[2] | 1 | #!/usr/bin/env python |
---|
| 2 | """ |
---|
| 3 | |
---|
| 4 | Data Transfer Script: Sequencer to Galaxy |
---|
| 5 | |
---|
| 6 | This script is called from Galaxy LIMS once the lab admin starts the data |
---|
| 7 | transfer process using the user interface. |
---|
| 8 | |
---|
| 9 | Usage: |
---|
| 10 | |
---|
| 11 | python data_transfer.py <data_transfer_xml> <config_id_secret> |
---|
| 12 | |
---|
| 13 | |
---|
| 14 | """ |
---|
| 15 | import ConfigParser |
---|
| 16 | import sys, os, time, traceback |
---|
| 17 | import optparse |
---|
| 18 | import urllib,urllib2, cookielib, shutil |
---|
| 19 | import logging, time, datetime |
---|
| 20 | import xml.dom.minidom |
---|
| 21 | |
---|
| 22 | sp = sys.path[0] |
---|
| 23 | |
---|
| 24 | from galaxydb_interface import GalaxyDbInterface |
---|
| 25 | |
---|
| 26 | assert sys.version_info[:2] >= ( 2, 4 ) |
---|
| 27 | new_path = [ sp ] |
---|
| 28 | new_path.extend( sys.path ) |
---|
| 29 | sys.path = new_path |
---|
| 30 | |
---|
| 31 | from galaxyweb_interface import GalaxyWebInterface |
---|
| 32 | |
---|
| 33 | assert sys.version_info[:2] >= ( 2, 4 ) |
---|
| 34 | new_path = [ os.path.join( os.getcwd(), "lib" ) ] |
---|
| 35 | new_path.extend( sys.path[1:] ) # remove scripts/ from the path |
---|
| 36 | sys.path = new_path |
---|
| 37 | |
---|
| 38 | |
---|
| 39 | from galaxy.util.json import from_json_string, to_json_string |
---|
| 40 | from galaxy.model import Sample |
---|
| 41 | from galaxy import eggs |
---|
| 42 | import pkg_resources |
---|
| 43 | pkg_resources.require( "pexpect" ) |
---|
| 44 | import pexpect |
---|
| 45 | |
---|
| 46 | pkg_resources.require( "simplejson" ) |
---|
| 47 | import simplejson |
---|
| 48 | |
---|
| 49 | log = logging.getLogger("datatx_"+str(os.getpid())) |
---|
| 50 | log.setLevel(logging.DEBUG) |
---|
| 51 | fh = logging.FileHandler("data_transfer.log") |
---|
| 52 | fh.setLevel(logging.DEBUG) |
---|
| 53 | formatter = logging.Formatter("%(asctime)s - %(name)s - %(message)s") |
---|
| 54 | fh.setFormatter(formatter) |
---|
| 55 | log.addHandler(fh) |
---|
| 56 | |
---|
| 57 | |
---|
| 58 | class DataTransfer(object): |
---|
| 59 | |
---|
| 60 | def __init__(self, msg, config_id_secret): |
---|
| 61 | log.info(msg) |
---|
| 62 | self.dom = xml.dom.minidom.parseString(msg) |
---|
| 63 | self.host = self.get_value(self.dom, 'data_host') |
---|
| 64 | self.username = self.get_value(self.dom, 'data_user') |
---|
| 65 | self.password = self.get_value(self.dom, 'data_password') |
---|
| 66 | self.sample_id = self.get_value(self.dom, 'sample_id') |
---|
| 67 | self.library_id = self.get_value(self.dom, 'library_id') |
---|
| 68 | self.folder_id = self.get_value(self.dom, 'folder_id') |
---|
| 69 | self.dataset_files = [] |
---|
| 70 | self.config_id_secret = config_id_secret |
---|
| 71 | count=0 |
---|
| 72 | while True: |
---|
| 73 | dataset_id = self.get_value_index(self.dom, 'dataset_id', count) |
---|
| 74 | file = self.get_value_index(self.dom, 'file', count) |
---|
| 75 | name = self.get_value_index(self.dom, 'name', count) |
---|
| 76 | if file: |
---|
| 77 | self.dataset_files.append(dict(name=name, |
---|
| 78 | dataset_id=int(dataset_id), |
---|
| 79 | file=file)) |
---|
| 80 | else: |
---|
| 81 | break |
---|
| 82 | count=count+1 |
---|
| 83 | try: |
---|
| 84 | # Retrieve the upload user login information from the config file |
---|
| 85 | config = ConfigParser.ConfigParser() |
---|
| 86 | config.read('transfer_datasets.ini') |
---|
