/**
* @brief Create a COinS (ContextObjects in Spans) for a reference
*
* COinS encodes an OpenURL in a <span> tag. See http://ocoins.info/.
*
* @param reference Reference object to be encoded
*
* @return HTML <span> tag containing a COinS
*/
function reference_to_coins($reference)
{
global $config;
$coins = '<span class="Z3988" title="' . reference_to_openurl($reference) . '"></span>';
return $coins;
}
/**
* @brief Create a COinS (ContextObjects in Spans) for a reference
*
* COinS encodes an OpenURL in a <span> tag. See http://ocoins.info/.
*
* @param reference Reference object to be encoded
*
* @return HTML <span> tag containing a COinS
*/
function reference_to_coins($reference)
{
global $config;
$coins = '';
switch ($reference->genre) {
case 'article':
$coins .= '<span class="Z3988" title="';
$coins .= reference_to_openurl($reference);
$coins .= '">';
$coins .= '</span>';
break;
default:
break;
}
return $coins;
}
/**
* @brief Pass refrence object to bioGUID openURL resolver to find it and add any identifiers found
*
* @param reference Reference object, this gets populated with additional fields (such as DOI) if found
*
* @return True if found in bioGUID, false otherwise.
*/
function bioguid_openurl_search(&$reference)
{
$found = false;
$url = 'http://bioguid.info/openurl.php?' . str_replace('&', '&', reference_to_openurl($reference)) . '&display=json';
//echo $url . "\n";
$json = get($url);
if ($json != '') {
$obj = json_decode($json);
$found = $obj->status == 'ok';
if ($found) {
// Flesh out
// Abstract
if (isset($obj->abstract)) {
if (!isset($reference->abstract)) {
$reference->abstract = $obj->abstract;
}
}
// epage
if (isset($obj->epage)) {
if (!isset($reference->epage)) {
$reference->epage = $obj->epage;
}
}
// ISSN
if (isset($obj->issn)) {
if (!isset($reference->issn)) {
$reference->issn = $obj->issn;
}
}
// DOI
if (isset($obj->doi)) {
if (!isset($reference->doi)) {
$reference->doi = $obj->doi;
}
}
// PMID
if (isset($obj->pmid)) {
if (!isset($reference->pmid)) {
$reference->pmid = $obj->pmid;
}
}
// Handle
if (isset($obj->hdl)) {
if (!isset($reference->hdl)) {
$reference->hdl = $obj->hdl;
}
}
// URL
if (isset($obj->url)) {
if (!isset($reference->url)) {
$reference->url = $obj->url;
}
}
// PDF
if (isset($obj->pdf)) {
if (!isset($reference->pdf)) {
$reference->pdf = $obj->pdf;
}
}
// Authors
if (isset($obj->authors)) {
if (count($reference->authors == 0)) {
foreach ($obj->authors as $author) {
$reference->authors[] = $author;
}
}
}
}
}
return $found;
}
function postprocess_citations($reference_id, $citations)
{
global $db;
$citation_count = 0;
// Avoid duplications
if ($reference_id != 0) {
$sql = 'DELETE FROM rdmp_reference_cites WHERE (reference_id=' . $reference_id . ')';
$result = $db->Execute($sql);
if ($result == false) {
die("failed [" . __FILE__ . ":" . __LINE__ . "]: " . $sql);
}
}
foreach ($citations as $citation) {
$citation_reference_id = 0;
if (isset($citation->genre)) {
// Lookup articles
if ($citation->genre == 'article') {
$citation_reference_id = 0;
// Do we have this already in BioStor?
