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index.html
executable file
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index.html
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<!DOCTYPE html>
<html lang="en" dir="ltr">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
<meta http-equiv="X-UA-Compatible" content="IE=edge" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<script src="js/jquery-3.6.0.min.js" ></script>
<script src="js/bootstrap.min.js" ></script>
<link rel="stylesheet" href="css/bootstrap.min.css" type="text/css" />
<link rel="stylesheet" href="css/bootstrap-icons.css " type="text/css" />
<meta name="keywords" content="" />
<meta name="description" content="" />
<title>.:PlamInteract:. .:Waller Lab:.</title>
<style>
#input_area {position: absolute; right:0 ; bottom:0 ; z-index: 1}
#show_hide_button {position: absolute; right:0 ; bottom:0 ; z-index: 500}
.overflowed{height:100%;overflow-y:auto}
.full{height:100%}
.half{height:50%}
.third{height:33%}
</style>
</head>
<body onload="resize_divs()">
<div id="show_hide_button" class="btn btn-success bi bi-arrow-down-square-fill" type="button" data-bs-toggle="collapse" data-bs-target="#input_area" aria-expanded="false" aria-controls="input_area" onclick="toggle_up_down('down')"></div>
<div class="card col-5 collapse show" id="input_area">
<input type="hidden" name="protein_info_str" id="protein_info_str" value="" />
<div class="card card-header bg-primary text-white text-center font-weight-bold"><h3>Input area</h3></div>
<div class="card card-body">
<div class="row">
<div class="col-5">
<label class="control-label font-weight-bold" for="accession_number">Accession number
<span id="str_search_span" class="bi bi-search" onclick=""></span>
</label>
<input type="text" class="form-control" id="accession_number" name="accession_number" oninput="update_search_button()"/>
</div>
<div class="col-5">
<label class="control-label font-weight-bold" for="tsv_file">From file</label>
<input type="file" class="form-control-file" id="tsv_file" name="tsv_file" onchange="enable_upload_button(this.value);"/>
</div>
<div class="col-2">
<div class="btn btn-primary form-control bi bi-upload" id="upload_button" onclick="tsv2idlist()"></div>
</div>
</div>
</div>
</div>
<div class="row" id="container">
<div class="col-4 full">
<div class="card full">
<div class="card card-header bg-secondary text-white text-center font-weight-bold"><h3>Accession number list</h3></div>
<div class="card card-body overflowed">
<div class="accordion" id="accession_number_list"></div>
</div>
</div>
</div>
<div class="col-4 full">
<div class="card half">
<div class="card card-header bg-secondary text-white text-center font-weight-bold"><h3>Literature info</h3></div>
<div class="card card-body overflowed" id="literature">
<div class="accordion" id="literature_accordion"></div>
</div>
</div>
<div class="card half">
<div class="card card-header bg-secondary text-white text-center font-weight-bold"><h3>Protein info</h3></div>
<div class="card card-body overflowed" id="link_list"></div>
</div>
</div>
<div class="col-4 full" id="article_div"></div>
</div>
<div id="status_dialog" name="status_dialog" class="modal" aria-hidden="true">
<div class="modal-dialog">
<div class="modal-content">
