Changeset 1798

Timestamp:

May 2, 2011, 11:55:13 AM (12 years ago)

Author:

robert@…

Message:

After searching, several actions can be performed on search results. These actions are called by sending data to a URL. This was done using the HTTP GET method, but that resulted in error with the length of the query string (see #422). This is solved by sending all data using the HTTP POST method.

Location:

trunk

Files:

• . (modified) (1 prop)
• grails-app/controllers/dbnp/exporter/ExporterController.groovy (modified) (2 diffs)
• grails-app/controllers/dbnp/query/AdvancedQueryController.groovy (modified) (6 diffs)
• grails-app/controllers/dbnp/studycapturing/AssayController.groovy (modified) (8 diffs)
• grails-app/controllers/dbnp/studycapturing/StudyController.groovy (modified) (2 diffs)
• grails-app/views/advancedQuery/_resultbuttons.gsp (modified) (1 diff)
• grails-app/views/advancedQuery/assayresults.gsp (modified) (1 diff)
• grails-app/views/advancedQuery/results.gsp (modified) (1 diff)
• grails-app/views/advancedQuery/sampleresults.gsp (modified) (1 diff)
• grails-app/views/advancedQuery/studyresults.gsp (modified) (1 diff)
• src/groovy/dbnp/query/Search.groovy (modified) (1 diff)
• web-app/js/advancedQueryResults.js (modified) (3 diffs)

trunk

@@ -10 +10 @@
 .settings
 *.log
+dtd

@@ -10 +10 @@
 .settings
 *.log
+dtd

trunk/grails-app/controllers/dbnp/exporter/ExporterController.groovy

@@ -51 +51 @@
     def export = {
                 def ids = params.list( 'ids' );
+                def tokens = params.list( 'tokens' );
         def studies = []
                 
@@ -59 +60 @@
                                         studies << study
                         }
+                }
+                
+                // Also accept tokens for defining studies
+                tokens.each {
+                        def study = Study.findByStudyUUID( it );
+                        if( study )
+                                studies << study;
                 }
         

trunk/grails-app/controllers/dbnp/query/AdvancedQueryController.groovy

@@ -125 +125 @@
                 def view = determineView( s.entity );
                 render( view: view, model: [search: s, queryId: queryId, actions: determineActions(s)] );
-        }
-
-        /**
-         * Performs an action on specific searchResults 
-         * @param       queryId         queryId of the search to show
-         * @param       id                      list with the ids of the results to perform the action on
-         * @param       actionName      Name of the action to perform
-         */
-        def performAction = {
-                def queryId = params.int( 'queryId' );
-                def selectedIds = params.list( 'id' ).findAll { it.isLong() }.collect { Long.parseLong(it) }
-                def actionName = params.actionName;
-                def moduleName = params.moduleName;
-
-                if( !queryId ) {
-                        flash.error = "Incorrect search ID given to show"
-                        redirect( action: "index" );
-                        return
-                }
-                
-                // Retrieve the search from session
-                Search s = retrieveSearch( queryId );
-                if( !s ) {
-                        flash.message = "Specified search could not be found"
-                        redirect( action: "list" );
-                        return;
-                }
-
-                // Determine the possible actions and build correct urls
-                def actions = determineActions(s, selectedIds );
-
-                // Find the right action to perform
-                def redirectUrl;
-                for( action in actions ) {
-                        if( action.module == moduleName && action.name == actionName ) {
-                                redirectUrl = action.url;
-                                break;
-                        }
-                }
-                
-                if( !redirectUrl ) {
-                        flash.error = "No valid action is given to perform";
-                        redirect( action: "show", id: queryId );
-                        return;
-                }
-                
-                redirect( url: redirectUrl );
         }
         
@@ -578 +531 @@
          * Determine a list of actions that can be performed on specific entities by GSCF
          * @param entity        Name of the entity that the actions could be performed on
-         * @param selectedIds   List with ids of the selected items to perform an action on
-         */
-        protected List gscfActions(Search s, def selectedIds = null) {
+         * @param selectedTokens        List with tokens (UUID) of the selected items to perform an action on
+         */
+        protected List gscfActions(Search s, def selectedTokens = null) {
                 switch(s.entity) {
                         case "Study":
                                 def ids = []
-                                s.filterResults(selectedIds).each {
+                                s.filterResults(selectedTokens).each {
                                         ids << it.id
                                 }
+
+                                def paramString = ids.collect { return 'ids=' + it }.join( '&' );
                                 
