datasets.php

<?php

##########################################################################
# Copyright 2013, Philip Ewels (phil.ewels@babraham.ac.uk)               #
#                                                                        #
# This file is part of Labrador.                                         #
#                                                                        #
# Labrador is free software: you can redistribute it and/or modify       #
# it under the terms of the GNU General Public License as published by   #
# the Free Software Foundation, either version 3 of the License, or      #
# (at your option) any later version.                                    #
#                                                                        #
# Labrador is distributed in the hope that it will be useful,            #
# but WITHOUT ANY WARRANTY; without even the implied warranty of         #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the          #
# GNU General Public License for more details.                           #
#                                                                        #
# You should have received a copy of the GNU General Public License      #
# along with Labrador.  If not, see <http://www.gnu.org/licenses/>.      #
##########################################################################

include('includes/start.php');

$project_id = false;

if(isset($_GET['id']) && is_numeric($_GET['id'])){
	$project_id = $_GET['id'];
}

if(isset($_GET['edit']) && is_numeric($_GET['edit'])){
	$edit = true;
	$project_id = $_GET['edit'];
} else {
	$edit = false;
}

if(isset($_GET['add']) && is_numeric($_GET['add'])){
	$add = true;
	$edit = false;
	$project_id = $_GET['add'];
} else {
	$add = false;
}

if($project_id){
	$projects = mysqli_query($dblink, "SELECT * FROM `projects` WHERE `id` = '".$project_id."'");
	if(mysqli_num_rows($projects) == 1){
		$project = mysqli_fetch_array($projects);
		$project_users = array();
		$project_users_q = mysqli_query($dblink, "SELECT `user_id` FROM `project_contacts` WHERE `project_id` = '$project_id'");
		if(mysqli_num_rows($project_users_q) > 0){
			while($project_user = mysqli_fetch_array($project_users_q)){
				$project_users[] = $project_user['user_id'];
			}
		}
	} else {
		header("Location: index.php");
	}
} else {
	header("Location: index.php");
}

$error = false;

// DELETE DATASETS
if(!empty($_POST['delete_datasets_submit']) && $_POST['delete_datasets_submit'] == 'I’m sure - delete the datasets'){
	$dataset_query = "SELECT * FROM `datasets` WHERE `project_id` = '$project_id'";
	$datasets = mysqli_query($dblink, $dataset_query);
	$counter = 0;
	if(mysqli_num_rows($datasets) > 0){
		while ($dataset = mysqli_fetch_array($datasets)){
			$id = $dataset['id'];
			if(isset($_POST["check_$id"]) && $_POST["check_$id"] == 'on'){
				$query = "DELETE FROM `datasets` WHERE `id` = '$id'";
				if(!mysqli_query($dblink, $query)){
					$error = true;
					$msg[] = "Could not delete dataset. mySQL error: <code>".mysqli_error()."</code><br>mySQL query: <code>$query</code>";
				} else {
					$counter++;
				}
			}
		}
	}
	// Save history message
	$query = sprintf("INSERT INTO `history` (`project_id`, `user_id`, `note`, `time`) VALUES ('%d', '%d', '%s', '%d')", $project_id, $user['id'], mysqli_real_escape_string($dblink, "Deleted $counter datasets."), time());
	if(!mysqli_query($dblink, $query)){
		$error = true;
		$msg[] = "Could not save history log to database. mySQL error: <code>".mysqli_error()."</code><br>mySQL query: <code>$query</code>";
	}

