/**
* @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, $search_hits);
break;
}
}
function db_store_article($article, $PageID = 0, $updating = false)
{
global $db;
global $config;
$update = false;
$id = 0;
// If we are editing an existing reference then we already know its id
if (isset($article->reference_id)) {
$id = $article->reference_id;
} else {
$id = db_find_article($article);
}
if ($id != 0) {
if ($updating) {
$update = true;
} else {
return $id;
}
}
// Try and trap empty references
if ($id == 0) {
$ok = false;
if (isset($article->title)) {
$ok = $article->title != '';
}
if (!$ok) {
return 0;
}
}
if (!isset($article->genre)) {
$article->genre = 'article';
}
$keys = array();
$values = array();
// Article metadata
foreach ($article as $k => $v) {
switch ($k) {
// Ignore as it's an array
case 'authors':
break;
case 'date':
$keys[] = 'date';
$values[] = $db->qstr($v);
if (!isset($article->year)) {
$keys[] = 'year';
$values[] = $db->qstr(year_from_date($v));
}
break;
// Don't store BHL URL here
// Don't store BHL URL here
case 'url':
if (preg_match('/^http:\\/\\/(www\\.)?biodiversitylibrary.org\\/page\\/(?<pageid>[0-9]+)/', $v)) {
} else {
// extract Handle if it exists
if (preg_match('/^http:\\/\\/hdl.handle.net\\/(?<hdl>.*)$/', $v, $m)) {
$keys[] = 'hdl';
$values[] = $db->qstr($m['hdl']);
} else {
$keys[] = $k;
$values[] = $db->qstr($v);
}
}
break;
// Things we store as is
// Things we store as is
case 'title':
case 'secondary_title':
case 'volume':
case 'series':
case 'issue':
case 'spage':
case 'epage':
case 'year':
case 'date':
case 'issn':
case 'genre':
case 'doi':
case 'hdl':
case 'lsid':
case 'oclc':
case 'pdf':
case 'abstract':
case 'pmid':
$keys[] = $k;
$values[] = $db->qstr($v);
break;
// Things we ignore
// Things we ignore
default:
break;
}
}
// Date
if (!isset($article->date) && isset($article->year)) {
$keys[] = 'date';
$values[] = $db->qstr($article->year . '-00-00');
}
// BHL PageID
if ($PageID != 0) {
$keys[] = 'PageID';
$values[] = $PageID;
}
// SICI
$s = new Sici();
$sici = $s->create($article);
if ($sici != '') {
$keys[] = 'sici';
$values[] = $db->qstr($sici);
}
if ($update) {
// Versioning?
// Delete links (author, pages, etc)
// Don't delete page range as we may loose plates, etc. outside range
/*
$sql = 'DELETE FROM rdmp_reference_page_joiner WHERE reference_id=' . $id;
$result = $db->Execute($sql);
if ($result == false) die("failed [" . __FILE__ . ":" . __LINE__ . "]: " . $sql);
*/
$sql = 'DELETE FROM rdmp_author_reference_joiner WHERE reference_id = ' . $id;
$result = $db->Execute($sql);
if ($result == false) {
die("failed [" . __FILE__ . ":" . __LINE__ . "]: " . $sql);
}
// update (updated timestamp will be automatically updated)
$sql = 'UPDATE rdmp_reference SET ';
$num_values = count($keys);
for ($i = 0; $i < $num_values; $i++) {
if ($i > 0) {
$sql .= ', ';
}
$sql .= $keys[$i] . '=' . $values[$i];
}
$sql .= ' WHERE reference_id=' . $id;
/* $cache_file = @fopen('/tmp/update.sql', "w+") or die("could't open file");
@fwrite($cache_file, $sql);
fclose($cache_file);
*/
$result = $db->Execute($sql);
if ($result == false) {
die("failed [" . __FILE__ . ":" . __LINE__ . "]: " . $sql);
}
} else {
// Adding article for first time so add 'created' and 'updated' timestamp
$keys[] = 'created';
$values[] = 'NOW()';
$keys[] = 'updated';
$values[] = 'NOW()';
$sql = 'INSERT INTO rdmp_reference (' . implode(",", $keys) . ') VALUES (' . implode(",", $values) . ')';
$result = $db->Execute($sql);
if ($result == false) {
die("failed [" . __FILE__ . ":" . __LINE__ . "]: " . $sql);
}
$id = $db->Insert_ID();
// Store reference_cluster_id which we can use to group duplicates, by default
// reference_cluster_id = reference_id
$sql = 'UPDATE rdmp_reference SET reference_cluster_id=' . $id . ' WHERE reference_id=' . $id;
$result = $db->Execute($sql);
if ($result == false) {
die("failed [" . __FILE__ . ":" . __LINE__ . "]: " . $sql);
}
}
// Indexing-------------------------------------------------------------------------------------
if (1) {
// solr
// this code is redundant with code in reference.php but I use different objects
// here and there (doh!). Also once we've added old stuff to solr this is the only place we
// should be calling solr
$solr = new Apache_Solr_Service('localhost', '8983', '/solr');
if (!$solr->ping()) {
echo 'Solr service not responding.';
exit;
}
$item = array();
