Changeset 4

Timestamp:

Jan 17, 2011, 3:49:20 PM (12 years ago)

Author:

robert@…

Message:

Implemented trash in order to prevent deletion of data

Location:

trunk

Files:

• grails-app/conf/BaseFilters.groovy (modified) (2 diffs)
• grails-app/controllers/metagenomics (deleted)
• grails-app/controllers/nl/tno/metagenomics/AssayController.groovy (modified) (1 diff)
• grails-app/controllers/nl/tno/metagenomics/AssaySampleController.groovy (added)
• grails-app/controllers/nl/tno/metagenomics/RunController.groovy (modified) (2 diffs)
• grails-app/controllers/nl/tno/metagenomics/StudyController.groovy (modified) (2 diffs)
• grails-app/controllers/nl/tno/metagenomics/integration/RestController.groovy (modified) (1 diff)
• grails-app/controllers/nl/tno/metagenomics/integration/SynchronizeController.groovy (modified) (2 diffs)
• grails-app/controllers/nl/tno/metagenomics/integration/TrashController.groovy (added)
• grails-app/domain/nl/tno/metagenomics/AssaySample.groovy (modified) (1 diff)
• grails-app/domain/nl/tno/metagenomics/Study.groovy (modified) (3 diffs)
• grails-app/services/metagenomics (deleted)
• grails-app/services/nl/tno/metagenomics/FastaService.groovy (modified) (2 diffs)
• grails-app/services/nl/tno/metagenomics/integration/GscfService.groovy (modified) (1 diff)
• grails-app/services/nl/tno/metagenomics/integration/SynchronizationService.groovy (modified) (14 diffs)
• grails-app/services/nl/tno/metagenomics/integration/TrashService.groovy (added)
• grails-app/taglib/nl/tno/metagenomics/UploadTagLib.groovy (modified) (1 diff)
• grails-app/views/assay/_addRunDialog.gsp (modified) (2 diffs)
• grails-app/views/assay/_editRunDialog.gsp (deleted)
• grails-app/views/assay/_showRunDialog.gsp (deleted)
• grails-app/views/assay/_showSampleDialog.gsp (deleted)
• grails-app/views/assay/show.gsp (modified) (4 diffs)
• grails-app/views/assaySample (added)
• grails-app/views/assaySample/show.gsp (added)
• grails-app/views/run/editForm.gsp (added)
• grails-app/views/run/show.gsp (added)
• grails-app/views/trash (added)
• grails-app/views/trash/index.gsp (added)
• test/unit/metagenomics/FastaControllerTests.groovy (deleted)
• test/unit/metagenomics/RunControllerTests.groovy (deleted)
• test/unit/metagenomics/SynchronizeControllerTests.groovy (deleted)
• test/unit/metagenomics/TrashControllerTests.groovy (added)
• test/unit/nl/tno/metagenomics/integration (added)
• test/unit/nl/tno/metagenomics/integration/TrashServiceTests.groovy (added)
• web-app/css/metagenomics.css (modified) (1 diff)
• web-app/images/icons (deleted)
• web-app/js/assay.show.runDialogs.js (modified) (2 diffs)
• web-app/js/assay.show.showRunDialog.js (modified) (1 diff)
• web-app/js/assay.show.showSampleDialog.js (modified) (1 diff)
• web-app/js/paginate.js (modified) (1 diff)
• web-app/js/trash.js (added)

trunk/grails-app/conf/BaseFilters.groovy

@@ -49 +49 @@
                                 // 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
+                                        // raising errors later on (Lazy loading errors)
+                                        session.user.refresh();
+                                        
                                         return true;
                                 }
@@ -78 +82 @@
                                                 if (!session.user){ // when not found, create a new user
                                                         session.user = new User(identifier: user.id, username: user.username).save(flush: true)
-                                                }                                                       
-                                                
+                                                }
                                         } catch(Exception e) {
                                                 log.error("Unable to fetch user from GSCF", e)

