/*
*/
/*
*
*
*
*
* 10.04.08: added Reflect_nestedFrameURL( url ): reflect the urls sent by the
* content iframe
* 07.01.08: browser detection and appopriate page navigation added
* 06.01.08: added methods required for the main web page
* (content iframe creation and reseting implemented as generic
* iFrameHandling methods)
* 15.12.07: url encoding is required -> back in the code
* 14.12.07: not encoding the url to be send anymore - updating the iframe
* overlib + pop-up script injection in the head modularised
* 09.12.07: pointing to reflect.embl.de (public) posting only the proxy server
* (the proxy will communicate with the tagging server)
* 16.11.07: switched to synchronous xmlhttp request
* 09.11.07: main functionality retrieve a url via proxy and 'reflect' page
*
* 14.10.08: added a security check to prevent content leaking for certain journals
*
*/
//
//
//var Reflect_proxyURL = 'cgi-bin/reflectProxy.cgi'; // the servlet exists in the same server
var Reflect_proxyURL = 'REST/GetEntities'; // the servlet exists in the same server
var Reflect_debugging = false;
var Reflect_WorkInProgressPage = 'Reflection in progress' +
'' +
'' +
'
' +
' '+
'
';
var Reflect_content_iframe_name = 'reflect_content_iframe';
var Reflect_FirefoxDownloadPage = "FirefoxDownload.html";
var Reflect_IEDownloadPage = "IEDownload.html";
var Reflect_BookmarkletDownloadPage = "BookmarkletDownload.html";
var input_is_url = 1;
//
//
//var Reflect_pageDoc = this.document;
var Reflect_iFrame = parent.reflect_content_iframe;//Reflect_pageDoc.getElementById(Reflect_content_iframe_name);
var Reflect_iFrameDoc = Reflect_getIFrameDoc( Reflect_iFrame );
//
//
function Reflect_setDownloadPage(){
var link = Reflect_defineProperDownloadPage();
Reflect_iFrame.location = link;
}
function Reflect_reflectRequestedURL() {
var requestedURL = Reflect_getRequestedURL();
// if (Reflect_URLIsAllowed( requestedURL ))
// {
Reflect_reflectURL(requestedURL);
// }
// else
// {
// alert('The Reflect web page is not allowed to process \n full text articles from this journal. \n\n Please try using the Reflect browser plug-in instead.' );
// }
}
function Reflect_URLIsAllowed( url ){
var allowed = true;
//journal specific content leaking prevention rules
if ( /dev\.biologists\.org\/cgi\/content\/full/.test( url ) )
{
allowed = false;
}
else if ( /journals\.royalsociety\.org\/content/.test( url ) )
{
allowed = false;
}
return allowed;
}
function Reflect_processRequestedURL( url ){
input_is_url = 1;
if ( /\s/.test( url ) )
{ /* true if there is any white space in the provided url */
// url = "http://www.google.com/search?ie=UTF-8&oe=UTF-8&q=" + Reflect_encodeURL( url );
input_is_url = 0;
}
else if ( !(/\./.test(url)) )
{ /* there is not dot (and no white space) => single word, no IP */
// url = "http://www.google.com/search?ie=UTF-8&oe=UTF-8&q=" + url;
input_is_url = 0;
}
url = Reflect_appendHTTPProtocolIfMissing(url);
return url;
}
function Reflect_isOpera(){
if (navigator.userAgent.indexOf("Opera") != -1)
{
return true;
}
else
{
return false;
}
}
/* NXT: merge with Reflect_reflectRequestedURL */
function Reflect_reflectURL( url ) {
var requestedURL = url;
if (requestedURL == "") { return; }
/* /_reg_ex_/.test("target") returns true if the target string matches the regEx */
if ( /type\ or\ paste\ a\ URL/.test( requestedURL ) ){ return; }
requestedURL = Reflect_processRequestedURL( requestedURL );
// requestedURL = "http://reflect.cbs.dtu.dk/REST/GetPopup?name="+encodeURIComponent(requestedURL)+"&entity_types=9606%20-1";
if(input_is_url == 1){
Reflect_iFrame.location = "http://reflect.cbs.dtu.dk/REST/GetHTML?uri="+encodeURIComponent(requestedURL);
}else{
var runAsynchronously = true;
var reflectRequestData = "document="+requestedURL+"&format=tsv";
var reflectedPage = Reflect_retrieveTaggedPageContents_updateIFrame(
Reflect_proxyURL, reflectRequestData, runAsynchronously);
// requestedURL = "http://reflect.cbs.dtu.dk/REST/GetPopup?name="+encodeURIComponent(requestedURL);
// Reflect_iFrame.document.body.innerHTML = "";
// Reflect_iFrame.document.write("");
}
return;
//updates input field (displays the http if it were missing)
Reflect_pageDoc.getElementById('reflect_urlInputField').value = requestedURL;
/* before doing anything else, reset the reflect_content_iframe */
// if (Reflect_isOpera()){alert('opera 4a');}
Reflect_resetIFrame(Reflect_content_iframe_name);
// if (Reflect_isOpera()){alert('opera 4b');}
// if (Reflect_isOpera()){alert('opera 1');}
var org = document.getElementById("reflect_organism_selection").value;
var reflectRequestData = 'url='+ Reflect_encodeURL(requestedURL) + '&entity_types=' + org;
var runAsynchronously = true;
