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|
########################################################################################
# #
# Author: Bertrand Neron, #
# Organization:'Biological Software and Databases' Group, Institut Pasteur, Paris. #
# Distributed under GPLv2 Licence. Please refer to the COPYING.LIB document. #
# #
########################################################################################
import unittest2 as unittest
import os
import sys
import shutil
MOBYLEHOME = os.path.abspath( os.path.join( os.path.dirname( __file__ ) , "../../../" ) )
os.environ['MOBYLEHOME'] = MOBYLEHOME
if ( MOBYLEHOME ) not in sys.path:
sys.path.append( MOBYLEHOME )
if ( os.path.join( MOBYLEHOME , 'Src' ) ) not in sys.path:
sys.path.append( os.path.join( MOBYLEHOME , 'Src' ) )
import Mobyle.Test.MobyleTest
from Mobyle.Transaction import Transaction
from Mobyle.MobyleError import MobyleError, SessionError
from Mobyle.Classes.DataType import DataTypeFactory
from Mobyle.Service import MobyleType
from Mobyle.Session import Session
#import Mobyle.Utils
DATADIR = os.path.dirname( __file__ )
class TransactionTest(unittest.TestCase):
"""Tests the functionalities of Transaction"""
def setUp(self):
"""
setting up the configuration for the test, including:
- test configuration that does not check dns or try to send confirmation emails
- test session email
"""
self.cfg = Mobyle.ConfigManager.Config()
shutil.rmtree(self.cfg.test_dir, ignore_errors=True)
os.makedirs(self.cfg.test_dir)
self.sessionKey = "Q12345678901234"
self.sessionDir = os.path.join( self.cfg.test_dir , self.sessionKey )
os.makedirs( self.sessionDir )
self.email = 'dummy@domain.fr'
self.passwd = 'dummypass'
self.actkey = 'dummykey'
self.xmlSourcePath = os.path.join( DATADIR , 'session_test.xml')
self.sessionPath = os.path.join( self.sessionDir , Session.FILENAME )
self.dataID = [ "f835ddf28cb6aa776a41d7c71ec9cb5a.out" , "16bd6f89e732eb7cb0bbc13c65d202d3.aln" ]
dtf = DataTypeFactory()
dataType1 = dtf.newDataType( 'Sequence' )
mobyleType1 = MobyleType( dataType1 , bioTypes = [ 'Protein' , 'Nucleic' ] , dataFormat = 'SWISSPROT' )
dataType2 = dtf.newDataType( 'Alignment' )
mobyleType2 = MobyleType( dataType2 , dataFormat = 'PHYLIPI' )
self.datas = [ {'dataName' : 'f835ddf28cb6aa776a41d7c71ec9cb5a.out' ,
'userName' : 'golden.out' ,
'size' : 4410 ,
'Type' : mobyleType1 ,
'dataBegin' : 'ID 104K_THEPA Reviewed; 924' ,
'inputModes' : [ 'result' ] ,
'producedBy' : [ 'file://tmp/mobyle/results/dnadist/G25406684175968' ] ,
'usedBy' : []
} ,
{'dataName' : '16bd6f89e732eb7cb0bbc13c65d202d3.aln' ,
'userName' : 'clustal.aln' ,
'size' : 90044 ,
'Type' : mobyleType2 ,
'dataBegin' : ' 47 1618\nF_75 ---------------------------' ,
'inputModes' : [ 'upload' , 'paste' ] ,
'producedBy' : [] ,
'usedBy' : [ 'file://tmp/mobyle/results/dnadist/G25406684175968' ,
'file://tmp/mobyle/results/dnadist/X25423048243999' ]
}
]
self.jobID = [ "file://tmp/mobyle/results/dnadist/X25423048243999" ,
"file://tmp/mobyle/results/dnadist/G25406684175968" ]
self.jobs = [ {'jobID' : 'file://tmp/mobyle/results/dnadist/X25423048243999' ,
'userName' : 'mon programme a moi' ,
'programName' : 'prog 1' ,
'status' : Mobyle.Status.Status( code = 6 ) , #killed
'date' : (2008, 11, 20, 12, 0, 0, 3, 325, -1) ,
'dataProduced': [] ,
'dataUsed' : ['16bd6f89e732eb7cb0bbc13c65d202d3.aln'] ,
} ,
{'jobID' : 'file://tmp/mobyle/results/dnadist/G25406684175968' ,
'userName' : 'file://tmp/mobyle/results/dnadist/G25406684175968' ,
'programName' : 'dnadist' ,
'status' : Mobyle.Status.Status( code = 3 ) , #running
'date' : (2008, 11, 19, 10, 50, 33, 2, 324, -1) ,
'dataProduced': ['f835ddf28cb6aa776a41d7c71ec9cb5a.out'] ,
