/
expandFns.php
3191 lines (3036 loc) · 131 KB
/
expandFns.php
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<?php
declare(strict_types=1);
require_once 'constants.php'; // @codeCoverageIgnore
require_once 'Template.php'; // @codeCoverageIgnore
require_once 'big_jobs.php'; // @codeCoverageIgnore
final class HandleCache {
// Greatly speed-up by having one array of each kind and only look for hash keys, not values
private const MAX_CACHE_SIZE = 100000;
public const MAX_HDL_SIZE = 1024;
private const BAD_DOI_ARRAY = [
'10.1126/science' => true,
'' => true,
'10.7556/jaoa' => true,
'10.1267/science.040579197' => true,
'10.0000/Rubbish_bot_failure_test' => true,
'10.0000/Rubbish_bot_failure_test2' => true,
'10.0000/Rubbish_bot_failure_test.x' => true];
/** @var array<bool> $cache_active */
public static array $cache_active = []; // DOI is in CrossRef and works
/** @var array<bool> $cache_inactive */
public static array $cache_inactive = []; // DOI either is not in CrossRef or does not work
/** @var array<bool> $cache_good */
public static array $cache_good = []; // DOI works
/** @var array<string> $cache_hdl_loc */
public static array $cache_hdl_loc = []; // Final HDL location URL
/** @var array<bool> $cache_hdl_bad */
public static array $cache_hdl_bad = self::BAD_DOI_ARRAY; // HDL/DOI does not resolve to anything
/** @var array<bool> $cache_hdl_null */
public static array $cache_hdl_null = []; // HDL/DOI resolves to null
public static function check_memory_use(): void {
$usage = count(self::$cache_inactive) +
count(self::$cache_active) +
count(self::$cache_good) +
count(self::$cache_hdl_bad) +
10*count(self::$cache_hdl_loc) + // These include a path too
count(self::$cache_hdl_null);
if ($usage > self::MAX_CACHE_SIZE) {
self::free_memory(); // @codeCoverageIgnore
}
}
public static function free_memory(): void {
self::$cache_active = [];
self::$cache_inactive = [];
self::$cache_good = [];
self::$cache_hdl_loc = [];
self::$cache_hdl_bad = self::BAD_DOI_ARRAY;
self::$cache_hdl_null = [];
gc_collect_cycles();
}
}
// ============================================= DOI functions ======================================
function doi_active(string $doi): ?bool {
$doi = trim($doi);
if (isset(HandleCache::$cache_active[$doi])) {
return true;
}
if (isset(HandleCache::$cache_inactive[$doi])) {
return false;
}
$works = doi_works($doi);
if ($works !== true) {
return $works;
}
$works = is_doi_active($doi);
if ($works === null) { // Temporary problem - do not cache
return null; // @codeCoverageIgnore
}
if ($works === false) {
HandleCache::$cache_inactive[$doi] = true;
return false;
}
HandleCache::$cache_active[$doi] = true;
return true;
}
function doi_works(string $doi): ?bool {
$doi = trim($doi);
if (strlen($doi) > HandleCache::MAX_HDL_SIZE) {
return null;
}
if (isset(HandleCache::$cache_good[$doi])) {
return true;
}
if (isset(HandleCache::$cache_hdl_bad[$doi])) {
return false;
}
if (isset(HandleCache::$cache_hdl_null[$doi])) {
return null;
}
HandleCache::check_memory_use();
$works = is_doi_works($doi);
if ($works === null) {
// These are unexpected nulls
HandleCache::$cache_hdl_null[$doi] = true;
return null; // @codeCoverageIgnoreEnd
}
if ($works === false) {
HandleCache::$cache_hdl_bad[$doi] = true;
return false;
}
HandleCache::$cache_good[$doi] = true;
return true;
}
function is_doi_active(string $doi): ?bool {
static $ch = null;
if ($ch === null) {
$ch = bot_curl_init(1.0,[
CURLOPT_HEADER => true,
CURLOPT_NOBODY => false,
CURLOPT_USERAGENT => BOT_CROSSREF_USER_AGENT]);
}
$doi = trim($doi);
$url = "https://api.crossref.org/v1/works/" . doi_encode($doi) . "?mailto=".CROSSREFUSERNAME; // do not encode crossref email
curl_setopt($ch, CURLOPT_URL, $url);
$return = bot_curl_exec($ch);
$header_length = (int) @curl_getinfo($ch, CURLINFO_HEADER_SIZE);
$header = substr($return, 0, $header_length);
$body = substr($return, $header_length);
$response_code = curl_getinfo($ch, CURLINFO_RESPONSE_CODE);
if ($header === "" || ($response_code === 503)) {
sleep(4); // @codeCoverageIgnoreStart
$return = bot_curl_exec($ch);
$response_code = curl_getinfo($ch, CURLINFO_RESPONSE_CODE);
$header_length = (int) @curl_getinfo($ch, CURLINFO_HEADER_SIZE);
$header = substr($return, 0, $header_length);
$body = substr($return, $header_length); // @codeCoverageIgnoreEnd
}
if ($header === "" || ($response_code === 503)) {
return null;
}
if ($body === 'Resource not found.'){
return false;
}
if ($response_code === 200) {
return true;
}
if ($response_code === 404) { // @codeCoverageIgnoreStart
return false;
}
$err = "CrossRef server error loading headers for DOI " . echoable($doi . " : " . (string) $response_code);
bot_debug_log($err);
report_warning($err);
return null; // @codeCoverageIgnoreEnd
}
function throttle_dx (): void {
static $last = 0.0;
$min_time = 40000.0;
$now = microtime(true);
$left = (int) ($min_time - ($now - $last));
if ($left > 0 && $left < $min_time) {
usleep($left); // less than min_time is paranoia, but do not want an inifinite delay
}
$last = $now;
}
function throttle_archive (): void {
static $last = 0.0;
$min_time = 1000000.0; // One second
$now = microtime(true);
$left = (int) ($min_time - ($now - $last));
if ($left > 0 && $left < $min_time) {
usleep($left); // less than min_time is paranoia, but do not want an inifinite delay
}
$last = $now;
}
function is_doi_works(string $doi): ?bool {
$doi = trim($doi);
