view WebServiceExtensionsV1.1/install.py~ @ 0:049760c677de default tip

Galaxy WSExtensions added successfully

# To change this template, choose Tools | Templates
# and open the template in the editor.

__author__ = "Chaitanya Guttula"


import os
import sys
from shutil import copytree, ignore_patterns

galaxyhome=os.environ.get('GALAXY_HOME')
#print galaxyhome

#os.mkdir(galaxyhome+'/GAL')
dirfilelist=os.listdir(galaxyhome+'/tools')
exist = False
for dirfile in dirfilelist:
    if dirfile == 'WebServiceToolWorkflow_REST_SOAP':
        exist = True
        break

if exist:
    print 'WebServiceToolWorkflow_REST_SOAP is already present in '+galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP'
else:
    copytree('WebServiceToolWorkflow_REST_SOAP',galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP', ignore=ignore_patterns('*.pyc', 'tmp*'))
    print 'Copied the folder \'WebServiceToolWorkflow_REST_SOAP\' to '+galaxyhome+'/tools'

f1=open(galaxyhome+'/tool_conf.xml','r')
f1.seek(0,0)
f2=open(galaxyhome+'/tool_conf_backup.xml','w')
f2.seek(0,0)

#copy the first line <toolbox> into another file f2
line = f1.readline()
#f2.write(line)

lineStripped=line.lstrip()
lineStripped=lineStripped.rstrip()

#Flags for verifying that the tool is not already installed
tool_present = False
webservice_present = False
workflow_present = False

# Check of the tools are already installed or not
# and sets the flags to true if they are already installed 
while not lineStripped == '</toolbox>':
    line = f1.readline()
    lineStripped = line.lstrip()
    lineStripped=lineStripped.rstrip()          
    if(lineStripped.find('<!--')>-1):
        line = f1.readline()
        while(not line.find('-->')>-1):
            line = f1.readline()
    
    if lineStripped == '<section name="Add Web service tool" id="RegisterWebService">':
        tool_present = True
    elif lineStripped == '<section name="Web Service Tools" id="WebServices">':
        webservice_present = True
    elif lineStripped == '<section name="Web Service Workflow Tools" id="WebServiceWorkflow">':
        workflow_present = True


f1.seek(0,0)
line = f1.readline()
f2.write(line)

lineStripped=line.lstrip()
lineStripped=lineStripped.rstrip()

# copy to the file f2 till <toolbox>
while not lineStripped == '<toolbox>':
    line = f1.readline()
    f2.write(line)
    lineStripped = line.lstrip()
    lineStripped = lineStripped.rstrip()

# Check if the tool is not installed and then add it to the file f2
if not tool_present:
    f2.write('  <section name="Add Web service tool" id="RegisterWebService">\n')
    f2.write('    <tool file="WebServiceToolWorkflow_REST_SOAP/WebServiceTool_input_url_REST_SOAP.xml"/>\n')
    f2.write('    <tool file="WebServiceToolWorkflow_REST_SOAP/WebServiceTool_input_method_REST_SOAP.xml"/>\n')
    f2.write('    <tool file="WebServiceToolWorkflow_REST_SOAP/refreshTool.xml"/>\n')
    f2.write('  </section>\n')
    print 'The "Add Web Service Tool" added successfully'
else:
    print 'The "Add Web service tool" tool is already present'


# Check if the section "Web Service Tools" is not installed and then add it to the file f2
if not webservice_present:
    f2.write('  <section name="Web Service Tools" id="WebServices">\n')
    f2.write('\n')
    f2.write('  </section>\n')
    print 'The "Web Service Tools" added successfully'
else:
    print 'The section "Web Service Tools" is already present'


# Check if the Section "Web Service Workflow Tools" is not installed and then add it to the file f2
if not workflow_present:
    f2.write('  <section name="Web Service Workflow Tools" id="WebServiceWorkflow">\n')
    f2.write('\n')
    f2.write('  </section>\n')
    print 'The section "Web Service Workflow Tools" is added successfully'
else:
    print 'The section "Web Service Workflow Tools" is already present'


