[galaxy-commits] galaxy-dist commit c8173a50bc9b: sample_tracking fixes

20 Nov 2010

# HG changeset patch -- Bitbucket.org
# Project galaxy-dist
# URL http://bitbucket.org/galaxy/galaxy-dist/overview
# User rc
# Date 1287030296 14400
# Node ID c8173a50bc9bdb0c8e07807c1b73be746557647f
# Parent  4d5b00b6fe741a35320a572302d1fb8bb7eb6971
sample_tracking fixes

--- a/templates/requests/common/sample_datasets.mako
+++ b/templates/requests/common/sample_datasets.mako
@@ -1,5 +1,5 @@
-<%def name="render_sample_datasets( cntrller, sample )">
-    <a href="${h.url_for( controller='requests_common', action='view_dataset_transfer', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${sample.transferred_dataset_files} / ${len( sample.datasets )}</a>
+<%def name="render_sample_datasets( sample )">
+    ${sample.transferred_dataset_files} / ${len( sample.datasets )}
 </%def>
 
-${render_sample_datasets( cntrller, sample )}
+${render_sample_datasets( sample )}

--- a/test/functional/test_forms_and_requests.py
+++ b/test/functional/test_forms_and_requests.py
@@ -160,8 +160,8 @@ class TestFormsAndRequests( TwillTestCas
         name = 'Test Requestype'
         self.create_request_type( name,
                                   "test sequencer configuration",
-                                  str( request_form.id ),
-                                  str( sample_form.id ),
+                                  self.security.encode_id( request_form.id ),
+                                  self.security.encode_id( sample_form.id ),
                                   sample_states,
                                   strings_displayed=[ 'Create a new sequencer configuration' ],
                                   strings_displayed_after_submit=[ "Sequencer configuration (%s) has been created" % name ] )

--- a/lib/galaxy/web/controllers/requests_common.py
+++ b/lib/galaxy/web/controllers/requests_common.py
@@ -88,7 +88,7 @@ class RequestsGrid( grids.Grid ):
         StateColumn( "State", 
                      key='state',
                      filterable="advanced",
-                     link=( lambda item: iff( item.deleted, None, dict( operation="events", id=item.id ) ) )
+                     link=( lambda item: iff( item.deleted, None, dict( operation="request_events", id=item.id ) ) )
                    )
     ]
     columns.append( grids.MulticolFilterColumn( "Search", 
@@ -105,7 +105,7 @@ class RequestsGrid( grids.Grid ):
 
 class RequestsCommon( BaseController, UsesFormDefinitionWidgets ):
     @web.json
-    def sample_state_updates( self, trans, cntrller, ids=None, states=None ):
+    def sample_state_updates( self, trans, ids=None, states=None ):
         # Avoid caching
         trans.response.headers['Pragma'] = 'no-cache'
         trans.response.headers['Expires'] = '0'
@@ -120,12 +120,10 @@ class RequestsCommon( BaseController, Us
                     rval[ id ] = { "state": sample.state.name,
                                    "datasets": len( sample.datasets ),
                                    "html_state": unicode( trans.fill_template( "requests/common/sample_state.mako",
-                                                                               sample=sample,
-                                                                               cntrller=cntrller ),
+                                                                               sample=sample),
                                                                                'utf-8' ),
                                    "html_datasets": unicode( trans.fill_template( "requests/common/sample_datasets.mako",
-                                                                                  sample=sample,
-                                                                                  cntrller=cntrller ),
+                                                                                  sample=sample ),
                                                                                   'utf-8' ) }
         return rval
     @web.expose
@@ -865,8 +863,6 @@ class RequestsCommon( BaseController, Us
                     library_id = current_samples[ copy_sample_index][ 'library_select_field' ].get_selected( return_value=True )
                     folder_id = current_samples[ copy_sample_index ][ 'folder_select_field' ].get_selected( return_value=True )
                     name = current_samples[ copy_sample_index ][ 'name' ] + '_%i' % ( len( current_samples ) + 1 )
-                    library_id = 'none'
-                    folder_id = 'none'
                     field_values = [ val for val in current_samples[ copy_sample_index ][ 'field_values' ] ]
                 else:
                     # The user has not selected a sample to copy (may just be adding a sample).