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

@@ -433 +433 @@
         }
 
-        /**
-         * Updates existing run 
-         */
-        def updateRun = {
-                // load study with id specified by param.id
-                def assay = Assay.get(params.id as Long)
-
-                if (!assay) {
-                        flash.message = "No assay found with id: $params.id"
-                        redirect('action': 'errorPage')
-                        return
-                }
-
-                if( !params.run_id ) {
-                        flash.message = "No run id given"
-                        redirect(action: 'show', id: params.id)
-                        return
-                }
-
-                def run
-
-                try {
-                        run = Run.findById( params.run_id as Long )
-                } catch( Exception e ) {
-                        throw e
-                        flash.message = "Incorrect run id given: "
-                        redirect(action: 'show', id: params.id)
-                        return
-                }
-
-                // Set properties to the run
-                params.parameterFile = params.editParameterFile
-                run.setPropertiesFromForm( params );
-
-                if( run.save() ) {
-                        flash.message = "Run succesfully saved";
-                } else {
-                        flash.error = "Run could not be saved: " + run.getErrors();
-                }
-
-                redirect( action: 'show', id: params.id)
-        }
-
         def errorPage = {
                 render "An error has occured. $flash.message"

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

@@ -7 +7 @@
 class RunController {
         def fileService
+        
+        /**  
+         * Shows information about this run in dialog style
+         */
+        def show = {
+                Run run = Run.get( params.id as long );
+                Assay assay = Assay.get( params.assayId as long );
+                
+                if( !run ) {
+                        render "Run not found";
+                        return
+                }
+                
+                if( !assay ) { 
+                        render "Assay not found";
+                        return
+                }
+                
+                [assay: assay, run: run]
+        }
+        
+        /**
+         * Shows a form to edit the specified run in dialog mode
+         */
+        def editForm = {
+                Run run = Run.get( params.id as long );
+                Assay assay = Assay.get( params.assayId as long );
+                
+                if( !run ) {
+                        render "Run not found";
+                        return
+                }
+                
+                if( !assay ) {
+                        render "Assay not found";
+                        return
+                }
+                
+                [assay: assay, run: run]
+        }
         
     def create = { 
@@ -26 +66 @@
                 redirect( controller: "assay", action: "show", id: params.id )
         }
+        
+        def update = {
+                if( !params.assayId ) {
+                        flash.error = "No assay id given"
+                        redirect(controller: 'assay', action: 'errorpage')
+                        return
+                }
+                def assay = Assay.get(params.assayId as Long)
+                
+                // load run with id specified by param.id
+                if (!assay) {
+                        flash.message = "No assay found with id: ${params.assayId}"
+                        redirect(controller: 'assay', 'action': 'errorPage')
+                        return
+                }
+
+
+                def run
+
+                try {
+                        run = Run.get( params.id as Long );
+                } catch( Exception e ) {
+                        throw e
+                        flash.message = "Incorrect run id given: "
+                        redirect(controller: 'assay', action: 'show', id: params.assayId)
+                        return
+                }
+
+                // Set properties to the run
+                params.parameterFile = params.editParameterFile
+                run.setPropertiesFromForm( params );
+
+                if( run.save() ) {
+                        flash.message = "Run succesfully saved";
+                } else {
+                        flash.error = "Run could not be saved: " + run.getErrors();
+                }
+
+                redirect( controller: 'assay', action: 'show', id: params.assayId)
+        }
+        
+        def delete = {
+                Run run = Run.get( params.id as long );
+
+                // 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.";
+                        redirect( controller: "assay", action: "show", id: params.assayId )
+                }
+                
+                // Remove all associations
+                run.assays.each {
+                        run.removeFromAssays( it );
+                }
+                
+                def name = run.name
+                run.delete();
+                flash.message = "Run " + name + " has been deleted from the system."
+
+                redirect( controller: "assay", action: "show", id: params.assayId )
+                
+        }
 }

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

@@ -5 +5 @@
         def gscfService
         def fileService
+        def trashService
         
         def index = {
@@ -16 +17 @@
                 fileService.cleanDirectory();
                 
+                // Clean the trash if needed
+                trashService.cleanTrash();
+                
                 // Filter studies for the ones the user is allowed to see
-                def studies = Study.findAll();
-                [studies: studies.findAll { it.canRead( session.user ) }, gscfAddUrl: gscfService.urlAddStudy(), lastSynchronized: synchronizationService.lastFullSynchronization ] 
+                def studies = Study.list();
+                [studies: studies.findAll { it.canRead( session.user ) }, 
+                        gscfAddUrl: gscfService.urlAddStudy(), 
+                        lastSynchronized: synchronizationService.lastFullSynchronization ] 
         }
 

trunk/grails-app/controllers/nl/tno/metagenomics/integration/RestController.groovy

