Changeset 518

Timestamp:

Jun 3, 2010, 12:27:08 PM (13 years ago)

Author:

roberth

Message:

Publications can be added to a study in the create study wizard. Publications are searched for on Pubmed, and when needed, added to the system.

Location:

trunk

Files:

• grails-app/controllers/dbnp/studycapturing/PublicationController.groovy (modified) (1 diff)
• grails-app/controllers/dbnp/studycapturing/WizardController.groovy (modified) (3 diffs)
• grails-app/domain/dbnp/studycapturing/Publication.groovy (modified) (1 diff)
• grails-app/taglib/dbnp/studycapturing/WizardTagLib.groovy (modified) (1 diff)
• grails-app/views/file (added)
• grails-app/views/publication/add.gsp (modified) (1 diff)
• grails-app/views/wizard/index.gsp (modified) (2 diffs)
• grails-app/views/wizard/pages/_study.gsp (modified) (1 diff)
• test/integration/dbnp (added)
• web-app/css/wizard.css (modified) (1 diff)
• web-app/js/publication-chooser.js (modified) (7 diffs)
• web-app/js/publication-chooser.pubmed.js (modified) (4 diffs)
• web-app/js/wizard.js (modified) (1 diff)

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

@@ -144 +144 @@
         }
     }
+
+    /**
+     * Searches for an ID in the current database, based on the pubMedID
+     * If the publication is not found in the database, it is added
+     */
+    def getID = {
+        // Find the ID
+        def pubMedID = params.get( 'publication-pubMedID' );
+        if( pubMedID ) {
+            def publication = Publication.findByPubMedID( pubMedID );
+            if( !publication ) {
+                publication = new Publication(
+                    title: params.get( 'publication-title' ),
+                    authorsList: params.get( 'publication-authorsList' ),
+                    pubMedID: params.get( 'publication-pubMedID' ),
+                    DOI: params.get( 'publication-doi' )
+                ).save(flush:true);
+            }
+
+            // Return the ID
+            render publication.id;
+        } else {
+            response.status = 500;
+            render "No pubMedID found in request";
+        }
+    }
 }

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

@@ -133 +133 @@
                                 success()
                         }.to "study"
-                        on("switchTemplate") {
+                        on("switchTemplate") {
                                 flash.values = params
 
@@ -604 +604 @@
                 }
 
+                // handle Publications
+                handlePublications(flow, flash, params)
+
                 // validate study
                 if (flow.study.validate()) {
@@ -614 +617 @@
                 }
         }
+
+        /**
+         * re-usable code for handling publications form data in a web flow
+         * @param Map LocalAttributeMap (the flow scope)
+         * @param Map localAttributeMap (the flash scope)
+         * @param Map GrailsParameterMap (the flow parameters = form data)
+         * @returns boolean
+         */
+        def handlePublications(flow, flash, params) {
+                // create study instance if we have none
+                if (!flow.study) flow.study = new Study();
+                if (!flow.study.publications ) flow.study.publications = [];
+
+                // Check the ids of the pubblications that should be attached
+                // to this study. If they are already attached, keep 'm. If
+                // studies are attached that are not in the selected (i.e. the
+                // user deleted them), remove them
+                def publicationIDs = params.get( 'publication_ids' );
+                if( publicationIDs ) {
+                    // Find the individual IDs and make integers
+                    publicationIDs = publicationIDs.split(',').collect { Integer.parseInt( it, 10 ) };
+
+                    // First remove the publication that are not present in the array
+                    flow.study.publications.removeAll { publication -> !publicationIDs.find { id -> id == publication.id } }
+
+                    // Add those publications not yet present in the database
+                    publicationIDs.each { id ->
+                        if( !flow.study.publications.find { publication -> id == publication.id } ) {
+                            def publication = Publication.get( id );
+                            if( publication ) {
+                                flow.study.addToPublications( publication );
+                            } else {
+                                println( 'Publication with ID ' + id + ' not found in database.' );
+                            }
+                        }
+                    }
+
+                } else {
+                    println( 'No publications selected.')
+                    flow.study.publications.clear();
+                }
+
+        }
+
 
