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file_top.php
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file_top.php
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<?php
include_once 'data.php';
include_once 'functions.php';
session_write_close();
if (isset($_SESSION['auth'])) {
$cache_name = cache_name();
$db_change = database_change(array(
'library',
'shelves',
'projectsusers',
'projectsfiles',
'filescategories',
'notes'
));
cache_start($db_change);
}
database_connect($database_path, 'library');
$shelf_files = array();
$shelf_files = read_shelf($dbHandle);
$desktop_projects = array();
$desktop_projects = read_desktop($dbHandle);
if (isset($_GET['select'])) {
if ($_GET['select'] != 'library' &&
$_GET['select'] != 'shelf' &&
$_GET['select'] != 'project' &&
$_GET['select'] != 'clipboard') {
$_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']);
$paper['title'] = htmlspecialchars($paper['title']);
$paper['abstract'] = htmlspecialchars($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]));
}
}
print '<div id="file-panel2"><div id="file-item-' . $paper['id'] . '" class="items alternating_row" data-file="' . $paper['file'] . '">';
print '<div class="titles file-title">' . $paper['title'] . '</div>';
$authors_string = '';
if (!empty($paper['authors'])) {
$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[] = $last.', '.$first;
}
$authors_string = join('; ', $new_authors);
}
print '<div class="authors"><span class="author_expander ui-icon ui-icon-circlesmall-plus" style="float:left"></span><div>'.htmlspecialchars($authors_string).'</div></div>';
}
if (!empty($paper['affiliation']))
print '<div class="authors"><span class="author_expander ui-icon ui-icon-circlesmall-plus" style="float:left"></span><div>' . $paper['affiliation'] . '</div></div>';
print '<i>';
if (!empty($paper['journal'])) {
print $paper['journal'];
} elseif (!empty($paper['secondary_title'])) {
print $paper['secondary_title'];
}
if (!empty($date))
print " ($date)";
if (!empty($paper['volume']))
print " <b>$paper[volume]</b>";
if (!empty($paper['issue']))
print " ($paper[issue])";
if (!empty($paper['pages']))
print ": $paper[pages].";
print "</i><br>";
if (isset($_SESSION['auth'])) {
print '<div class="star ' . (($paper['rating'] >= 1) ? 'ui-state-error-text' : 'ui-priority-secondary') . '" id="file-star-' . $paper['id'] . '-1"><span class="ui-icon ui-icon-star"></span></div>';
print '<div class="star ' . (($paper['rating'] >= 2) ? 'ui-state-error-text' : 'ui-priority-secondary') . '" id="file-star-' . $paper['id'] . '-2"><span class="ui-icon ui-icon-star"></span></div>';
print '<div class="star ' . (($paper['rating'] == 3) ? 'ui-state-error-text' : 'ui-priority-secondary') . '" id="file-star-' . $paper['id'] . '-3"><span class="ui-icon ui-icon-star"></span></div>';
}
$result = $dbHandle->query("SELECT categoryID,category
FROM categories
WHERE categoryID IN (SELECT categoryID
FROM filescategories
WHERE fileID=$query)
ORDER BY category COLLATE NOCASE ASC");
while ($categories = $result->fetch(PDO::FETCH_ASSOC)) {
$category_array[] = htmlspecialchars($categories['category']);
}
if (empty($category_array[0]))
$category_array[0] = '!unassigned';
$category_string = join(", ", $category_array);
$category_array = null;
if (is_file("library/$paper[file]") && isset($_SESSION['auth'])) {
if (!isset($_SESSION['pdfviewer']) || (isset($_SESSION['pdfviewer']) && $_SESSION['pdfviewer'] == 'external'))
print ' <b>·</b> <a title="Open PDF in new window" href="'.htmlspecialchars('downloadpdf.php?file='.urlencode($paper['file']).'#pagemode=none&scrollbar=1&navpanes=0&toolbar=1&statusbar=0&page=1&view=FitH,0').'" target="_blank" class="pdf_link">
<span class="ui-state-highlight" style="padding:0px 2px 0px 2px;margin-right:2px"> PDF </span></a>';
if (isset($_SESSION['pdfviewer']) && $_SESSION['pdfviewer'] == 'internal')
