class AlignerSlave(JobSlave):
"""
See also: Aligner.py, AlignerMaster.py
"""
def initialize(self, params):
"""
Initialize AlignerSlave.
@param params: dictionary with init parameters
@type params: {param:value}
"""
self.__dict__.update( params )
self.params = params
## Only the PATH must be updated from the master to run properly
os.environ["PATH"]=self.params['os.environ']["PATH"]
self.errorLog = LogFile( self.ferror, mode='a' )
def reportError(self, msg, d ):
"""
Report error.
@param msg: error message
@type msg: str
@param d: error data
@type d: any
"""
try:
s = '%s on %s, job %r\n' % (msg, os.uname()[1], d)
s += '\nErrorTrace:\n' + T.lastErrorTrace() + '\n'
self.errorLog.add( s )
try:
print msg
except:
pass
except Exception, why:
f = open('ErrorReportError_XRefineSlave','a')
f.write( str(why) )
try:
f.write( T.lastErrorTrace() )
except:
pass
f.close()
def go(self, dict):
"""
Run alignment job.
@param dict: dictionary with run parameters
@type dict: {param:value}
"""
d = {}
val = None
try:
T.flushPrint(self.progress_str)
for id, val in dict.items():
aligner_log = LogFile('%s/Aligner.log' % val["outFolder"])
d[id] = val
aligner_log.add('Slave aligns %s on %s' % (id, os.uname()[1]))
a = Aligner(outFolder=val["outFolder"], log=aligner_log)
## For the cross validation
if not os.path.exists(val["outFolder"] + TC.F_COFFEE):
input_file = val["outFolder"] + VS.F_TCOFFEE
alpha_path = self.prepareT_coffee(input_file)
a.align_for_modeller_inp(
pdbFiles=alpha_path,
fasta_templates=val["fastaTemplates"],
fasta_sequences=val["fastaSequences"],
fasta_target=val["fastaTarget"])
## For a classic project folder
else:
a.align_for_modeller_inp(
pdbFiles=val["pdbFiles"],
fasta_templates=val["fastaTemplates"],
fasta_sequences=val["fastaSequences"],
fasta_target=val["fastaTarget"])
a.go()
except Exception, why:
self.reportError('ERROR ' + str(why), val)
def go(self, dict):
"""
Run alignment job.
@param dict: dictionary with run parameters
@type dict: {param:value}
"""
d = {}
val = None
try:
T.flushPrint( self.progress_str )
for id, val in dict.items():
aligner_log = LogFile( '%s/Aligner.log' %val["outFolder"] )
d[id] = val
aligner_log.add('Slave aligns %s on %s' % (id,os.uname()[1]) )
a = Aligner( outFolder= val["outFolder"], log=aligner_log)
## For the cross validation
if not os.path.exists(val["outFolder"] + TC.F_COFFEE):
input_file = val["outFolder"] + VS.F_TCOFFEE
alpha_path = self.prepareT_coffee(input_file)
a.align_for_modeller_inp( pdbFiles=alpha_path,
fasta_templates=val["fastaTemplates"],
fasta_sequences=val["fastaSequences"],
fasta_target=val["fastaTarget"])
## For a classic project folder
else:
a.align_for_modeller_inp(pdbFiles=val["pdbFiles"],
fasta_templates=val["fastaTemplates"],
fasta_sequences=val["fastaSequences"],
fasta_target=val["fastaTarget"])
a.go()
except Exception, why:
self.reportError( 'ERROR '+str(why), val )
class AlignerSlave(JobSlave):
"""
See also: Aligner.py, AlignerMaster.py
"""
def initialize(self, params):
"""
Initialize AlignerSlave.
@param params: dictionary with init parameters
@type params: {param:value}
"""
self.__dict__.update(params)
self.params = params
## Only the PATH must be updated from the master to run properly
os.environ["PATH"] = self.params['os.environ']["PATH"]
self.errorLog = LogFile(self.ferror, mode='a')
def reportError(self, msg, d):
"""
Report error.