#copy rest of tool_conf.xml file to f2
while not lineStripped == '</toolbox>':
    line = f1.readline()
    f2.write(line)
    lineStripped = line.lstrip()
    lineStripped=lineStripped.rstrip()          
#else:
#    print line

##close f1 and f2
f1.close()
f2.close()

##interchange modes of f1 and f2
f1=open(galaxyhome+'/tool_conf.xml','w')
f1.seek(0,0)
f2=open(galaxyhome+'/tool_conf_backup.xml','r')
f2.seek(0,0)

line = f2.readline()
f1.write(line)

lineStripped=line.lstrip()
lineStripped = lineStripped.rstrip()

##write entire f2 into f1 (reverse roles)
while not lineStripped == '</toolbox>':
    line = f2.readline()
    f1.write(line)
    lineStripped = line.lstrip()
    lineStripped = lineStripped.rstrip()        
#else:
#    print line

f1.close()
f2.close()


# Adding Code to __init__.py in lib/galaxy/tools folder in Galaxy for disabling Web service stand alone tools in Workflows
f1 = open(galaxyhome+'/lib/galaxy/tools/__init__.py','r')
f1.seek(0,0)

exist = False
line = f1.readline()
linestripped = line.lstrip()
linestripped = linestripped.rstrip()
while line != '':
#    if(linsetripped.find('\'\'\'')>-1):
#        line = f1.readline()
#        while(not line.find('\'\'\'')>-1):
#            line = f1.readline()
    if(linestripped == 'if self.id.find("WebService")>-1:'):
        exist = True
        break
    line = f1.readline()
    linestripped = line.lstrip()
    linestripped = linestripped.rstrip()

if exist :
    print 'Workflow code is already present in __init__.py'
else:
    f2 = open(galaxyhome+'/lib/galaxy/tools/__init__backup.py','w')
    f2.seek(0,0)
    f1.seek(0,0)
    line = f1.readline()
    f2.write(line)
    linestripped = line.lstrip()
    linestripped = linestripped.rstrip()
    while not (linestripped.find('def check_workflow_compatible(')>-1): 
        line = f1.readline()
        linestripped = line.lstrip()
        linestripped = linestripped.rstrip()
        f2.write(line)
    if line.find('(')>-1:
        while not line.find(')')>-1:
            line = f1.readline()
            f2.write(line)
        
    line = f1.readline()
    while line.find('#')>-1:
        f2.write(line)
        line = f1.readline()
        
    indent=0
    while (line[indent] == ' '):
        indent = indent+1
    
    space = ''
    for i in range(0,indent):    
        space +=' '
        
    f2.write(space+'#############\n')    
    f2.write(space+'#added by Chaitany Guttula, [e-mail] - to disable webservice standalone tools in Workflows\n')
    f2.write(space+'if self.id.find("WebService")>-1:\n')
    f2.write(space+'    return False\n')
    f2.write(space+'#############\n')

    f2.write(line)
    line = f1.readline()
    f2.write(line)

    while line != '':
        line = f1.readline()
        f2.write(line)
    
    f1.close()
    f2.close()

    f1 = open(galaxyhome+'/lib/galaxy/tools/__init__backup.py','r')
    f2 = open(galaxyhome+'/lib/galaxy/tools/__init__.py','w')

    line = f1.readline()
    f2.write(line)

    while line != '':
        line = f1.readline()
        f2.write(line)
    
    f1.close()
    f2.close()
    print 'Workflow disabling Code added to __init__.py'
    


# Adding Code to __init__.py in lib/galaxy/tools folder in Galaxy for invoking the refresh functionality
f1 = open(galaxyhome+'/lib/galaxy/tools/__init__.py','r')
f1.seek(0,0)

exist = False
line = f1.readline()
linestripped = line.lstrip()
linestripped = linestripped.rstrip()
while line != '':
#    if(linsetripped.find('\'\'\'')>-1):
#        line = f1.readline()
#        while(not line.find('\'\'\'')>-1):
#            line = f1.readline()
    if(linestripped == 'if self.id == \'WebService_REFRESH_ID\':'):
        exist = True
        break
    line = f1.readline()
    linestripped = line.lstrip()
    linestripped = linestripped.rstrip()

