$divs = array();
database_connect(IL_DATABASE_PATH, 'library');
$query = join(",", $display_files);
$result = $dbHandle->query("SELECT id,file,title FROM library WHERE id IN (" . $query . ")");
$dbHandle = null;
$result = $result->fetchAll(PDO::FETCH_ASSOC);
//SORT QUERY RESULTS
$tempresult = array();
foreach ($result as $row) {
$key = array_search($row['id'], $export_files);
$tempresult[$key] = $row;
}
ksort($tempresult);
$result = $tempresult;
foreach ($result as $item) {
$divs[] = '<div id="list-item-' . $item['id'] . '" data-id="' . $item['id'] . '" data-file="' . $item['file'] . '" class="items listleft">' . lib_htmlspecialchars($item['title']) . '</div>';
}
$result = null;
$hr = '<div class="separator"></div>';
print join($hr, $divs);
if ($offset < count($export_files) - 20) {
print '<button id="nav-next" data-id="' . $export_files[$offset + 20] . '"><i class="fa fa-caret-down"></i></button>';
}
?>
</div>
<div class="alternating_row middle-panel"
style="float:left;width:6px;height:100%;overflow:hidden;border-right:1px solid rgba(0,0,0,0.2);border-left:1px solid rgba(0,0,0,0.2);cursor:pointer">
<i class="fa fa-caret-left" style="position:relative;left:1px;top:48%"></i>
</div>
<div style="width:auto;height:100%;overflow:hidden" id="items-right" data-file="<?php
echo $_GET['file'];
empty($_POST['custom1']) ? $custom1 = '' : ($custom1 = trim($_POST['custom1']));
empty($_POST['custom2']) ? $custom2 = '' : ($custom2 = trim($_POST['custom2']));
empty($_POST['custom3']) ? $custom3 = '' : ($custom3 = trim($_POST['custom3']));
empty($_POST['custom4']) ? $custom4 = '' : ($custom4 = trim($_POST['custom4']));
empty($_POST['bibtex']) ? $bibtex = '' : ($bibtex = trim($_POST['bibtex']));
empty($_POST['bibtex_type']) ? $bibtex_type = '' : ($bibtex_type = trim($_POST['bibtex_type']));
if (!empty($title)) {
$database_update = $stmt->execute();
}
if ($database_update == false) {
$error = "Error! The database has not been updated.";
}
$stmt = null;
$dbHandle = null;
if (empty($error)) {
die('title:' . lib_htmlspecialchars($title));
}
} elseif (isset($_POST['form_sent'])) {
$error = 'Error! Title is mandatory.';
}
if (!empty($error)) {
die($error);
}
########## read reference data ##########
database_connect(IL_DATABASE_PATH, 'library');
$file_query = $dbHandle->quote($_GET['file']);
$record = $dbHandle->query("SELECT * FROM library WHERE id={$file_query} LIMIT 1");
$paper = $record->fetch(PDO::FETCH_ASSOC);
$paper_urls = array();
if (!empty($paper['url'])) {
$paper_urls = explode('|', $paper['url']);
function show_search_results($result, $select, $display, $shelf_files, $desktop_projects, $tempdbHandle)
{
$project = '';
if (!empty($_GET['project'])) {
$project = $_GET['project'];
}
$i = 0;
if ($display == 'icons') {
print '<table cellspacing=0 id="icon-container" style="border:0;width:100%">
<tr><td class="alternating_row" style="width:100%;border-bottom:1px #c5c6c8 solid;border-top:1px #c5c6c8 solid;padding-bottom:11px">';
}
while (list($key, $paper) = each($result)) {
$pmid_url = '';
$pmcid_url = '';
$nasaads_url = '';
$arxiv_url = '';
$jstor_url = '';
$other_urls = '';
$urls = '';
$other_urls = '';
$uids = array();
$pmid = '';
$pmid_related_url = '';
$pmid_citedby_pmc = '';
$nasaid = '';
$nasa_related_url = '';
$nasa_citedby_pmc = '';
$ieeeid = '';
if (!empty($paper['uid'])) {
$uids = explode("|", $paper['uid']);
while (list($key, $uid) = each($uids)) {
if (preg_match('/PMID:/', $uid)) {
$pmid = preg_replace('/PMID:/', '', $uid);
}