'dataUsed' : ['16bd6f89e732eb7cb0bbc13c65d202d3.aln'] ,
}
]
def tearDown(self):
shutil.rmtree( self.cfg.test_dir , ignore_errors= True )
def testTransaction(self):
Transaction.create( self.sessionPath , False , False )
# Check locks types
transaction = Transaction( self.sessionPath, Transaction.WRITE )
transaction.rollback()
transaction = Transaction( self.sessionPath, Transaction.READ )
transaction.rollback()
self.assertRaises(MobyleError, Transaction, self.sessionPath, None )
# Invalid file
self.assertRaises(SessionError, Transaction, str(None), Transaction.READ)
def testCreation(self):
#create( filename , authenticated , activated , activatingKey = None , email = None , passwd = None)
#test anonymous session without email
Transaction.create( self.sessionPath , False , False )
os.unlink( self.sessionPath )
#test anonymous session with passwd
self.assertRaises( SessionError , Transaction.create , self.sessionPath , False , False , passwd = self.passwd )
#test anonymous session with email
Transaction.create( self.sessionPath , False , False , userEmail = self.email )
os.unlink( self.sessionPath )
#test authenticated session without passwd -> SessionError
self.assertRaises( SessionError , Transaction.create , self.sessionPath , True , False , userEmail = self.email )
#test authenticated session without email -> SessionError
self.assertRaises( SessionError , Transaction.create , self.sessionPath , True , False , passwd = self.passwd )
#test authenticated session with email and passwd
Transaction.create( self.sessionPath , True , False , userEmail = self.email , passwd = self.passwd )
os.unlink( self.sessionPath )
#test authenticated session with activatingKey
Transaction.create( self.sessionPath , True , False , activatingKey = self.actkey , userEmail = self.email , passwd = self.passwd )
os.unlink( self.sessionPath )
#test that session creation fails if already exists
Transaction.create( self.sessionPath , False , False )
self.assertRaises( SessionError , Transaction.create , self.sessionPath , False , False )
os.unlink( self.sessionPath )
def testCommit(self):
Transaction.create( self.sessionPath , False , False )
# Ensure that transaction with modification update the file
bef = os.stat( self.sessionPath )
transaction = Transaction( self.sessionPath , Transaction.WRITE )
transaction._setModified( True )
transaction.commit()
aft = os.stat( self.sessionPath )
self.assertFalse( bef.st_ino == aft.st_ino and bef.st_mtime == aft.st_mtime )
# Ensure that transaction without modification does not update the file
bef = os.stat( self.sessionPath )
transaction = Transaction( self.sessionPath , Transaction.WRITE )
transaction._setModified( False )
transaction.commit()
aft = os.stat( self.sessionPath )
self.assertTrue( bef.st_ino == aft.st_ino and bef.st_mtime == aft.st_mtime )
# By default, an empty transaction should have no effect on the file
bef = os.stat( self.sessionPath )
transaction = Transaction( self.sessionPath , Transaction.WRITE )
transaction.commit()
aft = os.stat( self.sessionPath )
self.assertTrue( bef.st_ino == aft.st_ino and bef.st_mtime == aft.st_mtime )
def testRollback(self):
shutil.copy( self.xmlSourcePath , self.sessionPath )
transaction = Transaction( self.sessionPath , Transaction.WRITE )
transaction.removeData( self.dataID[0] )
self. assertFalse( transaction.hasData(self.dataID[0] ) )
transaction.rollback()
transaction = Transaction( self.sessionPath , Transaction.READ )
self.assertTrue( transaction.hasData( self.dataID[0] ) )
transaction.commit()
def testConcurency(self):
Transaction.create( self.sessionPath , False , False )
transaction = Transaction( self.sessionPath , Transaction.READ )
## sub-process start
childPid = os.fork()