@@ -343 +343 @@
                         render url as JSON
                 }
-        }.metagenomics.baseURL
+        }
         
         /***************************************************/

trunk/grails-app/controllers/nl/tno/metagenomics/integration/SynchronizeController.groovy

@@ -17 +17 @@
                 //              /synchronize    -> fails with an error, redirects to /study
                 //                      etc...
-                synchronizationService.lastFullSynchronization = new Date();
+                // synchronizationService.lastFullSynchronization = new Date();
                         
                 [ url: redirectUrl ]
@@ -27 +27 @@
 
                 synchronizationService.fullSynchronization();
-                
+
                 render "";
         }

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

@@ -142 +142 @@
                 _averageQuality = -1;
         }
+        
+        /**
+         * Check whether this assay-sample combination contains information that should be saved in trash on a delete
+         * @return
+         */
+        public boolean containsData() {
+                return tagSequence || oligoNumber || numFiles() > 0;
+        }
+        
+        /**
+         * Move information that should be kept on delete to another assaySample object.
+         * 
+         * N.B. The sequencedata objects are really moved, so removed from the original object!
+         * 
+         * @param otherAssaySample      Object to move
+         */
+        public void moveValuableDataTo( AssaySample otherAssaySample ) {
+                // Copy properties
+                otherAssaySample.tagSequence = tagSequence;
+                otherAssaySample.oligoNumber = oligoNumber;
+                
+                // Move attached data
+                def dataList = sequenceData?.toList()
+                def otherAssay = otherAssaySample.assay;
+                
+                if( dataList && dataList.size() > 0 ) {
+                        for( def j = dataList.size() - 1; j >= 0; j-- ) {
+                                // Check whether the run of this sequenceData object is also connected to the assay
+                                def run = dataList[j].run;
+                                
+                                if( !otherAssay.runs || !otherAssay.runs.contains( run ) ) {
+                                        otherAssay.addToRuns( run );
+                                }
+                                
+                                // Copy data
+                                dataList[j].sample = otherAssaySample;
+                                this.removeFromSequenceData( dataList[j] );
+                                otherAssaySample.addToSequenceData( dataList[j] );
+                                dataList[j].save();
+                        }
+                }
+        }
 }

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

@@ -13 +13 @@
         String studyToken
         String name
+
+        // Set to true only on the specific study object that acts as
+        // a trash can for deleted objects. If objects are deleted in GSCF but still
+        // contain data in this module, they will be moved to the trashcan.
+        Boolean trashcan = false 
         
         // If a study is set to be dirty, it should be updated
@@ -31 +36 @@
         static constraints = {
                 studyToken(unique:true)
+                trashcan(nullable:true)
+                isDirty(nullable:true)
         }
         
@@ -70 +77 @@
                 return authorization.isOwner
         }
+
 }

trunk/grails-app/services/nl/tno/metagenomics/FastaService.groovy

@@ -131 +131 @@
 
                         // Best matching sample
+                        // TODO: Implement method to search for sample matches in a provided excel sheet
                         def sampleIdx = fuzzySearchService.mostSimilarWithIndex( matchWith, samples.sample.name );
                         def assaySample = null
@@ -316 +317 @@
                                                 lookingForFirstQualityScores = false;
 
-                                                quality = updateQuality( quality, line );
+                                                // Don't compute average quality because it takes too much time
+                                                //quality = updateQuality( quality, line );
                                         }
                                 } else {
-                                        quality = updateQuality( quality, line );
+                                        // Don't compute average quality because it takes too much time
+                                        //quality = updateQuality( quality, line );
                                 }
                                 

trunk/grails-app/services/nl/tno/metagenomics/integration/GscfService.groovy

@@ -213 +213 @@
          * @return ArrayList
          */
-        public HashMap getAuthorizationLevel(String sessionToken, String studyToken) {
+        public HashMap getAuthorizationLevel(String sessionToken, String studyToken) throws ResourceNotFoundException {
                 ArrayList list
 

trunk/grails-app/services/nl/tno/metagenomics/integration/SynchronizationService.groovy

@@ -7 +7 @@
 class SynchronizationService {
         def gscfService
+        def trashService
 
         String sessionToken = ""        // Session token to use for communication
@@ -81 +82 @@
                         return
 
-                def previousEager = eager
-                eager = true
-                synchronizeStudies();
-                eager = previousEager
+                def previousEager = this.eager
+                this.eager = true
+                this.synchronizeStudies();
+                this.eager = previousEager
                 
