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Merged
mapoferri merged 20 commits into from
Aug 20, 2026
Merged

Interactive tools features and fixes #39

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2a64c8c
fix: add network name to globals file
nicodr97 Aug 17, 2026
d5cc32e
fix: lua script return values
nicodr97 Aug 17, 2026
1679f0e
fix: set rewrite tag on apache conf
nicodr97 Aug 17, 2026
2c61ac4
feat: open interactive tool in new tab
nicodr97 Aug 18, 2026
991f0de
fix: don't check stage out file for interactive tools
nicodr97 Aug 18, 2026
9cb6f5a
refactor: remove legacy debug code
nicodr97 Aug 18, 2026
b118b4c
fix: interactive tool stop session
nicodr97 Aug 18, 2026
f0d471b
feat: synchronize interactive tool folder content
nicodr97 Aug 18, 2026
86dc5cd
fix: disable EGA files tab by default
nicodr97 Aug 18, 2026
2eb8e50
chore: remove legacy code
nicodr97 Aug 18, 2026
3beaa3c
fix: minor fixes
nicodr97 Aug 18, 2026
950b3de
chore: include production Vault files
nicodr97 Aug 19, 2026
46b38ec
chore: set lower cpus (slots) at SGE
nicodr97 Aug 19, 2026
8a9c9a4
feat: hide linked accounts
nicodr97 Aug 19, 2026
bba759c
fix: some mail functions
nicodr97 Aug 19, 2026
14743d0
feat: show html files properly
nicodr97 Aug 19, 2026
e693c80
fix: job parameters and check tool already running
nicodr97 Aug 19, 2026
6a93ca4
feat: restablish intermediate page for interactive session wait
nicodr97 Aug 19, 2026
8a72fb4
feat: add actions logs collection and store some test info
nicodr97 Aug 19, 2026
5b656aa
feat: include persistent logs for job execution
nicodr97 Aug 19, 2026
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8 changes: 4 additions & 4 deletions front_end/openVRE/apache/check_tool_access.lua
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Original file line number Diff line number Diff line change
Expand Up @@ -6,14 +6,14 @@ function check_access(r)
local tool_segment = r.uri:match("^/interactive%-tool/([^/]+)")
if not tool_segment then
r:err("check_tool_access: no tool_segment found, passing through")
return 200
return apache2.OK
end
r:err("check_tool_access: tool_segment=" .. tool_segment)

local project_id = tool_segment:match("__PROJ.+$")
if not project_id then
r:err("check_tool_access: could not parse project_id from: " .. tool_segment)
return 403
return apache2.HTTP_FORBIDDEN
end
r:err("check_tool_access: project_id=" .. project_id)

Expand All @@ -30,9 +30,9 @@ function check_access(r)
r:err("check_tool_access: http status=" .. tostring(status))

if status == "200" then
return 200
return apache2.OK
else
r:err("check_tool_access: denied user=" .. user .. " project=" .. project_id)
return 403
return apache2.HTTP_FORBIDDEN
end
end
2 changes: 2 additions & 0 deletions front_end/openVRE/apache/server.conf
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Expand Up @@ -39,6 +39,8 @@
Require valid-user
</LocationMatch>

RewriteEngine on

RewriteRule ^/interactive-tool/([^/]+)/?(.*) http://$1:8787/$2 [P,L]

ErrorLog /var/log/apache/vre-error.log
Expand Down
1 change: 1 addition & 0 deletions front_end/openVRE/config/globals.inc.php.sample
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Original file line number Diff line number Diff line change
Expand Up @@ -43,6 +43,7 @@ $GLOBALS['logs_datetime'] = "dd.M.Y HH:mm:ss";

// Interactive tools
$GLOBALS['NETWORK_IP'] = "172.17.0.1"; # default host ip for docker
$GLOBALS['NETWORK_NAME'] = getenv('NETWORK_NAME');
$GLOBALS['interactive_range_start_port'] = 9001;
$GLOBALS['max_parallel_independent_tools'] = 10;
$GLOBALS['toolsPath'] = "/tools/";
Expand Down
4 changes: 2 additions & 2 deletions front_end/openVRE/public/assets/pages/scripts/actions-home.js
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Original file line number Diff line number Diff line change
Expand Up @@ -698,7 +698,7 @@ function closeModalTool() {
}


function goInteractiveTool(toolContainerName) {
location.href = "interactive-tool/" + toolContainerName + "/";
function goInteractiveTool(id) {
window.open('launch-interactive/?pid=' + id, "_blank");
}

146 changes: 75 additions & 71 deletions front_end/openVRE/public/getdata/uploadForm.php
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@

require __DIR__ . "/../../config/bootstrap.php";
redirectOutside();
$includeEgaFiles = false;

