache_updating: n = self._get(locator) if n: return n, False else: # Add a new cache slot for the locator self._resize_cache(self.cache_max, self._max_slots-1) while len(self._cache) >= self._max_slots: # If there isn't a slot available, need to wait # for something to happen that releases one of the # cache slots. Idle for 200 ms or woken up by # another thread self._cache_updating.wait(timeout=0.2) self._resize_cache(self.cache_max, self._max_slots-1) if self._disk_cache: n = arvados.diskcache.DiskCacheSlot(locator, self._disk_cache_dir) else: n = KeepBlockCache.CacheSlot(locator) self._cache.insert(0, n) return n, True def set(self, slot, blob): try: slot.set(blob) return except OSError as e: if e.errno == errno.ENOMEM: # Reduce max slots to current - 4, cap cache and retry with self._cache_lock: self._max_slots = max(4, len(self._cache) - 4) elif e.errno == errno.ENOSPC: # Reduce disk max space to current - 256 MiB, cap cache and retry with self._cache_lock: sm = sum([st.size() for st in self._cache]) self.cache_max = max((256 * 1024 * 1024), sm - (256 * 1024 * 1024)) elif e.errno == errno.ENODEV: _logger.error("Unable to use disk cache: The underlying filesystem does not support memory mapping.") except Exception as e: pass finally: # Check if we should evict things from the cache. Either # because we added a new thing or there was an error and # we possibly adjusted the limits down, so we might need # to push something out. self.cap_cache() try: # Only gets here if there was an error the first time. The # exception handler adjusts limits downward in some cases # to free up resources, which would make the operation # succeed. slot.set(blob) except Exception as e: # It failed again. Give up. slot.set(None) raise arvados.errors.KeepCacheError("Unable to save block %s to disk cache: %s" % (slot.locator, e)) self.cap_cache()Class variables
var CacheSlot
Methods
def cap_cache(self)-
Cap the cache size to self.cache_max
def get(self, locator)def reserve_cache(self, locator)-
Reserve a cache slot for the specified locator, or return the existing slot.
def set(self, slot, blob)
class KeepClient (api_client=None, proxy=None, timeout=(2, 256, 32768), proxy_timeout=(20, 256, 32768), api_token=None, local_store=None, block_cache=None, num_retries=10, session=None)-
Initialize a new KeepClient.
Arguments: :api_client: The API client to use to find Keep services. If not provided, KeepClient will build one from available Arvados configuration.
:proxy: If specified, this KeepClient will send requests to this Keep proxy. Otherwise, KeepClient will fall back to the setting of the ARVADOS_KEEP_SERVICES or ARVADOS_KEEP_PROXY configuration settings. If you want to KeepClient does not use a proxy, pass in an empty string.
:timeout: The initial timeout (in seconds) for HTTP requests to Keep non-proxy servers. A tuple of three floats is interpreted as (connection_timeout, read_timeout, minimum_bandwidth). A connection will be aborted if the average traffic rate falls below minimum_bandwidth bytes per second over an interval of read_timeout seconds. Because timeouts are often a result of transient server load, the actual connection timeout will be increased by a factor of two on each retry. Default: (2, 256, 32768).
:proxy_timeout: The initial timeout (in seconds) for HTTP requests to Keep proxies. A tuple of three floats is interpreted as (connection_timeout, read_timeout, minimum_bandwidth). The behavior described above for adjusting connection timeouts on retry also applies. Default: (20, 256, 32768).
:api_token: If you're not using an API client, but only talking directly to a Keep proxy, this parameter specifies an API token to authenticate Keep requests. It is an error to specify both api_client and api_token. If you specify neither, KeepClient will use one available from the Arvados configuration.
:local_store: If specified, this KeepClient will bypass Keep services, and save data to the named directory. If unspecified, KeepClient will fall back to the setting of the $KEEP_LOCAL_STORE environment variable. If you want to ensure KeepClient does not use local storage, pass in an empty string. This is primarily intended to mock a server for testing.
:num_retries: The default number of times to retry failed requests. This will be used as the default num_retries value when get() and put() are called. Default 10.