// And now some obvious fails
if (strpos($doi, '/') === false){
return false;
}
if (strpos($doi, 'CITATION_BOT_PLACEHOLDER') !== false) {
return false;
}
if (preg_match('~^10\.1007/springerreference~', $doi)) {
return false;
}
if (!preg_match('~^([^\/]+)\/~', $doi, $matches)) {
return false;
}
if (isset(NULL_DOI_ANNOYING[$doi])) {
return false;
}
$registrant = $matches[1];
// TODO this will need updated over time. See registrant_err_patterns on https://en.wikipedia.org/wiki/Module:Citation/CS1/Identifiers
// 16:42, November 25, 2023 version is last check
if (strpos($registrant, '10.') === 0) { // We have to deal with valid handles in the DOI field - very rare, so only check actual DOIs
$registrant = substr($registrant,3);
if (preg_match('~^[^1-3]\d\d\d\d\.\d\d*$~', $registrant) || // 5 digits with subcode (0xxxx, 40000+); accepts: 10000–39999
preg_match('~^[^1-7]\d\d\d\d$~', $registrant) || // 5 digits without subcode (0xxxx, 60000+); accepts: 10000–69999
preg_match('~^[^1-9]\d\d\d\.\d\d*$~', $registrant) || // 4 digits with subcode (0xxx); accepts: 1000–9999
preg_match('~^[^1-9]\d\d\d$~', $registrant) || // 4 digits without subcode (0xxx); accepts: 1000–9999
preg_match('~^\d\d\d\d\d\d+~', $registrant) || // 6 or more digits
preg_match('~^\d\d?\d?$~', $registrant) || // less than 4 digits without subcode (3 digits with subcode is legitimate)
preg_match('~^\d\d?\.[\d\.]+~', $registrant) || // 1 or 2 digits with subcode
$registrant === '5555' || // test registrant will never resolve
preg_match('~[^\d\.]~', $registrant)) { // any character that isn't a digit or a dot
return false;
}
}
throttle_dx();
$url = "https://doi.org/" . doi_encode($doi);
$headers_test = get_headers_array($url);
if ($headers_test === false) {
if (strpos($doi, '10.2277/') === 0 || // Rogue
preg_match('~^10\.1038/nature\d{5}$~i', $doi) || // Nature dropped the ball
stripos($doi, '10.17312/harringtonparkpress/') === 0 ||
stripos($doi, '10.3149/csm.') === 0 ||
stripos($doi, '10.5047/meep.') === 0 ||
stripos($doi, '10.4435/BSPI.') === 0) {
return false;
}
if (isset(NULL_DOI_LIST[$doi])) {
return false;
}
foreach (NULL_DOI_STARTS_BAD as $bad_start) {
if (stripos($doi, $bad_start) === 0) {
return false; // all gone
}
}
if (isset(NULL_DOI_BUT_GOOD[$doi])) {
return true; // @codeCoverageIgnoreStart
}
$headers_test = get_headers_array($url);
bot_debug_log('Got null for HDL: ' . str_ireplace(['<', '>'], ['<', '>'],echoable($doi))); // @codeCoverageIgnoreEnd
}
if ($headers_test === false) {
$headers_test = get_headers_array($url); // @codeCoverageIgnore
}
if ($headers_test === false) { // most likely bad - note that null means do not add or remove doi-broken-date from pages
return null; // @codeCoverageIgnore
}
if (stripos($doi, '10.1126/scidip.') === 0) {
if ((string) @$headers_test['1'] === 'HTTP/1.1 404 Forbidden') {
unset($headers_test['1']); // https://doi.org/10.1126/scidip.ado5059
}
}
if (interpret_doi_header($headers_test) !== false) {
return interpret_doi_header($headers_test);
}
// Got 404 - try again, since we cache this and add doi-broken-date to pages, we should be double sure
$headers_test = get_headers_array($url);
/** We trust previous failure, so fail and null are both false */
if ($headers_test === false) {
return false;
}
return (bool) interpret_doi_header($headers_test);
}
/** @param array<mixed> $headers_test */
function interpret_doi_header(array $headers_test): ?bool {
if (empty($headers_test['Location']) && empty($headers_test['location'])) {
return false; // leads nowhere
}
/** @psalm-suppress InvalidArrayOffset */
$resp0 = (string) @$headers_test['0'];
/** @psalm-suppress InvalidArrayOffset */
$resp1 = (string) @$headers_test['1'];
/** @psalm-suppress InvalidArrayOffset */
$resp2 = (string) @$headers_test['2'];
if (strpos($resp2, '40') !== false) {
if ($resp1 === 'HTTP/1.1 302 Redirected') {
$resp2 = ''; // https://doi.org/10.1107/S2056989021000116
}
if ($resp1 === 'HTTP/1.1 301 Moved Permanently') {
$resp2 = ''; // https://doi.org/10.5152/UCD.2016.3683
}
}
if (stripos($resp0 . $resp1 . $resp2, '404 Not Found') !== false || stripos($resp0 . $resp1 . $resp2, 'HTTP/1.1 404') !== false) {
return false; // Bad
}
if (stripos($resp0, '302 Found') !== false || stripos($resp0, 'HTTP/1.1 302') !== false) {
return true; // Good
}
if (stripos((string) @json_encode($headers_test), 'dtic.mil') !== false) {
return true; // grumpy
}
if (stripos($resp0, '301 Moved Permanently') !== false || stripos($resp0, 'HTTP/1.1 301') !== false) { // Could be DOI change or bad prefix
if (stripos($resp1, '302 Found') !== false || stripos($resp1, 'HTTP/1.1 302') !== false) {
return true; // Good
} elseif (stripos($resp1, '301 Moved Permanently') !== false || stripos($resp1, 'HTTP/1.1 301') !== false) { // @codeCoverageIgnoreStart
if (stripos($resp2, '200 OK') !== false || stripos($resp2, 'HTTP/1.1 200') !== false) {
return true;
} else {
return false;
}
} else {
return false;
}
}
report_minor_error("Unexpected response in is_doi_works " . echoable($resp0));
return null; // @codeCoverageIgnoreEnd
}
/** @param array<mixed> $headers_test */
function get_loc_from_hdl_header(array $headers_test): ?string {
if (isset($headers_test['Location'][0]) && is_array(@$headers_test['Location'])) { // Should not be an array, but on rare occasions we get one
return (string) $headers_test['Location'][0]; // @codeCoverageIgnore
