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editFile.php
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<?php
require "../phplib/genlibraries.php";
redirectOutside();
?>
<?php require "../htmlib/header.inc.php"; ?>
<body class="page-header-fixed page-sidebar-closed-hide-logo page-content-white page-container-bg-solid page-sidebar-fixed">
<div class="page-wrapper">
<?php require "../htmlib/top.inc.php"; ?>
<?php require "../htmlib/menu.inc.php"; ?>
<!-- BEGIN CONTENT -->
<div class="page-content-wrapper">
<!-- BEGIN CONTENT BODY -->
<div class="page-content">
<!-- BEGIN PAGE HEADER-->
<!-- BEGIN PAGE BAR -->
<div class="page-bar">
<ul class="page-breadcrumb">
<li>
<a href="/home/">Home</a>
<i class="fa fa-circle"></i>
</li>
<li>
<span>Get Data</span>
<i class="fa fa-circle"></i>
</li>
<li>
<span>Edit File Metadata</span>
</li>
</ul>
</div>
<!-- END PAGE BAR -->
<!-- BEGIN PAGE TITLE-->
<h1 class="page-title"> Edit File
<small>edit file metadata</small>
</h1>
<!-- END PAGE TITLE-->
<!-- END PAGE HEADER-->
<?php
//recover REQUEST data if comming from failed form processing
//print "<br/>SESSION<br/>";
//var_dump($_SESSION);
/*if (isset($_REQUEST['requestID'])){
print "<br/>VARDUMP REQUEST INI<br/>";
var_dump($_REQUEST);
$requestID = $_REQUEST['requestID'];
print "<br/>RECOVERING from REQUEST[REQUEST_$requestID]<br/>";
$_REQUEST = $_SESSION["REQUEST_$requestID"];
print "<br/>VARDUMP REQUEST FIN<br/>";
var_dump($_REQUEST);
unset($_SESSION["REQUEST_$requestID"]);
}*/
//chek input files from REQUEST[fn]
$filesData=Array();
$filesMeta=Array();
if (!isset($_REQUEST['fn']) || !$_REQUEST['fn'] || !count($_REQUEST['fn']) ) {
$_SESSION['errorData']['Error'][]="No file selected. Please, select or upload a file to edit.";
// TODO: Go back to uploadForm.php?
}else{
if (!is_array($_REQUEST['fn'])){
$_REQUEST['fn']=Array($_REQUEST['fn']);
}
foreach ( $_REQUEST['fn'] as $idx => $v) {
$file = $_REQUEST['fn'][$idx];
$fileData = $GLOBALS['filesCol'] ->findOne(array('_id' => $file, 'owner' => $_SESSION['User']['id']));
$fileMeta = $GLOBALS['filesMetaCol']->findOne(array('_id' => $file));
if (empty($fileData)){
$_SESSION['errorData']['Error'][]="Problems while loading data. $file not found in the database.";
continue;
}else{
$filesData[$idx]=$fileData;
$filesMeta[$idx]=$fileMeta;
}
}
}
/*var_dump($filesData);
echo '<br><br>';
var_dump($filesMeta);*/
?>
<div class="row">
<div class="col-md-12">
<?php
$error_data = false;
if ($_SESSION['errorData']){
$error_data = true;
?>
<div class="alert alert-danger">
<?php
foreach($_SESSION['errorData'] as $subTitle=>$txts){
print "<strong>$subTitle</strong><br/>";
foreach($txts as $txt){
print "<div>$txt</div>";
}
}
unset($_SESSION['errorData']);
?>
</div>
<?php } ?>
<?php if (!$error_data){ ?>
<div class="mt-element-step">
<div class="row step-line">
<div class="mt-step-desc">
Add metadata to validate the file. Once the file has the <em>Validated</em> state, you will be able to use it in the workspace.
If you don't set the metadata at this moment, you can edit the file afterwards clicking the <em>Edit</em> button on the workspace table.