                 SynchronizationService.lastFullSynchronization = new Date();
@@ -95 +96 @@
         public ArrayList<Study> synchronizeStudies() {
                 if( !performSynchronization() )
-                        return Study.findAll()
+                        return Study.list()
 
                 // When eager fetching is enabled, ask for all studies, otherwise only ask for studies marked dirty
@@ -102 +103 @@
                 def studies
                 if( eager ) {
-                        studies = Study.findAll()
+                        studies = Study.list().findAll { !it.trashcan };
+                        log.trace "Eager synchronization: " + studies.size();
                 } else {
                         studies = Study.findAllWhere( [isDirty: true] );
-                }
-
+                        log.trace "Default synchronization: " + studies.size()
+                }
+                
                 // Perform no synchronization if no studies have to be synchronized
                 // Perform synchronization on only one study directly, because otherwise
@@ -235 +238 @@
                         return null
 
+                // Trashcan should never be synchronized
+                if( study.trashcan )
+                        return study
+                        
                 // If the study hasn't changed, don't update anything
                 if( !eager && !study.isDirty )
@@ -249 +256 @@
                 } catch( ResourceNotFoundException e ) {
                         // Study can't be found within GSCF.
-                        // TODO: How to handle the data that remains
-                        study.delete()
+                        trashService.moveToTrash( study );
                         return null
                 } catch( Exception e ) { // All other exceptions
@@ -335 +341 @@
                         for( int i = numStudyAssays - 1; i >= 0; i-- ) {
                                 def existingAssay = studyAssays[i];
-
-                                existingAssay.delete()
-                                study.removeFromAssays( existingAssay );
+                                
+                                // Move data to trash
+                                trashService.moveToTrash( existingAssay );
                         }
 
@@ -408 +414 @@
 
                                 // The assay has been removed
-                                // TODO: What to do with the data associated with this Assay (e.g. sequences)? See also GSCF ticket #255
-                                existingAssay.delete();
-                                study.removeFromAssays( existingAssay );
+                                trashService.moveToTrash( existingAssay );
                         }
                 }
@@ -446 +450 @@
                 } catch( ResourceNotFoundException e ) {
                         // Study has been deleted, remove all authorization on that study
-                        // TODO: handle deletion
                         log.trace( "Study " + study.studyToken + " has been deleted. Remove all authorization on that study")
-
-                        Auth.findAllByStudy( study ).each {
-                                it.delete()
-                        }
+                        trashService.moveToTrash( study );
 
                         return null
@@ -501 +501 @@
                 } catch( ResourceNotFoundException e ) {
                         // Assay can't be found within GSCF.
-                        // TODO: How to handle the data that remains
-                        assay.delete()
+                        trashService.moveToTrash( assay );
                         return null
                 } catch( Exception e ) { // All other exceptions are thrown
@@ -511 +510 @@
                 }
 
-                // If new assay is empty, something went wrong
+                // If new assay is empty, this means that the assay does exist, but now belongs to another module. Remove it from our system
                 if( newAssay.size() == 0 ) {
-                        throw new Exception( "No data returned for assay " + assay.assayToken + " but no error has occurred either. Please contact your system administrator" );
+                        log.info( "No data is returned by GSCF for assay  " + assay.assayToken + "; probably the assay is connected to another module." )
+                        trashService.moveToTrash( assay );
                         return null;
                 }
@@ -577 +577 @@
                 } catch( ResourceNotFoundException e ) {
                         // Assay can't be found within GSCF. Samples will be removed
-                        // TODO: How to handle the data that remains
-                        assay.removeAssaySamples();
+                        trashService.moveToTrash( assay );
 
                         return null
@@ -593 +592 @@
                         return []
                 }
-
 
                 synchronizeAssaySamples( assay, newSamples );
@@ -678 +676 @@
 
                                         // The sample has been removed
-                                        // TODO: What to do with the data associated with this AssaySample (e.g. sequences)? See also GSCF ticket #255
-                                        existingSample.delete();
-                                        assay.removeFromAssaySamples( existingSample );
+                                        trashService.moveToTrash( existingSample.sample );
                                 }
                         }

trunk/grails-app/taglib/nl/tno/metagenomics/UploadTagLib.groovy

@@ -23 +23 @@
                 out << '<script type="text/javascript">';
                 out << '  $(document).ready( function() { ';
-                out << '    var filename = "' + attrs.value + '";';
+                out << '    var filename = "' + ( attrs.value ?: '' ) + '";';
                 out << '    fileUploadField( "' + attrs.name + '", ' + ( multiple ? 'true' : 'false' ) + ( attrs.onUpload ? ', function(params) { ' + attrs.onUpload + '(params); }' : '' ) + ( attrs.onDelete ? ', function(params) { ' + attrs.onDelete + '(params); }' : '' ) + ');';
                 out << '    if( filename != "" ) {';