} elseif (isset($headers_test['location'][0]) && is_array(@$headers_test['location'])) {
return (string) $headers_test['location'][0]; // @codeCoverageIgnore
} elseif (isset($headers_test['location'])) {
return (string) $headers_test['location'];
} elseif (isset($headers_test['Location'])) {
return (string) $headers_test['Location'];
} else { // @codeCoverageIgnoreStart
bot_debug_log("Got weird header from handle: " . echoable(print_r($headers_test, true))); // Is this even possible
return null;
} // @codeCoverageIgnoreEnd
}
/** @psalm-suppress UnusedParam
@param array<string> $ids
@param array<Template> $templates */
function query_jstor_api(array $ids, array &$templates): void { // $ids not used // Pointer to save memory
foreach ($templates as $template) {
expand_by_jstor($template);
}
}
function sanitize_doi(string $doi): string {
if (substr($doi, -1) === '.') {
$try_doi = substr($doi, 0, -1);
if (doi_works($try_doi)) { // If it works without dot, then remove it
$doi = $try_doi;
} elseif (doi_works($try_doi . '.x')) { // Missing the very common ending .x
$doi = $try_doi . '.x';
} elseif (!doi_works($doi)) { // It does not work, so just remove it to remove wikipedia error. It's messed up
$doi = $try_doi;
}
}
$doi = safe_preg_replace('~^https?://d?x?\.?doi\.org/~i', '', $doi); // Strip URL part if present
$doi = safe_preg_replace('~^/?d?x?\.?doi\.org/~i', '', $doi);
$doi = safe_preg_replace('~^doi:~i', '', $doi); // Strip doi: part if present
$doi = str_replace("+" , "%2B", $doi); // plus signs are valid DOI characters, but in URLs are "spaces"
$doi = str_replace(HTML_ENCODE_DOI, HTML_DECODE_DOI, trim(urldecode($doi)));
$pos = (int) strrpos($doi, '.');
if ($pos) {
$extension = (string) substr($doi, $pos);
if (in_array(strtolower($extension), ['.htm', '.html', '.jpg', '.jpeg', '.pdf', '.png', '.xml', '.full'], true)) {
$doi = (string) substr($doi, 0, $pos);
}
}
$pos = (int) strrpos($doi, '#');
if ($pos) {
$extension = (string) substr($doi, $pos);
if (strpos(strtolower($extension), '#page_scan_tab_contents') === 0) {
$doi = (string) substr($doi, 0, $pos);
}
}
$pos = (int) strrpos($doi, ';');
if ($pos) {
$extension = (string) substr($doi, $pos);
if (strpos(strtolower($extension), ';jsessionid') === 0) {
$doi = (string) substr($doi, 0, $pos);
}
}
$pos = (int) strrpos($doi, '/');
if ($pos) {
$extension = (string) substr($doi, $pos);
if (in_array(strtolower($extension), ['/abstract', '/full', '/pdf', '/epdf', '/asset/', '/summary', '/short', '/meta', '/html', '/'], true)) {
$doi = (string) substr($doi, 0, $pos);
}
}
$new_doi = str_replace('//', '/', $doi);
if ($new_doi !== $doi) {
if (doi_works($new_doi) || !doi_works($doi)) {
$doi = $new_doi; // Double slash DOIs do exist
}
}
// And now for 10.1093 URLs
// The add chapter/page stuff after the DOI in the URL and it looks like part of the DOI to us
// Things like 10.1093/oxfordhb/9780199552238.001.0001/oxfordhb-9780199552238-e-003 and 10.1093/acprof:oso/9780195304923.001.0001/acprof-9780195304923-chapter-7
if (strpos($doi, '10.1093') === 0 && doi_works($doi) === false) {
if (preg_match('~^(10\.1093/oxfordhb.+)(?:/oxfordhb.+)$~', $doi, $match) ||
preg_match('~^(10\.1093/acprof.+)(?:/acprof.+)$~', $doi, $match) ||
preg_match('~^(10\.1093/acref.+)(?:/acref.+)$~', $doi, $match) ||
preg_match('~^(10\.1093/ref:odnb.+)(?:/odnb.+)$~', $doi, $match) ||
preg_match('~^(10\.1093/ww.+)(?:/ww.+)$~', $doi, $match) ||
preg_match('~^(10\.1093/anb.+)(?:/anb.+)$~', $doi, $match)) {
$new_doi = $match[1];
if (doi_works($new_doi)) {
$doi = $new_doi;
}
}
}
return $doi;
}
/* extract_doi
* Returns an array containing:
* 0 => text containing a DOI, possibly encoded, possibly with additional text
* 1 => the decoded DOI
*/
/** @return array<string> */
function extract_doi(string $text): array {
if (preg_match(
"~(10\.\d{4}\d?(/|%2[fF])..([^\s\|\"\?&>]|&l?g?t;|<[^\s\|\"\?&]*>)+)~",
$text, $match)) {
$doi = $match[1];
if (preg_match(
"~^(.*?)(/abstract|/e?pdf|/full|/figure|/default|</span>|[\s\|\"\?]|</).*+$~",
$doi, $new_match)
) {
$doi = $new_match[1];
}
$doi_candidate = sanitize_doi($doi);
while (preg_match(REGEXP_DOI, $doi_candidate) && !doi_works($doi_candidate)) {
$last_delimiter = 0;
foreach (['/', '.', '#', '?'] as $delimiter) {
$delimiter_position = (int) strrpos($doi_candidate, $delimiter);
$last_delimiter = ($delimiter_position > $last_delimiter) ? $delimiter_position : $last_delimiter;
}
$doi_candidate = substr($doi_candidate, 0, $last_delimiter);
}
if (doi_works($doi_candidate)) {
$doi = $doi_candidate;
}
if (!doi_works($doi) && !doi_works(sanitize_doi($doi))) { // Reject URLS like ...../25.10.2015/2137303/default.htm
if (preg_match('~^10\.([12]\d{3})~', $doi, $new_match)) {
if (preg_match("~[0-3][0-9]\.10\." . $new_match[1] . "~", $text)) {
return ['', ''];
}
}
}
return [$match[0], sanitize_doi($doi)];
}
return ['', ''];
}
// ============================================= String/Text functions ======================================
function wikify_external_text(string $title): string {
$replacement = [];
$placeholder = [];
$title = safe_preg_replace_callback('~(?:\$\$)([^\$]+)(?:\$\$)~iu',
static function (array $matches): string {return "<math>" . $matches[1] . "</math>";},
$title);
if (preg_match_all("~<(?:mml:)?math[^>]*>(.*?)</(?:mml:)?math>~", $title, $matches)) {
$num_matches = count($matches[0]);
for ($i = 0; $i < $num_matches; $i++) {
$replacement[$i] = '<math>' .