         /**

trunk/grails-app/domain/dbnp/studycapturing/Publication.groovy

@@ -46 +46 @@
  */
 
-class Publication {
+class Publication implements Serializable {
 
     String title

trunk/grails-app/taglib/dbnp/studycapturing/WizardTagLib.groovy

@@ -983 +983 @@
                 }
         }
+
+        def PublicationSelectElement = { attrs, body ->
+
+            attrs.description = 'Publications';
+            // render list with publications currently available
+            baseElement.call(
+                    '_publicationList',
+                    attrs,
+                    body
+            )
+
+            attrs.description = '';
+
+            // render 'Add publication button'
+            baseElement.call(
+                    '_publicationAddButton',
+                    attrs,
+                    body
+            )
+        }
+
+        /**
+         * Renders a input box for publications
+         */
+        def publicationSelect = { attrs, body ->
+                if( attrs.get( 'value' ) == null ) {
+                    attrs.value = [];
+                }
+                if( attrs.get( 'description' ) == null ) {
+                    attrs.description = '';
+                }
+                out << '<form id="' + attrs.name + '_form">';
+                out << textField(
+                            name: attrs.get( "name" ),
+                            value: '',
+                            rel: 'publication-pubmed',
+                            style: 'width: 400px;'
+                );
+                out << '</form>';
+                out << '<script type="text/javascript">';
+                out << '  iField = $( "#' + attrs.get( 'name' ) + '" );';
+                out << '  new PublicationChooser().initAutocomplete( iField );';
+                out << '</script>';
+        }
+
+        def _publicationList = { attrs, body ->
+           def display_none = 'none';
+           if( !attrs.get( 'value' ) || attrs.get( 'value' ).size() == 0 ) {
+                display_none =  'inline';
+           }
+           
+            // Add a unordered list
+            out << '<ul class="publication_list" id="' + attrs.name + '_list">';
+
+            out << '<li>';
+            out << '<span class="publication_none" id="' + attrs.name + '_none" style="display: ' + display_none + ';">';
+            out << 'No publications selected';
+            out << '</span>';
+            out << '</li>';
+
+            out << '</ul>';
+
+           // Add the publications using javascript
+           out << '<script type="text/javascript">'
+           if( attrs.get( 'value' ) && attrs.get( 'value' ).size() > 0 ) {
+               def i = 0;
+               attrs.get( 'value' ).each {
+                    out << 'showPublication( ';
+                    out << '  "' + attrs.name + '",';
+                    out << '  ' + it.id + ',';
+                    out << '  "' + it.title + '",';
+                    out << '  "' + it.authorsList + '",';
+                    out << '  ' + i++;
+                    out << ');';
+                }
+            }
+            out << '</script>';
+
+            def ids;
+            if( attrs.get( 'value' ) && attrs.get( 'value' ).size() > 0 ) {
+                ids = attrs.get( 'value' ).id.join( ',' )
+            } else {
+                ids = '';
+            }
+            out << '<input type="hidden" name="' + attrs.name + '_ids" value="' + ids + '" id="' + attrs.name + '_ids" value="' + ids + '">';
+        }
+
+        def _publicationAddButton = { attrs, body ->
+
+            // Output the dialog for the publications
+            out << '<div id="' + attrs.name + '_dialog">';
+            out << publicationSelect( attrs, body );
+            out << '</div>';
+            out << '<script type="text/javascript">';
+            out << '     $("#' + attrs.name + '_dialog").dialog({';
+            out << '         title   : "Add publication",';
+            out << '         autoOpen: false,';
+            out << '         width   : 800,';
+            out << '         height  : 400,';
+            out << '         modal   : true,';
+            out << '         position: "center",';
+            out << '         buttons : {';
+            out << '            Add  : function() { addPublication( "' + attrs.name + '" ); $(this).dialog("close"); },';
+            out << '            Close  : function() { $(this).dialog("close"); }';
+            out << '         },';
+            out << '         close   : function() {';
+            out << '             /* closeFunc(this); */';
+            out << '         }';
+            out << '     }).width(790).height(400);';
+            out << '</script>';
+
+            out << '<input type="button" onClick="var field = $( \'#' + attrs.name + '\' ); field.autocomplete( \'close\' ); field.val( \'\' );$( \'#' + attrs.name + '_dialog\' ).dialog( \'open\' ); field.focus();" value="Add Publication">';
+        }
+
 }

