lims:

- bug fix - the data transfer module now works for file/folder names with spaces in them
- UI cleanup

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', 

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)

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)

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

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( '<label>'+data+'</label>' )
-            }
-        });
+       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( '<label>'+data+'</label>' )
+                }
+            });
+        }
+        else 
+        {
+            cell.html( '' )
+        }
+        
        
    }
 </script>
@@ -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( '<label>'+data.name+'</label>' )
                     for(i=0; i<data.length; i++) 
                     {
                         var newOpt = new Option(data[i], data[i]);
@@ -72,7 +76,10 @@ $(document).ready(function(){
                 }
             });
        }
-       
+        else 
+        {
+            cell.html( '' )
+        }
    }
 </script>