def __init__(self, messagelogger):
self.messagelogger = messagelogger
try:
self.base_output_folder = None
self.last_server_submitted_to = None
self.BlastServices = []
self.BlastServers = {}
self.samples_and_inputs = {}
self.samples_and_databases = {}
self.samples_and_algorithms = {}
self.batchSize = 500
self.list_splits = {}
self.list_jobs = {}
self.list_jobs_submitted = {}
self.list_jobs_completed = {}
self.serverLoads = {}
self.performance = Performance()
self.list_jobs_submitted_file = 'list_jobs_submitted.txt'
self.pending_job = None
self.displaylen = 0
self.migrationMatrix = {}
self.messagelogger.write("OK: Blast Broker initialized!\n")
except:
self.messagelogger.write(
"ERROR: Failed to initialize Blast Broker!\n")
sys.exit(0)
return None
def __init__(self, gridParams):
self.user = None
self.service = None
self.walltime= None
self.remoteActiveFiles = {}
self.remoteActiveFolders= {}
self.remoteFormattedDBs = {}
self.serverUp = False
self.isaws=False
self.awsparams={}
self.remote_home_dir = '~'
self.working_directory='~'
self.base_output_folder= None
self.max_parallel_jobs = 4
self.os = 'mac'
self.bits = 'bit64'
self.type ='ordinary'
self.sub_string = ""
self.performance = Performance()
self.A =1
self.B =1
self.C =1
self.D =1
try:
for key, value in gridParams.iteritems():
setattr(self, key, value)
except:
print "ERROR : in creating BlastService"
pass
if not self.user:
self.messagelogger.write("ERROR: User for Grid service not specified\n")
sys.exit(0)
if not self.server:
self.messagelogger.write("ERROR: Service for Grid service not specified\n")
sys.exit(0)
self.Folders = [ 'MetaPathways', 'MetaPathways/databases', 'MetaPathways/executables', 'MetaPathways/samples', \
'MetaPathways/samples/.qstatdir']
self.Files = {
'blastp': [ 'executables' + PATHDELIM + self.os + PATHDELIM + self.bit, 'MetaPathways/executables/'],
'blastn': [ 'executables' + PATHDELIM + self.os + PATHDELIM + self.bit, 'MetaPathways/executables/'],\
'lastal': [ 'executables' + PATHDELIM + self.os + PATHDELIM + self.bit, 'MetaPathways/executables/'],\
'lastdb': [ 'executables' + PATHDELIM + self.os + PATHDELIM + self.bit, 'MetaPathways/executables/'],\
'makeblastdb': [ 'executables' + PATHDELIM + self.os + PATHDELIM + self.bit, 'MetaPathways/executables/'],\
'daemon.py': [ 'libs' + PATHDELIM + 'python_scripts', '']
}