</div>
<div> </div>
</div>
</div>
<!--<form name="uploadFiles" id="uploadFiles" action="" method="post" enctype="multipart/form-data">
<input type="hidden" name="op" id="op" value="1">
<input type="hidden" id="base-url" value="<?php echo $GLOBALS['BASEURL']; ?>"/>-->
<div class="note note-info">
<div class="mt-radio-list" style="padding-bottom:0;">
<?php
$FN = $filesData[0]['_id'];
foreach ( $filesData as $idx => $v) {
$fn = $filesData[$idx]['_id'];
$fnPath = $filesData[$idx]['path'];
$validated = $filesMeta[$idx]['validated'];
//get file compression
//if (!isset($_REQUEST['compressed'][$idx])){
// $fileExtensionFN = strtoupper(pathinfo($fn,PATHINFO_EXTENSION));
// $fileExtensionFN = preg_replace('/_\d$/',"",$fileExtensionFN);
// if (in_array(".".$fileExtensionFN,Array(".BZ2",".GZ",".RAR",".ZIP",".TGZ",".TAR"))){
// $_REQUEST['compressed'][$idx]=1;
// }else{
// $_REQUEST['compressed'][$idx]=0;
// }
//}
$file = formatData($filesData[$idx]);
switch ($validated){
case '0':
$validationState ="NOT VALIDATED";
$classState = $GLOBALS['STATES_COLOR'][4];
break;
case '1':
$validationState ="VALIDATED";
$classState = $GLOBALS['STATES_COLOR'][2];
break;
case '2':
$validationState ="READY";
$classState = $GLOBALS['STATES_COLOR'][1];
break;
case '3':
$validationState ="PROCESSING";
$classState = $GLOBALS['STATES_COLOR'][3];
break;
default:
$validationState = "NOT VALIDATED";
$classState = $GLOBALS['STATES_COLOR'][4];
}
?>
<label class="mt-radio mt-radio-outline" style="padding-left:0; margin-bottom:0; cursor:default;">
<h4><?php echo basename($fnPath);?> •
<small>
<strong><?php echo $file['size'];?></strong>
<?php echo $file['mtime'];?></small>
• <span id="file<?php echo $idx; ?>-state" class="<?php echo $classState; ?> file-state"><?php echo $validationState;?></span>
</h4>
<input type="hidden" name="fn[]" id='fn' value="<?php echo $fn;?>"/>
<!--<span></span>-->
</label>
<?php } ?>
</div>
</div>
<?php
//TODO add $defs as global like reference genomes?¿
//metadata default values
/*$defs = Array(
//general
'format' => 'UNK',
'description'=> "",
'compressed' => 0,
'validated' => 0,
//specific for aligned coords (BW, GFF, FASTQ aligned, etc..)
'refGenome' => "",
//specific for BAM
'paired' => 'paired',
'sorted' => TRUE,
);*/
//extract or guess file formats
foreach ($filesData as $idx => $v ) {
$fn = $filesData[$idx]['_id'];
$fileExtension = "";
if (isset($_REQUEST['format']) && isset($_REQUEST['format'][$idx]) && $_REQUEST['format'][$idx]){
$fileExtension=$_REQUEST['format'][$idx];
}elseif (isset($filesMeta[$idx]['format']) && $filesMeta[$idx]['format']){
$fileExtension=$filesMeta[$idx]['format'];
}elseif(isset($filesData[$idx]['_id'])){
$fnPath = $filesData[$idx]['path'];
list($fileExtension,$compressionType) = getFileExtension($fnPath);
if ($compressionType){
$_REQUEST['compressed'][$idx]=1;
}
/*
$fileInfo = pathinfo($fnPath);
if (isset($fileInfo['extension'])){
$fileExtension = strtoupper($fileInfo['extension']);
$fileExtension = preg_replace('/_\d$/',"",$fileExtension);
if (in_array(".".$fileExtension,Array(".BZ2",".GZ",".RAR",".ZIP",".TGZ",".TAR") )){
$fileExtension = strtoupper(pathinfo(str_replace(".".$fileInfo['extension'],"",$fnPath), PATHINFO_EXTENSION));
$fileExtension = preg_replace('/_\d+$/',"",$fileExtension);
$_REQUEST['compressed'][$idx]=1;
}else{
$_REQUEST['compressed'][$idx]=0;
}
}
*/
}
