import ConfigParser import sys, os import array import time import optparse,array import shutil, traceback import urllib,urllib2, cookielib assert sys.version_info[:2] >= ( 2, 4 ) new_path = [ os.path.join( os.getcwd(), "lib" ) ] new_path.extend( sys.path[1:] ) # remove scripts/ from the path sys.path = new_path from galaxy import eggs import pkg_resources import pkg_resources pkg_resources.require( "pycrypto" ) from Crypto.Cipher import Blowfish from Crypto.Util.randpool import RandomPool from Crypto.Util import number class GalaxyWebInterface(object): def __init__(self, server_host, server_port, datatx_email, datatx_password, config_id_secret): self.server_host = server_host self.server_port = server_port self.datatx_email = datatx_email self.datatx_password = datatx_password self.config_id_secret = config_id_secret # create url self.base_url = "http://%s:%s" % (self.server_host, self.server_port) # login url = "%s/user/login?email=%s&password=%s&login_button=Login" % (self.base_url, self.datatx_email, self.datatx_password) cj = cookielib.CookieJar() self.opener = urllib2.build_opener(urllib2.HTTPCookieProcessor(cj)) #print url f = self.opener.open(url) if f.read().find("ogged in as "+self.datatx_email) == -1: # if the user doesnt exist, create the user url = "%s/user/create?email=%s&username=%s&password=%s&confirm=%s&create_user_button=Submit" % ( self.base_url, self.datatx_email, self.datatx_email, self.datatx_password, self.datatx_password ) f = self.opener.open(url) if f.read().find("ogged in as "+self.datatx_email) == -1: raise Exception("The "+self.datatx_email+" user could not login to Galaxy") def add_to_library(self, server_dir, library_id, folder_id, dbkey=''): ''' This method adds the dataset file to the target data library & folder by opening the corresponding url in Galaxy server running. ''' params = urllib.urlencode(dict( cntrller='library_admin', tool_id='upload1', tool_state='None', library_id=self.encode_id(library_id), folder_id=self.encode_id(folder_id), upload_option='upload_directory', file_type='auto', server_dir=os.path.basename(server_dir), dbkey=dbkey, show_dataset_id='True', runtool_btn='Upload to library')) url = self.base_url+"/library_common/upload_library_dataset" print url print params try: f = self.opener.open(url, params) if f.read().find("Data Library") == -1: raise Exception("Dataset could not be uploaded to the data library. URL: %s, PARAMS=%s" % (url, params)) except: return 'ERROR', url, params def import_to_history(self, ldda_id, library_id, folder_id): params = urllib.urlencode(dict( cntrller='library_admin', show_deleted='False', library_id=self.encode_id(library_id), folder_id=self.encode_id(folder_id), ldda_ids=self.encode_id(ldda_id), do_action='import_to_history', use_panels='False')) #url = "http://lion.bx.psu.edu:8080/library_common/act_on_multiple_datasets?library_id=adb5f5c93f827949&show_deleted=False&ldda_ids=adb5f5c93f827949&cntrller=library_admin&do_action=import_to_history&use_panels=False" url = self.base_url+"/library_common/act_on_multiple_datasets" f = self.opener.open(url, params) x = f.read() if x.find("1 dataset(s) have been imported into your history.") == -1: raise Exception("Dataset could not be imported into history") def run_workflow(self, workflow_id, hid, workflow_step): input = str(workflow_step)+'|input' params = urllib.urlencode({'id':self.encode_id(workflow_id), 'run_workflow': 'Run workflow', input: hid}) url = self.base_url+"/workflow/run" f = self.opener.open(url, params) def logout(self): # finally logout f = self.opener.open(self.base_url+'/user/logout') def encode_id(self, obj_id ): id_cipher = Blowfish.new( self.config_id_secret ) # Convert to string s = str( obj_id ) # Pad to a multiple of 8 with leading "!" s = ( "!" * ( 8 - len(s) % 8 ) ) + s # Encrypt return id_cipher.encrypt( s ).encode( 'hex' ) def update_request_state(self, request_id): params = urllib.urlencode(dict( cntrller='requests_admin', request_id=request_id)) url = self.base_url + "/requests_common/update_request_state" f = self.opener.open(url, params) print url print params x = f.read()