def run(self):
_LOG.debug('launching %s.' % " ".join(self._invocation))
k = self._k
proc_cwd = k.get('cwd', os.curdir)
stdout_file_path = k.get('stdout', None)
stderr_file_path = k.get('stderr', None)
if stdout_file_path:
_stdout_fo = open_with_intermediates(stdout_file_path, 'w')
else:
_stdout_fo = open_with_intermediates(
os.path.join(proc_cwd, '.Job.stdout.txt'), 'w')
k['stdout'] = _stdout_fo
if stderr_file_path:
_stderr_fo = open_with_intermediates(stderr_file_path, 'w')
else:
_stderr_fo = open_with_intermediates(
os.path.join(proc_cwd, '.Job.stderr.txt'), 'w')
k['stderr'] = _stderr_fo
for key, v in self.environ.items():
os.environ[key] = v
process = Popen(self._invocation, stdin=PIPE, **k)
err_msg = []
err_msg.append(
"PASTA failed because one of the programs it tried to run failed.")
err_msg.append('The invocation that failed was: \n "%s"\n' %
'" "'.join(self._invocation))
try:
self.return_code = process.wait()
_stdout_fo.close()
_stderr_fo.close()
process.stdin.close()
if self.return_code:
errorFromFile = self.read_stderr(_stderr_fo)
if errorFromFile:
err_msg.append(errorFromFile)
self.error = "\n".join(err_msg)
raise Exception("")
_LOG.debug(
'Finished %s.\n Return code: %s; %s' %
(" ".join(self._invocation), self.return_code, self.error))
except Exception as e:
err_msg.append(str(e))
self.error = "\n".join(err_msg)
_LOG.error(self.error)
def save_to_filepath(self, filepath):
if filepath is None:
filepath = os.path.expanduser(os.path.join( '~', '.pasta', 'pasta.cfg'))
f = open_with_intermediates(filepath, 'w')
for g in self.get_categories():
g.set_config_parser_fields(self._config_parser)
self._config_parser.write(f)
f.close()
def create_input_files(self, job_subdir, input_subdir=None):
src_paths = []
seq_dir = os.path.join(self.top_dir, job_subdir)
if input_subdir is not None:
seq_dir = os.path.join(seq_dir, input_subdir)
for i in range(5):
fp = os.path.join(seq_dir, "data%d.fasta" % (i + 1))
src_paths.append(fp)
f = filemgr.open_with_intermediates(fp, "w")
f.close()
return src_paths
def run(self):
_LOG.debug('launching %s.' % " ".join(self._invocation))
k = self._k
proc_cwd = k.get('cwd', os.curdir)
stdout_file_path = k.get('stdout', None)
stderr_file_path = k.get('stderr', None)
if stdout_file_path:
_stdout_fo = open_with_intermediates(stdout_file_path, 'w')
else:
_stdout_fo = open_with_intermediates(os.path.join(proc_cwd, '.Job.stdout.txt'), 'w')
k['stdout'] = _stdout_fo
if stderr_file_path:
_stderr_fo = open_with_intermediates(stderr_file_path, 'w')
else:
_stderr_fo = open_with_intermediates(os.path.join(proc_cwd, '.Job.stderr.txt'), 'w')
k['stderr'] = _stderr_fo
for key,v in self.environ.items():
os.environ[key] = v
process = Popen(self._invocation, stdin = PIPE, **k)
err_msg = []
err_msg.append("PASTA failed because one of the programs it tried to run failed.")