if (preg_match('/NASAADS:/', $uid)) {
$nasaid = preg_replace('/NASAADS:/', '', $uid);
}
if (preg_match('/IEEE:/', $uid)) {
$ieeeid = preg_replace('/IEEE:/', '', $uid);
}
}
}
if (!empty($paper['url'])) {
$urls = explode("|", $paper['url']);
while (list($key, $url) = each($urls)) {
if (preg_match('/pubmed\\.org/', $url)) {
$pmid_url = $url;
} elseif (preg_match('/pubmedcentral\\.nih\\.gov/', $url) || preg_match('/\\/pmc\\//', $url)) {
$pmcid_url = $url;
} elseif (preg_match('/adsabs\\.harvard\\.edu/', $url)) {
$nasaads_url = $url;
} elseif (preg_match('/arxiv\\.org/', $url)) {
$arxiv_url = $url;
} elseif (preg_match('/jstor\\.org/', $url)) {
$jstor_url = $url;
} else {
$other_urls[] = $url;
}
}
}
if (!empty($pmid)) {
$pmid_related_url = 'http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=link&linkname=pubmed_pubmed&uid=' . $pmid;
$pmid_citedby_pmc = 'http://www.ncbi.nlm.nih.gov/pubmed?db=pubmed&cmd=link&linkname=pubmed_pubmed_citedin&uid=' . $pmid;
}
if (!empty($nasaid)) {
$nasa_related_url = 'http://adsabs.harvard.edu/cgi-bin/nph-abs_connect?return_req=no_params&text=' . urlencode($paper['abstract']) . '&title=' . urlencode($paper['title']);
$nasa_citedby_pmc = 'http://adsabs.harvard.edu/cgi-bin/nph-data_query?bibcode=' . $nasaid . '&link_type=CITATIONS';
}
if (!empty($ieeeid)) {
$ieee_url = 'http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=' . $ieeeid;
}
if (!empty($paper['authors'])) {
$array = array();
$new_authors = array();
$array = explode(';', $paper['authors']);
$array = array_filter($array);
if (!empty($array)) {
foreach ($array as $author) {
$array2 = explode(',', $author);
$last = trim($array2[0]);
$last = substr($array2[0], 3, -1);
$first = trim($array2[1]);
$first = substr($array2[1], 3, -1);
$new_authors[] = '<a href="display.php?select=' . $select . '&browse[' . urlencode($last . ', ' . $first) . ']=authors" class="navigation">' . htmlspecialchars($last . ', ' . $first) . '</a>';
}
$paper['authors'] = join('; ', $new_authors);
}
}
$paper['journal'] = htmlspecialchars($paper['journal']);
$paper['title'] = lib_htmlspecialchars($paper['title']);
$paper['abstract'] = lib_htmlspecialchars($paper['abstract']);
$paper['year'] = htmlspecialchars($paper['year']);
#######new date#########
$date = '';
if (!empty($paper['year'])) {
$date_array = array();
$date_array = explode('-', $paper['year']);
if (count($date_array) == 1) {
$date = $paper['year'];
} else {
if (empty($date_array[0])) {
$date_array[0] = '1969';
}
if (empty($date_array[1])) {
$date_array[1] = '01';
}
if (empty($date_array[2])) {
$date_array[2] = '01';
}
$date = date('Y M j', mktime(0, 0, 0, $date_array[1], $date_array[2], $date_array[0]));
}
}
$result2 = $tempdbHandle->query("SELECT notesID,notes FROM temp_notes WHERE fileID=" . intval($paper['id']) . " LIMIT 1");
$fetched = $result2->fetch(PDO::FETCH_ASSOC);
$result2 = null;
$paper['notesID'] = $fetched['notesID'];
$paper['notes'] = $fetched['notes'];
$i = $i + 1;
if ($display == 'icons') {
if (!extension_loaded('gd')) {
die('<p> Error! Icon view requires GD extension and Ghostscript.</p>');
}
$first_author = ' ';
$auth_arr = explode(';', $paper['authors']);
$auth_arr2 = explode(',', strip_tags($auth_arr[0]));
if (!empty($auth_arr2[0])) {
$first_author = $auth_arr2[0];
}
$etal = '';
if (count($auth_arr) > 1) {
$etal = ', et al.';
}
print '<div class="thumb-items" id="display-item-' . $paper['id'] . '" data-file="' . $paper['file'] . '"><div>';
