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getMetaWS.php
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getMetaWS.php
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<?php
require __DIR__."/../../config/bootstrap.php";
redirectOutside();
$asRoot = checkAdmin();
if($_REQUEST["type"] != 2) {
// EXTRACT FILE METADATA FROM DMP FILE
$mt = getGSFile_fromId($_REQUEST["id"],"",$asRoot);
$tool = getTool_fromId($mt["tool"],1);
}else{
// EXTRACT JOB METADATA FROM USER JOBS
$login = ($_REQUEST['user']?$_REQUEST['user']:$_SESSION['User']['_id']);
$job = getUserJobPid($login,$_REQUEST["id"]);
$mt = $job[$_REQUEST["id"]];
$job_path = getAttr_fromGSFileId($mt["_id"],"path",$asRoot);
if ($job_path){
$mt["path"]=$job_path;
}
}
// check Metadata
if (!$mt){
print "Sorry, no metadata accessible for this resource";
exit(0);
}
?> <h3>Item Metadata</h3><?php
// File Project and Name
if($mt["path"] != "") {
$name_th = ((isset($mt['type']) && $mt['type']=="dir")? "Directory Name":"File Name");
$p = explode("/", $mt['path']);
$project_name="foo project";
if (isset($mt['project']) && isProject($mt['project'])){
$project = getProject($mt['project']);
$project_name = $project['name'];
}
?>
<table class="table table-striped table-bordered">
<tbody>
<tr>
<th><b><?php echo $name_th;?></b></th>
</tr>
<tr>
<td><?php print printFilePath_fromPath($mt['path'],$asRoot);?></td>
</tr>
</tbody>
</table>
<?php
}
// Description
if($mt["description"] != "") {
?>
<table class="table table-striped table-bordered">
<tbody><tr>
<th><b>Description </b></th>
</tr>
<tr>
<td><?php echo nl2br ($mt["description"]); ?></td>
</tr>
</tbody>
</table>
<?php
}
// Validated
if(!isset($mt["validated"]) || $mt["validated"]) {
$mt['validated'] = "TRUE";
}else{
$mt['validated'] = "FALSE";
}
if ($mt['validated'] == "FALSE"){
?>
<table class="table table-striped table-bordered">
<tbody><tr>
<th><b>Valid Metadata
<i class="icon-question tooltips" data-container="body" data-html="true" data-placement="right" data-original-title="<p align='left' style='margin:0'>This file has missing or incorrect metadata. Please, click 'Validate Metadata' and fill in the form.</p>"></i>
</b></th>
</tr>
<tr>
<td><?php echo nl2br ($mt["validated"]);?>
<?php if($mt["validated"] == "FALSE") { ?>
<a style="margin-left:10px;" href="getdata/editFile.php?fn[]=<?php echo $mt["_id"]; ?>" class="btn btn-xs green">Validate Metadata</a>
<?php } ?>
</td>
</tr>
</tbody>
</table>
<?php
}
// Data_type, file_type, and OTHER METADATA (for files)
if($_REQUEST["type"] == 1) {
// show data_type, file_type
$dt = $GLOBALS['dataTypesCol']->findOne(array('_id' => $mt["data_type"]));
// show taxon_id and assembly
if(!isset($mt["oeb_dataset_id"])){
$datasetId = "N/A";
}else{
$datasetId = $mt['oeb_dataset_id'];
}
if(!isset($mt["oeb_community_ids"])){
$community = "N/A";
}else{
$communities = getCommunities();
if (!is_array($mt['oeb_community_ids'])){$mt['oeb_community_ids'] = array($mt['oeb_community_ids']);}
foreach ($mt['oeb_community_ids'] as $comm){
if ( isset($communities[$comm]) ){
$community = '<a href="https://openebench.bsc.es/html/scientific/'.$comm.'" target="_blank">'.$communities[$comm]["acronym"].'</a> ';
}else{
$community = "$comm";
