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_dataset.php
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_dataset.php
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<?php
/**
* @file _dataset.php
* @brief module that display information about a single dataset refered to by its DOI.
*
* at this point, Headers have been sent and the page already has had some writing on...
*
* The module takes information for a dataset, placed in database or json file and display it in this page.
*
* Keep replacing the fields with data from the JSON file.
*
* @author Nathalie Castells
* @date 9/27/2018
* @date 11/28/2019
*/
$Parsedown = new Parsedown();
$dsinfo = $GLOBALS['dsinfo']; //added 2023-02-21 to circumvent undefined variable error
if ($dsinfo['isReady'] == 1 ) {
$info .= $checkThisOne;
$identifierLink = "";
$actualURL = "";
$datasetCheckURL = "<span class=\"text-warning\">DRAFT VERSION: </span>" ;
if (substr($dsinfo['identifier'],0,3)=== '10.') {
$identifierLink = "<b>DOI : https://doi.org/". $dsinfo['identifier']. "</b>"; # DOI not minted so no link
$actualURL = "DOI: https://doi.org/". $dsinfo['identifier'];
} else {
$identifierLink = "<b>URL : " . $dsinfo['url']." - " .$dsinfo['identifier']. "</b>";
$actualURL = "URL : " . $dsinfo['url']." - " .$dsinfo['identifier'];
}
}
else
{
if (substr($dsinfo['identifier'],0,3) === '10.') {
$identifierLink = "<b>DOI : <a target=\"_BLANK\" href=\"https://doi.org/". $dsinfo['identifier']."\">https://doi.org/". $dsinfo['identifier']."</a>. </b>"; # DOI not minted so no link
$actualURL = "DOI: https://doi.org/". $dsinfo['identifier'];
} else {
$actualURL = "URL : " . $dsinfo['url']." - " .$dsinfo['identifier'];
$identifierLink = "<a target=\"_BLANK\" href=\"dsinfo/".$expt."/". $dsinfo['version']."-".$dsinfo['shortName'] . "\">".$expt."/". $dsinfo['version']."-".$dataset['shortName'] . " - ". $dataset['identifier']."</a>. </b>";
}
}
?>
<div id="idExpt">
<div id="greenTitle" class="d-flex py-3 p3-3 bg-primary text-white mt-0 ">
<h1 class="mx-3"><?php echo $datasetTitle?> </h1>
</div>
<div class="row m-3">
<div class=" p-3 border border-success rounded b">
<div class="pb-3 "><strong>Citation: </strong><?php echo $refAuthor; ?> (<?php echo $year;?>).
<?php echo $dsinfo['name'];?> <em><?php echo $getPublisher; ?></em>
<?php echo $identifierLink ?></div>
<!-- The text field -->
<?php
$reference = $refAuthor. " (".$year.") ". $dsinfo['name']. " - ". $getPublisher . " - ". $actualURL;
?>
<div class="d-flex justify-content-end align-items-center">
<div id="div1" class="btn btn-warning m-1 align-items-center" style="display:none">
<i class="fa fa-copy"></i> <b>Copied to clipboard</b></div>
<button address="<?php echo $reference; ?>" title="Copy to Clipboard"
class="btn btn-success m-1 copyToClipboard align-items-center">
<i class="fa fa-copy"></i> <b id="copyID">to Clipboard</b></button>
<?php if (file_exists($risfile)) {
$risURL = "<a title=\"Download Citation\" class=\"btn btn-success m-1 align-items-center\" href=\"".$risfile."\" download>
<i class=\"fa-solid fa-quote-right\"></i> <b>to RefMan</b></a>";
echo $risURL;
}?>
<?php if (file_exists($enwfile)) {
$enwURL = "<a title=\"Download Citation\" class=\"btn btn-success m-1 align-items-center\" href=\"".$enwfile."\" download>
<i class=\"fa-solid fa-quote-right\"></i> <b>to EndNote</b></a>";
echo $enwURL;
}?>
</div>
</div>
</div>
<div class="row mx-0 mb-3">
<?php
if ($dsinfo['isReady'] <= $displayValue) {
?><p>This dataset is in preparation - come back very soon! </p>
<?php
} else {
?>
<div class="col-sm-4">
<div class="card card-summary ">
<div class="card-body">
<ul class="list-group list-group-flush ">
<?php
if ($dsinfo['isExternal'] == 0) {
if (file_exists($zipfile)) {
echo $strDownload;
}
