/
Zotero.php
2052 lines (1971 loc) · 94.6 KB
/
Zotero.php
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<?php
declare(strict_types=1);
require_once 'constants.php'; // @codeCoverageIgnore
require_once 'Template.php'; // @codeCoverageIgnore
const MAGIC_STRING_URLS = 'CITATION_BOT_PLACEHOLDER_URL_POINTER_';
const CITOID_ZOTERO = "https://en.wikipedia.org/api/rest_v1/data/citation/zotero/";
/**
@param array<string> $_ids
@param array<Template> $templates
*/
function query_url_api(array $_ids, array &$templates): void { // Pointer to save memory
Zotero::query_url_api_class($templates);
}
final class Zotero {
private const ZOTERO_GIVE_UP = 5;
private const ZOTERO_SKIPS = 100;
private const ERROR_DONE = 'ERROR_DONE';
private static int $zotero_announced = 0;
private static CurlHandle $zotero_ch;
private static CurlHandle $ch_ieee;
private static CurlHandle $ch_jstor;
private static CurlHandle $ch_dx;
private static CurlHandle $ch_pmc;
private static CurlHandle $ch_doi;
private static CurlHandle $ch_pii;
private static int $zotero_failures_count = 0;
public static function create_ch_zotero(): void {
static $is_setup = false;
if ($is_setup) {
return;
}
$is_setup = true;
if (TRAVIS) {
$time = 3.0;
} else {
$time = 1.0; // @codeCoverageIgnore
}
self::$zotero_ch = bot_curl_init($time, [
CURLOPT_URL => CITOID_ZOTERO,
CURLOPT_HTTPHEADER => ['accept: application/json; charset=utf-8', 'Cache-Control: no-cache, must-revalidate']]);
self::$ch_ieee = bot_curl_init($time, [CURLOPT_USERAGENT => 'curl']); // IEEE requires JavaScript, unless curl is specified
self::$ch_jstor = bot_curl_init($time, []);
self::$ch_dx = bot_curl_init($time, []);
self::$ch_pmc = bot_curl_init($time, []);
self::$ch_doi = bot_curl_init($time, []);
self::$ch_pii = bot_curl_init($time, []);
}
public static function block_zotero(): void {
self::$zotero_failures_count = 1000000;
}
public static function unblock_zotero(): void {
self::$zotero_failures_count = 0;
}
/**
@param array<Template> $templates
*/
public static function query_url_api_class(array &$templates): void { // Pointer to save memory
foreach ($templates as $template) {
if (preg_match('~pii/(S\d{16})(?:|\/|\?|\:|\&|\;)$~i', $template->get('url'), $matches)) { // PII
if ($template->blank('doi')) {
$doi = self::get_doi_from_pii($matches[1]);
if (doi_works($doi)) {
$template->add_if_new('doi', $doi);
}
}
unset($doi, $matches);
}
}
if (!SLOW_MODE) {
return; // Zotero takes time
}
self::$zotero_announced = 1;
foreach ($templates as $template) {
self::expand_by_zotero($template);
}
self::$zotero_announced = 2;
foreach ($templates as $template) {
if ($template->has('biorxiv')) {
if ($template->blank('doi')) {
$template->add_if_new('doi', '10.1101/' . $template->get('biorxiv'));
expand_by_doi($template, true); // this data is better than zotero
} elseif (strstr($template->get('doi') , '10.1101') === false) {
expand_doi_with_dx($template, '10.1101/' . $template->get('biorxiv')); // dx data is better than zotero
self::expand_by_zotero($template, 'https://dx.doi.org/10.1101/' . $template->get('biorxiv')); // Rare case there is a different DOI
}
}
$doi = $template->get('doi');
if (!doi_active($doi)) {
if ($template->has('citeseerx')) {
self::expand_by_zotero($template, ' https://citeseerx.ist.psu.edu/viewdoc/summary?doi=' . $template->get('citeseerx'));
}
// Has a CAPCHA -- if ($template->has('jfm'))
// Has a CAPCHA -- if ($template->has('zbl'))
// Do NOT do MR -- it is a review not the article itself. Note that html does have doi, but do not use it.
if ($template->has('hdl')) {
self::expand_by_zotero($template, 'https://hdl.handle.net/' . $template->get('hdl'));
}
if ($template->has('osti')) {
self::expand_by_zotero($template, 'https://www.osti.gov/biblio/' . $template->get('osti'));
}
if ($template->has('rfc')) {
self::expand_by_zotero($template, 'https://tools.ietf.org/html/rfc' . $template->get('rfc'));
}
if ($template->has('ssrn')) {
self::expand_by_zotero($template, 'https://papers.ssrn.com/sol3/papers.cfm?abstract_id=' . $template->get('ssrn'));
}
}
if ($template->has('doi')) {
$doi = $template->get('doi');
if (!doi_active($doi) && doi_works($doi) && !preg_match(REGEXP_DOI_ISSN_ONLY, $doi)) {
self::expand_by_zotero($template, 'https://dx.doi.org/' . $doi); // DOIs without meta-data
}
if (doi_works($doi) && $template->blank('title') && stripos($doi, "10.1023/A:") === 0) {
self::expand_by_zotero($template, 'https://link.springer.com/article/' . $doi); // DOIs without title meta-data
}
}
}
}
/**
@param array<Template> $templates
*/
public static function query_ieee_webpages(array &$templates): void { // Pointer to save memory
foreach (['url', 'chapter-url', 'chapterurl'] as $kind) {
foreach ($templates as $template) {
set_time_limit(120);
/** @psalm-taint-escape ssrf */
$the_url = $template->get($kind);
if (preg_match("~^https://ieeexplore\.ieee\.org/document/(\d{5,})$~", $the_url, $matches_url)) {
curl_setopt(self::$ch_ieee, CURLOPT_URL, $the_url);
if ($template->blank('doi')) {
usleep(100000); // 0.10 seconds
$return = bot_curl_exec(self::$ch_ieee);
if ($return !== "" && preg_match_all('~"doi":"(10\.\d{4}/[^\s"]+)"~', $return, $matches, PREG_PATTERN_ORDER)) {