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

@@ -31 +31 @@
                                                         <th nowrap>date</th>
                                                         <th nowrap>other assays</th>
+                                                        <th class="nonsortable"></th>
                                                 </tr>
                                         </thead>                                
@@ -49 +50 @@
                                                                         </g:else>
                                                                 </td>
+                                                                <td>
+                                                                        <g:if test="${run.sequenceData?.size()}">
+                                                                                <img src="${fam.icon(name: 'delete')}" class="disabled" title="You can't delete this run because samples are associated with this run." />
+                                                                        </g:if>
+                                                                        <g:else>
+                                                                                <g:if test="${run.assays?.size() > 0}">
+                                                                                        <g:link onClick="return confirm( 'Are you sure you want to delete this run from the system? If you delete this run, it will also be deleted from the other assays it is associated to!' );" controller="run" action="delete" id="${run.id}" params="[assayId: assay.id]"><img src="${fam.icon(name: 'delete')}" /></g:link> 
+                                                                                </g:if>
+                                                                                <g:else>
+                                                                                        <g:link onClick="return confirm( 'Are you sure you want to delete this run from the system?' );" controller="run" action="delete" id="${run.id}" params="[assayId: assay.id]"><img src="${fam.icon(name: 'delete')}" /></g:link>
+                                                                                </g:else> 
+                                                                        </g:else>
+                                                                </td>
                                                         </tr>
                                                 </g:each>

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

@@ -27 +27 @@
                         </g:each>
                         
-                        $(function() {
-                                $('.uploadedFile').each( function( idx, el ) { 
+                        function initializeUploadedFiles( selector ) {
+                                if( selector == undefined )
+                                        selector = "";
+                                
+                                $( selector + ' .uploadedFile').each( function( idx, el ) { 
                                         $(el).html( createFileHTML( $(el).text(), 'getPermanent' ) );
                                 });
-                        });
+                        }
+
+                        // Initializefiles on load
+                        $(function() { initializeUploadedFiles(); });
                 </script>
         </head>
@@ -97 +103 @@
                         <g:render template="addFilesDialog" model="[assay: assay]" />
                 </g:if>
-                <g:render template="showSampleDialog" model="[assay: assay]" />
+                <div id="showSampleDialog" class="dialog"></div>
         </g:else>       
 
@@ -140 +146 @@
                                                 </td>
                                                 <td class="button"><a href="#" onClick="showEditRunDialog( ${run.id}, '${run.name?.encodeAsJavaScript()}', '${run.date ? run.date.format( 'yyyy-mm-dd' ).encodeAsJavaScript() : ''}', '${run.machine?.encodeAsJavaScript()}', '${run.supplier?.encodeAsJavaScript()}', '${run.parameterFile?.encodeAsJavaScript()}' ); return false;"><img src="${fam.icon(name: 'application_edit')}" /></a></td>
-                                                <td class="button"><g:link onClick="return confirm( 'Are you sure you want to remove the selected run from this assay?' );" controller="assay" action="removeRun" id="${assay.id}" params="${[run_id: run.id]}" ><img src="${fam.icon(name: 'application_delete')}" /></g:link></td>
+                                                <td class="button">
+                                                        <g:if test="${run.samples(assay.id).size()}">
+                                                                <img src="${fam.icon(name: 'application_delete')}" class="disabled" title="You can't remove this assay because sequences from this assay are coupled to this run." />
+                                                        </g:if>
+                                                        <g:else>
+                                                                <g:link onClick="return confirm( 'Are you sure you want to remove the selected run from this assay?' );" controller="assay" action="removeRun" id="${assay.id}" params="${[run_id: run.id]}" ><img src="${fam.icon(name: 'application_delete')}" /></g:link>
+                                                        </g:else>
+                                                </td>
                                         </tr>
                                 </g:each>
@@ -149 +162 @@
                 <input type="button" value="Add run" onClick="showAddRunDialog();">
                 <g:render template="addRunDialog" model="[assay: assay]" />
-                <g:render template="editRunDialog" model="[assay: assay]" />
+                <div id="editRunDialog" class="dialog"></div>
         </g:if> 
-        <g:render template="showRunDialog" model="[assay: assay]" />
-        
+        <div id="showRunDialog" class="dialog"></div>
 </body>
 </html>