$citation_reference_id = db_find_article($citation);
if ($citation_reference_id == 0) {
// Try BioStor OpenURL search
$citation_reference_id = import_from_openurl(reference_to_openurl($citation));
}
if ($citation_reference_id == 0) {
// Try bioGUID
if (bioguid_openurl_search($citation)) {
$citation_reference_id = db_store_article($citation);
}
}
}
}
// At this stage if citation_reference_id is 0 we haven't found it
// 1. store citation string (we are building a list of all such strings)
$citation_string_id = store_citation_string($citation);
// 2. If we've found it in BioStor, record link between citation string and reference id
if ($citation_reference_id != 0) {
$sql = 'DELETE FROM rdmp_reference_citation_string_joiner WHERE(reference_id=' . $citation_reference_id . ')
AND (citation_string_id=' . $citation_string_id . ')';
$result = $db->Execute($sql);
if ($result == false) {
die("failed [" . __FILE__ . ":" . __LINE__ . "]: " . $sql);
}
$sql = 'INSERT INTO rdmp_reference_citation_string_joiner (reference_id,citation_string_id)
VALUES(' . $citation_reference_id . ',' . $citation_string_id . ')';
$result = $db->Execute($sql);
if ($result == false) {
die("failed [" . __FILE__ . ":" . __LINE__ . "]: " . $sql);
}
}
// 3. Store link between source reference and citation string (which we will use to display literature cited)
if ($reference_id != 0) {
$sql = 'INSERT INTO rdmp_reference_cites (reference_id, citation_string_id, citation_order)
VALUES(' . $reference_id . ',' . $citation_string_id . ',' . $citation_count . ')';
$result = $db->Execute($sql);
if ($result == false) {
die("failed [" . __FILE__ . ":" . __LINE__ . "]: " . $sql);
}
$citation_count++;
}
}
}
function display_publication($publication)
{
global $couch;
global $config;
echo html_html_open();
echo html_head_open();
echo html_title($publication->title . ' - ' . $config['site_name']);
echo html_include_css('css/main.css');
echo html_include_css('css/viewer.css');
echo html_include_script('js/jquery-1.4.4.min.js');
echo html_include_script('js/viewer.js');
echo html_head_close();
echo html_body_open();
if (1) {
echo '<div style="position:relative;">';
// Metadata
echo '<div style="position:absolute;top:0px;left:620px;padding:10px;">';
echo '<div><span><a href="' . $config['web_root'] . '">' . $config['site_name'] . '</a></span></div>';
echo '<p></p>';
echo '<span style="font-weight:bold;font-size:18px;">' . $publication->title . '</span>';
echo '<div>' . 'by ' . reference_authors_to_text_string($publication->authors, false, true) . '</div>';
$outlet = $publication->publication_outlet;
// This ensures we double urlencode "&"
$outlet = str_replace("&", urlencode("&"), $outlet);
echo '<div>' . '<a href="' . $config['web_root'] . 'publication_outlet/' . urlencode($outlet) . '">' . '<i>' . $publication->publication_outlet . '</i>' . '</a>' . ' ' . $publication->volume . ':' . $publication->pages . ' (' . $publication->year . ')' . '</div>';
// External links ---------------------------------------------------------------------------------------
echo '<div>';
echo '<ul>';
if ($publication->_id) {
echo '<li><a href="http://lsid.tdwg.org/summary/urn:lsid:biodiversity.org.au:afd.publication:' . $publication->_id . '" target="_new">urn:lsid:biodiversity.org.au:afd.publication:' . $publication->_id . '</li>';
}
if (isset($publication->identifiers)) {
if (isset($publication->identifiers->doi)) {
echo '<li>' . '<a href="http://dx.doi.org/' . $publication->identifiers->doi . '" target="_new">doi:' . $publication->identifiers->doi . '</a></li>';
}
if (isset($publication->identifiers->hdl)) {
echo '<li>' . '<a href="http://hdl.handle.net/' . $publication->identifiers->hdl . '" target="_new">hdl:' . $publication->identifiers->hdl . '</a></li>';
}
if (isset($publication->identifiers->biostor)) {
echo '<li>' . '<a href="http://biostor.org/reference/' . $publication->identifiers->biostor . '" target="_new">BioStor</a></li>';
}
if (isset($publication->pageIdentifiers)) {
echo '<li>' . '<a href="http://biodiversitylibrary.org/page/' . $publication->pageIdentifiers[0] . '" target="_new">BHL</a></li>';
