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freetext_search.html
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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1">
<meta name="description" content="">
<meta name="author" content="">
<title>Text Mining Assertions Search</title>
<link href="https://cdn.jsdelivr.net/npm/[email protected]/dist/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-F3w7mX95PdgyTmZZMECAngseQB83DfGTowi0iMjiWaeVhAn4FJkqJByhZMI3AhiU" crossorigin="anonymous">
<script src="https://cdn.jsdelivr.net/npm/[email protected]/dist/js/bootstrap.bundle.min.js" integrity="sha384-/bQdsTh/da6pkI1MST/rWKFNjaCP5gBSY4sEBT38Q/9RBh9AH40zEOg7Hlq2THRZ" crossorigin="anonymous"></script>
<link href = "https://code.jquery.com/ui/1.10.4/themes/ui-lightness/jquery-ui.css" rel = "stylesheet">
<script src="https://code.jquery.com/jquery-3.6.0.min.js" integrity="sha256-/xUj+3OJU5yExlq6GSYGSHk7tPXikynS7ogEvDej/m4=" crossorigin="anonymous"></script>
<script src = "https://code.jquery.com/ui/1.10.4/jquery-ui.js"></script>
<link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/[email protected]/font/bootstrap-icons.css">
</head>
<body>
<main role="main" class="container-fluid">
<div class="col-lg-12 card">
<form class="card-body">
<!-- <div class="row"><input id="query" class="form-control" type="text" placeholder="query" aria-label="Query display field" disabled readonly></div> -->
<div class="row">
<div class="col-md-2 col-sm-12">
<label for="subjectSelect" class="form-label">Subject</label>
<input id="subjectSelect" class="form-control" type="text" list="subject-options">
<datalist id="subject-options"></datalist>
</div>
<div class="col-md-5 col-sm-12">
<label for="predicateSelect" class="form-label">Predicate</label>
<select id="predicateSelect" class="form-select" aria-label="Default select example">
<option selected>Any</option>
{% for pre in predicates %}
<option value="{{ pre }}">{{ pre }}</option>
{% endfor %}
</select>
</div>
<div class="col-md-2 col-sm-12">
<label for="objectSelect" class="form-label">Object</label>
<input id="objectSelect" class="form-control" type="text" list="object-options">
<datalist id="object-options"></datalist>
</div>
<div class="col-md-2 position-relative">
<button class="btn btn-primary position-absolute bottom-0" type="button" id="executeQueryButton">Execute Query</button>
</div>
</div>
</form>
</div>
<div class="col-lg-12 card" id="queryResultsCard">
<div class="card-body">
<h5 class="card-title" id="queryDescription">This is the plaintext of the query described above.</h5>
<h6 class="card-subtitle mb-2 text-muted" id="queryResultsCount">The number of results for the query.</h6>
<div class="form-inline">
<label for="pmidFilter" class="form-label">PMID filter:</label>
<input id="pmidFilter" type="text" placeholder="PMID:12345678">
<button class="btn btn-primary btn-sm" id="applyFilterButton">Filter</button>
<button class="btn btn-secondary btn-sm" id="clearFilterButton">Clear Filter</button>
</div>
<!--
<div class="btn-group" role="group" aria-label="Toggle display results page size">
<input type="radio" class="btn-check" name="btnradio" id="display10RadioButton" autocomplete="off" checked>
<label class="btn btn-outline-primary" for="display10RadioButton">10</label>
<input type="radio" class="btn-check" name="btnradio" id="display25RadioButton" autocomplete="off">
<label class="btn btn-outline-primary" for="display25RadioButton">25</label>
<input type="radio" class="btn-check" name="btnradio" id="display50RadioButton" autocomplete="off">
<label class="btn btn-outline-primary" for="display50RadioButton">50</label>
<input type="radio" class="btn-check" name="btnradio" id="displayAllRadioButton" autocomplete="off">
<label class="btn btn-outline-primary" for="displayAllRadioButton">All</label>
</div>
-->
<ul class="list-group" id="resultsListGroup"></ul>
<nav aria-label="Results navigation" class="invisible">
<ul class="pagination justify-content-center" id="results-pagination-list">
</ul>
</nav>
</div>
</div>
</main>
<script type="text/javascript">
