1. Cleanup of old files.

2. Fix for the NIHVIVO-2818 issue.
This commit is contained in:
tankchintan 2011-07-12 22:05:41 +00:00
parent 0959ead1cc
commit a83c1180f4
3 changed files with 1 additions and 756 deletions

View file

@ -1,276 +0,0 @@
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
function getWellFormedURLs(given_uri, type) {
// general best practice is to put javascript code inside document.ready
// but in this case when i do that the function does not get called
// properly.
// so removing it for now.
// $(document).ready(function() {
if (type == "coauthorship") {
var finalURL = $.ajax({
url: contextPath + "/visualization",
data: ({vis: "utilities", vis_mode: "COAUTHORSHIP_URL", uri: given_uri}),
dataType: "text",
async: false,
success:function(data){
// console.log("COA - " + data);
}
}).responseText;
return finalURL;
} else if (type == "profile") {
var finalURL = $.ajax({
url: contextPath + "/visualization",
data: ({vis: "utilities", vis_mode: "PROFILE_URL", uri: given_uri}),
dataType: "text",
async: false,
success:function(data){
}
}).responseText;
return finalURL;
} else if (type == "image") {
var finalURL = $.ajax({
url: contextPath + "/visualization",
data: ({vis: "utilities", vis_mode: "IMAGE_URL", uri: given_uri}),
dataType: "text",
async: false,
success:function(data){
}
}).responseText;
return finalURL;
} else if (type == "profile_info") {
var profileInfoJSON = $.ajax({
url: contextPath + "/visualization",
data: ({vis: "utilities", vis_mode: "PROFILE_INFO", uri: given_uri}),
dataType: "json",
async: false,
success:function(data){
}
}).responseText;
return profileInfoJSON;
}
// });
}
$.fn.image = function(src, successFunc, failureFunc){
return this.each(function(){
var profileImage = new Image();
profileImage.src = src;
profileImage.width = 150;
profileImage.onerror = failureFunc;
profileImage.onload = successFunc;
return profileImage;
});
}
function setProfileImage(imageContainerID, rawPath, contextPath) {
if (imageContainerID == "") {
return;
}
var imageLink = contextPath + rawPath;
var imageContainer = $("#" + imageContainerID);
imageContainer.image(imageLink,
function(){
imageContainer.empty().append(this);
},
function(){
//For performing any action on failure to
//find the image.
imageContainer.empty();
}
);
}
function setProfileMoniker(monikerContainerID, moniker) {
if (monikerContainerID == "") {
return;
}
$("#" + monikerContainerID).empty().text(moniker);
}
function setProfileName(nameContainerID, name) {
if (nameContainerID == "") {
return;
}
$("#" + nameContainerID).empty().text(name);
}
function processProfileInformation(nameContainerID,
monikerContainerID,
imageContainerID,
profileInfoJSON) {
var name, imageRawPath, imageContextPath, moniker;
$.each(profileInfoJSON, function(key, set){
if (key.search(/imageThumb/i) > -1) {
imageRawPath = set[0];
} else if (key.search(/imageContextPath/i) > -1) {
imageContextPath = set[0];
} else if (key.search(/moniker/i) > -1) {
moniker = set[0];
} else if (key.search(/label/i) > -1) {
name = set[0];
}
});
setProfileName(nameContainerID, name);
setProfileMoniker(monikerContainerID, moniker);
setProfileImage(imageContainerID, imageRawPath, imageContextPath);
}
function nodeClickedJS(json){
var obj = jQuery.parseJSON(json);
$("#newsLetter").attr("style","visibility:visible");
$("#authorName").empty().append(obj.name);
$("#works").empty().append(obj.number_of_authored_works);