	// Set up page
	if(!$error){
		$msg[] = "Deleted $counter datasets.";
	}
}

// SAVE EDITED DATASETS
if(!empty($_POST['edit_datasets']) && $_POST['edit_datasets'] == 'Edit Datasets'){
	$dataset_query = "SELECT * FROM `datasets` WHERE `project_id` = '$project_id'";
	$datasets = mysqli_query($dblink, $dataset_query);
	$counter = 0;
	if(mysqli_num_rows($datasets) > 0){
		while ($dataset = mysqli_fetch_array($datasets)){
			$id = $dataset['id'];
			$sql = array();
			$sql['name'] = $_POST["name_$id"];
			$sql['species'] = $_POST["species_$id"];
			$sql['cell_type'] = $_POST["cell_type_$id"];
			$sql['data_type'] = $_POST["data_type_$id"];
			$sql['accession_geo'] = $_POST["accession_geo_$id"];
			$sql['accession_sra'] = $_POST["accession_sra_$id"];
			$sql['notes'] = $_POST["notes_$id"];
			$sql['modified'] = time();
			$query = "UPDATE `datasets` SET ";
			foreach($sql as $field => $var){
				$query .= "`$field` = '".mysqli_real_escape_string($dblink, $var)."', ";
			}
			$query = substr($query, 0, -2)." WHERE `id` = '$id'";
			// Save to database
			if(!mysqli_query($dblink, $query)){
				$error = true;
				$msg[] = "Could not save dataset to database. mySQL error: <code>".mysqli_error()."</code><br>mySQL query: <code>$query</code>";
			} else {
				$counter++;
			}
		}
	}
	// Save history message
	$query = sprintf("INSERT INTO `history` (`project_id`, `user_id`, `note`, `time`) VALUES ('%d', '%d', '%s', '%d')", $project_id, $user['id'], mysqli_real_escape_string($dblink, "Edited datasets."), time());
	if(!mysqli_query($dblink, $query)){
		$error = true;
		$msg[] = "Could not save history log to database. mySQL error: <code>".mysqli_error()."</code><br>mySQL query: <code>$query</code>";
	}

	// Set up page
	if($error){
		$edit = true;
	} else {
		$msg[] = "Successfully edited $counter datasets.";
	}
}

// SAVE ADDED DATASETS
if(!empty($_POST['add_datasets']) && $_POST['add_datasets'] == 'Save All Datasets'){
	$i = 1;
	while(isset($_POST["name_$i"])){
		$sql = array();
		$sql['project_id'] = $project_id;
		$sql['name'] = $_POST["name_$i"];
		$sql['species'] = $_POST["species_$i"];
		$sql['cell_type'] = $_POST["cell_type_$i"];
		$sql['data_type'] = $_POST["data_type_$i"];
		$sql['accession_geo'] = $_POST["accession_geo_$i"];
		$sql['accession_sra'] = $_POST["accession_sra_$i"];
		$sql['modified'] = time();

		$query = "INSERT INTO `datasets` (";
		foreach($sql as $field => $var){
			$query .= "`$field`, ";
		}
		$query = substr($query, 0, -2).") VALUES (";
		foreach($sql as $field => $var){
			$query .= "'".mysqli_real_escape_string($dblink, $var)."', ";
		}
		$query = substr($query, 0, -2).")";
		// Save to database
		if(!mysqli_query($dblink, $query)){
			$error = true;
			$msg[] = "Could not save dataset to database. mySQL error: <code>".mysqli_error()."</code><br>mySQL query: <code>$query</code>";
		}
		$i++;
	}
	$i--;

	// Save history message
	$query = sprintf("INSERT INTO `history` (`project_id`, `user_id`, `note`, `time`) VALUES ('%d', '%d', '%s', '%d')", $project_id, $user['id'], mysqli_real_escape_string($dblink, "Added $i datasets."), time());
	if(!mysqli_query($dblink, $query)){
		$error = true;
		$msg[] = "Could not save history log to database. mySQL error: <code>".mysqli_error()."</code><br>mySQL query: <code>$query</code>";
	}

	// Set up page
	if($error){
		$add = true;
	} else {
		$msg[] = "Successfully added $i datasets.";
	}

	// Email support if no-one is assigned
	if(strlen($project['assigned_to']) < 3 && !$error && !$admin){
		mail($support_email, "[Labrador] $i datasets added to ".$project['name'], "Hi there,

$i datasets have just been added to the project ".$project['name']." on Labrador by ".$user['firstname'].' '.$user['surname']." (".$user['email']."). The project doesn't have anyone assigned yet.

