diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 4f68a70d01c..5f77a398281 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -1543,7 +1543,7 @@ class Sample( object ):
def print_ticks(d):
pass
datatx_info = self.request.type.datatx_info
- cmd = 'ssh %s@%s "du -sh %s"' % ( datatx_info['username'],
+ cmd = 'ssh %s@%s "du -sh \'%s\'"' % ( datatx_info['username'],
datatx_info['host'],
filepath)
output = pexpect.run(cmd, events={'.ssword:*': datatx_info['password']+'\r\n',
diff --git a/lib/galaxy/web/controllers/requests_admin.py b/lib/galaxy/web/controllers/requests_admin.py
index 5989b1358ab..2ea0967a61e 100644
--- a/lib/galaxy/web/controllers/requests_admin.py
+++ b/lib/galaxy/web/controllers/requests_admin.py
@@ -228,7 +228,7 @@ class RequestsAdmin( BaseController ):
trans.response.headers['Expires'] = '0'
sample = trans.sa_session.query( self.app.model.Sample ).get( int(id) )
datatx_info = sample.request.type.datatx_info
- cmd = 'ssh %s@%s "ls -oghp %s"' % ( datatx_info['username'],
+ cmd = 'ssh %s@%s "ls -oghp \'%s\'"' % ( datatx_info['username'],
datatx_info['host'],
folder_path )
output = pexpect.run(cmd, events={'.ssword:*': datatx_info['password']+'\r\n',
@@ -1528,7 +1528,7 @@ class RequestsAdmin( BaseController ):
message=message))
def print_ticks(d):
pass
- cmd = 'ssh %s@%s "ls -p %s"' % ( datatx_info['username'],
+ cmd = 'ssh %s@%s "ls -p \'%s\'"' % ( datatx_info['username'],
datatx_info['host'],
folder_path)
output = pexpect.run(cmd, events={'.ssword:*': datatx_info['password']+'\r\n',
@@ -1541,7 +1541,8 @@ class RequestsAdmin( BaseController ):
sample_id=trans.security.encode_id(sample.id),
message=message, status='error',
folder_path=folder_path ))
- return output.split()
+
+ return output.splitlines()
def __get_files_in_dir(self, trans, sample, folder_path):
tmpfiles = self.__get_files(trans, sample, folder_path)
diff --git a/scripts/galaxy_messaging/server/data_transfer.py b/scripts/galaxy_messaging/server/data_transfer.py
index 39fb0fa3ef0..dccea539051 100755
--- a/scripts/galaxy_messaging/server/data_transfer.py
+++ b/scripts/galaxy_messaging/server/data_transfer.py
@@ -151,11 +151,11 @@ class DataTransfer(object):
for i, df in enumerate(self.dataset_files):
self.update_status(Sample.transfer_status.TRANSFERRING, df['index'])
try:
- cmd = "scp %s@%s:%s %s/%s" % ( self.username,
+ cmd = "scp %s@%s:'%s' '%s/%s'" % ( self.username,
self.host,
- df['file'],
- self.server_dir,
- df['name'])
+ df['file'].replace(' ', '\ '),
+ self.server_dir.replace(' ', '\ '),
+ df['name'].replace(' ', '\ '))
log.debug(cmd)
output = pexpect.run(cmd, events={'.ssword:*': self.password+'\r\n',
pexpect.TIMEOUT:print_ticks},
@@ -182,7 +182,8 @@ class DataTransfer(object):
galaxyweb = GalaxyWebInterface(self.server_host, self.server_port,
self.datatx_email, self.datatx_password,
self.config_id_secret)
- galaxyweb.add_to_library(self.server_dir, self.library_id, self.folder_id)
+ retval = galaxyweb.add_to_library(self.server_dir, self.library_id, self.folder_id)
+ log.debug(str(retval))
galaxyweb.logout()
except Exception, e:
log.debug(e)
diff --git a/scripts/galaxy_messaging/server/galaxyweb_interface.py b/scripts/galaxy_messaging/server/galaxyweb_interface.py
index 779697f561f..7df5345af48 100644
--- a/scripts/galaxy_messaging/server/galaxyweb_interface.py
+++ b/scripts/galaxy_messaging/server/galaxyweb_interface.py
@@ -60,14 +60,15 @@ class GalaxyWebInterface(object):
dbkey=dbkey,
show_dataset_id='True',
runtool_btn='Upload to library'))