}
}
}
?>
<table class="table table-striped table-bordered">
<tbody>
<tr>
<th style="width:50%;"><b>Data Type</b></th>
<th><b>File Type</b></th>
</tr>
<tr>
<td><?php echo $dt["name"];if(!isset($dt["name"])) echo "N/A"; ?></td>
<td><?php echo $mt["format"]; if(!isset($mt["format"])) echo "N/A"; ?></td>
</tr>
</tbody>
</table>
<?php
if(isset($mt["paired"]) || isset($mt["sorted"])){
?>
<table class="table table-striped table-bordered">
<tbody>
<tr>
<th style="width:50%;"><b>BAM type</b></th>
<th><b>BAM sorted</b></th>
</tr>
<tr>
<td><?php echo $mt["paired"]. " end"; ?></td>
<td><?php if($mt["sorted"] == "sorted"){echo "TRUE";}else{echo "FALSE";} ?></td>
</tr>
</tbody>
</table>
<?php
}
}
?>
<?php
// Expiration date
$expiration ="";
if (isset($mt['expiration'])){
if (is_object($mt['expiration'])){
$expiration_date = $mt['expiration']->toDateTime()->format('U');
$days2expire = intval(( $expiration_date - time() ) / (24 * 3600));
$mt['expiration'] = strftime('%Y/%m/%d %H:%M', $expiration_date);
if ($days2expire < 0 ){
$expiration = "File/folder has not expiration date";
}else{
if ($days2expire < 7)
$expiration = $mt['expiration'] ." ( in <span style=\"color:#b30000;font-weight:bold;\">".$days2expire."</span> days)";
else
$expiration =$mt['expiration'] ." ( in $days2expire days)";
}
}elseif ($mt['expiration'] == -1){
$expiration = "This file/folder never expires";
}else{
$expiration = $mt['expiration'];
}
}else{
$expiration = "File/folder has not expiration date";
}
?>
<table class="table table-striped table-bordered">
<tbody><tr>
<th><b>File expiration</b></th>
</tr>
<tr>
<td><?php echo $expiration; ?></td>
</tr>
</tbody>
</table>
<?php
// Tool
if(isset($mt["tool"]) ) {
?>
<table class="table table-striped table-bordered">
<tbody><tr>
<th><b>Generated by Tool</b></th>
</tr>
<tr>
<td><?php echo $tool["name"]; ?></td>
</tr>
</tbody>
</table>
<?php
}
// Input File/s or URL
if(isset($mt['input_files']) || $mt['source_url'] ) {
?>
<table class="table table-striped table-bordered">
<tbody>
<tr>
<th><b>File source/s</b></th>
</tr>
<tr>
<td><?php
if (count($mt['input_files'])){ ?>
<ul class="feeds" id="list-files-run-tools">
<?php
foreach ($mt['input_files'] as $input_name => $inps ){
if (!is_array($inps)){
$inps = array($inps);
}
foreach ( $inps as $inp ){
if ($inp == "0"){
print "Data externally loaded or created";
}else{
$path = getAttr_fromGSFileId($inp, 'path',$asRoot);
if ($path){
print printFilePath_fromPath($path,$asRoot);
}else{
print "Data provenance lost. Internally annotated as $inp";
}
}
}
}?>
</ul>
<?php } ?>
</td>
</tr>
<?php if(isset($mt['source_url']) ) { ?>
<tr>
<th><b>Source URL</b></th>
</tr>
<tr>
<td><a href="<?php echo $mt["source_url"];?>" target="_blank" ><?php echo $mt["source_url"];?></a></td>
</tr>
<?php } ?>
</tbody>
</table>
<?php
}
// Associated Files
if(isset($mt["associated_files"])) {
?>
<table class="table table-striped table-bordered">
<tbody><tr>
<th><b>Associated Files</b></th>
</tr>
<tr>
<td><?php
if (count($mt['associated_files'])){
?>
<ul class="feeds" id="list-files-run-tools">
<?php
foreach ($mt['associated_files'] as $inp){
$path = getAttr_fromGSFileId($inp, 'path',$asRoot);
print printFilePath_fromPath($path,$asRoot);
}
?>
