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Votre Nom authored and Votre Nom committed Jul 1, 2022
1 parent 85bf2e2 commit 3e78bf3
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2 changes: 1 addition & 1 deletion html/HTTP-NCBI/date-update.js
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var DateUpdate=' Sat, 02 Nov 2019 ';
var DateUpdate=' Thu, 23 Apr 2020 ';
44 changes: 22 additions & 22 deletions html/HTTP-NCBI/index.html
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Expand Up @@ -332,7 +332,7 @@
<p><i class='fa fa-file-text-o fa-fw fa-lg' style='color:grey;'></i>&nbsp;<u>Reference:</u> de Vienne DM (2016) Lifemap: Exploring the Entire Tree of Life. <i>PLOS Biology</i> <b>14</b>(12):e2001624. <a href="https://doi.org/10.1371/journal.pbio.2001624">https://doi.org/10.1371/journal.pbio.2001624"</a></p>
</div>
<p style="font-size: x-small; text-align: center;"><i>For any question, remark, suggestion, or bug report, please contact Damien de Vienne: [email protected]</i><br>
<a rel="license" href="http://creativecommons.org/licenses/by-nc/4.0/"><img alt="Creative Commons License" style="border-width:0" src="https://i.creativecommons.org/l/by-nc/4.0/80x15.png" /></a>&nbsp;<span xmlns:dct="http://purl.org/dc/terms/" property="dct:title">Lifemap</span> by <a xmlns:cc="http://creativecommons.org/ns#" href="https://lbbe.univ-lyon1.fr/-de-Vienne-Damien-.html" property="cc:attributionName" rel="cc:attributionURL">Damien de Vienne / CNRS</a> is licensed under a <a rel="license" href="http://creativecommons.org/licenses/by-nc/4.0/">Creative Commons Attribution-NonCommercial 4.0 International License</a>.<br></p>
<!--<a rel="license" href="http://creativecommons.org/licenses/by-nc/4.0/"><img alt="Creative Commons License" style="border-width:0" src="https://i.creativecommons.org/l/by-nc/4.0/80x15.png" /></a>&nbsp;<span xmlns:dct="http://purl.org/dc/terms/" property="dct:title">Lifemap</span> by <a xmlns:cc="http://creativecommons.org/ns#" href="https://lbbe.univ-lyon1.fr/-de-Vienne-Damien-.html" property="cc:attributionName" rel="cc:attributionURL">Damien de Vienne / CNRS</a> is licensed under a <a rel="license" href="http://creativecommons.org/licenses/by-nc/4.0/">Creative Commons Attribution-NonCommercial 4.0 International License</a>.<br></p>-->
<div class="modal-footer">
<div style="text-align:center;">
<img src="https://upload.wikimedia.org/wikipedia/en/thumb/2/2c/CNRS.svg/200px-CNRS.svg.png" height="40px">
Expand Down Expand Up @@ -445,11 +445,11 @@
<script src="server-address.js" type="text/javascript"></script>
<!--HERE IS WHAT CONCERNS THE MAP AND MAP FUNCTION (focus, etc...)-->
<!-- FOR TREE MANIPULATION -->
<script src="http://jnuno.com/tree-model-js/vendor/jnuno/TreeModel-min.js"></script>
<!--<script src="http://jnuno.com/tree-model-js/vendor/jnuno/TreeModel-min.js"></script>-->

<script>
var map = L.map('map', {zoomControl: false, attributionControl: false});
var tolUrl="http://"+ServerAddress+"/osm_tiles/{z}/{x}/{y}.png";
var tolUrl="https://"+ServerAddress+"/osm_tiles/{z}/{x}/{y}.png";
var tol = new L.TileLayer(tolUrl, {minZoom: 4, maxZoom: 42});
map.addLayer(tol);
map.setView([-5,0], 5);
Expand Down Expand Up @@ -644,7 +644,7 @@
}
}
//this lists all required taxid, each once only. From those we will get lat/lon coordinates
var URL_PREFIX_FINAL = "http://"+ServerAddress+"/solr/taxo/select?q=taxid:(";
var URL_PREFIX_FINAL = "https://"+ServerAddress+"/solr/taxo/select?q=taxid:(";
var URL_SUFFIX = ")&wt=json&rows=10000";
var URL = URL_PREFIX_FINAL + alreadymet.join(' ') + URL_SUFFIX;
$.ajax({
Expand Down Expand Up @@ -838,7 +838,7 @@

