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isa-json.html
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<!DOCTYPE html>
<html>
<head>
<meta http-equiv="Content-Type" charset="utf-8" name="viewport" content="width=device-width, initial-scale=1">
<meta name="description" content="MARS: Multi-omics Adapter for Repository Submissions">
<meta name="keywords" content="MARS,">
<meta http-equiv="Cache-Control" content="no-cache, no-store, must-revalidate" />
<meta http-equiv="Pragma" content="no-cache" />
<meta http-equiv="Expires" content="0" />
<style>
.center {
position: relative;
text-align: center;
}
.uploadarea {
padding: 6px;
border: 4px solid #4fb3d9;
border-style: outset;
border-radius: 5px;
-khtml-opacity: 0.5;
-moz-opacity: 0.5;
opacity: 0.5;
height: 20vh;
background-image: url("data:image/svg+xml;utf8,<svg xmlns='http://www.w3.org/2000/svg' width='16' height='16' fill='%234fb3d9' class='bi bi-cloud-upload' viewBox='0 0 16 16'><path fill-rule='evenodd' d='M4.406 1.342A5.53 5.53 0 0 1 8 0c2.69 0 4.923 2 5.166 4.579C14.758 4.804 16 6.137 16 7.773 16 9.569 14.502 11 12.687 11H10a.5.5 0 0 1 0-1h2.688C13.979 10 15 8.988 15 7.773c0-1.216-1.02-2.228-2.313-2.228h-.5v-.5C12.188 2.825 10.328 1 8 1a4.53 4.53 0 0 0-2.941 1.1c-.757.652-1.153 1.438-1.153 2.055v.448l-.445.049C2.064 4.805 1 5.952 1 7.318 1 8.785 2.23 10 3.781 10H6a.5.5 0 0 1 0 1H3.781C1.708 11 0 9.366 0 7.318c0-1.763 1.266-3.223 2.942-3.593.143-.863.698-1.723 1.464-2.383'/><path fill-rule='evenodd' d='M7.646 4.146a.5.5 0 0 1 .708 0l3 3a.5.5 0 0 1-.708.708L8.5 5.707V14.5a.5.5 0 0 1-1 0V5.707L5.354 7.854a.5.5 0 1 1-.708-.708z'/></svg>");
background-position: center;
background-repeat: no-repeat;
background-size: 64px 64px;
}
td {
overflow-wrap: break-all;
word-break: break-all;
}
datalist {
display: flex;
justify-content: space-between;
color: #4fb3d9;
width: 100%;
}
.uploadarea:hover,
.uploadarea.dragging,
.uploadarea.uploading {
filter: alpha(opacity=100);
-khtml-opacity: 1;
-moz-opacity: 1;
opacity: 1;
}
.uploadarea input {
margin: auto;
width: 100%;
height: 100%;
border: none;
cursor: pointer;
opacity: 0;
}
.uploadarea input:focus {
outline: none;
}
span.json {
display: inline-block;
margin: 4px;
padding: 6px;
border: 4px solid #4fb3d9;
border-style: solid;
border-radius: 5px;
}
*[title]:hover:after {
background-color: #4fb3d9;
content: attr(name) '\A' attr(description);
z-index: 1;
position: absolute;
}
span.studies {
background-color: #fff9e6;
}
span.collapsed {
font-weight: bold;
border: 4px #4fb3d9;
border-style: inset;
box-shadow: 0 8px 6px -6px #4fb3d9;
cursor: pointer;
}
span.missingKey {
font-weight: bold;
border: 4px #b005ad;
border-style: dotted;
box-shadow: 0 8px 6px -6px #c50070;
}
span.collapsed::before {
content: "+";
color: #4fb3d9;
}
span.assays {
background-color: #F8E8EB;
}
.form-range {
appearance: auto !important;
}
input[type="range"]::-webkit-slider-thumb {
height: 15px;
width: 15px;
background-color: #fff;
border-radius: 50%;
border: 2px solid #4fb3d9;
}
input[type="range"]::-moz-range-thumb {
height: 15px;
width: 15px;
background-color: #fff;
border-radius: 50%;
border: 1px solid #4fb3d9;
}
input[type="range"]::-moz-range-track {
padding: 0 10px;
background: repeating-linear-gradient(to right,
#ccc,
#ccc 10%,
#000 10%,
#000 11%,
#ccc 11%,
#ccc 20%);
}
.scrollTable{
max-height : 200px;
overflow-y: scroll;
max-width: 80vw;
}
</style>
<!--<script src="https://cdn.jsdelivr.net/pyodide/v0.21.3/full/pyodide.js"></script>-->
<link href="./css/bootstrap.min.css" rel="stylesheet">
<script src="./js/bootstrap.bundle.min.js"></script>
<link href="./css/custom0220.css" rel="stylesheet" />
<link href="./css/bs5-intro-tour.css" rel="stylesheet" />