$filetypes = getFileTypesList();
//fill in form defaults from: REQUEST > FILEMETA DB > DEFAULTS $def
/*foreach ($defs as $attr => $v ){
if (isset($_REQUEST[$attr][$idx])){
$filesMeta[$idx][$attr]=$_REQUEST[$attr][$idx];
}elseif (!isset($filesMeta[$idx][$attr])){
$filesMeta[$idx][$attr]=$v;
}
}*/
?>
<form name="uploadFiles<?php echo $idx;?>" id="uploadFiles<?php echo $idx;?>" class="uploadFiles" action="" method="post" enctype="multipart/form-data">
<input type="hidden" name="op" id="op<?php echo $idx;?>" value="1">
<input type="hidden" id="base-url<?php echo $idx;?>" value="<?php echo $GLOBALS['BASEURL']; ?>"/>
<input type="hidden" name="idx" id="idx" value="<?php echo $idx;?>" />
<!-- Start Metadata Division per File. Displayed only if File is active (according radio button) -->
<div class="note note-info formInputs" id="formInputs<?php echo $idx;?>" style="position:relative;">
<div class="disable-form display-hide"></div>
<!-- While showing changes to be done, make Metadata Division Readonly
<?php if ( $state[$idx]=="disabled" || $_REQUEST['compressed'][$idx] ){ ?>
<div id="disableFormInputs" style="position:absolute;z-index:11;top:0;left:0;width:100%;height:100%;background-color:#FFFFFF;opacity: 0.6;"></div>
<?php } ?>
TODO "conversions" should be included as "actions" -->
<div class="form-group formatTR" id="formatTR<?php echo $idx;?>">
<label>File Format *</label>
<select id="format<?php echo $idx;?>" name="format" onchange="customfromFormat(this.value, <?php echo $idx;?>)" class="form-control formatSelector file-type-selector">
<option value="" >Select the file format</option>
<?php foreach($filetypes as $ft) { ?>
<option value="<?php echo $ft['_id']; ?>" <?php if (in_array($fileExtension,$ft['extension'])){echo "selected";}?>><?php echo $ft['_id']; ?></option>
<?php } ?>
<!--<option value="BAM" <?php if ($fileExtension =="BAM") {echo "selected";}?> >BAM</option>
<option value="BED" <?php if ($fileExtension =="BED") {echo "selected";}?> >BED </option>
<option value="BEDGRAPH" <?php if ($fileExtension=="BEDGRAPH"){echo "selected";}?>>BEDGRAPH</option>
<option value="WIG" <?php if ($fileExtension =="WIG") {echo "selected";}?> >WIG</option>
<option value="BW" <?php if ($fileExtension =="BW") {echo "selected";}?> >BIGWIG</option>
<option value="GFF" <?php if (in_array($fileExtension,Array("GTF","GFF"))){echo "selected";}?> >GFF/GTF</option>
<option value="GFF3" <?php if ($fileExtension =="GFF3"){echo "selected";}?> >GFF3</option>
<option value="FASTQ" <?php if (in_array($fileExtension,Array("FASTQ","FQ"))){echo "selected";}?>>FASTQ</option>
<option value="FASTA" <?php if (in_array($fileExtension,Array("FA","FASTA","FN"))){echo "selected";}?>>FASTA</option>
<option value="PDB" <?php if ($fileExtension =="PDB") {echo "selected";}?> >PDB</option>
<option value="JSON" <?php if ($fileExtension =="JSON"){echo "selected";}?> >JSON</option>
<option value="TXT" <?php if ($fileExtension =="TXT"){echo "selected";}?> >TXT</option>
<option value="DCD" <?php if ($fileExtension =="DCD") {echo "selected";}?> >DCD</option>
<option value="GRO" <?php if ($fileExtension =="GRO") {echo "selected";}?> >GRO</option>
<option value="GEM" <?php if ($fileExtension =="GEM") {echo "selected";}?> >GEM</option>
<option value="PARMTOP" <?php if (in_array($fileExtension,Array("PARMTOP","PRMTOP","TOP"))){echo "selected";}?> >PARMTOP</option>
