######################################################################################## # # # 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()