$dois = array_unique($matches[1]);
if (count($dois) === 1) {
if ($template->add_if_new('doi', $dois[0])) {
if (strpos($template->get('doi'), $matches_url[1]) !== false && doi_works($template->get('doi'))) {
// SEP 2020 $template->forget($kind); // It is one of those DOIs with the document number in it
}
}
}
}
} elseif (doi_works($template->get('doi'))) {
usleep(100000); // 0.10 seconds
$return = bot_curl_exec(self::$ch_ieee);
if ($return !== "" && strpos($return, "<title> - </title>") !== false) {
report_forget("Existing IEEE no longer works - dropping URL"); // @codeCoverageIgnore
$template->forget($kind); // @codeCoverageIgnore
}
}
}
}
}
}
/**
@param array<Template> $templates
*/
public static function drop_urls_that_match_dois(array &$templates): void { // Pointer to save memory
// Now that we have expanded URLs, try to lose them
foreach ($templates as $template) {
$doi = $template->get_without_comments_and_placeholders('doi');
if ($template->has('url')) {
$url = $template->get('url');
$url_kind = 'url';
} elseif ($template->has('chapter-url')) {
$url = $template->get('chapter-url');
$url_kind = 'chapter-url';
} elseif ($template->has('chapterurl')) {
$url = $template->get('chapterurl'); // @codeCoverageIgnore
$url_kind = 'chapterurl'; // @codeCoverageIgnore
} else {
$url = '';
$url_kind = '';
}
if ($doi && // IEEE code does not require "not incomplete"
$url &&
!preg_match(REGEXP_DOI_ISSN_ONLY, $doi) &&
$template->blank(DOI_BROKEN_ALIASES) &&
preg_match("~^https?://ieeexplore\.ieee\.org/document/\d{5,}/?$~", $url) && strpos($doi, '10.1109') === 0) {
// SEP 2020 report_forget("Existing IEEE resulting from equivalent DOI; dropping URL");
// SEP 2020 $template->forget($url_kind);
}
if ($doi &&
$url &&
!$template->profoundly_incomplete() &&
!preg_match(REGEXP_DOI_ISSN_ONLY, $doi) &&
(strpos($doi, '10.1093/') === false) &&
$template->blank(DOI_BROKEN_ALIASES))
{
set_time_limit(120);
if (str_ireplace(PROXY_HOSTS_TO_DROP,'', $url) !== $url && $template->get('doi-access') === 'free') {
report_forget("Existing proxy URL resulting from equivalent free DOI; dropping URL");
$template->forget($url_kind);
} elseif (str_ireplace(PROXY_HOSTS_TO_ALWAYS_DROP,'', $url) !== $url && $template->get('doi-access') === 'free') {
report_forget("Existing proxy URL resulting from equivalent free DOI; dropping URL");
$template->forget($url_kind);
} elseif (str_ireplace(PROXY_HOSTS_TO_ALWAYS_DROP,'', $url) !== $url && $template->blank(['archive-url', 'archiveurl'])) {
report_forget("Existing proxy URL resulting from equivalent DOI; fixing URL");
$template->set($url_kind, "https://dx.doi.org/" . doi_encode($doi));
} elseif (preg_match('~www.sciencedirect.com/science/article/B[^/\-]*\-[^/\-]+\-[^/\-]+/~', $url)) {
report_forget("Existing Invalid ScienceDirect URL when DOI is present; fixing URL");
$template->set($url_kind, "https://dx.doi.org/" . doi_encode($doi));
} elseif (preg_match('~www.sciencedirect.com/science/article/pii/\S{0,16}$~i', $url)) { // Too Short
report_forget("Existing Invalid ScienceDirect URL when DOI is present; fixing URL");
$template->set($url_kind, "https://dx.doi.org/" . doi_encode($doi));
} elseif (preg_match('~www.springerlink.com/content~i', $url)) { // Dead website
report_forget("Existing Invalid Springer Link URL when DOI is present; fixing URL");
$template->set($url_kind, "https://dx.doi.org/" . doi_encode($doi));
} elseif (str_ireplace('insights.ovid.com/pubmed','', $url) !== $url && $template->has('pmid')) {
// SEP 2020 report_forget("Existing OVID URL resulting from equivalent PMID and DOI; dropping URL");
// SEP 2020 $template->forget($url_kind);
} elseif ($template->has('pmc') && str_ireplace('iopscience.iop.org','', $url) !== $url) {
// SEP 2020 report_forget("Existing IOP URL resulting from equivalent DOI; dropping URL");
// SEP 2020 $template->forget($url_kind);;
$template->set($url_kind, "https://dx.doi.org/" . doi_encode($doi));
} elseif (str_ireplace('wkhealth.com','', $url) !== $url) {
report_forget("Existing Outdated WK Health URL resulting from equivalent DOI; fixing URL");
$template->set($url_kind, "https://dx.doi.org/" . doi_encode($doi));
} elseif ($template->has('pmc') && str_ireplace('bmj.com/cgi/pmidlookup','', $url) !== $url && $template->has('pmid') && $template->get('doi-access') === 'free' && stripos($url, 'pdf') === false) {
report_forget("Existing The BMJ URL resulting from equivalent PMID and free DOI; dropping URL");
$template->forget($url_kind);
} elseif ($template->get('doi-access') === 'free' && $template->get('url-status') === 'dead' && $url_kind === 'url') {
report_forget("Existing free DOI; dropping dead URL");
$template->forget($url_kind);
} elseif (doi_active($template->get('doi')) &&
!preg_match(REGEXP_DOI_ISSN_ONLY, $template->get('doi')) &&
$url_kind !== '' &&
(str_ireplace(CANONICAL_PUBLISHER_URLS, '', $template->get($url_kind)) !== $template->get($url_kind)) &&
$template->has_good_free_copy() &&
(stripos($template->get($url_kind), 'pdf') === false)) {
report_forget("Existing canonical URL resulting in equivalent free DOI/pmc; dropping URL");
$template->forget($url_kind);
} elseif (stripos($url, 'pdf') === false && $template->get('doi-access') === 'free' && $template->has('pmc')) {