/*
* Here obj.url points to the uri of that individual
*/
if(obj.url){
$("#profileUrl").attr("href", getWellFormedURLs(obj.url, "profile"));
$("#coAuthorshipVisUrl").attr("href", getWellFormedURLs(obj.url, "coauthorship"));
processProfileInformation("",
"profileMoniker",
"profileImage",
jQuery.parseJSON(getWellFormedURLs(obj.url, "profile_info")));
} else{
$("#profileUrl").attr("href","#");
$("#coAuthorshipVisUrl").attr("href","#");
}
$("#coAuthorName").empty().append(obj.name);
$("#coAuthors").empty().append(obj.num_coauthors);
$("#firstPublication").empty().append((obj.earliest_publication)?obj.earliest_publication+" First Publication":"");
$("#lastPublication").empty().append((obj.latest_publication)?obj.latest_publication+" Last Publication":"");
// obj.url:the url parameter for node
}
function renderSparklineVisualization(visualizationURL) {
$(document).ready(function() {
//$("#ego_sparkline").empty().html('<img src="${loadingImageLink}" />');
$.ajax({
url: visualizationURL,
dataType: "html",
success:function(data){
$("#ego_sparkline").html(data);
}
});
});
}
function renderCoAuthorshipVisualization() {
//Version check for the Flash Player that has the ability to start Player
//Product Install (6.0r65)
var hasProductInstall = DetectFlashVer(6, 0, 65);
//Version check based upon the values defined in globals
var hasRequestedVersion = DetectFlashVer(requiredMajorVersion, requiredMinorVersion, requiredRevision);
if ( hasProductInstall && !hasRequestedVersion ) {
// DO NOT MODIFY THE FOLLOWING FOUR LINES
// Location visited after installation is complete if installation is
// required
var MMPlayerType = (isIE == true) ? "ActiveX" : "PlugIn";
var MMredirectURL = window.location;
document.title = document.title.slice(0, 47) + " - Flash Player Installation";
var MMdoctitle = document.title;
AC_FL_RunContent(
"src", "playerProductInstall",
"FlashVars", "MMredirectURL="+MMredirectURL+'&MMplayerType='+MMPlayerType+'&MMdoctitle='+MMdoctitle+"",
"width", "600",
"height", "800",
"align", "middle",
"id", "CoAuthor",
"quality", "high",
"bgcolor", "#ffffff",
"name", "CoAuthor",
"allowScriptAccess","sameDomain",
"type", "application/x-shockwave-flash",
"pluginspage", "http://www.adobe.com/go/getflashplayer"
);
} else if (hasRequestedVersion) {
// if we've detected an acceptable version
// embed the Flash Content SWF when all tests are passed
AC_FL_RunContent(
"src", swfLink,
"flashVars", "graphmlUrl=" + egoCoAuthorshipDataURL,
"width", "600",
"height", "800",
"align", "middle",
"id", "CoAuthor",
"quality", "high",
"bgcolor", "#ffffff",
"name", "CoAuthor",
"allowScriptAccess","sameDomain",
"type", "application/x-shockwave-flash",
"pluginspage", "http://www.adobe.com/go/getflashplayer"
);
} else { // flash is too old or we can't detect the plugin
var alternateContent = 'Alternate HTML content should be placed here. '
+ 'This content requires the Adobe Flash Player. '
+ '<a href=http://www.adobe.com/go/getflash/>Get Flash</a>';
document.write(alternateContent); // insert non-flash content
}
}

View file

@ -1,479 +0,0 @@
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
function getWellFormedURLs(given_uri, type) {
if (!given_uri || given_uri == "") {
return;
}
// general best practice is to put javascript code inside document.ready
// but in this case when i do that the function does not get called
// properly.
// so removing it for now.
