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https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
lims:
- ui enhancements to the remote file browser: file details available on demand & the browser saves state after each transfer - code cleanup
This commit is contained in:
Ramkrishna Chakrabarty
@@ -204,19 +204,6 @@ class RequestTypeGrid( grids.Grid ):
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grids.GridAction( "Create new request type", dict( controller='requests_admin',
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action='create_request_type' ) )
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]
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class DataTransferThread(threading.Thread):
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def __init__(self, **kwargs):
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threading.Thread.__init__(self, name=kwargs['name'])
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self.dataset_index = kwargs['dataset_index']
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self.cmd = kwargs['cmd']
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def run(self):
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try:
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retcode = subprocess.call(self.cmd)
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except Exception, e:
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error_msg = "Data transfer failed. " + str(e) + "<br/>"
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log.debug(error_msg)
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#
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# ---- Request Controller ------------------------------------------------------
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@@ -231,6 +218,29 @@ class RequestsAdmin( BaseController ):
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@web.require_admin
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def index( self, trans ):
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return trans.fill_template( "/admin/requests/index.mako" )
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@web.json
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def get_file_details( self, trans, id=None, file=None, folder_path=None ):
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print >> sys.stderr, 'get_file_details', id, file
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def print_ticks(d):
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pass
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# Avoid caching
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trans.response.headers['Pragma'] = 'no-cache'
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trans.response.headers['Expires'] = '0'
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sample = trans.sa_session.query( self.app.model.Sample ).get( int(id) )
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datatx_info = sample.request.type.datatx_info
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cmd = 'ssh %s@%s "ls -oghp %s"' % ( datatx_info['username'],
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datatx_info['host'],
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os.sep.join([folder_path, file]))
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output = pexpect.run(cmd, events={'.ssword:*': datatx_info['password']+'\r\n',
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pexpect.TIMEOUT:print_ticks},
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timeout=10)
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#return output.split('\t')[0]
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# Create new HTML for any that have changed
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rval = {}
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rval['name'] = unicode(output.replace('\n', '<br/>'))
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return rval
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@web.json
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def sample_state_updates( self, trans, ids=None, states=None ):
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@@ -1486,10 +1496,10 @@ class RequestsAdmin( BaseController ):
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status='error',
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message="Set a data library and folder for <b>%s</b> to transfer dataset(s)." % sample.name,
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id=trans.security.encode_id(sample.request.id) ) )
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if sample.request.type.datatx_info.get('data_dir', ''):
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folder_path = util.restore_text( sample.request.type.datatx_info.get('data_dir', '') )
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else:
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if params.get( 'folder_path', '' ):
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folder_path = util.restore_text( params.get( 'folder_path', '' ) )
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else:
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folder_path = util.restore_text( sample.request.type.datatx_info.get('data_dir', '') )
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return trans.fill_template( '/admin/requests/get_data.mako',
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sample=sample, dataset_files=sample.dataset_files,
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message=message, status=status, files=[],
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@@ -1508,9 +1518,9 @@ class RequestsAdmin( BaseController ):
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message=message))
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def print_ticks(d):
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pass
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cmd = 'ssh %s@%s "ls -F %s"' % ( datatx_info['username'],
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datatx_info['host'],
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folder_path)
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cmd = 'ssh %s@%s "ls -p %s"' % ( datatx_info['username'],
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datatx_info['host'],
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folder_path)
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output = pexpect.run(cmd, events={'.ssword:*': datatx_info['password']+'\r\n',
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pexpect.TIMEOUT:print_ticks},
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timeout=10)
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@@ -1602,8 +1612,14 @@ class RequestsAdmin( BaseController ):
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filepath = os.path.join(folder_path, f)
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if f[-1] == os.sep:
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# the selected item is a folder so transfer all the
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# folder contents
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self.__get_files_in_dir(trans, sample, filepath)
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# folder contents
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# FIXME
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#self.__get_files_in_dir(trans, sample, filepath)
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return trans.response.send_redirect( web.url_for( controller='requests_admin',
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action='get_data',
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sample_id=sample.id,
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folder_path=folder_path,
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open_folder=True))
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else:
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sample.dataset_files.append(dict(filepath=filepath,
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status=sample.transfer_status.NOT_STARTED,
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@@ -1613,9 +1629,10 @@ class RequestsAdmin( BaseController ):
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trans.sa_session.add( sample )
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trans.sa_session.flush()
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return trans.response.send_redirect( web.url_for( controller='requests_admin',
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action='show_datatx_page',
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sample_id=trans.security.encode_id(sample.id),
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folder_path=folder_path))
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action='get_data',
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sample_id=sample.id,
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folder_path=folder_path,
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open_folder=True))
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return trans.response.send_redirect( web.url_for( controller='requests_admin',
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action='show_datatx_page',