print ' <b>·</b> <a title="Open PDF in new window" href="'.htmlspecialchars('viewpdf.php?file='.urlencode($paper['file']).'&title='.urlencode($paper['title'])).'" target="_blank" class="pdf_link">
<span class="ui-state-highlight ui-corner-all" style="padding:0px 2px 0px 2px;margin-right:2px"> PDF </span></a>';
}
if (!empty($paper['doi'])) {
print ' <b>·</b> <a href="http://dx.doi.org/' . urlencode($paper['doi']) . '" target="_blank">Publisher Website</a>';
}
if (!empty($paper['url'])) {
$pmid_url = '';
$pmcid_url = '';
$nasaads_url = '';
$arxiv_url = '';
$jstor_url = '';
$pmid_related_url = '';
$pmid_citedby_pmc = '';
$nasa_related_url = '';
$nasa_citedby_pmc = '';
$other_urls = array();
$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[] = $url;
}
}
}
if (!empty($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);
}
$uids = null;
}
if (!empty($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($pmid_url)) {
print " <b>·</b> <a href=\"" . htmlspecialchars($pmid_url) . "\" target=\"_blank\">PubMed</a>";
}
if (!empty($pmid_related_url)) {
print ' <b>·</b> <a href="' . htmlspecialchars($pmid_related_url) . '" target="_blank">
Related Articles</a>';
}
if (!empty($pmid_citedby_pmc)) {
print ' <b>·</b> <a href="' . htmlspecialchars($pmid_citedby_pmc) . '" target="_blank">
Cited by</a>';
}
if (!empty($pmcid_url)) {
print " <b>·</b> <a href=\"" . htmlspecialchars($pmcid_url) . "\" target=\"_blank\">PubMed Central</a>";
}
if (!empty($nasaads_url)) {
print " <b>·</b> <a href=\"" . htmlspecialchars($nasaads_url) . "\" target=\"_blank\">NASA ADS</a>";
}
if (!empty($nasa_related_url)) {
print ' <b>·</b> <a href="' . htmlspecialchars($nasa_related_url) . '" target="_blank" title="Related Articles">Related Articles</a>';
}
if (!empty($nasa_citedby_pmc)) {
print ' <b>·</b> <a href="' . htmlspecialchars($nasa_citedby_pmc) . '" target="_blank" title="Cited by">Cited by</a>';
}
if (!empty($arxiv_url)) {
print " <b>·</b> <a href=\"" . htmlspecialchars($arxiv_url) . "\" target=\"_blank\">arXiv</a>";
}
if (!empty($jstor_url)) {
print " <b>·</b> <a href=\"" . htmlspecialchars($jstor_url) . "\" target=\"_blank\">
JSTOR</a>";
}
if (!empty($ieee_url)) {
print ' <b>·</b> <a href="' . htmlspecialchars($ieee_url) . '" target="_blank">IEEE</a>';
}
if (!empty($other_urls)) {
foreach ($other_urls as $another_url) {
$url_host = htmlspecialchars(parse_url($another_url, PHP_URL_HOST));
print " <b>·</b> <a href=\"" . htmlspecialchars($another_url) . "\" target=\"_blank\" class=\"another_url\" title=\"$url_host\">Link</a>";
}
}
print '<div style="clear:both"></div>';
if (isset($_SESSION['auth'])) {
print ' <div class="noprint">';
if (isset($shelf_files) && !in_array($paper['id'], $shelf_files))
print '<div class="update_shelf add">
<span class="update_shelf ui-icon ui-icon-circlesmall-close" style="float:left"></span>Shelf </div>';
if (isset($shelf_files) && in_array($paper['id'], $shelf_files))
print '<div class="update_shelf remove ui-state-error-text">
<span class="update_shelf ui-icon ui-icon-check" style="float:left"></span>Shelf </div>';
if (!isset($_SESSION['session_clipboard']) || (isset($_SESSION['session_clipboard']) && !in_array($paper['id'], $_SESSION['session_clipboard'])))
print '<div class="update_clipboard add">
<span class="update_clipboard ui-icon ui-icon-circlesmall-close" style="float:left"></span>Clipboard </div>';
if (isset($_SESSION['session_clipboard']) && in_array($paper['id'], $_SESSION['session_clipboard']))
print '<div class="update_clipboard remove ui-state-error-text">
<span class="update_clipboard ui-icon ui-icon-check" style="float:left"></span>Clipboard </div>';
foreach ($desktop_projects as $desktop_project) {
$project_rowid = $dbHandle->query("SELECT ROWID FROM projectsfiles WHERE projectID=" . intval($desktop_project['projectID']) . " AND fileID=" . intval($paper['id']) . " LIMIT 1");
