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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="elab2ARC, convert eLabFTW experiments to ARCs">
<meta name="keywords" content="elab2ARC">
<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" />
<link rel="icon" type="image/x-icon" href="favicon.png">
<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;
}
button:hover span{
content: "under construction" !important;
}
</style>
<link href="./css/bootstrap.min.css" rel="stylesheet">
<script src="./js/bootstrap.bundle.min.js"></script>
<link href="./css/custom2607.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/git.js"></script>
<script src="./js/main060924.js" type="text/javascript"></script>
<script src="./js/turndown.js" type="text/javascript"></script>
<script type="module">
import http from './js/http.js'
window.http = http;
// 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 g-0 d-md-block dropdown col-auto">
<button type="button" onclick="location.href=location.href.split('#')[0]+'#elab'" class="btn d-none btn-nav"
id="submitNavBtn">
Fetch eLabFTW
</button>
<button class="btn btn-nav dropdown-toggle" id="instance" type="button" data-bs-toggle="dropdown" aria-expanded="false">
eLabFTW Instance: HHU
</button>
<ul class="dropdown-menu">
<li><button class="dropdown-item" onclick="setelabURL('https://demo.elabftw.net/api/v2/') " type="button">eLabFTW Instance: Demo</button></li>
<li><button class="dropdown-item" onclick=" setelabURL('https://elabftw.hhu.de/api/v2/')" type="button">eLabFTW Instance: HHU</button></li>
</ul>
<button type="button" onclick="location.href=location.href.split('#')[0]+'#arc'" class="btn btn-nav d-none"
id="a2jNavBtn">
Fetch ARCs
</button>
<button type="button" onclick="location.href=location.href.split('#')[0]+'#submit'" class="btn btn-nav d-none"
id="isacheckNavBtn">
Update ARC and Resubmit
</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" target="_blank" href="https://github.com/nfdi4plants/elab2arc">GitHub</a>
</li>
<li>
<a id="aboutlong" class="dropdown-item d-none" href=''>About</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="#elab">
<h1>Fetch eLabFTW experiments </h1>
</a>
</div>
<div name="tab" class="row justify-content-center d-none" id="elabTab">
<h1 class="center"> eLabFTW to ARC </h1>
<form id="authForm" action="/elab2arc/#elab" class="row justify-content-center align-items-center">
<div class="mb-3 col-lg-3">
<label for="elabexperimentid" class="form-label">eLabFTW Experiment ID (use comma "," to seperate multiple IDs)</label>
<textarea type="text" name="elabid" class="form-control" autocomplete="username" id="elabexperimentid" aria-describedby="elabexpHelp" required></textarea>
<div id="elabexpHelp" class="form-text d-none">Experiment ID can be found in the address bar of the browser.
</div>
</div>
<div class="mb-3 col-lg-2 ">
<label for="elabToken" class="form-label">eLabFTW API Key</label>
<input type="text" name="elabtoken" class="form-control" autocomplete="password" id="elabToken" required>
</div>
<div class="mb-3 col-lg-2">
<label for="datahubToken" class="form-label">DataHub Access Token</label>
<input type="text" name="datahubtoken" class="form-control" autocomplete="password" id="datahubToken" required>
</div>
<div class="mb-3 col-lg-2 d-none">
<label for="elabURLInput" class="form-label">elabURL</label>
<input type="text" name="elabURL" value="https://elabftw.hhu.de/api/v2/" class="form-control" autocomplete="password" id="elabURLInput" required>
</div>
<div class="mb-3 col-lg-3 ">
<label for="elabsubmit" class="form-label">Submit Options</label><br>
<button class="btn btn-primary" type="submit" data-bs-toggle="collapse" data-bs-target="#submitStatus" aria-expanded="true" aria-controls="submitStatus" > One Click Submission </button>
<span class="d-inline-block" tabindex="0" data-bs-toggle="tooltip" data-bs-title="Under Construction">
<button type="button" class="btn btn-primary" disabled><span> Step by Step </span></button>
