[2] | 1 | import ConfigParser |
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| 2 | import sys, os |
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| 3 | import array |
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| 4 | import time |
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| 5 | import optparse,array |
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| 6 | import shutil, traceback |
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| 7 | import urllib,urllib2, cookielib |
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| 8 | |
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| 9 | assert sys.version_info[:2] >= ( 2, 4 ) |
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| 10 | new_path = [ os.path.join( os.getcwd(), "lib" ) ] |
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| 11 | new_path.extend( sys.path[1:] ) # remove scripts/ from the path |
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| 12 | sys.path = new_path |
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| 13 | |
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| 14 | from galaxy import eggs |
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| 15 | import pkg_resources |
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| 16 | |
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| 17 | import pkg_resources |
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| 18 | pkg_resources.require( "pycrypto" ) |
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| 19 | |
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| 20 | from Crypto.Cipher import Blowfish |
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| 21 | from Crypto.Util.randpool import RandomPool |
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| 22 | from Crypto.Util import number |
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| 23 | |
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| 24 | |
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| 25 | class GalaxyWebInterface(object): |
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| 26 | def __init__(self, server_host, server_port, datatx_email, datatx_password, config_id_secret): |
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| 27 | self.server_host = server_host |
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| 28 | self.server_port = server_port |
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| 29 | self.datatx_email = datatx_email |
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| 30 | self.datatx_password = datatx_password |
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| 31 | self.config_id_secret = config_id_secret |
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| 32 | # create url |
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| 33 | self.base_url = "http://%s:%s" % (self.server_host, self.server_port) |
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| 34 | # login |
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| 35 | url = "%s/user/login?email=%s&password=%s&login_button=Login" % (self.base_url, self.datatx_email, self.datatx_password) |
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| 36 | cj = cookielib.CookieJar() |
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| 37 | self.opener = urllib2.build_opener(urllib2.HTTPCookieProcessor(cj)) |
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| 38 | #print url |
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| 39 | f = self.opener.open(url) |
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| 40 | if f.read().find("ogged in as "+self.datatx_email) == -1: |
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| 41 | # if the user doesnt exist, create the user |
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| 42 | 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 ) |
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| 43 | f = self.opener.open(url) |
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| 44 | if f.read().find("ogged in as "+self.datatx_email) == -1: |
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| 45 | raise Exception("The "+self.datatx_email+" user could not login to Galaxy") |
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| 46 | |
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| 47 | def add_to_library(self, server_dir, library_id, folder_id, dbkey=''): |
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| 48 | ''' |
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| 49 | This method adds the dataset file to the target data library & folder |
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| 50 | by opening the corresponding url in Galaxy server running. |
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| 51 | ''' |
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| 52 | params = urllib.urlencode(dict( cntrller='library_admin', |
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| 53 | tool_id='upload1', |
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| 54 | tool_state='None', |
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| 55 | library_id=self.encode_id(library_id), |
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| 56 | folder_id=self.encode_id(folder_id), |
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| 57 | upload_option='upload_directory', |
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| 58 | file_type='auto', |
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| 59 | server_dir=os.path.basename(server_dir), |
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| 60 | dbkey=dbkey, |
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| 61 | show_dataset_id='True', |
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| 62 | runtool_btn='Upload to library')) |
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| 63 | url = self.base_url+"/library_common/upload_library_dataset" |
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| 64 | print url |
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| 65 | print params |
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| 66 | try: |
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| 67 | f = self.opener.open(url, params) |
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| 68 | if f.read().find("Data Library") == -1: |
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| 69 | raise Exception("Dataset could not be uploaded to the data library. URL: %s, PARAMS=%s" % (url, params)) |
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| 70 | except: |
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| 71 | return 'ERROR', url, params |
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| 72 | |
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| 73 | def import_to_history(self, ldda_id, library_id, folder_id): |
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| 74 | params = urllib.urlencode(dict( cntrller='library_admin', |
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| 75 | show_deleted='False', |
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| 76 | library_id=self.encode_id(library_id), |
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| 77 | folder_id=self.encode_id(folder_id), |
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| 78 | ldda_ids=self.encode_id(ldda_id), |
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| 79 | do_action='import_to_history', |
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| 80 | use_panels='False')) |
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| 81 | #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" |
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| 82 | url = self.base_url+"/library_common/act_on_multiple_datasets" |
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| 83 | f = self.opener.open(url, params) |
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| 84 | x = f.read() |
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| 85 | if x.find("1 dataset(s) have been imported into your history.") == -1: |
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| 86 | raise Exception("Dataset could not be imported into history") |
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| 87 | |
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| 88 | def run_workflow(self, workflow_id, hid, workflow_step): |
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| 89 | input = str(workflow_step)+'|input' |
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| 90 | params = urllib.urlencode({'id':self.encode_id(workflow_id), |
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| 91 | 'run_workflow': 'Run workflow', |
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| 92 | input: hid}) |
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| 93 | url = self.base_url+"/workflow/run" |
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| 94 | f = self.opener.open(url, params) |
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| 95 | |
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| 96 | def logout(self): |
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| 97 | # finally logout |
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| 98 | f = self.opener.open(self.base_url+'/user/logout') |
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| 99 | |
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| 100 | def encode_id(self, obj_id ): |
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| 101 | id_cipher = Blowfish.new( self.config_id_secret ) |
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| 102 | # Convert to string |
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| 103 | s = str( obj_id ) |
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| 104 | # Pad to a multiple of 8 with leading "!" |
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| 105 | s = ( "!" * ( 8 - len(s) % 8 ) ) + s |
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| 106 | # Encrypt |
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| 107 | return id_cipher.encrypt( s ).encode( 'hex' ) |
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| 108 | |
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| 109 | def update_request_state(self, request_id): |
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| 110 | params = urllib.urlencode(dict( cntrller='requests_admin', |
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| 111 | request_id=request_id)) |
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| 112 | url = self.base_url + "/requests_common/update_request_state" |
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| 113 | f = self.opener.open(url, params) |
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| 114 | print url |
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| 115 | print params |
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| 116 | x = f.read() |
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| 117 | |
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| 118 | |
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| 119 | |
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| 120 | |
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| 121 | |
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| 122 | |
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