?>

Expand Down Expand Up @@ -51,7 +52,8 @@
them over the area below. You can also
<a href="javascript:$('.nav-tabs a[href=\'#create_file\']').click();">create a text file</a> from
a sequence or <a href="javascript:$('.nav-tabs a[href=\'#load_from_url\']').click();">load a file</a>
to your workspace from an external URL.</p>
to your workspace from an external URL.
</p>

</div>

Expand Down Expand Up @@ -79,9 +81,9 @@
<li class="uppercase">
<a href="#load_from_url" data-toggle="tab"> Load file from an external URL </a>
</li>
<li class="uppercase">
<!-- <li class="uppercase">
<a href="#load_from_ega" data-toggle="tab"> Load file from EGA </a>
</li>
</li> -->
</ul>
<div class="tab-content">
<div class="tab-pane active" id="upload_files">
Expand Down Expand Up @@ -127,7 +129,7 @@

if (isset($_SESSION['errorData'])) {
if (isset($_SESSION['errorData']['Info'])) {
?>
?>
<div class="alert alert-info">
<?php
} else {
Expand All @@ -142,91 +144,93 @@
}
unset($_SESSION['errorData']);
?>
</div>
</div>

<?php } ?>
<?php } ?>

<form class="down-form" action="javascript:;" method="post">
<div class="alert alert-danger display-hide" id="alert-down-form2">
Error downloading file, please, try again.
</div>
<div class="form-group">
<label>External URL *</label>

<div class="input-icon">
<i class="fa-li fa fa-cloud-download font-green" style="line-height:10px;"></i>
<input type="url" class="form-control" id="dfUrl" name="url" placeholder="http://public/path/to/file">
<input type="hidden" id="dfUploadType" name="uploadType" value="url" />
<br />
<p style="font-size:0.9em"><i>For password-protected sites, include the credentials in the URL. Format: [protocol]://[username]:[password]@server/path/to/file.<br />Notice that strange characters should be UTF-8 codified.</i></p>
<form class="down-form" action="javascript:;" method="post">
<div class="alert alert-danger display-hide" id="alert-down-form2">
Error downloading file, please, try again.
</div>
<button class="btn green" type="submit" id="btn-down-remote" style="margin-top:20px;">SEND DATA</button>
<div class="form-group">
<label>External URL *</label>

<div class="input-icon">
<i class="fa-li fa fa-cloud-download font-green" style="line-height:10px;"></i>
<input type="url" class="form-control" id="dfUrl" name="url" placeholder="http://public/path/to/file">
<input type="hidden" id="dfUploadType" name="uploadType" value="url" />
<br />
<p style="font-size:0.9em"><i>For password-protected sites, include the credentials in the URL. Format: [protocol]://[username]:[password]@server/path/to/file.<br />Notice that strange characters should be UTF-8 codified.</i></p>
</div>
<button class="btn green" type="submit" id="btn-down-remote" style="margin-top:20px;">SEND DATA</button>

<div class="progress-bar-down progress display-hide" style="margin-top:20px;">
<div class="progress-bar progress-bar-success" role="progressbar" aria-valuenow="20" aria-valuemin="0" aria-valuemax="100" style="width:0%;">
<span class="sr-only"> 20% Complete </span>
<div class="progress-bar-down progress display-hide" style="margin-top:20px;">
<div class="progress-bar progress-bar-success" role="progressbar" aria-valuenow="20" aria-valuemin="0" aria-valuemax="100" style="width:0%;">
<span class="sr-only"> 20% Complete </span>
</div>
</div>

</div>

</form>
</div>
<?php if ($includeEgaFiles): ?>
<div class="tab-pane" id="load_from_ega">
<p> Load data from EGA </p>
<?php
try {
require 'fetchEgaDatasets.php';
} catch (Exception $e) {
$_SESSION['errorData']['Error']['EGA'] = 'Failed to fetch EGA datasets: ' . $e->getMessage();
}

</form>
</div>
<div class="tab-pane" id="load_from_ega">
<p> Load data from EGA </p>
<?php
try {
require 'fetchEgaDatasets.php';
} catch (Exception $e) {
$_SESSION['errorData']['Error']['EGA'] = 'Failed to fetch EGA datasets: ' . $e->getMessage();
}

try {
require 'egaFiles.php';
} catch (Exception $e) {
$_SESSION['errorData']['Error']['EGA'] = 'Failed to fetch EGA files: ' . $e->getMessage();
}

