/
apiFunctions.php
1550 lines (1499 loc) · 66.1 KB
/
apiFunctions.php
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<?php
declare(strict_types=1);
require_once 'constants.php'; // @codeCoverageIgnore
require_once 'user_messages.php'; // @codeCoverageIgnore
require_once 'Template.php'; // @codeCoverageIgnore
require_once 'NameTools.php'; // @codeCoverageIgnore
/** @param array<string> $pmids
@param array<Template> $templates */
function query_pmid_api (array $pmids, array &$templates): void { entrez_api($pmids, $templates, 'pubmed'); } // Pointer to save memory
/** @param array<string> $pmcs
@param array<Template> $templates */
function query_pmc_api (array $pmcs, array &$templates): void { entrez_api($pmcs, $templates, 'pmc'); } // Pointer to save memory
final class AdsAbsControl {
private const MAX_CACHE_SIZE = 50000;
private static int $big_counter = 0;
private static int $small_counter = 0;
/** @var array<string> $doi2bib */
private static array $doi2bib = [];
/** @var array<string> $bib2doi */
private static array $bib2doi = [];
public static function big_gave_up_yet(): bool {
self::$big_counter = max(self::$big_counter - 1, 0);
return self::$big_counter !== 0;
}
public static function big_give_up(): void {
self::$big_counter = 1000;
}
public static function big_back_on(): void {
self::$big_counter = 0;
}
public static function small_gave_up_yet(): bool {
self::$small_counter = max(self::$small_counter - 1, 0);
return self::$small_counter !== 0;
}
public static function small_give_up(): void {
self::$small_counter = 1000;
}
public static function small_back_on(): void {
self::$small_counter = 0;
}
public static function add_doi_map(string $bib, string $doi): void {
self::check_memory_use();
if ($bib === '' || $doi === '') {
report_minor_error('Bad parameter in add_doi_map: ' . echoable($bib) . ' : ' . echoable($doi)); // @codeCoverageIgnore
return; // @codeCoverageIgnore
}
if ($doi === 'X') {
self::$bib2doi[$bib] = 'X';
} elseif (doi_works($doi)) { // paranoid
self::$bib2doi[$bib] = $doi;
if (stripos($bib, 'tmp') === false && stripos($bib, 'arxiv') === false) {
self::$doi2bib[$doi] = $bib;
}
}
}
public static function get_doi2bib(string $doi): string {
return (string) @self::$doi2bib[$doi];
}
public static function get_bib2doi(string $bib): string {
return (string) @self::$bib2doi[$bib];
}
public static function check_memory_use(): void {
$usage = count(self::$doi2bib) + count(self::$bib2doi);
if ($usage > self::MAX_CACHE_SIZE) {
self::free_memory(); // @codeCoverageIgnore
}
}
public static function free_memory(): void {
self::$doi2bib = [];
self::$bib2doi = [];
gc_collect_cycles();
}
}
/**
@param array<string> $ids
@param array<Template> $templates
*/
function entrez_api(array $ids, array &$templates, string $db): void { // Pointer to save memory
set_time_limit(120);
if (!count($ids) ||
$ids === ['XYZ'] ||
$ids === ['1'] ||
$ids === ['']) {
return; // junk data from test suite
}
if ($db !== 'pubmed' && $db !== 'pmc') {
report_error("Invalid Entrez type passed in: " . echoable($db)); // @codeCoverageIgnore
}
report_action("Using $db API to retrieve publication details: ");
$xml = get_entrez_xml($db, implode(',', $ids));
if ($xml === null) {
report_warning("Error in PubMed search: No response from Entrez server"); // @codeCoverageIgnore
return; // @codeCoverageIgnore
}
// A few PMC do not have any data, just pictures of stuff