You can see the project here: ".$labrador_url."project.php?id=$project_id

--
This is an automated e-mail sent from Labrador
$labrador_url
", $email_headers);

	// Email person assigned
	} else if(!$error && $project['assigned_to'] !== $user['email']){
		mail($project['assigned_to'], "[Labrador] $i datasets added to ".$project['name'], "Hi there,

$i datasets have just been added to the project ".$project['name']." on Labrador by ".$user['firstname'].' '.$user['surname']." (".$user['email']."). The project is assigned to you.

You can see the project here: ".$labrador_url."project.php?id=$project_id

--
This is an automated e-mail sent from Labrador
$labrador_url
", $email_headers);
	}
}



include('includes/header.php'); ?>

<div class="sidebar-nav">
	<h3 id="sidebar_project_title">
	<?php echo '<a href="project.php?id='.$project_id.'">'.$project['name'].'</a>'; ?></h3>
	<ul class="project-tabs">
		<li>
			<a href="project.php?id=<?php echo $project_id; ?>">Project Details</a>
		</li>
		<li class="active">
			<a href="datasets.php?id=<?php echo $project_id; ?>">Datasets</a>
		</li>
		<li>
			<a href="reports.php?id=<?php echo $project_id; ?>">Reports</a>
		</li>
		<li>
			<a href="files.php?id=<?php echo $project_id; ?>">Files</a>
		</li>
	</ul>
</div>

<?php if(!$edit && !$add){ ?>

<div class="sidebar-mainpage project-mainpage">

	<?php if(!empty($msg)): ?>
		<div class="alert alert-<?php echo $error ? 'error' : 'success'; ?>">
			<button type="button" class="close" data-dismiss="alert">×</button>
			<?php echo $error ? '<strong>Error!</strong><br>' : ''; ?>
			<?php foreach($msg as $var)	echo $var.'<br>'; ?>
		</div>
	<?php endif; ?>

	<?php if($admin || in_array($user['id'], $project_users)){ ?>
		<div class="pull-right">
			<a class="btn" href="datasets.php?edit=<?php echo $project['id']; ?>">Edit Datasets</a> &nbsp; 
			<a class="btn" href="datasets.php?add=<?php echo $project['id']; ?>">Add Datasets</a> &nbsp; 
			<a href="#sra-links-modal" role="button" class="btn btn-primary" data-toggle="modal">Get SRA Links</a>
		</div>
	<?php } ?>


	<a class="labrador_help_toggle pull-right" href="#labrador_help" title="Help"><i class="icon-question-sign"></i></a>
	<?php project_header($project); ?>

	<div class="labrador_help" style="display:none;">
		<div class="well">
			<h3>The Datasets Page</h3>
			<p>The datasets page shows all datasets associated with a given project. You can download data for specific datasets by selecting their row and clicking 'Download Checked Datasets'.</p>
			<p>Each dataset has a name, species, cell type, data type and accession codes. These are important as they allow the dataset to be found by other people through Labrador.
			Accession codes help Labrador to know which file names relate to which datasets and speed up processing as they can be used to automate processing pipelines.
			Clicking an accession code will load a new window showing that dataset in its respective repository.</p>
			<p>For projects with many datasets or poorly named datasets, it can be useful to use the 'Filter Datasets' box at the top to quickly find those which you are interested in or would like to download.
			Ticking the check-box at in the table header will select all currently visible datasets.</p>
			<p>You can read the full <a href="<?php echo $labrador_url; ?>/documentation/">Labrador documenation here</a>.</p>
		</div>
	</div>


	<?php
	$dataset_query = "SELECT * FROM `datasets` WHERE `project_id` = '$project_id'";
	$datasets = mysqli_query($dblink, $dataset_query);
	$existing_datasets = array();
	if(mysqli_num_rows($datasets) > 0){
	?>
	
