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466e55d
feat: do print sge logs when no job is running
nicodr97 Nov 28, 2025
198061a
chore: update monolog version
nicodr97 Nov 28, 2025
91f79c3
refactor: use boolean instead of 0/1
nicodr97 Dec 2, 2025
0a8c3df
feat: add logger to launch tool script and some other functions
nicodr97 Dec 3, 2025
738b321
refactor: delete unused file
nicodr97 Dec 3, 2025
fbe5f42
feat: set mongo version to v8.0 inside front_end image
nicodr97 Dec 3, 2025
61c9c81
refactor: remove unused variables and format
nicodr97 Dec 3, 2025
e4dfe1b
refactor: format and remove useless code
nicodr97 Dec 3, 2025
959c7e7
feat: set sge docker version to 26.1
nicodr97 Dec 3, 2025
d954ec8
feat: add logs and exceptions
nicodr97 Dec 3, 2025
ad36af6
fix: import of logger
nicodr97 Dec 4, 2025
208f103
refactor: separate get and check file id
nicodr97 Dec 4, 2025
4e06c3d
refactor: logs and errors
nicodr97 Dec 5, 2025
4091477
refactor: use lowercase for boolean constants
nicodr97 Dec 9, 2025
61b1416
refactor: use lowercase for 'null'
nicodr97 Dec 9, 2025
dbf50b1
refactor: include logs and exceptions and clean code
nicodr97 Dec 9, 2025
e39190d
refactor: logs, exceptions and old code
nicodr97 Dec 9, 2025
7fcf30e
refactor: formats and logs
nicodr97 Dec 9, 2025
7749c64
refactor: format, logs, exceptions and old code
nicodr97 Dec 10, 2025
c1f28a1
refactor: remove PMES and OEB code and some other log and error changes
nicodr97 Dec 10, 2025
b52774b
refactor: logs, exceptions and clean code
nicodr97 Dec 11, 2025
1804dd1
feat: remove current tool edition by admin
nicodr97 Dec 16, 2025
54775d4
feat: start removing old attributes from MUG
nicodr97 Dec 16, 2025
009b763
feat: change "file_type" to "format" and remove old genome edition code
nicodr97 Dec 16, 2025
592768f
feat: remove "sources" attribute from file metadata
nicodr97 Dec 17, 2025
67e7e99
feat: restore old file attributes conversion
nicodr97 Dec 17, 2025
47203dc
refactor: clean code and logs
nicodr97 Dec 17, 2025
ad6704d
refactor: clean error messages and logs
nicodr97 Jan 13, 2026
9a25c72
refactor: errors, logs and warnings
nicodr97 Jan 13, 2026
30da556
refactor: warnings and logs
nicodr97 Jan 13, 2026
ed84513
refactor: clean code and update logs
nicodr97 Jan 16, 2026
7377c41
fix: class autoload, error handling and minor fixes
nicodr97 Jan 19, 2026
53ee624
fix: wrong condition on sge submission
nicodr97 Jan 20, 2026
66f208a
fix: imports and some minor changes
nicodr97 Jan 20, 2026
0915270
fix: sge docker hostname issue
nicodr97 Jan 21, 2026
2240648
feature: replace default tool
nicodr97 Jan 23, 2026
bcd8096
fix: recover needed metadata on files and some missing parameters
nicodr97 Jan 23, 2026
c83932b
feature: default validated files for internal tools
nicodr97 Jan 23, 2026
74fca0a
fix: uncomment code
nicodr97 Jan 23, 2026
2a2d3ff
chore: add mock tool files to build image
nicodr97 Jan 26, 2026
3b1e2b9
fix: metadata attributes 'format' and 'path'
nicodr97 Jan 28, 2026
61d4857
feature: include login logs and use oauth2 token object instead of array
nicodr97 Jan 30, 2026
7dec118
fix: new user login
nicodr97 Jan 30, 2026
f34d987
fix: job execution progress and add logs
nicodr97 Jan 30, 2026
14ffca9
feature: remove empty menus
nicodr97 Feb 2, 2026
f37ce66
refactor: reuse isset to avoid warnings
nicodr97 Feb 2, 2026
e0985f8
fix: avoid warning on session headers
nicodr97 Feb 2, 2026
fa517bf
refactor: Vault class, functions and variables
nicodr97 Feb 2, 2026
f83a6b7
refactor: separate vault Client (stateless) and Vault token provider
nicodr97 Feb 3, 2026
a343adf
fix: update secrets id on existing users
nicodr97 Feb 4, 2026
81f462b
refactor: replace function with existing one
nicodr97 Feb 4, 2026
bdaa363
fix: hide unavailable links
nicodr97 Feb 4, 2026
0172674
refactor: make Vault data retrieval generic and refactor EGA datasets…
nicodr97 Feb 4, 2026
f9be6e8
refactor: make Vault upload generic and rename EGA to uppercase
nicodr97 Feb 4, 2026
63cc2d1
chore: remove template file
nicodr97 Feb 4, 2026
b1d3c55
feat: add .gitignore files for tools folder
nicodr97 Feb 4, 2026
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2 changes: 2 additions & 0 deletions docker-compose.yml
Original file line number Diff line number Diff line change
Expand Up @@ -138,6 +138,8 @@ services:
- net_vre
ports:
- "6444:6444"
extra_hosts:
- "front_end:172.21.0.14"
restart: on-failure:2