err_msg.append('The invocation that failed was: \n "%s"\n' % '" "'.join(self._invocation))
try:
self.return_code = process.wait()
_stdout_fo.close()
_stderr_fo.close()
process.stdin.close()
if self.return_code:
errorFromFile = self.read_stderr(_stderr_fo)
if errorFromFile:
err_msg.append(errorFromFile)
self.error = "\n".join(err_msg)
raise Exception("")
_LOG.debug('Finished %s.\n Return code: %s; %s' % (" ".join(self._invocation), self.return_code, self.error))
except Exception as e:
err_msg.append(str(e))
self.error = "\n".join(err_msg)
_LOG.error(self.error)
def create_input_files(self,
job_subdir,
input_subdir=None):
src_paths = []
seq_dir = os.path.join(self.top_dir, job_subdir)
if input_subdir is not None:
seq_dir = os.path.join(seq_dir, input_subdir)
for i in range(5):
fp = os.path.join(seq_dir, "data%d.fasta" % (i+1))
src_paths.append(fp)
f = filemgr.open_with_intermediates(fp, "w")
f.close()
return src_paths
def _write_partition_filepath(self, parfn, partitions, model):
# partition --- list of tuples, [("DNA", 1, 30), ("DNA", 31, 60), ("PROTEIN", 61, 100)]
file_obj = open_with_intermediates(parfn,'w')
count = 0
for item in partitions:
key = ""
count += 1
if item[0] == "DNA":
key = "DNA"
elif item[0] == "PROTEIN":
if model.startswith("PROTGAMMA"):
key = model[len("PROTGAMMAI"):] if model.startswith("PROTGAMMAI") else model[len("PROTGAMMA"):]
if model.startswith("PROTCAT"):
key = model[len("PROTCATI"):] if model.startswith("PROTCATI") else model[len("PROTCAT"):]
file_obj.write("%s, p%s=%s-%s\n" % (key, count, item[1], item[2]) )
file_obj.close()
def _write_partition_filepath(self, parfn, partitions, model):
# partition --- list of tuples, [("DNA", 1, 30), ("DNA", 31, 60), ("PROTEIN", 61, 100)]
file_obj = open_with_intermediates(parfn, 'w')
count = 0
for item in partitions:
key = ""
count += 1
if item[0] == "DNA":
key = "DNA"
elif item[0] == "PROTEIN":
if model.startswith("PROTGAMMA"):
key = model[len("PROTGAMMAI"):] if model.startswith(
"PROTGAMMAI") else model[len("PROTGAMMA"):]
if model.startswith("PROTCAT"):
key = model[len("PROTCATI"):] if model.startswith(
"PROTCATI") else model[len("PROTCAT"):]
file_obj.write("%s, p%s=%s-%s\n" % (key, count, item[1], item[2]))
file_obj.close()
def run(self):
_LOG.debug('launching %s.' % " ".join(self._invocation))
k = self._k
proc_cwd = k.get('cwd', os.curdir)
stdout_file_path = k.get('stdout', None)
stderr_file_path = k.get('stderr', None)
if stdout_file_path:
_stdout_fo = open_with_intermediates(stdout_file_path, 'w')
else:
_stdout_fo = open_with_intermediates(os.path.join(proc_cwd, '.Job.stdout.txt'), 'w')
k['stdout'] = _stdout_fo
if stderr_file_path:
_stderr_fo = open_with_intermediates(stderr_file_path, 'w')
else:
_stderr_fo = open_with_intermediates(os.path.join(proc_cwd, '.Job.stderr.txt'), 'w')
k['stderr'] = _stderr_fo
for key, v in self.environ.items():
os.environ[key] = v
err_msg = []
err_msg.append("PASTA failed because one of the programs it tried to run failed.")
