def _updateProtocol(self, prot):
prot2 = getProtocolFromDb(prot.getProject().path, prot.getDbPath(),
prot.getObjId())
# Close DB connections
prot2.getProject().closeMapper()
prot2.closeMappers()
return prot2
def _loadProt():
# Load the last version of the protocol from its own database
loadedProt = getProtocolFromDb(prot.getProject().path,
prot.getDbPath(), prot.getObjId())
# Close DB connections
loadedProt.getProject().closeMapper()
loadedProt.closeMappers()
return loadedProt
def _getUpdatedProtocol(self):
prot = self.protocol
prot2 = getProtocolFromDb(self.protocol.getProject().path,
prot.getDbPath(), prot.getObjId())
# Close DB connections
prot2.getProject().closeMapper()
prot2.closeMappers()
return prot2
def _updateProtocol(self, prot):
prot2 = getProtocolFromDb(prot.getProject().path,
prot.getDbPath(),
prot.getObjId())
# Close DB connections
prot2.getProject().closeMapper()
prot2.closeMappers()
return prot2
def _updateProtocol(self, protocol):
""" Retrieve the updated protocol
"""
prot2 = getProtocolFromDb(protocol.getProject().path,
protocol.getDbPath(), protocol.getObjId())
# Close DB connections
prot2.closeMappers()
return prot2
def getUpdatedProtocol(protocol):
""" Retrieve the updated protocol and close db connections
"""
prot2 = getProtocolFromDb(os.getcwd(), protocol.getDbPath(),
protocol.getObjId())
# Close DB connections
prot2.getProject().closeMapper()
prot2.closeMappers()
return prot2
def _loadProt():
# Load the last version of the protocol from its own database
prot2 = getProtocolFromDb(prot.getProject().path,
prot.getDbPath(),
prot.getObjId())
# Close DB connections
prot2.getProject().closeMapper()
prot2.closeMappers()
return prot2
def updateProtocol(cls, prot):
""" Method used for streaming when we need to update
the protocol to check if there are new outputs.
"""
prot2 = getProtocolFromDb(prot.getProject().path, prot.getDbPath(),
prot.getObjId())
# Close DB connections
prot2.getProject().closeMapper()
prot2.closeMappers()
return prot2
def _updateProtocol(self, protocol, tries=0, checkPid=False):
# If this is read only exit
if self.isReadOnly(): return
# If we are already updated, comparing timestamps
if pwprot.isProtocolUpToDate(protocol): return
try:
# Backup the values of 'jobId', 'label' and 'comment'
# to be restored after the .copy
jobId = protocol.getJobId()
label = protocol.getObjLabel()
comment = protocol.getObjComment()
# If the protocol database has ....
# Comparing date will not work unless we have a reliable
# lastModificationDate of a protocol in the project.sqlite
# TODO: when launching remote protocols, the db should be
# TODO: retrieved in a different way.
prot2 = pwprot.getProtocolFromDb(self.path,
protocol.getDbPath(),
protocol.getObjId())
if checkPid:
self.checkPid(prot2)
# Copy is only working for db restored objects
protocol.setMapper(self.mapper)
protocol.copy(prot2, copyId=False)
# Restore backup values
protocol.setJobId(jobId)
protocol.setObjLabel(label)
protocol.setObjComment(comment)
protocol.lastUpdateTimeStamp.set(datetime.datetime.now())
self.mapper.store(protocol)
# Close DB connections
prot2.getProject().closeMapper()
prot2.closeMappers()
except Exception, ex:
print("Error trying to update protocol: %s(jobId=%s)\n "
"ERROR: %s, tries=%d"
% (protocol.getObjName(), jobId, ex, tries))
if tries == 3: # 3 tries have been failed
traceback.print_exc()
# If any problem happens, the protocol will be marked
# with a FAILED status
protocol.setFailed(str(ex))
self.mapper.store(protocol)
else:
time.sleep(0.5)
self._updateProtocol(protocol, tries + 1)
def _updateProtocol(self, protocol, tries=0):
if not self.isReadOnly():
try:
# Backup the values of 'jobId', 'label' and 'comment'
# to be restored after the .copy
jobId = protocol.getJobId()
label = protocol.getObjLabel()
comment = protocol.getObjComment()