print '<div class="thumb-titles"><div style="overflow:hidden;white-space:nowrap"><b>' . $paper['title'] . '</b><br>' . $first_author . $etal;
if (!empty($paper['year'])) {
print ' (' . substr($paper['year'], 0, 4) . ')';
}
print '</div></div>';
if (date('Y-m-d') == $paper['addition_date']) {
print '<div class="new-item ui-state-error-text">New!</div>';
}
if (is_readable('library/' . $paper['file'])) {
if (isset($_SESSION['pdfviewer']) && $_SESSION['pdfviewer'] == 'external') {
print '<a href="' . htmlspecialchars('downloadpdf.php?file=' . urlencode($paper['file']) . '#pagemode=none&scrollbar=1&navpanes=0&toolbar=1&statusbar=0&page=1&view=FitH,0') . '" target="_blank" style="display:block">';
}
if (!isset($_SESSION['pdfviewer']) || isset($_SESSION['pdfviewer']) && $_SESSION['pdfviewer'] == 'internal') {
print '<a href="' . htmlspecialchars('viewpdf.php?file=' . urlencode($paper['file']) . '&title=' . urlencode($paper['title'])) . '" target="_blank" style="width:360px;height:240px;display:block">';
}
print '<img src="icon.php?file=' . $paper['file'] . '" style="width:360px;height:240px;border:0" alt="Loading PDF..."></a>';
} else {
print '<div style="margin-top:90px;margin-left:150px;font-size:18px;color:#b5b6b8">No PDF</div>';
}
print '</div>';
print PHP_EOL . '<table class="item-sticker" style="margin:6px 0;width:100%"><tr><td class="noprint ui-corner-all" style="padding:5px 8px;border:1px solid #c5c6c8">';
print '<i class="fa fa-plus-circle expander view-icon" style="margin-right:0.5em"></i>';
print '<span><i class="star ' . ($paper['rating'] >= 1 ? 'ui-state-error-text' : 'ui-priority-secondary') . ' fa fa-star"></i>';
print ' <i class="star ' . ($paper['rating'] >= 2 ? 'ui-state-error-text' : 'ui-priority-secondary') . ' fa fa-star"></i>';
print ' <i class="star ' . ($paper['rating'] == 3 ? 'ui-state-error-text' : 'ui-priority-secondary') . ' fa fa-star"></i></span> ';
print '<b style="margin:0 0.5em">·</b>';
if (isset($shelf_files) && in_array($paper['id'], $shelf_files)) {
print ' <span class="update_shelf clicked"><i class="update_shelf fa fa-check-square ui-state-error-text"></i> Shelf </span>';
} else {
print ' <span class="update_shelf"><i class="update_shelf fa fa-square-o"></i> Shelf </span>';
}
if (isset($_SESSION['session_clipboard']) && in_array($paper['id'], $_SESSION['session_clipboard'])) {
print ' <span class="update_clipboard clicked"><i class="update_clipboard fa fa-check-square ui-state-error-text"></i> Clipboard </span>';
} else {
print ' <span class="update_clipboard"><i class="update_clipboard fa fa-square-o"></i> Clipboard </span>';
}
foreach ($desktop_projects as $desktop_project) {
$project_rowid = $tempdbHandle->query("SELECT ROWID FROM temp_projects WHERE projectID=" . intval($desktop_project['projectID']) . " AND fileID=" . intval($paper['id']) . " LIMIT 1");
$project_rowid = $project_rowid->fetchColumn();
if (!empty($project_rowid)) {
print ' <span data-projid="' . $desktop_project['projectID'] . '" class="update_project clicked" style="white-space:nowrap;padding-right:0.5em"><i class="update_project fa fa-check-square ui-state-error-text"></i> ' . htmlspecialchars($desktop_project['project']) . '</span>';
}
if (empty($project_rowid)) {
print ' <span data-projid="' . $desktop_project['projectID'] . '" class="update_project" style="white-space:nowrap;padding-right:0.5em"><i class="update_project fa fa-square-o"></i> ' . htmlspecialchars($desktop_project['project']) . '</span>';
}
$project_rowid = null;
}
print PHP_EOL . '</td></tr></table></div>';
} else {
