def tests():
print "In tests"
VISHNU.vishnuInitialize(os.getenv("VISHNU_CONFIG_FILE"))
session = VISHNU.Session()
err = VISHNU.connect("root", "vishnu_user", session)
sessionKey = session.getSessionKey()
workId = 0
submitRequest = WebboardData(
sessionKey, "cluster1", '1', '1', workId,
"/home/ubuntu/Source/ApplicationScripts/Disseq/scripts/disseq_generic.sh",
"/home/ubuntu/Source/ApplicationScripts/Disseq/scripts/disseq.py", {
'query_file':
'/home/ubuntu/Source/ApplicationScripts/Disseq/examples/input1.fasta',
'base_file':
'/home/ubuntu/Source/ApplicationScripts/Disseq/examples/base.fas'
}, {
'disseq_algo': 'sw',
'disseq_dispSeqLen': 'no',
'disseq_printSeqID': 'no',
'nbSequence': '1'
})
execute(submitRequest)
print "out tests"
def test_update_machine(self):
ma = VISHNU.Machine()
ma.setName("bunny")
ma.setSite("test")
ma.setLanguage("fr")
ma.setMachineDescription("desc")
ma.setStatus(1)
r = VISHNU.addMachine(self.k, ma)
# Check with bad session key : fail
try:
VISHNU.updateMachine(self.k+"b'ad", ma)
except VISHNU.VishnuException, e :
self.assertEqual(28, e.getMsgI())
def test_update_user(self):
u = VISHNU.User()
u.setFirstname("bob")
u.setLastname("bob")
u.setEmail("*****@*****.**")
u.setPrivilege(0)
r = VISHNU.addUser(self.k, u)
self.assertEqual(0, r)
# Check with bad session key : fail
try:
r = VISHNU.updateUser(self.k + "ba'd", u)
except VISHNU.VishnuException, e:
self.assertEqual(28, e.getMsgI())
def tests():
print "In tests"
VISHNU.vishnuInitialize(os.getenv("VISHNU_CONFIG_FILE"))
session = VISHNU.Session()
err = VISHNU.connect("root", "vishnu_user", session)
sessionKey = session.getSessionKey()
workId =0
submitRequest = WebboardData(sessionKey,"cluster1",'1', '1',workId,"/home/ubuntu/Source/ApplicationScripts/Disseq/scripts/disseq_generic.sh","/home/ubuntu/Source/ApplicationScripts/Disseq/scripts/disseq.py",{'query_file': '/home/ubuntu/Source/ApplicationScripts/Disseq/examples/input1.fasta', 'base_file': '/home/ubuntu/Source/ApplicationScripts/Disseq/examples/base.fas' },{'disseq_algo':'sw','disseq_dispSeqLen' :'no','disseq_printSeqID' :'no','nbSequence' :'1' })
execute(submitRequest)
print "out tests"
def test_update_machine(self):
ma = VISHNU.Machine()
ma.setName("bunny")
ma.setSite("test")
ma.setLanguage("fr")
ma.setMachineDescription("desc")
ma.setStatus(1)
r = VISHNU.addMachine(self.k, ma)
# Check with bad session key : fail
try:
VISHNU.updateMachine(self.k + "b'ad", ma)
except VISHNU.VishnuException, e:
self.assertEqual(28, e.getMsgI())
def test_update_user(self):
u = VISHNU.User()
u.setFirstname("bob")
u.setLastname("bob")
u.setEmail("*****@*****.**")
u.setPrivilege(0)
r = VISHNU.addUser(self.k, u)
self.assertEqual(0, r)
# Check with bad session key : fail
try:
r = VISHNU.updateUser(self.k+"ba'd", u)
except VISHNU.VishnuException, e :
self.assertEqual(28, e.getMsgI())
def test_delete_machine(self):
ma = VISHNU.Machine()
ma.setName("bunny")
ma.setSite("test")
ma.setLanguage("fr")
ma.setMachineDescription("desc")
ma.setStatus(1)
r = VISHNU.addMachine(self.k, ma)
r = VISHNU.deleteMachine(self.k, ma.getMachineId())
r = VISHNU.addMachine(self.k, ma)
try:
r = VISHNU.deleteMachine(self.k+"ba'd", ma.getMachineId())
except VISHNU.VishnuException, e:
self.assertEqual(28, e.getMsgI())
def test_define_user_id(self):
# Define a format with quote
identifier = "$NAME'voila"
VISHNU.defineUserIdentifier(self.k,identifier)
# Create a user
u = VISHNU.User()
u.setFirstname("bob")
u.setLastname("'bob")