$(function() {
let pageSize = 25;
var curPage = 0;
var isFiltered = false;
var searchResults = [];
var resultsView = []
var subject_curies = [], object_curies = [];
function insertStringAt(originalString, stringToAdd, index) {
return originalString.slice(0, index) + stringToAdd + originalString.slice(index);
}
function spliceStrings(originalString, spliceList) {
outputString = originalString;
spliceList.sort((a, b) => a[1] - b[1]);
var priorInsertLength = 0;
for(let i = 0; i < spliceList.length; i++) {
outputString = insertStringAt(outputString, spliceList[i][0], spliceList[i][1] + priorInsertLength);
priorInsertLength += spliceList[i][0].length;
}
return outputString;
}
function createListItem(item) {
let subject_start = parseInt(item.subject_span.split('|')[0], 10);
let subject_end = parseInt(item.subject_span.split('|')[1], 10);
let object_start = parseInt(item.object_span.split('|')[0], 10);
let object_end = parseInt(item.object_span.split('|')[1], 10);
let spliceList = [
['<span class="badge bg-primary" data-bs-toggle="tooltip" title="' + item.subject_curie + '">', subject_start],
['</span>', subject_end],
['<span class="badge bg-info" data-bs-toggle="tooltip" title="' + item.object_curie + '">', object_start],
['</span>', object_end]
];
let sentenceHTML = spliceStrings(item.sentence, spliceList);
let evidenceHTML = '<a target="_blank" href="https://pubmed.ncbi.nlm.nih.gov/' + item.document_pmid.split(':')[1] + '/">'
+ item.document_pmid + '<small><i class="bi bi-box-arrow-up-right"></i></small></a> ' + item.document_year + ' ' + item.document_zone
+ ' (Confidence - ' + item.confidence_score + ') [' + item.predicate_curie + ']'
+ '<a target="_blank" href="https://tmui.text-mining-kp.org/assertion/' + item.assertion_id + '">'
+ 'Assertion Feedback<small><i class="bi bi-box-arrow-up-right"></i></small></a>'
+ '<a target="_blank" href="https://tmui.text-mining-kp.org/evidence/' + item.evidence_id + '">'
+ 'Evidence Feedback<small><i class="bi bi-box-arrow-up-right"></i></small></a>: <br>';
listElement = document.createElement('li');
listElement.className = 'list-group-item';
listElement.innerHTML = evidenceHTML + sentenceHTML;
return listElement;
}
nextPage = function() {
setPage(curPage + 1);
}
previousPage = function() {
setPage(curPage - 1);
}
function setUpPagination() {
if(!isFiltered) {
resultsView = searchResults;
}
if(resultsView.length == 0) {
$('#results-pagination-list').html('');
$('#results-pagination-list').parent().addClass("invisible");
return;
}
var pageList = document.getElementById('results-pagination-list');
$('#results-pagination-list').parent().removeClass("invisible");
var linkList = '<li class="page-item disabled"><a id="results-previous" class="page-link" aria-label="Previous">'
+ '<i class="bi bi-arrow-left"></i></a></li>';
var numberOfLinks = Math.floor((resultsView.length - 1) / pageSize) + 1;
for(var i = 0; i < numberOfLinks; i++)
linkList += '<li id="results-page-' + i + '" class="page-item"><a class="page-link" data-page="' + i + '">' + (i + 1) + '</a></li>';
linkList += '<li class="page-item"><a id="results-next" class="page-link" aria-label="Next" onclick="nextPage()">'
+ '<i class="bi bi-arrow-right"></i></a></li>';
pageList.innerHTML = linkList;
for(i = 0; i < numberOfLinks; i++) {
document.getElementById('results-page-' + i).firstElementChild.onclick = function () {
var newPage = parseInt(this.dataset.page);
setPage(newPage);
}
}
$('#results-page-0').addClass('active');
}
function updatePagination() {
if(!isFiltered) {
resultsView = searchResults;
}
var numberOfLinks = Math.floor((resultsView.length - 1) / pageSize) + 1;
if(curPage == 0) {
console.log('start of the journey');
document.getElementById('results-previous').onclick = undefined;
$('#results-previous').parent().addClass("disabled");
} else if(curPage > 0) {
document.getElementById('results-previous').onclick = previousPage;
$('#results-previous').parent().removeClass("disabled");
}
if(curPage + 1 >= numberOfLinks) {
console.log((curPage + 1) + ' end of the line ' + numberOfLinks);