} else {
?>
<li class="list-group-item"><b>Data is at: </b><a target="_BLANK"
href="<?php echo $dsinfo['url'];?>"><?php echo $dsinfo['identifier'];?></a>
<?php
}
if ($dsinfo['isExternal'] == 0) { echo $strUserArea;
?>
<li class="list-group-item"><b>DOI: </b><a
href="https://doi.org/<?php echo $dsinfo['identifier'];?>"><?php echo $dsinfo['identifier'];?></a>
</li>
<?php if ($hasNVersion == 1) { ?>
<li class="list-group-item text-warning "><b>Newer Version: </b>
<?php
echo $newVersionShort;
?>
</li>
<?php } }?>
<?php if ($expt == "rro") { ?><li class="list-group-item"><b>Experiment:
</b> <a href="orphans.php">Other</a></li>
<?php } else {?>
<li class="list-group-item"><b>Experiment: </b> <a
href="experiment/<?php echo $expt;?>"><?php echo $pageinfo['Experiment']; ?></a></li>
<?php
}
if ($dsinfo['isExternal'] == 0) {
?>
<li class="list-group-item"><b>Files included in the download: </b> <?php echo $distribution; ?>
</li> <?php ?>
<li class="list-group-item"><b>Version: </b> <?php echo $dsinfo['version']; ?></li>
<?php }
echo $dateCreation . $datePublication .$dateUpdate; ?>
<li class="list-group-item"><b>Keywords: </b>
<?php
$localwords = $dsinfo['keywords'];
echo printVocab($localwords);
?></li>
<li class="list-group-item"><b>Author(s): </b> <?php echo $refAuthor; ?></li>
<li class="list-group-item"><b>Publisher: </b><?php echo $getPublisher; ?></li>
<?php echo $strDownload;?>
</ul>
</div>
</div>
</div>
<div class="col-sm-8">
<p class="text-right">
<a href="https://twitter.com/share?ref_src=twsrc%5Etfw" class="twitter-share-button"
data-via="eRA_curator" data-size="large"
data-text=" <?php echo $dsinfo['name']; ?> <?php echo $dsinfo['identifier'];?> "
data-url="<?php echo $dsinfo['url'];?>" data-hashtags="eRAdatasets"
data-related="eRA_Curator,Rothamsted" data-related="Rothamsted" data-show-count="false">Tweet this
dataset</a>
</p>
<?php echo $illustration; // if it is available ?>
<h3 class="my-3">Summary</h3>
<?php
echo $Parsedown->text($arrDescription['Abstract']);
if (isset($arrDescription['Methods'])) {
?>
<h3>Methods</h3>
<?php
echo $Parsedown->text($arrDescription['Methods']);
}
if (isset($arrDescription['TechnicalInfo'])) {
?>
<h3>Technical Information</h3>
<?php
echo $Parsedown->text($arrDescription['TechnicalInfo']);
}
if ($hasDocuments == 1) {
echo $relDocuments;
}
if ($hasDatasets == 1) {
echo $relDatasets;
}
if ($dsinfo['isExternal'] == 0) {
if ($hasPVersion == 1) {
echo $prevVersions;
}
if ($hasNVersion == 1) {
echo $newVersions;
}
}
if ($hasCT == 1) {
echo $tblContributors;
}
if ($dsinfo['isExternal'] == 0) {
?>
<h3>Dataset Access and Conditions</h3>
<h4>Rights Holder</h4>
<p>Rothamsted Research</p>
<h4>License</h4>
<p>
<a rel="license" target="_blank" href="http://creativecommons.org/licenses/by/4.0/" target="out">
<img
style="width: 50px;"
alt="Creative Commons License"
src="images/logos/cc4.png"
/></a> This dataset is
available under a <a rel="license" href="http://creativecommons.org/licenses/by/4.0/">Creative Commons
Attribution Licence (4.0)</a>.
</p>
<h4>Cite this Dataset</h4>
<p>
<strong>YOU MUST CITE AS: </strong><?php echo $refAuthor; ?> (<?php echo $year;?>).
<?php echo $datasetTitle;?> <em><?php echo $getPublisher; ?></em>
<a target="_blank"
href="https://doi.org/<?php echo $dsinfo['identifier'];?>">https://doi.org/<?php echo $dsinfo['identifier'];?></a>
<p>
Please review our <a href="info/howtocredit">How to Credit Datasets</a>
guidance for more information.
</p>
<h4>Conditions of Use</h4>
<p>
Rothamsted relies on the integrity of users to ensure that datasets
are used appropriately and Rothamsted Research receives suitable
acknowledgment as being the originators of these data. Please review
the <a href="info/conditions">Conditions of Use</a> before
downloading.