<script src="./js/bs5-intro-tour.js" type="text/javascript" charset="utf-8"></script>
<!--script src="js/example.js" type="text/javascript" charset="utf-8"></script-->
<script src="./js/test_json_dataplant_no_investigation_small.js"></script>
<script src="./js/test_json_datahub.js"></script>
<script src="./js/dataplant_biosamples_returned_json.js"></script>
<script src="./js/datahub_biosamples_returned_json.js"></script>
<script src="./js/git.js"></script>
<script src="./js/main060924.js" type="text/javascript"></script>
<script src="./js/jsonata.min.js"></script>
<script type="module">
import http from './js/http.js'
window.http = http;
window.googleJSON = await fetchGoogleCSV();
// window.fs = new LightningFS('fs')
// window.pfs = window.fs.promises
</script>
</head>
<body>
<div class="col-12" style="background: rgb(45, 62, 80); height: 3.25rem; margin: 0 0 0 0px; padding: 0 0 0 0; ">
<a class="" href="https://nfdi4plants.org/" style="">
<img src="images/logo.png" alt="Logo" width="32" height="32"
style="position: absolute; margin: 8px 12px 8px 12px; left: 0px; padding-top: 4px;" />
</a>
<div class="justify-content-center row d-flex align-items-center"
style="margin: 0 0 0 0; ; padding: 0 0 0 0; height: 3.25rem; ">
<div class="btn-group d-md-none g-0 dropdown col-auto d-flex align-items-center" style="">
<button type="button" class="btn rounded-0 border-0 g-0 btn-nav " data-bs-toggle="dropdown"
aria-expanded="false" id="menu">
Menu
<a
style="display: inline-block; color: rgb(79, 179, 217); letter-spacing: 2px; font-size: 1em; transform: scaleX(2); transform-origin: 1 0;">
∨ </a>
</button>
<ul class="dropdown-menu">
<li>
<button id="convertershort" class="dropdown-item d-none" onclick=''>Converter</button>
</li>
<li>
<a id="ghlinkshort" class="dropdown-item" href="https://github.com/elixir-europe/MARS">GitHub</a>
</li>
<li>
<a id="specshort" class="dropdown-item" onclick='dlText(JSON.stringify(googleJSON), "ISA-JSON_Specification_MARS")'>Download Specification</a>
</li>
</ul>
</div>
<div class="btn-group d-none g-0 d-md-block dropdown col-auto">
<button type="button" onclick="location.href=location.href.split('#')[0]+'#isacheck'" class="btn btn-nav"
id="isacheckNavBtn">
ISA Check
</button>
<button type="button" class="btn border-0 rounded-0 g-0 btn-nav" data-bs-toggle="dropdown" aria-expanded="false"
id="conversion_tools">
Menu
<a
style="display: inline-block; color: rgb(79, 179, 217); letter-spacing: 2px; font-size: 1em; transform: scaleX(2); transform-origin: 1 0;">
∨ </a>
</button>
<ul class="dropdown-menu">
<li>
<button id="converterlong" class="dropdown-item d-none" onclick=''>Converter</button>
</li>
<li>
<a id="ghlinklong" class="dropdown-item" href="https://github.com/elixir-europe/MARS">GitHub</a>
</li>
<li>
<a id="speclong" class="dropdown-item" onclick='dlText(JSON.stringify(googleJSON), "ISA-JSON_Specification_MARS")'>Download Specification</a>
</li>
</ul>
</div>
</div>
</div>
<div class="container">
<div name="tab" class=" col-12 justify-content-center nav-link text-center" id="introTab">
<a href="#isacheck">
<h1>Checks, validate and auto complete of ISA-JSON </h1>
</a>
</div>
<div name="tab" class="row justify-content-center d-none" id="submissionTab">
<h1 class="center">MARS: Multi-omics Adapter for Repository Submissions </h1>
<form id="authForm" class="row justify-content-center">
<div class="mb-3 col-2">
<label for="username" class="form-label">ENA Username</label>
<input type="text" class="form-control" id="username" aria-describedby="usernameHelp">
<div id="usernameHelp" class="form-text d-none">The user name and password are used for token generation.