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class KeepClient(object): DEFAULT_TIMEOUT = PyCurlHelper.DEFAULT_TIMEOUT DEFAULT_PROXY_TIMEOUT = PyCurlHelper.DEFAULT_PROXY_TIMEOUT class KeepService(PyCurlHelper): """Make requests to a single Keep service, and track results. A KeepService is intended to last long enough to perform one transaction (GET or PUT) against one Keep service. This can involve calling either get() or put() multiple times in order to retry after transient failures. However, calling both get() and put() on a single instance -- or using the same instance to access two different Keep services -- will not produce sensible behavior. """ HTTP_ERRORS = ( socket.error, ssl.SSLError, arvados.errors.HttpError, ) def __init__(self, root, user_agent_pool=queue.LifoQueue(), upload_counter=None, download_counter=None, headers={}, insecure=False): super(KeepClient.KeepService, self).__init__() self.root = root self._user_agent_pool = user_agent_pool self._result = {'error': None} self._usable = True self._session = None self._socket = None self.get_headers = {'Accept': 'application/octet-stream'} self.get_headers.update(headers) self.put_headers = headers self.upload_counter = upload_counter self.download_counter = download_counter self.insecure = insecure def usable(self): """Is it worth attempting a request?""" return self._usable def finished(self): """Did the request succeed or encounter permanent failure?""" return self._result['error'] == False or not self._usable def last_result(self): return self._result def _get_user_agent(self): try: return self._user_agent_pool.get(block=False) except queue.Empty: return pycurl.Curl() def _put_user_agent(self, ua): try: ua.reset() self._user_agent_pool.put(ua, block=False) except: ua.close() def get(self, locator, method="GET", timeout=None): # locator is a KeepLocator object. url = self.root + str(locator) _logger.debug("Request: %s %s", method, url) curl = self._get_user_agent() ok = None try: with timer.Timer() as t: self._headers = {} response_body = BytesIO() curl.setopt(pycurl.NOSIGNAL, 1) curl.setopt(pycurl.OPENSOCKETFUNCTION, lambda *args, **kwargs: self._socket_open(*args, **kwargs)) curl.setopt(pycurl.URL, url.encode('utf-8')) curl.setopt(pycurl.HTTPHEADER, [ '{}: {}'.format(k,v) for k,v in self.get_headers.items()]) curl.setopt(pycurl.WRITEFUNCTION, response_body.write) curl.setopt(pycurl.HEADERFUNCTION, self._headerfunction) if self.insecure: curl.setopt(pycurl.SSL_VERIFYPEER, 0) curl.setopt(pycurl.SSL_VERIFYHOST, 0) else: curl.setopt(pycurl.CAINFO, arvados.util.ca_certs_path()) if method == "HEAD": curl.setopt(pycurl.NOBODY, True) else: curl.setopt(pycurl.HTTPGET, True) self._setcurltimeouts(curl, timeout, method=="HEAD") try: curl.perform() except Exception as e: raise arvados.errors.HttpError(0, str(e)) finally: if self._socket: self._socket.close() self._socket = None self._result = { 'status_code': curl.getinfo(pycurl.RESPONSE_CODE), 'body': response_body.getvalue(), 'headers': self._headers, 'error': False, } ok = retry.check_http_response_success(self._result['status_code']) if not ok: self._result['error'] = arvados.errors.HttpError( self._result['status_code'], self._headers.get('x-status-line', 'Error')) except self.HTTP_ERRORS as e: self._result = { 'error': e, } self._usable = ok != False if self._result.get('status_code', None): # The client worked well enough to get an HTTP status # code, so presumably any problems are just on the # server side and it's OK to reuse the client. self._put_user_agent(curl) else: # Don't return this client to the pool, in case it's # broken. curl.close() if not ok: _logger.debug("Request fail: GET %s => %s: %s", url, type(self._result['error']), str(self._result['error'])) return None if method == "HEAD": _logger.info("HEAD %s: %s bytes", self._result['status_code'], self._result.get('content-length')) if self._result['headers'].get('x-keep-locator'): # This is a response to a remote block copy request, return # the local copy block locator. return self._result['headers'].get('x-keep-locator') return True _logger.info("GET %s: %s bytes in %s msec (%.3f MiB/sec)", self._result['status_code'], len(self._result['body']), t.msecs, 1.0*len(self._result['body'])/2**20/t.secs if t.secs > 0 else 0) if self.download_counter: self.download_counter.add(len(self._result['body'])) resp_md5 = hashlib.md5(self._result['body']).hexdigest() if resp_md5 != locator.md5sum: _logger.warning("Checksum fail: md5(%s) = %s", url, resp_md5) self._result['error'] = arvados.errors.HttpError( 0, 'Checksum fail') return None return self._result['body'] def put(self, hash_s, body, timeout=None, headers={}): put_headers = copy.copy(self.put_headers) put_headers.update(headers) url = self.root + hash_s _logger.debug("Request: PUT %s", url) curl = self._get_user_agent() ok = None try: with timer.Timer() as t: self._headers = {} body_reader = BytesIO(body) response_body = BytesIO() curl.setopt(pycurl.NOSIGNAL, 1) curl.setopt(pycurl.OPENSOCKETFUNCTION, lambda *args, **kwargs: self._socket_open(*args, **kwargs)) curl.setopt(pycurl.URL, url.encode('utf-8')) # Using UPLOAD tells cURL to wait for a "go ahead" from the # Keep server (in the form of a HTTP/1.1 "100 Continue" # response) instead of sending the request body immediately. # This allows the server to reject the request if the request # is invalid or the server is read-only, without waiting for # the client to send the entire block. curl.setopt(pycurl.UPLOAD, True) curl.setopt(pycurl.INFILESIZE, len(body)) curl.setopt(pycurl.READFUNCTION, body_reader.read) curl.setopt(pycurl.HTTPHEADER, [ '{}: {}'.format(k,v) for k,v in put_headers.items()]) curl.setopt(pycurl.WRITEFUNCTION, response_body.write) curl.setopt(pycurl.HEADERFUNCTION, self._headerfunction) if self.insecure: curl.setopt(pycurl.SSL_VERIFYPEER, 0) curl.setopt(pycurl.SSL_VERIFYHOST, 0) else: curl.setopt(pycurl.CAINFO, arvados.util.ca_certs_path()) self._setcurltimeouts(curl, timeout) try: curl.perform() except Exception as e: raise arvados.errors.HttpError(0, str(e)) finally: if self._socket: self._socket.close() self._socket = None self._result = { 'status_code': curl.getinfo(pycurl.RESPONSE_CODE), 'body': response_body.getvalue().decode('utf-8'), 'headers': self._headers, 'error': False, } ok = retry.check_http_response_success(self._result['status_code']) if not ok: self._result['error'] = arvados.errors.HttpError( self._result['status_code'], self._headers.get('x-status-line', 'Error')) except self.HTTP_ERRORS as e: self._result = { 'error': e, } self._usable = ok != False # still usable if ok is True or None if self._result.get('status_code', None): # Client is functional. See comment in get(). self._put_user_agent(curl) else: curl.close() if not ok: _logger.debug("Request fail: PUT %s => %s: %s", url, type(self._result['error']), str(self._result['error'])) return False _logger.info("PUT %s: %s bytes in %s msec (%.3f MiB/sec)", self._result['status_code'], len(body), t.msecs, 1.0*len(body)/2**20/t.secs if t.secs > 0 else 0) if self.upload_counter: self.upload_counter.add(len(body)) return True class KeepWriterQueue(queue.Queue): def __init__(self, copies, classes=[]): queue.Queue.__init__(self) # Old-style superclass self.wanted_copies = copies self.wanted_storage_classes = classes self.successful_copies = 0 self.confirmed_storage_classes = {} self.response = None self.storage_classes_tracking = True self.queue_data_lock = threading.RLock() self.pending_tries = max(copies, len(classes)) self.pending_tries_notification = threading.Condition() def write_success(self, response, replicas_nr, classes_confirmed): with self.queue_data_lock: self.successful_copies += replicas_nr if classes_confirmed is None: self.storage_classes_tracking = False elif self.storage_classes_tracking: for st_class, st_copies in classes_confirmed.items(): try: self.confirmed_storage_classes[st_class] += st_copies except KeyError: self.confirmed_storage_classes[st_class] = st_copies self.pending_tries = max(self.wanted_copies - self.successful_copies, len(self.pending_classes())) self.response = response with self.pending_tries_notification: self.pending_tries_notification.notify_all() def write_fail(self, ks): with self.pending_tries_notification: self.pending_tries += 1 self.pending_tries_notification.notify() def pending_copies(self): with self.queue_data_lock: return self.wanted_copies - self.successful_copies def satisfied_classes(self): with self.queue_data_lock: if not self.storage_classes_tracking: # Notifies disabled storage classes expectation to # the outer loop. return None return list(set(self.wanted_storage_classes) - set(self.pending_classes())) def pending_classes(self): with self.queue_data_lock: if (not self.storage_classes_tracking) or (self.wanted_storage_classes is None): return [] unsatisfied_classes = copy.copy(self.wanted_storage_classes) for st_class, st_copies in self.confirmed_storage_classes.items(): if st_class in unsatisfied_classes and st_copies >= self.wanted_copies: unsatisfied_classes.remove(st_class) return unsatisfied_classes def get_next_task(self): with self.pending_tries_notification: while True: if self.pending_copies() < 1 and len(self.pending_classes()) == 0: # This notify_all() is unnecessary -- # write_success() already called notify_all() # when pending<1 became true, so it's not # possible for any other thread to be in # wait() now -- but it's cheap insurance # against deadlock so we do it anyway: self.pending_tries_notification.notify_all() # Drain the queue and then raise Queue.Empty while True: self.get_nowait() self.task_done() elif self.pending_tries > 0: service, service_root = self.get_nowait() if service.finished(): self.task_done() continue self.pending_tries -= 1 return service, service_root elif self.empty(): self.pending_tries_notification.notify_all() raise queue.Empty else: self.pending_tries_notification.wait() class KeepWriterThreadPool(object): def __init__(self, data, data_hash, copies, max_service_replicas, timeout=None, classes=[]): self.total_task_nr = 0 if (not max_service_replicas) or (max_service_replicas >= copies): num_threads = 1 else: num_threads = int(math.ceil(1.0*copies/max_service_replicas)) _logger.debug("Pool max threads is %d", num_threads) self.workers = [] self.queue = KeepClient.KeepWriterQueue(copies, classes) # Create workers for _ in range(num_threads): w = KeepClient.KeepWriterThread(self.queue, data, data_hash, timeout) self.workers.append(w) def add_task(self, ks, service_root): self.queue.put((ks, service_root)) self.total_task_nr += 1 def done(self): return self.queue.successful_copies, self.queue.satisfied_classes() def join(self): # Start workers for worker in self.workers: worker.start() # Wait for finished work self.queue.join() def response(self): return self.queue.response class KeepWriterThread(threading.Thread): class TaskFailed(RuntimeError): pass def __init__(self, queue, data, data_hash, timeout=None): super(KeepClient.KeepWriterThread, self).