if childPid: #father
pid , status = os.wait()
self.assertFalse( status )
else: #child
cmd = [ sys.executable, 'openTransaction.py' , self.sessionPath , str( Transaction.READ ) ]
os.execv( cmd[0] , cmd )
## sub-process end
transaction.commit()
transaction = Transaction( self.sessionPath , Transaction.WRITE )
## sub-process start
childPid = os.fork()
if childPid: #father
pid , status = os.wait()
self.assertTrue( status )
else: #child
cmd = [ sys.executable, 'openTransaction.py' , self.sessionPath , str( Transaction.READ ) ]
os.execv( cmd[0] , cmd )
## sub-process end
transaction.commit()
def testgetID(self):
Transaction.create( self.sessionPath , False , False )
transaction = Transaction( self.sessionPath , Transaction.READ )
receivedID = transaction.getID()
transaction.commit()
self.assertEqual( receivedID , self.sessionKey )
def testEmail(self):
Transaction.create( self.sessionPath , False , False )
transaction = Transaction( self.sessionPath , Transaction.WRITE )
transaction.setEmail( self.email )
transaction.commit()
transaction = Transaction( self.sessionPath , Transaction.READ )
receivedEmail = transaction.getEmail()
transaction.commit()
self.assertTrue( receivedEmail == self.email )
def testisActivated(self):
# Test unactivated session
Transaction.create( self.sessionPath , False , False )
transaction = Transaction( self.sessionPath , Transaction.READ )
active = transaction.isActivated()
transaction.commit()
self.assertFalse( active )
os.unlink( self.sessionPath )
# Test already activated session
Transaction.create( self.sessionPath , False , True )
transaction = Transaction( self.sessionPath , Transaction.READ )
active = transaction.isActivated()
transaction.commit()
self.assertTrue( active )
os.unlink( self.sessionPath )
# Test session after activation
Transaction.create( self.sessionPath , False , False )
transaction = Transaction( self.sessionPath , Transaction.WRITE )
transaction.activate()
transaction.commit()
transaction = Transaction( self.sessionPath , Transaction.READ )
active = transaction.isActivated()
transaction.commit()
self.assertTrue( active )
os.unlink( self.sessionPath )
# Test session after inactivation
Transaction.create( self.sessionPath , False , True )
transaction = Transaction( self.sessionPath , Transaction.WRITE )
active = transaction.isActivated()
self.assertTrue( active )
transaction.inactivate()
transaction.commit()
active = transaction.isActivated()
self.assertFalse( active )
os.unlink( self.sessionPath )
def testActivatingKey(self):
Transaction.create( self.sessionPath , False , True , activatingKey = self.actkey , userEmail = None)
transaction = Transaction( self.sessionPath , Transaction.READ )
actKey = transaction.getActivatingKey()
transaction.commit()
self.assertTrue( actKey == self.actkey )
def testAuthenticated(self):
Transaction.create( self.sessionPath , True , True , activatingKey = self.actkey , userEmail = self.email , passwd = self.passwd )
transaction = Transaction( self.sessionPath , Transaction.READ )
auth = transaction.isAuthenticated()
transaction.commit()
self.assertTrue( auth )
def testPasswd(self):
Transaction.create( self.sessionPath , False , False )
transaction = Transaction( self.sessionPath , Transaction.WRITE )
sendPasswd = "monBeauMotDePasse"
transaction.setPasswd( sendPasswd )
transaction.commit()
transaction = Transaction( self.sessionPath , Transaction.READ )
receivedPasswd = transaction.getPasswd()
transaction.commit()
self.assertTrue( sendPasswd == receivedPasswd )
def testCaptchaSolution( self ):
sendSoluce = 'solution'
Transaction.create( self.sessionPath , False , False )
transaction = Transaction( self.sessionPath , Transaction.WRITE )