</span>
</div>
</form>
<div id="toolstatus" class="col-10 m-auto">
<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 class="accordion" id="accordionUI">
<div class="accordion-item">
<h2 class="accordion-header" id="statusHeading">
<button class="accordion-button" id="pbarLabel" type="button" data-bs-toggle="collapse" data-bs-target="#submitStatus" aria-expanded="true" aria-controls="submitStatus">
Submission Status
</button>
</h2>
<div id="submitStatus" class="accordion-collapse collapse" aria-labelledby="statusHeading" data-bs-parent="#accordionUI">
<div class="accordion-body" id="detailedStatus">
</div>
</div>
</div>
<div class="accordion-item">
<h2 class="accordion-header" id="elabHeading">
<button class="accordion-button" type="button" data-bs-toggle="collapse" id="filesAcc" data-bs-target="#elabInfo" aria-expanded="true" aria-controls="elabInfo">
Files Changed in ARC
</button>
</h2>
<div id="elabInfo" class="accordion-collapse collapse" aria-labelledby="elabHeading" data-bs-parent="#accordionUI">
<div class="accordion-body">
<div class="center" id="filesChanged">
</div>
</div>
</div>
</div>
</div>
</div>
<div class="row justify-content-center m-3">
<img id="bbb"></img>
</div>
</div>
<div name="tab" class=" col-12 d-none" id="arcTab">
<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">
</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="updateTab">
<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 id="alertPlace"> </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>
</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 fs = FS.fs;
var elabJSON;
var statusInfo;
const version = "08-11-25";
var blobb = [];
const detailedInfo = document.getElementById("detailedStatus");
const filesChanged =document.getElementById("filesChanged");
var turndownService = new TurndownService();
var mainOrMaster = "main";
turndownService.keep(['table']);
function setelabURL(elabURL){
var elabURL1 = unescape(elabURL);
window.localStorage.setItem('elabURL',elabURL1);
document.getElementById('elabURLInput').value=elabURL1 ;
document.getElementById('instance').innerHTML = 'instance: '+elabURL1;
document.getElementById('elabURLInput').value = elabURL1;
}
async function fetchElabJSON( elabToken, query='experiments/', elabURL , corsproxy ='https://corsproxy.cplantbox.com/'){
// Define the API endpoint
const elabftwServerUrl = corsproxy + elabURL + query;
// Define the API key
const headers = {'accept': 'application/json', 'Authorization': elabToken, 'Origin': 'x-requested-with'};
// Make the fetch request
try {
const response = await fetch(elabftwServerUrl, { headers, method: 'GET'});
const json = await response.json();
return json;
} catch (error) {
if (error.message.includes(`Unexpected token 'N', "No corresp"... is not valid JSON`) || error.message.includes(`!DOCTYPE`)){
showError("Access of eLabFTW is not successful, the eLabFTW API key might be wrong, or you are using a wrong instance. Please first check the eLabFTW instance and then go to the settings of the eLabFTW to create a new API key and use it");
}else{
showError("Access of eLabFTW is not successful, error message is "+ error);
}
return error;
}
}
async function fetchElabFiles( elabToken, query='experiments/', elabURL, corsproxy ='https://corsproxy.cplantbox.com/' ){
// Define the API endpoint
const elabftwServerUrl = corsproxy + elabURL + query;
// Define the API key
const headers = {'accept': 'application/json', 'Authorization': elabToken, 'Origin': 'x-requested-with'};
// Make the fetch request
try {
var response = await fetch(`${elabftwServerUrl}`, { headers, method: 'GET'});
return response.blob();
} catch (error) {
if (error.message.includes(`Unexpected token 'N', "No corresp"... is not valid JSON`)){
console.error(error);
showError("Access of eLabFTW is not successful, the eLabFTW API key might be wrong, please go to settings to create a new API key and use it");
}else{
showError("Access of eLabFTW is not successful, error message is "+ error);
