/scripts/galaxy_messaging/server/galaxyweb_interface.py

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' )