curl_setopt(self::$ch_dx, CURLOPT_URL, "https://dx.doi.org/" . doi_encode($doi));
$ch_return = bot_curl_exec(self::$ch_dx);
if (strlen($ch_return) > 50) { // Avoid bogus tiny pages
$redirectedUrl_doi = curl_getinfo(self::$ch_dx, CURLINFO_EFFECTIVE_URL); // Final URL
if (stripos($redirectedUrl_doi, 'cookie') !== false) {
break;
}
if (stripos($redirectedUrl_doi, 'denied') !== false) {
break;
}
$redirectedUrl_doi = self::url_simplify($redirectedUrl_doi);
$url_short = self::url_simplify($url);
if (preg_match('~^https?://.+/pii/?(S?\d{4}[^/]+)~i', $redirectedUrl_doi, $matches ) === 1 ) { // Grab PII numbers
$redirectedUrl_doi = $matches[1] ; // @codeCoverageIgnore
}
if (stripos($url_short, $redirectedUrl_doi) !== false ||
stripos($redirectedUrl_doi, $url_short) !== false) {
report_forget("Existing canonical URL resulting from equivalent free DOI; dropping URL");
$template->forget($url_kind);
} else { // See if $url redirects
/** @psalm-taint-escape ssrf */
$the_url = $url;
curl_setopt(self::$ch_doi, CURLOPT_URL, $the_url);
$ch_return = bot_curl_exec(self::$ch_doi);
if (strlen($ch_return) > 60) {
$redirectedUrl_url = curl_getinfo(self::$ch_doi, CURLINFO_EFFECTIVE_URL);
$redirectedUrl_url = self::url_simplify($redirectedUrl_url);
if (stripos($redirectedUrl_url, $redirectedUrl_doi) !== false ||
stripos($redirectedUrl_doi, $redirectedUrl_url) !== false) {
report_forget("Existing canonical URL resulting from equivalent free DOI; dropping URL");
$template->forget($url_kind);
}
}
}
}
unset($ch_return);
}
}
$url = $template->get($url_kind);
if ($url && !$template->profoundly_incomplete() && str_ireplace(PROXY_HOSTS_TO_ALWAYS_DROP,'', $url) !== $url) {
if (!$template->blank_other_than_comments('pmc')) {
report_forget("Existing proxy URL resulting from equivalent PMC; dropping URL");
$template->forget($url_kind);
}
}
}
}
private static function zotero_request(string $url): string {
set_time_limit(120);
if (self::$zotero_failures_count > self::ZOTERO_GIVE_UP) {
self::$zotero_failures_count -= 1;
if (self::$zotero_failures_count === self::ZOTERO_GIVE_UP) {
self::$zotero_failures_count = 0;
}
}
/** @psalm-taint-escape ssrf */
$the_url = CITOID_ZOTERO . urlencode($url);
curl_setopt(self::$zotero_ch, CURLOPT_URL, $the_url);
if (self::$zotero_failures_count > self::ZOTERO_GIVE_UP) {
return self::ERROR_DONE;
}
$delay = max(min(100000*(1+self::$zotero_failures_count), 10), 0); // 0.10 seconds delay, with paranoid bounds checks
usleep($delay);
$zotero_response = bot_curl_exec(self::$zotero_ch);
if ($zotero_response === '') {
sleep(2); // @codeCoverageIgnore
$zotero_response = bot_curl_exec(self::$zotero_ch); // @codeCoverageIgnore
}
if ($zotero_response === '') {
// @codeCoverageIgnoreStart
report_warning(curl_error(self::$zotero_ch) . " For URL: " . echoable($url));
if (strpos(curl_error(self::$zotero_ch), 'timed out after') !== false) {
self::$zotero_failures_count += 1;
if (self::$zotero_failures_count > self::ZOTERO_GIVE_UP) {
report_warning("Giving up on URL expansion for a while");
self::$zotero_failures_count += self::ZOTERO_SKIPS;
}
}
$zotero_response = self::ERROR_DONE;
// @codeCoverageIgnoreEnd
}
return $zotero_response;
}
public static function expand_by_zotero(Template $template, ?string $url = null): void {
$access_date = 0;
if (is_null($url)) {
if (in_array($template->get('url-status'), ['usurped', 'unfit', 'dead', 'deviated'], true)) {
return;
}
$access_date = (int) strtotime(tidy_date($template->get('accessdate') . ' ' . $template->get('access-date')));
$archive_date = (int) strtotime(tidy_date($template->get('archivedate') . ' ' . $template->get('archive-date')));
if ($access_date && $archive_date) {
$access_date = min($access_date, $archive_date); // Whichever was first
} elseif ($archive_date) {
$access_date = $archive_date;
}
if ($template->has('url')) {
$url = $template->get('url');
} elseif ($template->has('chapter-url')) {
$url = $template->get('chapter-url');
} elseif ($template->has('chapterurl')) {
$url = $template->get('chapterurl');
} else {
return;
}
if (preg_match('~^https?://(?:dx\.|)doi\.org~i', $url)) {
return;
}
if (preg_match('~^https?://semanticscholar\.org~i', $url)) {
return;
}
if (preg_match(REGEXP_BIBCODE, urldecode($url))) {
return;
}
if (preg_match("~^https?://citeseerx\.ist\.psu\.edu~i", $url)) {
return;
}
if (preg_match("~\barxiv\.org/.*(?:pdf|abs|ftp/arxiv/papers/\d{4})/(.+?)(?:\.pdf)?$~i", $url)) {
return;
}
}
if (!$template->profoundly_incomplete($url)) {
return; // Only risk unvetted data if there's little good data to sully
}
if (stripos($url, 'CITATION_BOT_PLACEHOLDER') !== false) {
return; // That's a bad url
}
// Clean up URLs
if (preg_match('~^(https?://(?:www\.|)nature\.com/articles/[a-zA-Z0-9\.]+)\.pdf(?:|\?.*)$~i', $url, $matches)) { // remove .PDF from Nature urls
$url = $matches[1]; // @codeCoverageIgnore
}
if (preg_match('~^(https?://(?:www\.|)mdpi\.com/.+)(?:/pdf\-vor|/pdf)$~', $url, $matches)) {
$url = $matches[1];
}
$bad_url = implode('|', ZOTERO_AVOID_REGEX);
if (preg_match("~^https?://(?:www\.|m\.|)(?:" . $bad_url . ")~i", $url)) {
return;
}
// Is it actually a URL. Zotero will search for non-url things too!