transaction.setCaptchaSolution( sendSoluce )
transaction.commit()
transaction = Transaction( self.sessionPath , Transaction.READ )
receivedSoluce = transaction.getCaptchaSolution()
transaction.commit()
self.assertTrue( sendSoluce == receivedSoluce )
transaction2 = Transaction( self.sessionPath , Transaction.READ )
receivedSoluce = transaction2.getCaptchaSolution()
self.assertTrue( sendSoluce == receivedSoluce )
transaction2.commit()
################################
#
# operations on Data
#
#################################
def testHasData(self):
shutil.copy( self.xmlSourcePath , self.sessionPath)
transaction = Transaction( self.sessionPath , Transaction.READ )
self.assertTrue( transaction.hasData( self.dataID[1] ) )
transaction.commit()
def testRenameData( self ):
shutil.copy( self.xmlSourcePath , self.sessionPath)
newUserName = '__new_user_name_for_the_data__'
transaction = Transaction( self.sessionPath , Transaction.WRITE )
transaction.renameData( self.dataID[0] , newUserName )
transaction.commit()
transaction = Transaction( self.sessionPath , Transaction.READ )
data = transaction.getData( self.dataID[0] )
transaction.commit()
self.assertTrue( newUserName == data[ 'userName' ] )
def testGetAllData(self):
shutil.copy( self.xmlSourcePath , self.sessionPath)
transaction = Transaction( self.sessionPath , Transaction.READ )
receivedData = transaction.getAllData()
transaction.commit()
self.assertTrue( len( receivedData ) == 2 )
for data in receivedData:
self.assertTrue( data in self.datas )
def testRemoveData( self ):
shutil.copy( self.xmlSourcePath , self.sessionPath )
transaction = Transaction( self.sessionPath , Transaction.WRITE )
transaction.removeData( self.dataID[0] )
transaction.commit()
transaction = Transaction( self.sessionPath , Transaction.READ )
self.assertFalse( transaction.hasData( self.dataID[0] ) )
transaction.commit()
def testLinkJobInput2Data( self ):
Transaction.create( self.sessionPath , False , True )
transaction = Transaction( self.sessionPath , Transaction.WRITE )
sendData = self.datas[0]
transaction.createData( sendData[ 'dataName' ] ,
sendData[ 'userName' ] ,
sendData[ 'size' ] ,
sendData[ 'Type' ] ,
sendData[ 'dataBegin' ] ,
sendData[ 'inputModes' ] ,
producedBy = [] ,
usedBy = []
)
sendJob = self.jobs[ 0 ]
transaction.createJob( sendJob['jobID'] ,
sendJob['userName'] ,
sendJob['programName'] ,
sendJob['status'] ,
sendJob['date'] ,
[] ,
[]
)
transaction.commit()
transaction = Transaction( self.sessionPath , Transaction.WRITE )
transaction.linkJobInput2Data( [ sendData[ 'dataName' ] ] , [ sendJob['jobID'] ])
transaction.commit()
transaction = Transaction( self.sessionPath , Transaction.READ )
data = transaction.getData( sendData[ 'dataName' ] )
job = transaction.getJob( sendJob['jobID'])
transaction.commit()
self.assertEqual( data[ 'usedBy' ][0] , sendJob[ 'jobID' ] )
self.assertEqual( job[ 'dataUsed' ][0] , sendData[ 'dataName' ] )
def testLinkJobOutput2Data( self ):
Transaction.create( self.sessionPath , False , True )
transaction = Transaction( self.sessionPath , Transaction.WRITE )
sendData = self.datas[0]
transaction.createData( sendData[ 'dataName' ] ,
sendData[ 'userName' ] ,
sendData[ 'size' ] ,
sendData[ 'Type' ] ,
sendData[ 'dataBegin' ] ,
sendData[ 'inputModes' ] ,
producedBy = [] ,
usedBy = []
)
sendJob = self.jobs[ 0 ]
transaction.createJob( sendJob['jobID'] ,
sendJob['userName'] ,
sendJob['programName'] ,
sendJob['status'] ,
sendJob['date'] ,
[] ,
[]
)
transaction.commit()
transaction = Transaction( self.sessionPath , Transaction.WRITE )
transaction.linkJobOutput2Data( [ sendData[ 'dataName' ] ] , [ sendJob['jobID'] ])
transaction.commit()
transaction = Transaction( self.sessionPath , Transaction.READ )
