X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/1afb8044b6b82dba5546464ecc42b7361f75cd2e..da96cadf6038f819d4bb30b30de78449f958a9f5:/sdk/python/arvados.py diff --git a/sdk/python/arvados.py b/sdk/python/arvados.py index 6973358195..f4fe070786 100644 --- a/sdk/python/arvados.py +++ b/sdk/python/arvados.py @@ -1,4 +1,5 @@ import gflags +import httplib import httplib2 import logging import os @@ -14,11 +15,16 @@ import string import bz2 import zlib import fcntl +import time +import threading from apiclient import errors from apiclient.discovery import build -class CredentialsFromEnv: +if 'ARVADOS_DEBUG' in os.environ: + logging.basicConfig(level=logging.DEBUG) + +class CredentialsFromEnv(object): @staticmethod def http_request(self, uri, **kwargs): from httplib import BadStatusLine @@ -43,9 +49,17 @@ class CredentialsFromEnv: url = ('https://%s/discovery/v1/apis/' '{api}/{apiVersion}/rest' % os.environ['ARVADOS_API_HOST']) credentials = CredentialsFromEnv() -http = httplib2.Http() + +# Use system's CA certificates (if we find them) instead of httplib2's +ca_certs = '/etc/ssl/certs/ca-certificates.crt' +if not os.path.exists(ca_certs): + ca_certs = None # use httplib2 default + +http = httplib2.Http(ca_certs=ca_certs) http = credentials.authorize(http) -http.disable_ssl_certificate_validation=True +if re.match(r'(?i)^(true|1|yes)$', + os.environ.get('ARVADOS_API_HOST_INSECURE', '')): + http.disable_ssl_certificate_validation=True service = build("arvados", "v1", http=http, discoveryServiceUrl=url) def task_set_output(self,s): @@ -79,12 +93,15 @@ def current_job(): _current_job = t return t +def getjobparam(*args): + return current_job()['script_parameters'].get(*args) + def api(): return service -class JobTask: - def __init__(self, parameters=dict(), resource_limits=dict()): - print "init jobtask %s %s" % (parameters, resource_limits) +class JobTask(object): + def __init__(self, parameters=dict(), runtime_constraints=dict()): + print "init jobtask %s %s" % (parameters, runtime_constraints) class job_setup: @staticmethod @@ -135,16 +152,29 @@ class job_setup: exit(0) class util: + @staticmethod + def clear_tmpdir(path=None): + """ + Ensure the given directory (or TASK_TMPDIR if none given) + exists and is empty. + """ + if path == None: + path = current_task().tmpdir + if os.path.exists(path): + p = subprocess.Popen(['rm', '-rf', path]) + stdout, stderr = p.communicate(None) + if p.returncode != 0: + raise Exception('rm -rf %s: %s' % (path, stderr)) + os.mkdir(path) + @staticmethod def run_command(execargs, **kwargs): - if 'stdin' not in kwargs: - kwargs['stdin'] = subprocess.PIPE - if 'stdout' not in kwargs: - kwargs['stdout'] = subprocess.PIPE - if 'stderr' not in kwargs: - kwargs['stderr'] = subprocess.PIPE - p = subprocess.Popen(execargs, close_fds=True, shell=False, - **kwargs) + kwargs.setdefault('stdin', subprocess.PIPE) + kwargs.setdefault('stdout', subprocess.PIPE) + kwargs.setdefault('stderr', sys.stderr) + kwargs.setdefault('close_fds', True) + kwargs.setdefault('shell', False) + p = subprocess.Popen(execargs, **kwargs) stdoutdata, stderrdata = p.communicate(None) if p.returncode != 0: raise Exception("run_command %s exit %d:\n%s" % @@ -308,6 +338,11 @@ class util: collection -- collection locator path -- where to extract: absolute, or relative to job tmp """ + matches = re.search(r'^([0-9a-f]+)(\+[\w@]+)*$', collection) + if matches: + collection_hash = matches.group(1) + else: + collection_hash = hashlib.md5(collection).hexdigest() if not re.search('^/', path): path = os.path.join(current_job().tmpdir, path) lockfile = open(path + '.lock', 'w') @@ -318,7 +353,7 @@ class util: os.mkdir(path) already_have_it = False try: - if os.readlink(os.path.join(path, '.locator')) == collection: + if os.readlink(os.path.join(path, '.locator')) == collection_hash: already_have_it = True except OSError: pass @@ -331,24 +366,26 @@ class util: os.unlink(os.path.join(path, '.locator')) files_got = [] - for f in CollectionReader(collection).all_files(): - if (files == [] or - ((f.name() not in files_got) and - (f.name() in files or - (decompress and f.decompressed_name() in files)))): - outname = f.decompressed_name() if decompress else f.name() - files_got += [outname] - if os.path.exists(os.path.join(path, outname)): - continue - util.mkdir_dash_p(os.path.dirname(os.path.join(path, outname))) - outfile = open(os.path.join(path, outname), 'wb') - for buf in (f.readall_decompressed() if decompress - else f.readall()): - outfile.write(buf) - outfile.close() + for s in CollectionReader(collection).all_streams(): + stream_name = s.name() + for f in s.all_files(): + if (files == [] or + ((f.name() not in files_got) and + (f.name() in files or + (decompress and f.decompressed_name() in files)))): + outname = f.decompressed_name() if decompress else f.name() + files_got += [outname] + if os.path.exists(os.path.join(path, stream_name, outname)): + continue + util.mkdir_dash_p(os.path.dirname(os.path.join(path, stream_name, outname))) + outfile = open(os.path.join(path, stream_name, outname), 'wb') + for buf in (f.readall_decompressed() if decompress + else f.readall()): + outfile.write(buf) + outfile.close() if len(files_got) < len(files): raise Exception("Wanted files %s but only got %s from %s" % (files, files_got, map(lambda z: z.name(), list(CollectionReader(collection).all_files())))) - os.symlink(collection, os.path.join(path, '.locator')) + os.symlink(collection_hash, os.path.join(path, '.locator')) lockfile.close() return path @@ -416,30 +453,7 @@ class util: allfiles += [ent_base] return allfiles -class DataReader: - def __init__(self, data_locator): - self.data_locator = data_locator - self.p = subprocess.Popen(["whget", "-r", self.data_locator, "-"], - stdout=subprocess.PIPE, - stdin=None, stderr=subprocess.PIPE, - shell=False, close_fds=True) - def __enter__(self): - pass - def __exit__(self): - self.close() - def read(self, size, **kwargs): - return self.p.stdout.read(size, **kwargs) - def close(self): - self.p.stdout.close() - if not self.p.stderr.closed: - for err in self.p.stderr: - print >> sys.stderr, err - self.p.stderr.close() - self.p.wait() - if self.p.returncode != 0: - raise Exception("whget subprocess exited %d" % self.p.returncode) - -class StreamFileReader: +class StreamFileReader(object): def __init__(self, stream, pos, size, name): self._stream = stream self._pos = pos @@ -511,7 +525,7 @@ class StreamFileReader: return string.join(self._stream.tokens_for_range(self._pos, self._size), " ") + "\n" -class StreamReader: +class StreamReader(object): def __init__(self, tokens): self._tokens = tokens self._current_datablock_data = None @@ -623,7 +637,7 @@ class StreamReader: self._pos += len(data) return data -class CollectionReader: +class CollectionReader(object): def __init__(self, manifest_locator_or_text): if re.search(r'^\S+( [a-f0-9]{32,}(\+\S+)*)+( \d+:\d+:\S+)+\n', manifest_locator_or_text): self._manifest_text = manifest_locator_or_text @@ -660,7 +674,7 @@ class CollectionReader: self._populate() return self._manifest_text -class CollectionWriter: +class CollectionWriter(object): KEEP_BLOCK_SIZE = 2**26 def __init__(self): self._data_buffer = [] @@ -676,7 +690,36 @@ class CollectionWriter: pass def __exit__(self): self.finish() + def write_directory_tree(self, + path, stream_name='.', max_manifest_depth=-1): + self.start_new_stream(stream_name) + todo = [] + if max_manifest_depth == 0: + dirents = sorted(util.listdir_recursive(path)) + else: + dirents = sorted(os.listdir(path)) + for dirent in dirents: + target = os.path.join(path, dirent) + if os.path.isdir(target): + todo += [[target, + os.path.join(stream_name, dirent), + max_manifest_depth-1]] + else: + self.start_new_file(dirent) + with open(target, 'rb') as f: + while True: + buf = f.read(2**26) + if len(buf) == 0: + break + self.write(buf) + self.finish_current_stream() + map(lambda x: self.write_directory_tree(*x), todo) + def write(self, newdata): + if hasattr(newdata, '__iter__'): + for