                                 return [[
@@ -592 +547 @@
                                                 name:"simpletox",
                                                 description: "Export as SimpleTox",
-                                                url: createLink( controller: "exporter", action: "export", params: [ 'format': 'list', 'ids' : ids ] )
+                                                url: createLink( controller: "exporter", action: "export", params: [ 'format': 'list', 'ids' : ids ] ),
+                                                submitUrl: createLink( controller: "exporter", action: "export", params: [ 'format': 'list' ] ),
+                                                paramString: paramString
                                         ], [
                                                 module: "gscf",
                                                 name:"excel",
                                                 description: "Export as Excel",
-                                                url: createLink( controller: "study", action: "exportToExcel", params: [ 'format': 'list', 'ids' : ids ] )
+                                                url: createLink( controller: "study", action: "exportToExcel", params: [ 'format': 'list', 'ids' : ids ] ),
+                                                submitUrl: createLink( controller: "study", action: "exportToExcel", params: [ 'format': 'list' ] ),
+                                                paramString: paramString
                                         ]]
                         case "Assay":
                                 def ids = []
-                                s.filterResults(selectedIds).each {
+                                s.filterResults(selectedTokens).each {
                                         ids << it.id
                                 }
+
+                                def paramString = ids.collect { return 'ids=' + it }.join( '&' );
                                 
                                 return [[
@@ -609 +570 @@
                                                 name:"excel",
                                                 description: "Export as Excel",
-                                                url: createLink( controller: "assay", action: "exportToExcel", params: [ 'format': 'list', 'ids' : ids ] )
+                                                url: createLink( controller: "assay", action: "exportToExcel", params: [ 'format': 'list', 'ids' : ids ] ),
+                                                submitUrl: createLink( controller: "assay", action: "exportToExcel", params: [ 'format': 'list' ] ),
+                                                paramString: paramString
                                         ]]
                         case "Sample":
@@ -622 +585 @@
          * @param entity        Name of the entity that the actions could be performed on
          */
-        protected List moduleActions(Search s, def selectedIds = null) {
+        protected List moduleActions(Search s, def selectedTokens = null) {
                 def actions = []
 
@@ -639 +602 @@
                                 if( json[ s.entity ] ) {
                                         json[ s.entity ].each { action ->
-                                                def url = action.url ?: module.url + "/action/" + action.name
+                                                def baseUrl = action.url ?: module.url + "/action/" + action.name
+                                                def paramString = s.filterResults(selectedTokens).collect { "tokens=" + it.giveUUID() }.join( "&" )
                                                 
-                                                if( url.find( /\?/ ) )
-                                                        url += "&"
+                                                if( baseUrl.find( /\?/ ) )
+                                                        baseUrl += "&"
                                                 else
-                                                        url += "?"
+                                                        baseUrl += "?"
                                                 
-                                                url += "entity=" + s.entity
-                                                url += "&" + s.filterResults(selectedIds).collect { "tokens=" + it.giveUUID() }.join( "&" )
+                                                baseUrl += "entity=" + s.entity
+                                                
+                                                def url = baseUrl;
+                                                
                                                 actions << [
                                                                         module: moduleName,
                                                                         name: action.name,
                                                                         description: action.description + " (" + moduleName + ")",
-                                                                        url: url
+                                                                        url: url + "&" + paramString,
+                                                                        submitUrl: baseUrl,
+                                                                        paramString: paramString
                                                                 ];
                                         }

trunk/grails-app/controllers/dbnp/studycapturing/AssayController.groovy

@@ -5 +5 @@
         def assayService
         def authenticationService
-    def fileService
+        def fileService
 
         static allowedMethods = [save: "POST", update: "POST", delete: "POST"]
@@ -174 +174 @@
                                 flow.rowData            = assayService.convertColumnToRowStructure(assayData)
 
-                def previewRows         = Math.min(flow.rowData.size()    as int, 5) - 1
-                def previewCols         = Math.min(flow.rowData[0].size() as int, 5) - 1
+                                def previewRows         = Math.min(flow.rowData.size()    as int, 5) - 1
+                                def previewCols         = Math.min(flow.rowData[0].size() as int, 5) - 1
 
                                 flow.assayDataPreview   = flow.rowData[0..previewRows].collect{ it[0..previewCols] as ArrayList }
@@ -198 +198 @@
         }
 
-    /**
-     * Export the row data in session.rowData to the outputStream of the http
-     * response.
-     */
+        /**
+         * Export the row data in session.rowData to the outputStream of the http
+         * response.
+         */
         def doExport = {
 
@@ -209 +209 @@
                 try {
 
-//                      assayService.exportRowWiseDataToExcelFile(session.rowData, response.outputStream)
+                        //                      assayService.exportRowWiseDataToExcelFile(session.rowData, response.outputStream)
                         assayService.exportRowWiseDataToCSVFile(session.rowData, response.outputStream)
 