<div class="modal-header bg-success text-white text-center font-weight-bold"><h4 class="modal-title">Status</h4></div>
<div class="modal-body" id="spinner_container"></div>
</div>
</div>
</div>
</body>
<script type="text/javascript">
function resize_divs(){
var body_height = $(window).height() ;
var body_width = $(window).width() ;
$("#container").css({"height":body_height,"width":body_width,"position":"fixed","top":0,"left":0});
}
function update_search_button(){
var accession_number = $("#accession_number").val()
$("#str_search_span").attr("onclick","clear_divs();get_uniprot_accession('"+accession_number+"');get_pubmed_list('"+accession_number+"');")
}
function toggle_up_down(direction){
if(direction == "up"){
$("#show_hide_button").attr("onclick","toggle_up_down('down')")
$("#show_hide_button").removeClass("bi-arrow-up-square-fill").addClass("bi-arrow-down-square-fill")
}
else{
$("#show_hide_button").attr("onclick","toggle_up_down('up')")
$("#show_hide_button").removeClass("bi-arrow-down-square-fill").addClass("bi-arrow-up-square-fill")
}
}
function get_uniprot_accession(accession_number){
clear_divs();
spinner_str = " <div id=\"pubmed_direct_status\" class=\"row\">\n"+
" <div class=\"col-6\">\n"+
" <div class=\"spinner-border text-primary\" id=\"pubmed_direct_spinner\"></div>\n"+
" </div>\n"+
" <div class=\"col-6\">PubMed Direct search</div>\n"+
" </div>\n"+
" <div id=\"pubmed_xt_status\" class=\"row\">\n"+
" <div class=\"col-6\">\n"+
" <div class=\"spinner-border text-info\" id=\"pubmed_xt_spinner\"></div>\n"+
" </div>\n"+
" <div class=\"col-6\">PubMed extended search</div>\n"+
" </div>\n"+
" <div id=\"gene2pubmed_status\" class=\"row\">\n"+
" <div class=\"col-6\">\n"+
" <div class=\"spinner-border text-success\" id=\"gene2pubmed_spinner\"></div>\n"+
" </div>\n"+
" <div class=\"col-6\">gene2pubmed search</div>\n"+
" </div>\n"+
" <div id=\"uniprot_status\" class=\"row\">\n"+
" <div class=\"col-6\">\n"+
" <div class=\"spinner-border text-danger\" id=\"uniprot_spinner\"></div>\n"+
" </div>\n"+
" <div class=\"col-6\">UniProt search</div>\n"+
" <div id=\"scidir_status\" class=\"row\">\n"+
" <div class=\"col-6\">\n"+
" <div class=\"spinner-border text-warning\" id=\"scidir_spinner\"></div>\n"+
" </div>\n"+
" <div class=\"col-6\">Sciencedirect search</div>\n"+
" </div>\n";
$("#spinner_container").html(spinner_str);
$("#status_dialog").modal('show');
get_pubmed_list(accession_number);
var form_data = new FormData() ;
var target_url = "get_uniprot_accession.php" ;
form_data.append("accession_number", accession_number) ;
$.ajax({
url: target_url,
dataType: 'script',
cache: false,
contentType: false,
processData: false,
data: form_data,
type: 'post',
complete: function (uniprot){
var uniprot_xml_data = uniprot.responseText ;
var xml_data = $.parseXML(uniprot_xml_data);
$xml_data = $(xml_data);
var query_str = $xml_data.find("query_str").text();
var accession_number = $xml_data.find("accession_number").text();
var gene_name = $xml_data.find("gene").children("name").text().split(".")[0];
if(query_str==0){
var uniprot_accession = $xml_data.find("entry").children("accession").text();
if (uniprot_accession != ""){
get_uniprot_description(uniprot_accession);
var protein_gene_id = $xml_data.find("entry").children('dbReference[type="GeneID"]').attr("id");