u.setEmail("*****@*****.**")
u.setPrivilege(0)
r = VISHNU.addUser(self.k, u)
self.assertEqual(0, r)
# Delete him
VISHNU.deleteUser(self.k, u.getUserId())
def test_delete_machine(self):
ma = VISHNU.Machine()
ma.setName("bunny")
ma.setSite("test")
ma.setLanguage("fr")
ma.setMachineDescription("desc")
ma.setStatus(1)
r = VISHNU.addMachine(self.k, ma)
r = VISHNU.deleteMachine(self.k, ma.getMachineId())
r = VISHNU.addMachine(self.k, ma)
try:
r = VISHNU.deleteMachine(self.k + "ba'd", ma.getMachineId())
except VISHNU.VishnuException, e:
self.assertEqual(28, e.getMsgI())
def test_add_machine(self):
ma = VISHNU.Machine()
ma.setName("bunny")
ma.setSite("test")
ma.setLanguage("fr")
ma.setMachineDescription("desc")
# Check we can add a machine
r = VISHNU.addMachine(self.k, ma)
self.assertEqual(0, r)
VISHNU.deleteMachine(self.k, ma.getMachineId())
# Check with bad session key : fail
try:
VISHNU.addMachine(self.k+"b'ad", ma)
except VISHNU.VishnuException, e :
self.assertEqual(28, e.getMsgI())
def test_delete_user(self):
u = VISHNU.User()
u.setFirstname("bob")
u.setLastname("bob")
u.setEmail("*****@*****.**")
u.setPrivilege(0)
VISHNU.addUser(self.k, u)
VISHNU.deleteUser(self.k, u.getUserId())
VISHNU.addUser(self.k, u)
try:
VISHNU.deleteUser(self.k + "ba'd", u.getUserId())
except VISHNU.VishnuException, e:
self.assertEqual(28, e.getMsgI())
def test_delete_user(self):
u = VISHNU.User()
u.setFirstname("bob")
u.setLastname("bob")
u.setEmail("*****@*****.**")
u.setPrivilege(0)
VISHNU.addUser(self.k, u)
VISHNU.deleteUser(self.k, u.getUserId())
VISHNU.addUser(self.k, u)
try:
VISHNU.deleteUser(self.k+"ba'd", u.getUserId())
except VISHNU.VishnuException, e:
self.assertEqual(28, e.getMsgI())
def tests():
print "In tests"
VISHNU.vishnuInitialize(os.getenv("VISHNU_CONFIG_FILE"))
session = VISHNU.Session()
err = VISHNU.connect("root", "vishnu_user", session)
sessionKey = session.getSessionKey()
workId = 0
submitRequest = WebboardData(
sessionKey, "cluster1", '1', '1', workId,
"/home/ubuntu/Source/ApplicationScripts/Blastp/scripts/blastp_generic.sh",
"/home/ubuntu/Source/ApplicationScripts/Blastp/scripts/pblastp.py", {
'query_file':
'/home/ubuntu/Source/ApplicationScripts/Blastp/examples/input3.fasta'
}, {
'blastp_used_db': 'Default',
'blastp_evalue': '1e-5',
'blastp_outfmt': '7',
'nbSequence': '2'
})
execute(submitRequest)
print "out tests"
class testUMS(unittest.TestCase):
def setUp(self):
self.sess = VISHNU.Session()
self.op = VISHNU.ConnectOptions()
VISHNU.vishnuInitialize(os.getenv("VISHNU_CONFIG_FILE"))
VISHNU.connect('root', 'vishnu_user', self.sess, self.op)
self.k = self.sess.getSessionKey()
def test_bad_key(self):
try:
VISHNU.listMachines(self.k + "b'ad")
except VISHNU.VishnuException, e:
self.assertEqual(28, e.getMsgI())
try:
VISHNU.listUsers(self.k + "b'ad")
except VISHNU.VishnuException, e:
self.assertEqual(28, e.getMsgI())
def test_define_user_id(self):
# Define a format with quote
identifier = "$NAME'voila"
VISHNU.defineUserIdentifier(self.k, identifier)
# Create a user
u = VISHNU.User()
u.setFirstname("bob")
u.setLastname("'bob")
u.setEmail("*****@*****.**")
u.setPrivilege(0)
r = VISHNU.addUser(self.k, u)
self.assertEqual(0, r)
# Delete him
VISHNU.deleteUser(self.k, u.getUserId())
def test_add_machine(self):
ma = VISHNU.Machine()
ma.setName("bunny")
ma.setSite("test")
ma.setLanguage("fr")
ma.setMachineDescription("desc")
# Check we can add a machine
r = VISHNU.addMachine(self.k, ma)
self.assertEqual(0, r)
