details: http://www.bx.psu.edu/hg/galaxy/rev/205d55699a10 changeset: 3381:205d55699a10 user: rc date: Fri Feb 12 14:01:45 2010 -0500 description: LIMS data transfer: - Fixed some config variable issues - Now for the time being, Galaxy can transfer one dataset at a time.
diffstat:
lib/galaxy/web/controllers/requests_admin.py | 5 +-- scripts/galaxy_messaging/server/data_transfer.py | 39 +++++++++++------------ transfer_datasets.ini.sample | 14 +++++++- 3 files changed, 31 insertions(+), 27 deletions(-)
diffs (154 lines):
diff -r 971389b682c7 -r 205d55699a10 lib/galaxy/web/controllers/requests_admin.py --- a/lib/galaxy/web/controllers/requests_admin.py Fri Feb 12 13:13:12 2010 -0500 +++ b/lib/galaxy/web/controllers/requests_admin.py Fri Feb 12 14:01:45 2010 -0500 @@ -1527,7 +1527,7 @@ messagetype='error', msg=msg)) error_msg = '' - transfer_script = "scripts/galaxy_messaging/server/daemon.py" + transfer_script = "scripts/galaxy_messaging/server/data_transfer.py" for index, dataset in enumerate(sample.dataset_files): dfile = dataset[0] status = dataset[1] @@ -1573,9 +1573,6 @@ action='show_datatx_page', sample_id=trans.security.encode_id(sample.id), folder_path=os.path.dirname(dfile))) - - - ## #### Request Type Stuff ################################################### ## diff -r 971389b682c7 -r 205d55699a10 scripts/galaxy_messaging/server/data_transfer.py --- a/scripts/galaxy_messaging/server/data_transfer.py Fri Feb 12 13:13:12 2010 -0500 +++ b/scripts/galaxy_messaging/server/data_transfer.py Fri Feb 12 14:01:45 2010 -0500 @@ -17,12 +17,11 @@ <library_id> <folder_id> """ - import ConfigParser import sys, os, time, traceback import optparse import urllib,urllib2, cookielib, shutil -import logging +import logging, time from galaxydb_interface import GalaxyDbInterface
assert sys.version_info[:2] >= ( 2, 4 ) @@ -40,7 +39,7 @@ import simplejson
curr_dir = os.getcwd() -logfile = os.path.join('/Users/rc/tmp', 'data_transfer.log') +logfile = os.path.join(os.getcwd(), 'data_transfer.log') logging.basicConfig(filename=logfile, level=logging.DEBUG, format="%(asctime)s [%(levelname)s] %(message)s")
@@ -66,11 +65,13 @@ try: # Retrieve the upload user login information from the config file config = ConfigParser.ConfigParser() - config.read('universe_wsgi.ini') - self.server_host = config.get("server:main", "host") - self.server_port = config.get("server:main", "port") - self.database_connection = config.get("app:main", "database_connection") - self.import_dir = config.get("app:main", "library_import_dir") + config.read('transfer_datasets.ini') + self.datatx_email = config.get("data_transfer_user_login_info", "email") + self.datatx_password = config.get("data_transfer_user_login_info", "password") + self.server_host = config.get("universe_wsgi_config", "host") + self.server_port = config.get("universe_wsgi_config", "port") + self.database_connection = config.get("universe_wsgi_config", "database_connection") + self.import_dir = config.get("universe_wsgi_config", "library_import_dir") # create the destination directory within the import directory self.server_dir = os.path.join( self.import_dir, 'datatx_'+str(os.getpid()) ) os.mkdir(self.server_dir) @@ -90,7 +91,7 @@ ''' # datatx self.transfer_file() - # add the dataset to the given library + # add the dataset to the given library self.add_to_library() # update the data transfer status in the db self.update_status('Complete') @@ -104,6 +105,7 @@ before adding the same to the data library ''' try: + time.sleep(60) shutil.rmtree( self.server_dir ) except: self.error_and_exit() @@ -151,24 +153,19 @@ ''' try: logging.debug('Adding %s to library...' % os.path.basename(self.remote_file)) - # Retrieve the upload user login information from the config file - config = ConfigParser.ConfigParser() - config.read('transfer_datasets.ini') - email = config.get("data_transfer_user_login_info", "email") - password = config.get("data_transfer_user_login_info", "password") # create url base_url = "http://%s:%s" % (self.server_host, self.server_port) # login - url = "%s/user/login?email=%s&password=%s" % (base_url, email, password) + url = "%s/user/login?email=%s&password=%s" % (base_url, self.datatx_email, self.datatx_password) cj = cookielib.CookieJar() opener = urllib2.build_opener(urllib2.HTTPCookieProcessor(cj)) f = opener.open(url) - if f.read().find("Now logged in as "+email) == -1: + if f.read().find("Now logged 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" % ( base_url, email, email, password, password ) + url = "%s/user/create?email=%s&username=%s&password=%s&confirm=%s&create_user_button=Submit" % ( base_url, self.datatx_email, self.datatx_email, self.datatx_password, self.datatx_password ) f = opener.open(url) - if f.read().find("Now logged in as "+email) == -1: - raise DataTransferException("The "+email+" user could not login to Galaxy") + if f.read().find("Now logged in as "+self.datatx_email) == -1: + raise DataTransferException("The "+self.datatx_email+" user could not login to Galaxy") # after login, add dataset to the library params = urllib.urlencode(dict( cntrller='library_admin', tool_id='upload1', @@ -191,7 +188,7 @@ # finally logout f = opener.open(base_url+'/user/logout') if f.read().find("You are no longer logged in.") == -1: - raise DataTransferException("The "+email+" user could not logout of Galaxy") + raise DataTransferException("The "+self.datatx_email+" user could not logout of Galaxy") except DataTransferException, (e): self.error_and_exit(e.msg) except: @@ -199,7 +196,7 @@
def update_status(self, status): ''' - + Update the data transfer status for this dataset in the database ''' try: galaxy = GalaxyDbInterface(self.database_connection) diff -r 971389b682c7 -r 205d55699a10 transfer_datasets.ini.sample --- a/transfer_datasets.ini.sample Fri Feb 12 13:13:12 2010 -0500 +++ b/transfer_datasets.ini.sample Fri Feb 12 14:01:45 2010 -0500 @@ -1,5 +1,15 @@ # Galaxy LIMS Transfer Datasets Configuration File
[data_transfer_user_login_info] -#email = user@example.com -#password = +#email = datatx@bx.psu.edu +#password = datatx + +# The following section contains 4 config variables neede for the data transfer. +# Please copy the exact values for each of these variables from the universe_wsgi.ini +# configuration file for this installation + +[universe_wsgi_config] +#host = 127.0.0.1 +#port = +#database_connection = +#library_import_dir = \ No newline at end of file