run.py
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Created: Sat, Jun 8, 17:15

run.py
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	#!/usr/bin/env python

	from __future__ import print_function

	import job
	import runconfig
	import conffile
	import sqlobject
	import base
	import sys
	import bdparser as bdp
	import re
	import numpy as np
	import datetime

	class Run(sqlobject.SQLObject):
	"""
	"""


	def attachToJob(self,job):
	self["job_id"] = job.id
	self.base.insert(self)
	self.addConfigFile(self.execfile)
	for cnffile in self.configfiles:
	self.addConfigFile(cnffile)

	def getExecFile(self):
	return self.getUpdatedConfigFile(self.entries["exec"])


	def addConfigFiles(self,file_list,regex_params=None):
	self.prepare()
	params_list = self.types.keys()
	myjob = job.Job(self.base)
	myjob.prepare()
	params_list += myjob.types.keys()

	#print (regex_params)
	self.configfiles += [ conffile.addFile(fname,self.base,\
	regex_params=regex_params,\
	params=params_list) for fname in file_list]
	return self.configfiles

	def addConfigFile(self,configfile):
	myrun_config = runconfig.RunConfig(self.base)
	myrun_config.prepare()
	myrun_config.attachToRun(self)
	myrun_config.addConfigFile(configfile)
	self.base.insert(myrun_config)

	def getConfigFiles(self):
	# myjob = job.Job(self.base)
	# myjob["id"] = self.entries["job_id"]
	# myjob = self.getMatchedObjectList()[0]

	runconf = runconfig.RunConfig(self.base)
	runconf["run_id"] = self.id
	runconf_list = runconf.getMatchedObjectList()
	conffiles = [self.getUpdatedConfigFile(f["configfile_id"]) for f in runconf_list]
	return conffiles

	def getConfigFile(self,file_id):
	runconf = runconfig.RunConfig(self.base)
	conf = conffile.ConfFile(self.base)
	conf.prepare()
	conf["id"] = file_id
	conf = conf.getMatchedObjectList()[0]
	return conf

	def getUpdatedConfigFile(self,file_id):
	conf = self.getConfigFile(file_id)

	myjob = job.Job(self.base)
	myjob.prepare()
	myjob["id"] = self.entries["job_id"]
	myjob = myjob.getMatchedObjectList()[0]
	for key,val in myjob.entries.iteritems():
	tmp = conf["file"].replace("__BLACKDYNAMITE__" + key + "__",str(val))
	if ((not tmp == conf["file"]) and val is None):
	raise Exception( "unset job parameter " + key)
	conf["file"] = tmp

	for key,val in self.entries.iteritems():
	tmp = conf["file"].replace("__BLACKDYNAMITE__" + key + "__",str(val))
	if ((not tmp == conf["file"]) and not val):
	raise Exception( "unset run parameter " + key)
	conf["file"] = tmp

	conf["file"] = conf["file"].replace("__BLACKDYNAMITE__dbhost__",self.base.dbhost)
	conf["file"] = conf["file"].replace("__BLACKDYNAMITE__study__",self.base.schema)
	conf["file"] = conf["file"].replace("__BLACKDYNAMITE__run_id__",str(self.id))
	return conf

	def listQuantities(self):
	request = "SELECT id,name FROM {0}.quantities WHERE (is_vector) = (false)".format(self.base.schema)
	curs = self.base.performRequest(request)
	all_quantities = [res[1] for res in curs]
	return all_quantities

	def getScalarQuantities(self,names,additional_request=None):


	request = "SELECT id,name FROM {0}.quantities WHERE (is_vector) = (false)".format(self.base.schema)
	params = []
	if (names):
	if (not type(names) == list):
	names = [names]
	request += " and ("
	for name in names:
	similar_op_match = re.match(r"\s(~)\s(.*)", name)
	op = " = "
	if (similar_op_match):
	op = " ~ "
	name = similar_op_match.group(2)
	request += " name " + op + "%s or"
	params.append(str(name))
	request = request[:len(request)-3] + ")"
	# print (request)
	# print (params)
	curs = self.base.performRequest(request,params)

	quantities = [res[1] for res in curs]
	if (len(quantities) == 0):
	print ("No quantity matches " + str(names))
	print ("Quantities declared in the database are \n" + "\n".join([res for res in self.listQuantities()]))
	sys.exit(-1)
	return None

	try:
	quant_indexes = [quantities.index(n) for n in names]
	quantities = names
	except:
	quant_indexes = None