}
return error;
}
}
function gitUrlCheck(url){
if (/(?:git|ssh|https?|git@[-\w.]+):(\/\/)?(.*?)(\.git)(\/?|\#[-\d\w._]+?)$/.test(url)){
updateInfo("DataHub URL collected successfully" ,"30");
return url;
}
else{
//updateInfo("DataHub URL is not correct, automatic patches are done " ,"30");
if (!url.endsWith(".git")){
url = url + ".git";
//updateInfo("Added \" .git\" at the end, current url is "+ url ,"30");
}
if (!url.startsWith("https://")){
url = "https://" + url ;
updateInfo("Added \" https:// \" at the start, current url is "+ url ,"30");
}
return url;
}
}
async function datahubClone(datahubURL, dir, datahubtoken){
const [begin, end] = datahubURL.split("//");
url = begin + "//oath2:" + datahubtoken + "@" + end;
console.log(url);
try {
const cloneResponse = await git.clone({
fs,
http,
dir,
corsProxy: 'https://gitcors.cplantbox.com',
url: url,
ref: 'main',
singleBranch:true,
depth: 1,
force: true,
onProgress: event => {
updateLabel(event.phase)
if (event.total) {
updateProgressBar(10 + (event.loaded / event.total)*30)
} else {
updateIndeterminateProgressBar(10 + (event.loaded / 100)*30)
}
}
});
mainOrMaster = "main";
} catch (error) {
console.error(error);
updateInfo("Clone branch main failed, now try to clone branch master", "50")
const cloneResponse = await git.clone({
fs,
http,
dir,
corsProxy: 'https://gitcors.cplantbox.com',
url: url,
ref: 'master',
singleBranch:true,
depth: 1,
force: true,
onProgress: event => {
updateLabel(event.phase)
if (event.total) {
updateProgressBar(50 + (event.loaded / event.total)*30)
} else {
updateIndeterminateProgressBar(50 + (event.loaded / 100)*30)
}
}
});
mainOrMaster = "master";
}
}
async function commitPush( datahubtoken, datahubURL, fullname, email, dir ){
let sha = await git.commit({
fs,
dir: dir,
author: {
name: fullname,
email: email,
},
message: "Automatically commited by eLabFTW2ARC tool with version"+ version +". "+ statusInfo
});
console.log("commit finished");
try {
let pushResult = await git.push({
fs,
http,
dir: dir,
remote: 'origin',
force: true,
ref: 'main',
onAuth: () => ({ username: datahubtoken }),
});
console.log(pushResult) ;
updateInfo("Success pushed, ARC updated Successfully <br>", "100")
//
} catch (error) {
console.error(error);
updateInfo( error+" Push to main failed, now try to push to branch master", "0");
let pushResult = await git.push({
fs,
http,
dir: dir,
force: true,
remote: 'origin',
ref: 'master',
onAuth: () => ({ username: datahubtoken }),
});
console.log(pushResult) ;
showError( datahubURL +"ARC has been updated")
//showError( "push to git failed. The error is "+ error)
}
}
async function createAssay(assayId, dir){
try {
fs.statSync(dir+"/assays/"+assayId+"/protocols");
} catch (error) {
console.error(error);
fs.mkdirSync(dir+"/assays/"+assayId+"/protocols",{ recursive: true } )
};
try {
fs.statSync(dir+"/assays/"+assayId+"/dataset");
} catch (error) {
console.error(error);
fs.mkdirSync(dir+"/assays/"+assayId+"/dataset",{ recursive: true } )
}
}
function updateInfo(text, percent){
updateLabel(text);
updateProgressBar(percent);
const event = new Date();
statusInfo += event.toLocaleString('en-GB', { timeZone: 'UTC' }) +" " + text +"\t " + "<br>";
detailedInfo.innerHTML = statusInfo;
}
async function updateAll(elabid, elabtoken, datahubtoken, instance="https://elabftw.hhu.de/api/v2/"){
try {
filesChanged.innerHTML="";
statusInfo = "";
elabid = elabid || document.getElementById("elabexperimentid").value;
elabtoken = elabtoken || document.getElementById("elabToken").value;
datahubtoken = datahubtoken || document.getElementById("datahubToken").value;
setelabURL(instance);
instance = unescape(instance);
const maxage = 60*60*24*31; //max age is one month
document.cookie = "elabid="+elabid+"; SameSite=lax; max-age=2678400; Secure";
document.cookie = "elabtoken="+elabtoken+"; SameSite=lax; max-age=2678400; Secure";
document.cookie = "datahubtoken="+datahubtoken+"; SameSite=lax; max-age=2678400; Secure";
elabid = decodeURIComponent(elabid);
