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', ''] }