</div>
</div>
<div class="mb-3 col-2">
<label for="password" class="form-label">Password</label>
<input type="password" class="form-control" id="password">
</div>
<div class="mb-3 form-check d-none">
<input type="checkbox" class="form-check-input " id="passwordCheck">
<label class="form-check-label" for="passwordCheck">Check me out</label>
</div>
<div class="mb-3 col-2 d-none">
<label id="tokenHelp" class="form-text">Only collect token if you need.</label>
<br>
<button type="submit" id="formSubmit" class="btn btn-primary" aria-describedby="tokenHelp">Collect
Token</button>
</div>
</form>
<div class="col-6 m-auto">
</div>
<div class="row justify-content-center m-3">
<!-- <div class="col-2">
<button class="btn btn-primary" style="display:inline" data-bs-toggle="modal" data-bs-target="#cModal"
id="cModalButton"> Start Submissions </button>
</div> -->
</div>
</div>
<div name="tab" class=" col-12 d-none" id="ARC2JSONTab">
<div class="" style="height: 50vh; overflow-y: scroll">
<table class="table table-striped table-hover" style="table-layout:auto ; width:100%; ">
<thead>
<tr>
<th scope="col">Number</th>
<th scope="col">User/Group</th>
<th scope="col">Repo Name</th>
<th scope="col">Actions</th>
</tr>
</thead>
<tbody id="datahubTable">
</tbody>
</table>
</div>
<div class="row m-3">
<div class="col-5">
<h4> Imported ARCs </h4>
<table class="table table-striped table-hover" style="table-layout:auto ; width:100%; ">
<thead>
<tr>
<th scope="col">ARC Name</th>
<th scope="col">Import Time</th>
<th scope="col">Actions</th>
</tr>
</thead>
<tbody id="importedARCTable">
</tbody>
</table>
</div>
<div class="col-7">
<form class="">
<div class="row g-3 align-items-center">
<div class="col-3 text-end">
<label for="repoURL" class="col-form-label">ARC gitlab URL</label>
</div>
<div class="col-5">
<input type="text" id="repoURL"
value='https://git.nfdi4plants.org/ai.krueger/2024_GrowthCoupledHemeBiosensor.git'
class="form-control" aria-describedby="repoURLLabel" required>
</div>
<div class="col-4">
<span id="repoURLLabel" class="form-text">
ARC Repository URL can be copied from the "Clone with HTTPS" section under code. It should start with
"https://" and end with ".git"
</span>
</div>
</div>
<div class="row g-3 align-items-center d-none">
<div class="col-3 text-end">
<label for="gitusername" class="col-form-label">Username</label>
</div>
<div class="col-5">
<input type="Gitusername" id="gitusername" class="form-control" aria-describedby="UsernameHelpInline">
</div>
<div class="col-4">
<span id="UsernameHelpInline" class="form-text">
The username or of DataHUB
</span>
</div>
</div>
<div class="row g-3 align-items-center">
<div class="col-3 text-end">
<label for="gitpassword" class="col-form-label">Access Token</label>
</div>
<div class="col-5">
<input type="Gitpassword" placeholder="can be left empty" id="gitpassword" class="form-control"
aria-describedby="passwordHelpInline">
</div>
<div class="col-4">
<span id="passwordHelpInline" class="form-text">
The personal access token can be left empty if the repository is publicly accessible.