str_replace(array_keys(MML_TAGS), array_values(MML_TAGS),
str_replace(['<mml:', '</mml:'], ['<', '</'], $matches[1][$i]))
. '</math>';
$placeholder[$i] = sprintf(TEMP_PLACEHOLDER, $i);
// Need to use a placeholder to protect contents from URL-safening
$title = str_replace($matches[0][$i], $placeholder[$i], $title);
}
$title = str_replace(['<mo stretchy="false">', "<mo stretchy='false'>"], '', $title);
}
// Sometimes stuff is encoded more than once
$title = html_entity_decode($title, ENT_COMPAT | ENT_HTML401, "UTF-8");
$title = html_entity_decode($title, ENT_COMPAT | ENT_HTML401, "UTF-8");
$title = html_entity_decode($title, ENT_COMPAT | ENT_HTML401, "UTF-8");
$title = safe_preg_replace("~\s+~"," ", $title); // Remove all white spaces before
if (mb_substr($title, -6) === " ") {
$title = mb_substr($title, 0, -6);
}
// Special code for ending periods
while (mb_substr($title, -2) === "..") {
$title = mb_substr($title, 0, -1);
}
if (mb_substr($title, -1) === ".") { // Ends with a period
if (mb_substr_count($title, '.') === 1) { // Only one period
$title = mb_substr($title, 0, -1);
} elseif (mb_substr_count($title, ' ') === 0) { // No spaces at all and multiple periods
;
} else { // Multiple periods and at least one space
$last_word_start = (int) mb_strrpos(' ' . $title, ' ');
$last_word = mb_substr($title, $last_word_start);
if (mb_substr_count($last_word, '.') === 1 && // Do not remove if something like D.C. or D. C.
mb_substr($title, $last_word_start-2, 1) !== '.') {
$title = mb_substr($title, 0, -1);
}
}
}
$title = safe_preg_replace('~[\*]$~', '', $title);
$title = title_capitalization($title, true);
$htmlBraces = ["<", ">"];
$angleBraces = ["<", ">"];
$title = str_ireplace($htmlBraces, $angleBraces, $title);
$originalTags = ['<title>', '</title>', '</ title>', 'From the Cover: '];
$wikiTags = ['','','',''];
$title = str_ireplace($originalTags, $wikiTags, $title);
$originalTags = ['<inf>', '</inf>'];
$wikiTags = ['<sub>', '</sub>'];
$title = str_ireplace($originalTags, $wikiTags, $title);
$originalTags = ['.<br>', '.</br>', '.</ br>', '.<p>', '.</p>', '.</ p>', '.<strong>', '.</strong>', '.</ strong>'];
$wikiTags = ['. ','. ','. ','. ','. ','. ','. ','. ','. '];
$title = str_ireplace($originalTags, $wikiTags, $title);
$originalTags = ['<br>', '</br>', '</ br>', '<p>', '</p>', '</ p>', '<strong>', '</strong>', '</ strong>'];
$wikiTags = ['. ','. ','. ','. ','. ','. ', ' ',' ',' '];
$title = trim(str_ireplace($originalTags, $wikiTags, $title));
if (preg_match("~^\. (.+)$~", $title, $matches)) {
$title = trim($matches[1]);
}
if (preg_match("~^(.+)(\.\s+)\.$~s", $title, $matches)) {
$title = trim($matches[1] . ".");
}
$title_orig = '';
while ($title !== $title_orig) {
$title_orig = $title; // Might have to do more than once. The following do not allow < within the inner match since the end tag is the same :-( and they might nest or who knows what
$title = safe_preg_replace_callback('~(?:<Emphasis Type="Italic">)([^<]+)(?:</Emphasis>)~iu',
static function (array $matches): string {return "''" . $matches[1] . "''";},
$title);
$title = safe_preg_replace_callback('~(?:<Emphasis Type="Bold">)([^<]+)(?:</Emphasis>)~iu',
static function (array $matches): string {return "'''" . $matches[1] . "'''";},
$title);
$title = safe_preg_replace_callback('~(?:<em>)([^<]+)(?:</em>)~iu',
static function (array $matches): string {return "''" . $matches[1] . "''";},
$title);
$title = safe_preg_replace_callback('~(?:<i>)([^<]+)(?:</i>)~iu',
static function (array $matches): string {return "''" . $matches[1] . "''";},
$title);
$title = safe_preg_replace_callback('~(?:<italics>)([^<]+)(?:</italics>)~iu',
static function (array $matches): string {return "''" . $matches[1] . "''";},
$title);
}
if (mb_substr($title, -1) === '.') {
$title = sanitize_string($title) . '.';
} else {
$title = sanitize_string($title);
}
$title = str_replace([''],[' '], $title); // Funky spaces
$title = str_ireplace('<p class="HeadingRun \'\'In\'\'">', ' ', $title);
$title = str_ireplace([' ', ' ', ' '], [' ', ' ', ' '], $title);
if (mb_strlen($title) === strlen($title)) {
$title = trim($title," \t\n\r\0\x0B\xc2\xa0");
} else {
$title = trim($title," \t\n\r\0");
}
$num_replace = count($replacement);
for ($i = 0; $i < $num_replace; $i++) {
$title = str_replace($placeholder[$i], $replacement[$i], $title); // @phan-suppress-current-line PhanTypePossiblyInvalidDimOffset
}
foreach (['<msup>', '<msub>', '<mroot>', '<msubsup>', '<munderover>', '<mrow>', '<munder>', '<mtable>', '<mtr>', '<mtd>'] as $mathy) {
if (strpos($title, $mathy) !== false) {
return '<nowiki>' . $title . '</nowiki>';
}
}
return $title;
}
function restore_italics (string $text): string {