$project_rowid = $project_rowid->fetchColumn();
if (empty($project_rowid))
print '<div class="' . $desktop_project['projectID'] . ' update_project add">
<span class="update_project ui-icon ui-icon-circlesmall-close" style="float:left"></span>' . htmlspecialchars($desktop_project['project']) . ' </div>';
if (!empty($project_rowid))
print '<div class="' . $desktop_project['projectID'] . ' update_project remove ui-state-error-text">
<span class="update_project ui-icon ui-icon-check" style="float:left"></span>' . htmlspecialchars($desktop_project['project']) . ' </div>';
$project_rowid = null;
}
print ' </div>';
}
print '<div style="clear:both"></div>';
print " </div>";
print '<div style="margin:4px 0 4px 4px">';
print '<div class="item-sticker ui-widget-content ui-corner-all" style="margin-left:4px;margin-top:4px;width:361px;float:left">
<div class="ui-widget-header ui-dialog-titlebar items ui-corner-top" style="border:0">Abstract</div><div class="separator" style="margin:0"></div>
<div class="alternating_row abstract ui-corner-bottom" style="padding:4px 7px;overflow:auto;height:299px;column-count:auto;-moz-column-count:auto;-webkit-column-count:auto">' . $paper['abstract'] . '
</div></div>';
$notes = null;
if (isset($_SESSION['auth'])) {
$user_query = $dbHandle->quote($_SESSION['user_id']);
$result = $dbHandle->query("SELECT notesID,notes FROM notes WHERE fileID=$query AND userID=$user_query LIMIT 1");
$fetched = $result->fetch(PDO::FETCH_ASSOC);
$result = null;
$notesid = $fetched['notesID'];
$notes = $fetched['notes'];
}
print '<div class="item-sticker ui-widget-content ui-corner-all" style="margin-left:4px;margin-top:4px;width:361px;float:left">
<div class="ui-widget-header ui-dialog-titlebar items ui-corner-top" style="border:0">Notes</div><div class="separator" style="margin:0"></div>
<div class="alternating_row ui-corner-bottom" style="padding:4px 7px;height:299px;overflow:auto">' . $notes . '
</div></div>';
$integer = sprintf("%05d", intval($paper['file']));
$files_to_display = glob('library/supplement/' . $integer . '*');
$url_filename = null;
if (count($files_to_display) > 0) {
foreach ($files_to_display as $supplementary_file) {
$isimage = null;
$image_array = array();
$extension = pathinfo($supplementary_file, PATHINFO_EXTENSION);
if ($extension == 'jpg' || $extension == 'jpeg' || $extension == 'gif' || $extension == 'png') {
$image_array = @getimagesize($supplementary_file);
$image_mime = $image_array['mime'];
if ($image_mime == 'image/jpeg' || $image_mime == 'image/gif' || $image_mime == 'image/png')
$isimage = true;
}
if ($isimage)
$url_filenames[] = '<li><a href="' . htmlspecialchars($supplementary_file) . '" target="_blank">' . substr(basename($supplementary_file), 5) . '</a>';
if (!$isimage)
$url_filenames[] = '<li><a href="' . htmlspecialchars('attachment.php?attachment=' . basename($supplementary_file)) . '">' . substr(basename($supplementary_file), 5) . '</a>';
}
$url_filename = join('<br>', $url_filenames);
}
print '<div class="item-sticker ui-widget-content ui-corner-all" style="margin-left:4px;margin-top:4px;width:239px;float:left">
<div class="ui-widget-header ui-dialog-titlebar items ui-corner-top" style="border:0">Supplementary Files</div><div class="separator" style="margin:0"></div>
<div class="alternating_row ui-corner-bottom" style="padding:4px 7px;overflow:auto;height:128px"><ul style="padding-left:16px">' . $url_filename . '</ul>
</div></div>';
print '<div class="item-sticker ui-widget-content ui-corner-all" style="margin-left:4px;margin-top:4px;width:239px;float:left">
<div class="ui-widget-header ui-dialog-titlebar items ui-corner-top" style="border:0">IDs</div><div class="separator" style="margin:0"></div>
<div class="alternating_row ui-corner-bottom" style="padding:4px 7px;overflow:auto;height:128px">';