volumes:
Expand Down
6 changes: 3 additions & 3 deletions front_end/Dockerfile
Original file line number Diff line number Diff line change
Expand Up @@ -24,9 +24,9 @@ RUN apt-get update && apt-get install -y libmcrypt-dev \
&& docker-php-ext-configure gd --with-freetype=/usr/include/ --with-jpeg=/usr/include/ \
&& docker-php-ext-install gd

RUN apt-get update && apt-get install gnupg curl
RUN curl -fsSL https://www.mongodb.org/static/pgp/server-7.0.asc |gpg -o /usr/share/keyrings/mongodb-server-7.0.gpg --dearmor
RUN echo "deb [ signed-by=/usr/share/keyrings/mongodb-server-7.0.gpg ] http://repo.mongodb.org/apt/debian bookworm/mongodb-org/7.0 main" | tee /etc/apt/sources.list.d/mongodb-org-7.0.list
RUN apt-get update && apt-get install -y gnupg curl
RUN curl -fsSL https://www.mongodb.org/static/pgp/server-8.0.asc |gpg -o /usr/share/keyrings/mongodb-server-8.0.gpg --dearmor
RUN echo "deb [ signed-by=/usr/share/keyrings/mongodb-server-8.0.gpg ] http://repo.mongodb.org/apt/debian bookworm/mongodb-org/8.0 main" | tee /etc/apt/sources.list.d/mongodb-org-8.0.list
RUN apt-get update
RUN apt-get install -y mongodb-org

Expand Down
10 changes: 4 additions & 6 deletions front_end/openVRE/composer.json
Original file line number Diff line number Diff line change
Expand Up @@ -3,12 +3,14 @@
"ext-openssl": "*",
"auth0/auth0-php": "^8.0",
"chadicus/slim-oauth2": "^3.1",
"erusev/parsedown": "^1.7",
"firebase/php-jwt": "^6.11",
"guzzlehttp/guzzle": "*",
"justinrainbow/json-schema": "^5.2",
"league/oauth2-google": "^2.0",
"mongodb/mongodb": "^2.1",
"monolog/monolog": "^2.5",
"monolog/monolog": "^3.9",
"phpmailer/phpmailer": "^7.0.0",
"phpseclib/phpseclib": "~3.0",
"slim/extras": "*",
"slim/http": "^1.3.0",
Expand All @@ -20,11 +22,7 @@
},
"autoload": {
"psr-4": {
"App\\": "app/",
"App\\Controllers\\": "app/controllers",
"App\\Models\\": "app/models",
"App\\Middleware\\": "app/Middleware",
"App\\Handlers\\": "app/Handlers"
"OpenVRE\\": "public/phplib/classes/"
}
},
"autoload-dev": {
Expand Down
41 changes: 31 additions & 10 deletions front_end/openVRE/config/bootstrap.php
Original file line number Diff line number Diff line change
@@ -1,21 +1,42 @@
<?php

// import vendor libs
require dirname(__FILE__) . "/../vendor/autoload.php";

use OpenVRE\LoggerFactory;

set_exception_handler(function (Throwable $e) {
#$_SESSION['errorData']['Error'][] = $e->getMessage();
$logger = LoggerFactory::getLogger("Bootstrap interface");
$logger->error($e->getTraceAsString());
$logger->error(sprintf(
"%s in %s:%d",
$e->getMessage(),
$e->getFile(),
$e->getLine()
));

http_response_code(500);
echo "<!DOCTYPE html><html><body>";
echo "<h1>Application error</h1>";
echo "<div class='alert alert-danger'>"
. htmlspecialchars($e->getMessage(), ENT_QUOTES, 'UTF-8')
. "</div>";
echo "</body></html>";

exit;
});