$text = trim(str_replace([' ', ' ', ' ', ' ', ' '], [' ', ' ', ' ', ' ', ' '], $text));
// <em> tags often go missing around species names in CrossRef
/** $old = $text; */
$text = str_replace(ITALICS_HARDCODE_IN, ITALICS_HARDCODE_OUT, $text); // Ones to always do, since they keep popping up in our logs
$text = str_replace("xAzathioprine therapy for patients with systemic lupus erythematosus", "Azathioprine therapy for patients with systemic lupus erythematosus", $text); // Annoying stupid bad data
$text = trim(str_replace([' ', ' ', ' ', ' ', ' '], [' ', ' ', ' ', ' ', ' '], $text));
while (preg_match('~([a-z])(' . ITALICS_LIST . ')([A-Z\-\?\:\.\)\(\,]|species|genus| in| the|$)~', $text, $matches)) {
if (in_array($matches[3], [':', '.', '-', ','], true)) {
$pad = "";
} else {
$pad = " ";
}
$text = str_replace($matches[0], $matches[1] . " ''" . $matches[2] . "''" . $pad . $matches[3], $text);
}
$text = trim(str_replace([' ', ' ', ' ', ' ', ' '], [' ', ' ', ' ', ' ', ' '], $text));
$padded = ' '. $text . ' ';
if (str_replace(CAMEL_CASE, '', $padded) !== $padded) {
return $text; // Words with capitals in the middle, but not the first character
}
$new = safe_preg_replace('~([a-z]+)([A-Z][a-z]+\b)~', "$1 ''$2''", $text);
if ($new === $text) {
return $text;
}
// Do not return $new, since we are wrong much more often here than wrong with new CrossRef Code
bot_debug_log('restore_italics: ' . $text . ' SHOULD BE ' . $new); // @codeCoverageIgnore
return $text; // @codeCoverageIgnore
}
function sanitize_string(string $str): string {
// ought only be applied to newly-found data.
if ($str === '') {
return '';
}
if (strtolower(trim($str)) === 'science (new york, n.y.)') {
return 'Science';
}
if (preg_match('~^\[http.+\]$~', $str)) {
return $str; // It is a link out
}
$replacement = [];
$placeholder = [];
$math_templates_present = preg_match_all("~<\s*math\s*>.*<\s*/\s*math\s*>~", $str, $math_hits);
if ($math_templates_present) {
$num_maths = count($math_hits[0]);
for ($i = 0; $i < $num_maths; $i++) {
$replacement[$i] = $math_hits[0][$i];
$placeholder[$i] = sprintf(TEMP_PLACEHOLDER, $i);
}
$str = str_replace($replacement, $placeholder, $str);
}
$dirty = ['[', ']', '|', '{', '}', " what�s "];
$clean = ['[', ']', '|', '{', '}', " what's "];
$str = trim(str_replace($dirty, $clean, safe_preg_replace('~[;.,]+$~', '', $str)));
if ($math_templates_present) {
$str = str_replace($placeholder, $replacement, $str);
}
return $str;
}
function truncate_publisher(string $p): string {
return safe_preg_replace("~\s+(group|inc|ltd|publishing)\.?\s*$~i", "", $p);
}
function str_remove_irrelevant_bits(string $str): string {
if ($str === '') {
return '';
}
$str = trim($str);
$str = str_replace('�', 'X', $str);
$str = safe_preg_replace(REGEXP_PLAIN_WIKILINK, "$1", $str); // Convert [[X]] wikilinks into X
$str = safe_preg_replace(REGEXP_PIPED_WIKILINK, "$2", $str); // Convert [[Y|X]] wikilinks into X
$str = trim($str);
$str = safe_preg_replace("~^the\s+~i", "", $str); // Ignore leading "the" so "New York Times" == "The New York Times"
$str = safe_preg_replace("~\s~u", ' ', $str);
// punctuation
$str = str_replace(['.', ',', ';', ': ', "…"], [' ', ' ', ' ', ' ', ' '], $str);
$str = str_replace([':', '-', '—', '–', '—', '–'], ['', '', '', '', '', ''], $str);
$str = str_replace([' ', ' '], [' ', ' '], $str);
$str = str_replace(" & ", " and ", $str);
$str = str_replace(" / ", " and ", $str);
$str = trim($str);
$str = str_ireplace(['Proceedings', 'Proceeding', 'Symposium', 'Huffington ', 'the Journal of ', 'nytimes.com' , '& ' , '(Clifton, N.J.)'],
['Proc', 'Proc', 'Sym', 'Huff ', 'journal of ', 'New York Times', 'and ', ''], $str);
$str = str_ireplace(['<sub>', '<sup>', '<i>', '<b>', '</sub>', '</sup>', '</i>', '</b>', '<p>', '</p>', '<title>', '</title>'], '', $str);
$str = str_ireplace(['SpringerVerlag', 'Springer Verlag Springer', 'Springer Verlag', 'Springer Springer'],
['Springer', 'Springer', 'Springer', 'Springer' ], $str);
$str = straighten_quotes($str, true);
$str = str_replace("′","'", $str);
$str = safe_preg_replace('~\(Incorporating .*\)$~i', '', $str); // Physical Chemistry Chemical Physics (Incorporating Faraday Transactions)
$str = safe_preg_replace('~\d+ Volume Set$~i', '', $str); // Ullmann's Encyclopedia of Industrial Chemistry, 40 Volume Set
$str = safe_preg_replace('~^Retracted~i', '', $str);
$str = safe_preg_replace('~\d?\d? ?The ?sequence ?of ?\S+ ?has ?been ?deposited ?in ?the ?GenBank ?database ?under ?accession ?number ?\S+ ?\d?~i', '', $str);
$str = safe_preg_replace('~(?:\:\.\,)? ?(?:an|the) official publication of the.+$~i', '', $str);
$str = trim($str);
$str = strip_diacritics($str);
return $str;
}
// See also titles_are_similar()