document.getElementById('results-next').onclick = undefined;
$('#results-next').parent().addClass("disabled");
} else if(curPage + 1 < numberOfLinks) {
document.getElementById('results-next').onclick = nextPage;
$('#results-next').parent().removeClass("disabled");
}
}
function setPage(newPage) {
$('#results-page-' + curPage).removeClass('active');
curPage = newPage;
$('#results-page-' + curPage).addClass('active');
displayResults();
updatePagination();
}
function displayResults() {
$("#resultsListGroup").children().remove();
if(!isFiltered) {
resultsView = searchResults;
}
if(resultsView.length > 0) {
resultsView.sort((a,b) => parseFloat(b.confidence_score) - parseFloat(a.confidence_score));
$('#queryResultsCount').text(resultsView.length + ' sentence(s) found');
let listContainer = document.getElementById('resultsListGroup');
for(var i = 0; i < pageSize && i < resultsView.length; i++) {
listContainer.append(createListItem(resultsView[(curPage * pageSize) + i]));
}
/*
resultsData.forEach((item) => {
listContainer.append(createListItem(item));
});
*/
} else {
$("#queryResultsCount").text('No results found');
}
var tooltipTriggerList = [].slice.call(document.querySelectorAll('[data-bs-toggle="tooltip"]'));
var tooltipList = tooltipTriggerList.map(function (tooltipTriggerEl) {
return new bootstrap.Tooltip(tooltipTriggerEl);
})
}
function getSubjectCuries() {
$.ajax({
method: "GET",
url: "/api/curies/subject",
}).done(function(results) {
subjects = JSON.parse(results);
optionsList = [];
dataList = document.getElementById('subject-options');
subjects.curies.forEach(curie => dataList.appendChild(new Option(curie, curie)))
$('#subjectSelect').attr('placeholder', subjects.namespaces.join(', '))
});
}
function getObjectCuries() {
$.ajax({
method: "GET",
url: "/api/curies/object",
}).done(function(results) {
objects = JSON.parse(results);
optionsList = [];
dataList = document.getElementById('object-options');
objects.curies.forEach(curie => dataList.appendChild(new Option(curie, curie)))
$('#objectSelect').attr('placeholder', objects.namespaces.join(', '))
});
}
function filterResultsByDocumentID(docID) {
if(searchResults.length == 0 || docID.length == 0) {
return;
}
resultsView = []
actualID = docID.toUpperCase();
searchResults.forEach(function(item) {
if(isNaN(actualID)) {
if(item.document_pmid.toUpperCase() == actualID) {
resultsView.push(item);
}
} else {
recordDocID = item.document_pmid.toUpperCase().replace('PMID:', '').replace('PMC', '');
if(recordDocID == actualID) {
resultsView.push(item);
}
}
});
isFiltered = true;
}
$("#executeQueryButton").on("click", function() {
sub = $("#subjectSelect").val();
obj = $("#objectSelect").val();
pred = $("#predicateSelect").val();
if(sub == '') {
sub = 'Any'
}
if(obj == '') {
obj = 'Any'
}
$.ajax({
method: "POST",
url: "/query/",
data: JSON.stringify({subject: sub, object: obj, predicate: pred}),
dataType: "json",
contentType: "application/json"
}).done(function(res) {
let queryInfo = res.query;
let resultsData = res.results;
$("#resultsListGroup").children().remove();
let subject_text = queryInfo.subject_text?.id?.label.toUpperCase?.() ?? sub;
let object_text = queryInfo.object_text?.id?.label.toUpperCase?.() ?? obj;
let queryHTML = 'Searching for: '
+ '<span class="badge bg-primary" data-bs-toggle="tooltip" title="' + queryInfo.subject_curie
+ '">' + subject_text + '</span> '
+ (queryInfo.predicate_curie.split(':')?.[1] ?? queryInfo.predicate_curie)
+ ' <span class="badge bg-info" data-bs-toggle="tooltip" title="' + queryInfo.object_curie
+ '">' + object_text + '</span>'
$('#queryDescription').html(queryHTML);
searchResults = resultsData;
setUpPagination();
displayResults();
});
});
$("#applyFilterButton").on("click", function() {
pmid = $("#pmidFilter").val();
filterResultsByDocumentID(pmid);
setUpPagination();
displayResults();
});
$("#clearFilterButton").on("click", function() {
resultsView = searchResults;
$("#pmidFilter").val("");
isFiltered = false;
setUpPagination();
displayResults();
});
(function () {
getSubjectCuries();
getObjectCuries();
})();
});
</script>
</body>