@param msg: error message
@type msg: str
@param d: error data
@type d: any
"""
try:
s = '%s on %s, job %r\n' % (msg, os.uname()[1], d)
s += '\nErrorTrace:\n' + T.lastErrorTrace() + '\n'
self.errorLog.add(s)
try:
print msg
except:
pass
except Exception, why:
f = open('ErrorReportError_XRefineSlave', 'a')
f.write(str(why))
try:
f.write(T.lastErrorTrace())
except:
pass
f.close()
class ModelSlave(JobSlave):
def initialize(self, params):
"""
Initialize AlignerSlave.
@param params: dictionary with init parameters
@type params: {param:value}
"""
self.__dict__.update( params )
self.params = params
self.errorLog = LogFile( self.ferror, mode='a' )
def reportError(self, msg, d ):
"""
Report error.
@param msg: error message
@type msg: str
@param d: error data
@type d: any
"""
try:
s = '%s on %s, job %r\n' % (msg, os.uname()[1], d)
s += '\nErrorTrace:\n' + T.lastErrorTrace() + '\n'
self.errorLog.add( s )
try:
print msg
except:
pass
except Exception, why:
f = open('ErrorReportError_XRefineSlave','a')
f.write( str(why) )
try:
f.write( T.lastErrorTrace() )
except:
pass
f.close()
class ModelSlave(JobSlave):
def initialize(self, params):
"""
Initialize AlignerSlave.
@param params: dictionary with init parameters
@type params: {param:value}
"""
self.__dict__.update(params)
self.params = params
self.errorLog = LogFile(self.ferror, mode='a')
def reportError(self, msg, d):
"""
Report error.
@param msg: error message
@type msg: str
@param d: error data
@type d: any
"""
try:
s = '%s on %s, job %r\n' % (msg, os.uname()[1], d)
s += '\nErrorTrace:\n' + T.lastErrorTrace() + '\n'
self.errorLog.add(s)
try:
print msg
except:
pass
except Exception, why:
f = open('ErrorReportError_XRefineSlave', 'a')
f.write(str(why))
try:
f.write(T.lastErrorTrace())
except:
pass
f.close()
class AmberEntropySlave( JobSlave ):
"""
Collect AmberEntropist jobs from AmberEntropyMaster and return result.
"""
def initialize(self, params):
"""
expects::
{'nice':int, 'ferror':str, .. }
@param params: initialisation parameters passed from the master
@type params: dict
"""
self.__dict__.update( params )
self.errorLog = LogFile( self.ferror, mode='a' )
def reportError(self, msg, id ):
try:
try:
print msg
except:
pass
msg = 'trouble with ' + msg
s = '%s on %s, run %s\n' % (msg, os.uname()[1], id)
s += '\Error:' + T.lastError()
s += '\nErrorTrace:\n' + T.lastErrorTrace() + '\n'
s += '\n'
self.errorLog.add( s )
except Exception, why:
f = open('ErrorReportError_AmberEntropySlave','a')
f.write( str(type(why)) )
try:
f.write( T.lastErrorTrace() )
except:
pass
f.close()
class AmberEntropySlave( JobSlave ):
"""
Collect AmberEntropist jobs from AmberEntropyMaster and return result.
"""
def initialize(self, params):
"""
expects::
{'nice':int, 'ferror':str, .. }
@param params: initialisation parameters passed from the master
@type params: dict
"""
self.__dict__.update( params )
self.errorLog = LogFile( self.ferror, mode='a' )
def reportError(self, msg, id ):
try:
try:
print msg
except:
pass
msg = 'trouble with ' + msg
s = '%s on %s, run %s\n' % (msg, os.uname()[1], id)
s += '\Error:' + T.lastError()
s += '\nErrorTrace:\n' + T.lastErrorTrace() + '\n'
s += '\n'
self.errorLog.add( s )
except Exception, why:
f = open('ErrorReportError_AmberEntropySlave','a')
f.write( str(type(why)) )
try:
f.write( T.lastErrorTrace() )
except:
pass
f.close()