VISHNU.deleteMachine(self.k, ma.getMachineId())
# Check with bad session key : fail
try:
VISHNU.addMachine(self.k + "b'ad", ma)
except VISHNU.VishnuException, e:
self.assertEqual(28, e.getMsgI())
def test_connection_bad_name(self):
sess = VISHNU.Session()
k = sess.getSessionKey()
VISHNU.vishnuInitialize(os.getenv("VISHNU_CONFIG_FILE"))
l = ["bad", "vishnu_user", sess]
self.assertRaises(VISHNU.VishnuException, VISHNU.connect, *l)
def test_connection(self):
sess = VISHNU.Session()
VISHNU.vishnuInitialize(os.getenv("VISHNU_CONFIG_FILE"))
VISHNU.connect("root", "vishnu_user", sess)
k = sess.getSessionKey()
self.assertTrue(k != "")
def submitToVishnu(webboardDataRequest, errorHandler=None):
myErrorHandler = errorHandler
if (myErrorHandler == None):
myErrorHandler = ErrorHandler()
myErrorHandler.submitStatus = ""
vsession = webboardDataRequest.vsession
scriptPath = webboardDataRequest.application
workId = webboardDataRequest.workId
estimatedHours = webboardDataRequest.estimatedHours
nbcpus = webboardDataRequest.nbcpus
machineId = webboardDataRequest.machine
specparams = webboardDataRequest.specparams
memory = webboardDataRequest.memory
parameters = dictToVishnu(webboardDataRequest.parameters)
inputFiles = dictToVishnu(webboardDataRequest.files)
criterion = VISHNU.LoadCriterion()
vishnuOptions = VISHNU.SubmitOptions()
vishnuOptions.setWorkId(workId)
if (estimatedHours and estimatedHours != "0"):
vishnuOptions.setWallTime(int(estimatedHours))
if (nbcpus and nbcpus != "0"):
vishnuOptions.setNbCpu(int(nbcpus))
vishnuOptions.setTextParams(str(parameters))
vishnuOptions.setFileParams(str(inputFiles))
#Handling optional values
#memory
if (memory and memory != "0"):
vishnuOptions.setMemory(memory)
#specific params
if (specparams != ""):
vishnuOptions.setSpecificParams(str(specparams))
print "Specific parameters : ", str(specparams)
#end optional
#vishnuOptions.setSelectQueueAutom(True)
#vishnuOptions.setNbCpu(int())
job = VISHNU.Job()
try:
print "vsession %s, machine %s, application %s" % (
str(vsession), str(machineId), str(scriptPath))
VISHNU.submitJob(str(vsession), str(machineId), str(scriptPath), job,
vishnuOptions)
print "Submit Ok"
myErrorHandler.submitStatus = "Success"
myErrorHandler.jobid = job.getJobId()
print job.getJobId()
except VISHNU.SystemException as e:
myErrorHandler.errors = myErrorHandler.errors + 1
myErrorHandler.submitStatus = "VISHNU System exception : " + e.what()
myErrorHandler.jobid = job.getJobId()
print "VISHNU : ", e.what()
print job.getJobId()
except VISHNU.VishnuException as e:
myErrorHandler.errors = myErrorHandler.errors + 1
myErrorHandler.submitStatus = "VISHNU exception : " + e.what()
myErrorHandler.jobid = job.getJobId()
print "Vishnu Exception : ", e.what()
print job.getJobId()
except Exception as e:
myErrorHandler.errors = myErrorHandler.errors + 1
myErrorHandler.submitStatus = "Exception : " + e
myErrorHandler.jobid = job.getJobId()
print "Exception Bizarre ", e
print job.getJobId()
return job
def test_bad_key(self):
try:
VISHNU.listMachines(self.k + "b'ad")
except VISHNU.VishnuException, e:
self.assertEqual(28, e.getMsgI())
def displayOut(jr):
print "JobId: ", jr.getJobId()
print "output: ", jr.getOutputPath()
print "error: ", jr.getErrorPath()
def displayComp(lijr):
for i in range(len(lijr[1])):
displayOut(lijr[1][i])
print " "
def displayListJ(lij):
for i in range(len(lij[1])):
displayJob(lij[1][i], i)
print " "
VISHNU.vishnuInitialize(os.getenv("VISHNU_CONFIG_FILE"))
j = VISHNU.Job()