	# print (quant)
	results = []
	for key in quantities:
	q = self.getScalarQuantity(key,additional_request)
	if (q is not None):
	results.append([key,q])
	print ("got Quantity " + str(key) + " : " + str(q.shape[0]) + " values")
	return results

	def getScalarQuantity(self,name,additional_request=None):
	request = "SELECT id,is_integer FROM {0}.quantities WHERE (name,is_vector) = (%s,false)".format(self.base.schema)
	curs = self.base.performRequest(request,[name])
	item = curs.fetchone()
	if (item is None):
	raise Exception("unknown quantity \"" + name + "\"")
	quantity_id = item[0]
	is_integer = item[1]
	request = "SELECT step,measurement from {0}.{1} WHERE (run_id,quantity_id) = ({2},{3})".format(self.base.schema,"scalar_real" if (is_integer == False) else "scalar_integer",self.id,quantity_id)
	if (additional_request):
	request += " and " + " and ".join(additional_request)
	request += " ORDER BY step"
	curs.execute(request,[name])
	fetch = curs.fetchall()
	if (not fetch):
	return None
	return (np.array([(val[0],val[1]) for val in fetch]))


	def getVectorQuantity(self,name, step):
	request = "SELECT id,is_integer FROM {0}.quantities WHERE (name,is_vector) = (%s,true)".format(self.base.schema)
	curs = self.base.performRequest(request,[name])
	item = curs.fetchone()
	if (item is None):
	raise Exception("unknown quantity \"" + name + "\"")
	quantity_id = item[0]
	is_integer = item[1]
	request = "SELECT measurement from {0}.{1} WHERE (run_id,quantity_id,step) = ({2},{3},{4})".format(self.base.schema,"vector_real" if (is_integer == False) else "vector_integer",self.id,quantity_id,step)
	curs.execute(request,[name])
	fetch = curs.fetchone()
	if (fetch):
	return np.array(fetch[0])
	return None

	def getAllVectorQuantity(self,name):
	request = "SELECT id,is_integer FROM {0}.quantities WHERE (name,is_vector) = (%s,true)".format(self.base.schema)
	curs = self.base.performRequest(request,[name])
	item = curs.fetchone()
	if (item is None):
	raise Exception("unknown quantity \"" + name + "\"")
	quantity_id = item[0]
	is_integer = item[1]
	request = "SELECT step,measurement from {0}.{1} WHERE (run_id,quantity_id) = ({2},{3}) order by step".format(self.base.schema,"vector_real" if (is_integer == False) else "vector_integer",self.id,quantity_id)
	curs.execute(request,[name])
	fetch = curs.fetchall()
	if (not fetch):
	return None
	matres = np.array([val[1] for val in fetch])
	stepres = np.array([val[0] for val in fetch])
	return (stepres,matres)


	def __init__ (self,base):
	sqlobject.SQLObject.__init__(self,base)
	self.table_name = "runs"
	self.foreign_keys["job_id"] = "jobs"
	self.types["machine_name"] = str
	self.types["run_path"] = str
	self.allowNull["run_path"] = True
	self.types["job_id"] = int
	self.types["nproc"] = int
	self.types["run_name"] = str
	self.types["wait_id"] = int
	self.allowNull["wait_id"] = True
	self.types["start_time"] = datetime.datetime
	self.allowNull["start_time"] = True
	self.types["state"] = str
	self.allowNull["state"] = True
	self.execfile = None
	self.configfiles = []
	self.types["exec"] = str

	################################################################

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