var reflectedPage = Reflect_retrieveTaggedPageContents_updateIFrame(
Reflect_proxyURL, reflectRequestData, runAsynchronously);
// if ( Reflect_isOpera() ){ alert('opera 3'); }
}
function Reflect_appendHTTPProtocolIfMissing( url ) {
var urlWithProtocol="";
var containsHTTPProtocol = false;
//RegEx \^http.?:\/\/.* matches either http://something or https://something
containsHTTPProtocol = /^http.?:\/\/.*/.test(url);
if (!containsHTTPProtocol)
{
// urlWithProtocol = "http://" + url;
urlWithProtocol = url;
return urlWithProtocol;
}
else
{
return url;
}
}
/* cross-browser retrieval of the iFrame document */
function Reflect_getIFrameDoc( iFrame ){
if (!iFrame) { return; }
var iFrameDoc = '';
if (iFrame.contentDocument) { //NS6, Safari, Opera
iFrameDoc = iFrame.contentDocument;
}
else if (iFrame.contentWindow) { //IE5.5 and IE6
iFrameDoc = iFrame.contentWindow.document;
}
else if (iFrame.document) { //IE5
iFrameDoc = iFrame.document;
}
return iFrameDoc;
}
function Reflect_removeIFrame ( iframe ) {
var parent = iframe.parentNode;
parent.removeChild(iframe);
}
function Reflect_getRequestedURL() {
var url = Reflect_trim(Reflect_extractURL());
if (url == "") { alert("You must enter a URL"); }
if (Reflect_debugging) {alert('requestedURL, not-encoded:' + url); }
return url;
}
function Reflect_updateIFrameURL( iFrameDoc, newURL ) {
iFrameDoc.location.href = newURL;
}
function Reflect_updateIFrameContents( iFrameDoc, newContents ) {
iFrameDoc.open();
try { iFrameDoc.write( newContents ); } catch (e){alert(e);}
iFrameDoc.close();
}
function Reflect_encodeURL( url ){
var encodedURL = encodeURIComponent(url);
if (Reflect_debugging) {alert('requestedURL, encoded:' + encodedURL); }
return encodedURL;
}
/*
* @param data "param=value" pairs
*
* update IFrame action takes place as a callback inside
* http_request.onreadystatechange (after the tagged text has been retrieved)
* (readyState == 4 && http_request.status == 200)
*
*/
function Reflect_retrieveTaggedPageContents_updateIFrame(middleware_url, data, runAsynchronously) {
var http_request = false;
if (window.XMLHttpRequest) { // Mozilla, Safari,...
http_request = new XMLHttpRequest();
if (http_request.overrideMimeType) { http_request.overrideMimeType('text/html'); }
}
else if (window.ActiveXObject) { // IE
try { http_request = new ActiveXObject("Msxml2.XMLHTTP"); }
catch (e) {
try { http_request = new ActiveXObject("Microsoft.XMLHTTP"); }
catch (e) {alert(e)}
}
}
if (!http_request) { alert('Cannot create XMLHTTP instance'); return false; }
http_request.onreadystatechange = function() {
if (http_request.readyState < 4) {
if (Reflect_debugging) { alert('1. http_request.readyState: ' + http_request.readyState); }
//Reflect_updateIFrameContents( Reflect_iFrameDoc, Reflect_WorkInProgressPage );
//Reflect_setContents (Reflect_content_iframe_name, Reflect_WorkInProgressPage );
}
else //if (http_request.readyState == 4)
{
if (http_request.status == 200) {
if (Reflect_debugging) { alert('2. http_request.status:' + http_request.status); }
result = http_request.responseText;
if (Reflect_debugging) {alert('retrieved ' + result); }
var array = result.split("\n");
var entities = new Array();
for (var i=0;i";
if(entities.length > 0){
Reflect_iFrame.document.location.href = "iframe.html?"+entities.join(";");
}else{
Reflect_iFrame.document.location.href = "noresult.html";
}
// Reflect_iFrame.document.body.innerHTML = "";
// Reflect_iFrame.document.write(""+iFrame+"");
// Reflect_setURL( Reflect_content_iframe_name, result);
}
else {
alert(http_request.status + ' error ' + http_request.statusText);
return;
}
}
}
if (Reflect_debugging) {alert('POSTing: ' + middleware_url + ' to retrieve ' + data + ' contents ' ); }
try
{
http_request.open("POST", middleware_url, runAsynchronously); //async (T/F)
}
catch (e)
{
//alert('Error: ' + e + ' middleware_url: ' + middleware_url + ' data: ' + data);
}
//http_request.setRequestHeader("User-agent", "Mozilla/4.0");
http_request.setRequestHeader("Content-type", "application/x-www-form-urlencoded");
http_request.setRequestHeader("Accept", "application/atom+xml,application/xml,text/xml");
http_request.setRequestHeader("Connection", "close");
http_request.send(data); //parameter-value pair
}
function Reflect_getIFrameDocumentHead() {
var head = Reflect_iFrameDoc.getElementsByTagName('head')[0];
if(!head) {
alert('html page without "head"');
return '';
}
return head;
}
function Reflect_extractURL() {
var url = document.getElementById("reflect_urlInputField").value;
return url;
}
// will trim all leading and trailing whitespace
// from the incoming string, and convert all runs of more than one whitespace
// character into a single space. The altered string gets returned.