if (preg_match('~^https?://[^/]+/?$~', $url) === 1) {
return; // Just a host name
}
set_time_limit(120); // This can be slow
if (preg_match(REGEXP_IS_URL, $url) !== 1) {
return; // See https://mathiasbynens.be/demo/url-regex/ This regex is more exact than validator. We only spend time on this after quick and dirty check is passed
}
set_time_limit(120);
if (self::$zotero_announced === 1) {
report_action("Using Zotero translation server to retrieve details from URLs.");
self::$zotero_announced = 0;
} elseif (self::$zotero_announced === 2) {
report_action("Using Zotero translation server to retrieve details from identifiers.");
self::$zotero_announced = 0;
}
$zotero_response = self::zotero_request($url);
self::process_zotero_response($zotero_response, $template, $url, $access_date);
return;
}
public static function process_zotero_response(string $zotero_response, Template $template, string $url, int $access_date): void {
if ($zotero_response === self::ERROR_DONE) {
return; // Error message already printed in zotero_request()
}
switch (trim($zotero_response)) {
case '':
report_info("Nothing returned for URL " . echoable($url));
return;
case 'Internal Server Error':
report_info("Internal server error with URL " . echoable($url));
return;
case 'Remote page not found':
report_info("Remote page not found for URL " . echoable($url));
return;
case 'No items returned from any translator':
report_info("Remote page not interpretable for URL " . echoable($url));
return;
case 'An error occurred during translation. Please check translation with the Zotero client.':
report_info("An error occurred during translation for URL " . echoable($url));
return;
}
if (strpos($zotero_response, '502 Bad Gateway') !== false) {
report_warning("Bad Gateway error for URL ". echoable($url));
return;
}
if (strpos($zotero_response, '503 Service Temporarily Unavailable') !== false) {
report_warning("Temporarily Unavailable error for URL " . echoable($url)); // @codeCoverageIgnore
return; // @codeCoverageIgnore
}
if (strpos($zotero_response, '<title>Wikimedia Error</title>') !== false) {
report_warning("Temporarily giving an error for URL " . echoable($url)); // @codeCoverageIgnore
return; // @codeCoverageIgnore
}
$zotero_data = @json_decode($zotero_response, false);
if (!isset($zotero_data)) {
report_warning("Could not parse JSON for URL ". echoable($url) . ": " . $zotero_response);
return;
} elseif (!is_array($zotero_data)) {
if (is_object($zotero_data)) {
$zotero_data = (array) $zotero_data;
} else {
report_warning("JSON did not parse correctly for URL ". echoable($url) . ": " . $zotero_response);
return;
}
}
if (!isset($zotero_data[0])) {
$result = $zotero_data;
} else {
$result = $zotero_data[0];
}
$result = (object) $result ;
if (empty($result->publicationTitle) && empty($result->bookTitle) && !isset($result->title)) {
if (!empty($result->subject)) {
$result->title = $result->subject;
} elseif (!empty($result->caseName)) {
$result->title = $result->caseName;
} elseif (!empty($result->nameOfAct)) {
$result->title = $result->nameOfAct;
}
}
if (!isset($result->title)) {
if (strpos($zotero_response, 'unknown_error') !== false) { // @codeCoverageIgnoreStart
report_info("Did not get a title for URL ". echoable($url));
} else {
report_minor_error("Did not get a title for URL ". echoable($url) . ": " . $zotero_response); // Odd Error
}
return; // @codeCoverageIgnoreEnd
}
if (substr(strtolower(trim($result->title)), 0, 9) === 'not found') {
report_info("Could not resolve URL " . echoable($url));
return;
}
// Remove unused stuff
unset($result->abstractNote);
unset($result->version);
unset($result->accessDate);
unset($result->libraryCatalog);
unset($result->url);
unset($result->tags);
unset($result->key);
unset($result->websiteTitle);
unset($result->journalAbbreviation);
unset($result->ISSN);
unset($result->subject);
unset($result->caseName);
unset($result->nameOfAct);
if (stripos($url, 'www.royal.uk') !== false) {
unset($result->creators); // @codeCoverageIgnore
unset($result->author); // @codeCoverageIgnore
}
if (stripos($url, 'newrepublic.com') !== false) { // Bad data for all but first one
unset($result->creators['1']);
unset($result->author['1']);
}
$result->title = convert_to_utf8($result->title);
// Reject if we find more than 5 or more than 10% of the characters are �. This means that character
// set was not correct in Zotero and nothing is good. We allow a couple of � for German umlauts that arer easily fixable by humans.