elabidList = elabid.split(",");
totalExp = elabidList.length
for (const [expIndex, elabid] of Object.entries(elabidList) ){
if (elabid){
const ratio = (expIndex+1)/totalExp;
updateInfo("Fetching eLabFTW experiment <b> "+ elabid +"</b>, instance is "+instance, ratio* 10);
const res = await fetchElabJSON(elabtoken, "experiments/"+elabid, instance);
const users = await fetchElabJSON(elabtoken, "users", instance);
const extra_fields = res.metadata_decoded.extra_fields;
const datahubURL = gitUrlCheck(extra_fields.datahub_url.value);;
// const assayId = res.title.replaceAll(".", "-dot-").replaceAll("/", "-slash-");
const assayId = res.title.replace(/\//g, "|").replace(/[^a-zA-Z0-9_.,\-+%$|(){}\[\]*=#?&$!^°<>;]/g, "_");
const fullname = res.fullname;
const user = users.find(e=> e.fullname == fullname)
const email = user.email;
let protocol = res.body;
const elabWWW= instance.replace("api/v2/", "");
protocol = protocol.replace(/\w+\.php\?mode=view/g, elabWWW+"/$&" );
console.log("protocol is" + protocol);
let markdown = turndownService.turndown(protocol);
updateInfo("DataHUB URL fetched from elab is \""+datahubURL, "\"" + ratio*20 );
const dir = "arc"+elabid;
await datahubClone(datahubURL, dir, datahubtoken);
let ls;
try {
ls = fs.readdirSync(dir+"/assays")
} catch (error) {
ls = fs.readdirSync(dir)
}
//updateInfo("Assays are "+ ls.toString().replaceAll(",", "<br>") +". Updating assay <b>" + assayId+ "</b>", "30" );
await createAssay(assayId, dir);
await fullAssay2(assayId, "new metadata table", res.lastname, res.firstname, email, res.team_name, "Generated by elab2ARC tool on "+Date() , dir);
updateInfo("isa.assay.xlsx has been updated at <b>"+assayId+"</b> ", ratio*35);
await git.add({ fs, dir: dir, filepath: "assays/"+assayId+"/isa.assay.xlsx"})
statusHTML =
`
<table class="table table-striped table-hover">
<thead>
<tr>
<th scope="col">eLabFTW Experiment `+elabid +`</th>
<th scope="col">ARC files updated</th>
</tr>
</thead>
<tbody>
<tr>
<td id="protocolHTML">
`+ protocol +`
</td>
<td>
ARC file path is `+ dir+`assays/`+encodeURIComponent(assayId)+`/protocols/eLabFTW_protocol.md
<br>
<a href="`+datahubURL.slice(0,-4)+`/-/blob/`+mainOrMaster+`/assays/`+encodeURIComponent(assayId)+`/protocols/eLabFTW_protocol.md" target="_blank" >click to check the file</a>
</td>
</tr>
`
const uploads = res.uploads;
let fileList = [];
//let filedict = {};
for (const [index, ele] of Object.entries(uploads)){
const blobs = await fetchElabFiles( elabtoken, "experiments/"+ elabid+ "/uploads/"+ ele.id +"?format=´binary´",instance);
blobb.push(blobs);
let objectURL = URL.createObjectURL(blobs)
objectURL= objectURL.replace( /&storage=./g , "" );
let data = new Uint8Array(await blobs.arrayBuffer());
// const extension = blobs.type.split("/").slice(-1)[0];
const realname = ele.real_name.replace(/[^a-zA-Z0-9_,\-+%$|(){}\[\]*=#?&$!^°<>;]/g, "_");
const longname = ele.long_name;
const path = "assays/"+assayId+"/dataset/"+index+"_"+realname;
const markdownPath = "assays/"+encodeURIComponent(assayId)+"/dataset/"+index+"_"+realname;
//filedict[longname] = datahubURL.slice(0,-4)+`/-/raw/main/`+path;
//statusHTML = statusHTML.replaceAll( "app/download.php?f="+longname , objectURL );
statusHTML = statusHTML.replace( /app\/download\.php(.*)f=/g, "" );
statusHTML = statusHTML.replaceAll( longname , objectURL );
statusHTML = statusHTML.replaceAll( "&storage=1" , "" );
statusHTML = statusHTML.replaceAll( "&storage=2" , "" );
markdown = markdown.replace(/app\/download\.php(.*)f=/g, "")
markdown = markdown.replace(/&storage=./g, "")
markdown = markdown.replaceAll( longname , datahubURL.slice(0,-4)+`/-/raw/`+mainOrMaster+`/`+markdownPath );
await fs.promises.writeFile(dir+"/"+path , data);
await git.add({ fs, dir: dir, filepath: path });
updateInfo("Added file " + realname, ratio*(10+(index/uploads.length * 10)) );
if(blobs.type.includes("image") ){
statusHTML +=
`
<tr>
<td>
<img src="`+ objectURL +`">
</td>
<td>
Submitted
ARC file path is: `+path+`.