-            // clear the data from the session
-            session.removeAttribute('rowData')
+                        // clear the data from the session
+                        session.removeAttribute('rowData')
 
                 } catch (Exception e) {
@@ -245 +245 @@
          */
         def exportToExcelAsSheets = {
-                def ids = params.list( 'ids' ).findAll { it.isLong() }.collect { Long.valueOf( it ) };
-
-                if( !ids ) {
-                        flash.errorMessage = "No assay ids given";
-                        redirect( action: "errorPage" );
+                def assays = getAssaysFromParams( params );
+                
+                if( !assays )
                         return;
-                }
-
-                // Find all assays for the given ids
-                def assays = ids.unique().collect { id -> Assay.get( id ) }.findAll { it }
 
                 // Send headers to the browser so the user can download the file
@@ -293 +287 @@
          */
         def exportToExcelAsList = {
-                def ids = params.list( 'ids' ).findAll { it.isLong() }.collect { Long.valueOf( it ) };
-
-                if( !ids ) {
-                        flash.errorMessage = "No assay ids given";
-                        redirect( action: "errorPage" );
+                def assays = getAssaysFromParams( params );
+                
+                if( !assays )
                         return;
-                }
 
                 // If only 1 assay is asked for, don't bother with merging multiple assays.
                 // In that case just use the export method to export one assay per sheet
-                if( ids.size() == 1 )
+                if( assays.size() == 1 )
                         return exportToExcelAsSheets( params );
-
-                // Find all assays for the given ids
-                def assays = ids.unique().collect { id -> Assay.get( id ) }.findAll { it }
 
                 // Send headers to the browser so the user can download the file
@@ -325 +313 @@
                                 // Retrieve row based data for this assay
                                 def assayData = assayService.collectAssayData( assay, fieldMap, measurementTokens );
-                                
+
                                 // Prepend study and assay data to the list
                                 assayData = assayService.prependAssayData( assayData, assay, assay.samples?.size() )
                                 assayData = assayService.prependStudyData( assayData, assay, assay.samples?.size() )
-                                
+
                                 // Put each assay on another sheet
                                 columnWiseAssayData << assayData;
                         }
-                        
+
                         // Merge data from all assays
                         def mergedColumnWiseData = assayService.mergeColumnWiseDataOfMultipleStudies( columnWiseAssayData );
@@ -347 +335 @@
         }
 
+        def getAssaysFromParams( params ) {
+                def ids = params.list( 'ids' ).findAll { it.isLong() }.collect { Long.valueOf( it ) };
+                def tokens = params.list( 'tokens' );
+
+                if( !ids && !tokens ) {
+                        flash.errorMessage = "No assay ids given";
+                        redirect( action: "errorPage" );
+                        return [];
+                }
+
+                // Find all assays for the given ids
+                def assays = [];
+                ids.each { id ->
+                        def assay = Assay.get( id );
+                        if( assay )
+                                assays << assay;
+                }
+
+                // Also accept tokens for defining studies
+                tokens.each { token ->
+                        def assay = Assay.findByAssayUUID( token );
+                        if( assay )
+                                assays << assay;
+                }
+                
+                if( !assays ) {
+                        flash.errorMessage = "No assays found";
+                        redirect( action: "errorPage" );
+                        return [];
+                }
+                
+                return assays.unique();
+        }
 
         def errorPage = {

trunk/grails-app/controllers/dbnp/studycapturing/StudyController.groovy

@@ -396 +396 @@
         def exportToExcel = {
                 def ids = params.list( 'ids' ).findAll { it.isLong() }.collect { Long.valueOf( it ) };
-
-                if( !ids ) {
+                def tokens = params.list( 'tokens' );
+
+                if( !ids && !tokens ) {
                         flash.errorMessage = "No study ids given";
                         redirect( controller: "assay", action: "errorPage" );
@@ -404 +405 @@
                 
                 // Find all assay ids for these studies
-                def assayIds = ids.collect { id ->
+                def assayIds = [];
+                ids.each { id ->
                         def study = Study.get( id );
                         if( study ) {
-                                return study.assays.collect { assay -> assay.id }
-                        } else {
-                                return []
+                                assayIds += study.assays.collect { assay -> assay.id }
                         }
-                }.flatten()
+                }
                 
