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++;
}
}
}
/**
* @brief Handle OpenURL request
*
* We may have more than one parameter with same name, so need to access QUERY_STRING, not _GET
* http://stackoverflow.com/questions/353379/how-to-get-multiple-parameters-with-same-name-from-a-url-in-php
*
*/
function main()
{
global $config;
global $debug;
global $format;
$id = 0;
$callback = '';
// If no query parameters
if (count($_GET) == 0) {
display_form();
exit(0);
}
if (isset($_GET['format'])) {
switch ($_GET['format']) {
case 'html':
$format = 'html';
break;
case 'json':
$format = 'json';
break;
default:
$format = 'html';
break;
}
}
if (isset($_GET['callback'])) {
$callback = $_GET['callback'];
}
$debug = false;
if (isset($_GET['debug'])) {
$debug = true;
}
// Handle query and display results.
$query = explode('&', html_entity_decode($_SERVER['QUERY_STRING']));
$params = array();
foreach ($query as $param) {
list($key, $value) = explode('=', $param);
$key = preg_replace('/^\\?/', '', urldecode($key));
$params[$key][] = trim(urldecode($value));
}
if ($debug) {
echo '<h1>Params</h1>';
echo '<pre>';
print_r($params);
echo '</pre>';
}
// This is what we got from user
$referent = new stdclass();
parse_openurl($params, $referent);
// Flesh it out
// If we are looking for an article we need an ISSN, or at least an OCLC
// Ask whether have this in our database (assumes we have ISSN)
if (!isset($referent->issn)) {
// Try and get ISSN from bioGUID
$issn = issn_from_title($referent->secondary_title);
if ($issn != '') {
$referent->issn = $issn;
} else {
// No luck with ISSN, look for OCLC
if (!isset($referent->oclc)) {
$oclc = oclc_for_title($referent->secondary_title);
if ($oclc != 0) {
$referent->oclc = $oclc;
}
}
}
}
if ($debug) {
echo '<h1>Referent</h1>';
echo '<pre>';
print_r($referent);
echo '</pre>';
}
// Handle identifiers
if (isset($referent->url)) {
// BHL URL, for example if we have already mapped article to BHL
// in Zotero,
if (preg_match('/^http:\\/\\/(www\\.)?biodiversitylibrary.org\\/page\\/(?<pageid>[0-9]+)/', $referent->url, $matches)) {
//print_r($matches);
$PageID = $matches['pageid'];
$references = bhl_reference_from_pageid($PageID);
//print_r($references);
if (count($references) == 0) {
// We don't have an article for this PageID
$search_hit = bhl_score_page($PageID, $referent->title);
// Store
$id = db_store_article($referent, $PageID);
} else {
// Have a reference with this PageID already
// Will need to handle case where > 1 article on same page, e.g.
// http://www.biodiversitylibrary.org/page/3336598
$id = $references[0];
}
// Did we get a hit?
if ($id != 0) {
// We have this reference in our database
switch ($format) {
case 'json':
// Display object
$reference = db_retrieve_reference($id);
header("Content-type: text/plain; charset=utf-8\n\n");
if ($callback != '') {
echo $callback . '(';
}
echo json_format(json_encode($reference));
if ($callback != '') {
echo ')';
}
break;
case 'html':
default:
// Redirect to reference display
header('Location: ' . $config['web_root'] . 'reference/' . $id . "\n\n");
break;
}
exit;
}
}
}
// OK, we're not forcing a match to BHL, so do we have this article?
$id = db_find_article($referent);
//echo "<b>id=$id</b><br/>";
if ($id != 0) {
// We have this reference in our database
switch ($format) {
case 'json':
// Display object
$reference = db_retrieve_reference($id);
header("Content-type: text/plain; charset=utf-8\n\n");
if ($callback != '') {
echo $callback . '(';
}
echo json_format(json_encode($reference));
if ($callback != '') {
echo ')';
}
break;
case 'html':
default:
// Twitter as log
if ($config['twitter']) {
$tweet_this = false;
$tweet_this = isset($_GET['rfr_id']);
if ($tweet_this) {
$url = $config['web_root'] . 'reference/' . $id . ' ';
// . '#openurl'; // url + hashtag
$url = $id;
$url_len = strlen($url);
$status = '';
//$text = $_GET['rfr_id'];
$text = '#openurl ' . $_SERVER["HTTP_REFERER"];
//$text .= ' @rdmpage';
if (isset($article->title)) {
}
$status = $text;
$status_len = strlen($status);
$extra = 140 - $status_len - $url_len - 1;
if ($extra < 0) {
$status_len += $extra;
$status_len -= 1;
$status = substr($status, 0, $status_len);
$status .= '…';
}
$status .= ' ' . $url;
tweet($status);
}
}
// Redirect to reference display
header('Location: reference/' . $id . "\n\n");
break;
}
exit;
}
// OK, not found, so let's go look for it...
// Search BHL
$atitle = '';
if (isset($referent->title)) {
$atitle = $referent->title;
}
$search_hits = bhl_find_article($atitle, $referent->secondary_title, $referent->volume, isset($referent->spage) ? $referent->spage : $referent->pages, isset($referent->series) ? $referent->series : '', isset($referent->date) ? $referent->date : '', isset($referent->issn) ? $referent->issn : '');
if (count($search_hits) == 0) {
// try alternative way of searching using article title
$search_hits = bhl_find_article_from_article_title($referent->title, $referent->secondary_title, $referent->volume, isset($referent->spage) ? $referent->spage : $referent->pages, isset($referent->series) ? $referent->series : '', isset($referent->issn) ? $referent->issn : '');
}
// At this point if we haven't found it in BHL we could go elsewhere, e.g. bioGUID,
// in which case we'd need to take this into account when displaying HTML and JSON
if ($debug) {
echo '<h3>Search hits</h3>';
echo '<pre>';
print_r($search_hits);
echo '</pre>';
}
if (1) {
// Check whether we already have an article that starts on this
foreach ($search_hits as $hit) {
$references = bhl_reference_from_pageid($hit->PageID);
//print_r($references);
if (count($references) != 0) {
// We have this reference in our database
switch ($format) {
case 'json':
// Display object
$reference = db_retrieve_reference($references[0]);
header("Content-type: text/plain; charset=utf-8\n\n");
if ($callback != '') {
echo $callback . '(';
}
echo json_format(json_encode($reference));
if ($callback != '') {
echo ')';
}
break;
case 'html':
default:
// Redirect to reference display
header('Location: reference/' . $references[0] . "\n\n");
break;
}
exit;
}
}
}
// Output search results in various formats...
switch ($format) {
case 'json':
display_bhl_result_json($referent, $search_hits, $callback);
break;
case 'html':
default:
display_bhl_result_html($referent, $search_hits);
break;
}
}
case 'authors':
$value = trim($value);
if ($value != '') {
$authors = explode("\n", $value);
foreach ($authors as $v) {
$parts = parse_name($v);
$author = new stdClass();
if (isset($parts['last'])) {
$author->lastname = $parts['last'];
}
if (isset($parts['suffix'])) {
$author->suffix = $parts['suffix'];
}
if (isset($parts['first'])) {
$author->forename = $parts['first'];
if (array_key_exists('middle', $parts)) {
$author->forename .= ' ' . $parts['middle'];
}
}
$reference->authors[] = $author;
}
}
break;
default:
break;
}
}
db_store_article($reference, $PageID, $updating);
}
header("Content-type: text/plain; charset=utf-8\n\n");
echo json_encode($response);