print PHP_EOL . '<div id="display-item-' . $paper['id'] . '" class="items" data-file="' . $paper['file'] . '" style="padding:0 0 10px 0">';
include 'coins.php';
print '<div class="ui-widget-header" style="overflow:hidden;border-left:0;border-right:0;padding:2px 6px">';
if (is_file('library/' . $paper['file']) && isset($_SESSION['auth'])) {
if (isset($_SESSION['pdfviewer']) && $_SESSION['pdfviewer'] == 'external') {
print '<div class="noprint titles-pdf" style="float:left;text-shadow:1px 1px 1px white">
<a class="ui-state-error-text" href="' . htmlspecialchars('downloadpdf.php?file=' . urlencode($paper['file']) . '#pagemode=none&scrollbar=1&navpanes=0&toolbar=1&statusbar=0&page=1&view=FitH,0') . '" target="_blank" style="display:block">
PDF</a></div>';
}
if (!isset($_SESSION['pdfviewer']) || isset($_SESSION['pdfviewer']) && $_SESSION['pdfviewer'] == 'internal') {
print '<div class="noprint titles-pdf" style="float:left;text-shadow:1px 1px 1px white">
<a class="ui-state-error-text" href="' . htmlspecialchars('viewpdf.php?file=' . urlencode($paper['file']) . '&title=' . urlencode($paper['title'])) . '" target="_blank" style="display:block">
PDF</a></div>';
}
} else {
print PHP_EOL . '<div class="ui-state-error-text noprint titles-pdf" style="float:left;color:#c5c6c8;cursor:auto">PDF</div>';
}
print PHP_EOL . '<div class="titles brief">' . $paper['title'] . '</div>';
print '</div>';
print '<div style="clear:both"></div>';
print '<table class="noprint"><tr><td style="width:24px;padding-top:8px;padding-left:12px">';
if ($display != 'abstract') {
print PHP_EOL . '<i class="expander fa fa-plus-circle view-' . $display . '"></i>';
}
print '</td><td style="padding-top:8px">';
if (isset($shelf_files) && in_array($paper['id'], $shelf_files)) {
print '<span class="update_shelf clicked"><i class="update_shelf fa fa-check-square ui-state-error-text"></i> Shelf </span>';
} else {
print '<span class="update_shelf"><i class="update_shelf fa fa-square-o"></i> Shelf </span>';
}
if (isset($_SESSION['session_clipboard']) && in_array($paper['id'], $_SESSION['session_clipboard'])) {
print ' <span class="update_clipboard clicked"><i class="update_clipboard fa fa-check-square ui-state-error-text"></i> Clipboard </span>';
} else {
print ' <span class="update_clipboard"><i class="update_clipboard fa fa-square-o"></i> Clipboard </span>';
}
foreach ($desktop_projects as $desktop_project) {
$project_rowid = $tempdbHandle->query("SELECT ROWID FROM temp_projects WHERE projectID=" . intval($desktop_project['projectID']) . " AND fileID=" . intval($paper['id']) . " LIMIT 1");
$project_rowid = $project_rowid->fetchColumn();
if (!empty($project_rowid)) {
print ' <span data-projid="' . $desktop_project['projectID'] . '" class="update_project clicked" style="white-space:nowrap;padding-right:0.5em"><i class="update_project fa fa-check-square ui-state-error-text"></i> ' . htmlspecialchars($desktop_project['project']) . '</span>';
}
if (empty($project_rowid)) {
print ' <span data-projid="' . $desktop_project['projectID'] . '" class="update_project" style="white-space:nowrap;padding-right:0.5em"><i class="update_project fa fa-square-o"></i> ' . htmlspecialchars($desktop_project['project']) . '</span>';
}
$project_rowid = null;
}
print PHP_EOL . '</td></tr></table>';
print PHP_EOL . '<div class="display-summary" style="margin:0 30px;';
print $display == 'brief' ? 'display:none">' : '">';
if (!empty($paper['authors'])) {
print PHP_EOL . '<div class="authors"><i class="author_expander fa fa-plus-circle"></i> ' . $paper['authors'] . '</div>';