__init__() self.timeout = timeout self.queue = queue self.data = data self.data_hash = data_hash self.daemon = True def run(self): while True: try: service, service_root = self.queue.get_next_task() except queue.Empty: return try: locator, copies, classes = self.do_task(service, service_root) except Exception as e: if not isinstance(e, self.TaskFailed): _logger.exception("Exception in KeepWriterThread") self.queue.write_fail(service) else: self.queue.write_success(locator, copies, classes) finally: self.queue.task_done() def do_task(self, service, service_root): classes = self.queue.pending_classes() headers = {} if len(classes) > 0: classes.sort() headers['X-Keep-Storage-Classes'] = ', '.join(classes) success = bool(service.put(self.data_hash, self.data, timeout=self.timeout, headers=headers)) result = service.last_result() if not success: if result.get('status_code'): _logger.debug("Request fail: PUT %s => %s %s", self.data_hash, result.get('status_code'), result.get('body')) raise self.TaskFailed() _logger.debug("KeepWriterThread %s succeeded %s+%i %s", str(threading.current_thread()), self.data_hash, len(self.data), service_root) try: replicas_stored = int(result['headers']['x-keep-replicas-stored']) except (KeyError, ValueError): replicas_stored = 1 classes_confirmed = {} try: scch = result['headers']['x-keep-storage-classes-confirmed'] for confirmation in scch.replace(' ', '').split(','): if '=' in confirmation: stored_class, stored_copies = confirmation.split('=')[:2] classes_confirmed[stored_class] = int(stored_copies) except (KeyError, ValueError): # Storage classes confirmed header missing or corrupt classes_confirmed = None return result['body'].strip(), replicas_stored, classes_confirmed def __init__(self, api_client=None, proxy=None, timeout=DEFAULT_TIMEOUT, proxy_timeout=DEFAULT_PROXY_TIMEOUT, api_token=None, local_store=None, block_cache=None, num_retries=10, session=None): """Initialize a new KeepClient. Arguments: :api_client: The API client to use to find Keep services. If not provided, KeepClient will build one from available Arvados configuration. :proxy: If specified, this KeepClient will send requests to this Keep proxy. Otherwise, KeepClient will fall back to the setting of the ARVADOS_KEEP_SERVICES or ARVADOS_KEEP_PROXY configuration settings. If you want to KeepClient does not use a proxy, pass in an empty string. :timeout: The initial timeout (in seconds) for HTTP requests to Keep non-proxy servers. A tuple of three floats is interpreted as (connection_timeout, read_timeout, minimum_bandwidth). A connection will be aborted if the average traffic rate falls below minimum_bandwidth bytes per second over an interval of read_timeout seconds. Because timeouts are often a result of transient server load, the actual connection timeout will be increased by a factor of two on each retry. Default: (2, 256, 32768). :proxy_timeout: The initial timeout (in seconds) for HTTP requests to Keep proxies. A tuple of three floats is interpreted as (connection_timeout, read_timeout, minimum_bandwidth). The behavior described above for adjusting connection timeouts on retry also applies. Default: (20, 256, 32768). :api_token: If you're not using an API client, but only talking directly to a Keep proxy, this parameter specifies an API token to authenticate Keep requests. It is an error to specify both api_client and api_token. If you specify neither, KeepClient will use one available from the Arvados configuration. :local_store: If specified, this KeepClient will bypass Keep services, and save data to the named directory. If unspecified, KeepClient will fall back to the setting of the $KEEP_LOCAL_STORE environment variable. If you want to ensure KeepClient does not use local storage, pass in an empty string. This is primarily intended to mock a server for testing. :num_retries: The default number of times to retry failed requests. This will be used as the default num_retries value when get() and put() are called. Default 10. """ self.lock = threading.Lock() if proxy is None: if config.get('ARVADOS_KEEP_SERVICES'): proxy = config.get('ARVADOS_KEEP_SERVICES') else: proxy = config.get('ARVADOS_KEEP_PROXY') if api_token is None: if api_client is None: api_token = config.get('ARVADOS_API_TOKEN') else: api_token = api_client.api_token elif api_client is not None: raise ValueError( "can't build KeepClient with both API client and token") if local_store is None: local_store = os.environ.get('KEEP_LOCAL_STORE') if api_client is None: self.insecure = config.flag_is_true('ARVADOS_API_HOST_INSECURE') else: self.insecure = api_client.insecure self.block_cache = block_cache if block_cache else KeepBlockCache() self.timeout = timeout self.proxy_timeout = proxy_timeout self._user_agent_pool = queue.LifoQueue() self.upload_counter = Counter() self.download_counter = Counter() self.put_counter = Counter() self.get_counter = Counter() self.hits_counter = Counter() self.misses_counter = Counter() self._storage_classes_unsupported_warning = False self._default_classes = [] if local_store: self.local_store = local_store self.head = self.local_store_head self.get = self.local_store_get self.put = self.local_store_put else: self.num_retries = num_retries self.max_replicas_per_service = None if proxy: proxy_uris = proxy.split() for i in range(len(proxy_uris)): if not proxy_uris[i].endswith('/'): proxy_uris[i] += '/' # URL validation url = urllib.parse.urlparse(proxy_uris[i]) if not (url.scheme and url.netloc): raise arvados.errors.ArgumentError("Invalid proxy URI: {}".format(proxy_uris[i])) self.api_token = api_token self._gateway_services = {} self._keep_services = [{ 'uuid': "00000-bi6l4-%015d" % idx, 'service_type': 'proxy', '_service_root': uri, } for idx, uri in