trunk/grails-app/views/publication/add.gsp

@@ -22 +22 @@
   <script type="text/javascript" src="${resource(dir: 'js', file: 'publication-chooser.pubmed.js')}"></script>
   <script type="text/javascript" src="${resource(dir: 'js', file: 'publication-chooser.programminglanguages.js')}"></script>
-
+  <script type="text/javascript">
+    PublicationChooser.prototype.availableDBs[ "pubmed" ].select = selectPubMedAdd;
+    PublicationChooser.prototype.availableDBs[ "pubmed" ].close  = closePubMedAdd;
+</script>
  </head>
  <body>
-
- <g:form action="createFromPubmed">
-  <g:textField name="publication" rel="publication-pubmed" style="width:300px;"/>
-  <g:submitButton name="add" value="Add publication" />
- </g:form>
-
-
+   <p>
+     Search for a publication on pubmed. You can search on a part of the title or authors.
+   </p>
+   <g:form action="createFromPubmed">
+    <g:textField name="publication" rel="publication-pubmed" style="width:500px;"/>
+    <!-- <g:submitButton name="add" value="Add publication" /> -->
+   </g:form>
 
  ${errors}

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

@@ -23 +23 @@
         <script type="text/javascript" src="${resource(dir: 'js', file: 'table-editor.min.js')}"></script>
         <script type="text/javascript" src="${resource(dir: 'js', file: 'ontology-chooser.min.js')}"></script>
+        <script type="text/javascript" src="${resource(dir: 'js', file: 'publication-chooser.js')}"></script>
+        <script type="text/javascript" src="${resource(dir: 'js', file: 'publication-chooser.pubmed.js')}"></script>
         <script type="text/javascript" src="${resource(dir: 'js', file: 'SelectAddMore.min.js')}"></script>
         <script type="text/javascript" src="${resource(dir: 'js', file: 'timepicker-0.2.1.min.js')}"></script>
@@ -33 +35 @@
         <script type="text/javascript" src="${resource(dir: 'js', file: 'table-editor.js')}"></script>
         <script type="text/javascript" src="${resource(dir: 'js', file: 'ontology-chooser.js')}"></script>
+        <script type="text/javascript" src="${resource(dir: 'js', file: 'publication-chooser.js')}"></script>
+        <script type="text/javascript" src="${resource(dir: 'js', file: 'publication-chooser.pubmed.js')}"></script>
         <script type="text/javascript" src="${resource(dir: 'js', file: 'SelectAddMore.js')}"></script>
         <script type="text/javascript" src="${resource(dir: 'js', file: 'timepicker-0.2.1.js')}"></script>

trunk/grails-app/views/wizard/pages/_study.gsp

@@ -30 +30 @@
         </wizard:templateElement>
         <g:if test="${study}"><wizard:templateElements entity="${study}" /></g:if>
+
+        <wizard:publicationSelectElement name="publication" value="${study?.publications}" />
+
 </wizard:pageContent>

trunk/web-app/css/wizard.css

@@ -348 +348 @@
     color: red;
 }
-}
+
+.wizard ul.publication_list {
+    list-style-type: none;
+    margin: -10px 0 0 255px;
+    padding: 0;
+}
+
+.wizard ul.publication_list li {
+    margin-left: 0px;
+    padding: 4px 6px;
+}
+
+.wizard ul.publication_list li.even {
+    background-color: #F0F0F0;
+}
+.wizard ul.publication_list li.odd {
+    background-color: #F8F8F8;
+}
+
+.wizard ul.publication_list li .delete_button { float: right; margin-left: 10px; }
+.wizard ul.publication_list li .authors { font-size: 10px; margin-top: 3px; color: #333; }

trunk/web-app/js/publication-chooser.js

@@ -149 +149 @@
  * initialize object
  */
-PublicationChooser.init = function() {
+PublicationChooser.init = function( events ) {
     // find all ontology elements
     $("input[rel*='publication']").each(function() {
-        new PublicationChooser().initAutocomplete(this);
+        new PublicationChooser().initAutocomplete( this, events );
     });
 };
@@ -159 +159 @@
     minLength       : 3,        // minimum input length before launching Ajax request
     cache           : [],       // ontology cache
-    maxResults      : 10,       // Max number of results retrieved
+    maxResults      : 8,        // Max number of results retrieved
     database        : '',       // Default database to be used. As for now, also the only possible database
     availableDBs    : {},       // Available databases, filled by extensions. Key is databasename and value is reference to method to be called
+    events          : {},       // Stores the events to fire
     
     /**
@@ -167 +168 @@
      * @param element
      */
-    initAutocomplete: function(element) {
+    initAutocomplete: function( element, customEvents ) {
         var that = this
         var inputElement = $(element);
         var selected = false;
 