</span>
</div>
</div>
<div class="col-3 m-auto align-items-center">
<br>
<button class="btn btn-primary" id="submitURL" onclick="event.preventDefault(); cloneARC()">Export
ARC-JSON</button>
</div>
</form>
</div>
</div>
<div id="ARCInfo" class="row m-auto">
</div>
</div>
<div name="tab" class=" col-8 d-none align-items-center m-auto" id="isacheckTab">
<!-- <div class=" area uploadarea my-3" id="importArea" ondragenter="this.className='area uploadarea dragging'"
ondrop=";DragAndDrop(event)" style=" width:100%">
<input type="file" id="import" multiple>
</div> -->
<div class="text-center m-auto">
<button class="text btn btn-primary d-none" id="toSubmit" onclick="location.href=location.href.split('#')[0]+'#submit'" >
Start Submission
</button>
</div>
<div class="accordion" id="accordionExample">
<div class="accordion-item">
<!-- <h2 class="accordion-header" id="headingOne">
<button class="accordion-button" type="button" data-bs-toggle="collapse" data-bs-target="#exampleTest" aria-expanded="true" aria-controls="exampleTest">
Use prepared ISA-JSON example to test the basic functions
</button>
</h2> -->
<div id="exampleTest" class="accordion-collapse collapse" aria-labelledby="headingOne" data-bs-parent="#accordionExample">
<div class="accordion-body">
<div class="center">
DataPLANT test JSON <a href="#" onclick="isaVis(dataplant_json)">here</a>
<br>
DataHub test JSON <a href="#" onclick="isaVis(datahub_json)">here</a> <br>
<br>
<input class="btn btn-primary d-inline d-none" type="file" id="input_json" name="json" multiple />
<br>
<div class="d-flex justify-content-center d-none" id="waiting">
<div class="spinner-grow btn-primary" style="width: 3rem; height: 3rem;" role="status">
<br>
<span class="sr-only d-none">Loading...</span>
</div>
</div>
<div class="m-auto" id="xml_output">
</div>
</div>
</div>
</div>
</div>
</div>
<div class="row m-3"></div>
<div class="col-12">
<h4> MARS ISA-JSON Specification </h4>
<table class="table table-striped table-hover" style="table-layout:auto ; width:100%; ">
<thead>
<tr>
<th scope="col">Human Readable Location</th>
<th scope="col">Cardinality</th>
<th scope="col">Machine Readable</th>
<!-- <th scope="col">Check Passed</th> -->
</tr>
</thead>
<tbody id="marsTable">
</tbody>
</table>
</div>
<!-- <div id="alertPlace"> </div>
<h4> ISA JSON Visualization: </h4>
<label for="jsonRange" class="form-label">Chose the level of details by slides (larger number = more details). The
blocks can collapsed or explanded by clicks and the values will show when the blocks are hovered.
</label>
<input type="range" class="form-range" id="jsonRange" min="2" max="2" onchange="setRange(this)" list="steplist">
<datalist id="steplist">
</datalist>
<div class="col-12 m-auto">
<span id="jsonVisualize" class="json m-auto">
</span>
</div> -->
</div>
</div>
<button type="button" class="btn btn-primary d-none" id="loadingModalBtn" data-bs-toggle="modal"
data-bs-target="#loadingModal">
Launch loading modal
</button>
<div class="modal" id="loadingModal" data-bs-backdrop="static" data-bs-keyboard="false" tabindex="-1"
aria-labelledby="#loadingModalLabel" aria-hidden="true">
<div class="modal-dialog">
<div class="modal-content">
<div class="modal-header">
<h1 class="modal-title fs-5" id="loadingModalLabel">Processing</h1>
<button type="button" class="btn-close" data-bs-dismiss="modal" aria-label="Close"></button>
</div>
<div class="modal-body">
<div class="d-flex justify-content-center">
<div class="spinner-border" role="status">
<span class="visually-hidden">Loading...</span>
</div>
</div>
<span id="pbarLabel"> </span>
<div class="progress">
<div class="progress-bar progress-bar-striped progress-bar-animated" id="pbarModal" role="progressbar"
aria-label="Animated striped example" aria-valuenow="1" aria-valuemin="0" aria-valuemax="100"