<option value="MDCRD" <?php if (in_array($fileExtension,Array("MDCRD","TRJ"))){echo "selected";}?> >MDCRD</option>
<option value="UNK" <?php if ($fileExtension =="UNK"){echo "selected";}?> >OTHER</option>-->
</select>
</div>
<input type="hidden" id="data_type_selected" value="<?php echo $filesMeta[$idx]['data_type']; ?>" >
<div class="form-group display-hide" id="dataType<?php echo $idx;?>">
<label>Data Type * <i class="icon-question tooltips" data-container="body" data-placement="right" data-original-title="Data type description"></i></span></label>
<select name="data_type" id="data_type_sel<?php echo $idx;?>" class="form-control data-type-selector" onchange="customfromDataType(this.value, <?php echo $idx;?>)" disabled>
</select>
<!--<span class="help-block font-red warn1" style="display:none;">This field is required.</span>-->
</div>
<div class="form-group display-hide" id="taxonG<?php echo $idx;?>">
<label class="control-label" id="label-taxon<?php echo $idx;?>">Taxon * <i class="icon-question tooltips" data-container="body" data-html="true" data-placement="right" data-original-title="<p align='left' style='margin:0'>Insert the taxon for this file. You can provide it by name, ID, or avoid this step.</p>"></i></label>
<div class="input-group">
<input type="text" class="form-control field_dependency<?php echo $idx;?> field_dependency<?php echo $idx;?>_1 taxon_name" name="taxon_name_id" id="taxonName" placeholder="Please enter the taxon name" value="<?php echo fromTaxonID2TaxonName($filesMeta[$idx]['taxon_id'])." (".$filesMeta[$idx]['taxon_id'].")"; ?>">
<input type="text" class="form-control field_dependency<?php echo $idx;?> field_dependency<?php echo $idx;?>_2 taxon_id" style="display:none;" name="taxon_id_name" id="taxonID" placeholder="Please enter the taxon ID" disabled value="<?php echo $filesMeta[$idx]['taxon_id']; ?>">
<input type="text" class="form-control field_dependency<?php echo $idx;?> field_dependency<?php echo $idx;?>_3" style="display:none;" id="" disabled placeholder="No taxon provided">
<div class="input-group-btn">
<img class="Typeahead-spin" src="assets/layouts/layout/img/loading-spinner-blue.gif" style="display:none;">
<button type="button" class="btn green dropdown-toggle" data-toggle="dropdown"><span class="arg_dependency<?php echo $idx;?>">Taxon Name</span>
<i class="fa fa-angle-down"></i>
</button>
<ul class="dropdown-menu pull-right">
<li>
<a class="arg_dependency<?php echo $idx;?>_1" href="javascript:changeArgDependency('<?php echo $idx;?>', '1', true);"> Taxon Name </a>
</li>
<li>
<a class="arg_dependency<?php echo $idx;?>_2" href="javascript:changeArgDependency('<?php echo $idx;?>', '2', true);"> Taxon ID </a>
</li>
<li>
<a class="arg_dependency<?php echo $idx;?>_3" href="javascript:changeArgDependency('<?php echo $idx;?>', '3', false);"> No Taxon </a>
</li>
</ul>
</div>
</div>
</div>
<input type="hidden" name="taxon_id" value="<?php echo $filesMeta[$idx]['taxon_id']; ?>" />
<div class="form-group display-hide" id="refGenomeTR<?php echo $idx;?>">
<label>Assembly * <i class="icon-question tooltips" data-container="body" data-placement="right" data-original-title="Assembly description"></i></span></label>
<select name="refGenome" id="refGenome<?php echo $idx;?>" class="form-control" disabled>
<option value="">Select the assembly</option>