// set up app settings
require dirname(__FILE__)."/../config/globals.inc.php";
require dirname(__FILE__) . "/../config/globals.inc.php";

// import vendor libs
require dirname(__FILE__)."/../vendor/autoload.php";
require dirname(__FILE__) . "/../vendor/autoload.php";

// import local classes
foreach(glob(dirname(__FILE__)."/../public/phplib/classes/*.php") as $lib){
require $lib;
}
// import local libs
foreach(glob(dirname(__FILE__)."/../public/phplib/*.php") as $lib){
foreach (glob(dirname(__FILE__) . "/../public/phplib/*.php") as $lib) {
require $lib;
}

// initialize session
require dirname(__FILE__)."/../public/phplib/session.inc";

?>
require dirname(__FILE__) . "/../public/phplib/session.inc";
39 changes: 1 addition & 38 deletions front_end/openVRE/config/globals.inc.php.sample
Original file line number Diff line number Diff line change
Expand Up @@ -157,44 +157,7 @@ $GLOBALS['clouds'] = Array(
"pubDir_virtual" => $GLOBALS['pubDir'],
"dataDir_host" => $GLOBALS["host_path"].$GLOBALS['dataDir'],
"pubDir_host" => $GLOBALS["host_path"].$GLOBALS['pubDir'],
"PMESserver_domain" => "pmes.mydomain.com",
"PMESserver_port" => "80",
"PMESserver_address"=> "/",
"imageTypes" => array(), // list of cloud OCCI templates indexed by RAM (GB)
"auth" => array("required" => False)
),
'my_remote_2' => array(
"http_host" => "www.mydomain2.com", // used in getCurrentCloud
"dataDir_fs" => "/NFS/export/path2/userdata/", // export path for NFS server
"pubDir_fs" => "/NFS/export/path2/public/", // export path for NFS server
"dataDir_virtual" => "/shared/path/for/userdata",
"pubDir_virtual" => "/shared/path/for/public",
"PMESserver_domain" => "pmes.mydomain2.com",
"PMESserver_port" => "8080",
"PMESserver_address"=> "/",
"imageTypes" => array( // list of cloud OCCI templates indexed by RAM (GB)
"2" => array(
"1" => array("id" => "small", "disk" => null, "name" => "small"),
"8" => array("id" => "large-small", "disk" => null, "name" => "large-small"),
"16" => array("id" => "extra_large-small", "disk" => null, "name" => "large-small")
),
"4" => array(
"2" => array("id" => "medium", "disk" => null, "name" => "medium"),
"4" => array("id" => "medium-medium", "disk" => null, "name" => "medium-medium"),
"8" => array("id" => "large-medium", "disk" => null, "name" => "large-medium"),
"16" => array("id" => "extra_large-medium", "disk" => null, "name" => "extra_large-medium")
)
),
"auth" => array(
"required" => True,
"OS_NO_CACHE" => "True",
"OS_CLOUDNAME" => "overcloud",
"OS_AUTH_URL" => "https://extcloud05.ebi.ac.uk:13000/v2.0",
"NOVA_VERSION" => "1.2",
"COMPUTE_API_VERSION" => "1.2",
"OS_USERNAME" => "username@mail.es",
"OS_PASSWORD" => "s3cr3t",
"OS_TENANT_NAME" => "tenancy_name"
)
)
)
);
Original file line number Diff line number Diff line change
@@ -1,8 +1,7 @@
[
{
"file_path": "uploads",
"path": "uploads",
"type":"dir",
"sources": [0],
"meta_data": {
"expiration":-1,
"description": "Uploaded personal data",
Expand Down
Original file line number Diff line number Diff line change
@@ -1,12 +1,9 @@
[
{
"file_path": "uploads/README.md",
"path": "uploads/README.md",
"data_type": "configuration_file",
"file_type": "TXT",
"format": "TXT",
"type": "file",
"sources": [
0
],
"meta_data": {
"expiration": -1,
"description": "my first VRE file"
Expand Down
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