var protein_name = $xml_data.find("entry").children("protein").children("submittedName").children("fullName").text();
var organism_name = $xml_data.find("entry").children("organism").children("name").text();
var organism_tax_id = $xml_data.find("entry").children("organism").children('dbReference[type="NCBI Taxonomy"]').attr("id");
search_pubmed(organism_name,protein_name);
search_gene2pubmed(organism_tax_id,protein_gene_id);
search_elsevier(organism_name,protein_name);
check_progress();
}
else{
$("#link_list").html("");
$("#pubmed_direct_spinner").removeClass("spinner-border").addClass("bi").addClass("bi-triangle-fill")
$("#pubmed_xt_spinner").removeClass("spinner-border").addClass("bi").addClass("bi-triangle-fill")
$("#gene2pubmed_spinner").removeClass("spinner-border").addClass("bi").addClass("bi-triangle-fill")
$("#uniprot_spinner").removeClass("spinner-border").addClass("bi").addClass("bi-triangle-fill")
$("#scidir_spinner").removeClass("spinner-border").addClass("bi").addClass("bi-triangle-fill")
}
}
}
})
}
function get_uniprot_description(uniprot_accession){
var form_data = new FormData() ;
var target_url = "get_uniprot_description.php" ;
form_data.append("uniprot_accession", uniprot_accession) ;
$.ajax({
url: target_url,
dataType: 'script',
cache: false,
contentType: false,
processData: false,
data: form_data,
type: 'post',
complete: function (uniprot){
var uniprot_xml_data = uniprot.responseText ;
var xml_data = $.parseXML(uniprot_xml_data);
$xml_data = $(xml_data);
var query_str = $xml_data.find("query_str").text()
var accession_number = $xml_data.find("accession_number").text()
if(query_str==0){
var uniprot_accession = $xml_data.find("entry").children("accession").text();
var list_html_str = ""
var protein_name = $xml_data.find("entry").children("protein").children("submittedName").children("fullName").text()
list_html_str = "<div class=\"alert bg-danger text-white text-center font-weight-bold\"><h5>"+protein_name+"</h5></div>\n";
list_html_str += "<ul class=\"list-group\">\n";
list_html_str += "<li class=\"list-group-item list-group-item-success\">UniProt: <a href=\"https://www.uniprot.org/uniprot/"+uniprot_accession+"\" target=\"_blank\">"+uniprot_accession+"</a></li>\n";
$xml_data.find("entry").children("dbReference").each(function (){
var dbreference_type = $(this).attr("type");
var dbreference_id = $(this).attr("id");
var dest_url = "" ;
var reactome_path = "" ;
switch(dbreference_type){
case "EMBL" :
dest_url = "https://www.ebi.ac.uk/ena/browser/view"+dbreference_id ;
class_str="list-group-item-success" ;
list_html_str += "<li class=\"list-group-item "+class_str+"\">"+dbreference_type+": <a href=\""+dest_url+"\" target=\"_blank\">"+dbreference_id+"</a></li>\n";
break;
case "RefSeq" :
dest_url = "https://www.ncbi.nlm.nih.gov/protein/"+dbreference_id ;
class_str="list-group-item-primary" ;
list_html_str += "<li class=\"list-group-item "+class_str+"\">"+dbreference_type+": <a href=\""+dest_url+"\" target=\"_blank\">"+dbreference_id+"</a></li>\n";
break;
case "IntAct" :
dest_url = "https://www.ebi.ac.uk/intact/query/"+dbreference_id ;
class_str="list-group-item-warning" ;
list_html_str += "<li class=\"list-group-item "+class_str+"\">"+dbreference_type+": <a href=\""+dest_url+"\" target=\"_blank\">"+dbreference_id+"</a></li>\n";
break;
case "KEGG" :
dest_url = "https://www.genome.jp/entry/"+dbreference_id ;