// We also get a lot of % and $ if the encoding was something like iso-2022-jp and converted wrong
$bad_count = substr_count($result->title, '�') + mb_substr_count($result->title, '$') + mb_substr_count($result->title, '%');
$total_count = mb_strlen($result->title);
if (isset($result->bookTitle)) {
$result->bookTitle = convert_to_utf8($result->bookTitle);
$bad_count += substr_count($result->bookTitle, '�') + mb_substr_count($result->bookTitle, '$') + mb_substr_count($result->bookTitle, '%');
$total_count += mb_strlen($result->bookTitle);
}
if (($bad_count > 5) || ($total_count > 1 && (($bad_count/$total_count) > 0.1))) {
report_info("Could parse unicode characters in " . echoable($url));
return;
}
report_info("Retrieved info from " . echoable($url));
// Verify that Zotero translation server did not think that this was a website and not a journal
if (strtolower(substr(trim($result->title), -9)) === ' on jstor') { // Not really "expanded", just add the title without " on jstor"
$template->add_if_new('title', substr(trim($result->title), 0, -9)); // @codeCoverageIgnore
return; // @codeCoverageIgnore
}
$test_data = '';
if (isset($result->bookTitle)) {
$test_data .= $result->bookTitle . ' ';
}
if (isset($result->title)) {
$test_data .= $result->title;
}
foreach (BAD_ZOTERO_TITLES as $bad_title ) {
if (mb_stripos($test_data, $bad_title) !== false) {
report_info("Received invalid title data for URL " . echoable($url) . ": $test_data");
return;
}
}
if ($test_data === '404' || $test_data === '/404') {
return;
}
if (isset($result->bookTitle) && strtolower($result->bookTitle) === 'undefined') {
unset($result->bookTitle); // S2 without journals
}
if (isset($result->publicationTitle) && strtolower($result->publicationTitle) === 'undefined') {
unset($result->publicationTitle); // S2 without journals
}
if (isset($result->bookTitle)) {
foreach (array_merge(BAD_ACCEPTED_MANUSCRIPT_TITLES, IN_PRESS_ALIASES) as $bad_title ) {
if (str_i_same($result->bookTitle, $bad_title)) {
report_info("Received invalid book title data for URL " . echoable($url) . ": $result->bookTitle");
return;
}
}
}
if (isset($result->title)) {
foreach (array_merge(BAD_ACCEPTED_MANUSCRIPT_TITLES, IN_PRESS_ALIASES) as $bad_title ) {
if (str_i_same($result->title, $bad_title)) {
report_info("Received invalid title data for URL ". echoable($url) . ": $result->title");
return;
}
}
}
if (isset($result->publicationTitle)) {
foreach (array_merge(BAD_ACCEPTED_MANUSCRIPT_TITLES, IN_PRESS_ALIASES) as $bad_title ) {
if (str_i_same($result->publicationTitle, $bad_title)) {
report_info("Received invalid publication title data for URL ". echoable($url) . ": $result->publicationTitle");
return;
}
}
// Specific bad data that is correctable
$tester = strtolower($result->publicationTitle);
if ($tester === 'nationalpost') {
$result->publicationTitle = 'National Post';
} elseif ($tester === 'financialpost') {
$result->publicationTitle = 'Financial Post';
} elseif ($tester === 'bloomberg.com') {
$result->publicationTitle = 'Bloomberg';
} elseif ($tester === 'advanced books') {
unset($result->issue);
unset($result->volume);
unset($result->pages);
unset($result->publicationTitle);
}
}
if (preg_match('~^([^\]]+)\|([^\]]+)\| ?THE DAILY STAR$~i', (string) @$result->title, $matches)) {
$result->title = $matches[1];
$result->publicationTitle = 'The Daily Star';
}
if (isset($result->extra)) { // [extra] => DOI: 10.1038/546031a has been seen in the wild
if (preg_match('~\sdoi:\s?([^\s]+)\s~i', ' ' . $result->extra . ' ', $matches)) {
if (!isset($result->DOI)) {
$result->DOI = trim($matches[1]);
}
$result->extra = trim(str_replace(trim($matches[0]), '', $result->extra));
}
if (preg_match('~\stype:\s?([^\s]+)\s~i', ' ' . $result->extra . ' ', $matches)) { // [extra] => type: dataset has been seen in the wild
$result->extra = trim(str_replace(trim($matches[0]), '', $result->extra));
}
if (preg_match('~\sPMID: (\d+)\s+PMCID: PMC(\d+)\s~i', ' ' . $result->extra . ' ', $matches)) {
$result->extra = trim(str_replace(trim($matches[0]), '', $result->extra));
$template->add_if_new('pmid', $matches[1]);
$template->add_if_new('pmc', $matches[2]);
}
if (preg_match('~\sPMID: (\d+), (\d+)\s~i', ' ' . $result->extra . ' ', $matches)) {
$result->extra = trim(str_replace(trim($matches[0]), '', $result->extra));
if ($matches[1] === $matches[2]) {
$template->add_if_new('pmid', $matches[1]);
}
}
if (preg_match('~\sPMID: (\d+)\s~i', ' ' . $result->extra . ' ', $matches)) {
$result->extra = trim(str_replace(trim($matches[0]), '', $result->extra));
$template->add_if_new('pmid', $matches[1]);
}
if (preg_match('~\sOCLC: (?:|ocn|ocm)(\d+)\s~i', ' ' . $result->extra . ' ', $matches)) {
$result->extra = trim(str_replace(trim($matches[0]), '', $result->extra));
$template->add_if_new('oclc', $matches[1]);
}
if (preg_match('~\sOpen Library ID: OL(\d+M)\s~i', ' ' . $result->extra . ' ', $matches)) {
$result->extra = trim(str_replace(trim($matches[0]), '', $result->extra));
$template->add_if_new('ol', $matches[1]);
}
// UNUSED stuff goes below
if (preg_match('~\sFormat: PDF\s~i', ' ' . $result->extra . ' ', $matches)) {
$result->extra = trim(str_replace(trim($matches[0]), '', $result->extra));
}
if (preg_match('~\sIMDb ID: ((?:tt|co|nm)\d+)\s~i', ' ' . $result->extra . ' ', $matches)) { // We don't use it
