comparison peakMotifs_wrapper.py @ 52:a1d369ead6d7 draft default tip

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51:9e193aa2b9d2

import zipfile
import time
import platform
from suds.client import Client

###########################################################'

###########################################################'
## Define log options for suds

# Import log package
#import logging

# Import log package
#import logging
# création de l'objet logger qui va nous servir à écrire dans les logs
#logger = logging.getLogger()
# on met le niveau du logger à DEBUG, comme ça il écrit tout
#logger.setLevel(logging.DEBUG)
# Configure log of suds clients to DEBUG for verbose output concerning Client request
#logging.getLogger('suds.client').setLevel(logging.ERROR)
#logging.getLogger('suds.transport').setLevel(logging.ERROR)
#logging.getLogger('suds.xsd.schema').setLevel(logging.ERROR)
#logging.getLogger('suds.wsdl').setLevel(logging.ERROR)


# création d'un second handler qui va rediriger chaque écriture de log
# sur la console
#steam_handler = logging.StreamHandler()
#steam_handler.setLevel(logging.DEBUG)
#logger.addHandler(steam_handler)

#logger.info('Hello')

#print(client.factory.create('peak_motifs'))

#	  (PeakMotifsRequest){
#		 output = None -> ok
#		 verbosity = None
#		 test = None -> ok
#		 tmp_test_infile = None
#		 control = None
#		 tmp_control_infile = None
#		 max_seq_length = None
#		 max_motif_number = None
#		 ref_motif = None
#		 top_peaks = None
#		 min_length = None
#		 max_length = None
#		 markov = None
#		 min_markov = None
#		 max_markov = None
#		 noov = None
#		 class_int = None
#		 str = None
#		 graph_title = None
#		 image_format = None
#		 disco = None
#		 source = None
#		 task = None
#	  }
# }


################################ functions ############################################################
## Define a function to make a service perform the desired request using provided arguments
def call_run_service(service, args):
	"""
	Run job in RSAT server.

	"""

	###########################################################'
	## Download RSAT results
	urllib.urlretrieve(urlResult, nameFile)
	#except IOError:
	#logFile.write("\nResult URL is false")
	#Logger.error("Result URL is false")
	#logFile.write("\n"+nameFile+"\n")

	###########################################################'
	## Decompress results
	#try:
	zfile = zipfile.ZipFile(nameFile, 'r')
	#except IOError:
	#logFile.write("No zip file")
	#Logger.error("No zip file")

	tempflag = 0
	folderName =""

	for i in zfile.namelist():  ## On parcourt l'ensemble des fichiers de l'archive

	###########################################################'
	## Run job in RSAT server
	result = call_run_service(rsat_service, peakMotifsRequest)

	#logFile = open("/bioinfo/users/jbrayet/Bureau/peak_motifs.log","w")

	#logFile.write("###############################################\n")
	#logFile.write("Command performed on server\n")
	#logFile.write(result.command)
	#logFile.write("\n")
	#logFile.write("###############################################\n")
	#logFile.write("Result\n")
	#logFile.write(result.server)

	print("###############################################\n")
	print("Command performed on server\n")
	print(result.command)
	print("\n")
	print("###############################################\n")

		"mx":"http://prokaryotes.rsat.eu/rsa-tools/"
	
		}
	"""

	nameFile = "peak-motifs_results.zip"
	urlResult=buildZipUrl(result.server)
	print urlResult

	#ogFile.write("\n"+urlResult)

	###########################################################'
	## Wait RSAT server
	while urllib.urlopen(urlResult).getcode() != 200:
	#logFile.write(str(urllib.urlopen(urlResult).getcode())+"\n")
		time.sleep(5)

	#logFile.write(str(nameFile)+"\n")
	#time.sleep(5)
	#while urllib.urlretrieve(urlResult, nameFile) 
	#try:

	folderName=recupRSATResult(urlResult,nameFile)
	
	while(not(os.path.exists(folderName+"peak-motifs_synthesis.html"))):
		os.popen("rm -rf "+folderName)
		recupRSATResult(urlResult,nameFile)

	#logFile.write("\n"+folderName+"\n")
	#logFile.write("\n"+outGalaxyValue+"\n")

        os.popen("cp "+folderName+"peak-motifs_synthesis.html "+outGalaxyValue)
	os.popen("cp "+nameFile+" "+folderName)
        #logFile.close()
        #os.popen("sed -i \"1iHHEELLLOOO\" "+outGalaxyValue)
        #os.popen("sed -i \"1i<style type=\'text/css\'></style>\" "+outGalaxyValue)

        ###########################################################'
        ##Create results folder name
        outGalaxyValueDir = outGalaxyValue.replace(".dat","_files")

        #logFile.write("\noutGalaxyValueDir : " +outGalaxyValueDir)

        #logFile.close()

        # Create results folder
        os.popen("mkdir "+outGalaxyValueDir)

        # Copy results files in results folder
        os.popen("cp -R "+folderName+"data " + outGalaxyValueDir+"/data")
        os.popen("cp -R "+folderName+"reports " + outGalaxyValueDir+"/reports")
        os.popen("cp -R "+folderName+"results " + outGalaxyValueDir+"/results")
        
        if not outGalaxyValue2 =="":
            os.popen("cp "+folderName+"results/sites/peak-motifs_all_motifs_seqcoord.bed "+outGalaxyValue2)
        
        
        

52:a1d369ead6d7

import zipfile
import time
import platform
from suds.client import Client

################################ functions ############################################################
## Define a function to make a service perform the desired request using provided arguments
def call_run_service(service, args):
	"""
	Run job in RSAT server.

	"""

	###########################################################'
	## Download RSAT results
	urllib.urlretrieve(urlResult, nameFile)

	###########################################################'
	## Decompress results
	zfile = zipfile.ZipFile(nameFile, 'r')

	tempflag = 0
	folderName =""

	for i in zfile.namelist():  ## On parcourt l'ensemble des fichiers de l'archive

	###########################################################'
	## Run job in RSAT server
	result = call_run_service(rsat_service, peakMotifsRequest)

	print("###############################################\n")
	print("Command performed on server\n")
	print(result.command)
	print("\n")
	print("###############################################\n")

		"mx":"http://prokaryotes.rsat.eu/rsa-tools/"
	
		}
	"""

	nameFile = "peak-motifs_archive.zip"
	urlResult=buildZipUrl(result.server)
	print urlResult

	###########################################################'
	## Wait RSAT server
	while urllib.urlopen(urlResult).getcode() != 200:
		time.sleep(5)

	folderName=recupRSATResult(urlResult,nameFile)
	
	while(not(os.path.exists(folderName+"peak-motifs_synthesis.html"))):
		os.popen("rm -rf "+folderName)
		recupRSATResult(urlResult,nameFile)

        os.popen("cp "+folderName+"peak-motifs_synthesis.html "+outGalaxyValue)

        ###########################################################'
        ##Create results folder name

        # Create results folder
	outGalaxyValueDir = outGalaxyValue.replace(".dat","_files")
	os.popen("mkdir "+outGalaxyValueDir)

        # Copy results files in results folder

	os.popen("cp "+nameFile+" "+outGalaxyValueDir+"/"+nameFile)
        os.popen("cp -R "+folderName+"* " + outGalaxyValueDir+"/")
        
        if not outGalaxyValue2 =="":
            os.popen("cp "+folderName+"results/sites/peak-motifs_all_motifs_seqcoord.bed "+outGalaxyValue2)