+                // Also accept tokens for defining studies
+                tokens.each { token ->
+                        def study = Study.findByStudyUUID( token );
+                        if( study )
+                                assayIds += study.assays.collect { assay -> assay.id }
+                }
+                 
                 if( !assayIds ) {
                         flash.errorMessage = "No assays found for the given studies";

trunk/grails-app/views/advancedQuery/_resultbuttons.gsp

@@ -18 +18 @@
                 </g:if>
                 <g:else>
-                        <a class="performAction ${action.name}" href="${action.url}" onClick="performAction( $('form#results'), '${action.name}', '${action.module}' ); return false;">${action.description}</a>
+                        <a class="performAction ${action.name}" href="${action.url}" onClick="performAction( $('form#results'), '${action.name}', '${action.module}', '${action.submitUrl}' ); return false;">${action.description}</a>
                 </g:else>
                 <br />

trunk/grails-app/views/advancedQuery/assayresults.gsp

@@ -41 +41 @@
                                                 also http://datatables.net/examples/api/form.html and advancedQueryResults.js
                                         */ %>
-                                        <g:checkBox name="id" value="${assayInstance.id}" checked="${false}" onClick="updateCheckAll(this);" />
+                                        <g:checkBox name="uuid" value="${assayInstance.giveUUID()}" checked="${false}" onClick="updateCheckAll(this);" />
                                 </td>
                                 <td>

trunk/grails-app/views/advancedQuery/results.gsp

@@ -40 +40 @@
                                                 also http://datatables.net/examples/api/form.html and advancedQueryResults.js
                                         */ %>
-                                        <g:checkBox name="id" value="${result.id}" checked="${false}" onClick="updateCheckAll(this);" />
+                                        <g:checkBox name="uuid" value="${result.giveUUID()}" checked="${false}" onClick="updateCheckAll(this);" />
                                 </td>                   
                                 <td>${search.entity}</td>

trunk/grails-app/views/advancedQuery/sampleresults.gsp

@@ -41 +41 @@
                                                 also http://datatables.net/examples/api/form.html and advancedQueryResults.js
                                         */ %>
-                                        <g:checkBox name="id" value="${sampleInstance.id}" checked="${false}" onClick="updateCheckAll(this);" />
+                                        <g:checkBox name="uuid" value="${sampleInstance.giveUUID()}" checked="${false}" onClick="updateCheckAll(this);" />
                                 </td>
                                 <td>${fieldValue(bean: sampleInstance, field: "name")}</td>

trunk/grails-app/views/advancedQuery/studyresults.gsp

@@ -44 +44 @@
                                                 also http://datatables.net/examples/api/form.html and advancedQueryResults.js
                                         */ %>
-                                        <g:checkBox name="id" value="${studyInstance.id}" checked="${false}" onClick="updateCheckAll(this);" />
+                                        <g:checkBox name="uuid" value="${studyInstance.giveUUID()}" checked="${false}" onClick="updateCheckAll(this);" />
                                 </td>
                                 <td>

trunk/src/groovy/dbnp/query/Search.groovy

@@ -795 +795 @@
         * @return       A list with only those results for which the id is in the selectedIds
         */
-   public List filterResults( List selectedIds ) {
-           if( !selectedIds || !results )
+   public List filterResults( List selectedTokens ) {
+           if( !selectedTokens || !results )
                    return results
 
            return results.findAll {
-                   selectedIds.contains( it.id )
+                   selectedTokens.contains( it.giveUUID() )
            }
    }

trunk/web-app/js/advancedQueryResults.js

@@ -58 +58 @@
 }
 
-function performAction( form, action, module ) {
+function performAction( form, action, module, url ) {
         // Make sure the data from the paginated table is submitted
         // This is performed with javascript, because otherwise
         // checkboxes of hidden rows won't be taken into account
         // See also http://datatables.net/examples/api/form.html
+        
+        if( url == undefined )
+                url = '/advancedQuery/performAction';
         
         // First remove all previously created inputs, in order to avoid any collissions
@@ -74 +77 @@
         $('input', oTable.fnGetNodes()).each(function(idx,el) {
                 var $el = $(el);
-                if( $el.attr( 'name' ) == "id" && $(el).attr( 'checked' ) ) {
+                if( $el.attr( 'name' ) == "uuid" && $(el).attr( 'checked' ) ) {
                         checked = true;
-                        form.append( $( '<input type="hidden" name="id" value="' + $el.attr( 'value' ) + '" class="created" />' ) );
+                        form.append( $( '<input type="hidden" name="tokens" value="' + $el.attr( 'value' ) + '" class="created" />' ) );
                 }
         })
@@ -88 +91 @@
         $( '[name=actionName]', form ).val( action );
         $( '[name=moduleName]', form ).val( module );
-        submitForm( form, '/advancedQuery/performAction' );
+        
+        form.attr( 'action', url );
+        form.submit();
 }

@@ -10 +10 @@
 .settings
 *.log
+dtd