| 87 | self.datatx_email = config.get("data_transfer_user_login_info", "email") |
---|
| 88 | self.datatx_password = config.get("data_transfer_user_login_info", "password") |
---|
| 89 | self.server_host = config.get("universe_wsgi_config", "host") |
---|
| 90 | self.server_port = config.get("universe_wsgi_config", "port") |
---|
| 91 | self.database_connection = config.get("universe_wsgi_config", "database_connection") |
---|
| 92 | self.import_dir = config.get("universe_wsgi_config", "library_import_dir") |
---|
| 93 | # create the destination directory within the import directory |
---|
| 94 | self.server_dir = os.path.join( self.import_dir, 'datatx_'+str(os.getpid())+'_'+datetime.date.today().strftime("%d%b%Y") ) |
---|
| 95 | os.mkdir(self.server_dir) |
---|
| 96 | if not os.path.exists(self.server_dir): |
---|
| 97 | raise Exception |
---|
| 98 | # connect to db |
---|
| 99 | self.galaxydb = GalaxyDbInterface(self.database_connection) |
---|
| 100 | except: |
---|
| 101 | log.error(traceback.format_exc()) |
---|
| 102 | log.error('FATAL ERROR') |
---|
| 103 | if self.database_connection: |
---|
| 104 | self.error_and_exit('Error') |
---|
| 105 | sys.exit(1) |
---|
| 106 | |
---|
| 107 | def start(self): |
---|
| 108 | ''' |
---|
| 109 | This method executes the file transfer from the sequencer, adds the dataset |
---|
| 110 | to the data library & finally updates the data transfer status in the db |
---|
| 111 | ''' |
---|
| 112 | # datatx |
---|
| 113 | self.transfer_files() |
---|
| 114 | # add the dataset to the given library |
---|
| 115 | self.add_to_library() |
---|
| 116 | # update the data transfer status in the db |
---|
| 117 | self.update_status(Sample.transfer_status.COMPLETE) |
---|
| 118 | # cleanup |
---|
| 119 | #self.cleanup() |
---|
| 120 | sys.exit(0) |
---|
| 121 | |
---|
| 122 | def cleanup(self): |
---|
| 123 | ''' |
---|
| 124 | remove the directory created to store the dataset files temporarily |
---|
| 125 | before adding the same to the data library |
---|
| 126 | ''' |
---|
| 127 | try: |
---|
| 128 | time.sleep(60) |
---|
| 129 | shutil.rmtree( self.server_dir ) |
---|
| 130 | except: |
---|
| 131 | self.error_and_exit() |
---|
| 132 | |
---|
| 133 | |
---|
| 134 | def error_and_exit(self, msg=''): |
---|
| 135 | ''' |
---|
| 136 | This method is called any exception is raised. This prints the traceback |
---|
| 137 | and terminates this script |
---|
| 138 | ''' |
---|
| 139 | log.error(traceback.format_exc()) |
---|
| 140 | log.error('FATAL ERROR.'+msg) |
---|
| 141 | self.update_status('Error', 'All', msg+"\n"+traceback.format_exc()) |
---|
| 142 | sys.exit(1) |
---|
| 143 | |
---|
| 144 | def transfer_files(self): |
---|
| 145 | ''' |
---|
| 146 | This method executes a scp process using pexpect library to transfer |
---|
| 147 | the dataset file from the remote sequencer to the Galaxy server |
---|
| 148 | ''' |
---|
| 149 | def print_ticks(d): |
---|
| 150 | pass |
---|
| 151 | for i, df in enumerate(self.dataset_files): |
---|
| 152 | self.update_status(Sample.transfer_status.TRANSFERRING, df['dataset_id']) |
---|
| 153 | try: |
---|
| 154 | cmd = "scp %s@%s:'%s' '%s/%s'" % ( self.username, |
---|
| 155 | self.host, |
---|
| 156 | df['file'].replace(' ', '\ '), |
---|
| 157 | self.server_dir.replace(' ', '\ '), |
---|
| 158 | df['name'].replace(' ', '\ ')) |
---|
| 159 | log.debug(cmd) |
---|
| 160 | output = pexpect.run(cmd, events={'.ssword:*': self.password+'\r\n', |
---|
| 161 | pexpect.TIMEOUT:print_ticks}, |