class_str="list-group-item-secondnary" ;
list_html_str += "<li class=\"list-group-item "+class_str+"\">"+dbreference_type+": <a href=\""+dest_url+"\" target=\"_blank\">"+dbreference_id+"</a></li>\n";
break;
case "InterPro":
dest_url = "https://www.ebi.ac.uk/interpro/entry/InterPro/"+dbreference_id ;
class_str="list-group-item-danger" ;
list_html_str += "<li class=\"list-group-item "+class_str+"\">"+dbreference_type+": <a href=\""+dest_url+"\" target=\"_blank\">"+dbreference_id+"</a></li>\n";
break;
case "Reactome":
dest_url = "https://reactome.org/content/detail/"+dbreference_id ;
reactome_type = $(this).children("property").attr("type");
reactome_value = $(this).children("property").attr("value");
class_str="list-group-item-info";
list_html_str += "<li class=\"list-group-item "+class_str+"\">"+dbreference_type+": <a href=\""+dest_url+"\" target=\"_blank\">"+dbreference_id+"</a></li>\n";
break;
}
});
$("#link_list").html(list_html_str);
$("#uniprot_status").remove()
}
else{
$("#link_list").html("");
$("#uniprot_spinner").removeClass("spinner-border").addClass("bi").addClass("bi-triangle-fill")
}
}
})
}
function get_pubmed_list(accession_number){
var form_data = new FormData() ;
var target_url = "get_pubmed_list.php" ;
form_data.append("accession_number", accession_number) ;
$.ajax({
url: target_url,
dataType: 'script',
cache: false,
contentType: false,
processData: false,
data: form_data,
type: 'post',
complete: function (eSearchResult){
var eSearchResult_xml_data = eSearchResult.responseText ;
var xml_data = $.parseXML(eSearchResult_xml_data);
$xml_data = $(xml_data);
var query_str = $xml_data.find("query_str").text();
var accession_number = $xml_data.find("accession_number").text();
var html_str = "";
if(query_str==0){
var num_hits = $xml_data.children("eSearchResult").children("Count").text();
html_str = "<div class=\"accordion-item\">\n"+
" <div class=\"list-group-item list-group-item-primary\""+
" data-bs-toggle=\"collapse\""+
" data-bs-target=\"#pubmed_direct_list\""+
" aria-expanded=\"true\""+
" aria-controls=\"pubmed_direct_list\" >PubMed direct hits"+
" <span class=\"badge rounded-pill bg-secondary\">"+num_hits+"</span>\n"+
" </div>\n";
if (num_hits>=1){
html_str += " <div id=\"pubmed_direct_list\" class=\"accordion-collapse collapse\" data-bs-parent=\"#literature_accordion\">\n"+
" <ul class=\"list-group\">\n";
$xml_data.find("IdList").children("Id").each(function (){
html_str += " <li class=\"list-group-item\">"+
" <a href=\"https://pubmed.ncbi.nlm.nih.gov/"+$(this).text()+"\" "+
" target=\"_blank\">"+$(this).text()+"</a>\n"+
" <span class=\"bi bi-search\" onclick=\"get_pubmed_info("+$(this).text()+")\" ></span>\n"+
" </li>\n";
});
html_str += " </ul>\n"+
" </div>\n"+
"</div>\n";
}
else{
html_str += "</div>\n";
}
$("#pubmed_direct_status").remove();
}
else{
$("#pubmed_direct_spinner").removeClass("spinner-border").addClass("bi").addClass("bi-triangle-fill")
html_str = "<div class=\"accordion-item\">\n"+
" <div class=\"list-group-item list-group-item-secondary\""+
" data-bs-toggle=\"collapse\""+
" data-bs-target=\"#pubmed_direct_list\""+
" aria-expanded=\"true\""+
" aria-controls=\"pubmed_direct_list\" >PubMed direct hits"+
" <span class=\"badge rounded-pill bg-danger\">0</span>\n"+
" </div>\n"+
"</div>\n";
}