style="width: 1%">
</div>
</div>
</div>
<div class="modal-footer">
<button type="button" class="btn btn-secondary" data-bs-dismiss="modal">Close</button>
</div>
</div>
</div>
</div>
<script type="text/javascript">
var v_list, csv_content, cleanend_global, token, ena_return = 0, biosamples_return = 0;
var input_json = "test_input";
var log_backup = console.log;
var fs = FS.fs;
var alert_place_holder = document.getElementById('alertPlace');
var log_messages = [];
var current_file;
var steps = [{
title: "Converter and validators",
content: '<p> Welcome! Our converter can convert an ISA-JSON file to multiple endpoint repositories such as ENA, Metabolites, EGA, EVA'
//
}
];
// addEventListener("load", (event) =>
// {
// // try{var repoList;
// // fetch('https://git.nfdi4plants.org/api/v4/projects')
// // .then(data => {
// // if (data.status >= 400 && data.status < 600) {
// // throw alert("Bad response from server, please check the availability of the server");
// // }
// // return data.json();
// // })
// // .then(post => {
// // window.repoList = post;
// // var tableHTML = '';
// // let newIndex = 0;
// // post.forEach((element, index) => {
// // if (element.description !== null) {
// // const pathName = element.path_with_namespace.split("/");
// // newIndex += 1;
// // tableHTML += `
// // <tr>
// // <th scope="row">`+ newIndex + ` </th>
// // <td>
// // `+ pathName[0] + `
// // </td>
// // <td>
// // <a href="`+ element.web_url + `" target="_blank">` + pathName[1] + `</a>
// // </td>
// // <td>
// // <div class="btn-group" role="group" aria-label="Basic example">
// // <button type="button" onclick="document.getElementById('repoURL').value='`+ element.http_url_to_repo + `'; cloneARC()" class="btn btn-primary">Import and Get ISA-JSON</button>
// // <button type="button" onclick="document.getElementById('repoURL').value='`+ element.http_url_to_repo + `'; cloneARC(false)" class="btn btn-secondary">Only Import</button>
// // </div>
// // </td>
// // </tr>
// // `
// // }
// // }), document.getElementById("datahubTable").innerHTML = tableHTML;
// // }).catch((error) => {
// // // Your error is here!
// // alert(error)
// // });}catch(e){
// // alert(e);
// // }
// });
var checklist_biosamples = [
{
"description" : "To check if investigation exists as a wraper",
"key": "investigation",
"jsonata": "$.$keys()",
"error": "element.key + \" can not be found in\" element.jsonata",
"fixfunction": '{"investigation":$}'
},
{
"description" : "To check if studies exsits",
"key": "studies",
"jsonata": "$.investigation.$keys()",
"error": "element.key + \" can not be found in\" element.jsonata",
"fixfunction": '$~>| $.investigation| {"studies":"missing_key"} |'
},
// {
// "description" : "To check if assays exsits",
// "key": "assays",
// "jsonata": "$.investigation.studies[0].$keys()",
// "error": "element.key + \" can not be found in\" element.jsonata",
// "fixfunction": '$assert($.investigation.studies.$keys(), "error, no assays in studies")'
// },
{
"description" : "check if organisms are added to the $.investigation.studies.materials.sources.characteristics ",
"jsonata" : '$assert($boolean($.investigation.studies.materials.sources.characteristics."@id"[$contains("organism=")].%.category."@id".$not($contains("organism"))).$not(), "error. Organism is not found" )',
"fixfunction" : '$~> |$.investigation.studies.materials.sources.characteristics."@id"[$contains("organism=")].%| {"category":{"@id": "#MaterialAttribute/organism/OBI:0100026" }} |'
},
{
"description" : "To check if organisms exists in the ids in characteristicCategories",
"jsonata" : '$assert($boolean($.**.`@id`.$contains("#MaterialAttribute/OBI:0100026")).$not() , "error, no organisms in characteristicCategories")',
"fixfunction" : '$~>| $.**[`@id`="#MaterialAttribute/OBI:0100026"]| {"@id":"#MaterialAttribute/organism/OBI:0100026"} |'