data = transaction.getData( sendData[ 'dataName' ] )
job = transaction.getJob( sendJob['jobID'])
transaction.commit()
self.assertEqual( data[ 'producedBy' ][0] , sendJob[ 'jobID' ] )
self.assertEqual( job[ 'dataProduced' ][0] , sendData[ 'dataName' ] )
def testAddInputModes(self ):
shutil.copy( self.xmlSourcePath , self.sessionPath )
transaction = Transaction( self.sessionPath , Transaction.WRITE )
transaction.addInputModes( self.dataID[0] , [ 'paste' , 'db' ] )
transaction.commit()
transaction = Transaction( self.sessionPath , Transaction.READ )
data = transaction.getData( self.dataID[0] )
transaction.commit()
result = ['paste' , 'db' , 'result']
result.sort()
data[ 'inputModes' ].sort()
self.assertEqual( data[ 'inputModes' ] , result )
#an inputMode must not be twice in the xml
transaction = Transaction( self.sessionPath , Transaction.WRITE )
transaction.addInputModes( self.dataID[0] , [ 'paste' ] )
transaction.commit()
transaction = Transaction( self.sessionPath , Transaction.READ )
data = transaction.getData( self.dataID[0] )
transaction.commit()
data[ 'inputModes' ].sort()
self.assertEqual( data[ 'inputModes' ] , result )
def testCreateAndGetData( self ):
Transaction.create( self.sessionPath , True , True , activatingKey = 'uneJolieCle' , userEmail = self.email , passwd = self.passwd )
transaction = Transaction( self.sessionPath , Transaction.WRITE )
sendData = self.datas[0]
transaction.createData( sendData[ 'dataName' ] ,
sendData[ 'userName' ] ,
sendData[ 'size' ] ,
sendData[ 'Type' ] ,
sendData[ 'dataBegin' ] ,
sendData[ 'inputModes' ] ,
producedBy = sendData[ 'producedBy' ] ,
usedBy = sendData[ 'usedBy' ]
)
transaction.commit()
transaction = Transaction( self.sessionPath , Transaction.READ )
receivedData = transaction.getData( sendData[ 'dataName' ] )
transaction.commit()
self.assertTrue( receivedData == sendData )
####################
#
# jobs methods
#
####################
def testHasJob( self ):
shutil.copy( self.xmlSourcePath , self.sessionPath )
jobid = "file://tmp/mobyle/results/dnadist/G25406684175968"
transaction = Transaction( self.sessionPath , Transaction.READ )
self.assertTrue( transaction.hasJob( jobid ) )
self.assertFalse( transaction.hasJob( jobid.replace('G','Z') ) )
transaction.commit()
def testGetAllJobs( self ):
shutil.copy( self.xmlSourcePath , self.sessionPath)
transaction = Transaction( self.sessionPath , Transaction.READ )
receivedJobs = transaction.getAllJobs()
transaction.commit()
self.assertTrue( len( receivedJobs ) == 2 )
for job in receivedJobs:
self.assertTrue( job in self.jobs )
def testCreateAndGetJob( self ):
Transaction.create( self.sessionPath , False , True )
sendJob = self.jobs[ 1 ]
transaction = Transaction( self.sessionPath , Transaction.WRITE )
transaction.createJob( sendJob['jobID'] ,
sendJob['userName'] ,
sendJob['programName'] ,
sendJob['status'] ,
sendJob['date'] ,
sendJob['dataUsed'] ,
sendJob['dataProduced']
)
transaction.commit()
transaction = Transaction( self.sessionPath , Transaction.READ )
receivedJob = transaction.getJob( sendJob[ 'jobID' ] )
transaction.commit()
self.assertEqual( sendJob , receivedJob )
def testRemoveJob( self ):
shutil.copy( self.xmlSourcePath , self.sessionPath )
transaction = Transaction( self.sessionPath , Transaction.WRITE )
transaction.removeJob( self.jobID[1] )
transaction.commit()
transaction = Transaction( self.sessionPath , Transaction.READ )
self.assertFalse( transaction.hasJob( self.jobID[1] ) )
transaction.commit()
def testRenameJob( self ):
shutil.copy( self.xmlSourcePath , self.sessionPath )
newUserName = "mon beau job"
transaction = Transaction( self.sessionPath , Transaction.WRITE )
transaction.renameJob( self.jobID[1] , newUserName )