# TODO: when launching remote protocols, the db should be retrieved
# in a different way.
# join(protocol.getHostConfig().getHostPath(), protocol.getDbPath())
prot2 = pwprot.getProtocolFromDb(self.path,
protocol.getDbPath(),
protocol.getObjId())
# Copy is only working for db restored objects
protocol.setMapper(self.mapper)
protocol.copy(prot2, copyId=False)
# Restore backup values
protocol.setJobId(jobId)
protocol.setObjLabel(label)
protocol.setObjComment(comment)
self.mapper.store(protocol)
# Close DB connections
prot2.getProject().closeMapper()
prot2.closeMappers()
except Exception, ex:
print "Error trying to update protocol: %s(jobId=%s)\n ERROR: %s, tries=%d" % (
protocol.getObjName(), jobId, ex, tries)
if tries == 3: # 3 tries have been failed
traceback.print_exc()
# If any problem happens, the protocol will be marked with a status fail
protocol.setFailed(str(ex))
self.mapper.store(protocol)
else:
time.sleep(0.5)
self._updateProtocol(protocol, tries + 1)
mode = sys.argv[1]
if mode not in ['run', 'stop']:
usage("Mode should be 'run' or 'stop'. Received: '%s'" % mode)
projectPath = os.path.join(os.environ['SCIPION_USER_DATA'], 'projects',
sys.argv[2])
print "projectPath: ", projectPath
protDbPath = sys.argv[3]
protId = int(sys.argv[4])
from pyworkflow.protocol import getProtocolFromDb
from pyworkflow.protocol.launch import launch, stop
protocol = getProtocolFromDb(projectPath, protDbPath, protId, chdir=False)
# We need to change the hostname to localhost, since it will
# be considered 'local' from now on to either run or stop
protocol.setHostName('localhost')
if mode == 'run':
FNULL = open(os.devnull, 'w')
jobId = launch(protocol,
stdin=None,
stdout=FNULL,
stderr=subprocess.STDOUT)
print "Scipion remote jobid: %d" % jobId
elif mode == 'stop':
stop(protocol)
else:
usage()
usage("Received only %d arguments" % n)
mode = sys.argv[1]
if mode not in ['run', 'stop']:
usage("Mode should be 'run' or 'stop'. Received: '%s'" % mode)
projectPath = os.path.join(os.environ['SCIPION_USER_DATA'], 'projects', sys.argv[2])
print "projectPath: ", projectPath
protDbPath = sys.argv[3]
protId = int(sys.argv[4])
from pyworkflow.protocol import getProtocolFromDb
from pyworkflow.protocol.launch import launch, stop
protocol = getProtocolFromDb(projectPath, protDbPath, protId, chdir=False)
# We need to change the hostname to localhost, since it will
# be considered 'local' from now on to either run or stop
protocol.setHostName('localhost')
if mode == 'run':
FNULL = open(os.devnull, 'w')
jobId = launch(protocol, stdin=None, stdout=FNULL, stderr=subprocess.STDOUT)
print "Scipion remote jobid: %d" % jobId
elif mode == 'stop':
stop(protocol)
else:
usage()
def _loadProtocol(self):
return getProtocolFromDb(self._args.projPath,
self._args.dbPath,
self._args.protId,
chdir=True)
try:
from rpdb2 import start_embedded_debugger
from signal import signal, SIGUSR2
signal(SIGUSR2, lambda sig, frame: start_embedded_debugger('a'))
except ImportError:
pass
if __name__ == '__main__':
if len(sys.argv) > 2:
projPath = sys.argv[1]
dbPath = sys.argv[2]
protId = int(sys.argv[3])
from pyworkflow.protocol import runProtocolMain, getProtocolFromDb
# Enter to the project directory and load protocol from db
protocol = getProtocolFromDb(projPath, dbPath, protId, chdir=True)
mapper = protocol.getMapper()
log = open(protocol._getLogsPath('schedule.log'), 'w')
pid = os.getpid()
protocol.setPid(pid)
def _log(msg):
print >> log, "%s: %s" % (pwutils.prettyTimestamp(), msg)
log.flush()
_log("Scheduling protocol %s, pid: %s" % (protId, pid))
mapper.store(protocol)
mapper.commit()
mapper.close()
def _loadProtocol(self):
return getProtocolFromDb(self._args.projPath,
self._args.dbPath,
self._args.protId, chdir=True)