if exist :
    print 'Refresh code is already present in __init__.py'
else:
    f2 = open(galaxyhome+'/lib/galaxy/tools/__init__backup.py','w')
    f2.seek(0,0)
    f1.seek(0,0)
    line = f1.readline()
    f2.write(line)
    linestripped = line.lstrip()
    linestripped = linestripped.rstrip()
    while not (linestripped.find('def execute(')>-1): 
        line = f1.readline()
        linestripped = line.lstrip()
        linestripped = linestripped.rstrip()
        f2.write(line)
    if line.find('(')>-1:
        while not line.find(')')>-1:
            line = f1.readline()
            f2.write(line)
        
    line = f1.readline()
    while line.find('#')>-1:
        f2.write(line)
        line = f1.readline()
        
    indent=0
    while (line[indent] == ' '):
        indent = indent+1
    
    space = ''
    for i in range(0,indent):    
        space +=' '
        
    f2.write(space+'#############\n')    
    f2.write(space+'#add code to verify if user has administrative privileges\n')
    f2.write(space+'#added by sumedha ganjoo, [e-mail] - to refresh toolbox\n')
    f2.write(space+'if self.id == \'WebService_REFRESH_ID\':\n')
    f2.write(space+'    self.app.refreshToolBox()\n')
    f2.write(space+'#############\n')

    f2.write(line)
    line = f1.readline()
    f2.write(line)

    while line != '':
        line = f1.readline()
        f2.write(line)
    
    f1.close()
    f2.close()

    f1 = open(galaxyhome+'/lib/galaxy/tools/__init__backup.py','r')
    f2 = open(galaxyhome+'/lib/galaxy/tools/__init__.py','w')

    line = f1.readline()
    f2.write(line)

    while line != '':
        line = f1.readline()
        f2.write(line)
    
    f1.close()
    f2.close()
    print 'Refresh Code added to __init__.py'
    
    
# Adding Code to app.py in lib/galaxy folder in Galaxy for invoking the refresh functionality
f1 = open(galaxyhome+'/lib/galaxy/app.py','r')

f1.seek(0,0)

exist = False
line = f1.readline()
linestripped = line.lstrip()
linestripped = linestripped.rstrip()
while line != '':
    if(linestripped == 'def refreshToolBox( self ):'):
        exist = True
        break
    line = f1.readline()
    linestripped = line.lstrip()
    linestripped = linestripped.rstrip()

if exist:
    print 'Refresh code is already present in app.py'
else:
    f2 = open(galaxyhome+'/lib/galaxy/app_backup.py','w')
    f2.seek(0,0)
    f1.seek(0,0)
    line = f1.readline()
    f2.write(line)
    linestripped = line.lstrip()
    linestripped = linestripped.rstrip()
    while not (line.find('class UniverseApplication')>-1): 
        line = f1.readline()
        linestripped = line.lstrip()
        linestripped = linestripped.rstrip()
        f2.write(line)
    if line.find('(')>-1:
        while not line.find(')')>-1:
            line = f1.readline()
            f2.write(line)
        
    line = f1.readline()
    
    while line.find('#')>-1:
        f2.write(line)
        line = f1.readline()
    
    
    indent=0
    while (line[indent] == ' '):
        indent = indent+1

    space = ''
    for i in range(0,indent):    
        space +=' '
    
    f2.write(space+'#############\n')    
    f2.write(space+'#added by sumedha ganjoo, [e-mail]\n')
    f2.write(space+'def refreshToolBox( self ):\n')
    f2.write(space+'    self.toolbox = tools.ToolBox( self.config.tool_config, self.config.tool_path, self )\n')
    f2.write(space+'#############\n\n')

    f2.write(line)
    line = f1.readline()
    f2.write(line)

    while line != '':
        line = f1.readline()
        f2.write(line)

    f1.close()
    f2.close()

    f1 = open(galaxyhome+'/lib/galaxy/app_backup.py','r')
    f2 = open(galaxyhome+'/lib/galaxy/app.py','w')
    
    line = f1.readline()
    f2.write(line)

    while line != '':
        line = f1.readline()
        f2.write(line)

    f1.close()
    f2.close()
    print 'Refresh code is added to app.py'
    
    
    
print '****Installation of tool is complete. Now reload galaxy to use the installed tool****'