$("#literature_accordion").append(html_str);
}
})
}
function search_pubmed(organism_name,protein_name){
var form_data = new FormData() ;
var target_url = "search_pubmed.php" ;
form_data.append("organism_name", organism_name) ;
form_data.append("protein_name", protein_name) ;
$.ajax({
url: target_url,
dataType: 'script',
cache: false,
contentType: false,
processData: false,
data: form_data,
type: 'post',
complete: function (eSearchResult){
var eSearchResult_xml_data = eSearchResult.responseText ;
var xml_data = $.parseXML(eSearchResult_xml_data);
$xml_data = $(xml_data);
var query_str = $xml_data.find("query_str").text();
var html_str = "";
if(query_str==0){
var num_hits = $xml_data.children("eSearchResult").children("Count").text();
html_str = "<div class=\"accordion-item\">\n"+
" <div class=\"list-group-item list-group-item-info\""+
" data-bs-toggle=\"collapse\""+
" data-bs-target=\"#pubmed_xt_list\""+
" aria-expanded=\"true\""+
" aria-controls=\"pubmed_xt_list\" >PubMed extended hits"+
" <span class=\"badge rounded-pill bg-secondary\">"+num_hits+"</span>\n"+
" </div>\n";
if (num_hits>=1){
html_str += " <div id=\"pubmed_xt_list\" class=\"accordion-collapse collapse\" data-bs-parent=\"#literature_accordion\">\n"+
" <ul class=\"list-group\">\n";
$xml_data.find("IdList").children("Id").each(function (){
html_str += " <li class=\"list-group-item\">"+
" <a href=\"https://pubmed.ncbi.nlm.nih.gov/"+$(this).text()+"\" "+
" target=\"_blank\">"+$(this).text()+"</a>\n"+
" <span class=\"bi bi-search\" onclick=\"get_pubmed_info("+$(this).text()+")\" ></span>\n"+
" </li>\n";
});
html_str += " </ul>\n"+
" </div>\n"+
"</div>\n";
}
else{
html_str += "</div>\n";
}
$("#pubmed_xt_status").remove()
}
else{
$("#pubmed_xt_spinner").removeClass("spinner-border").addClass("bi").addClass("bi-triangle-fill")
html_str = "<div class=\"accordion-item\">\n"+
" <div class=\"list-group-item list-group-item-secondary\""+
" data-bs-toggle=\"collapse\""+
" data-bs-target=\"#pubmed_xt_list\""+
" aria-expanded=\"true\""+
" aria-controls=\"pubmed_xt_list\" >PubMed extended hits"+
" <span class=\"badge rounded-pill bg-danger\">0</span>\n"+
" </div>\n"+
"</div>\n";
}
$("#literature_accordion").append(html_str);
}
})
}
function search_gene2pubmed(organism_tax_id,protein_gene_id){
var form_data = new FormData() ;
var target_url = "search_gene2pubmed.php" ;
form_data.append("protein_gene_id", protein_gene_id);
form_data.append("organism_tax_id", organism_tax_id);
$.ajax({
url: target_url,
dataType: 'script',
cache: false,
contentType: false,
processData: false,
data: form_data,
type: 'post',
complete: function (gene2pubmed){
var gene2pubmed_xml_data = gene2pubmed.responseText ;
var xml_data = $.parseXML(gene2pubmed_xml_data);
$xml_data = $(xml_data);
var query_str = $xml_data.find("query_str").text();
var html_str = "";
var pmid = "";
var link = "";
if(query_str==0){
var num_direct_hits = $xml_data.find("num_direct_hits").text()
var num_xt_hits = $xml_data.find("num_xt_hits").text()
html_str = "<div class=\"accordion-item\">\n"+
" <div class=\"list-group-item list-group-item-success\""+
" data-bs-toggle=\"collapse\""+
" data-bs-target=\"#gene2pubmed_direct_list\""+
" aria-expanded=\"true\""+
" aria-controls=\"gene2pubmed_direct_list\" >gene2pubmed direct hits"+
" <span class=\"badge rounded-pill bg-secondary\">"+num_direct_hits+"</span>\n"+