},
{
"description" : "To check if there are multiple studies exist. Only the first will be slected if there is not submission specifications",
"jsonata" : '$assert ($count($.investigation.studies)=1, "error. More than one studies are found" )',
"fixfunction" : '$~> |$.investigation | {"studies" : [$.studies[0]]} |'
},
{
"description": "To check if all investigation.studies.materials.sources have at least one characteristics",
"jsonata": '$assert($count($.investigation.studies.materials.sources[$lookup("characteristics")]) = $count($.investigation.studies.materials.sources), "Not all sources in materials have characteristics ")',
"fixfunction": '$~>| $.investigation.studies.materials| {"sources" : sources[$lookup("characteristics")] } |'
},{
"description" : "To evaluate the type of \"value\" key, try auto fix if the value is numbers or strings",
"jsonata" : '$assert(($nopeople := $ ~> |$.investigation.studies[0]| {"people":[]} |; $not($exists($nopeople.investigation.studies.**[($type(value) = "string") or ($type(value) = "number")]))), "error, the strings or numbers type of value exist in the values")',
"error": "string and number values exist in the 'value' keys",
"fixfunction" : '($people := $.investigation.studies.people ;$c1 := $ ~> | $.investigation.studies.**[($type(value) = "string") or ($type(value) = "number") ] | { "value": {"@id": "","annotationValue": value.$string(), "termAccession":"", "termSource":"" } }| ; $c1 ~> | $.investigation.studies| {"people" : $people} | )'
},{
"description": "To check if all investigation.studies.materials.sources.characteristics.category has correct format",
"jsonata" : '($p := $.investigation.studies.materials.sources.characteristics; $assert( $count($p) = $count($p.category) , "Some characteristics do not have categories" ))',
"fixfunction" :'($dic := $.investigation.studies.materials.sources.characteristics[$lookup("value")]{ `@id` : category}; $getvalue := function($id){($dic.$lookup($id))}; $ ~> |$.investigation.studies.materials.sources.characteristics| {"category": `@id`.$getvalue($) }| )'
},
{
"description": "To check investigation.studies.materials.sources.characteristics.value ",
"jsonata" : '($p := $.investigation.studies.materials.sources.characteristics[[$contains(`@id`, "Empty" ).$not()]]; $assert( $count($p) = $count($p.value) , "Some characteristics do not have values" ))',
"fixfunction" :'($dic := $.investigation.studies.materials.sources.characteristics[$lookup("value")]{ `@id` : value};$getvalue := function($id){($dic.$lookup($id))}; $ ~> |$.investigation.studies.materials.sources.characteristics| {"value": `@id`.$getvalue($) }| )'
}
]
var checklist_ena = [
{
"description" : "evaluate the type of \"value\" key, try auto fix if the value is ",
"jsonata" : '$assert($.studies.**[($type(value) = "string") or ($type(value) = "number")], "error")',
"error": "string and number values exist in the 'value' keys",
"fixfunction" : '$ ~> | $.investigation.studies.**[($type(value) = "string") or ($type(value) = "number") ] | { "value": {"@id": "","annotationValue": value.$string(), "termAccession":"", "termSource":"" } }|'
}
]
function csvJSON(csv){
var lines=csv.split("\n");
var result = [];
var headers=lines[1].split(",");
for(var i=2;i<lines.length;i++){
var obj = {};
var currentline=lines[i].split(",");
for(var j=0;j<headers.length;j++){
obj[headers[j]] = currentline[j];
}
result.push(obj);
}
//return result; //JavaScript object
return JSON.stringify(result); //JSON
}
async function fetchGoogleCSV(){
try {
//read .csv file on a server
const target = `https://docs.google.com/spreadsheets/d/e/2PACX-1vQvgQoUByiJgGcJ4jtD8bG9AyQrh4TYVQE8aq7AqJRxLdfyLFATKspu_vkyqbVsTyEnNIBHqWtpgV6X/pub?gid=0&single=true&output=csv`;