// $(document).ready(function() {
var finalURL;
if (type == "coauthorship") {
finalURL = $.ajax({
url: contextPath + "/visualization",
data: ({vis: "utilities", vis_mode: "PERSON_LEVEL_URL", uri: given_uri}),
dataType: "text",
async: false,
success:function(data){
}
}).responseText;
return finalURL;
} else if (type == "copi") {
finalURL = $.ajax({
url: contextPath + "/visualization",
data: ({vis: "utilities", vis_mode: "COPI_URL", uri: given_uri}),
dataType: "text",
async: false,
success:function(data){
}
}).responseText;
return finalURL;
}else if (type == "profile") {
finalURL = $.ajax({
url: contextPath + "/visualization",
data: ({vis: "utilities", vis_mode: "PROFILE_URL", uri: given_uri}),
dataType: "text",
async: false,
success:function(data){
}
}).responseText;
return finalURL;
} else if (type == "image") {
finalURL = $.ajax({
url: contextPath + "/visualization",
data: ({vis: "utilities", vis_mode: "IMAGE_URL", uri: given_uri}),
dataType: "text",
async: false,
success:function(data){
}
}).responseText;
return finalURL;
} else if (type == "profile_info") {
var profileInfoJSON = $.ajax({
url: contextPath + "/visualization",
data: ({vis: "utilities", vis_mode: "PROFILE_INFO", uri: given_uri}),
dataType: "json",
async: false,
success:function(data){
}
}).responseText;
return profileInfoJSON;
}
// });
}
$.fn.image = function(src, successFunc, failureFunc){
return this.each(function(){
var profileImage = new Image();
profileImage.onerror = failureFunc;
profileImage.onload = successFunc;
profileImage.src = src;
return profileImage;
});
};
function setProfileImage(imageContainerID, mainImageURL, contextPath) {
if (imageContainerID == "") {
return;
}
if (!mainImageURL || mainImageURL == "") {
$("#" + imageContainerID).empty();
return;
}
var rawPath = getWellFormedURLs(mainImageURL, "image");
var imageLink = contextPath + rawPath;
var imageContainer = $("#" + imageContainerID);
imageContainer.image(imageLink,
function(){
imageContainer.empty().append(this);
},
function(){
// For performing any action on failure to
// find the image.
imageContainer.empty();
}
);
}
function setProfileMoniker(monikerContainerID, moniker, doEllipsis) {
if (monikerContainerID == "") {
return;
}
if (!moniker) {
$("#" + monikerContainerID).empty();
return;
}
var finalDisplayMoniker;
if (moniker.length > 30 && doEllipsis) {
finalDisplayMoniker = moniker.substr(0,30) + "...";
} else {
finalDisplayMoniker = moniker;
}
$("#" + monikerContainerID).empty().text(finalDisplayMoniker);
$("#" + monikerContainerID).attr('title', moniker);
}
function setProfileName(nameContainerID, name, doNameEllipsis) {
if (nameContainerID == "") {
return;
}
if (!name) {
$("#" + nameContainerID).empty();
return;
}
var finalDisplayName;
if (name.length > 30 && doNameEllipsis) {
finalDisplayName = name.substr(0,30) + "...";
} else {
finalDisplayName = name;
}
$("#" + nameContainerID).empty().text(finalDisplayName);
$("#" + nameContainerID).attr('title', name);
}
function processProfileInformation(nameContainerID,
monikerContainerID,
imageContainerID,
profileInfoJSON,
doMonikerEllipsis,
doNameEllipsis) {
var name, mainImageURL, imageContextPath, moniker;
if (jQuery.isEmptyObject(profileInfoJSON)) {
return;
}
$.each(profileInfoJSON, function(key, set){
if (key.search(/mainImage/i) > -1) {
mainImageURL = set[0];
} else if (key.search(/imageContextPath/i) > -1) {
imageContextPath = set[0];
} else if (key.search(/moniker/i) > -1) {
moniker = set[0];
} else if (key.search(/label/i) > -1) {
name = set[0];
}
});
setProfileName(nameContainerID, name, doNameEllipsis);
setProfileMoniker(monikerContainerID, moniker, doMonikerEllipsis);
setProfileImage(imageContainerID, mainImageURL, imageContextPath);
}
function visLoaded(nodes){
var jsonedNodes = jQuery.parseJSON(nodes);
var tableID = "";
var tableContainer = "";
if(visMode == "coauthorship"){