	<table id="existing_datasets_table" class="display compact sortable order-column hover">
		<thead>
			<tr>
				<th data-sort="string-ins">Name</th>
				<th data-sort="string-ins">Species</th>
				<th data-sort="string-ins">Cell Type</th>
				<th data-sort="string-ins">Data Type</th>
				<th style="width:20%;">Accession Codes</th>
				<th data-sort="string-ins">Last Modified</th>
			</tr>
		</thead>
		<tbody>
	<?php while ($dataset = mysqli_fetch_array($datasets)){ ?>
			<tr>
				<td>
				<?php if(!empty($dataset['notes'])) { ?>
					<i class="icon-tag pull-right" title="<?php echo $dataset['notes']; ?>"></i>
				<?php } ?>
					<label for="check_<?php echo $dataset['id']; ?>" class="dataset_name"><?php echo $dataset['name']; ?></label>
				</td>
				<td><?php echo $dataset['species']; ?></td>
				<td><?php echo $dataset['cell_type']; ?></td>
				<td><?php echo $dataset['data_type']; ?></td>
				<td class="dataset-accessions"><?php
				echo accession_badges ($dataset['accession_geo'], 'geo');
				echo accession_badges ($dataset['accession_sra'], 'sra');
				?></td>
				<td class="text-right"><?php echo $dataset['modified'] === NULL ? '' : date('Y/m/d', $dataset['modified']); ?></td>
			</tr>
	<?php } // dataset while loop ?>
		</tbody>
	</table>

	<?php } //check for existing datasets ?>
</div>

<!-- SRA links Modal -->
<div id="sra-links-modal" class="modal hide fade" tabindex="-1" role="dialog" aria-labelledby="sra-links-modal-header" aria-hidden="true">
  <div class="modal-header">
    <button type="button" class="close" data-dismiss="modal" aria-hidden="true">×</button>
    <h3 id="sra-links-modal-header">SRA Download Links</h3>
  </div>
  <div class="modal-body"><pre style="overflow-x: scroll; white-space: nowrap; font-size: 0.8em;">[ loading ]</pre></div>
  <div class="modal-footer">
	<p class="muted pull-left">NB: Works with <a href="http://clusterflow.io">Cluster Flow</a>.</p>
    <button class="btn" data-dismiss="modal" aria-hidden="true">Close</button>
	<button class="btn" id="datasets_download_file">Download</button>
	<button class="btn btn-primary" id="datasets_save_to_server" data-projectid="<?php echo $project_id; ?>">Save to cluster</button>
	<p class="text-left muted">
		Cluster location:<br>
		<code style="font-size: 10px;" id="datasetsr_save_to_server_path"><?php echo $data_root.$project['name'].'/'.$project['name'].'_labrador_downloads_'.date('d_m_Y').'.txt'; ?></code>
	</p>
  </div>
</div>

<?php } // if(!$edit && !$add)

if($edit) { ?>

<div class="sidebar-mainpage project-mainpage">

	<?php if(!empty($msg)): ?>
		<div class="alert alert-<?php echo $error ? 'error' : 'success'; ?>">
			<button type="button" class="close" data-dismiss="alert">×</button>
			<?php echo $error ? '<strong>Error!</strong><br>' : ''; ?>
			<?php foreach($msg as $var)	echo $var.'<br>'; ?>
		</div>
	<?php endif; ?>

	<?php project_header($project); ?>

	<form class="form-inline well">
		Batch update checked datasets: &nbsp;
		<input type="text" class="input-small bulk_update" id="name" placeholder="Name"> &nbsp;
		<input type="text" class="input-small bulk_update" id="species" placeholder="Species"> &nbsp;
		<input type="text" class="input-small bulk_update" id="cell_type" placeholder="Cell Type"> &nbsp;
		<input type="text" class="input-small bulk_update" id="data_type" placeholder="Data Type"> &nbsp;
		<input type="text" class="input-small bulk_update" id="notes" placeholder="Notes"> &nbsp;
		<small><em>(overwrites current values)</em></small>
	</form>

	<form action="datasets.php?id=<?php echo $project_id; ?>" method="post" class="form-horizontal">