function str_equivalent(string $str1, string $str2): bool {
return str_i_same(str_remove_irrelevant_bits($str1), str_remove_irrelevant_bits($str2));
}
// See also str_equivalent()
function titles_are_similar(string $title1, string $title2): bool {
if (!titles_are_dissimilar($title1, $title2)) {
return true;
}
// Try again but with funky stuff mapped out of existence
$title1 = str_replace('�', '', str_replace(array_keys(MAP_DIACRITICS), '', $title1));
$title2 = str_replace('�', '', str_replace(array_keys(MAP_DIACRITICS), '', $title2));
if (!titles_are_dissimilar($title1, $title2)) {
return true;
}
return false;
}
function de_wikify(string $string): string {
return str_replace(["[", "]", "'''", "''", "&"], ["", "", "'", "'", ""], preg_replace(["~<[^>]*>~", "~\&[\w\d]{2,7};~", "~\[\[[^\|\]]*\|([^\]]*)\]\]~"], ["", "", "$1"], $string));
}
function titles_are_dissimilar(string $inTitle, string $dbTitle): bool {
// Blow away junk from OLD stuff
if (stripos($inTitle, 'CITATION_BOT_PLACEHOLDER_') !== false) {
$possible = preg_replace("~# # # CITATION_BOT_PLACEHOLDER_[A-Z]+ \d+ # # #~isu", ' ' , $inTitle);
if ($possible !== null) {
$inTitle = $possible;
} else { // When PHP fails with unicode, try without it
$inTitle = preg_replace("~# # # CITATION_BOT_PLACEHOLDER_[A-Z]+ \d+ # # #~i", ' ' , $inTitle); // @codeCoverageIgnore
if ($inTitle === null) {
return true;
}
}
}
// Strip diacritics before decode
$inTitle = strip_diacritics($inTitle);
$dbTitle = strip_diacritics($dbTitle);
// always decode new data
$dbTitle = titles_simple(htmlentities(html_entity_decode($dbTitle)));
// old data both decoded and not
$inTitle2 = titles_simple($inTitle);
$inTitle = titles_simple(htmlentities(html_entity_decode($inTitle)));
$dbTitle = strip_diacritics($dbTitle);
$inTitle = strip_diacritics($inTitle);
$inTitle2 = strip_diacritics($inTitle2);
$dbTitle = mb_strtolower($dbTitle);
$inTitle = mb_strtolower($inTitle);
$inTitle2 = mb_strtolower($inTitle2);
$drops = [" ", "<strong>", "</strong>", "<em>", "</em>", " ", "&ensp", "&emsp", "&thinsp", "&zwnj",
"-", "‐", "ʼ", "'", "", "&", "'", ",", ".", ";", '"', "\n", "\r", "\t", "\v", "\e", "‐",
"-", "ʼ", "`", "]", "[", "(", ")", ":", "′", "−"];
$inTitle = str_replace($drops, "", $inTitle);
$inTitle2 = str_replace($drops, "", $inTitle2);
$dbTitle = str_replace($drops, "", $dbTitle);
// This will convert &delta into delta
return ((strlen($inTitle) > 254 || strlen($dbTitle) > 254)
? (strlen($inTitle) !== strlen($dbTitle)
|| similar_text($inTitle, $dbTitle) / strlen($inTitle) < 0.98)
: (levenshtein($inTitle, $dbTitle) > 3)
)
&&
((strlen($inTitle2) > 254 || strlen($dbTitle) > 254)
? (strlen($inTitle2) !== strlen($dbTitle)
|| similar_text($inTitle2, $dbTitle) / strlen($inTitle2) < 0.98)
: (levenshtein($inTitle2, $dbTitle) > 3)
);
}
function titles_simple(string $inTitle): string {
// Failure leads to null or empty strings!!!!
// Leading Chapter # - Use callback to make sure there are a few characters after this
$inTitle = safe_preg_replace_callback('~^(?:Chapter \d+ \- )(.....+)~iu',
static function (array $matches): string {
return $matches[1];
}, trim($inTitle));
// Chapter number at start
$inTitle = safe_preg_replace('~^\[\d+\]\s*~iu', '', trim($inTitle));
// Trailing "a review"
$inTitle = safe_preg_replace('~(?:\: | |\:)a review$~iu', '', trim($inTitle));
// Strip trailing Online
$inTitle = safe_preg_replace('~ Online$~iu', '', $inTitle);
// Strip trailing (Third Edition)
$inTitle = safe_preg_replace('~\([^\s\(\)]+ Edition\)^~iu', '', $inTitle);
// Strip leading International Symposium on
$inTitle = safe_preg_replace('~^International Symposium on ~iu', '', $inTitle);
// Strip leading the
$inTitle = safe_preg_replace('~^The ~iu', '', $inTitle);
// Strip trailing
$inTitle = safe_preg_replace('~ A literature review$~iu', '', $inTitle);
$inTitle = safe_preg_replace("~^Editorial: ~ui", "", $inTitle);
$inTitle = safe_preg_replace("~^Brief communication: ~ui", "", $inTitle);
// Reduce punctuation
$inTitle = straighten_quotes(mb_strtolower($inTitle), true);
$inTitle = safe_preg_replace("~(?: |‐|−|-|—|–|’|—|–)~u", "", $inTitle);
$inTitle = str_replace(["\n", "\r", "\t", "‐", ":", "–", "—", "&ndash", "&mdash"], "", $inTitle);
// Retracted
$inTitle = safe_preg_replace("~\[RETRACTED\]~ui", "", $inTitle);
$inTitle = safe_preg_replace("~\(RETRACTED\)~ui", "", $inTitle);
$inTitle = safe_preg_replace("~RETRACTED~ui", "", $inTitle);
// Drop normal quotes
$inTitle = str_replace(["'", '"'], "", $inTitle);
// Strip trailing periods
$inTitle = trim(rtrim($inTitle, '.'));
// &
$inTitle = str_replace(" & ", " and ", $inTitle);
$inTitle = str_replace(" / ", " and ", $inTitle);
// greek
$inTitle = strip_diacritics($inTitle);
$inTitle = str_remove_irrelevant_bits($inTitle);