j1 = VISHNU.Job()
j2 = VISHNU.Job()
j3 = VISHNU.Job()
criterion = VISHNU.LoadCriterion()
op = VISHNU.SubmitOptions()
mid = "machine_1"
mid2 = "machine_2"
#path = "/home/traore/VishnuProject/vishnu/TMS/test/src/scripts/torque_script"
#path = "scripts/torque_script"
path = "scripts/testScriptGen"
waitingScriptPath = "scripts/testScriptGenWaiting"
#The first argument in command line corresponds to the machine id
def setUp(self):
self.sess = VISHNU.Session()
self.op = VISHNU.ConnectOptions()
VISHNU.vishnuInitialize(os.getenv("VISHNU_CONFIG_FILE"))
VISHNU.connect('root', 'vishnu_user', self.sess, self.op)
self.k = self.sess.getSessionKey()
newFileName = "FMS_test_file" newDirName = "FMS_test_dir" newSubDirName = "FMS_test_sub_dir" #local paths workingDirFullPath1 = machineId1 + sep + FMSWORKINGDIR workingDirFullPath2 = machineId2 + sep + FMSWORKINGDIR baseDirFullPath1 = machineId1 + sep + FMSDIR1 baseDirFullPath2 = machineId2 + sep + FMSDIR2 fileFullPath1 = baseDirFullPath1 + slash + newFileName fileFullPath2 = baseDirFullPath2 + slash + newFileName dirFullPath1 = baseDirFullPath1 + slash + newDirName recursiveDirFullPath1 = dirFullPath1 + slash + newSubDirName dirFullPath2 = baseDirFullPath2 + slash + newDirName #Objects initialization headOpt = VISHNU.HeadOfFileOptions() tailOpt = VISHNU.TailOfFileOptions() dirContent = [] dirContent2 = [] lsOpt = VISHNU.LsDirOptions() fileInfo = VISHNU.FileStat() dirEntryInfo = VISHNU.DirEntry() transferOpt = VISHNU.CpFileOptions() fileTransferInfo = VISHNU.FileTransfer() fileTransferList = [] stopTransferOptions = VISHNU.StopTransferOptions() lsTransferOptions = VISHNU.LsTransferOptions() session = VISHNU.Session() contentOfFile = "" # preconditions if (os.path.exists(FMSDIR1)):
print "Name: ", newAuthSys.getName()
print "URI: ", newAuthSys.getURI()
print "AuthLogin: "******"AuthPassword: "******"UserPasswordEncryption: ", newAuthSys.getUserPasswordEncryption()
print "Type: ", newAuthSys.getType()
print "LdapBase: ", newAuthSys.getLdapBase()
def displayAuthSystems(li):
print "length li:", len(li[1])
for i in range(len(li[1])):
displayAuthSys(li[1][i])
print " "
try:
sess = VISHNU.Session()
# Initialisation of vishnu, the parameter is the path to the configuration file (cf shell script for the content of this file)
VISHNU.vishnuInitialize(os.getenv("VISHNU_CONFIG_FILE"))
# Connection of the user root with the password vishnu_user, getting in return the error code r and the session key k
VISHNU.connect("root", "vishnu_user", sess)
k = sess.getSessionKey()
print "Session key: ",k
# Creation of a listsession object
#l = VISHNU.ListSessions()
# Calling the vishnu service listSession for the session key k, filling the list l
res = VISHNU.listSessions(k)
# Getting the size of the list
#l.getSessions().size()
# Getting the userid of the 24th session of the list
def setUp(self):
self.sess = VISHNU.Session()
self.op = VISHNU.ConnectOptions()
VISHNU.vishnuInitialize(os.getenv("VISHNU_CONFIG_FILE"))
VISHNU.connect('root', 'vishnu_user', self.sess, self.op)
self.k = self.sess.getSessionKey()
ma.setName("bunny")
ma.setSite("test")
ma.setLanguage("fr")
ma.setMachineDescription("desc")
# Check we can add a machine
r = VISHNU.addMachine(self.k, ma)
self.assertEqual(0, r)
VISHNU.deleteMachine(self.k, ma.getMachineId())
# Check with bad session key : fail
try:
VISHNU.addMachine(self.k+"b'ad", ma)
except VISHNU.VishnuException, e :
self.assertEqual(28, e.getMsgI())
# For each in param check injection
ma.setName("bunn'y")