if (isset($xml->DocSum->Item) && count($xml->DocSum->Item) > 0) {
foreach($xml->DocSum as $document) {
report_info("Found match for $db identifier " . echoable((string) $document->Id));
foreach($ids as $template_key => $an_id) { // Cannot use array_search since that only returns first
$an_id = (string) $an_id;
if (!array_key_exists($template_key, $templates)) {
bot_debug_log('Key not found in entrez_api ' . (string) $template_key . ' ' . $an_id); // @codeCoverageIgnore
$an_id = '-3333'; // @codeCoverageIgnore
}
if ($an_id === (string) $document->Id) {
$this_template = $templates[$template_key];
$this_template->record_api_usage('entrez', $db === 'pubmed' ? 'pmid' : 'pmc');
foreach ($document->Item as $item) {
if (preg_match("~10\.\d{4}/[^\s\"']*~", (string) $item, $match)) {
$this_template->add_if_new('doi', $match[0], 'entrez');
}
switch ($item["Name"]) {
case "Title":
$this_template->add_if_new('title', str_replace(["[", "]"], "", (string) $item), 'entrez'); // add_if_new will format the title
break;
case "PubDate":
if (preg_match("~(\d+)\s*(\w*)~", (string) $item, $match)) {
$this_template->add_if_new('year', $match[1], 'entrez');
}
break;
case "FullJournalName":
$this_template->add_if_new('journal', mb_ucwords((string) $item), 'entrez'); // add_if_new will format the title
break;
case "Volume":
$this_template->add_if_new('volume', (string) $item, 'entrez');
break;
case "Issue":
$this_template->add_if_new('issue', (string) $item, 'entrez');
break;
case "Pages":
$this_template->add_if_new('pages', (string) $item, 'entrez');
break;
case "PmId":
$this_template->add_if_new('pmid', (string) $item, 'entrez');
break;
case "AuthorList":
$i = 0;
foreach ($item->Item as $key => $subItem) {
$subItem = (string) $subItem;
if (preg_match('~^\d~', $subItem)) { // Author started with a number, skip all remaining authors.
break; // @codeCoverageIgnore
} elseif ((string) $key === "CollectiveName") { // This is often really long string of gibberish
break; // @codeCoverageIgnore
} elseif (strlen($subItem) > 100) {
break; // @codeCoverageIgnore
} elseif (author_is_human($subItem)) {
$jr_test = junior_test($subItem);
$subItem = $jr_test[0];
$junior = $jr_test[1];
if (preg_match("~(.*) (\w+)$~", $subItem, $names)) {
$first = trim(preg_replace('~(?<=[A-Z])([A-Z])~', ". $1", $names[2]));
if (strpos($first, '.') && substr($first, -1) !== '.') {
$first .= '.';
}
$i++;
$this_template->add_if_new("author$i", $names[1] . $junior . ',' . $first, 'entrez');
}
} else {
// We probably have a committee or similar. Just use 'author$i'.
$i++;
$this_template->add_if_new("author$i", $subItem, 'entrez');
}
}
break;
case "LangList":
case 'ISSN':
break;
case "ArticleIds":
foreach ($item->Item as $subItem) {
switch ($subItem["Name"]) {
case "pubmed":
case "pmid":
preg_match("~\d+~", (string) $subItem, $match);
$this_template->add_if_new("pmid", $match[0], 'entrez');
break;
case "pmc":
preg_match("~\d+~", (string) $subItem, $match);
$this_template->add_if_new('pmc', $match[0], 'entrez');
break;
case "pmcid":
if (preg_match("~embargo-date: ?(\d{4})\/(\d{2})\/(\d{2})~", (string) $subItem, $match)) {
$date_emb = date("F j, Y", mktime(0, 0, 0, (int) $match[2], (int) $match[3], (int) $match[1])); // @codeCoverageIgnore
$this_template->add_if_new('pmc-embargo-date', $date_emb, 'entrez'); // @codeCoverageIgnore
}
break;
case "doi":
case "pii":
