diff --git a/front_end/openVRE/config/bootstrap.php b/front_end/openVRE/config/bootstrap.php index e2863a5b..12972244 100644 --- a/front_end/openVRE/config/bootstrap.php +++ b/front_end/openVRE/config/bootstrap.php @@ -6,9 +6,6 @@ // import vendor libs require dirname(__FILE__)."/../vendor/autoload.php"; -// initialize session -require dirname(__FILE__)."/../public/phplib/session.inc"; - // import local classes foreach(glob(dirname(__FILE__)."/../public/phplib/classes/*.php") as $lib){ require $lib; @@ -18,4 +15,7 @@ require $lib; } +// initialize session +require dirname(__FILE__)."/../public/phplib/session.inc"; + ?> diff --git a/front_end/openVRE/config/globals.inc.php.sample b/front_end/openVRE/config/globals.inc.php.sample index 83cf18cc..caebd769 100644 --- a/front_end/openVRE/config/globals.inc.php.sample +++ b/front_end/openVRE/config/globals.inc.php.sample @@ -34,7 +34,7 @@ $GLOBALS['shared'] = "/shared_data/"; // VRE data directory $GLOBALS['logFile'] = $GLOBALS['root']."/logs/application.log"; // Log file path $GLOBALS['dataDir'] = $GLOBALS['shared']."userdata/"; // User data directory $GLOBALS['pubDir'] = $GLOBALS['shared']."public/"; // Public data directory -$GLOBALS['sampleData'] = "/var/www/html/openVRE/data"; +$GLOBALS['sampleDataPath'] = "/var/www/html/openVRE/data/sampleData/"; // Sample data directory $GLOBALS['sampleData_default'] = "basic"; // Default workspace's dataset entry // File manager config @@ -78,12 +78,16 @@ $GLOBALS['adminToken'] = $GLOBALS['authServer']."/realms/master/prot $GLOBALS['adminRealm'] = $GLOBALS['authServer']."/admin/realms/".$GLOBALS['authRealm']; // admin keycloak users // Vault integration and roles -$GLOBALS['vaultUrl'] = 'https://localhost:8200'; +$GLOBALS['vaultUrl'] = 'http://localhost:8200'; $GLOBALS['vaultToken'] = 'root'; //$jwtToken = $_SESSION['User']['JWT']; $GLOBALS['vaultRolename'] = 'demo'; $GLOBALS['secretPath'] = 'secret/mysecret/data/'; +// EGA +$GLOBALS['EGA_METADATA_TOKEN_ENDPOINT'] = 'https://idp.ega-archive.org/realms/EGA/protocol/openid-connect/token'; +$GLOBALS['EGA_METADATA_API'] = 'https://metadata.ega-archive.org'; + // Google Analytics #$GLOBALS['GA_TAG']; // if used, set the id for: https://www.googletagmanager.com/gtag/js?id= diff --git a/front_end/openVRE/data/basic/.sample_metadata.json b/front_end/openVRE/data/sampleData/basic/.sample_metadata.json similarity index 100% rename from front_end/openVRE/data/basic/.sample_metadata.json rename to front_end/openVRE/data/sampleData/basic/.sample_metadata.json diff --git a/front_end/openVRE/data/basic/uploads/.sample_metadata.json b/front_end/openVRE/data/sampleData/basic/uploads/.sample_metadata.json similarity index 100% rename from front_end/openVRE/data/basic/uploads/.sample_metadata.json rename to front_end/openVRE/data/sampleData/basic/uploads/.sample_metadata.json diff --git a/front_end/openVRE/data/basic/uploads/README.md b/front_end/openVRE/data/sampleData/basic/uploads/README.md similarity index 100% rename from front_end/openVRE/data/basic/uploads/README.md rename to front_end/openVRE/data/sampleData/basic/uploads/README.md diff --git a/front_end/openVRE/public/admin/adminTools.php b/front_end/openVRE/public/admin/adminTools.php index d9fd965c..0c78abe5 100644 --- a/front_end/openVRE/public/admin/adminTools.php +++ b/front_end/openVRE/public/admin/adminTools.php @@ -1,69 +1,67 @@ find(array()); - -}elseif ($_SESSION['User']['Type'] == 1){ - if ($_SESSION['User']['ToolsDev']){ +if ($_SESSION['User']['Type'] == UserType::Admin->value) { + // do query + $result = $GLOBALS['toolsCol']->find(array()); +} elseif ($_SESSION['User']['Type'] == UserType::ToolDev->value) { + if ($_SESSION['User']['ToolsDev']) { // do query $result = $GLOBALS['toolsCol']->find(array("_id" => array('$in' => $_SESSION['User']['ToolsDev']))); // prepare stats filter $stats_filter = array("toolId" => array('$in' => $_SESSION['User']['ToolsDev'])); - - }else{ + } else { // return error - $_SESSION['errorData']['Error'][]="Sorry, your account has no tool ownership. Sorry, cannot adminstrate them."; + $_SESSION['errorData']['Error'][] = "Sorry, your account has no tool ownership. Sorry, cannot adminstrate them."; // do dump query $result = $GLOBALS['toolsCol']->find(array("_id" => "force_empty")); // prepare dump stats filter $stats_filter = array("force" => "empty"); } -}else{ - redirect($GLOBALS['URL']); +} else { + redirect($GLOBALS['URL']); } // format query result -foreach (array_values(iterator_to_array($result)) as $v){ - $toolId = $v['_id']; - $tools[$toolId]['json'] = $v; - //$tools[$toolId]['json']["owners"] = getToolDev_fromTool($toolId); - if ( $tools[$toolId]['json']['owner']['user'] ){ - $tools[$toolId]['json']["owners"] = array($tools[$toolId]['json']['owner']['user']); - }else{ - $tools[$toolId]['json']["owners"] = array($tools[$toolId]['json']['owner']['author']); - } +foreach (array_values(iterator_to_array($result)) as $v) { + $toolId = $v['_id']; + $tools[$toolId]['json'] = $v; + if ($tools[$toolId]['json']['owner']['user']) { + $tools[$toolId]['json']["owners"] = array($tools[$toolId]['json']['owner']['user']); + } else { + $tools[$toolId]['json']["owners"] = array($tools[$toolId]['json']['owner']['author']); + } } // get statistics -if ($_REQUEST['tools']){ - if (! is_array($_REQUEST['tools'])){ $_REQUEST['tools'] = array($_REQUEST['tools']); } - $stats_filter = array("toolId" => array('$in' => $_REQUEST['tools'])); +if ($_REQUEST['tools']) { + if (! is_array($_REQUEST['tools'])) { + $_REQUEST['tools'] = array($_REQUEST['tools']); + } + $stats_filter = array("toolId" => array('$in' => $_REQUEST['tools'])); } $jobs = aggregateJobLogs($stats_filter); -$stats = getStatsFromJobLogs($jobs,array_keys($tools)); +$stats = getStatsFromJobLogs($jobs, array_keys($tools)); //// if export=true, generate CSV and exit -if ($_REQUEST['export'] == 1){ +if ($_REQUEST['export'] == 1) { // set CSV name - $filename='VRE_jobstats_'.date('m-d-Y').".csv"; + $filename = 'VRE_jobstats_' . date('m-d-Y') . ".csv"; // print job entry per line ob_start(); @@ -74,17 +72,16 @@ header('Cache-Control: must-revalidate, post-check=0, pre-check=0'); header('Cache-Control: private', false); header('Content-Type: text/csv'); - header('Content-Disposition: attachment;filename=' . $filename); + header('Content-Disposition: attachment;filename=' . $filename); - printCSVJobLogs($jobs,'php://output'); + printCSVJobLogs($jobs, 'php://output'); ob_flush(); die(0); - } - + //// if no export, print logs html page @@ -95,155 +92,160 @@ -
- - - - - - -
- -
- - -
-
    -
  • - Admin - -
    • -
  • - My installed Tools -
    • -
-
- - -