$result->extra = trim(str_replace(trim($matches[0]), '', $result->extra));
}
if (preg_match('~\s(original-date: \S+)\s~i', ' ' . $result->extra . ' ', $matches)) { // We don't use it
$result->extra = trim(str_replace(trim($matches[0]), '', $result->extra)); // @codeCoverageIgnore
}
if (preg_match('~\s(Google-Books-ID: \S+)\s~i', ' ' . $result->extra . ' ', $matches)) { // We don't use it
$result->extra = trim(str_replace(trim($matches[0]), '', $result->extra)); // @codeCoverageIgnore
}
if (preg_match('~\s(ISSN: \S+)\s~i', ' ' . $result->extra . ' ', $matches)) { // We don't use it
$result->extra = trim(str_replace(trim($matches[0]), '', $result->extra)); // @codeCoverageIgnore
}
if (preg_match('~\s(Page Version ID: \S+)\s~i', ' ' . $result->extra . ' ', $matches)) { // We don't use it
$result->extra = trim(str_replace(trim($matches[0]), '', $result->extra)); // @codeCoverageIgnore
}
if (preg_match('~\s(Citation Key: \S+)\s~i', ' ' . $result->extra . ' ', $matches)) { // We don't use it
$result->extra = trim(str_replace(trim($matches[0]), '', $result->extra)); // @codeCoverageIgnore
}
if (preg_match('~\s(number-of-pages: [ivx]+, \d+)\s~i', ' ' . $result->extra . ' ', $matches)) { // We don't use it
$result->extra = trim(str_replace(trim($matches[0]), '', $result->extra)); // @codeCoverageIgnore
}
if (preg_match('~\s(number-of-pages: \S+)\s~i', ' ' . $result->extra . ' ', $matches)) { // We don't use it
$result->extra = trim(str_replace(trim($matches[0]), '', $result->extra)); // @codeCoverageIgnore
}
if (preg_match('~\s(Version: \S+)\s~i', ' ' . $result->extra . ' ', $matches)) { // We don't use it
$result->extra = trim(str_replace(trim($matches[0]), '', $result->extra)); // @codeCoverageIgnore
}
if (preg_match('~\s(RSLID: \S+)\s~i', ' ' . $result->extra . ' ', $matches)) { // We don't use it
$result->extra = trim(str_replace(trim($matches[0]), '', $result->extra)); // @codeCoverageIgnore
}
if (preg_match('~\s(QID: \S+)\s~i', ' ' . $result->extra . ' ', $matches)) { // We don't use it
$result->extra = trim(str_replace(trim($matches[0]), '', $result->extra)); // @codeCoverageIgnore
}
if (preg_match('~\s(National Archives Identifier: \S+)\s~i', ' ' . $result->extra . ' ', $matches)) { // We don't use it
$result->extra = trim(str_replace(trim($matches[0]), '', $result->extra)); // @codeCoverageIgnore
}
if (preg_match('~\s(Catalog Number: \S+)\s~i', ' ' . $result->extra . ' ', $matches)) { // We don't use it
$result->extra = trim(str_replace(trim($matches[0]), '', $result->extra)); // @codeCoverageIgnore
}
if (preg_match('~\s(BMCR ID: \S+)\s~i', ' ' . $result->extra . ' ', $matches)) { // We don't use it
$result->extra = trim(str_replace(trim($matches[0]), '', $result->extra)); // @codeCoverageIgnore
}
if (preg_match('~\s(PubAg AGID: \S+)\s~i', ' ' . $result->extra . ' ', $matches)) { // We don't use it
$result->extra = trim(str_replace(trim($matches[0]), '', $result->extra)); // @codeCoverageIgnore
}
if (preg_match('~\s(IP-\d+)\s~i', ' ' . $result->extra . ' ', $matches)) { // We don't use it
$result->extra = trim(str_replace(trim($matches[0]), '', $result->extra)); // @codeCoverageIgnore
}
if (preg_match('~\s(Accession Number: \S+)\s~i', ' ' . $result->extra . ' ', $matches)) { // We don't use it
$result->extra = trim(str_replace(trim($matches[0]), '', $result->extra)); // @codeCoverageIgnore
}
if (preg_match('~\sADS Bibcode: (\d{4}\S{15})\s~i', ' ' . $result->extra . ' ', $matches)) {
$result->extra = trim(str_replace(trim($matches[0]), '', $result->extra));
$template->add_if_new('bibcode', $matches[1]);
}
if (preg_match('~\s(arXiv: \S+)\s~i', ' ' . $result->extra . ' ', $matches)) { // We don't use it - only comes from arXiv DOIs
$result->extra = trim(str_replace(trim($matches[0]), '', $result->extra)); // @codeCoverageIgnore
}
if (preg_match('~\s(INIS Reference Number: \d+)\s~i', ' ' . $result->extra . ' ', $matches)) { // We don't use it - https://inis.iaea.org
$result->extra = trim(str_replace(trim($matches[0]), '', $result->extra)); // @codeCoverageIgnore
}
if (preg_match('~\s(ERIC Number: \S+)\s~i', ' ' . $result->extra . ' ', $matches)) { // We don't use it
$result->extra = trim(str_replace(trim($matches[0]), '', $result->extra)); // @codeCoverageIgnore
}
if (preg_match('~\s(\d+ cm\.)\s~i', ' ' . $result->extra . ' ', $matches)) { // We don't use it - size of book
$result->extra = trim(str_replace(trim($matches[0]), '', $result->extra)); // @codeCoverageIgnore
}
// These go at end since it is unbound on end often with linefeeds and such
if (preg_match('~submitted:[\s\S]*$~i', ' ' . $result->extra . ' ', $matches)) { // We don't use it
$result->extra = trim(str_replace(trim($matches[0]), '', $result->extra)); // @codeCoverageIgnore
}
if (preg_match('~event\-location:[\s\S]*$~i', ' ' . $result->extra . ' ', $matches)) { // We don't use it and it is long verbose
$result->extra = trim(str_replace(trim($matches[0]), '', $result->extra)); // @codeCoverageIgnore
}
if (preg_match('~Translated title:[\s\S]*$~i', ' ' . $result->extra . ' ', $matches)) { // We don't use it
$result->extra = trim(str_replace(trim($matches[0]), '', $result->extra)); // @codeCoverageIgnore
}
if (preg_match('~reviewed\-title:[\s\S]*$~i', ' ' . $result->extra . ' ', $matches)) { // We don't use it
$result->extra = trim(str_replace(trim($matches[0]), '', $result->extra)); // @codeCoverageIgnore