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@@ -1747,42 +1764,6 @@ class RequestsAdmin( BaseController ):
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action='show_datatx_page',
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sample_id=trans.security.encode_id(sample.id),
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folder_path=datatx_info['data_dir']))
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error_message = ''
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transfer_script = "scripts/galaxy_messaging/server/data_transfer.py"
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for index, dataset in enumerate(sample.dataset_files):
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dfile = dataset[0]
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status = dataset[1]
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if status == sample.transfer_status.NOT_STARTED:
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cmd = ( "python",
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transfer_script,
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datatx_info['host'],
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datatx_info['username'],
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datatx_info['password'],
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dfile,
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str(sample.id),
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str(index),
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trans.security.encode_id(sample.library.id),
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trans.security.encode_id(sample.folder.id) )
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# # set the transfer status
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sample.dataset_files[index][1] = sample.transfer_status.IN_PROGRESS
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trans.sa_session.add( sample )
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trans.sa_session.flush()
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dtt = DataTransferThread(name='thread_'+str(index),
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dataset_index=index,
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cmd=cmd)
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dtt.start()
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if error_message:
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return trans.response.send_redirect( web.url_for( controller='requests_admin',
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action='show_datatx_page',
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sample_id=trans.security.encode_id(sample.id),
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folder_path=os.path.dirname(dfile),
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status='error',
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message=error_message))
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return trans.response.send_redirect( web.url_for( controller='requests_admin',
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action='show_datatx_page',
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sample_id=trans.security.encode_id(sample.id),
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folder_path=os.path.dirname(dfile)))
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@web.expose
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@web.require_admin
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def dataset_details( self, trans, **kwd ):
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@@ -15,7 +15,34 @@ $(document).ready(function(){
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$(this).next(".msg_body").slideToggle(450);
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});
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});
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</script>
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<script type="text/javascript">
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function display_file_details(sample_id, folder_path)
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{
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var w = document.get_data.files_list.selectedIndex;
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var selected_value = document.get_data.files_list.options[w].value;
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var cell = $("#file_details");
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//var sample_id = sample.id
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// Make ajax call
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$.ajax( {
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type: "POST",
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url: "${h.url_for( controller='requests_admin', action='get_file_details' )}",
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dataType: "json",
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data: { id: sample_id, file: selected_value, folder_path: folder_path },
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success : function ( data ) {
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cell.html( '<label>'+data.name+'</label>' )
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}
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});
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}
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</script>
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<style type="text/css">
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.msg_head {
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padding: 0px 0px;
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@@ -92,7 +119,7 @@ $(document).ready(function(){
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%endif
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##<div class="toolForm">
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<form name="get_data" action="${h.url_for( controller='requests_admin', action='get_data', sample_id=sample.id)}" method="post" >
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<form name="get_data" id="get_data" action="${h.url_for( controller='requests_admin', action='get_data', sample_id=sample.id)}" method="post" >
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<div class="form-row">
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##<div class="toolFormTitle">Select files for transfer</div>
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<h4>Select files for transfer</h4>
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@@ -104,12 +131,16 @@ $(document).ready(function(){
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<input type="submit" name="open_folder" value="Open folder"/>
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<input type="submit" name="folder_up" value="Up"/>
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</div>
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<div class="form-row">
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<select name="files_list" id="files_list" style="max-width: 98%; width: 98%; height: 150px; font-size: 100%;" multiple>
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%for index, f in enumerate(files):
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<option value="${f}">${f}</option>
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%endfor
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</select>
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<div class="form-row">
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<select name="files_list" id="files_list" style="max-width: 98%; width: 98%; height: 150px; font-size: 100%;" onChange="display_file_details(${sample.id}, '${folder_path}')" multiple>
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%for index, f in enumerate(files):
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<option value="${f}">${f}</option>
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%endfor
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</select>
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<br/>
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<div id="file_details" class="toolParamHelp" style="clear: both;">
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</div>
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</div>
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<div class="form-row">
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<div class="toolParamHelp" style="clear: both;">
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@@ -1,5 +1,5 @@
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<%def name="render_sample_datasets( sample )">
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<a href="${h.url_for(controller='requests_admin', action='show_datatx_page', sample_id=trans.security.encode_id(sample.id))}">${sample.transferred_dataset_files()}</a>
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<a href="${h.url_for(controller='requests_admin', action='show_datatx_page', sample_id=trans.security.encode_id(sample.id))}">${sample.transferred_dataset_files()}/${len(sample.dataset_files)}</a>
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</%def>
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