err_msg.append('The invocation that failed was: \n "%s"\n' % '" "'.join(self._invocation))
self.return_code = 0 # Initialization of return code
try:
command = ""
for item in self._invocation:
command = command + " "+item
# MESSENGER.send_info("[JMAbuin] Initial command "+command)
if configure_spark.isSpark():
fileIndex = 0
if(self._invocation[fileIndex] == "java"): # Case of opal
# MESSENGER.send_info("[JMAbuin] We are launching OPAL")
fileIndex = 3
# Check if Java is in our path
# MESSENGER.send_info("[JMAbuin] JAVA_HOME is " + os.getenv('JAVA_HOME'))
# MESSENGER.send_info("[JMAbuin] PATH is " + os.getenv('PATH'))
newJava = os.getenv('JAVA_HOME')+"/bin/java"
if newJava is not None:
self._invocation[0] = newJava
'''
current_dir = os.getcwd()
current_theoretical_dir = ""
currentItem = 0
totalItems = len(self._invocation[5].split("/"))
for item in self._invocation[5].split("/"):
if(currentItem > 0) and (totalItems - currentItem > 7):
current_theoretical_dir = current_theoretical_dir + "/" + item
currentItem += 1
if(current_dir != current_theoretical_dir):
self._invocation[5] = self._invocation[5].replace(current_theoretical_dir, current_dir)
self._invocation[7] = self._invocation[5].replace(current_theoretical_dir, current_dir)
self._invocation[9] = self._invocation[5].replace(current_theoretical_dir, current_dir)
'''
# Example: tempAHc28U/step0/centroid/pw/r5d2_r5d1/tempopal_waXAP/out.fasta
# First file:
self.changePermissions(self._invocation[5], 7)
self.changePermissions(self._invocation[7], 7)
self.changePermissions(self._invocation[9], 7)
execname = os.path.basename(self._invocation[fileIndex])
if (not os.path.isfile(self._invocation[fileIndex])):
MESSENGER.send_warning("[JMAbuin] " + self._invocation[fileIndex] + " does not exists! Finding it.")
if(os.path.isfile(os.getcwd() + "/pasta.zip/bin/" + execname)):
MESSENGER.send_info("[JMAbuin] Found " + execname + "!! => " + os.getcwd() + "/pasta.zip/bin/" + execname)
self._invocation[fileIndex] = os.getcwd() + "/pasta.zip/bin/" + execname
else:
newInvocationPath = self.findFile("../", execname)
if (os.path.isfile(newInvocationPath)):
MESSENGER.send_info("[JMAbuin] new " + execname + " path is " + newInvocationPath)
self._invocation[fileIndex] = newInvocationPath
else:
MESSENGER.send_error("[JMAbuin] Could not find " + execname + "!!")
# MESSENGER.send_info("[JMAbuin] Final " + execname + " => " + self._invocation[fileIndex])
command = ""
for item in self._invocation:
command = command + " " + item
#number_of_cpus = os.environ["OMP_NUM_THREADS"]
#MESSENGER.send_info("[JMAbuin] Final command " + command + "with " + number_of_cpus + " CPUS")
startTime = time.time()
process = Popen(self._invocation, stdin=PIPE, **k)
self.return_code = process.wait() # Chema aqui
endTime = time.time()
# process = Popen(self._invocation, stdin=PIPE, **k)
# (output, output_err) = process.communicate()
# self.return_code = process.returncode
MESSENGER.send_info("[JMAbuin] :: run :: return code from " + self._invocation[0] + " is: " + str(self.return_code) + " and execution time is: " + str(endTime - startTime) + " seconds.")
if "fasttreeMP" in self._invocation[0]:
MESSENGER.send_info("[JMAbuin] running fastree in parallel")
command = ""
for item in self._invocation:
command = command + " " + item
number_of_cpus = os.environ["OMP_NUM_THREADS"]
MESSENGER.send_info("[JMAbuin] Final command " + command + " with " + number_of_cpus+" CPUS")
_stdout_fo.close()
_stderr_fo.close()
process.stdin.close()
if self.return_code < 0:
errorFromFile = self.read_stderr(_stderr_fo)
if errorFromFile:
err_msg.append(errorFromFile)
# err_msg.append(output_err)
self.error = "\n".join(err_msg)
raise Exception("")
_LOG.debug('Finished %s.\n Return code: %s; %s' % (" ".join(self._invocation), self.return_code, self.error))
except OSError as ose:
err_msg.append(str(ose))
self.error = "\n".join(err_msg)
MESSENGER.send_error("[JMAbuin] " + ose.message)
MESSENGER.send_error("[JMAbuin] " + ose.child_traceback)
_LOG.error(self.error)
sys.exit(ose.message + " :: "+ose.child_traceback)
except Exception as e:
err_msg.append(str(e.message))
self.error = "\n".join(err_msg)
MESSENGER.send_error("[JMAbuin] " + self.error)
_LOG.error(self.error)
sys.exit(e.message)