<br>
<a href="`+datahubURL.slice(0,-4)+`/-/blob/`+mainOrMaster+`/`+encodeURIComponent(path)+`" target="_blank" >click to check the file</a>
</td>
</tr>
`
} else {
statusHTML +=
`
<tr>
<td>
file name is `+realname+`
</tb>
<td>
Submitted
ARC file path is: `+path+`.
<br>
<a href="`+datahubURL.slice(0,-4)+`/-/blob/`+mainOrMaster+`/`+encodeURIComponent(path)+`" target="_blank" >click to check the file</a>
</td>
</tr>
`
}
}
await fs.promises.writeFile(dir+'/assays/'+assayId+'/protocols/eLabFTW_protocol.md' , markdown);
await git.add({ fs, dir: dir, filepath: 'assays/'+assayId+'/protocols/eLabFTW_protocol.md' });
await fs.promises.writeFile(dir+'/assays/'+assayId+'/dataset/readme.md' , "# Data files");
await git.add({ fs, dir: dir, filepath: "assays/"+assayId+"/dataset/readme.md"})
updateInfo("Finished adding protocol files in ARC", ratio*70 );
updateInfo("All files have been added to ARC, starting to push ARC to", ratio*80 );
await commitPush(datahubtoken, datahubURL, fullname, email, dir );
//updateInfo("ARC updated Successfully<br>" , "100" );
document.getElementById("filesAcc").click();
statusHTML += "</tbody> </table>";
statusHTML = statusHTML.replaceAll( "<img", "<img class='img-fluid'" );
filesChanged.innerHTML += statusHTML;
}
}
} catch (error) {
if (error.message.includes("401")){
showError( "ELabFTW to ARC conversion failed, error is "+ error+". Please check the DataHub Token is matched to the datahub_url in the eLabFTW extra_fields. ");
console.error(error);
}else{
showError( "ELabFTW to ARC conversion failed, error is "+ error);
console.error(error);
}
updateInfo("ARC updated failed" , "0" );
}
}
addEventListener("hashchange", (event) => {
if (true) {
softRoute();
}
});
const loading = new bootstrap.Modal(document.getElementById('loadingModal'), {
keyboard: true, show: false
});
addEventListener("load", (event) => {
//showError("sorry there is currently a connection problem between this tool and DataHUB, please try again later.")
const tooltipTriggerList = document.querySelectorAll('[data-bs-toggle="tooltip"]');
const tooltipList = [...tooltipTriggerList].map(tooltipTriggerEl => new bootstrap.Tooltip(tooltipTriggerEl));
softRoute();
// try{var repoList;
// fetch('https://git.nfdi4plants.org/api/v4/projects')
// .then(data => {
// if (data.status >= 400 && data.status < 600) {
// throw showError("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(false)" class="btn btn-secondary">Import ARC</button>
// </div>
// </td>
// </tr>
// `
// }
// }), document.getElementById("datahubTable").innerHTML = tableHTML;
// }).catch((error) => {
// // Your error is here!