var zoomTo = function(taxid) {
// $("#route-details").hide();
var url = "http://"+ServerAddress+"/solr/taxo/select?q=taxid:"+taxid+"&wt=json&rows=1000";
var url = "https://"+ServerAddress+"/solr/taxo/select?q=taxid:"+taxid+"&wt=json&rows=1000";
if (taxid === 1) {
map.setView( L.latLng([-4.226497,0]),7);
}
Expand Down Expand Up @@ -895,7 +895,7 @@
}
getmultiRoute(RESUROUTES, action);
RESUFINAL = RESUFINAL.join(' ')
var URL_PREFIX_FINAL = "http://"+ServerAddress+"/solr/taxo/select?q=taxid:(";
var URL_PREFIX_FINAL = "https://"+ServerAddress+"/solr/taxo/select?q=taxid:(";
var URL_SUFFIX = ")&wt=json&rows=1000";
var URL = URL_PREFIX_FINAL + RESUFINAL + URL_SUFFIX;
console.log(URL)
Expand Down Expand Up @@ -951,7 +951,7 @@
var lon2 = bb._northEast.lng;
var lat1 = bb._southWest.lat;
var lat2 = bb._northEast.lat;
var URL2 = "http://"+ServerAddress+"/solr/taxo/select?q=*:*&fq=zoom:[0 TO " + z + "]&fq=lat:[" + lat1 + " TO " + lat2 + "]&fq=lon:[" + lon1 + " TO " + lon2 + "]&wt=json&rows=1000";
var URL2 = "https://"+ServerAddress+"/solr/taxo/select?q=*:*&fq=zoom:[0 TO " + z + "]&fq=lat:[" + lat1 + " TO " + lat2 + "]&fq=lon:[" + lon1 + " TO " + lon2 + "]&wt=json&rows=1000";
$.ajax({
url : URL2,
success : function(data) {
Expand Down Expand Up @@ -1028,8 +1028,8 @@
//SEARCH FUNCTIONS
$(function() {
var str;
var URL_PREFIX = "http://"+ServerAddress+"/solr/taxo/suggesthandler?suggest.q=";
var URL_PREFIX_FINAL = "http://"+ServerAddress+"/solr/taxo/select?q=taxid:";
var URL_PREFIX = "https://"+ServerAddress+"/solr/taxo/suggesthandler?suggest.q=";
var URL_PREFIX_FINAL = "https://"+ServerAddress+"/solr/taxo/select?q=taxid:";
var URL_SUFFIX = "&wt=json";
$("#searchinput").autocomplete({
source : function(request, response) {
Expand Down Expand Up @@ -1130,8 +1130,8 @@
});
$(function() {
var str;
var URL_PREFIX = "http://"+ServerAddress+"/solr/taxo/suggesthandler?suggest.q=";
var URL_PREFIX_FINAL = "http://"+ServerAddress+"/solr/taxo/select?q=taxid:";
var URL_PREFIX = "https://"+ServerAddress+"/solr/taxo/suggesthandler?suggest.q=";
var URL_PREFIX_FINAL = "https://"+ServerAddress+"/solr/taxo/select?q=taxid:";
var URL_SUFFIX = "&wt=json";
$("#searchinput2").autocomplete({
source : function(request, response) {
Expand Down Expand Up @@ -1204,8 +1204,8 @@
});
$(function() {
var str;
var URL_PREFIX = "http://"+ServerAddress+"/solr/taxo/suggesthandler?suggest.q=";
var URL_PREFIX_FINAL = "http://"+ServerAddress+"/solr/taxo/select?q=taxid:";
var URL_PREFIX = "https://"+ServerAddress+"/solr/taxo/suggesthandler?suggest.q=";
var URL_PREFIX_FINAL = "https://"+ServerAddress+"/solr/taxo/select?q=taxid:";
var URL_SUFFIX = "&wt=json";
$("#searchinput3").autocomplete({
source : function(request, response) {
Expand Down Expand Up @@ -1297,7 +1297,7 @@