s in newdata: + self.write(s) + return self._data_buffer += [newdata] self._data_buffer_len += len(newdata) self._current_stream_length += len(newdata) @@ -692,6 +735,7 @@ class CollectionWriter: self.finish_current_file() self.set_current_file_name(newfilename) def set_current_file_name(self, newfilename): + newfilename = re.sub(r' ', '\\\\040', newfilename) if re.search(r'[ \t\n]', newfilename): raise AssertionError("Manifest filenames cannot contain whitespace") self._current_file_name = newfilename @@ -712,7 +756,7 @@ class CollectionWriter: def set_current_stream_name(self, newstreamname): if re.search(r'[ \t\n]', newstreamname): raise AssertionError("Manifest stream names cannot contain whitespace") - self._current_stream_name = newstreamname + self._current_stream_name = '.' if newstreamname=='' else newstreamname def current_stream_name(self): return self._current_stream_name def finish_current_stream(self): @@ -751,40 +795,202 @@ class CollectionWriter: manifest += "\n" return manifest +global_client_object = None + class Keep: @staticmethod - def put(data): - if 'KEEP_LOCAL_STORE' in os.environ: - return Keep.local_store_put(data) - p = subprocess.Popen(["whput", "-"], - stdout=subprocess.PIPE, - stdin=subprocess.PIPE, - stderr=subprocess.PIPE, - shell=False, close_fds=True) - stdoutdata, stderrdata = p.communicate(data) - if p.returncode != 0: - raise Exception("whput subprocess exited %d - stderr:\n%s" % (p.returncode, stderrdata)) - return stdoutdata.rstrip() + def global_client_object(): + global global_client_object + if global_client_object == None: + global_client_object = KeepClient() + return global_client_object + + @staticmethod + def get(locator, **kwargs): + return Keep.global_client_object().get(locator, **kwargs) + @staticmethod - def get(locator): + def put(data, **kwargs): + return Keep.global_client_object().put(data, **kwargs) + +class KeepClient(object): + + class ThreadLimiter(object): + """ + Limit the number of threads running at a given time to + {desired successes} minus {successes reported}. When successes + reported == desired, wake up the remaining threads and tell + them to quit. + + Should be used in a "with" block. + """ + def __init__(self, todo): + self._todo = todo + self._done = 0 + self._todo_lock = threading.Semaphore(todo) + self._done_lock = threading.Lock() + def __enter__(self): + self._todo_lock.acquire() + return self + def __exit__(self, type, value, traceback): + self._todo_lock.release() + def shall_i_proceed(self): + """ + Return true if the current thread should do stuff. Return + false if the current thread should just stop. + """ + with self._done_lock: + return (self._done < self._todo) + def increment_done(self): + """ + Report that the current thread was successful. + """ + with self._done_lock: + self._done += 1 + def done(self): + """ + Return how many successes were reported. + """ + with self._done_lock: + return self._done + + class KeepWriterThread(threading.Thread): + """ + Write a blob of data to the given Keep server. Call + increment_done() of the given ThreadLimiter if the write + succeeds. + """ + def __init__(self, **kwargs): + super(KeepClient.KeepWriterThread, self).__init__() + self.args = kwargs + def run(self): + with self.args['thread_limiter'] as limiter: + if not limiter.shall_i_proceed(): + # My turn arrived, but the job has been done without + # me. + return + logging.debug("KeepWriterThread %s proceeding %s %s" % + (str(threading.current_thread()), + self.args['data_hash'], + self.args['service_root'])) + h = httplib2.Http() + url = self.args['service_root'] + self.args['data_hash'] + api_token = os.environ['ARVADOS_API_TOKEN'] + headers = {'Authorization': "OAuth2 %s" % api_token} + try: + resp, content = h.request(url.encode('utf-8'), 'PUT', + headers=headers, + body=self.args['data']) + if (resp['status'] == '401' and + re.match(r'Timestamp verification failed', content)): + body = KeepClient.sign_for_old_server( + self.args['data_hash'], + self.args['data']) + h = httplib2.Http() + resp, content = h.request(url.encode('utf-8'), 'PUT', + headers=headers, + body=body) + if re.match(r'^2\d\d$', resp['status']): + logging.debug("KeepWriterThread %s succeeded %s %s" % + (str(threading.current_thread()), + self.args['data_hash'], + self.args['service_root'])) + return limiter.increment_done() + logging.warning("Request fail: PUT %s => %s %s" % + (url, resp['status'], content)) + except (httplib2.HttpLib2Error, httplib.HTTPException) as e: + logging.warning("Request fail: PUT %s => %s: %s" % + (url, type(e), str(e))) + + def __init__(self): + self.lock = threading.Lock() + self.service_roots = None + + def shuffled_service_roots(self, hash): + if self.service_roots == None: + self.lock.acquire() + keep_disks = api().keep_disks().list().execute()['items'] + roots = (("http%s://%s:%d/" % + ('s' if f['service_ssl_flag'] else '', + f['service_host'], + f['service_port'])) + for f in keep_disks) + self.service_roots = sorted(set(roots)) + logging.debug(str(self.service_roots)) + self.lock.release() + seed = hash + pool = self.service_roots[:] + pseq = [] + while len(pool) > 0: + if len(seed) < 8: + if len(pseq) < len(hash) / 4: # first time around + seed = hash[-4:] + hash + else: + seed += hash + probe = int(seed[0:8], 16) % len(pool) + pseq += [pool[probe]] + pool = pool[:probe] + pool[probe+1:] + seed = seed[8:] + logging.debug(str(pseq)) + return pseq + + def get(self, locator): if 'KEEP_LOCAL_STORE' in os.environ: - return Keep.local_store_get(locator) - p = subprocess.Popen(["whget", locator, "-"], - stdout=subprocess.PIPE, - stdin=None, - stderr=subprocess.PIPE, - shell=False, close_fds=True) - stdoutdata, stderrdata = p.communicate(None) - if p.returncode != 0: - raise Exception("whget subprocess exited %d - stderr:\n%s" % (p.returncode, stderrdata)) + return KeepClient.local_store_get(locator) + expect_hash = re.sub(r'\+.*', '', locator) + for service_root in self.shuffled_service_roots(expect_hash): + h = httplib2.Http() + url = service_root + expect_hash + api_token = os.environ['ARVADOS_API_TOKEN'] + headers = {'Authorization': "OAuth2 %s" % api_token, + 'Accept': 'application/octet-stream'} + try: + resp, content = h.request(url.encode('utf-8'), 'GET', + headers=headers) + if re.match(r'^2\d\d$', resp['status']): + m = hashlib.new('md5') + m.update(content) + md5 = m.hexdigest() + if md5 == expect_hash: + return content + logging.warning("Checksum fail: md5(%s) = %s" % (url, md5)) + except (httplib2.HttpLib2Error, httplib.ResponseNotReady) as e: + logging.info("Request fail: GET %s => %s: %s" % + (url, type(e), str(e))) + raise Exception("Not found: %s" % expect_hash) + + def put(self, data, **kwargs): + if 'KEEP_LOCAL_STORE' in os.environ: + return KeepClient.local_store_put(data) m = hashlib.new('md5') - m.update(stdoutdata) - try: - if locator.index(m.hexdigest()) == 0: - return stdoutdata - except ValueError: - pass - raise Exception("md5 checksum mismatch: md5(get(%s)) == %s" % (locator, m.hexdigest())) + m.update(data) + data_hash = m.hexdigest() + have_copies = 0 + want_copies = kwargs.get('copies', 2) + if not (want_copies > 0): + return data_hash + threads = [] + thread_limiter = KeepClient.ThreadLimiter(want_copies) + for service_root in self.shuffled_service_roots(data_hash): + t = KeepClient.KeepWriterThread(data=data, + data_hash=data_hash, + service_root=service_root, + thread_limiter=thread_limiter) + t.start() + threads += [t] + for t in threads: + t.join() + have_copies = thread_limiter.done() + if have_copies == want_copies: + return (data_hash + '+' + str(len(data))) + raise Exception("Write fail for %s: wanted %d but wrote %d" % + (data_hash, want_copies, have_copies)) + + @staticmethod + def sign_for_old_server(data_hash, data): + return (("-----BEGIN PGP SIGNED MESSAGE-----\n\n\n%d %s\n-----BEGIN PGP SIGNATURE-----\n\n-----END PGP SIGNATURE-----\n" % (int(time.time()), data_hash)) + data) + + @staticmethod def local_store_put(data): m = hashlib.new('md5')