+        // Add spinner element
+        if( !baseUrl ) {
+            var baseUrl = '..';
+        }
+        var imgEl = document.createElement( 'img' );
+        imgEl.setAttribute( 'id', inputElement.attr( 'id' ) + '_spinner' );
+        imgEl.setAttribute( 'src', baseUrl + '/images/spinner.gif' );
+        imgEl.setAttribute( 'style', 'margin-left: 5px;');
+
+        // Add the element next to the input box
+        inputElement.after( imgEl );
+        $( imgEl ).hide();
+
         // determine what database to use
         var values = inputElement.attr('rel').split("-");
+
+        // Check which database the user wants
         if( values.length > 1 ) {
             // check for supported databases
             if( this.availableDBs[ values[ 1 ] ] ) {
                 this.database = values[1];
+                this.events = this.availableDBs[ this.database ];
             } else {
-                alert( 'Database ' + values[1] + ' not supported. Using default: ' + this.database );
+                this.database = values[1] + " (custom)";
+                this.events = {};
             }
+        } else {
+            this.database = "(custom)";
+            this.events = {};
+        }
+
+        // Add custom events to this object
+        if( customEvents ) {
+            $.each( customEvents, function( id, func ) {
+                that.events[ id ] = func;
+            })
+        }
+        
+        // If no 'source' function is defined, nothing can be searched for
+        if( !this.events[ 'source' ]) {
+            alert( 'Database ' + this.database + ' not supported. Using none.' );
         }
 
@@ -189 +222 @@
         inputElement.autocomplete({
             minLength: that.minLength,
-            delay: 400,
+            delay: 300,
 
             source: function(request, response) {
@@ -199 +232 @@
                     response(that.cache[ that.database ][ q ]);
                 } else {
-                    if( that.database != "" && that.availableDBs[ that.database ] && that.availableDBs[ that.database ][ 'source' ] ) {
-                        that.availableDBs[ that.database ][ 'source' ]( that, q, response );
+                    if( that.database != "" && that.events[ 'source' ] ) {
+                       that.events[ 'source' ]( that, q, response );
                     }
                 }
@@ -206 +239 @@
             search: function(event, ui ) {
                 that.selected = false;
+                $( '#' + inputElement.attr( 'id' ) + '_spinner' ).show();
+            },
+            open: function(event, ui ) {
+                $( '#' + inputElement.attr( 'id' ) + '_spinner' ).hide();
             },
             select: function(event, ui) {
@@ -211 +248 @@
                 that.selected = true;
 
-                if( that.database != "" && that.availableDBs[ that.database ] && that.availableDBs[ that.database ][ 'select' ] ) {
-                    that.availableDBs[ that.database ][ 'select' ]( that, inputElement, event, ui );
+                if( that.database != "" && that.events[ 'select' ] ) {
+                    that.events[ 'select' ]( that, inputElement, event, ui );
                 }
             },
             close: function(event, ui) {
                 if( !that.selected ) {
-                    if( that.database != "" && that.availableDBs[ that.database ] && that.availableDBs[ that.database ][ 'close' ] ) {
-                        that.availableDBs[ that.database ][ 'close' ]( that, inputElement, event, ui );
+                    if( that.database != "" && that.events[ 'close' ] ) {
+                        that.events[ 'close' ]( that, inputElement, event, ui );
+                    }
+
+                    if( inputElement.closePublication ) {
+                        inputElement.closePublication( that, event, ui );
                     }
                 }

trunk/web-app/js/publication-chooser.pubmed.js

@@ -4 +4 @@
     var terms = searchterm.split( " " );
     for( var i = 0; i < terms.length; i++ ) {
-        searchFor[ searchFor.length ] = "(" + terms[i].trim() + "[title]" + " OR " + terms[i].trim() + "[author]" + ")";
+        searchFor[ searchFor.length ] = "(" + $.trim( terms[i] ) + "[title]" + " OR " + $.trim( terms[i] ) + "[author]" + ")";
     }
 
@@ -38 +38 @@
 };
 
-selectPubMed = function( chooserObject, inputElement, event, ui ) {
+// Handler that handles the select of a publication
+selectPubMedAdd = function( chooserObject, inputElement, event, ui ) {
 
     // option selected, set hidden fields
@@ -52 +53 @@
     element.removeClass('error');
 };
-closePubMed  = function( chooserObject, inputElement, event, ui ) {
+
+// Handler that handles the closing of the autocomplete
+closePubMedAdd  = function( chooserObject, inputElement, event, ui ) {
     // no he didn't, clear the field(s)
     var element = inputElement;
@@ -116 +119 @@
 }
 