trunk/web-app/css/metagenomics.css

@@ -473 +473 @@
     display: none;
 }
+
+.disabled { 
+        opacity: 0.5;
+        -moz-opacity:0.5;
+        -khtml-opacity:0.5;
+        filter:alpha(opacity=50);
+}
+
+.ui-dialog a:link, .ui-dialog a:visited, .ui-dialog a:hover {
+        color: #006dba;
+        text-decoration: none;
+}

trunk/web-app/js/assay.show.runDialogs.js

@@ -42 +42 @@
         
         // Initialize date picker for add run dialog
-        $( "#run_date, #edit_run_date" ).datepicker({
+        $( "#run_date" ).datepicker({
                 changeMonth: true,
                 changeYear: true,
@@ -66 +66 @@
  */
 function showEditRunDialog(id, name, date, machine, supplier, parameterFile) {
-        $( '#edit_run_id' ).val( id );
-        
-        $( '#edit_run_name' ).val( name );
-        $( '#edit_run_date' ).val( date );
-        $( '#edit_run_machine' ).val( machine );
-        $( '#edit_run_supplier' ).val( supplier );
-        
-        editFile( 'editParameterFile', parameterFile)
-        $( "#editRunDialog" ).dialog( "open" );
+        $( "#editRunDialog" ).load( baseUrl + "/run/editForm/" + id + "?assayId=" + assayId, [], function() {
+                // Initialize date picker for add run dialog
+                $( "#edit_run_date" ).datepicker({
+                        changeMonth: true,
+                        changeYear: true,
+                        dateFormat: 'yy-mm-dd'
+                });     
+                
+                $( "#editRunDialog" ).dialog( "open" );
+        } );
 }
 

trunk/web-app/js/assay.show.showRunDialog.js

@@ -15 +15 @@
  */
 function showRun( id ) {
-        $( '#showRunDialog div.showRun' ).hide()
-        $( '#showRunDialog div#showRun_' + id ).show()
-        
-        var titleEl = $( '#showRunDialog div#showRun_' + id + ' h2' ).first();
-        titleEl.hide();
-        $( "#showRunDialog" ).dialog( "option", "title", "Run " + titleEl.text() );
-        $( "#showRunDialog" ).dialog( "open" );
+        $( "#showRunDialog" ).load( baseUrl + "/run/show/" + id + "?assayId=" + assayId, [], function() {
+                var titleEl = $( '#showRunDialog h2' ).first();
+                titleEl.hide();
+                
+                initializeUploadedFiles( '#showRunDialog' );
+                initializePagination( '#showRunDialog' );
+                                
+                $( "#showRunDialog" ).dialog( "option", "title", "Run " + titleEl.text() );
+                $( "#showRunDialog" ).dialog( "open" );
+        } );
 }

trunk/web-app/js/assay.show.showSampleDialog.js

@@ -15 +15 @@
  */
 function showSample( id ) {
-        $( '#showSampleDialog div.showSample' ).hide()
-        $( '#showSampleDialog div#showSample_' + id ).show()
-        
-        var titleEl = $( '#showSampleDialog div#showSample_' + id + ' h2' ).first();
-        titleEl.hide();
-        $( "#showSampleDialog" ).dialog( "option", "title", "Sample " + titleEl.text() );
-        $( "#showSampleDialog" ).dialog( "open" );
+        $( "#showSampleDialog" ).load( baseUrl + "/assaySample/show/" + id, [], function() {
+                var titleEl = $( '#showSampleDialog h2' ).first();
+                titleEl.hide();
+                
+                initializeUploadedFiles( "#showSampleDialog" );
+                initializePagination( "#showSampleDialog" );
+                                
+                $( "#showSampleDialog" ).dialog( "option", "title", "Sample " + titleEl.text() );
+                $( "#showSampleDialog" ).dialog( "open" );
+        } );
 }