<?php
$refList = scanDir($GLOBALS['refGenomes']);
array_push($refList,"0"); //add Other
var_dump($refList);
foreach ($refList as $ref){
if ( preg_match('/^\./', $ref) || !is_dir($GLOBALS['refGenomes']) )
continue;
if (isset($GLOBALS['refGenomes_names'][$ref]))
$refName=$GLOBALS['refGenomes_names'][$ref];
else
$refName=$ref;
if ($filesMeta[$idx]['refGenome'] == $ref){
print "<option selected value=\"$ref\">$refName</option>";
}else{
print "<option value=\"$ref\">$refName</option>";
}
}
?>
</select>
</div>
<div class="form-group display-hide" id="pairedTR<?php echo $idx;?>">
<label>BAM type</label>
<div class="mt-radio-inline">
<label class="mt-radio mt-radio-outline">
<input type="radio" name="paired" class="paired<?php echo $idx;?>" value="paired" checked> Paired-End
<span></span>
</label>
<label class="mt-radio mt-radio-outline">
<input type="radio" name="paired" class="paired<?php echo $idx;?>" value="single"> Single-End
<span></span>
</label>
</div>
</div>
<div class="form-group display-hide" id="sortedTR<?php echo $idx;?>">
<label>Coordinates sorting</label>
<div class="mt-radio-inline">
<label class="mt-radio mt-radio-outline">
<input type="radio" name="sorted" class="sorted<?php echo $idx;?>" value="sorted" onclick="showHideSortInfo(0,<?php echo $idx;?>)" checked> Sorted
<span></span>
</label>
<label class="mt-radio mt-radio-outline">
<input type="radio" name="sorted" class="sorted<?php echo $idx;?>" value="unsorted" onclick="showHideSortInfo(1, <?php echo $idx;?>)" > Unsorted
<span></span>
</label>
</div>
</div>
<div class="alert alert-warning display-hide" id="sortInfo<?php echo $idx;?>">
<strong>BAM</strong> file will be authomatically sorted by coordinate order
</div>
<!--<div class="form-group refGenomeTR" id="refGenomeTR<?php echo $idx;?>">
<label>Assembly</label>
<span class="tooltip-mt-radio"><i class="icon-question tooltips" data-container="body" data-placement="right" data-original-title="Assembly description"></i></span>
<select name="refGenome" class="form-control">
<option value="">Select the assembly</option>
<?php
$refList = scanDir($GLOBALS['refGenomes']);
foreach ($refList as $specie){
if ( preg_match('/^\./', $specie) || !is_dir($GLOBALS['refGenomes']))
continue;
$scaffoldList = scanDir($GLOBALS['refGenomes']."/$specie");
foreach ($scaffoldList as $ref){
if ( preg_match('/^\./', $ref) || !is_dir($GLOBALS['refGenomes']."/$specie"))
continue;
if (isset($GLOBALS['refGenomes_names'][$ref]))
$refName=$GLOBALS['refGenomes_names'][$ref];
else
$refName=$ref;
if ($filesMeta[$idx]['refGenome'] == $ref){
print "<option selected value=\"$ref\">$refName</option>";
}else{
print "<option value=\"$ref\">$refName</option>";
}
}
} ?>
</select>
<span class="help-block font-red warn-ref-gen" style="display:none;">This field is required.</span>
</div>
<div class="form-group pairedTR" id="pairedTR<?php echo $idx;?>">
<label>BAM type</label>
<div class="mt-radio-inline">
<label class="mt-radio mt-radio-outline">
<input type="radio" name="paired<?php echo $idx; ?>" value="paired" checked> Paired-End
<span></span>
</label>
<label class="mt-radio mt-radio-outline">
<input type="radio" name="paired<?php echo $idx; ?>" value="single"> Single-End
<span></span>
</label>
</div>
</div>
<div class="form-group sortedTR" id="sortedTR<?php echo $idx;?>">
<label>Coordinates sorting</label>