if (preg_match("~10\.\d{4}/[^\s\"']*~", (string) $subItem, $match)) {
$this_template->add_if_new('doi', $match[0], 'entrez');
}
}
}
break;
}
}
}
}
}
}
return;
}
/**
@param array<string> $bibcodes
@param array<Template> $templates
*/
function query_bibcode_api(array $bibcodes, array &$templates): void { adsabs_api($bibcodes, $templates, 'bibcode'); } // Pointer to save memory
/**
@param array<Template> $templates
*/
function expand_arxiv_templates (array &$templates): void { // Pointer to save memory
$ids = [];
$arxiv_templates = [];
foreach ($templates as $this_template) {
if ($this_template->wikiname() === 'cite arxiv') {
$this_template->rename('arxiv', 'eprint');
} else {
$this_template->rename('eprint', 'arxiv');
}
$eprint = str_ireplace("arXiv:", "", $this_template->get('eprint') . $this_template->get('arxiv'));
if ($eprint && stripos($eprint, 'CITATION_BOT') === false) {
$ids[] = $eprint;
$arxiv_templates[] = $this_template;
}
}
arxiv_api($ids, $arxiv_templates);
}
/**
@param array<string> $ids
@param array<Template> $templates
*/
function arxiv_api(array $ids, array &$templates): void { // Pointer to save memory
static $ch = null;
if ($ch === null) {
$ch = bot_curl_init(1.0, []);
}
set_time_limit(120);
if (count($ids) === 0) {
return;
}
report_action("Getting data from arXiv API");
/** @psalm-taint-escape ssrf */
$request = "https://export.arxiv.org/api/query?start=0&max_results=2000&id_list=" . implode(',', $ids);
curl_setopt($ch, CURLOPT_URL, $request);
$response = bot_curl_exec($ch);
if ($response) {
$xml = @simplexml_load_string(
preg_replace("~(</?)(\w+):([^>]*>)~", "$1$2$3", $response)
);
unset($response);
} else {
report_warning("No response from arXiv."); // @codeCoverageIgnore
return; // @codeCoverageIgnore
}
if (!is_object($xml)) {
report_warning("No valid from arXiv."); // @codeCoverageIgnore
return; // @codeCoverageIgnore
}
if ((string)$xml->entry->title === "Error") {
$the_error = (string)$xml->entry->summary;
if (stripos($the_error, 'incorrect id format for') !== false) {
report_warning("arXiv search failed: " . echoable($the_error));
} else {
report_minor_error("arXiv search failed - please report the error: " . echoable($the_error)); // @codeCoverageIgnore
}
return;
}
$this_template = current($templates); // advance at end of foreach loop
foreach ($xml->entry as $entry) {
$i = 0;
report_info("Found match for arXiv " . echoable($ids[$i]));
if ($this_template->add_if_new("doi", (string) $entry->arxivdoi, 'arxiv')) {
if ($this_template->blank(['journal', 'volume', 'issue']) && $this_template->has('title')) {
// Move outdated/bad arXiv title out of the way
$the_arxiv_title = $this_template->get('title');
$the_arxiv_contribution = $this_template->get('contribution');
if ($the_arxiv_contribution !== '') {
$this_template->set('contribution', '');
}
$this_template->set('title', '');
expand_by_doi($this_template);
if ($this_template->blank('title')) {
$this_template->set('title', $the_arxiv_title);
if ($the_arxiv_contribution !== '') {
$this_template->set('contribution', $the_arxiv_contribution);
}
} else {
if ($the_arxiv_contribution !== '' && $this_template->blank('contribution')) {
$this_template->forget('contribution');
}
}
unset($the_arxiv_title);
unset($the_arxiv_contribution);
} else {
expand_by_doi($this_template);
}
}
foreach ($entry->author as $auth) {
$i++;
$name = (string) $auth->name;