trunk/web-app/js/paginate.js

@@ -1 @@
-        $(function() {
-                $('.paginate').each(function(idx, el) {
-                        var $el = $(el);
-                        $el.dataTable({ 
-                                bJQueryUI: true, 
-                                bFilter: false, 
-                                bLengthChange: false, 
-                                iCookieDuration: 86400,                         // Save cookie one day
-                                sPaginationType: 'full_numbers',
-                                iDisplayLength: 10,                                     // Number of items shown on one page.
-                                aoColumnDefs: [
-                                        { "bSortable": false, "aTargets": ["nonsortable"] }     // Disable sorting on all columns with th.nonsortable
-                                ]                                               
-                        });
-                });
-                
-                // Remove the top bar of the datatable and hide pagination with only one page
-                $(".dataTables_wrapper").each(function(idx, el) {
-                        var $el = $(el);
-                        
-                        // Hide pagination if only one page is present (that is: if no buttons can be clicked)
-                        if($el.find('span span.ui-state-default:not(.ui-state-disabled)').size() == 0 ){
-                                $el.find('div.fg-toolbar').css( 'display', 'none' );
-                        } else {
-                                $el.find('div.fg-toolbar').css( 'display', 'block' );
-                                $el.find( 'div.ui-toolbar' ).first().hide();
-                                
-                                // Check whether a h1, h2 or h3 is present above the table, and move it into the table
-                                /*
-                                var $previousElement = $el.prev();
-                                if( $previousElement != undefined && $previousElement.get(0) != undefined ) {
-                                        var tagName = $previousElement.get(0).tagName.toLowerCase();
-                                        if( tagName == "h1" || tagName == "h2" || tagName == "h3" ) {
-                                                // Put the margin that was on the title onto the table
-                                                $el.css( "margin-top", $previousElement.css( "margin-top" ) );
-                                                $previousElement.css( "margin-top", '4px' );
-                                                $previousElement.css( "marginBottom", '4px' );
-
-                                                // If so, move the element into the table
-                                                $previousElement.remove();
-                                                $el.find( 'div.ui-toolbar' ).first().append( $previousElement );
-                                        }
-                                }
-                                */                                              
-                        }
+function initializePagination( selector ) {
+        if( selector == undefined ) {
+                selector = ''
+        }
+        
+        $( selector + ' .paginate').each(function(idx, el) {
+                var $el = $(el);
+                $el.dataTable({ 
+                        bJQueryUI: true, 
+                        bFilter: false, 
+                        bLengthChange: false, 
+                        iCookieDuration: 86400,                         // Save cookie one day
+                        sPaginationType: 'full_numbers',
+                        iDisplayLength: 10,                                     // Number of items shown on one page.
+                        aoColumnDefs: [
+                                { "bSortable": false, "aTargets": ["nonsortable"] }     // Disable sorting on all columns with th.nonsortable
+                        ]                                               
                 });
         });
+        
+        // Remove the top bar of the datatable and hide pagination with only one page
+        $( selector + " .dataTables_wrapper").each(function(idx, el) {
+                var $el = $(el);
+                
+                // Hide pagination if only one page is present (that is: if no buttons can be clicked)
+                if($el.find('span span.ui-state-default:not(.ui-state-disabled)').size() == 0 ){
+                        $el.find('div.fg-toolbar').css( 'display', 'none' );
+                } else {
+                        $el.find('div.fg-toolbar').css( 'display', 'block' );
+                        $el.find( 'div.ui-toolbar' ).first().hide();
+                        
+                        // Check whether a h1, h2 or h3 is present above the table, and move it into the table
+                        /*
+                        var $previousElement = $el.prev();
+                        if( $previousElement != undefined && $previousElement.get(0) != undefined ) {
+                                var tagName = $previousElement.get(0).tagName.toLowerCase();
+                                if( tagName == "h1" || tagName == "h2" || tagName == "h3" ) {
+                                        // Put the margin that was on the title onto the table
+                                        $el.css( "margin-top", $previousElement.css( "margin-top" ) );
+                                        $previousElement.css( "margin-top", '4px' );
+                                        $previousElement.css( "marginBottom", '4px' );
+
+                                        // If so, move the element into the table
+                                        $previousElement.remove();
+                                        $el.find( 'div.ui-toolbar' ).first().append( $previousElement );
+                                }
+                        }
+                        */                                              
+                }
+        });
+        
+}
+
+$(function() { initializePagination(); });