		<table id="edit_existing_datasets_table" class="table table-bordered table-condensed table_form">
			<thead>
				<tr>
					<th class="select"><input type="checkbox" class="select-all"></th>
					<th style="width:30%;">Name</th>
					<th>Species</th>
					<th>Cell Type</th>
					<th>Data Type</th>
					<th>GEO Accession</th>
					<th>SRA Accessions</th>
					<th>Notes</th>
				</tr>
			</thead>
			<tbody>
		<?php $dataset_query = "SELECT * FROM `datasets` WHERE `project_id` = '$project_id'";
		$datasets = mysqli_query($dblink, $dataset_query);
		if(mysqli_num_rows($datasets) > 0){
			while ($dataset = mysqli_fetch_array($datasets)){ ?>
				<tr>
					<td class="select"><input type="checkbox" class="select-row" id="check_<?php echo $dataset['id']; ?>" name="check_<?php echo $dataset['id']; ?>"></td>
					<td><input class="name" type="text" name="name_<?php echo $dataset['id']; ?>" value="<?php echo $dataset['name']; ?>"></td>
					<td><input class="species" type="text" name="species_<?php echo $dataset['id']; ?>" value="<?php echo $dataset['species']; ?>"></td>
					<td><input class="cell_type" type="text" name="cell_type_<?php echo $dataset['id']; ?>" value="<?php echo $dataset['cell_type']; ?>"></td>
					<td><input class="data_type" type="text" name="data_type_<?php echo $dataset['id']; ?>" value="<?php echo $dataset['data_type']; ?>"></td>
					<td><input class="accession_geo" type="text" name="accession_geo_<?php echo $dataset['id']; ?>" value="<?php echo $dataset['accession_geo']; ?>"></td>
					<td><input class="accession_sra" type="text" name="accession_sra_<?php echo $dataset['id']; ?>" value="<?php echo $dataset['accession_sra']; ?>"></td>
					<td><input class="notes" type="text" name="notes_<?php echo $dataset['id']; ?>" value="<?php echo $dataset['notes']; ?>"></td>
				</tr>
		<?php } // dataset while loop
		} else { // existing datasets check ?>
				<tr>
					<td colspan="8"><em>No datasets to edit!</em></td>
				</tr>
		<?php } ?>
			</tbody>
		</table>

		<div class="form-actions">
			<input type="submit" class="btn btn-primary btn-large" name="edit_datasets" id="edit_datasets" value="Edit Datasets">
			&nbsp; <a href="#" id="delete_datasets_button" class="btn btn-large btn-danger popover_button" data-toggle="popover" data-html="true" title="Delete Checked Datasets" data-content="Are you sure? <strong>This cannot be undone</strong>. Data on the server will not be affected. <br><br> <input type='submit' class='btn btn-danger btn-block' name='delete_datasets_submit' value='I&#8217;m sure - delete the datasets'>" data-original-title="Delete Checked Datasets">Delete Checked Datasets</a>
		</div>

	</form>

</div>

<?php } // if($edit)

if($add) { ?>

<div class="sidebar-mainpage project-mainpage">

	<?php if(!empty($msg)): ?>
		<div class="alert alert-<?php echo $error ? 'error' : 'success'; ?>">
			<button type="button" class="close" data-dismiss="alert">×</button>
			<?php echo $error ? '<strong>Error!</strong><br>' : ''; ?>
			<?php foreach($msg as $var)	echo $var.'<br>'; ?>
		</div>
	<?php endif; ?>

	<?php project_header($project); ?>

	<div class="alert alert-warning" style="display:none;" id="lookup_error">
		<button type="button" class="close" data-dismiss="alert">×</button>
		<div class="msg_content">