enumerate(proxy_uris)] self._writable_services = self._keep_services self.using_proxy = True self._static_services_list = True else: # It's important to avoid instantiating an API client # unless we actually need one, for testing's sake. if api_client is None: api_client = arvados.api('v1') self.api_client = api_client self.api_token = api_client.api_token self._gateway_services = {} self._keep_services = None self._writable_services = None self.using_proxy = None self._static_services_list = False try: self._default_classes = [ k for k, v in self.api_client.config()['StorageClasses'].items() if v['Default']] except KeyError: # We're talking to an old cluster pass def current_timeout(self, attempt_number): """Return the appropriate timeout to use for this client. The proxy timeout setting if the backend service is currently a proxy, the regular timeout setting otherwise. The `attempt_number` indicates how many times the operation has been tried already (starting from 0 for the first try), and scales the connection timeout portion of the return value accordingly. """ # TODO(twp): the timeout should be a property of a # KeepService, not a KeepClient. See #4488. t = self.proxy_timeout if self.using_proxy else self.timeout if len(t) == 2: return (t[0] * (1 << attempt_number), t[1]) else: return (t[0] * (1 << attempt_number), t[1], t[2]) def _any_nondisk_services(self, service_list): return any(ks.get('service_type', 'disk') != 'disk' for ks in service_list) def build_services_list(self, force_rebuild=False): if (self._static_services_list or (self._keep_services and not force_rebuild)): return with self.lock: try: keep_services = self.api_client.keep_services().accessible() except Exception: # API server predates Keep services. keep_services = self.api_client.keep_disks().list() # Gateway services are only used when specified by UUID, # so there's nothing to gain by filtering them by # service_type. self._gateway_services = {ks['uuid']: ks for ks in keep_services.execute()['items']} if not self._gateway_services: raise arvados.errors.NoKeepServersError() # Precompute the base URI for each service. for r in self._gateway_services.values(): host = r['service_host'] if not host.startswith('[') and host.find(':') >= 0: # IPv6 URIs must be formatted like http://[::1]:80/... host = '[' + host + ']' r['_service_root'] = "{}://{}:{:d}/".format( 'https' if r['service_ssl_flag'] else 'http', host, r['service_port']) _logger.debug(str(self._gateway_services)) self._keep_services = [ ks for ks in self._gateway_services.values() if not ks.get('service_type', '').startswith('gateway:')] self._writable_services = [ks for ks in self._keep_services if not ks.get('read_only')] # For disk type services, max_replicas_per_service is 1 # It is unknown (unlimited) for other service types. if self._any_nondisk_services(self._writable_services): self.max_replicas_per_service = None else: self.max_replicas_per_service = 1 def _service_weight(self, data_hash, service_uuid): """Compute the weight of a Keep service endpoint for a data block with a known hash. The weight is md5(h + u) where u is the last 15 characters of the service endpoint's UUID. """ return hashlib.md5((data_hash + service_uuid[-15:]).encode()).hexdigest() def weighted_service_roots(self, locator, force_rebuild=False, need_writable=False): """Return an array of Keep service endpoints, in the order in which they should be probed when reading or writing data with the given hash+hints. """ self.build_services_list(force_rebuild) sorted_roots = [] # Use the services indicated by the given +K@... remote # service hints, if any are present and can be resolved to a # URI. for hint in locator.hints: if hint.startswith('K@'): if len(hint) == 7: sorted_roots.append( "https://keep.{}.arvadosapi.com/".format(hint[2:])) elif len(hint) == 29: svc = self._gateway_services.get(hint[2:]) if svc: sorted_roots.append(svc['_service_root']) # Sort the available local services by weight (heaviest first) # for this locator, and return their service_roots (base URIs) # in that order. use_services = self._keep_services if need_writable: use_services = self._writable_services self.using_proxy = self._any_nondisk_services(use_services) sorted_roots.extend([ svc['_service_root'] for svc in sorted( use_services, reverse=True, key=lambda svc: self._service_weight(locator.md5sum, svc['uuid']))]) _logger.debug("{}: {}".format(locator, sorted_roots)) return sorted_roots def map_new_services(self, roots_map, locator, force_rebuild, need_writable, headers): # roots_map is a dictionary, mapping Keep service root strings # to KeepService objects. Poll for Keep services, and add any # new ones to roots_map. Return the current list of local # root strings. headers.setdefault('Authorization', "OAuth2 %s" % (self.api_token,)) local_roots = self.weighted_service_roots(locator, force_rebuild, need_writable) for root in local_roots: if root not in roots_map: roots_map[root] = self.KeepService( root, self._user_agent_pool, upload_counter=self.upload_counter, download_counter=self.download_counter, headers=headers, insecure=self.insecure) return local_roots @staticmethod def _check_loop_result(result): # KeepClient RetryLoops should save results as a 2-tuple: the # actual result of the request, and the number of servers available # to receive the request this round. # This method returns True if there's a real result, False if # there are no more servers available, otherwise None. if isinstance(result, Exception): return None result, tried_server_count = result if (result is not None) and (result is not False): return