My Tools Administration - configure & test -
-
+
+ + + + + + +
+ +
+ + +
+
    +
  • + Admin + +
    • +
  • + My installed Tools +
    • +
+
+ + +

My Tools Administration + configure & test +
+
Download Statistics -
-

- - -
-
- - -
- -
- - - $txts){ - print "$subTitle
"; - foreach($txts as $txt){ - print "
$txt
"; - } - } - unset($_SESSION['errorData']); - ?> -
- -
-
- -
-
- -
- -
- - - - + + + + +
+
+ + +
+ +
+ + + $txts) { + print "$subTitle
"; + foreach ($txts as $txt) { + print "
$txt
"; + } + } + unset($_SESSION['errorData']); + ?> +
+ +
+
+ +
+
+ +
+ +
+ + +
+ + + + + + + + + + + $v) { + ?> - - - - - - - - - $v){ - ?> - - - - - - - - +

Download statistics

+ +
    +
    • +
+ + + + - -
Tool IdStatusOwner/sTool specificationStatistics
Tool IdStatusOwner/sTool specificationStatistics
Internal'; - } else { - // allow update status - if($_SESSION['User']['Type'] == 0 || ($_SESSION["User"]["Type"] == 1 && in_array($toolId,$_SESSION['User']['ToolsDev']))){ - - echo ' '; - } - // show status - switch($v["json"]["status"]){ - case 0: echo ' '.$GLOBALS['tool_status'][$v["json"]["status"]].' ';break; - case 1: echo ' '.$GLOBALS['tool_status'][$v["json"]["status"]].' ';break; - case 2: echo ' '.$GLOBALS['tool_status'][$v["json"]["status"]].' ';break; - case 3: echo ' '.$GLOBALS['tool_status'][$v["json"]["status"]].'';break; - } - - } - ?> - - ", $v["json"]["owners"]); ?> - - View JSON - - -
    -
    • -
    • -
    • -
    • -
- -

Download statistics

- -
    -
    • -
- -
-
+ + +
@@ -254,14 +256,14 @@
-