return $inTitle;
}
function strip_diacritics (string $input): string {
return str_replace(array_keys(MAP_DIACRITICS), array_values(MAP_DIACRITICS), $input);
}
function straighten_quotes(string $str, bool $do_more): string { // (?<!\') and (?!\') means that it cannot have a single quote right before or after it
// These Regex can die on Unicode because of backward looking
if ($str === '') {
return '';
}
$str = str_replace('Hawaiʻi', 'CITATION_BOT_PLACEHOLDER_HAWAII', $str);
$str = str_replace('Ha‘apai', 'CITATION_BOT_PLACEHOLDER_HAAPAI', $str);
$str = safe_preg_replace('~(?<!\')̵[679];|'|ȁ[89];|[\x{FF07}\x{2018}-\x{201B}`]|&[rl]s?[b]?quo;(?!\')~u', "'", $str);
if((mb_strpos($str, '›') !== false && mb_strpos($str, '&[lsaquo;') !== false) ||
(mb_strpos($str, '\x{2039}') !== false && mb_strpos($str, '\x{203A}') !== false) ||
(mb_strpos($str, '‹') !== false && mb_strpos($str, '›') !== false)) { // Only replace single angle quotes if some of both
$str = safe_preg_replace('~&[lr]saquo;|[\x{2039}\x{203A}]|[‹›]~u', "'", $str); // Websites tiles: Jobs ›› Iowa ›› Cows ›› Ames
}
$str = safe_preg_replace('~̶[013];|[\x{201C}-\x{201F}]|&[rlb][d]?quo;~u', '"', $str);
if((mb_strpos($str, '»') !== false && mb_strpos($str, '«') !== false) ||
(mb_strpos($str, '\x{00AB}') !== false && mb_strpos($str, '\x{00AB}') !== false) ||
(mb_strpos($str, '«') !== false && mb_strpos($str, '»') !== false)) { // Only replace double angle quotes if some of both // Websites tiles: Jobs » Iowa » Cows » Ames
if ($do_more){
$str = safe_preg_replace('~&[lr]aquo;|[\x{00AB}\x{00BB}]|[«»]~u', '"', $str);
} else { // Only outer funky quotes, not inner quotes
if (preg_match('~^(?:«|»|\x{00AB}|\x{00BB}|«|»)~u', $str) &&
preg_match( '~(?:«|»|\x{00AB}|\x{00BB}|«|»)$~u', $str) // Only if there is an outer quote on both ends
) {
$str = safe_preg_replace('~^(?:«|»|\x{00AB}|\x{00BB}|«|»)~u' , '"', $str);
$str = safe_preg_replace( '~(?:«|»|\x{00AB}|\x{00BB}|«|»)$~u', '"', $str);
} else {
; // No change
}
}
}
$str = str_ireplace('CITATION_BOT_PLACEHOLDER_HAAPAI', 'Ha‘apai', $str);
$str = str_ireplace('CITATION_BOT_PLACEHOLDER_HAWAII', 'Hawaiʻi', $str);
return $str;
}
// ============================================= Capitalization functions ======================================
function title_case(string $text): string {
if (stripos($text, 'www.') !== false || stripos($text, 'www-') !== false || stripos($text, 'http://') !== false) {
return $text; // Who knows - duplicate code below
}
return mb_convert_case($text, MB_CASE_TITLE, "UTF-8");
}
/** Returns a properly capitalized title.
* If $caps_after_punctuation is true (or there is an abundance of periods), it allows the
* letter after colons and other punctuation marks to remain capitalized.
* If not, it won't capitalize after : etc.
*/
function title_capitalization(string $in, bool $caps_after_punctuation): string {
// Use 'straight quotes' per WP:MOS
$new_case = straighten_quotes(trim($in), false);
if (mb_substr($new_case, 0, 1) === "[" && mb_substr($new_case, -1) === "]") {
return $new_case; // We ignore wikilinked names and URL linked since who knows what's going on there.
// Changing case may break links (e.g. [[Journal YZ|J. YZ]] etc.)
}
if (stripos($new_case, 'www.') !== false || stripos($new_case, 'www-') !== false || stripos($new_case, 'http://') !== false) {
return $new_case; // Who knows - duplicate code above
}
if ($new_case === mb_strtoupper($new_case)
&& mb_strlen(str_replace(["[", "]"], "", trim($in))) > 6
) {
// ALL CAPS to Title Case
$new_case = mb_convert_case($new_case, MB_CASE_TITLE, "UTF-8");
}
// Implicit acronyms
$new_case = ' ' . $new_case . ' ';
$new_case = safe_preg_replace_callback("~[^\w&][b-df-hj-np-tv-xz]{3,}(?=\W)~ui",
static function (array $matches): string {return mb_strtoupper($matches[0]);}, // Three or more consonants. NOT Y
$new_case);
$new_case = safe_preg_replace_callback("~[^\w&][aeiou]{3,}(?=\W)~ui",
static function (array $matches): string {return mb_strtoupper($matches[0]);}, // Three or more vowels. NOT Y
$new_case);
$new_case = mb_substr($new_case, 1, -1); // Remove added spaces
$new_case = mb_substr(str_replace(UC_SMALL_WORDS, LC_SMALL_WORDS, " " . $new_case . " "), 1, -1);
foreach(UC_SMALL_WORDS as $key=>$_value) {
$upper = UC_SMALL_WORDS[$key];
$lower = LC_SMALL_WORDS[$key];
foreach ([': ', ', ', '. ', '; '] as $char) {
$new_case = str_replace(mb_substr($upper, 0, -1) . $char, mb_substr($lower, 0, -1) . $char, $new_case);
}
}
if ($caps_after_punctuation || (substr_count($in, '.') / strlen($in)) > .07) {
// When there are lots of periods, then they probably mark abbreviations, not sentence ends
// We should therefore capitalize after each punctuation character.