function Reflect_trim(string) {
// If the incoming string is invalid, or nothing was passed in, return empty
if (!string)
return "";
string = string.replace(/^\s+/, ''); // Remove leading whitespace
string = string.replace(/\s+$/, ''); // Remove trailing whitespace
// Replace all whitespace runs with a single space
string = string.replace(/\s+/g, ' ');
return string; // Return the altered value
}
function Reflect_resetIFrame(iFrameName) {
var iFrame = Reflect_getIFrame (iFrameName);
var parentNode = iFrame.parentNode;
// if (Reflect_isOpera()){alert('opera 5a, iframe: ' + iFrame + " iFParent "+ parentNode );}
Reflect_removeIFrame(iFrame, parentNode);
// if (Reflect_isOpera()){alert('opera 5b');}
Reflect_createAndAdd(iFrameName, parentNode);
// if (Reflect_isOpera()){alert('opera 5c');}
}
function Reflect_getIFrame(iFrameName){
var iFrame = this.document.getElementById(iFrameName);
return iFrame;
}
function Reflect_removeIFrame(iFrame, parentNode){
// if (Reflect_isOpera()){alert('opera 5ai');}
parentNode.removeChild(iFrame);
// if (Reflect_isOpera()){alert('opera 5aii');}
}
/* creates the iframe with the "iFrameName" id and adds it to the "parentNode" */
function Reflect_createAndAdd(iFrameName, parentNode){
var iFrame = this.document.createElement('iframe'); /* Do not change */
iFrame.setAttribute('id', iFrameName);
iFrame.setAttribute('scrolling', 'auto');
iFrame.setAttribute('width', '100%');
iFrame.setAttribute('height', '1800');
iFrame.setAttribute('frameBorder', '0');
parentNode.appendChild(iFrame);
}
function Reflect_setURL( iFrameName, url){
var iFrameDoc = Reflect_getIFrameDoc( Reflect_getIFrame( iFrameName ) );
iFrameDoc.location.href = url;
}
function Reflect_setContents( iFrameName, newContents ) {
var iFrameDoc = Reflect_getIFrameDoc( Reflect_getIFrame( iFrameName ) );
iFrameDoc.open();
try { iFrameDoc.write( newContents ); } catch (e){alert(e);}
iFrameDoc.close();
}
/* reset the "iFrameName" iframe and sets its location to "url"*/
function Reflect_display(url, iFrameName){
Reflect_resetIFrame(iFrameName);
Reflect_setURL(iFrameName, url);
}
function Reflect_displayDownloadPage(){
var downloadPageName = Reflect_defineProperDownloadPage();
Reflect_display(downloadPageName, Reflect_content_iframe_name);
}
function Reflect_defineProperDownloadPage(){
var downloadPageName = "";
var browserName = Reflect_getBrowserName();
if (browserName == "firefox"){
downloadPageName = Reflect_FirefoxDownloadPage;
}
else if (browserName == "msie") {
downloadPageName = Reflect_IEDownloadPage;
}
else {
downloadPageName = Reflect_BookmarkletDownloadPage;
}
return downloadPageName;
}
/*
* source: http://quomon.com/question_How_Identify_browser_java_script_IE_Safari_Firefox_2311.aspx
* @returns A string which specifies which is the current
* browser in which we are running.
*
* Currently-supported browser detection and codes:
* * 'opera' -- Opera
* * 'msie' -- Internet Explorer
* * 'safari' -- Safari
* * 'firefox' -- FireFox
* * 'mozilla' -- Mozilla
*
* If we are unable to property identify the browser, we
* return an empty string.
*
* @type String
*/
function Reflect_getBrowserName() {
var browserName = "";
var ua = navigator.userAgent.toLowerCase();
if ( ua.indexOf( "opera" ) != -1 ) {
browserName = "opera";
}
else if ( ua.indexOf( "msie" ) != -1 ) {
browserName = "msie";
}
else if ( ua.indexOf( "safari" ) != -1 ) {
browserName = "safari";
}
else if ( ua.indexOf( "mozilla" ) != -1 ) {
if ( ua.indexOf( "firefox" ) != -1 ) {
browserName = "firefox";
}
else {
browserName = "mozilla";
}
}
return browserName;
};
'+
'