}
}
if (isset($publication->urls)) {
foreach ($publication->urls as $url) {
if (preg_match('/http:\\/\\/ci.nii.ac.jp\\/naid\\//', $url)) {
echo '<li>' . '<a href="' . $url . '" target="_new">' . $url . '</a></li>';
}
if (preg_match('/http:\\/\\/gallica.bnf.fr\\//', $url)) {
echo '<li>' . '<a href="' . $url . '" target="_new">' . $url . '</a></li>';
}
if (preg_match('/http:\\/\\/www.jstor.org\\//', $url)) {
echo '<li>' . '<a href="' . $url . '" target="_new">' . $url . '</a></li>';
}
}
}
echo '</div>';
echo reference_to_coins($publication);
echo '<div><a href="http://biostor.org/openurlhook.php?' . reference_to_openurl($publication) . '&webhook=' . urlencode($config['web_server'] . $config['web_root'] . 'webhook.php') . '" target="_new">OpenURL Hook</a></div>';
//------------------------------------------------------------------------------------------
// Names
$resp = $couch->send("GET", "/" . $config['couchdb'] . "/_design/publication/_view/taxonNames?key=" . urlencode('"' . $publication->_id . '"'));
$names = json_decode($resp);
if (count($names->rows) > 0) {
echo '<h3>Names published</h3>';
echo '<ul>';
foreach ($names->rows as $row) {
echo '<li>' . '<a href="id/' . $row->value->_id . '">' . $row->value->taxonName . '</a></li>';
}
echo '</ul>';
}
echo '</div>';
// --- end metadata
// Viewer
echo '<div style="position:absolute;top:0px;left:0px;width:600px;">';
$has_fulltext = isset($publication->identifiers->biostor) || isset($publication->pdf);
if (!$has_fulltext) {
if (isset($publication->identifiers->doi)) {
$url = 'http://dx.doi.org/' . $publication->identifiers->doi;
echo '<div style="width:600px;height:800px;border:1px solid rgb(192,192,192);">';
echo '<iframe src="' . $url . '" width="600" height="800" style="border: none;">';
echo '</iframe>';
echo '</div>';
} else {
if (count($publication->urls) > 0) {
$display_url = '';
foreach ($publication->urls as $url) {
if (preg_match('/http:\\/\\/ci.nii.ac.jp\\/naid\\//', $url)) {
$display_url = $url;
break;
}
if (preg_match('/http:\\/\\/gallica.bnf.fr\\//', $url)) {
$display_url = $url;
break;
}
if (preg_match('/http:\\/\\/www.jstor.org\\//', $url)) {
$display_url = $url;
break;
}
}
if ($display_url != '') {
echo '<div style="width:600px;height:800px;border:1px solid rgb(192,192,192);">';
echo '<iframe src="' . $display_url . '" width="600" height="800" style="border: none;">';
echo '</iframe>';
echo '</div>';
}
} else {
echo '<div style="width:600px;height:800px;border:1px solid rgb(192,192,192);">
<div style="position:absolute;top:300px;left:0px;width:600px;color:rgb(192,192,192);text-align:center;font-size:72px;">No content</div>
</div>';
}
}
} else {
// PDF
if (isset($publication->pdf)) {
echo '<div>';
echo '<iframe src="http://docs.google.com/viewer?url=';
echo str_replace(' ', '%20', $publication->pdf) . '&embedded=true" width="600" height="800" style="border: none;">';
echo '</iframe>';
echo '</div>';
} else {
// BioStor
if (isset($publication->identifiers->biostor)) {
echo '<script> pages=[' . join(",", $publication->pageIdentifiers) . ']; </script>';
echo '
<div style="position:relative;width:600px;height:800px;">
<div id="header" >
<div style="float:right;padding:8px;margin-right:10px;">
<span id="page_counter">1/?</span>
<span> </span>
<span> </span>
<img id="previous_page" src="images/previous.png" border="0" onclick="previous();" title="Show previous page">
<span> </span>
<img id="next_page" src="images/next.png" border="0" onclick="next();" title="Show next page">
<span> </span>
<span> </span>
<span> </span>
<img src="images/fourpages.png" border="0" onclick="show_all_pages();" title="Show all pages">
<span> </span>
<img src="images/onepage.png" border="0" onclick="show_page(-1);" title="Fit page to viewer">
</div>
</div>
<div id="page_container">
<img id="page_image" />
<div id="all_pages" ></div>
</div>
</div>
<script>
show_page(0);
</script>';
}
}
}
echo '</div>
</div>';
} else {
//----------------------------------------------------------------------------------------------