r = VISHNU.addMachine(self.k, ma)
self.assertEqual(0, r)
VISHNU.deleteMachine(self.k, ma.getMachineId())
ma.setSite("t'est")
r = VISHNU.addMachine(self.k, ma)
self.assertEqual(0, r)
VISHNU.deleteMachine(self.k, ma.getMachineId())
ma.setLanguage("f'r")
r = VISHNU.addMachine(self.k, ma)
self.assertEqual(0, r)
VISHNU.deleteMachine(self.k, ma.getMachineId())
ma.setMachineDescription("d'esc")
r = VISHNU.addMachine(self.k, ma)
self.assertEqual(0, r)
# Test inserted objects contain quotes
def test_connection_bad_name(self):
sess = VISHNU.Session()
k = sess.getSessionKey()
VISHNU.vishnuInitialize(os.getenv("VISHNU_CONFIG_FILE"))
l = ["bad", "vishnu_user", sess]
self.assertRaises(VISHNU.VishnuException, VISHNU.connect, *l)
lsTransferOptions = VISHNU.LsTransferOptions()
session = VISHNU.Session()
contentOfFile = ""
# preconditions
if os.path.exists(FMSDIR1):
shutil.rmtree(FMSDIR1)
if os.path.exists(FMSDIR2):
shutil.rmtree(FMSDIR2)
os.makedirs(FMSDIR1)
os.makedirs(FMSDIR2)
vishnu_client_file_path = os.getenv("VISHNU_CONFIG_FILE")
VISHNU.vishnuInitialize(vishnu_client_file_path)
##########################################################
try:
r = VISHNU.connect(userId, userPwd, session)
k = session.getSessionKey()
print "touch:", fileFullPath1
VISHNU.touch(k, fileFullPath1)
print "sessionKey:", k
print "==================stat===============:"
VISHNU.stat(k, fileFullPath1, fileInfo)
displayFileInfo(fileInfo)
print "rm: ", fileFullPath1
def test_connection(self):
sess = VISHNU.Session()
VISHNU.vishnuInitialize(os.getenv("VISHNU_CONFIG_FILE"))
VISHNU.connect("root", "vishnu_user", sess)
k = sess.getSessionKey()
self.assertTrue(k != "")
def test_bad_key(self):
try:
VISHNU.listMachines(self.k+"b'ad")
except VISHNU.VishnuException, e :
self.assertEqual(28, e.getMsgI())
return values.get(mtype)
def displayMetric(lic, machineId):
try :
for i in range(len(lic[1])):
print "Type: ", getMetricType(lic[1][i].getType())
mtype = getMetricType(lic[1][i].getType())
print "Value: ", lic[1][i].getValue()
mvalue = lic[1][i].getValue()
mtime = (date.fromtimestamp(lic[1][i].getTime())).strftime('%d-%b-%Y')
print "time : ", mtime
except VISHNU.VishnuException, e:
print e.what()
VISHNU.vishnuInitialize(os.getenv("VISHNU_CONFIG_FILE"))
mid = "machine_1"
pop = VISHNU.ProcessOp()
lip = []
lic = []
opc = VISHNU.CurMetricOp()
lih = []
oph = VISHNU.MetricHistOp()
sess = VISHNU.Session()
try :
VISHNU.connect("root", "vishnu_user", sess)
k = sess.getSessionKey()
print "Session key: ",k
lip = VISHNU.getProcesses(k, pop)
ma.setName("bunny")
ma.setSite("test")
ma.setLanguage("fr")
ma.setMachineDescription("desc")
# Check we can add a machine
r = VISHNU.addMachine(self.k, ma)
self.assertEqual(0, r)
VISHNU.deleteMachine(self.k, ma.getMachineId())
# Check with bad session key : fail
try:
VISHNU.addMachine(self.k + "b'ad", ma)
except VISHNU.VishnuException, e:
self.assertEqual(28, e.getMsgI())
# For each in param check injection
ma.setName("bunn'y")
r = VISHNU.addMachine(self.k, ma)
self.assertEqual(0, r)
VISHNU.deleteMachine(self.k, ma.getMachineId())
ma.setSite("t'est")
r = VISHNU.addMachine(self.k, ma)
self.assertEqual(0, r)
VISHNU.deleteMachine(self.k, ma.getMachineId())
ma.setLanguage("f'r")
r = VISHNU.addMachine(self.k, ma)
self.assertEqual(0, r)
VISHNU.deleteMachine(self.k, ma.getMachineId())
ma.setMachineDescription("d'esc")
r = VISHNU.addMachine(self.k, ma)
self.assertEqual(0, r)
# Test inserted objects contain quotes