---|
| 162 | timeout=10) |
---|
| 163 | log.debug(output) |
---|
| 164 | path = os.path.join(self.server_dir, os.path.basename(df['name'])) |
---|
| 165 | if not os.path.exists(path): |
---|
| 166 | msg = 'Could not find the local file after transfer (%s)' % path |
---|
| 167 | log.error(msg) |
---|
| 168 | raise Exception(msg) |
---|
| 169 | except Exception, e: |
---|
| 170 | msg = traceback.format_exc() |
---|
| 171 | self.update_status('Error', df['dataset_id'], msg) |
---|
| 172 | |
---|
| 173 | |
---|
| 174 | def add_to_library(self): |
---|
| 175 | ''' |
---|
| 176 | This method adds the dataset file to the target data library & folder |
---|
| 177 | by opening the corresponding url in Galaxy server running. |
---|
| 178 | ''' |
---|
| 179 | try: |
---|
| 180 | self.update_status(Sample.transfer_status.ADD_TO_LIBRARY) |
---|
| 181 | log.debug("dir:%s, lib:%s, folder:%s" % (self.server_dir, str(self.library_id), str(self.folder_id))) |
---|
| 182 | galaxyweb = GalaxyWebInterface(self.server_host, self.server_port, |
---|
| 183 | self.datatx_email, self.datatx_password, |
---|
| 184 | self.config_id_secret) |
---|
| 185 | retval = galaxyweb.add_to_library(self.server_dir, self.library_id, self.folder_id) |
---|
| 186 | log.debug(str(retval)) |
---|
| 187 | galaxyweb.logout() |
---|
| 188 | except Exception, e: |
---|
| 189 | log.debug(e) |
---|
| 190 | self.error_and_exit(str(e)) |
---|
| 191 | |
---|
| 192 | def update_status(self, status, dataset_id='All', msg=''): |
---|
| 193 | ''' |
---|
| 194 | Update the data transfer status for this dataset in the database |
---|
| 195 | ''' |
---|
| 196 | try: |
---|
| 197 | log.debug('Setting status "%s" for dataset "%s" of sample "%s"' % ( status, str(dataset_id), str(self.sample_id) ) ) |
---|
| 198 | if dataset_id == 'All': |
---|
| 199 | for dataset in self.dataset_files: |
---|
| 200 | self.galaxydb.set_sample_dataset_status(dataset['dataset_id'], status, msg) |
---|
| 201 | else: |
---|
| 202 | self.galaxydb.set_sample_dataset_status(dataset_id, status, msg) |
---|
| 203 | log.debug('done.') |
---|
| 204 | except: |
---|
| 205 | log.error(traceback.format_exc()) |
---|
| 206 | log.error('FATAL ERROR') |
---|
| 207 | sys.exit(1) |
---|
| 208 | |
---|
| 209 | def get_value(self, dom, tag_name): |
---|
| 210 | ''' |
---|
| 211 | This method extracts the tag value from the xml message |
---|
| 212 | ''' |
---|
| 213 | nodelist = dom.getElementsByTagName(tag_name)[0].childNodes |
---|
| 214 | rc = "" |
---|
| 215 | for node in nodelist: |
---|
| 216 | if node.nodeType == node.TEXT_NODE: |
---|
| 217 | rc = rc + node.data |
---|
| 218 | return rc |
---|
| 219 | |
---|
| 220 | def get_value_index(self, dom, tag_name, dataset_id): |
---|
| 221 | ''' |
---|
| 222 | This method extracts the tag value from the xml message |
---|
| 223 | ''' |
---|
| 224 | try: |
---|
| 225 | nodelist = dom.getElementsByTagName(tag_name)[dataset_id].childNodes |
---|
| 226 | except: |
---|
| 227 | return None |
---|
| 228 | rc = "" |
---|
| 229 | for node in nodelist: |
---|
| 230 | if node.nodeType == node.TEXT_NODE: |
---|
| 231 | rc = rc + node.data |
---|
| 232 | return rc |
---|
| 233 | |
---|
| 234 | if __name__ == '__main__': |
---|
| 235 | log.info('STARTING %i %s' % (os.getpid(), str(sys.argv))) |
---|
| 236 | # |
---|
| 237 | # Start the daemon |
---|
| 238 | # |
---|
| 239 | dt = DataTransfer(sys.argv[1], sys.argv[2]) |
---|
| 240 | dt.start() |
---|
| 241 | sys.exit(0) |
---|
| 242 | |
---|