}
print !empty($paper['journal']) ? $paper['journal'] : $paper['secondary_title'];
print !empty($date) ? ' (' . htmlspecialchars($date) . ')' : '';
if (!empty($paper['volume'])) {
print ' <b>' . htmlspecialchars($paper['volume']) . '</b>';
}
if (!empty($paper['pages'])) {
print ': ' . htmlspecialchars($paper['pages']);
}
if (date('Y-m-d') == $paper['addition_date']) {
$today = ' <span class="ui-state-error-text"><b>New!</b></span>';
} else {
$today = '';
}
$result2 = $tempdbHandle->query("SELECT categoryID,category FROM temp_categories WHERE fileID=" . intval($paper['id']) . " ORDER BY category COLLATE NOCASE ASC");
while ($categories = $result2->fetch(PDO::FETCH_ASSOC)) {
$category_array[] = '<a href="' . htmlspecialchars('display.php?browse[' . urlencode($categories['categoryID']) . ']=category&select=' . $select . '&project=' . $project) . '" class="navigation">' . htmlspecialchars($categories['category']) . '</a>';
}
if (empty($category_array[0])) {
$category_array[0] = '<a href="' . htmlspecialchars('display.php?browse[0]=category&select=' . $select) . '" class="navigation">!unassigned</a>';
}
print '<br><span><i class="star ' . ($paper['rating'] >= 1 ? 'ui-state-error-text' : 'ui-priority-secondary') . ' fa fa-star"></i>';
print ' <i class="star ' . ($paper['rating'] >= 2 ? 'ui-state-error-text' : 'ui-priority-secondary') . ' fa fa-star"></i>';
print ' <i class="star ' . ($paper['rating'] == 3 ? 'ui-state-error-text' : 'ui-priority-secondary') . ' fa fa-star"></i></span> ';
print '<b style="margin:0 0.5em">·</b>';
if (!empty($paper['bibtex'])) {
print htmlspecialchars($paper['bibtex']);
} else {
$bibtex_author = strip_tags($paper['authors']);
$bibtex_author = substr($bibtex_author, 0, strpos($bibtex_author, ','));
if (empty($bibtex_author)) {
$bibtex_author = 'unknown';
}
$bibtex_year = '0000';
$bibtex_year_array = explode('-', $paper['year']);
if (!empty($bibtex_year_array[0])) {
$bibtex_year = $bibtex_year_array[0];
}
$bibtex_key = utf8_deaccent($bibtex_author) . '-' . $bibtex_year . '-ID' . $paper['id'];
print htmlspecialchars($bibtex_key);
}
print '<b style="margin:0 0.5em">·</b>';
print 'Category: ';
$category_string = join(", ", $category_array);
$category_array = null;
print $category_string;
print '<b style="margin:0 0.5em">·</b> Added: <a href="display.php?select=' . $select . '&browse[' . $paper['addition_date'] . ']=addition_date" class="navigation">' . date('M jS, Y', strtotime($paper['addition_date'])) . '</a>' . $today;
print '<div class="noprint display-abstract"';
print $display != 'abstract' ? ' style="display:none"' : '';
print '>';
if (!empty($pmid_url)) {
print '<a href="' . htmlspecialchars($pmid_url) . '" target="_blank">PubMed</a> <b style="margin:0 0.5em">·</b> ';
}
if (!empty($pmid_related_url)) {
print '<a href="' . htmlspecialchars($pmid_related_url) . '" target="_blank">Related Articles</a> <b style="margin:0 0.5em">·</b> ';
}
if (!empty($pmid_citedby_pmc)) {
print '<a href="' . htmlspecialchars($pmid_citedby_pmc) . '" target="_blank">Cited by</a> <b style="margin:0 0.5em">·</b> ';
}
if (!empty($pmcid_url)) {
print '<a href="' . htmlspecialchars($pmcid_url) . '" target="_blank">PubMed Central</a> <b style="margin:0 0.5em">·</b> ';
}
if (!empty($nasaads_url)) {
print '<a href="' . htmlspecialchars($nasaads_url) . '" target="_blank">NASA ADS</a> <b style="margin:0 0.5em">·</b> ';
}
if (!empty($nasa_related_url)) {