		</div>
	</div>

	<form class="form-inline well action_buttons">
		<div class="input-prepend">
			<button class="btn" type="button" id="btn_add_datasets">Add datasets</button>
			<input style="width:20px;" id="num_datasets" type="text" value="1">
		</div>
		&nbsp; &nbsp;
		<?php if(strlen($project['accession_geo']) > 0) {
			$geo_accessions = explode(" ",$project['accession_geo']);
			foreach($geo_accessions as $acc) {
				$acc = trim($acc); ?>
			<button class="btn geo_accession_lookup" type="button" data-accession="<?php echo $acc; ?>">Look up accession <?php echo $acc; ?> &nbsp; <i class="icon-search"></i></button>
		<?php }
		}
		if(strlen($project['accession_sra']) > 0) {
			$sra_accessions = explode(" ",$project['accession_sra']);
			foreach($sra_accessions as $acc) {
				$acc = trim($acc); ?>
			<button class="btn geo_accession_lookup" type="button" data-accession="<?php echo $acc; ?>">Look up accession <?php echo $acc; ?> &nbsp; <i class="icon-search"></i></button>
		<?php }
		}
		if(strlen($project['accession_ena']) > 0) {
			$ena_accessions = explode(" ",$project['accession_ena']);
			foreach($ena_accessions as $acc) {
				$acc = trim($acc); ?>
			<button class="btn geo_accession_lookup" type="button" data-accession="<?php echo $acc; ?>">Look up accession <?php echo $acc; ?> &nbsp; <i class="icon-search"></i></button>
		<?php }
		}
		if(strlen($project['accession_ddjb']) > 0) {
			$ddjb_accessions = explode(" ",$project['accession_ddjb']);
			foreach($ddjb_accessions as $acc) {
				$acc = trim($acc); ?>
			<button class="btn geo_accession_lookup" type="button" data-accession="<?php echo $acc; ?>">Look up accession <?php echo $acc; ?> &nbsp; <i class="icon-search"></i></button>
		<?php }
		} ?>
		<hr>
		Batch update checked datasets: &nbsp;
		<input type="text" class="input-small bulk_update" id="name" placeholder="Name"> &nbsp;
		<input type="text" class="input-small bulk_update" id="species" placeholder="Species"> &nbsp;
		<input type="text" class="input-small bulk_update" id="cell_type" placeholder="Cell Type"> &nbsp;
		<input type="text" class="input-small bulk_update" id="data_type" placeholder="Data Type"> &nbsp;
		<small><em>(overwrites current values)</em></small>
	</form>

	<form action="datasets.php?id=<?php echo $project_id; ?>" method="post" class="form-horizontal form_validate">
		<table id="add_existing_datasets_table" class="table table-bordered table-condensed table_form">
			<thead>
				<tr>
					<th class="select"><input type="checkbox" class="select-all"></th>
					<th style="width:30%;">Name</th>
					<th>Species</th>
					<th>Cell Type</th>
					<th>Data Type</th>
					<th>GEO Accession</th>
					<th>SRA Accessions</th>
				</tr>
			</thead>
			<tbody>
				<tr>
					<td class="select"><input type="checkbox" class="select-row" id="check_1"></td>
					<td><input required class="name" type="text" id="name_1" name="name_1"></td>
					<td><input required class="species" type="text" id="species_1" name="species_1"></td>
					<td><input required class="cell_type" type="text" id="cell_type_1" name="cell_type_1"></td>
					<td><input required class="data_type" type="text" id="data_type_1" name="data_type_1"></td>
					<td><input class="accession_geo" type="text" id="accession_geo_1" name="accession_geo_1"></td>
					<td><input class="accession_sra" type="text" id="accession_sra_1" name="accession_sra_1"></td>
				</tr>
			</tbody>
		</table>

		<div class="alert alert-error" style="display:none;" id="lookup_warning">
			<button type="button" class="close" data-dismiss="alert">×</button>
			<strong>Please remember to remove any datasets that you don't need.</strong>
			Adding additional datasets will delay the processing of your project.
		</div>

		<div class="form-actions">
			<input type="submit" class="btn btn-primary btn-large" name="add_datasets" id="add_datasets_submit" value="Save All Datasets">
			&nbsp; <a href="#" id="remove_datasets_button" class="btn btn-large btn-danger popover_button">Remove Checked Datasets</a>
		</div>
	</form>
</div>

<?php } // if($add)

include('includes/javascript.php'); ?>
<script src="js/datasets.js" type="text/javascript"></script>
<?php include('includes/footer.php'); ?>