print "<u>I, Librarian ID:</u> <a href=\"stable.php?id=$paper[id]\" target=\"_blank\">" . $paper['id'] . " (stable link)</a>";
$uid_array = explode("|", $paper['uid']);
foreach ($uid_array as $uid) {
$uids[] = $uid;
}
$bibtex_author = substr($paper['authors'], 3);
$bibtex_author = substr($bibtex_author, 0, strpos($bibtex_author, '"'));
if (empty($bibtex_author))
$bibtex_author = 'unknown';
$bibtex_year_array = explode('-', $paper['year']);
$bibtex_year = '0000';
if (!empty($bibtex_year_array[0]))
$bibtex_year = $bibtex_year_array[0];
$bibtex_key = utf8_deaccent($bibtex_author) . '-' . $bibtex_year . '-ID' . $paper['id'];
print "<br><u>External IDs:</u> " . implode(", ", $uids);
print "<br><u>DOI:</u> " . $paper['doi'];
if (!empty($paper['bibtex'])) {
print '<br><u>BibTex:</u> <input type="text" class="bibtex" value="' . $paper['bibtex'] . '" style="outline:none;width:165px">';
} else {
print '<br><u>BibTex:</u> <input type="text" class="bibtex" value="' . $bibtex_key . '" style="outline:none;width:165px">';
}
print ' </div></div>';
print '<div class="item-sticker ui-widget-content ui-corner-all" style="margin-left:4px;margin-top:4px;width:239px;float:left">
<div class="ui-widget-header ui-dialog-titlebar items ui-corner-top" style="border:0">Graphical Abstract</div><div class="separator" style="margin:0"></div>
<div class="alternating_row ui-corner-bottom" style="padding:4px 7px;height:128px;overflow:auto">';
if (is_file(graphical_abstract($paper['file'])))
print '<a href="' . graphical_abstract($paper['file']) . '" target="_blank">
<img src="' . graphical_abstract($paper['file']) . '" style="width:100%"></a>';
print ' </div></div>';
print '<div class="item-sticker ui-widget-content ui-corner-all" style="margin-left:4px;margin-top:4px;width:239px;float:left">
<div class="ui-widget-header ui-dialog-titlebar items ui-corner-top" style="border:0">Categories</div><div class="separator" style="margin:0"></div>
<div class="alternating_row ui-corner-bottom" style="padding:4px 7px;overflow:auto;height:128px">' . $category_string . '
</div></div>';
print '<div class="item-sticker ui-widget-content ui-corner-all" style="margin-left:4px;margin-top:4px;width:239px;float:left">
<div class="ui-widget-header ui-dialog-titlebar items ui-corner-top" style="border:0">Keywords</div><div class="separator" style="margin:0"></div>
<div class="alternating_row ui-corner-bottom" style="padding:4px 7px;overflow:auto;height:128px">' . $paper['keywords'] . '
</div></div>';
print '<div class="item-sticker ui-widget-content ui-corner-all" style="margin-left:4px;margin-top:4px;width:239px;float:left">
<div class="ui-widget-header ui-dialog-titlebar items ui-corner-top" style="border:0">Miscellaneous</div><div class="separator" style="margin:0"></div>
<div class="alternating_row ui-corner-bottom" style="padding:4px 7px;overflow:auto;height:128px">';
print '<u>Publication type:</u> ' . $paper['reference_type'];
print '<br><u>Editor:</u> ' . $paper['editor'];
print '<br><u>Publisher:</u> ' . $paper['publisher'];
print '<br><u>Place published:</u> ' . $paper['place_published'];
print '<br><u>Custom 1:</u> ' . $paper['custom1'];
print '<br><u>Custom 2:</u> ' . $paper['custom2'];
print '<br><u>Custom 3:</u> ' . $paper['custom3'];
print '<br><u>Custom 4:</u> ' . $paper['custom4'];
print ' </div></div>';
print '<div style="clear:both"></div><br> <u>Added:</u> ' . date('F d, Y', strtotime($paper['addition_date'])) . ' by ' . get_username($dbHandle, $database_path, $paper['added_by']);
if (!empty($paper['modified_date']))
print " <b>·</b> <u>Last Modified:</u> " . date("F j, Y, g:i A", strtotime($paper['modified_date'])) . " by " . get_username($dbHandle, $database_path, $paper['modified_by']);
print '</div></div>';
print '<script type="text/javascript">$("title").text("'.$paper['title'].'")</script>';
}
}
if (isset($_SESSION['auth'])) cache_store();
?>