" </div>\n";
if (num_direct_hits>=1){
html_str += " <div id=\"gene2pubmed_direct_list\" class=\"accordion-collapse collapse\" data-bs-parent=\"#literature_accordion\">\n"+
" <ul class=\"list-group\">\n";
$xml_data.find("direct_hits").children("entry").each(function (){
html_str += " <li class=\"list-group-item\">"+
" <a href=\"https://pubmed.ncbi.nlm.nih.gov/"+$(this).text()+"\" "+
" target=\"_blank\">"+$(this).text()+"</a>\n"+
" <span class=\"bi bi-search\" onclick=\"get_pubmed_info("+$(this).text()+")\" ></span>\n"+
" </li>\n";
});
html_str += " </ul>\n"+
" </div>\n"+
"</div>\n";
}
else{
html_str += "</div>\n";
}
html_str += "<div class=\"accordion-item\">\n"+
" <div class=\"list-group-item list-group-item-warning\""+
" data-bs-toggle=\"collapse\""+
" data-bs-target=\"#gene2pubmed_xt_list\""+
" aria-expanded=\"true\""+
" aria-controls=\"gene2pubmed_xt_list\" >gene2pubmed extended hits"+
" <span class=\"badge rounded-pill bg-secondary\">"+num_xt_hits+"</span>\n"+
" </div>\n";
if (num_xt_hits>=1){
html_str += " <div id=\"gene2pubmed_xt_list\" class=\"accordion-collapse collapse\" data-bs-parent=\"#literature_accordion\">\n"+
" <ul class=\"list-group\">\n";
$xml_data.find("xt_hits").children("entry").each(function (){
html_str += " <li class=\"list-group-item\">"+
" <a href=\"https://pubmed.ncbi.nlm.nih.gov/"+$(this).text()+"\" "+
" target=\"_blank\">"+$(this).text()+"</a>\n"+
" <span class=\"bi bi-search\" onclick=\"get_pubmed_info("+$(this).text()+")\" ></span>\n"+
" </li>\n";
});
html_str += " </ul>\n"+
" </div>\n"+
"</div>\n";
}
else{
html_str += "</div>\n";
}
$("#gene2pubmed_status").remove()
}
else{
$("#pubmed_direct_spinner").removeClass("spinner-border").addClass("bi").addClass("bi-triangle-fill")
html_str = "<div class=\"accordion-item\">\n"+
" <div class=\"list-group-item list-group-item-secondary\""+
" data-bs-toggle=\"collapse\""+
" data-bs-target=\"#gene2pubmed_direct_list\""+
" aria-expanded=\"true\""+
" aria-controls=\"gene2pubmed_direct_list\" >gene2pubmed direct hits"+
" <span class=\"badge rounded-pill bg-danger\">0</span>\n"+
" </div>\n"+
"</div>\n"+
"<div class=\"accordion-item\">\n"+
" <div class=\"list-group-item list-group-item-secondary\""+
" data-bs-toggle=\"collapse\""+
" data-bs-target=\"#gene2pubmed_xt_list\""+
" aria-expanded=\"true\""+
" aria-controls=\"gene2pubmed_xt_list\" >gene2pubmed extended hits"+
" <span class=\"badge rounded-pill bg-danger\">0</span>\n"+
" </div>\n"+
"</div>\n";
}
$("#literature_accordion").append(html_str);
}
})
}
function search_elsevier(organism_name,protein_name){
var form_data = new FormData() ;
var target_url = "search_elsevier.php" ;
form_data.append("organism_name", organism_name) ;
form_data.append("protein_name", protein_name) ;
$.ajax({
url: target_url,
dataType: 'script',
cache: false,
contentType: false,
processData: false,
data: form_data,
type: 'post',
complete: function (elsevier_results){
var elsevier_xml_data = elsevier_results.responseText ;
var xml_data = $.parseXML(elsevier_xml_data);
$xml_data = $(xml_data);
var query_str = $xml_data.find("query_str").text();
var html_str = "";
var pii = "";
var link = "";
if(query_str==0){
var num_hits = $xml_data.find("count").text();
html_str = "<div class=\"accordion-item\">\n"+