+// Only the source method should be used for all pubmed autocompletes
+// The select and close handlers that are defined here, should only be used
+// on the add publication page. They can be overridden in the initialization
+// of the publication chooser class
 PublicationChooser.prototype.availableDBs[ "pubmed" ] = { 
     'source': sourcePubMed,
-    'select': selectPubMed,
-    'close':  closePubMed
+    'select': selectPubMedAdd,
+    'close':  closePubMedAdd
 };
+

trunk/web-app/js/wizard.js

@@ -351 +351 @@
     return '<a target="_blank" href="' + baseUrl + '/file/get/' + filename + '">' + filename + '</a>';
 }
+
+function addPublication( element_id ) {
+  /* Find publication ID and add to form */
+  jQuery.ajax({
+    type:"GET",
+    url: baseUrl + "/publication/getID?" +  $("#" + element_id + "_form").serialize(),
+    success: function(data,textStatus){
+        var id = parseInt( data );
+
+        // Put the ID in the array, but only if it does not yet exist
+        var ids = getPublicationIds( element_id );
+
+        if( $.inArray(id, ids ) == -1 ) {
+            ids[ ids.length ] = id;
+            $( '#' + element_id + '_ids' ).val( ids.join( ',' ) );
+
+            // Show the title and a remove button
+            showPublication( element_id, id, $("#" + element_id + "_form").find( '[name=publication-title]' ).val(), $("#" + element_id + "_form").find( '[name=publication-authorsList]' ).val(), ids.length - 1 );
+
+            // Hide the 'none box'
+            $( '#' + element_id + '_none' ).css( 'display', 'none' );
+        }
+    },
+    error:function(XMLHttpRequest,textStatus,errorThrown){ alert( "Publication could not be added." ) }
+  }); return false;
+}
+
+function removePublication( element_id, id ) {
+    var ids = getPublicationIds( element_id );
+    if( $.inArray(id, ids ) != -1 ) {
+        // Remove the ID
+        ids.splice($.inArray(id, ids ), 1);
+        $( '#' + element_id + '_ids' ).val( ids.join( ',' ) );
+
+        // Remove the title from the list
+        var li = $( "#" + element_id + '_item_' + id );
+        if( li ) {
+            li.remove();
+        }
+
+        // Show the 'none box' if needed
+        if( ids.length == 0 ) {
+            $( '#' + element_id + '_none' ).css( 'display', 'inline' );
+        }
+
+    }
+}
+
+function getPublicationIds( element_id ) {
+    var ids = $( '#' + element_id + '_ids' ).val();
+    if( ids == "" ) {
+        return new Array();
+    } else {
+        ids_array = ids.split( ',' );
+        for( var i = 0; i < ids_array.length; i++ ) {
+            ids_array[ i ] = parseInt( ids_array[ i ] );
+        }
+
+        return ids_array;
+    }
+}
+
+function showPublication( element_id, id, title, authors, nr ) {
+    var deletebutton = document.createElement( 'img' );
+    deletebutton.setAttribute( 'class', 'famfamfam delete_button' );
+    deletebutton.setAttribute( 'alt', 'remove this publication' );
+    deletebutton.setAttribute( 'src', baseUrl + '/images/icons/famfamfam/delete.png' );
+    deletebutton.setAttribute( 'onClick', 'removePublication( "' + element_id + '", ' + id + ' ); return false;' );
+    deletebutton.setAttribute( 'style', 'cursor: pointer;' );
+
+    var titleDiv = document.createElement( 'div' );
+    titleDiv.setAttribute( 'class', 'title' );
+    titleDiv.appendChild( document.createTextNode( title ) );
+
+    var authorsDiv = document.createElement( 'div' );
+    authorsDiv.setAttribute( 'class', 'authors' );
+    authorsDiv.appendChild( document.createTextNode( authors ) );
+
+    var li = document.createElement( 'li' );
+    li.setAttribute( 'id', element_id + '_item_' + id );
+    li.setAttribute( 'class', nr % 2 == 0 ? 'even' : 'odd' );
+    li.appendChild( deletebutton );
+    li.appendChild( titleDiv );
+    li.appendChild( authorsDiv );
+
+    $( '#' + element_id + '_list' ).append( li );
+}