<div class="mt-radio-inline">
<label class="mt-radio mt-radio-outline">
<input type="radio" name="sorted<?php echo $idx; ?>" value="sorted" onclick="showHideSortInfo(0,<?php echo $idx;?>)" checked> Sorted
<span></span>
</label>
<label class="mt-radio mt-radio-outline">
<input type="radio" name="sorted<?php echo $idx; ?>" value="unsorted" onclick="showHideSortInfo(1, <?php echo $idx;?>)" > Unsorted
<span></span>
</label>
</div>
</div>
<div class="alert alert-warning sortInfo" id="sortInfo<?php echo $idx;?>">
<strong>BAM</strong> file will be authomatically sorted by coordinate order
</div>-->
<div class="form-group descriptionTR" id="descriptionTR<?php echo $idx;?>">
<label>Description</label>
<textarea name="description" id="description<?php echo $idx;?>" class="form-control" rows="6" placeholder="Write a short description here..."><?php echo $filesMeta[$idx]['description'];?></textarea>
</div>
<!--<input type="hidden" name="validated[]" value="<?php print $filesMeta[$idx]['validated'];?>"/>-->
<input type="hidden" name="fn" value="<?php print $fn;?>"/>
<div class="form-actions btn-send-data">
<!--<input type="button" class="btn green snd-metadata-btn" value="SEND METADATA" onclick="sendMetadata(<?php echo $idx; ?>, 1);" style="position:relative;z-index:20;" >-->
<input type="button" class="btn green snd-metadata-btn" id="snd<?php echo $idx; ?>" value="SEND METADATA" style="position:relative;z-index:20;" >
</div>
</div>
</form>
<?php
if (isset($_SESSION['validation'][$fn]['msg'])){ ?>
<div class="note note-info">
<b>Validation summary:</b></br>
<ul style="list-style:disc">
<?php
foreach ($_SESSION['validation'][$fn]['msg'] as $line){
print "<li>$line</li>";
}?>
</ul>
<i>Press <b>"OK"</b> to record the proposed changes.</i>
</div>
<?php }
if (isset($_SESSION['enqueued'][$idx]['msg'])){ ?>
<div class="note note-info">
<?php echo $_SESSION['enqueued'][$IDX]['msg']?>
</div>
<?php
}?>
<div class="note feedback-file display-hide" id="feedback-file<?php echo $idx; ?>">
<h4 class="block"></h4>
<span></span>
</div>
<?php } //end main foreach!!! ?>
<div class="form-actions">
<div id="bottom-validated-files">
<div id="go-out-uploadform"><input type="button" class="btn default" value="BACK TO WORKSPACE" onclick="location.href='workspace/';" /></div>
</div>
</div>
<!-- </form>-->
<?php }else{ ?>
<div id="go-out-uploadform"><input type="button" class="btn default" value="BACK TO WORKSPACE" onclick="location.href='workspace/';" /></div>
<?php } //END if NOT ERROR ?>
</div>
</div>
</div>
<!-- END CONTENT BODY -->
</div>
<!-- END CONTENT -->
<div class="modal fade" id="myModal1" tabindex="-1" role="basic" aria-hidden="true">
<div class="modal-dialog">
<div class="modal-content">
<div class="modal-header">
<button type="button" class="close" data-dismiss="modal" aria-hidden="true"></button>
<h4 class="modal-title">Beware!</h4>
</div>
<div class="modal-body">You haven't completed the validation of this file, you should edit the metadata afterwards through the workspace table. </div>
<div class="modal-footer">
<button type="button" class="btn dark btn-outline" data-dismiss="modal">Cancel</button>
<button type="button" class="btn green btn-modal-ok">I'm aware</button>
</div>
</div>
<!-- /.modal-content -->
</div>
<!-- /.modal-dialog -->
</div>
<?php
require "../htmlib/footer.inc.php";
require "../htmlib/js.inc.php";
?>