" <div class=\"list-group-item list-group-item-info\""+
" data-bs-toggle=\"collapse\""+
" data-bs-target=\"#scidir_list\""+
" aria-expanded=\"true\""+
" aria-controls=\"scidir_list\" >Sciencedirect hits"+
" <span class=\"badge rounded-pill bg-secondary\">"+num_hits+"</span>\n"+
" </div>\n";
if (num_hits>=1){
html_str += " <div id=\"scidir_list\" class=\"accordion-collapse collapse\" data-bs-parent=\"#literature_accordion\">\n"+
" <ul class=\"list-group\">\n";
$xml_data.find("entry").each(function (){
pii = $(this).find("pii").text();
link = $(this).find("link").text();
html_str += " <li class=\"list-group-item\">\n"+
" <a href=\""+link+"\" target=\"_blank\">"+pii+"</a>"+
" <span class=\"bi bi-search\" onclick=\"get_scidir_info('"+pii+"')\" ></span>\n"+
" </li>\n";
});
html_str += " </ul>\n"+
" </div>\n"+
"</div>\n";
}
else{
html_str += "</div>\n";
}
$("#scidir_status").remove()
}
else{
$("#scidir_spinner").removeClass("spinner-border").addClass("bi").addClass("bi-triangle-fill")
html_str = "<div class=\"accordion-item\">\n"+
" <div class=\"list-group-item list-group-item-secondary\""+
" data-bs-toggle=\"collapse\""+
" data-bs-target=\"#scidir_list\""+
" aria-expanded=\"true\""+
" aria-controls=\"scidir_list\" >Sciencedirect hits"+
" <span class=\"badge rounded-pill bg-danger\">0</span>\n"+
" </div>\n"+
"</div>\n";
}
$("#literature_accordion").append(html_str);
}
})
}
function get_pubmed_info(pubmed_id){
var form_data = new FormData() ;
var target_url = "get_pubmed_info.php" ;
form_data.append("pubmed_id", pubmed_id) ;
$.ajax({
url: target_url,
dataType: 'script',
cache: false,
contentType: false,
processData: false,
data: form_data,
type: 'post',
complete: function (PubmedArticleSet){
var PubmedArticleSet_xml_data = PubmedArticleSet.responseText ;
var xml_data = $.parseXML(PubmedArticleSet_xml_data);
$xml_data = $(xml_data);
var query_str = $xml_data.find("query_str").text();
var accession_number = $xml_data.find("accession_number").text();
var html_str = "";
if(query_str==0){
var title_str = $xml_data.find("PubmedArticle").find("Article").find("ArticleTitle").text();
var abstract_str = $xml_data.find("PubmedArticle").find("Article").find("Abstract").find("AbstractText").text();
var author_str = ""
var auth_lastname = ""
var auth_firstname = ""
$xml_data.find("PubmedArticle").find("Article").find("AuthorList").find("Author").each(function(){
auth_lastname = $(this).find("LastName").text()
auth_firstname = $(this).find("ForeName").text()
author_str += auth_lastname+" "+auth_firstname+", "
});
var html_str = "<div class=\"card full\" >\n"+
" <div class=\"card-header bg-primary text-white text-center font-weight-bold\"><h3>"+title_str+"</h3></div>\n"+
" <div style=\"height:80%\" class=\"card-body text-justify overflowed\"><h4>"+abstract_str+"</h4></div>\n"+
" <div style=\"height:20%\" class=\"card-footer bg-light overflowed\"><h5>"+author_str+"</h5></div>\n"+
"</div>\n";
}
$("#article_div").html(html_str)
}
})
}
function get_scidir_info(pii){
var form_data = new FormData() ;
var target_url = "get_scidir_info.php" ;
form_data.append("pii", pii) ;
$.ajax({
url: target_url,
dataType: 'script',
cache: false,
contentType: false,
processData: false,
data: form_data,
type: 'post',
complete: function (sciencedirect_info){
var scidir_xml_data = sciencedirect_info.responseText ;