const res = await fetch(target, {
method: 'get',
headers: {
'content-type': 'text/csv;charset=UTF-8',
}
});
if (res.status === 200) {
const data = await res.text();
const result = JSON.parse(csvJSON(data));
showSpecs(result);
return result;
//document.getElementById("submission").disabled = false;
} else {
console.log(`Error code ${res.status}`);
}
} catch (err) {
console.log(err)
}
}
async function updateTable( ISAJSON ){
//googleJSON = await fetchGoogleCSV();
let tableHTML = "";
for (const [index, e] of Object.entries(googleJSON)){
if (e["Obligation-MARS"].replace(" ", "") == "Mandatory"){
const eva = e["JSONata_MARS_evaluation"];
const human = e.ISAjson;
const jsonataExp = "$assert('"+eva+", '"+human +"')"
let result;
try {
result = await jsonata(jsonataExp).evaluate(ISAJSON);
result = "Passed";
} catch (error) {
result = "<span class='text-danger'> failed " + error.message+"</span>";
}
console.log(human +" the eval result is"+result);
tableHTML += `
<tr>
<td>
`+ human + `
</td>
<td>
`+ e["Obligation-MARS"] + `
</td>
<td>
`+ jsonataExp + `
</td>
<td id=marsTableRow`+ index + `>
`+result+`
</td>
</tr>
`
}
}
document.getElementById("marsTable").innerHTML = tableHTML;
}
function showSpecs(result){
let tableHTML = "";
for (const [index, e] of Object.entries(result)){
if (e["Obligation-MARS"].replace(" ", "") == "Mandatory"){
const eva = e["JSONata_MARS_evaluation"];
const human = e.ISAjson;
const jsonataExp = "$assert('"+eva+", '"+human +"')"
tableHTML += `
<tr>
<td>
`+ human + `
</td>
<td>
`+ e["Obligation-MARS"] + `
</td>
<td>
`+ jsonataExp + `
</td>
</tr>
`
}
}
document.getElementById("marsTable").innerHTML = tableHTML;
}
async function checkJSONata(googleJSON, ){
}
const loading = new bootstrap.Modal(document.getElementById('loadingModal'), {
keyboard: true, show: false
});
function setRange(ele) {
loading.show()
const order = Number(ele.value);
const max = Number(ele.max);
const id = order - 1;
//const preid = order-2;
document.querySelectorAll('[data-order="' + id + '"]').forEach(e => { if (e.firstElementChild != null) { e.classList.add('collapsed'); } })
for (let i = 1; i < order - 1; i++) {
document.querySelectorAll('[data-order="' + i + '"]').forEach(e => { if (e.firstElementChild != null) { e.classList.remove('collapsed'); } })
}
for (let i = 1; i < order; i++) {
document.querySelectorAll('[data-order="' + i + '"]').forEach(e => {
e.classList.remove('d-none');
}
);
}
for (let i = order; i <= max; i++) {
document.querySelectorAll('[data-order="' + i + '"]').forEach(e => {
if (e.firstElementChild != null) {
e.classList.add('collapsed');
}
e.classList.add('d-none');
}
);
}
loading.hide();
}
const bootAlert = (message, type) => {
const wrapper = document.createElement('div')
wrapper.innerHTML = [
`<div class="alert alert-${type} alert-dismissible" role="alert">`,
` <div>${message}</div>`,
' <button type="button" class="btn-close" data-bs-dismiss="alert" aria-label="Close"></button>',
'</div>'
].join('')
alert_place_holder.append(wrapper)
}
function checkHas(key, location, error) {
const expression = "$assert('" + key + "' in " + location + ", '" + error + "')";
return expression;
}
async function jCheck(json, expression) {
var result = await jsonata(expression).evaluate(json);
return result;
}
async function checkall(checklist, isa) {
window.alert_place_holder.innerHTML = "";
var passed = 0;
for (const [index, element] of Object.entries(checklist,)) {
try { if(element.key){
await jCheck(isa, checkHas(element.key, element.jsonata, element.key + " can not be found in " + element.jsonata));
passed += 1;
bootAlert(element.description +". [Test passed]", "success")
} else {
await jCheck(isa, element.jsonata);
passed += 1;
bootAlert(element.description +". [Test passed]", "success")
}
} catch (e) {
try {
isa = await jCheck(isa, element.fixfunction);