}
if (preg_match('~Physical Description:[\s\S]*$~i', ' ' . $result->extra . ' ', $matches)) { // We don't use it
$result->extra = trim(str_replace(trim($matches[0]), '', $result->extra)); // @codeCoverageIgnore
}
if (preg_match('~BBK:[\s\S]*$~i', ' ' . $result->extra . ' ', $matches)) { // We don't use it
$result->extra = trim(str_replace(trim($matches[0]), '', $result->extra)); // @codeCoverageIgnore
}
if (preg_match('~Place Manufactured: [\s\S]*$~i', ' ' . $result->extra . ' ', $matches)) { // We don't use it
$result->extra = trim(str_replace(trim($matches[0]), '', $result->extra)); // @codeCoverageIgnore
}
if (preg_match('~Dimensions: [\s\S]*$~i', ' ' . $result->extra . ' ', $matches)) { // We don't use it
$result->extra = trim(str_replace(trim($matches[0]), '', $result->extra)); // @codeCoverageIgnore
}
if (preg_match('~Category: [\s\S]*$~i', ' ' . $result->extra . ' ', $matches)) { // We don't use it
$result->extra = trim(str_replace(trim($matches[0]), '', $result->extra)); // @codeCoverageIgnore
}
if (preg_match('~Credit: [\s\S]*$~i', ' ' . $result->extra . ' ', $matches)) { // We don't use it
$result->extra = trim(str_replace(trim($matches[0]), '', $result->extra)); // @codeCoverageIgnore
}
if (preg_match('~Manufacturer: [\s\S]*$~i', ' ' . $result->extra . ' ', $matches)) { // We don't use it
$result->extra = trim(str_replace(trim($matches[0]), '', $result->extra)); // @codeCoverageIgnore
}
if (preg_match('~pl., cartes, errata.+~i', ' ' . $result->extra . ' ', $matches)) { // We don't use it
$result->extra = trim(str_replace(trim($matches[0]), '', $result->extra)); // @codeCoverageIgnore
}
if (preg_match('~Post URL:.+~i', ' ' . $result->extra . ' ', $matches)) { // We don't use it
$result->extra = trim(str_replace(trim($matches[0]), '', $result->extra)); // @codeCoverageIgnore
}
if (preg_match('~Reference Number:.+~i', ' ' . $result->extra . ' ', $matches)) { // We don't use it
$result->extra = trim(str_replace(trim($matches[0]), '', $result->extra)); // @codeCoverageIgnore
}
if (preg_match('~jurisdiction:.+~i', ' ' . $result->extra . ' ', $matches)) { // We don't use it
$result->extra = trim(str_replace(trim($matches[0]), '', $result->extra)); // @codeCoverageIgnore
}
$result->extra = trim($result->extra);
if ($result->extra !== '') {
;// TODO - check back later on report_minor_error("Unhandled extra data: " . echoable($result->extra) . ' FROM ' . echoable($url)); // @codeCoverageIgnore
}
}
if (isset($result->DOI) && $template->blank('doi')) {
if (preg_match('~^(?:https://|http://|)(?:dx\.|)doi\.org/(.+)$~i', $result->DOI, $matches)) {
$result->DOI = $matches[1];
}
$possible_doi = sanitize_doi($result->DOI);
if (doi_works($possible_doi)) {
$template->add_if_new('doi', $possible_doi);
expand_by_doi($template);
if (stripos($url, 'jstor')) {
check_doi_for_jstor($template->get('doi'), $template);
}
if (!$template->profoundly_incomplete()) {
return;
}
}
}
if (isset($result->date)) {
foreach (NO_DATE_WEBSITES as $bad_website ) {
if (stripos($url, $bad_website) !== false) {
unset($result->date);
break;
}
}
}
if (isset($result->ISBN)) {
$template->add_if_new('isbn', $result->ISBN);
}
if ($access_date && isset($result->date)) {
$new_date = strtotime(tidy_date((string) $result->date)); // One time got an integer
if ($new_date) { // can compare
if ($new_date > $access_date) {
report_info("URL appears to have changed since access-date " . echoable($url));
return;
}
}
}
if (str_i_same(substr((string) @$result->publicationTitle, 0, 4), 'http') ||
str_i_same(substr((string) @$result->bookTitle, 0, 4), 'http') ||
str_i_same(substr((string) @$result->title, 0, 4), 'http')) {
report_info("URL returned in Journal/Newpaper/Title/Chapter field for " . echoable($url)); // @codeCoverageIgnore
return; // @codeCoverageIgnore
}
if (isset($result->bookTitle)) {
$result->bookTitle = safe_preg_replace('~\s*\(pdf\)$~i', '', $result->bookTitle);
$result->bookTitle = safe_preg_replace('~^\(pdf\)\s*~i', '', $result->bookTitle);
$result->bookTitle = safe_preg_replace('~ \- ProQuest\.?~i', '', $result->bookTitle);
}
if (isset($result->title)) {
$result->title = safe_preg_replace('~\s*\(pdf\)$~i', '', (string) $result->title);
$result->title = safe_preg_replace('~^\(pdf\)\s*~i', '', $result->title);
$result->title = safe_preg_replace('~ \- ProQuest\.?~i', '', $result->title);
}
if (strpos($url, 'biodiversitylibrary.org') !== false) {
unset($result->publisher); // Not reliably set
}
if (isset($result->title) && $result->title === 'Cultural Advice' && strpos($url, 'edu.au') !== false) {
unset($result->title); // A warning, not a title
}
if ($template->has('title')) {
if (isset($result->title) && titles_are_similar($template->get('title'), (string) $result->title)) {
unset($result->title);
}
}
if ($template->has('chapter')) {
if (isset($result->title) && titles_are_similar($template->get('chapter'), (string) $result->title)) {
unset($result->title);
}
}
if (isset($result->bookTitle)) {
$template->add_if_new('title', (string) $result->bookTitle);
if (isset($result->title)) {
$template->add_if_new('chapter', (string) $result->title);
}
if (isset($result->publisher)) {
$template->add_if_new('publisher', (string) $result->publisher);
}
} else {
if (isset($result->title)){
$template->add_if_new('title', (string) $result->title);
}