True elif tried_server_count < 1: _logger.info("No more Keep services to try; giving up") return False else: return None def get_from_cache(self, loc_s): """Fetch a block only if is in the cache, otherwise return None.""" locator = KeepLocator(loc_s) slot = self.block_cache.get(locator.md5sum) if slot is not None and slot.ready.is_set(): return slot.get() else: return None def refresh_signature(self, loc): """Ask Keep to get the remote block and return its local signature""" now = datetime.datetime.utcnow().isoformat("T") + 'Z' return self.head(loc, headers={'X-Keep-Signature': 'local, {}'.format(now)}) @retry.retry_method def head(self, loc_s, **kwargs): return self._get_or_head(loc_s, method="HEAD", **kwargs) @retry.retry_method def get(self, loc_s, **kwargs): return self._get_or_head(loc_s, method="GET", **kwargs) def _get_or_head(self, loc_s, method="GET", num_retries=None, request_id=None, headers=None, prefetch=False): """Get data from Keep. This method fetches one or more blocks of data from Keep. It sends a request each Keep service registered with the API server (or the proxy provided when this client was instantiated), then each service named in location hints, in sequence. As soon as one service provides the data, it's returned. Arguments: * loc_s: A string of one or more comma-separated locators to fetch. This method returns the concatenation of these blocks. * num_retries: The number of times to retry GET requests to *each* Keep server if it returns temporary failures, with exponential backoff. Note that, in each loop, the method may try to fetch data from every available Keep service, along with any that are named in location hints in the locator. The default value is set when the KeepClient is initialized. """ if ',' in loc_s: return ''.join(self.get(x) for x in loc_s.split(',')) self.get_counter.add(1) request_id = (request_id or (hasattr(self, 'api_client') and self.api_client.request_id) or arvados.util.new_request_id()) if headers is None: headers = {} headers['X-Request-Id'] = request_id slot = None blob = None try: locator = KeepLocator(loc_s) if method == "GET": while slot is None: slot, first = self.block_cache.reserve_cache(locator.md5sum) if first: # Fresh and empty "first time it is used" slot break if prefetch: # this is request for a prefetch to fill in # the cache, don't need to wait for the # result, so if it is already in flight return # immediately. Clear 'slot' to prevent # finally block from calling slot.set() slot = None return None blob = slot.get() if blob is not None: self.hits_counter.add(1) return blob # If blob is None, this means either # # (a) another thread was fetching this block and # failed with an error or # # (b) cache thrashing caused the slot to be # evicted (content set to None) by another thread # between the call to reserve_cache() and get(). # # We'll handle these cases by reserving a new slot # and then doing a full GET request. slot = None self.misses_counter.add(1) # If the locator has hints specifying a prefix (indicating a # remote keepproxy) or the UUID of a local gateway service, # read data from the indicated service(s) instead of the usual # list of local disk services. hint_roots = ['http://keep.{}.arvadosapi.com/'.format(hint[2:]) for hint in locator.hints if hint.startswith('K@') and len(hint) == 7] hint_roots.extend([self._gateway_services[hint[2:]]['_service_root'] for hint in locator.hints if ( hint.startswith('K@') and len(hint) == 29 and self._gateway_services.get(hint[2:]) )]) # Map root URLs to their KeepService objects. roots_map = { root: self.KeepService(root, self._user_agent_pool, upload_counter=self.upload_counter, download_counter=self.download_counter, headers=headers, insecure=self.insecure) for root in hint_roots } # See #3147 for a discussion of the loop implementation. Highlights: # * Refresh the list of Keep services after each failure, in case # it's being updated. # * Retry until we succeed, we're out of retries, or every available # service has returned permanent failure. sorted_roots = [] roots_map = {} loop = retry.RetryLoop(num_retries, self._check_loop_result, backoff_start=2) for tries_left in loop: try: sorted_roots = self.map_new_services( roots_map, locator, force_rebuild=(tries_left < num_retries), need_writable=False, headers=headers) except Exception as error: loop.save_result(error) continue # Query KeepService objects that haven't returned # permanent failure, in our specified shuffle order. services_to_try = [roots_map[root] for root in sorted_roots if roots_map[root].usable()] for keep_service in services_to_try: blob = keep_service.get(locator, method=method, timeout=self.current_timeout(num_retries-tries_left)) if blob is not None: break loop.save_result((blob, len(services_to_try))) # Always cache the result, then return it if we succeeded. if loop.success(): return blob finally: if slot is not None: self.block_cache.set(slot, blob) # Q: Including 403 is necessary for the Keep tests to continue # passing, but maybe they should expect KeepReadError instead? not_founds = sum(1 for key in sorted_roots if roots_map[key].last_result().get('status_code', None) in {403, 404, 410}) service_errors = ((key, roots_map[key].last_result()['error']) for key in sorted_roots) if not roots_map: raise arvados.errors.KeepReadError( "[{}] failed to read {}: no Keep services available ({})".format( request_id, loc_s, loop.last_result())) elif not_founds == len(sorted_roots): raise arvados.errors.NotFoundError( "[{}] {} not found".format(request_id, loc_s), service_errors) else: raise arvados.errors.KeepReadError( "[{}] failed