Changeset 26 for trunk/grails-app

Timestamp:

Apr 5, 2011, 12:10:29 PM (9 years ago)

Author:

robert@…

Message:

Small fixes

Location:

trunk/grails-app

Files:

• conf/BaseFilters.groovy (modified) (1 diff)
• controllers/nl/tno/metagenomics/RunController.groovy (modified) (4 diffs)
• domain/nl/tno/metagenomics/Run.groovy (modified) (2 diffs)
• views/assay/index.gsp (modified) (2 diffs)
• views/run/index.gsp (modified) (2 diffs)

trunk/grails-app/conf/BaseFilters.groovy

@@ -95 +95 @@
                                 // If a user is already logged in, let him continue
                                 if( session.user && session.user != null ) {
-                                        // If we don't refresh the user object, an old hiberante session could still be attached to the object
+                                        // If we don't refresh the user object, an old hibernate session could still be attached to the object
                                         // raising errors later on (Lazy loading errors)
-                                        session.user.refresh();
-                                        
-                                        return true;
+                                        try {
+                                                session.user.refresh();
+                                                return true;
+                                        } catch( Exception ex ) {
+                                                // If an exception occurs, the user is not correctly refreshed. Send the user back to gscf
+                                                session.user = null;
+                                                log.info( "User refresh failed" );
+                                        }
                                 }
                                 

trunk/grails-app/controllers/nl/tno/metagenomics/RunController.groovy

@@ -12 +12 @@
 
         def index = {
-                [runs: Run.list()]
+                [runs: Run.list(), user: session.user]
         }
 
@@ -129 +129 @@
 
                 // Don't remove runs for which data exists
-                if( run.sequenceData?.size() ) {
-                        flash.message = "Run could not be deleted because samples are associated with it.";
+                if( run.assaySamples*.sequenceData.flatten().size() ) {
+                        flash.message = "Run could not be deleted because samples with data are associated with it.";
                         redirect( controller: "assay", action: "show", id: params.assayId )
                 }
@@ -147 +147 @@
                 
                 // Remove all associations
-                run.assays.each {
+                def a = [] + run.assays
+                a.each {
                         run.removeFromAssays( it );
                 }
@@ -156 +157 @@
 
                 redirect( controller: "assay", action: "show", id: params.assayId )
+        }
+
+        def deleteRun = {
+                Run run = getRun( params.id );
+
+                if( !run ) {
+                        redirect(controller: 'run', action: 'index')
+                        return
+                }
+
+                // Don't remove runs for which data exists
+                if( run.assaySamples*.sequenceData.flatten().size() ) {
+                        flash.message = "Run could not be deleted because samples with data are associated with it.";
+                        redirect(controller: 'run', action: 'index')
+                }
+
+                // Check whether the user has sufficient privileges to remove the run from all assays
+                def hasPrivileges = true;
+                run.assays.each {
+                        if( !it.study.canWrite( session.user ) )
+                                hasPrivileges = false
+                }
+                
+                if( !hasPrivileges ) {
+                        flash.message = "Run could not be deleted because you don't have sufficient privileges to remove the run from all assays.";
+                        redirect(controller: 'run', action: 'index')
+                }
+                
+                // Remove all associations
+                def a = [] + run.assays
+                a.each {
+                        run.removeFromAssays( it );
+                }
+
+                def name = run.name
+                run.delete();
+                flash.message = "Run " + name + " has been deleted from the system."
+
+                redirect(controller: 'run', action: 'index')
         }
 

trunk/grails-app/domain/nl/tno/metagenomics/Run.groovy

@@ -1 +1 @@
 package nl.tno.metagenomics
 
+import nl.tno.metagenomics.auth.User
 import org.codehaus.groovy.grails.commons.ConfigurationHolder
 
@@ -112 +113 @@
                 return list.unique().toList();
         }
+        
+        /**
+         * Returns true if this run can be deleted
+         * 
+         * @return
+         */
+        public boolean deletable( User u ) {
+                // Don't remove runs for which data exists
+                if( this.assaySamples*.sequenceData.flatten().size() ) {
+                        return false;
+                }
+
+                // Check whether the user has sufficient privileges to remove the run from all assays
+                def hasPrivileges = true;
+                assays.each {
+                        if( !it.study.canWrite( u ) )
+                                hasPrivileges = false
+                }
+                
+                return hasPrivileges
+        }
 }

trunk/grails-app/views/assay/index.gsp

@@ -22 +22 @@
                                                 <th># samples</th>
                                                 <th>avg sequences / sample</th>
+                                                <th class="nonsortable"></th>
                                         </tr>
                                 </thead>
@@ -42 +43 @@
                                                                                 </g:else>
                                                                         </td>
+                                                                        <td><g:link controller="assay" action="show" id="${assay.id}"><img src="${fam.icon( name: 'application_form_magnify' )}" alt="view" title="view" /></g:link></td>
+                                                                        
                                                                 </tr>
                                                         </g:each>

trunk/grails-app/views/run/index.gsp

@@ -29 +29 @@
                                 <thead>
                                         <tr>
-                                                <th class="nonsortable"><input type="checkbox" id="checkAll" onClick="checkAllPaginated(this);" /></th>
-                                                <th>Run</th>
-                                                <th># samples</th>
-                                                <th># sequences</th>
+                                                <th width="5" class="nonsortable"><input type="checkbox" id="checkAll" onClick="checkAllPaginated(this);" /></th>
+                                                <th width="49%" >Run</th>
+                                                <th width="15%"># samples</th>
+                                                <th width="15%"># sequences</th>
+                                                <th width="5" class="nonsortable"></th>
+                                                <th width="5" class="nonsortable"></th>
                                         </tr>
                                 </thead>
@@ -42 +44 @@
                                                         <td>${run.assaySamples?.size()}</td>
                                                         <td>${run.numSequences()}</td>
+                                                        <td><g:link controller="run" action="show" id="${run.id}"><img src="${fam.icon( name: 'application_form_magnify' )}" alt="view" title="view" /></g:link></td>
+                                                        <td>
+                                                                <g:if test="${run.deletable(user)}">
+                                                                        <g:link controller="run" action="deleteRun" id="${run.id}"><img src="${fam.icon( name: 'delete' )}" alt="delete" title="delete" /></g:link>
+                                                                </g:if>
+                                                                <g:else>
+                                                                        <img src="${fam.icon( name: 'delete' )}" class="disabled" alt="Run can not be deleted because data is associated with it." title="Run can not be deleted because data is associated with it." />
+                                                                </g:else>
+                                                        </td>
                                                 </tr>
                                         </g:each>