tableID = "coauthorships_table";
tableContainer = "coauth_table_container";
} else{
tableID = "copis_table";
tableContainer = "copi_table_container";
}
$(document).ready(function() {
createTable("coauthorships_table" , "coauth_table_container" , jsonedNodes.slice(1));
});
}
function createTable(tableID, tableContainer, tableData) {
var number_of_works = "";
var tableCaption = "";
var tableColumnTitle1 = "";
var tableColumnTitle2 = "";
if(visMode == "coauthorship"){
tableCaption = "Co-authors ";
tableColumnTitle1 = "Author";
tableColumnTitle2 = "Publications with <br />";
}else{
tableCaption = "Co-pis ";
tableColumnTitle1 = "Principal Investigator";
tableColumnTitle2 = "Grants with <br />";
}
var table = $('<table>');
table.attr('id', tableID);
table.append($('<caption>').html(tableCaption + "<a href=\"" + egoCoAuthorsListDataFileURL + "\">(.CSV File)</a>"));
var header = $('<thead>');
var row = $('<tr>');
var authorTH = $('<th>');
authorTH.html(tableColumnTitle1);
row.append(authorTH);
row.append($('<th>').html(tableColumnTitle2 + "" + $('#ego_label').text()));
header.append(row);
table.append(header);
$.each(tableData, function(i, item){
if(visMode == "coauthorship"){
number_of_works = item.number_of_authored_works;
}else{
number_of_works = item.number_of_investigated_grants;
}
var row = $('<tr>');
row.append($('<td>').html(item.label));
row.append($('<td>').html(number_of_works));
table.append(row);
});
table.prependTo('#' + tableContainer);
$('#' + tableContainer + " #loadingData").remove();
}
//renderStatsOnNodeClicked, CoRelations, noOfCoRelations
//function nodeClickedJS(json){
function renderStatsOnNodeClicked(json){
//console.log(json);
var obj = jQuery.parseJSON(json);
var works = "";
var persons = "";
var relation = "";
var earliest_work = "";
var latest_work = "";
var number_of_works = "";
if(visMode == "coauthorship"){
works = "Publication(s)";
persons = "Co-author(s)";
relation = "coauthorship"
earliest_work = obj.earliest_publication;
latest_work = obj.latest_publication;
number_of_works = obj.number_of_authored_works;
}else{
works = "Grant(s)";
persons = "Co-PI(s)";
relation = "copi";
earliest_work = obj.earliest_grant;
latest_work = obj.latest_grant;
number_of_works = obj.number_of_investigated_grants;
}
$("#dataPanel").attr("style","visibility:visible");
$("#works").empty().append(number_of_works);
/*
* Here obj.url points to the uri of that individual
*/
if(obj.url){
if (obj.url == egoURI) {
$("#authorName").addClass('author_name').removeClass('neutral_author_name');
$('#num_works > .author_stats_text').text(works);
$('#num_authors > .author_stats_text').text(persons);
} else {
$("#authorName").addClass('neutral_author_name').removeClass('author_name');
$('#num_works > .author_stats_text').text('Joint ' + works);
$('#num_authors > .author_stats_text').text('Joint ' + persons);
}
$("#profileUrl").attr("href", getWellFormedURLs(obj.url, "profile"));
$("#coAuthorshipVisUrl").attr("href", getWellFormedURLs(obj.url, relation));
processProfileInformation("authorName",
"profileMoniker",
"profileImage",
jQuery.parseJSON(getWellFormedURLs(obj.url, "profile_info")),
true,
true);
} else{
$("#profileUrl").attr("href","#");
$("#coAuthorshipVisUrl").attr("href","#");
}
$("#coAuthors").empty().append(obj.noOfCorelations);
$("#firstPublication").empty().append(earliest_work);
(earliest_work)?$("#fPub").attr("style","visibility:visible"):$("#fPub").attr("style","visibility:hidden");
$("#lastPublication").empty().append(latest_work);
(latest_work)?$("#lPub").attr("style","visibility:visible"):$("#lPub").attr("style","visibility:hidden");
// obj.url:the url parameter for node
}
/*
* Inside both of these functions, '&' are replaced with '%26' because we are externally
* passing two parameters to the flash code using flashvars (see renderCoAuthorshipVisualization())
* and they are delimited using '&' too.