jCheck(isa, element.jsonata)
.catch(e =>{
bootAlert(e.message +". \n Validation failed and automatic patch is not successful. \n ", "danger");
return Promise.reject()
}
)
.then(e =>
{
passed += 1;
bootAlert(element.description +". \n Validation failed but automatic patching has been successfully done", "warning");
if (passed == checklist.length){
//document.getElementById("toSubmit").classList.remove("d-none");
console.log("all test passed");
}else{
//document.getElementById("toSubmit").classList.add("d-none");
}
}
);
} catch (e) {
bootAlert(e.message, "danger")
};
}
};
//console.log("returned isa is: " + JSON.stringify(isa));
return isa;
}
window.id = 0;
window.orderMax = 0;
function traverse(json, parentNode, order) {
if (typeof json !== 'object' || json === null) return;
order += 1;
window.orderMax = Math.max(order, window.orderMax)
document.getElementById("jsonRange").setAttribute("max", window.orderMax);
Object.entries(json).forEach(([key, value]) => {
const keyAttribute = key.replace("@", "at");
if (typeof (value) == 'string') {
try {
//parentNode.setAttribute(keyAttribute,value);
let childNode = document.createElement("span");
childNode.classList.add("json");
childNode.classList.add(key);
childNode.innerText = key;
childNode.setAttribute("title", value);
childNode.setAttribute("data-order", order);
value=="missing_key"? childNode.classList.add("missingKey") : {} ;
parentNode.appendChild(childNode);
} catch (error) {
alert(e);
};
if ((key == '@id') || (key == 'name')) {
//parentNode.innerText += key+ " "+ value+ " ";
//parentNode.classList.add(value);
};
} else if (typeof (value) == 'object') {
let childNode = document.createElement("span");
childNode.classList.add("json");
childNode.classList.add(key);
if ((Object.prototype.toString.call(json) === '[object Array]')) {
childNode.innerText = Number(key) + 1;
} else {
childNode.innerText = key;
}
childNode.setAttribute("data-order", order);
window.id += 1;
try {
childNode.setAttribute("id", "jsonId" + window.id);
} catch (error) {
alert(e);
}
childNode.setAttribute("name", key);
window.orderMax = Math.max(order, window.orderMax);
const nextOrder = order + 1;
document.getElementById("jsonRange").setAttribute("max", window.orderMax);
childNode.setAttribute("onclick", "event.stopPropagation();this.classList.toggle('collapsed'); +1;this.querySelectorAll('span[data-order=\"" + nextOrder + "\"]').forEach(e=> e.classList.toggle('d-none'))");
parentNode.appendChild(childNode);
traverse(value, childNode, order);
}
;
});
};
async function isaVis(json) {
json = await checkall(checklist_biosamples, json);
await updateTable( json );
window.orderMax = 0;
window.path = 0;
let ele1 = document.getElementById("jsonVisualize");
ele1.innerHTML = "";
var order = 0;
try {
traverse(json, ele1, order),
setTimeout(e => { loading.hide() }, 100);
} catch (error) {
alert(error);
}
let stepListText = "";
let jsonRange = document.getElementById("jsonRange");
for (let i = 2; i <= Number(jsonRange.max); i++) {
stepListText += "<option value=" + i + " label=" + i + " >" + i + "</option>"
}
document.getElementById("steplist").innerHTML = stepListText;
jsonRange.value = 3;
jsonRange.onchange()
}
function updateLabel(phrase) {
document.getElementById("pbarLabel").innerHTML = phrase;
}
function updateProgressBar(progress) {
const pbar = document.getElementById("pbarModal");
pbar.setAttribute("style", 'width:' + progress + '%;')
pbar.setAttribute("aria-valuenow", progress)
}
function updateIndeterminateProgressBar(progress) {
const pbar = document.getElementById("pbarModal");
pbar.setAttribute("style", 'width:' + progress + '%;')
pbar.setAttribute("aria-valuenow", progress)
}
async function cloneARC(convert = true) {
// try {
// document.getElementById("loadingModalBtn").click();
// var url;