function allRoutes(multiTaxid) {
return new Promise(function (resolve, reject) {
var url = "http://"+ServerAddress+"/solr/addi/select?q=*:*&fq=taxid:("+multiTaxid+")&wt=json&rows=1000";
var url = "https://"+ServerAddress+"/solr/addi/select?q=*:*&fq=taxid:("+multiTaxid+")&wt=json&rows=1000";
$.ajax({
url : url,
success : function(data) {
Expand All @@ -1315,7 +1315,7 @@
//get infos
taxidFrom = taxidFrom.replace(/\s+/g, '');
taxidTo = taxidTo.replace(/\s+/g, '');
var url = "http://"+ServerAddress+"/solr/addi/select?q=*:*&fq=taxid:("+taxidFrom+" "+taxidTo+")&wt=json&rows=1000";
var url = "https://"+ServerAddress+"/solr/addi/select?q=*:*&fq=taxid:("+taxidFrom+" "+taxidTo+")&wt=json&rows=1000";
$.ajax({
url : url,
success : function(data) {
Expand All @@ -1336,7 +1336,7 @@
}
var mrca = getMrca(asc1,asc2);
routeq = route.toString().replace(/,/g,' ');
url2 = "http://"+ServerAddress+"/solr/taxo/select?q=*:*&fq=taxid:(" + routeq + ")&wt=json&rows=10000";
url2 = "https://"+ServerAddress+"/solr/taxo/select?q=*:*&fq=taxid:(" + routeq + ")&wt=json&rows=10000";

$.ajax({
url : url2,
Expand Down Expand Up @@ -1468,10 +1468,10 @@
var getNbdesc = function(taxid) {
$("#NBDESC").empty();
if (taxid===1) {
var url = "http://"+ServerAddress+"/solr/taxo/select?q=taxid:(2 2157 2759)&wt=json";
var url = "https://"+ServerAddress+"/solr/taxo/select?q=taxid:(2 2157 2759)&wt=json";
}
else {
var url = "http://"+ServerAddress+"/solr/taxo/select?q=taxid:"+taxid+"&wt=json";
var url = "https://"+ServerAddress+"/solr/taxo/select?q=taxid:"+taxid+"&wt=json";
}
$.ajax({
url : url,
Expand All @@ -1498,7 +1498,7 @@
taxi = taxid;
spna = spname;
comna = comname;
var treeFileAddr = "http://"+ServerAddress+"/trees/" + taxid.replace(/\s+/g, '') + ".tre";
var treeFileAddr = "https://"+ServerAddress+"/trees/" + taxid.replace(/\s+/g, '') + ".tre";
$('#modaltitle').empty();
$('#modalbody-text').empty();
$('#modalbody-pict').empty();
Expand Down Expand Up @@ -1537,7 +1537,7 @@
text +="<li>Number of descendants: <b>"+nbdesc+"</b></li>";
}
text +="</ul><ul>"
text +='<li>Explore <b>' + spname + '</b> on <a href="http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=' + taxid.replace(/\s+/g, '') + '&mode=info" target="_blank">NCBI</a></li>';
text +='<li>Explore <b>' + spname + '</b> on <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=' + taxid.replace(/\s+/g, '') + '&mode=info" target="_blank">NCBI</a></li>';
//if (taxid!="1") {
// text += '<li><a href="' + treeFileAddr + '" download>Download</a> the complete NCBI subtree of <b>' + spname + '</b> in Newick Extended format (NHX) </li>';
//}
Expand Down Expand Up @@ -1578,7 +1578,7 @@
var lon2 = bb._northEast.lng;
var lat1 = bb._southWest.lat;
var lat2 = bb._northEast.lat;
var URL2 = "http://"+ServerAddress+"/solr/taxo/select?q=*:*&fq=zoom:[0 TO " + z + "]&fq=lat:[" + lat1 + " TO " + lat2 + "]&fq=lon:[" + lon1 + " TO " + lon2 + "]&wt=json&rows=1000";
var URL2 = "https://"+ServerAddress+"/solr/taxo/select?q=*:*&fq=zoom:[0 TO " + z + "]&fq=lat:[" + lat1 + " TO " + lat2 + "]&fq=lon:[" + lon1 + " TO " + lon2 + "]&wt=json&rows=1000";
$.ajax({
url : URL2,
success : function(data) {
Expand All @@ -1588,7 +1588,7 @@
$.each(ok, function( index, value ) {
var latlong = new L.LatLng(ok[index].lat[0], ok[index].lon[0]);
var taxid = String(ok[index].taxid[0]);
var URL3 = "http://"+ServerAddress+"/solr/addi/select?q=*:*&fq=taxid:"+taxid+"&wt=json";
var URL3 = "https://"+ServerAddress+"/solr/addi/select?q=*:*&fq=taxid:"+taxid+"&wt=json";
$.ajax({
url:URL3,
success : function(data2) {
Expand Down

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