</p>
<?php }?>
<div id="accordion">
<?php
if (isset($arrDescription['TableOfContents'])) {
?>
<div class="card">
<div class="card-header" id="TableOfContents">
<h3 class="mb-0">
<button class="btn btn-link collapsed" data-toggle="collapse" data-target="#collapseOne"
aria-expanded="false" aria-controls="collapseOne">Table Of Contents</button>
</h3>
</div>
<div id="collapseOne" class="collapse" aria-labelledby="TableOfContents"
data-parent="#accordion">
<div class="card-body">
<h3>Table Of Contents</h3>
<p><?php echo $Parsedown->text($arrDescription['TableOfContents']); ?></p>
</div>
</div>
</div> <?php
}
if (isset($arrDescription['Provenance'])) {
?>
<div class="card">
<div class="card-header" id="Provenance">
<h5 class="mb-0">
<button class="btn btn-link collapsed" data-toggle="collapse"
data-target="#collapseThree" aria-expanded="false"
aria-controls="collapseThree">Provenance</button>
</h5>
</div>
<div id="collapseThree" class="collapse" aria-labelledby="Provenance" data-parent="#accordion">
<div class="card-body">
<p><?php echo $Parsedown->text( $arrDescription['Provenance']); ?></p>
</div>
</div>
</div>
<?php
}
if (isset($arrDescription['Quality'])) {
?>
<div class="card">
<div class="card-header" id="Quality">
<h5 class="mb-0">
<button class="btn btn-link collapsed" data-toggle="collapse"
data-target="#collapseFour" aria-expanded="false"
aria-controls="collapseFour">Quality</button>
</h5>
</div>
<div id="collapseFour" class="collapse" aria-labelledby="Quality" data-parent="#accordion">
<div class="card-body">
<p><?php echo $Parsedown->text($arrDescription['Quality']); ?></p>
</div>
</div>
</div>
<?php
}
if (isset($arrDescription['Other'])) {
?>
<div class="card">
<div class="card-header" id="Other">
<h5 class="mb-0">
<button class="btn btn-link collapsed" data-toggle="collapse" data-target="#collapseSix"
aria-expanded="false" aria-controls="collapseSix">Additional Information</button>
</h5>
</div>
<div id="collapseSix" class="collapse" aria-labelledby="Other" data-parent="#accordion">
<div class="card-body">
<p><?php echo $Parsedown->text($arrDescription['Other']); ?></p>
</div>
</div>
</div>
<?php
}
if ($dsinfo['isExternal'] == 0) {
?>
<div class="card">
<div class="card-header" id="Funding">
<h5 class="mb-0">
<button class="btn btn-link collapsed" data-toggle="collapse"
data-target="#collapseFunding" aria-expanded="false"
aria-controls="collapseFunding">Funding</button>
</h5>
</div>
<div id="collapseFunding" class="collapse" aria-labelledby="Funding" data-parent="#accordion">
<div class="card-body">
<ul class="list-group mx-3">
<li class="list-group-item ">The dataset <b><?php echo $dsinfo['name'];?></b>
is a published dataset from the e-RA Database.
e-RA is part of the Rothamsted Long-Term Experiments - National Bioscience
Research Infrastructure (RLTE-NBRI), which also covers maintenance of the <a
href="https://www.rothamsted.ac.uk/national-capability/long-term-experiments-0">
Long-Term Experiments, </A> the <a
href=" https://www.rothamsted.ac.uk/facilities-and-resources/rothamsted-sample-archive">
Rothamsted Sample Archive </a> and Rothamsted's environmental monitoring
activities including the weather stations and its role in the <a
href="https://www.rothamsted.ac.uk/facilities-and-resources/environmental-change-network">
UK Environmental Change Network</A>
</li>
<li class="list-group-item ">The RLTE-NBRI is funded by UK Research and Innovation -
Biotechnology and Biological Sciences Research Council (UKRI-BBSRC) under award
BBS/E/RH/23NB0007 (2023-2028). The RLTE-NBRI is also supported by the Lawes
Agricultural Trust. e-RA has been part of a National Capability since 2012,
previous awards from the BBSRC were Grants BBS/E/C/00005189 (2012-2017) and
BBS/E/C/000J0300 (2017-2022)
</li>
</ul>
<?php echo $strFunders;?>
</div>
</div>
</div>
<?php } ?>
</div>
</div>
</div>
</div>
<!-- Modal OA-->
<?php
$formVisible = " ";
$modalSize = " modal-lg";
if (isset($_SESSION['user']['startSession'])) {
$formVisible = " d-none";
$modalSize = " ";
//$fullname = $_SESSION['user']['fullname'];
}
$fullname = "";
if (isset($_SESSION['user']['fullname'])) {
$formVisible = " d-none";
$modalSize = " ";
$fullname = $_SESSION['user']['fullname'];
}
$institution = "";
if(isset($_SESSION['user']['institution'])) {
$formVisible = " d-none";
$modalSize = " ";
$institution = $_SESSION['user']['institution'];
}
$positionValue = "";
if(isset($_SESSION['user']['positionValue'])) {
$formVisible = " d-none";
$modalSize = " ";
$positionValue = $_SESSION['user']['positionValue'];
}
$country = "";
if (isset($_SESSION['user']['country'])) {
$formVisible = " d-none";
$modalSize = " ";
$country = $_SESSION['user']['country'];
} else {$country = "GB";}
$information = "";
if (isset($_SESSION['user']['information'])) {
$information = $_SESSION['user']['information'];
}
?>
<div class="modal fade" id="modalClickTroughOA" tabindex="-1" role="dialog" aria-labelledby="exampleModalCenterTitle"
aria-hidden="true">
<div class="modal-dialog <?php echo $modalSize ; ?> modal-dialog-centered" role="document">
<div class="modal-content">
<div class="modal-header">
<h5 class="modal-title" id="exampleModalLongTitle">End User
Agreement</h5>
<button type="button" class="close" data-dismiss="modal" aria-label="Close">
<span aria-hidden="true">×</span>
</button>
</div>
<div class="modal-body">
<p>
<a rel="license" target="_blank" href="http://creativecommons.org/licenses/by/4.0/"
target="out"><img style="width: 50px;" alt="Creative Commons License" src="images/logos/cc4.png"
align="middle" /></a> This work is
licensed under a <a rel="license" href="http://creativecommons.org/licenses/by/4.0/">Creative
Commons Attribution 4.0 International License</a>.