$new_case = safe_preg_replace_callback("~[?.:!/]\s+[a-z]~u" /* Capitalize after punctuation */,
static function (array $matches): string {return mb_strtoupper($matches[0]);},
$new_case);
$new_case = safe_preg_replace_callback("~(?<!<)/[a-z]~u" /* Capitalize after slash unless part of ending html tag */,
static function (array $matches): string {return mb_strtoupper($matches[0]);},
$new_case);
// But not "Ann. Of...." which seems to be common in journal titles
$new_case = str_replace("Ann. Of ", "Ann. of ", $new_case);
}
$new_case = safe_preg_replace_callback(
"~ \([a-z]~u" /* uppercase after parenthesis */,
static function (array $matches): string {return mb_strtoupper($matches[0]);},
trim($new_case)
);
$new_case = safe_preg_replace_callback(
"~\w{2}'[A-Z]\b~u" /* Lowercase after apostrophes */,
static function (array $matches): string {return mb_strtolower($matches[0]);},
trim($new_case)
);
/** French l'Words and d'Words */
$new_case = safe_preg_replace_callback(
"~(\s[LD][\'\x{00B4}])([a-zA-ZÀ-ÿ]+)~u",
static function (array $matches): string {return mb_strtolower($matches[1]) . mb_ucfirst_force($matches[2]);},
' ' . $new_case
);
/** Italian dell'xxx words */
$new_case = safe_preg_replace_callback(
"~(\s)(Dell|Degli|Delle)([\'\x{00B4}][a-zA-ZÀ-ÿ]{3})~u",
static function (array $matches): string {return $matches[1] . mb_strtolower($matches[2]) . $matches[3];},
$new_case
);
$new_case = mb_ucfirst(trim($new_case));
// Solitary 'a' should be lowercase
$new_case = safe_preg_replace("~(\w\s+)A(\s+\w)~u", "$1a$2", $new_case);
// but not in "U S A"
$new_case = trim(str_replace(" U S a ", " U S A ", ' ' . $new_case . ' '));
// This should be capitalized
$new_case = str_replace(['(new Series)', '(new series)'] , ['(New Series)', '(New Series)'], $new_case);
// Catch some specific epithets, which should be lowercase
$new_case = safe_preg_replace_callback(
"~(?:'')?(?P<taxon>\p{L}+\s+\p{L}+)(?:'')?\s+(?P<nova>(?:(?:gen\.? no?v?|sp\.? no?v?|no?v?\.? sp|no?v?\.? gen)\b[\.,\s]*)+)~ui" /* Species names to lowercase */,
static function (array $matches): string {return "''" . mb_ucfirst(mb_strtolower($matches['taxon'])) . "'' " . mb_strtolower($matches["nova"]);},
$new_case);
// "des" at end is "Des" for Design not german "The"
if (mb_substr($new_case, -4, 4) === ' des') {
$new_case = mb_substr($new_case, 0, -4) . ' Des';
}
// Capitalization exceptions, e.g. Elife -> eLife
$new_case = str_replace(UCFIRST_JOURNAL_ACRONYMS, JOURNAL_ACRONYMS, " " . $new_case . " ");
$new_case = mb_substr($new_case, 1, mb_strlen($new_case) - 2); // remove spaces, needed for matching in LC_SMALL_WORDS
// Single letter at end should be capitalized J Chem Phys E for example. Obviously not the spanish word "e".
if (mb_substr($new_case, -2, 1) === ' ') {
$new_case = mb_strrev(mb_ucfirst(mb_strrev($new_case)));
}
if ($new_case === 'Now and then') {
$new_case = 'Now and Then'; // Odd journal name
}
// Trust existing "ITS", "its", ...
$its_in = preg_match_all('~ its(?= )~iu', ' ' . trim($in) . ' ', $matches_in, PREG_OFFSET_CAPTURE);
$new_case = trim($new_case);
$its_out = preg_match_all('~ its(?= )~iu', ' ' . $new_case . ' ', $matches_out, PREG_OFFSET_CAPTURE);
if ($its_in === $its_out && $its_in !== 0 && $its_in !== false) {
$matches_in = $matches_in[0];
$matches_out = $matches_out[0];
foreach ($matches_in as $key => $_value) {
if ($matches_in[$key][0] !== $matches_out[$key][0] &&
$matches_in[$key][1] === $matches_out[$key][1]) {
$new_case = substr_replace($new_case, trim($matches_in[$key][0]), $matches_out[$key][1], 3); // PREG_OFFSET_CAPTURE is ALWAYS in BYTES, even for unicode
}
}
}
// Trust existing "DOS", "dos", ...
$its_in = preg_match_all('~ dos(?= )~iu', ' ' . trim($in) . ' ', $matches_in, PREG_OFFSET_CAPTURE);
$new_case = trim($new_case);
$its_out = preg_match_all('~ dos(?= )~iu', ' ' . $new_case . ' ', $matches_out, PREG_OFFSET_CAPTURE);
if ($its_in === $its_out && $its_in !== 0 && $its_in !== false) {
$matches_in = $matches_in[0];
$matches_out = $matches_out[0];
foreach ($matches_in as $key => $_value) {
if ($matches_in[$key][0] !== $matches_out[$key][0] &&
$matches_in[$key][1] === $matches_out[$key][1]) {
$new_case = substr_replace($new_case, trim($matches_in[$key][0]), $matches_out[$key][1], 3); // PREG_OFFSET_CAPTURE is ALWAYS in BYTES, even for unicode
}
}
}
if (preg_match('~Series ([a-zA-Z] )(\&|and)( [a-zA-Z] )~', $new_case . ' ', $matches)) {
$replace_me = 'Series ' . $matches[1] . $matches[2] . $matches[3];
$replace = 'Series ' . strtoupper($matches[1]) . $matches[2] . strtoupper($matches[3]);
$new_case = trim(str_replace($replace_me, $replace, $new_case . ' '));
}
// 42th, 33rd, 1st, ...
if(preg_match('~\s\d+(?:st|nd|rd|th)[\s\,\;\:\.]~i', ' ' . $new_case . ' ', $matches)) {
$replace_me = $matches[0];
$replace = strtolower($matches[0]);
$new_case = trim(str_replace($replace_me, $replace, ' ' .$new_case . ' '));
}
// Part XII: Roman numerals
$new_case = safe_preg_replace_callback(
"~ part ([xvil]+): ~iu",
static function (array $matches): string {return " Part " . strtoupper($matches[1]) . ": ";},
$new_case);
$new_case = safe_preg_replace_callback(
"~ part ([xvi]+) ~iu",
static function (array $matches): string {return " Part " . strtoupper($matches[1]) . " ";},
$new_case);
$new_case = safe_preg_replace_callback(
"~ (?:Ii|Iii|Iv|Vi|Vii|Vii|Ix)$~u",
static function (array $matches): string {return strtoupper($matches[0]);},
$new_case);
$new_case = safe_preg_replace_callback(
"~^(?:Ii|Iii|Iv|Vi|Vii|Vii|Ix):~u",