--- a/lib/galaxy/web/controllers/requests.py
+++ b/lib/galaxy/web/controllers/requests.py
@@ -52,6 +52,12 @@ class Requests( BaseController ):
                                                                   action='undelete_request',
                                                                   cntrller='requests',
                                                                   **kwd ) )
+            if operation == "request_events":
+                return trans.response.send_redirect( web.url_for( controller='requests_common',
+                                                                  action='request_events',
+                                                                  cntrller='requests',
+                                                                  **kwd ) )
+
         # If there are requests that have been rejected, show a message as a reminder to the user
         rejected = 0
         for request in trans.sa_session.query( trans.app.model.Request ) \

--- a/templates/admin/requests/view_request_type.mako
+++ b/templates/admin/requests/view_request_type.mako
@@ -11,7 +11,7 @@
 
 <div class="toolForm"><div class="toolFormTitle">Sequencer configuration information</div>
-    <form name="view_request_type" action="${h.url_for( controller='requests_admin', action='create_request_type', rt_id=request_type.id)}" method="post" >
+    <form name="view_request_type" action="${h.url_for( controller='requests_admin', action='create_request_type', rt_id=trans.security.encode_id( request_type.id ))}" method="post" ><div class="form-row"><label>Name</label>
             ${request_type.name}

--- a/templates/requests/common/manage_request.mako
+++ b/templates/requests/common/manage_request.mako
@@ -62,7 +62,7 @@
             // Build request data
             var ids = []
             var states = []
-            $.each( sample_states, function ( id, state, cntrller ) {
+            $.each( sample_states, function ( id, state ) {
                 ids.push( id );
                 states.push( state );
             });
@@ -73,7 +73,7 @@
                 dataType: "json",
                 data: { ids: ids.join( "," ), states: states.join( "," ) },
                 success : function ( data ) {
-                    $.each( data, function( cntrller, id, val ) {
+                    $.each( data, function( id, val ) {
                         // Replace HTML
                         var cell1 = $("#sampleState-" + id);
                         cell1.html( val.html_state );
@@ -140,7 +140,6 @@
 	            <a class="action-button" confirm="More samples cannot be added to this request once it is submitted. Click OK to submit." href="${h.url_for( controller='requests_common', action='submit_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Submit</a>
 	        %endif
 	        <a class="action-button" href="${h.url_for( controller='requests_common', action='request_events', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">History</a>
-	        <a class="action-button"  href="${h.url_for( controller='requests_common', action='edit_basic_request_info', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Edit</a>
 	        %if is_admin:
 	            %if request.is_submitted:
 	                <a class="action-button" href="${h.url_for( controller='requests_admin', action='reject', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Reject</a>
@@ -178,6 +177,13 @@
 
 <h4><img src="/static/images/fugue/toggle-expand.png" alt="Show" onclick="showContent(this);" style="cursor:pointer;"/> Request Information</h4><div style="display:none;">
+    <div class="form-row">
+        <ul class="manage-table-actions">
+            <li>
+                <a class="action-button"  href="${h.url_for( controller='requests_common', action='edit_basic_request_info', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Edit request informaton</a>
+            </li>
+        </ul>
+    </div><table class="grid" border="0"><tbody><tr>
@@ -452,7 +458,7 @@
                             %if sample.request.is_unsubmitted:
                                 <td>Unsubmitted</td>
                             %else:
-                                <td id="sampleState-${sample.id}">${render_sample_state( cntrller, sample )}</td>
+                                <td><a id="sampleState-${sample.id}" href="${h.url_for( controller='requests_common', action='sample_events', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${render_sample_state( sample )}</a></td>
                             %endif
                             %if info['library']:
                                 %if cntrller == 'requests':
@@ -469,9 +475,9 @@
                                 <td></td>
                             %endif
                             %if request.is_submitted or request.is_complete: 
-                                <td id="sampleDatasets-${sample.id}">
-                                    ${render_sample_datasets( cntrller, sample )}
-                                </td>
+                                <td><a id="sampleDatasets-${sample.id}" href="${h.url_for( controller='requests_common', action='view_dataset_transfer', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">
+                                    ${render_sample_datasets( sample )}
+                                </a></td>
                             %endif
                         %else:                                                            
                             ${show_basic_info_form( sample_index, sample, info )}