// showError(error)
// });}catch(e){
// showError(e);
// }
}
);
function normalizePathSeparators (str) {
const normalizedPath = path.normalize(str)
return normalizedPath.replace(/\\/g, '/');
}
async function fulfillWriteContract (basePath, contract) {
function ensureDirectory (filePath) {
let dirPath = path.dirname(filePath)
if (!fs.existsSync(dirPath)){
fs.mkdirSync(dirPath, { recursive: true });
}
}
const p = path.join(basePath,contract.Path)
if (contract.Operation = "CREATE") {
if (contract.DTO == undefined) {
ensureDirectory(p)
fs.writeFileSync(p, "")
} else if (contract.DTOType == "ISA_Assay" || contract.DTOType == "ISA_Assay" || contract.DTOType == "ISA_Investigation") {
ensureDirectory(p)
await Xlsx.toFile(p, contract.DTO)
} else if (contract.DTOType == "PlainText") {
ensureDirectory(p)
fs.writeFileSync(p, contract.DTO)
} else {
console.log("Warning: The given contract is not a correct ARC write contract: ", contract)
}
}
}
// Read
async function fulfillReadContract (basePath, contract) {
async function fulfill() {
const normalizedPath = normalizePathSeparators(path.join(basePath, contract.Path))
switch (contract.DTOType) {
case "ISA_Assay":
case "ISA_Study":
case "ISA_Investigation":
let fswb = await Xlsx.fromXlsxFile(normalizedPath)
return fswb
break;
case "PlainText":
let content = fs.load(normalizedPath)
return content
break;
default:
console.log(`Handling of ${contract.DTOType} in a READ contract is not yet implemented`)
}
}
if (contract.Operation == "READ") {
return await fulfill()
} else {
console.error(`Error (fulfillReadContract): "${contract}" is not a READ contract`)
}
}
function getAllFilePaths(basePath) {
const filesList = []
function loop (dir) {
const files = fs.readdirSync(dir);
for (const file of files) {
const filePath = path.join(dir, file);
if (fs.statSync(filePath).isDirectory()) {
// If it's a directory, recursively call the function on that directory
loop(filePath);
} else {
// If it's a file, calculate the relative path and add it to the list
const relativePath = path.relative(basePath, filePath);
const normalizePath = normalizePathSeparators(relativePath)
filesList.push(normalizePath);
}
}
}
loop(basePath)
return filesList;
}
// put it all together
async function read(basePath) {
let allFilePaths = getAllFilePaths(basePath)
// Initiates an ARC from FileSystem but no ISA info.
let arc = arctrl.ARC.fromFilePaths(allFilePaths)
// Read contracts will tell us what we need to read from disc.
let readContracts = arc.GetReadContracts()
console.log(readContracts)
let fcontracts = await Promise.all(
readContracts.map(async (contract) => {
let content = await fulfillReadContract(basePath, contract)
contract.DTO = content
return (contract)
})
)
arc.SetISAFromContracts(fcontracts);
console.log(fcontracts);
return arc
}
// execution
// execution
window.ARC2JSON= async function(ARCName, JSONname ){
await read(ARCName).then(
arc => {try {
fs.writeFileSync(JSONname, arctrl.JsonController.Investigation.toISAJsonString(arc.ISA, void 0, true))
// file written successfully
} catch (err) {
console.error(err);
}}
)
}
window.fullAssay2= async function(assayName, tableName ="newtable", firstName=void 0, familyName=void 0, email= void 0, affiliation= void 0, comment="generated by elab2arc", dir ){
try {
// -------- 1. Create and manipulate object in datamodel ----------
const growth = arctrl.ArcTable.init(tableName);
// Add input column with one value to table
growth.AddColumn(arctrl.CompositeHeader.input(arctrl.IOType.source()), [arctrl.CompositeCell.createFreeText("Input1")]);
// Add characteristic column with one value
const oa_species = new arctrl.OntologyAnnotation("species", "GO", "GO:0123456");
const oa_chlamy = new arctrl.OntologyAnnotation("Chlamy", "NCBI", "NCBI:0123456");
//growth.AddColumn(arctrl.CompositeHeader.characteristic(oa_species), [arctrl.CompositeCell.createTerm(oa_chlamy)]);
// Create assay
//const mtype = new arctrl.OntologyAnnotation("measurement type", "1", "2");
//const mtech = new arctrl.OntologyAnnotation("technology type", "1", "2");
//const mplat = new arctrl.OntologyAnnotation("technology platform", "1", "2");
const roles = new arctrl.OntologyAnnotation("Researcher", "AGRO", "AGRO:00000373");
let comments_p = arctrl.Comment$.create("generation log",comment);