to read {} after {}".format(request_id, loc_s, loop.attempts_str()), service_errors, label="service") @retry.retry_method def put(self, data, copies=2, num_retries=None, request_id=None, classes=None): """Save data in Keep. This method will get a list of Keep services from the API server, and send the data to each one simultaneously in a new thread. Once the uploads are finished, if enough copies are saved, this method returns the most recent HTTP response body. If requests fail to upload enough copies, this method raises KeepWriteError. Arguments: * data: The string of data to upload. * copies: The number of copies that the user requires be saved. Default 2. * num_retries: The number of times to retry PUT requests to *each* Keep server if it returns temporary failures, with exponential backoff. The default value is set when the KeepClient is initialized. * classes: An optional list of storage class names where copies should be written. """ classes = classes or self._default_classes if not isinstance(data, bytes): data = data.encode() self.put_counter.add(1) data_hash = hashlib.md5(data).hexdigest() loc_s = data_hash + '+' + str(len(data)) if copies < 1: return loc_s locator = KeepLocator(loc_s) request_id = (request_id or (hasattr(self, 'api_client') and self.api_client.request_id) or arvados.util.new_request_id()) headers = { 'X-Request-Id': request_id, 'X-Keep-Desired-Replicas': str(copies), } roots_map = {} loop = retry.RetryLoop(num_retries, self._check_loop_result, backoff_start=2) done_copies = 0 done_classes = [] for tries_left in loop: try: sorted_roots = self.map_new_services( roots_map, locator, force_rebuild=(tries_left < num_retries), need_writable=True, headers=headers) except Exception as error: loop.save_result(error) continue pending_classes = [] if done_classes is not None: pending_classes = list(set(classes) - set(done_classes)) writer_pool = KeepClient.KeepWriterThreadPool(data=data, data_hash=data_hash, copies=copies - done_copies, max_service_replicas=self.max_replicas_per_service, timeout=self.current_timeout(num_retries - tries_left), classes=pending_classes) for service_root, ks in [(root, roots_map[root]) for root in sorted_roots]: if ks.finished(): continue writer_pool.add_task(ks, service_root) writer_pool.join() pool_copies, pool_classes = writer_pool.done() done_copies += pool_copies if (done_classes is not None) and (pool_classes is not None): done_classes += pool_classes loop.save_result( (done_copies >= copies and set(done_classes) == set(classes), writer_pool.total_task_nr)) else: # Old keepstore contacted without storage classes support: # success is determined only by successful copies. # # Disable storage classes tracking from this point forward. if not self._storage_classes_unsupported_warning: self._storage_classes_unsupported_warning = True _logger.warning("X-Keep-Storage-Classes header not supported by the cluster") done_classes = None loop.save_result( (done_copies >= copies, writer_pool.total_task_nr)) if loop.success(): return writer_pool.response() if not roots_map: raise arvados.errors.KeepWriteError( "[{}] failed to write {}: no Keep services available ({})".format( request_id, data_hash, loop.last_result())) else: service_errors = ((key, roots_map[key].last_result()['error']) for key in sorted_roots if roots_map[key].last_result()['error']) raise arvados.errors.KeepWriteError( "[{}] failed to write {} after {} (wanted {} copies but wrote {})".format( request_id, data_hash, loop.attempts_str(), (copies, classes), writer_pool.done()), service_errors, label="service") def local_store_put(self, data, copies=1, num_retries=None, classes=[]): """A stub for put(). This method is used in place of the real put() method when using local storage (see constructor's local_store argument). copies and num_retries arguments are ignored: they are here only for the sake of offering the same call signature as put(). Data stored this way can be retrieved via local_store_get(). """ md5 = hashlib.md5(data).hexdigest() locator = '%s+%d' % (md5, len(data)) with open(os.path.join(self.local_store, md5 + '.tmp'), 'wb') as f: f.write(data) os.rename(os.path.join(self.local_store, md5 + '.tmp'), os.path.join(self.local_store, md5)) return locator def local_store_get(self, loc_s, num_retries=None): """Companion to local_store_put().""" try: locator = KeepLocator(loc_s) except ValueError: raise arvados.errors.NotFoundError( "Invalid data locator: '%s'" % loc_s) if locator.md5sum == config.EMPTY_BLOCK_LOCATOR.split('+')[0]: return b'' with open(os.path.join(self.local_store, locator.md5sum), 'rb') as f: return f.read() def local_store_head(self, loc_s, num_retries=None): """Companion to local_store_put().""" try: locator = KeepLocator(loc_s) except ValueError: raise arvados.errors.NotFoundError( "Invalid data locator: '%s'" % loc_s) if locator.md5sum == config.EMPTY_BLOCK_LOCATOR.split('+')[0]: return True if os.path.exists(os.path.join(self.local_store, locator.md5sum)): return TrueClass variables
var DEFAULT_PROXY_TIMEOUTvar DEFAULT_TIMEOUTvar KeepService-
Make requests to a single Keep service, and track results.
A KeepService is intended to last long enough to perform one transaction (GET or PUT) against one Keep service. This can involve calling either get() or put() multiple times in order to retry after transient failures. However, calling both get() and put() on a single instance – or using the same instance to access two different Keep services – will not produce sensible behavior.
var KeepWriterQueue-
Create a queue object with a given maximum size.