</ul>
<?php
}else{
echo "";
}?>
</td>
</tr>
</tbody>
</table>
<?php
}
// Arguments
if(isset($mt["arguments"])) {
?>
<table class="table table-striped table-bordered">
<tbody><tr>
<th><b>Arguments</b></th>
</tr>
<tr>
<td>
<table class="table table-bordered">
<?php
foreach ($mt["arguments"] as $k => $v){
if (isset($tool['arguments'][$k]['description'])){
$k = $tool['arguments'][$k]['description'];
}
if(gettype($v) == "array") {
echo "<tr><td>$k</td><td>";
foreach($v as $val) echo $val."<br>";
echo "</td></tr>";
}elseif(gettype($v) == "boolean") {
$v = ($v?"TRUE":"FALSE");
echo "<tr><td>$k</td><td>$v</td></tr>";
} else {
echo "<tr><td>$k</td><td>$v</td></tr>";
}
}
?>
</table>
</td>
</tr>
</tbody>
</table>
<?php
}
// cloudName, memory and cpus
$mem = "";
$cpus = "";
if(!isset($mt['cloudName']) || strlen($mt["cloudName"]) == 0)
$mt['cloudName'] = $GLOBALS['cloud'];
if(isset($mt['imageType'])){
$mem = $mt['imageType']['memory'];
$cpus = $mt['imageType']['cpus'];
}elseif(isset($tool['infrastructure']['memory'])){
$mem = $tool['infrastructure']['memory'];
$cpus = $tool['infrastructure']['cpus'];
}
if($mt["cloudName"] != "") {
?>
<table class="table table-striped table-bordered">
<tbody><tr>
<th style="width:50%;"><b>Cloud infrastructure</b></th>
<th><b><?php if ($mem){echo "Resources";}?></b></th>
</tr>
<tr>
<td><?php echo $mt['cloudName'];?></td>
<td><?php if ($mem){echo "Cores: $cpus RAM: $mem GB";}?></td>
</tr>
</tbody>
</table>
<?php
}
?>
<!--- DATA ONLY FOR DEVEL USERS -->
<?php
if ($_SESSION['User']['Type']== 0 || $_SESSION['User']['Type'] == 1){
?>
<h3>Development data</h3>
<table class="table table-striped table-bordered">
<tbody><tr>
<th style="background-color: #e7ecf1;"><b>Metadata resource - <a href="http://multiscale-genomics.readthedocs.io/projects/mg-dm-api/rest.html" title="Data Management RESTful API" target="_blank">DMP</a></b></th>
</tr>
<tr>
<td>
<?php if ($_SESSION['User']['Type']== 0 || $_SESSION['User']['Type'] == 1){ ?>
<br/>
<pre style="font-size:0.7em;margin:10px 25px;"><?php echo json_encode($mt, JSON_PRETTY_PRINT);?></pre>
<?php } ?>
</td>
</tr>
</tbody>
</table>
<table class="table table-striped table-bordered">
<tbody><tr>
<th style="background-color: #e7ecf1;"><b>Resource location</b></th>
</tr>
<tr>
<td><?php
if ($mt['path']){echo $mt['path'];}else{echo "Job has no execution directory !!";}?>
</td>
</tr>
</tbody>
</table>
<?php
if($_REQUEST["type"] == 2) { ?>
<table class="table table-striped table-bordered">
<tbody><tr>
<th style="background-color: #e7ecf1;"><b>Job identifier</b></th>
</tr>
<tr>
<td><?php echo $_REQUEST['id'];?></td>
</tr>
</tbody>
</table>
<?php
}
}
?>
<!--- END OF DEVEL USERS -->
<!--- BLUE BUTTONS -->
<div id="meta-log">
<?php
// Log button
if(file_exists($mt['log_file'])) { ?>
<a href="workspace/workspace.php?op=openPlainFileFromPath&fnPath=<?php echo urlencode($mt['log_file']); ?>" class="btn green" target="_blank"><i class="fa fa-file-text-o"></i> VIEW LOG FILE </a>
<?php }else{ ?>
<a href="javascript:;" class="btn grey tooltips" data-container="body" data-html="true" data-placement="bottom" data-original-title="<p align='left' style='margin:0'>Fie not available</p>"><i class="fa fa-exclamation-triangle"></i> VIEW LOG FILE </a>