var xml_data = $.parseXML(scidir_xml_data);
$xml_data = $(xml_data);
var query_str = $xml_data.find("query_str").text();
var html_str = "";
if(query_str==0){
var title_str = $xml_data.find("title").text();
var abstract_str = $xml_data.find("abstract").text();
var author_str = ""
$xml_data.find("author").each(function(){
author_str += $(this).text()+" | "
});
author_str.replace(/ | $/, '')
var html_str = "<div class=\"card full\" >\n"+
" <div class=\"card-header bg-primary text-white text-center font-weight-bold\"><h3>"+title_str+"</h3></div>\n"+
" <div style=\"height:80%\" class=\"card-body text-justify overflowed\"><h4>"+abstract_str+"</h4></div>\n"+
" <div style=\"height:20%\" class=\"card-footer bg-light overflowed\"><h5>"+author_str+"</h5></div>\n"+
"</div>\n";
}
$("#article_div").html(html_str)
}
})
}
function enable_upload_button(value){
(value=="")? $("#upload_button").attr("disabled",true).attr("enabled",false): $("#upload_button").attr("disabled",false).attr("enabled",true) ;
}
function tsv2idlist() {
var form_data = new FormData();
var tsv_file = $("#tsv_file").prop("files")[0];
form_data.append("tsv_file",tsv_file);
$.ajax({
url: "tsv2idlist.php",
dataType: 'json',
cache: false,
contentType: false,
processData: false,
data: form_data,
type: 'post',
complete: function (tsv2idlist){
var tsv2idlist_xml_data = tsv2idlist.responseText ;
var xml_data = $.parseXML(tsv2idlist_xml_data);
$xml_data = $(xml_data);
var query_str = $xml_data.find("query_str").text();
var entry_name = ""
var accession = ""
var group_id = ""
var group_count = ""
if (query_str==0){
html_str = "";
var counter = parseInt(0);
$xml_data.find("entry").each(function(){
counter++;
group_id = "group_"+counter;
entry_name=$(this).find("name").text()
group_count = $(this).find("accession").length;
html_str += "<div class=\"accordion-item\">\n"+
" <div class=\"list-group-item list-group-item-warning\""+
" data-bs-toggle=\"collapse\""+
" data-bs-target=\"#"+group_id+"\""+
" aria-expanded=\"true\""+
" aria-controls=\""+group_id+"\" >"+entry_name+
" <span class=\"badge rounded-pill bg-secondary\">"+group_count+"</span>\n"+
" </div>\n";
if(group_count>0){
html_str += " <div id=\""+group_id+"\" class=\"accordion-collapse collapse\" data-bs-parent=\"#accession_number_list\">\n"+
" <ul class=\"list-group\">\n";
$(this).find("accession").each(function(){
accession = $(this).text()
html_str += " <li class=\"list-group-item font-weight-bold\">"+accession+" <span class=\"bi bi-search\" onclick=\"get_uniprot_accession('"+accession+"')\"></span></li>\n"
});
html_str += " </ul>\n"+
" </div>\n"+
"</div>\n";
}
});
$("#accession_number_list").html(html_str)
}
}
})
}
function clear_divs(){
$("#link_list").html("");
$("#literature_accordion").html("");
$("#article_div").html("");
}
function check_progress(){
var pubmed_direct_status = $("#pubmed_direct_status").length;
var pubmed_xt_status = $("#pubmed_xt_status").length;
var gene2pubmed_status = $("#gene2pubmed_status").length;
var uniprot_status = $("#uniprot_status").length;
var scidir_status = $("#scidir_status").length;
if(pubmed_direct_status == 0 && pubmed_xt_status == 0 && gene2pubmed_status == 0 && uniprot_status == 0 && scidir_status == 0){
$("#status_dialog").modal("hide");
}
else{
setTimeout(function(){check_progress();},500);
}
}
</script>
</html>