If maxsize is <= 0, the queue size is infinite.
var KeepWriterThread-
A class that represents a thread of control.
This class can be safely subclassed in a limited fashion. There are two ways to specify the activity: by passing a callable object to the constructor, or by overriding the run() method in a subclass.
var KeepWriterThreadPool
Methods
def build_services_list(self, force_rebuild=False)def current_timeout(self, attempt_number)-
Return the appropriate timeout to use for this client.
The proxy timeout setting if the backend service is currently a proxy, the regular timeout setting otherwise. The
attempt_numberindicates how many times the operation has been tried already (starting from 0 for the first try), and scales the connection timeout portion of the return value accordingly. def get(self, loc_s, **kwargs)def get_from_cache(self, loc_s)-
Fetch a block only if is in the cache, otherwise return None.
def head(self, loc_s, **kwargs)def local_store_get(self, loc_s, num_retries=None)-
Companion to local_store_put().
def local_store_head(self, loc_s, num_retries=None)-
Companion to local_store_put().
def local_store_put(self, data, copies=1, num_retries=None, classes=[])-
A stub for put().
This method is used in place of the real put() method when using local storage (see constructor's local_store argument).
copies and num_retries arguments are ignored: they are here only for the sake of offering the same call signature as put().
Data stored this way can be retrieved via local_store_get().
def map_new_services(self, roots_map, locator, force_rebuild, need_writable, headers)def put(self, data, copies=2, num_retries=None, request_id=None, classes=None)-
Save data in Keep.
This method will get a list of Keep services from the API server, and send the data to each one simultaneously in a new thread. Once the uploads are finished, if enough copies are saved, this method returns the most recent HTTP response body. If requests fail to upload enough copies, this method raises KeepWriteError.
Arguments: * data: The string of data to upload. * copies: The number of copies that the user requires be saved. Default 2. * num_retries: The number of times to retry PUT requests to each Keep server if it returns temporary failures, with exponential backoff. The default value is set when the KeepClient is initialized. * classes: An optional list of storage class names where copies should be written.
def refresh_signature(self, loc)-
Ask Keep to get the remote block and return its local signature
def weighted_service_roots(self, locator, force_rebuild=False, need_writable=False)-
Return an array of Keep service endpoints, in the order in which they should be probed when reading or writing data with the given hash+hints.
class KeepLocator (locator_str)-
Expand source code
class KeepLocator(object): EPOCH_DATETIME = datetime.datetime.utcfromtimestamp(0) HINT_RE = re.compile(r'^[A-Z][A-Za-z0-9@_-]+$') def __init__(self, locator_str): self.hints = [] self._perm_sig = None self._perm_expiry = None pieces = iter(locator_str.split('+')) self.md5sum = next(pieces) try: self.size = int(next(pieces)) except StopIteration: self.size = None for hint in pieces: if self.HINT_RE.match(hint) is None: raise ValueError("invalid hint format: {}".format(hint)) elif hint.startswith('A'): self.parse_permission_hint(hint) else: self.hints.append(hint) def __str__(self): return '+'.join( native_str(s) for s in [self.md5sum, self.size, self.permission_hint()] + self.hints if s is not None) def stripped(self): if self.size is not None: return "%s+%i" % (self.md5sum, self.size) else: return self.md5sum def _make_hex_prop(name, length): # Build and return a new property with the given name that # must be a hex string of the given length. data_name = '_{}'.format(name) def getter(self): return getattr(self, data_name) def setter(self, hex_str): if not arvados.util.is_hex(hex_str, length): raise ValueError("{} is not a {}-digit hex string: {!r}". format(name, length, hex_str)) setattr(self, data_name, hex_str) return property(getter, setter) md5sum = _make_hex_prop('md5sum', 32) perm_sig = _make_hex_prop('perm_sig', 40) @property def perm_expiry(self): return self._perm_expiry @perm_expiry.setter def perm_expiry(self, value): if not arvados.util.is_hex(value, 1, 8): raise ValueError( "permission timestamp must be a hex Unix timestamp: {}". format(value)) self._perm_expiry = datetime.datetime.utcfromtimestamp(int(value, 16)) def permission_hint(self): data = [self.perm_sig, self.perm_expiry] if None in data: return None data[1] = int((data[1] - self.EPOCH_DATETIME).total_seconds()) return "A{}@{:08x}".format(*data) def parse_permission_hint(self, s): try: self.perm_sig, self.perm_expiry = s[1:].split('@', 1) except IndexError: raise ValueError("bad permission hint {}".format(s)) def permission_expired(self, as_of_dt=None): if self.perm_expiry is None: return False elif as_of_dt is None: as_of_dt = datetime.datetime.now() return self.perm_expiry <= as_of_dtClass variables
var EPOCH_DATETIMEvar HINT_RE
Instance variables
prop md5sum-
Expand source code
def getter(self): return getattr(self, data_name) prop perm_expiry-
Expand source code
@property def perm_expiry(self): return self._perm_expiry prop perm_sig-
Expand source code
def getter(self): return getattr(self, data_name)
Methods
def parse_permission_hint(self, s)def permission_expired(self, as_of_dt=None)def permission_hint(self)def stripped(self)