<?php }
// Devel buttons
if(($_SESSION['User']['Type'] == 0) || ($_SESSION['User']['Type'] == 1)) { ?>
<?php if(file_exists($mt['submission_file'])) { ?>
<a href="workspace/workspace.php?op=openPlainFileFromPath&fnPath=<?php echo urlencode($mt['submission_file']); ?>" class="btn green" target="_blank"><i class="fa fa-paper-plane"></i> VIEW SUBMIT FILE </a>
<?php }else{ ?>
<a href="javascript:;" class="btn grey tooltips" data-container="body" data-html="true" data-placement="bottom" data-original-title="<p align='left' style='margin:0'>Fie not available</p>"><i class="fa fa-exclamation-triangle"></i> VIEW SUBMIT FILE </a>
<?php } ?>
<?php if(file_exists($mt['config_file'])){ ?>
<a href="workspace/workspace.php?op=openPlainFileFromPath&fnPath=<?php echo urlencode($mt['config_file']); ?>" class="btn green" target="_blank"><i class="fa fa-cog"></i> VIEW CONFIG FILE </a>
<?php }elseif(file_exists($GLOBALS['dataDir'].$mt['path']."/".$GLOBALS['tool_config_file']) ) { ?>
<a href="workspace/workspace.php?op=openPlainFileFromPath&fnPath=<?php echo urlencode($mt['path']."/".$GLOBALS['tool_config_file']); ?>" class="btn green" target="_blank"><i class="fa fa-cog"></i> VIEW CONFIG FILE </a>
<?php }else{ ?>
<a href="javascript:;" class="btn grey tooltips" data-container="body" data-html="true" data-placement="bottom" data-original-title="<p align='left' style='margin:0'>Fie not available</p>"><i class="fa fa-exclamation-triangle"></i> VIEW CONFIG FILE </a>
<?php } ?>
<?php if(file_exists($mt['metadata_file']) ){ ?>
<a href="workspace/workspace.php?op=openPlainFileFromPath&fnPath=<?php echo urlencode($mt['metadata_file']); ?>" class="btn green" target="_blank"><i class="fa fa-tags"></i> VIEW META FILE </a>
<?php }elseif(file_exists($GLOBALS['dataDir'].$mt['path']."/".$GLOBALS['tool_metadata_file']) ) { ?>
<a href="workspace/workspace.php?op=openPlainFileFromPath&fnPath=<?php echo urlencode($mt['path']."/".$GLOBALS['tool_metadata_file']); ?>" class="btn green" target="_blank"><i class="fa fa-tags"></i> VIEW META FILE </a>
<?php }else{ ?>
<a href="javascript:;" class="btn grey tooltips" data-container="body" data-html="true" data-placement="bottom" data-original-title="<p align='left' style='margin:0'>Fie not available</p>"><i class="fa fa-exclamation-triangle"></i> VIEW META FILE </a>
<?php } ?>
<?php if(file_exists($mt['stageout_file']) ){ ?>
<a href="workspace/workspace.php?op=openPlainFileFromPath&fnPath=<?php echo urlencode($mt['stageout_file']); ?>" class="btn green" target="_blank"><i class="fa fa-line-chart"></i> VIEW RESULTS FILE </a>
<?php }elseif(file_exists($GLOBALS['dataDir'].$mt['path']."/".$GLOBALS['tool_stageout_file']) ) { ?>
<a href="workspace/workspace.php?op=openPlainFileFromPath&fnPath=<?php echo urlencode($mt['path']."/".$GLOBALS['tool_stageout_file']); ?>" class="btn green" target="_blank"><i class="fa fa-line-chart"></i> VIEW RESULTS FILE </a>
<?php }else{ ?>
<a href="javascript:;" class="btn grey tooltips" data-container="body" data-html="true" data-placement="bottom" data-original-title="<p align='left' style='margin:0'>Fie not available</p>"><i class="fa fa-exclamation-triangle"></i> VIEW RESULTS FILE </a>
<?php }
} ?>
</div>