// Home
echo '<span><a href="' . $config['web_root'] . '">' . $config['site_name'] . '</a></span>';
echo html_search_box();
//----------------------------------------------------------------------------------------------
// Object
echo '<div>';
echo '<h1>' . $publication->title . '</h1>';
echo '<div>' . 'by ' . reference_authors_to_text_string($publication->authors, false, true) . '</div>';
echo '<div>' . '<i>' . $publication->publication_outlet . '</i>' . ' ' . $publication->volume . ':' . $publication->pages . ' (' . $publication->year . ')' . '</div>';
//echo '<div>' . $publication->_id . '</div>';
/*
if (isset($publication->abstract))
{
echo '<div>' . $publication->abstract . '</div>';
}
*/
// External links
echo '<ul>';
if (isset($publication->identifiers)) {
if (isset($publication->identifiers->doi)) {
echo '<li>' . '<a href="http://dx.doi.org/' . $publication->identifiers->doi . '" target="_new">doi:' . $publication->identifiers->doi . '</a></li>';
}
if (isset($publication->identifiers->hdl)) {
echo '<li>' . '<a href="http://hdl.handle.net/' . $publication->identifiers->hdl . '" target="_new">hdl:' . $publication->identifiers->hdl . '</a></li>';
}
if (isset($publication->identifiers->biostor)) {
echo '<li>' . '<a href="http://biostor.org/reference/' . $publication->identifiers->biostor . '" target="_new">BioStor</a></li>';
}
if (isset($publication->pageIdentifiers)) {
echo '<li>' . '<a href="http://biodiversitylibrary.org/page/' . $publication->pageIdentifiers[0] . '" target="_new">BHL</a></li>';
}
}
if (isset($publication->urls)) {
foreach ($publication->urls as $url) {
if (preg_match('/http:\\/\\/ci.nii.ac.jp\\/naid\\//', $url)) {
echo '<li>' . '<a href="' . $url . '" target="_new">' . $url . '</a></li>';
}
}
}
echo '</ul>';
echo '</div>';
//----------------------------------------------------------------------------------------------
// Names
$resp = $couch->send("GET", "/" . $config['couchdb'] . "/_design/publication/_view/taxonNames?key=" . urlencode('"' . $publication->_id . '"'));
$names = json_decode($resp);
if (count($names->rows) > 0) {
echo '<h2>Names published</h2>';
echo '<ul>';
foreach ($names->rows as $row) {
echo '<li>' . '<a href="id/' . $row->value->_id . '">' . $row->value->taxonName . '</a></li>';
}
echo '</ul>';
}
//----------------------------------------------------------------------------------------------
// Content
echo '<h2>Content</h2>';
$has_fulltext = isset($publication->identifiers->biostor) || isset($publication->pdf);
if (!$has_fulltext) {
if (isset($publication->identifiers->doi)) {
$url = 'http://dx.doi.org/' . $publication->identifiers->doi;
echo '<div>';
echo '<iframe src="' . $url . '" width="100%" height="700" style="border: none;">';
echo '</iframe>';
echo '</div>';
}
} else {
// PDF
if (isset($publication->pdf)) {
echo '<div>';
echo '<iframe src="http://docs.google.com/viewer?url=';
echo urlencode($publication->pdf) . '&embedded=true" width="700" height="700" style="border: none;">';
echo '</iframe>';
echo '</div>';
} else {
// BioStor
if (isset($publication->identifiers->biostor)) {
echo '<script> pages=[' . join(",", $publication->pageIdentifiers) . ']; </script>';
echo '
<div style="position:relative;width:700px;height:700px;">
<div id="header" >
<div style="float:right;padding:8px;margin-right:10px;">
<span id="page_counter">1/?</span>
<span> </span>
<span> </span>
<img id="previous_page" src="images/previous.png" border="0" onclick="previous();" title="Show previous page">
<span> </span>
<img id="next_page" src="images/next.png" border="0" onclick="next();" title="Show next page">
<span> </span>
<span> </span>
<span> </span>
<img src="images/fourpages.png" border="0" onclick="show_all_pages();" title="Show all pages">
<span> </span>
<img src="images/onepage.png" border="0" onclick="show_page(-1);" title="Fit page to viewer">
</div>
</div>
<div id="page_container">
<img id="page_image" />
<div id="all_pages" ></div>
</div>
</div>
<script>
show_page(0);
</script>';
}
}
}
}
echo html_body_close();
echo html_html_close();
}