?>

<?php

if (isset($_SESSION['errorData']) && isset($_SESSION['errorData']['Error']) && isset($_SESSION['errorData']['Error']['EGA'])) {
if (isset($_SESSION['errorData']['Info'])) {
?>
<div class="alert alert-info">
<?php
} else {
?>
<div class="alert alert-warning">
<?php } ?>
<?php foreach ($_SESSION['errorData'] as $subTitle => $txts) {
print "$subTitle<br/>";
foreach ($txts as $txt) {
print "<div style=\"margin-left:20px;\">$txt</div>";
try {
require 'egaFiles.php';
} catch (Exception $e) {
$_SESSION['errorData']['Error']['EGA'] = 'Failed to fetch EGA files: ' . $e->getMessage();
}
}
unset($_SESSION['errorData']);
?>
</div>

<?php } ?>
?>

<?php

if (isset($_SESSION['errorData']) && isset($_SESSION['errorData']['Error']) && isset($_SESSION['errorData']['Error']['EGA'])) {
if (isset($_SESSION['errorData']['Info'])) {
?>
<div class="alert alert-info">
<?php
} else {
?>
<div class="alert alert-warning">
<?php } ?>
<?php foreach ($_SESSION['errorData'] as $subTitle => $txts) {
print "$subTitle<br/>";
foreach ($txts as $txt) {
print "<div style=\"margin-left:20px;\">$txt</div>";
}
}
unset($_SESSION['errorData']);
?>
</div>

<?php } ?>
</div>
</div>
<?php endif; ?>
</div>
</div>
<!-- END TAB PORTLET-->
</div>
</div>
<!-- END TAB PORTLET-->
</div>
<!-- END CONTENT BODY -->
</div>
</div>
<!-- END CONTENT BODY -->
</div>
<!-- END CONTENT -->
<!-- END CONTENT -->


<?php
<?php

require "../htmlib/footer.inc.php";
require "../htmlib/js.inc.php";
require "../htmlib/footer.inc.php";
require "../htmlib/js.inc.php";

?>
?>
36 changes: 11 additions & 25 deletions front_end/openVRE/public/help/general.php
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Expand Up @@ -36,38 +36,24 @@
</div>
<!-- END PAGE BAR -->
<!-- BEGIN PAGE TITLE-->
<h1 class="page-title">What is the euCanSHare Virtual Research Envirnoment (VRE)?</h1>
<h1 class="page-title">What is the Virtual Research Envirnoment (VRE)?</h1>
<!-- END PAGE TITLE-->
<!-- END PAGE HEADER-->

<div class="note note-danger" style="background-color: #F3D8DD;border-color:#e4032e;">
<h4 class="block">
The Disc4All VRE is a computational platform designed for Data Sharing, Intervertevral Disc Degeneration Analysis, Machine Learning and Bioinformatics Data Analysis.
<h4 class="block">
The VRE is a computational platform designed for Data Sharing, Intervertevral Disc Degeneration Analysis, Machine Learning and Bioinformatics Data Analysis.
</h4>
</div>

<p><img src="https://disc4all.upf.edu/wp-content/uploads/2021/09/Interactions-consortium.png" style="margin:0 350px;width:50%;max-width:100%;" /></p>

<p>
The Disc4All VRE is being developed so as to cater for the needs of the scientific community, especially clinical researchers who need an objective and quantitative way to analyse their data in an unbiased way and make predictions with state-of-the art techniques. Its main objectives are:

<p>
<ul>
<li>The democratization of the use of Machine Learning methods by the whole community by providing a easy-to-use and high-level interface with detailed documentation.</li>
<li>To establish a reproducible and publicly available analysis pipeline to enhance repeatability of research results.</li>
</ul>
</p>
<p>
The main components of the Disc4All VRE are:
<ul>
<li>Tools for data quality control</li>
<li>The MRI Spine Image Analyzer consisting of various tools, such as Segmentation Tools and Radiomics Analysis Tools, all implemented into a single workflow.</li>
<li>Disagnosis Workflow Toolbox</li>
<li>Bioinformatics Toolbox</li>
</ul>

</p>
The VRE is being developed so as to cater for the needs of the scientific community, especially clinical researchers who need an objective and quantitative way to analyse their data in an unbiased way and make predictions with state-of-the art techniques. Its main objectives are:

<p>
<ul>
<li>The democratization of the use of Machine Learning methods by the whole community by providing a easy-to-use and high-level interface with detailed documentation.</li>
<li>To establish a reproducible and publicly available analysis pipeline to enhance repeatability of research results.</li>
</ul>
</p>
</div>
<!-- END CONTENT BODY -->
</div>
Expand All @@ -78,4 +64,4 @@
require "../htmlib/footer.inc.php";
require "../htmlib/js.inc.php";

?>
?>
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