$item['id'] = 'reference/' . $id;
$item['title'] = $article->title;
$item['publication_outlet'] = $article->secondary_title;
$item['year'] = $article->year;
$authors = array();
foreach ($article->authors as $a) {
$authors[] = $a->forename . ' ' . $a->surname;
}
$item['authors'] = $authors;
$citation = '';
$citation .= ' ' . $article->year;
$citation .= ' ' . $article->title;
$citation .= ' ' . $article->secondary_title;
$citation .= ' ' . $article->volume;
if (isset($article->issue)) {
$citation .= '(' . $article->issue . ')';
}
$citation .= ':';
$citation .= ' ';
$citation .= $article->spage;
if (isset($article->epage)) {
$citation .= '-' . $article->epage;
}
$item['citation'] = $citation;
$text = '';
$num_authors = count($article->authors);
$count = 0;
if ($num_authors > 0) {
foreach ($article->authors as $author) {
$text .= $author->forename . ' ' . $author->lastname;
if (isset($author->suffix)) {
$text .= ' ' . $author->suffix;
}
$count++;
if ($count == 2 && $num_authors > 3) {
$text .= ' et al.';
break;
}
if ($count < $num_authors - 1) {
$text .= ', ';
} else {
if ($count < $num_authors) {
$text .= ' and ';
}
}
}
}
$item['citation'] = $text . ' ' . $citation;
$parts = array();
$parts[] = $item;
//print_r($parts);
// add to solr
$documents = array();
foreach ($parts as $item => $fields) {
$part = new Apache_Solr_Document();
foreach ($fields as $key => $value) {
if (is_array($value)) {
foreach ($value as $datum) {
$part->setMultiValue($key, $datum);
}
} else {
$part->{$key} = $value;
}
}
$documents[] = $part;
}
//
//
// Load the documents into the index
//
try {
$solr->addDocuments($documents);
$solr->commit();
$solr->optimize();
} catch (Exception $e) {
echo $e->getMessage();
}
} else {
$sql = 'DELETE FROM rdmp_text_index WHERE (object_uri=' . $db->qstr($config['web_root'] . 'reference/' . $id) . ')';
$result = $db->Execute($sql);
if ($result == false) {
die("failed [" . __FILE__ . ":" . __LINE__ . "]: " . $sql);
}
// Only do this if we have a title, as sometimes we don't (e.g. CrossRef lacks metadata)
if (isset($article->title)) {
$sql = 'INSERT INTO rdmp_text_index(object_type, object_id, object_uri, object_text)
VALUES ("title"' . ', ' . $id . ', ' . $db->qstr($config['web_root'] . 'reference/' . $id) . ', ' . $db->qstr($article->title) . ')';
$result = $db->Execute($sql);
if ($result == false) {
die("failed [" . __FILE__ . ":" . __LINE__ . "]: " . $sql);
}
}
}
// Versioning-----------------------------------------------------------------------------------
// Store this object in version table so we can recover it if we overwrite item
$ip = getip();
$sql = 'INSERT INTO rdmp_reference_version(reference_id, ip, json) VALUES(' . $id . ', ' . 'INET_ATON(\'' . $ip . '\')' . ',' . $db->qstr(json_encode($article)) . ')';
$result = $db->Execute($sql);
if ($result == false) {
die("failed [" . __FILE__ . ":" . __LINE__ . "]: " . $sql);
}
// Author(s)------------------------------------------------------------------------------------
// Store author as and link to the article
if (isset($article->authors)) {
db_store_authors($id, $article->authors);
}
// Store page range (only if not updating, otherwise we may loose plates, etc.
// that aren't in page range)
if ($PageID != 0 && !$update) {
$page_range = array();
if (isset($article->spage) && isset($article->epage)) {
$page_range = bhl_page_range($PageID, $article->epage - $article->spage + 1);
} else {
// No epage, so just get spage (to do: how do we tell user we don't have page range?)
$page_range = bhl_page_range($PageID, 0);
}
//print_r($page_range);
$count = 0;
foreach ($page_range as $page) {
$sql = 'INSERT INTO rdmp_reference_page_joiner (reference_id, PageID, page_order)
VALUES (' . $id . ',' . $page . ',' . $count++ . ')';
$result = $db->Execute($sql);
if ($result == false) {
die("failed [" . __FILE__ . ":" . __LINE__ . "]: " . $sql);
}
}
}
// Tweet----------------------------------------------------------------------------------------
if (!$update) {
if ($config['twitter']) {
$url = $config['web_root'] . 'reference/' . $id . ' ' . '#bhlib';
// url + hashtag
$url_len = strlen($url);
$status = '';
if (isset($article->title)) {
$status = $article->title;
$status_len = strlen($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);
}
}
return $id;
}
function postprocess_citations($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++;
}
}
}