transaction.commit()
transaction = Transaction( self.sessionPath , Transaction.READ )
job = transaction.getJob( self.jobID[1] )
transaction.commit()
self.assertEqual( newUserName , job[ 'userName' ] )
def testUpdateJobStatus( self ):
shutil.copy( self.xmlSourcePath , self.sessionPath )
sendStatus = Mobyle.Status.Status( code = 7 ) #hold
transaction = Transaction( self.sessionPath , Transaction.WRITE )
transaction.updateJobStatus( self.jobID[0] , sendStatus )
transaction.commit()
transaction = Transaction( self.sessionPath , Transaction.READ )
job = transaction.getJob( self.jobID[0] )
transaction.commit()
self.assertEqual( sendStatus , job[ 'status' ] )
def testSetAndGetJobLabel(self):
shutil.copy( self.xmlSourcePath , self.sessionPath )
#there is not labels yet in jobs
transaction = Transaction( self.sessionPath , Transaction.READ )
label_recieved = transaction.getJobLabels(self.jobID[0])
transaction.commit()
self.assertEqual( label_recieved , [] )
#add one label
label_send = ['label_1']
transaction = Transaction( self.sessionPath , Transaction.WRITE )
transaction.setJobLabels( self.jobID[0] , label_send )
transaction.commit()
#get one label
transaction = Transaction( self.sessionPath , Transaction.READ )
label_recieved = transaction.getJobLabels(self.jobID[0])
transaction.commit()
self.assertEqual( label_recieved , label_send )
#add 2 labels
label_send = ['label_2', 'label_2_bis']
transaction = Transaction( self.sessionPath , Transaction.WRITE )
transaction.setJobLabels( self.jobID[1] , label_send )
transaction.commit()
#get 2 labels
transaction = Transaction( self.sessionPath , Transaction.READ )
label_recieved = transaction.getJobLabels(self.jobID[1])
transaction.commit()
self.assertEqual( label_recieved , label_send )
#add label in job which have already labels
new_label = [ 'label_3', 'label_3_bis' ]
transaction = Transaction( self.sessionPath , Transaction.WRITE )
transaction.setJobLabels( self.jobID[1] , new_label )
transaction.commit()
#get 2 new labels
transaction = Transaction( self.sessionPath , Transaction.READ )
label_recieved = transaction.getJobLabels( self.jobID[1] )
label_recieved = transaction.getJobLabels( self.jobID[1] )
transaction.commit()
self.assertEqual( label_recieved , new_label )
def testgetAllUniqueLabels(self):
shutil.copy( self.xmlSourcePath , self.sessionPath )
label_1= [ 'label_1', 'label_1_bis' ]
label_2= label_1 + [ 'label_2' ]
transaction = Transaction( self.sessionPath , Transaction.WRITE )
transaction.setJobLabels( self.jobID[0] , label_1 )
transaction.setJobLabels( self.jobID[1] , label_2 )
transaction.commit()
transaction = Transaction( self.sessionPath , Transaction.READ )
label_recieved = transaction.getJobLabels( self.jobID[1] )
transaction.commit()
s = set( label_1 + label_2 )
unique = list( s )
unique.sort()
label_recieved.sort()
self.assertEqual( label_recieved , unique )
def testSetAndGetJobDescription(self):
shutil.copy( self.xmlSourcePath , self.sessionPath )
job_description = "a new beautiful description for this job"
transaction = Transaction( self.sessionPath , Transaction.WRITE )
transaction.setJobDescription( self.jobID[0] , job_description)
transaction.commit()
transaction = Transaction( self.sessionPath , Transaction.READ )
jobDescription_recieved = transaction.getJobDescription( self.jobID[0] )
transaction.commit()
self.assertEqual( jobDescription_recieved , job_description )
transaction = Transaction( self.sessionPath , Transaction.READ )
jobDescription_recieved = transaction.getJobDescription( self.jobID[1] )
transaction.commit()
self.assertEqual( None , jobDescription_recieved )
if __name__ == '__main__':
unittest.main()
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