*/
function getEncodedCoAuthorURL(){
var queryString = "uri="+ egoURI + "&vis=coauthorship&render_mode=data";
// console.log('domainParam is '+ domainParam);
// console.log('CoAuthorURL is ' + domainParam + '?' + queryString.replace(/&/g, '%26'));
return domainParam + '?' + queryString.replace(/&/g, '%26');
}
function getEncodedCoPIURL(){
var queryString = "uri="+ egoURI+ "&vis=coprincipalinvestigator&render_mode=data";
// console.log('CoPIURL is ' + domainParam + '?' + queryString.replace(/&/g, '%26') );
return domainParam + '?' + queryString.replace(/&/g, '%26');
}
function renderCoAuthorshipVisualization() {
var visualization = "";
var encodedURL = "";
if(visMode == "coauthorship"){
visualization = "CoAuthor";
encodedURL = getEncodedCoAuthorURL();
} else {
visualization = "CoPI";
encodedURL = getEncodedCoPIURL();
}
// console.log('visualization is ' + visualization + ' and encodedURL is '+ encodedURL);
// Version check for the Flash Player that has the ability to start Player
// Product Install (6.0r65)
var hasProductInstall = DetectFlashVer(6, 0, 65);
// Version check based upon the values defined in globals
var hasRequestedVersion = DetectFlashVer(requiredMajorVersion, requiredMinorVersion, requiredRevision);
if ( hasProductInstall && !hasRequestedVersion ) {
// DO NOT MODIFY THE FOLLOWING FOUR LINES
// Location visited after installation is complete if installation is
// required
var MMPlayerType = (isIE == true) ? "ActiveX" : "PlugIn";
var MMredirectURL = window.location;
document.title = document.title.slice(0, 47) + " - Flash Player Installation";
var MMdoctitle = document.title;
AC_FL_RunContent(
"src", "playerProductInstall",
"FlashVars", "MMredirectURL="+MMredirectURL+'&MMplayerType='+MMPlayerType+'&MMdoctitle='+MMdoctitle+"",
"width", "800",
"height", "840",
"align", "middle",
"id", "EgoCentric",
"quality", "high",
"bgcolor", "#ffffff",
"name", "EgoCentric",
"allowScriptAccess","sameDomain",
"type", "application/x-shockwave-flash",
"pluginspage", "http://www.adobe.com/go/getflashplayer"
);
} else if (hasRequestedVersion) {
// if we've detected an acceptable version
// embed the Flash Content SWF when all tests are passed
//coAuthorUrl=/vivo1/visualization?vis=coauthorship%26render_mode=data%26uri=http%3A%2F%2Fvivo.iu.edu%2Findividual%2FBrnerKaty&labelField=label&coPIUrl=/vivo1/visualization?vis=coprincipalinvestigator%26render_mode=data%26uri=http%3A%2F%2Fvivo.iu.edu%2Findividual%2FBrnerKaty&labelField=label
AC_FL_RunContent(
"src", swfLink,
// "flashVars", 'coAuthorUrl='+ encodeURL(egoCoAuthorshipDataFeederURL) + '&coPIUrl=' + encodeURL(egoCoPIDataFeederURL) ,
// "flashVars", 'coAuthorUrl='+ getEncodedCoAuthorURL() + '&coPIUrl=' + getEncodedCoPIURL() ,
// "flashVars", 'graphmlUrl=' + getEncodedCoAuthorURL() + '&labelField=label&visType=CoAuthor',
"flashVars", 'graphmlUrl=' + encodedURL + '&labelField=label&visType='+visualization,
"width", "600",
"height", "850",
"align", "top",
"id", "EgoCentric",
"quality", "high",
"bgcolor", "#ffffff",
"name", "EgoCentric",
"allowScriptAccess","sameDomain",
"type", "application/x-shockwave-flash",
"pluginspage", "http://www.adobe.com/go/getflashplayer"
);
} else { // flash is too old or we can't detect the plugin
var alternateContent = '<br /><h3 style="color: red;">'
+ 'This content requires the Adobe Flash Player. '
+ '<a href=http://www.adobe.com/go/getflash/>Get Flash</a></h3>';
document.write(alternateContent); // insert non-flash content
}
}

View file

@ -66,7 +66,7 @@ public class UtilitiesRequestHandler implements VisualizationRequestHandler {
String filterRule = "?predicate = j.2:mainImage " String filterRule = "?predicate = j.2:mainImage "
+ "|| ?predicate = vitro:moniker " + "|| ?predicate = core:preferredTitle "
+ "|| ?predicate = rdfs:label"; + "|| ?predicate = rdfs:label";
QueryRunner<GenericQueryMap> profileQueryHandler = QueryRunner<GenericQueryMap> profileQueryHandler =