--- a/templates/requests/common/sample_state.mako
+++ b/templates/requests/common/sample_state.mako
@@ -1,5 +1,5 @@
-<%def name="render_sample_state( cntrller, sample )">
-    <a href="${h.url_for( controller='requests_common', action='sample_events', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${sample.state.name}</a>
+<%def name="render_sample_state( sample )">
+    ${sample.state.name}
 </%def>
 
-${render_sample_state( cntrller, sample )}
+${render_sample_state( sample )}

--- a/lib/galaxy/web/controllers/requests_admin.py
+++ b/lib/galaxy/web/controllers/requests_admin.py
@@ -163,6 +163,11 @@ class RequestsAdmin( BaseController, Use
                                                                   action='manage_request',
                                                                   cntrller='requests_admin',
                                                                   **kwd ) )
+            if operation == "request_events":
+                return trans.response.send_redirect( web.url_for( controller='requests_common',
+                                                                  action='request_events',
+                                                                  cntrller='requests_admin',
+                                                                  **kwd ) )
             if operation == "reject":
                 return self.reject_request( trans, **kwd )
             if operation == "view_type":
@@ -423,7 +428,6 @@ class RequestsAdmin( BaseController, Use
                                                                       request_id=request_id,
                                                                       folder_path=folder_path,
                                                                       sample_id=sample.id,
-                                                                      open_folder=True,
                                                                       message=message,
                                                                       status=status ) )
             # Get the filenames from the remote host
@@ -590,21 +594,31 @@ class RequestsAdmin( BaseController, Use
                            FOLDER_ID=str(sample.folder.id),
                            DATASETS=datasets )
         # Send the message 
-        conn = amqp.Connection( host=trans.app.config.amqp['host'] + ":" + trans.app.config.amqp['port'], 
-                                userid=trans.app.config.amqp['userid'], 
-                                password=trans.app.config.amqp['password'], 
-                                virtual_host=trans.app.config.amqp['virtual_host'], 
-                                insist=False )    
-        chan = conn.channel()
-        msg = amqp.Message( data.replace( '\n', '' ).replace( '\r', '' ), 
-                            content_type='text/plain', 
-                            application_headers={'msg_type': 'data_transfer'} )
-        msg.properties["delivery_mode"] = 2
-        chan.basic_publish( msg,
-                            exchange=trans.app.config.amqp['exchange'],
-                            routing_key=trans.app.config.amqp['routing_key'] )
-        chan.close()
-        conn.close()
+        try:
+            conn = amqp.Connection( host=trans.app.config.amqp['host'] + ":" + trans.app.config.amqp['port'], 
+                                    userid=trans.app.config.amqp['userid'], 
+                                    password=trans.app.config.amqp['password'], 
+                                    virtual_host=trans.app.config.amqp['virtual_host'], 
+                                    insist=False )    
+            chan = conn.channel()
+            msg = amqp.Message( data.replace( '\n', '' ).replace( '\r', '' ), 
+                                content_type='text/plain', 
+                                application_headers={'msg_type': 'data_transfer'} )
+            msg.properties["delivery_mode"] = 2
+            chan.basic_publish( msg,
+                                exchange=trans.app.config.amqp['exchange'],
+                                routing_key=trans.app.config.amqp['routing_key'] )
+            chan.close()
+            conn.close()
+        except Exception, e:
+            message = "Error in sending the data transfer message to the Galaxy AMQP message queue:<br/>%s" % str(e)
+            status = "error"
+            return trans.response.send_redirect( web.url_for( controller='requests_admin',
+                                                              action='manage_datasets',
+                                                              sample_id=trans.security.encode_id( sample.id ),
+                                                              status=status,
+                                                              message=message) )
+
     def __start_datatx( self, trans, sample, selected_sample_datasets ):
         datatx_user = self.__setup_datatx_user( trans, sample.library, sample.folder )
         # Validate sequencer information

    

[galaxy-commits] galaxy-dist commit c8173a50bc9b: sample_tracking fixes

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