print '<a href="' . htmlspecialchars($nasa_related_url) . '" target="_blank">Related Articles</a> <b style="margin:0 0.5em">·</b> ';
}
if (!empty($nasa_citedby_pmc)) {
print '<a href="' . htmlspecialchars($nasa_citedby_pmc) . '" target="_blank">Cited by</a> <b style="margin:0 0.5em">·</b> ';
}
if (!empty($arxiv_url)) {
print '<a href="' . htmlspecialchars($arxiv_url) . '" target="_blank">arXiv</a> <b style="margin:0 0.5em">·</b> ';
}
if (!empty($jstor_url)) {
print '<a href="' . htmlspecialchars($jstor_url) . '" target="_blank">JSTOR</a> <b style="margin:0 0.5em">·</b> ';
}
if (!empty($ieee_url)) {
print '<a href="' . htmlspecialchars($ieee_url) . '" target="_blank">IEEE</a> <b style="margin:0 0.5em">·</b> ';
}
if (!empty($paper['doi'])) {
print '<a href="' . htmlspecialchars('http://dx.doi.org/' . urlencode($paper['doi'])) . '" target="_blank">Publisher Website</a> <b style="margin:0 0.5em">·</b> ';
}
if (!empty($other_urls)) {
foreach ($other_urls as $another_url) {
print '<a href="' . htmlspecialchars($another_url) . '" target="_blank" class="anotherurl" title="' . htmlspecialchars(parse_url($another_url, PHP_URL_HOST)) . '">Link</a> <b style="margin:0 0.5em">·</b> ';
}
}
print '<a href="stable.php?id=' . $paper['id'] . '" target="_blank">Stable Link</a>';
print '</div>';
print '<div class="abstract display-abstract" style="';
print $display != 'abstract' ? 'display:none' : '';
print '">' . $paper['abstract'] . '</div>';
print '<div class="display-abstract" style="';
print $display != 'abstract' ? 'display:none' : '';
print '">';
if (!empty($paper['notes'])) {
print '<div class="item-sticker ui-widget-content ui-corner-all" style="margin:6px;width:340px;float:left">
<div class="ui-widget-header items ui-corner-top" style="border:0"><b class="ui-dialog-titlebar">Notes</b></div><div class="separator" style="margin:0"></div>
<div class="alternating_row ui-corner-bottom" style="padding:4px 7px;max-height:200px;overflow:auto">' . $paper['notes'] . '
</div></div>';
}
if (is_file(graphical_abstract($paper['file']))) {
print '<div class="item-sticker ui-widget-content ui-corner-all" style="margin:6px;width:340px;float:left">
<div class="ui-widget-header items ui-corner-top" style="border:0"><b class="ui-dialog-titlebar">Graphical Abstract</b></div><div class="separator" style="margin:0"></div>
<div class="alternating_row ui-corner-bottom" style="padding:4px 7px;max-height:200px;overflow:auto">
<img src="' . htmlspecialchars('attachment.php?mode=inline&attachment=' . basename(graphical_abstract($paper['file']))) . '">
</div></div>';
}
print '</div></div></div>';
}
}
if ($display == 'icons') {
print '</td></tr></table>';
}
}
$_GET['select'] = 'library';
}
$select = $_GET['select'];
} else {
$select = 'library';
}
if (isset($_GET['file'])) {
$query = $dbHandle->quote($_GET['file']);
if (!isset($paper)) {
$result = $dbHandle->query("SELECT * FROM library WHERE id={$query} LIMIT 1");
$paper = $result->fetch(PDO::FETCH_ASSOC);
}
if (!empty($paper['id'])) {
$paper['journal'] = htmlspecialchars($paper['journal']);
$paper['title'] = lib_htmlspecialchars($paper['title']);
$paper['abstract'] = lib_htmlspecialchars($paper['abstract']);
$paper['year'] = htmlspecialchars($paper['year']);
#######new date#########
$date = '';
if (!empty($paper['year'])) {
$date_array = array();
$date_array = explode('-', $paper['year']);
if (count($date_array) == 1) {
$date = $paper['year'];
} else {
if (empty($date_array[0])) {
$date_array[0] = '1969';
}
if (empty($date_array[1])) {
$date_array[1] = '01';
}