- #url = "http://localhost:8080/library_common/upload_library_dataset?cntrller=library_admin&tool_id=upload1&tool_state=None&library_id=adb5f5c93f827949&folder_id=adb5f5c93f827949&upload_option=upload_directory&file_type=auto&server_dir=003&dbkey=%3F&message=&runtool_btn=Upload+to+library"
- #url = base_url+"/library_common/upload_library_dataset?library_id=adb5f5c93f827949&tool_id=upload1&file_type=auto&server_dir=datatx_22858&dbkey=%3F&upload_option=upload_directory&folder_id=529fd61ab1c6cc36&cntrller=library_admin&tool_state=None&runtool_btn=Upload+to+library"
url = self.base_url+"/library_common/upload_library_dataset"
- #print url
- #print params
- 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))
+ 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',
@@ -78,14 +79,10 @@ class GalaxyWebInterface(object):
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 = base_url+"/library_common/upload_library_dataset?library_id=adb5f5c93f827949&tool_id=upload1&file_type=auto&server_dir=datatx_22858&dbkey=%3F&upload_option=upload_directory&folder_id=529fd61ab1c6cc36&cntrller=library_admin&tool_state=None&runtool_btn=Upload+to+library"
url = self.base_url+"/library_common/act_on_multiple_datasets"
- #print url
- #print params
f = self.opener.open(url, params)
x = f.read()
if x.find("1 dataset(s) have been imported into your history.") == -1:
- #print x
raise Exception("Dataset could not be imported into history")
def run_workflow(self, workflow_id, hid, workflow_step):
@@ -94,11 +91,7 @@ class GalaxyWebInterface(object):
'run_workflow': 'Run workflow',
input: hid})
url = self.base_url+"/workflow/run"
- #print url+'?'+params
f = self.opener.open(url, params)
-# if f.read().find("1 dataset(s) have been imported into your history.") == -1:
-# raise Exception("Error in running the workflow")
-
def logout(self):
# finally logout
diff --git a/templates/admin/requests/get_data.mako b/templates/admin/requests/get_data.mako
index 51b6fdf1f4e..bd185dc9b30 100644
--- a/templates/admin/requests/get_data.mako
+++ b/templates/admin/requests/get_data.mako
@@ -27,17 +27,24 @@ $(document).ready(function(){
var w = document.get_data.files_list.selectedIndex;
var selected_value = document.get_data.files_list.options[w].value;
var cell = $("#file_details");
- //var sample_id = sample.id
- // Make ajax call
- $.ajax( {
- type: "POST",
- url: "${h.url_for( controller='requests_admin', action='get_file_details' )}",
- dataType: "json",
- data: { id: sample_id, folder_path: document.get_data.folder_path.value+selected_value },
- success : function ( data ) {
- cell.html( '' )
- }
- });
+ if(selected_value.charAt(selected_value.length-1) != '/')
+ {
+ // Make ajax call
+ $.ajax( {
+ type: "POST",
+ url: "${h.url_for( controller='requests_admin', action='get_file_details' )}",
+ dataType: "json",
+ data: { id: sample_id, folder_path: document.get_data.folder_path.value+selected_value },
+ success : function ( data ) {
+ cell.html( '' )
+ }
+ });
+ }
+ else
+ {
+ cell.html( '' )
+ }
+
}
@@ -47,11 +54,10 @@ $(document).ready(function(){
{
var w = document.get_data.files_list.selectedIndex;
var selected_value = document.get_data.files_list.options[w].value;
+ var cell = $("#file_details");
if(selected_value.charAt(selected_value.length-1) == '/')
{
document.get_data.folder_path.value = document.get_data.folder_path.value+selected_value
- var cell = $("#file_details");
- //var sample_id = sample.id
// Make ajax call
$.ajax( {
type: "POST",
@@ -60,8 +66,6 @@ $(document).ready(function(){
data: { id: sample_id, folder_path: document.get_data.folder_path.value },
success : function ( data ) {
document.get_data.files_list.options.length = 0
- //alert(data)
- //cell.html( '' )
for(i=0; i