if (isset($result->itemType) && ($result->itemType === 'book' || $result->itemType === 'bookSection')) {
if (isset($result->publisher)) {
$template->add_if_new('publisher', (string) $result->publisher);
}
}
}
if (isset($result->issue)) {
$template->add_if_new('issue', (string) $result->issue);
}
if (isset($result->pages)) {
$pos_pages = (string) $result->pages;
if (preg_match('~\d~', $pos_pages) && !preg_match('~\d+\.\d+.\d+~', $pos_pages)) { // At least one number but not a dotted number from medRxiv
$pos_pages = str_ireplace(['σελ.', 'σελ ', 'pages ', 'page ', 'pages:', 'page:', 'pages', 'page'], [' ', ' ', ' ', ' ', ' ', ' ', ' ', ' '], $pos_pages);
$pos_pages = trim($pos_pages);
$pos_pages = str_ireplace([' ', ' ', ' '], [' ', ' ', ' '], $pos_pages);
$template->add_if_new('pages' , $pos_pages);
}
}
if (isset($result->itemType) && $result->itemType === 'newspaperArticle') {
if (isset($result->publicationTitle)) {
$new_title = (string) $result->publicationTitle;
if (in_array(strtolower($new_title), WORKS_ARE_PUBLISHERS, true)) {
$template->add_if_new('publisher', $new_title);
} else {
$template->add_if_new('newspaper', $new_title);
}
}
} else {
if (isset($result->publicationTitle)) {
if ((!$template->has('title') || !$template->has('chapter')) && // Do not add if already has title and chapter
(stripos((string) $result->publicationTitle, ' edition') === false)) { // Do not add if "journal" includes "edition"
if (str_replace(NON_JOURNALS, '', (string) $result->publicationTitle) === (string) $result->publicationTitle) {
$template->add_if_new('journal', (string) $result->publicationTitle);
}
}
}
}
if (isset($result->volume)) {
$volume = (string) $result->volume;
if (strpos($volume, "(") === false ) {
if (preg_match('~[a-zA-Z]~', $volume) && (bool) strtotime($volume)) {
; // Do not add date
} else {
$template->add_if_new('volume', $volume);
}
}
}
if (isset($result->date) && strlen((string) $result->date)>3) {
$new_date = tidy_date((string) $result->date);
if (stripos($url, 'indiatimes') !== false) { // "re-posted" website all at once
$maybe_date = (int) strtotime($new_date);
$end_date1 = strtotime('10 January 2017');
$end_date2 = strtotime('21 January 2017');
if ($maybe_date > $end_date1 && $maybe_date < $end_date2) {
$new_date = '';
}
}
if ($new_date) {
$template->add_if_new('date', $new_date);
}
}
if (isset($result->series) && stripos($url, '.acm.org')===false) {
$template->add_if_new('series' , (string) $result->series);
}
$i = 0;
while (isset($result->author[$i])) {
if (self::is_bad_author((string) @$result->author[$i][1])) {
unset($result->author[$i][1]);
}
if (self::is_bad_author((string) @$result->author[$i][0])) {
unset($result->author[$i][0]);
}
$i++;
}
unset($i);
if (isset($result->author[0]) && !isset($result->author[1]) &&
!author_is_human(@$result->author[0][0] . ' ' . @$result->author[0][1])) {
unset($result->author[0]); // Do not add a single non-human author
}
$i = 0;
while (isset($result->author[$i])) {
if (author_is_human(@$result->author[$i][0] . ' ' . @$result->author[$i][1])) {
$template->validate_and_add('author' . (string)($i+1), (string) @$result->author[$i][1], (string) @$result->author[$i][0],
isset($result->rights) ? (string) $result->rights : '', false);
}
$i++;
if ($template->blank(['author' . (string)($i), 'first' . (string)($i), 'last' . (string)($i)])) {
break; // Break out if nothing added
}
}
unset($i);
if ((stripos($url, '/sfdb.org') !== false || stripos($url, '.sfdb.org') !== false) && $template->blank(WORK_ALIASES)) {
$template->add_if_new('website', 'sfdb.org');
}
// see https://www.mediawiki.org/wiki/Citoid/itemTypes
if (isset($result->itemType)) {
switch ($result->itemType) {
case 'book':
case 'bookSection':
// Too much bad data to risk switching journal to book or vice versa.
// also reject 'review'
if ($template->wikiname() === 'cite web' &&
stripos($url . @$result->title . @$result->bookTitle . @$result->publicationTitle, 'review') === false &&
stripos($url, 'archive.org') === false && !preg_match('~^https?://[^/]*journal~', $url) &&
stripos($url, 'booklistonline') === false &&
stripos($url, 'catalogue.bnf') === false &&
stripos($url, 'finna.fi') === false &&
stripos($url, 'planetebd.com') === false &&
stripos($url, 'data.bnf.fr') === false &&
stripos($url, 'elonet.fi') === false
) {
$template->change_name_to('cite book');
}
break;
case 'journalArticle':
case 'conferencePaper':
case 'report': // ssrn uses this
if (($template->wikiname() === 'cite web') &&
(str_ireplace(NON_JOURNAL_WEBSITES, '', $url) === $url) &&
!$template->blank(WORK_ALIASES) &&
(str_ireplace('breakingnews', '', $url) === $url) &&
(str_ireplace('/blog/', '', $url) === $url)) {
$template->change_name_to('cite journal');
}
break;
case 'magazineArticle':
if ($template->wikiname() === 'cite web') {
$template->change_name_to('cite magazine');
}
break;
case 'newspaperArticle':
if ($template->wikiname() === 'cite web') {
$test_data = $template->get('work') . $template->get('website') .
$template->get('url') . $template->get('chapter-url') .
$template->get('title') . $template->get('encyclopedia') .
$template->get('encyclopædia') . $url; // Some things get called "news" in error
if (str_ireplace(['.gov', 'encyclopedia', 'encyclopædia'], '', $test_data) === $test_data) {
$template->change_name_to('cite news');
}
}
break;
case 'thesis':