X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/91876456cf62bbc18bb2e0b887182756596031ff..5620a47e20e004188e0f1d0245ae9e916575e806:/sdk/python/arvados.py diff --git a/sdk/python/arvados.py b/sdk/python/arvados.py index fd266b7b77..f017b1e06e 100644 --- a/sdk/python/arvados.py +++ b/sdk/python/arvados.py @@ -9,6 +9,10 @@ import subprocess import json import UserDict import re +import hashlib +import string +import bz2 +import zlib from apiclient import errors from apiclient.discovery import build @@ -59,6 +63,7 @@ def current_task(): t = service.job_tasks().get(uuid=os.environ['TASK_UUID']).execute() t = UserDict.UserDict(t) t.set_output = types.MethodType(task_set_output, t) + t.tmpdir = os.environ['TASK_TMPDIR'] _current_task = t return t @@ -68,6 +73,8 @@ def current_job(): if _current_job: return _current_job t = service.jobs().get(uuid=os.environ['JOB_UUID']).execute() + t = UserDict.UserDict(t) + t.tmpdir = os.environ['CRUNCH_WORK'] _current_job = t return t @@ -84,32 +91,50 @@ class job_setup: if if_sequence != current_task()['sequence']: return job_input = current_job()['script_parameters']['input'] - p = subprocess.Popen(["whls", job_input], - stdout=subprocess.PIPE, - stdin=None, stderr=None, - shell=False, close_fds=True) - for f in p.stdout.read().split("\n"): - if f != '': - task_input = job_input + '/' + re.sub(r'^\./', '', f) + cr = CollectionReader(job_input) + for s in cr.all_streams(): + for f in s.all_files(): + task_input = f.as_manifest() new_task_attrs = { 'job_uuid': current_job()['uuid'], - 'created_by_job_task': current_task()['uuid'], + 'created_by_job_task_uuid': current_task()['uuid'], 'sequence': if_sequence + 1, 'parameters': { 'input':task_input } } service.job_tasks().create(job_task=json.dumps(new_task_attrs)).execute() - p.stdout.close() - p.wait() - if p.returncode != 0: - raise Exception("whls exited %d" % p.returncode) if and_end_task: service.job_tasks().update(uuid=current_task()['uuid'], job_task=json.dumps({'success':True}) ).execute() exit(0) +class util: + @staticmethod + def run_command(execargs, **kwargs): + p = subprocess.Popen(execargs, close_fds=True, shell=False, + stdin=subprocess.PIPE, + stdout=subprocess.PIPE, + stderr=subprocess.PIPE, + **kwargs) + stdoutdata, stderrdata = p.communicate(None) + if p.returncode != 0: + raise Exception("run_command %s exit %d:\n%s" % + (execargs, p.returncode, stderrdata)) + return stdoutdata, stderrdata + + @staticmethod + def git_checkout(url, version, path): + if not re.search('^/', path): + path = os.path.join(current_job().tmpdir, path) + if not os.path.exists(path): + util.run_command(["git", "clone", url, path], + cwd=os.path.dirname(path)) + util.run_command(["git", "checkout", version], + cwd=path) + return path + class DataReader: def __init__(self, data_locator): self.data_locator = data_locator @@ -131,4 +156,355 @@ class DataReader: self.p.stderr.close() self.p.wait() if self.p.returncode != 0: - raise Exception("subprocess exited %d" % self.p.returncode) + raise Exception("whget subprocess exited %d" % self.p.returncode) + +class StreamFileReader: + def __init__(self, stream, pos, size, name): + self._stream = stream + self._pos = pos + self._size = size + self._name = name + self._filepos = 0 + def name(self): + return self._name + def decompressed_name(self): + return re.sub('\.(bz2|gz)$', '', self._name) + def size(self): + return self._size + def stream_name(self): + return self._stream.name() + def read(self, size, **kwargs): + self._stream.seek(self._pos + self._filepos) + data = self._stream.read(min(size, self._size - self._filepos)) + self._filepos += len(data) + return data + def readall(self, size, **kwargs): + while True: + data = self.read(size, **kwargs) + if data == '': + break + yield data + def bunzip2(self, size): + decompressor = bz2.BZ2Decompressor() + for chunk in self.readall(size): + data = decompressor.decompress(chunk) + if data and data != '': + yield data + def gunzip(self, size): + decompressor = zlib.decompressobj(16+zlib.MAX_WBITS) + for chunk in self.readall(size): + data = decompressor.decompress(decompressor.unconsumed_tail + chunk) + if data and data != '': + yield data + def readlines(self, decompress=True): + self._stream.seek(self._pos + self._filepos) + if decompress and re.search('\.bz2$', self._name): + datasource = self.bunzip2(2**10) + elif decompress and re.search('\.gz$', self._name): + datasource = self.gunzip(2**10) + else: + datasource = self.readall(2**10) + data = '' + for newdata in datasource: + data += newdata + sol = 0 + while True: + eol = string.find(data, "\n", sol) + if eol < 0: + break + yield data[sol:eol+1] + sol = eol+1 + data = data[sol:] + if data != '': + yield data + def as_manifest(self): + if self.size() == 0: + return ("%s d41d8cd98f00b204e9800998ecf8427e+0 0:0:%s\n" + % (self._stream.name(), self.name())) + return string.join(self._stream.tokens_for_range(self._pos, self._size), + " ") + "\n" + +class StreamReader: + def __init__(self, tokens): + self._tokens = tokens + self._current_datablock_data = None + self._current_datablock_pos = 0 + self._current_datablock_index = -1 + self._pos = 0 + + self._stream_name = None + self.data_locators = [] + self.files = [] + + for tok in self._tokens: + if self._stream_name == None: + self._stream_name = tok + elif re.search(r'^[0-9a-f]{32}(\+\S+)*$', tok): + self.data_locators += [tok] + elif re.search(r'^\d+:\d+:\S+', tok): + pos, size, name = tok.split(':',2) + self.files += [[int(pos), int(size), name]] + else: + raise Exception("Invalid manifest format") + def tokens_for_range(self, range_start, range_size): + resp = [self._stream_name] + return_all_tokens = False + block_start = 0 + token_bytes_skipped = 0 + for locator in self.data_locators: + sizehint = re.search(r'\+(\d+)', locator) + if not sizehint: + return_all_tokens = True + if return_all_tokens: + resp += [locator] + next + blocksize = int(sizehint.group(0)) + if range_start + range_size <= block_start: + break + if range_start < block_start + blocksize: + resp += [locator] + else: + token_bytes_skipped += blocksize + block_start += blocksize + for f in self.files: + if ((f[0] < range_start + range_size) + and + (f[0] + f[1] > range_start) + and + f[1] > 0): + resp += ["%d:%d:%s" % (f[0] - token_bytes_skipped, f[1], f[2])] + return resp + def name(self): + return self._stream_name + def all_files(self): + for f in self.files: + pos, size, name = f + yield StreamFileReader(self, pos, size, name) + def nextdatablock(self): + if self._current_datablock_index < 0: + self._current_datablock_pos = 0 + self._current_datablock_index = 0 + else: + self._current_datablock_pos += self.current_datablock_size() + self._current_datablock_index += 1 + self._current_datablock_data = None + def current_datablock_data(self): + if self._current_datablock_data == None: + self._current_datablock_data = Keep.get(self.data_locators[self._current_datablock_index]) + return self._current_datablock_data + def current_datablock_size(self): + if self._current_datablock_index < 0: + self.nextdatablock() + sizehint = re.search('\+(\d+)', self.data_locators[self._current_datablock_index]) + if sizehint: + return int(sizehint.group(0)) + return len(self.current_datablock_data()) + def seek(self, pos): + """Set the position of the next read operation.""" + self._pos = pos + def really_seek(self): + """Find and load the appropriate data block, so the byte at + _pos is in memory. + """ + if self._pos == self._current_datablock_pos: + return True + if (self._current_datablock_pos != None and + self._pos >= self._current_datablock_pos and + self._pos <= self._current_datablock_pos + self.current_datablock_size()): + return True + if self._pos < self._current_datablock_pos: + self._current_datablock_index = -1 + self.nextdatablock() + while (self._pos > self._current_datablock_pos and + self._pos > self._current_datablock_pos + self.current_datablock_size()): + self.nextdatablock() + def read(self, size): + """Read no more than size bytes -- but at least one byte, + unless _pos is already at the end of the stream. + """ + if size == 0: + return '' + self.really_seek() + while self._pos >= self._current_datablock_pos + self.current_datablock_size(): + self.nextdatablock() + if self._current_datablock_index >= len(self.data_locators): + return None + data = self.current_datablock_data()[self._pos - self._current_datablock_pos : self._pos - self._current_datablock_pos + size] + self._pos += len(data) + return data + +class CollectionReader: + 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 + self._manifest_locator = None + else: + self._manifest_locator = manifest_locator_or_text + self._manifest_text = None + self._streams = None + def __enter__(self): + pass + def __exit__(self): + pass + def _populate(self): + if self._streams != None: + return + if not self._manifest_text: + self._manifest_text = Keep.get(self._manifest_locator) + self._streams = [] + for stream_line in self._manifest_text.split("\n"): + stream_tokens = stream_line.split() + self._streams += [stream_tokens] + def all_streams(self): + self._populate() + resp = [] + for s in self._streams: + resp += [StreamReader(s)] + return resp + def all_files(self): + for s in self.all_streams(): + for f in s.all_files(): + yield f + +class CollectionWriter: + KEEP_BLOCK_SIZE = 2**26 + def __init__(self): + self._data_buffer = [] + self._data_buffer_len = 0 + self._current_stream_files = [] + self._current_stream_length = 0 + self._current_stream_locators = [] + self._current_stream_name = '.' + self._current_file_name = None + self._current_file_pos = 0 + self._finished_streams = [] + def __enter__(self): + pass + def __exit__(self): + self.finish() + def write(self, newdata): + self._data_buffer += [newdata] + self._data_buffer_len += len(newdata) + self._current_stream_length += len(newdata) + while self._data_buffer_len >= self.KEEP_BLOCK_SIZE: + self.flush_data() + def flush_data(self): + data_buffer = ''.join(self._data_buffer) + if data_buffer != '': + self._current_stream_locators += [Keep.put(data_buffer[0:self.KEEP_BLOCK_SIZE])] + self._data_buffer = [data_buffer[self.KEEP_BLOCK_SIZE:]] + def start_new_file(self, newfilename=None): + self.finish_current_file() + self.set_current_file_name(newfilename) + def set_current_file_name(self, newfilename): + if re.search(r'[ \t\n]', newfilename): + raise AssertionError("Manifest filenames cannot contain whitespace") + self._current_file_name = newfilename + def current_file_name(self): + return self._current_file_name + def finish_current_file(self): + if self._current_file_name == None: + if self._current_file_pos == self._current_stream_length: + return + raise Exception("Cannot finish an unnamed file (%d bytes at offset %d in '%s' stream)" % (self._current_stream_length - self._current_file_pos, self._current_file_pos, self._current_stream_name)) + self._current_stream_files += [[self._current_file_pos, + self._current_stream_length - self._current_file_pos, + self._current_file_name]] + self._current_file_pos = self._current_stream_length + def start_new_stream(self, newstreamname=None): + self.finish_current_stream() + self.set_current_stream_name(newstreamname) + 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 + def current_stream_name(self): + return self._current_stream_name + def finish_current_stream(self): + self.finish_current_file() + self.flush_data() + if len(self._current_stream_files) == 0: + pass + elif self._current_stream_name == None: + raise Exception("Cannot finish an unnamed stream (%d bytes in %d files)" % (self._current_stream_length, len(self._current_stream_files))) + else: + self._finished_streams += [[self._current_stream_name, + self._current_stream_locators, + self._current_stream_files]] + self._current_stream_files = [] + self._current_stream_length = 0 + self._current_stream_locators = [] + self._current_stream_name = None + self._current_file_pos = 0 + self._current_file_name = None + def finish(self): + return Keep.put(self.manifest_text()) + def manifest_text(self): + self.finish_current_stream() + manifest = '' + for stream in self._finished_streams: + manifest += stream[0] + if len(stream[1]) == 0: + manifest += " d41d8cd98f00b204e9800998ecf8427e+0" + else: + for locator in stream[1]: + manifest += " %s" % locator + for sfile in stream[2]: + manifest += " %d:%d:%s" % (sfile[0], sfile[1], sfile[2]) + manifest += "\n" + return manifest + +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() + @staticmethod + def get(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)) + 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())) + @staticmethod + def local_store_put(data): + m = hashlib.new('md5') + m.update(data) + md5 = m.hexdigest() + locator = '%s+%d' % (md5, len(data)) + with open(os.path.join(os.environ['KEEP_LOCAL_STORE'], md5 + '.tmp'), 'w') as f: + f.write(data) + os.rename(os.path.join(os.environ['KEEP_LOCAL_STORE'], md5 + '.tmp'), + os.path.join(os.environ['KEEP_LOCAL_STORE'], md5)) + return locator + @staticmethod + def local_store_get(locator): + r = re.search('^([0-9a-f]{32,})', locator) + if not r: + raise Exception("Keep.get: invalid data locator '%s'" % locator) + if r.group(0) == 'd41d8cd98f00b204e9800998ecf8427e': + return '' + with open(os.path.join(os.environ['KEEP_LOCAL_STORE'], r.group(0)), 'r') as f: + return f.read()