</p>
<p>
<strong>YOU MUST CITE AS: </strong><?php echo $refAuthor; ?> (<?php echo $year;?>).
<?php echo $dsinfo['name'];?> <em><?php echo $getPublisher; ?></em>
<a target="_blank"
href="https://doi.org/<?php echo $dsinfo['identifier'];?>"><?php echo $dsinfo['identifier'];?></a>
</p>
<p>Rothamsted relies on the integrity of users to ensure that
Rothamsted Research receives suitable acknowledgment as being the
originators of these data. This enables us to monitor the use of
each dataset and to demonstrate their value.</p>
</div>
<div class="modal-footer">
<form method="POST" class="was-validated">
<div class="<?php echo $formVisible ; ?>">
<div class="form-group">
<label for="InputName">
<h5>Full Name</h5>
</label>
<input type="text" class="form-control" id="InputName" name="InputName"
placeholder="Your name" value="<?php echo $fullname; ?>">
<div class="valid-feedback"></div>
<div class="invalid-feedback">Please fill out this field.</div>
</div>
<div class="form-group">
<label for="InputInstitute">
<h5>Name and Type of Organisation (Academic, Industry, Farm, School or Other)</h5>
</label>
<input type="text" class="form-control" id="InputInstitute" name="InputInstitute"
placeholder="Organisation's name and type" value="<?php echo $institution; ?>"> <small
id="instHelp" class="form-text text-muted"></small>
<div class="valid-feedback"></div>
<div class="invalid-feedback">Please fill out this field.</div>
</div>
<div class="form-group">
<label for="inputCountry">
<h5>Country</h5>
</label>
<select class="form-control selectpicker countrypicker" data-flag="true"
data-default="<?php echo $country; ?>" id="inputCountry" name="inputCountry">
</select>
</div>
<div class="form-group">
<label for="information">
<h5>How will the data be used?</h5>
</label>
<textarea class="form-control" id="information" name="information"
rows="3"><?php echo $information; ?></textarea>
</div>
</div>
<div class="form-group">
<label class="form-check-label" for="understandCheck"> <b>e-RA collects information to
understand how the data is used and for justification of continued
funding</b> - Please read our <a target="_BLANK" href="info/privacy">privacy
information</a></label>
</div>
<br />
<button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
<button type="submit" class="btn btn-primary" name="dlform" value="isDownload">Agree and
Download</button>
</div>
<!-- div class="modal-footer">
<button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
<a type="button" download class="btn btn-primary"
href="<?php // echo $zipfile; ?>">Agree and Download</a>
</div> -->
</div>
</div>
</div>
<!-- Modal Other-->
<div class="modal fade" id="modalClickTroughOther" tabindex="-1" role="dialog" aria-labelledby="exampleModalCenterTitle"
aria-hidden="true">
<div class="modal-dialog modal-dialog-centered" role="document">
<div class="modal-content">
<div class="modal-header">
<h5 class="modal-title" id="exampleModalLongTitle">End User
Agreement</h5>
<button type="button" class="close" data-dismiss="modal" aria-label="Close">
<span aria-hidden="true">×</span>
</button>
</div>
<div class="modal-body">
<p>
<a rel="license" target="_blank" href="http://creativecommons.org/licenses/by/4.0/"
target="out"><img style="width: 50px;" alt="Creative Commons License" src="images/logos/cc4.png"
align="middle" /></a> This work is
licensed under a <a rel="license" href="http://creativecommons.org/licenses/by/4.0/">Creative
Commons Attribution 4.0 International License</a>.
</p>
<p>
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