if (preg_match("~(.+\.)(.+?)$~", $name, $names) || preg_match('~^\s*(\S+) (\S+)\s*$~', $name, $names)) {
$this_template->add_if_new("last$i", $names[2], 'arxiv');
$this_template->add_if_new("first$i", $names[1], 'arxiv');
} else {
$this_template->add_if_new("author$i", $name, 'arxiv');
}
if ($this_template->blank(["last$i", "first$i", "author$i"])) {
$i--; // Deal with authors that are empty or just a colon as in https://export.arxiv.org/api/query?start=0&max_results=2000&id_list=2112.04678
}
}
$the_title = (string) $entry->title;
// arXiv fixes these when it sees them
while (preg_match('~\$\^{(\d+)}\$~', $the_title, $match)) {
$the_title = str_replace($match[0], '<sup>' . $match[1] . '</sup>', $the_title); // @codeCoverageIgnore
}
while (preg_match('~\$_(\d+)\$~', $the_title, $match)) {
$the_title = str_replace($match[0], '<sub>' . $match[1] . '</sub>', $the_title); // @codeCoverageIgnore
}
while (preg_match('~\\ce{([^}{^ ]+)}~', $the_title, $match)) { // arXiv fixes these when it sees them
$the_title = str_replace($match[0], ' ' . $match[1] . ' ', $the_title); // @codeCoverageIgnore
$the_title = str_replace(' ', ' ', $the_title); // @codeCoverageIgnore
}
$this_template->add_if_new("title", $the_title, 'arxiv'); // Formatted by add_if_new
$this_template->add_if_new("class", (string) $entry->category["term"], 'arxiv');
$int_time = strtotime((string) $entry->published);
if ($int_time) {
$this_template->add_if_new("year", date("Y", $int_time), 'arxiv');
}
if ($this_template->has('publisher')) {
if (stripos($this_template->get('publisher'), 'arxiv') !== false) {
$this_template->forget('publisher');
}
}
$this_template = next($templates);
}
if ($this_template !== false) {
report_minor_error('Unexpected error in arxiv_api()' . echoable($this_template->parsed_text())); // @codeCoverageIgnore
}
return;
}
/**
@param array<string> $ids
@param array<Template> $templates
*/
function adsabs_api(array $ids, array &$templates, string $identifier): void { // Pointer to save memory
set_time_limit(120);
if (count($ids) === 0) {
return;
}
foreach ($ids as $key => $bibcode) {
if (stripos($bibcode, 'CITATION') !== false || strlen($bibcode) !== 19) {
unset($ids[$key]); // @codeCoverageIgnore
}
}
// Use cache
foreach ($templates as $template) {
if ($template->has('bibcode') && $template->blank('doi')) {
$doi = AdsAbsControl::get_bib2doi($template->get('bibcode'));
if (doi_works($doi)) {
$template->add_if_new('doi', $doi);
}
}
}
$NONE_IS_INCOMPLETE = true;
foreach ($templates as $template) {
if ($template->has('bibcode') && $template->incomplete()) {
$NONE_IS_INCOMPLETE = false;
break;
}
if (stripos($template->get('bibcode'), 'tmp') !== false || stripos($template->get('bibcode'), 'arxiv') !== false) {
$NONE_IS_INCOMPLETE = false;
break;
}
}
if ($NONE_IS_INCOMPLETE ||
AdsAbsControl::big_gave_up_yet() ||
!PHP_ADSABSAPIKEY) {
return;
}
// API docs at https://github.com/adsabs/adsabs-dev-api/blob/master/Search_API.ipynb
$adsabs_url = "https://" . (TRAVIS ? 'qa' : 'api')
. ".adsabs.harvard.edu/v1/search/bigquery?q=*:*"
. "&fl=arxiv_class,author,bibcode,doi,doctype,identifier,"
. "issue,page,pub,pubdate,title,volume,year&rows=2000";
report_action("Expanding from BibCodes via AdsAbs API");
$curl_opts=[
CURLOPT_URL => $adsabs_url,
CURLOPT_HTTPHEADER => ['Content-Type: big-query/csv', 'Authorization: Bearer ' . PHP_ADSABSAPIKEY],
CURLOPT_HEADER => true,
CURLOPT_CUSTOMREQUEST => 'POST',
CURLOPT_POSTFIELDS => "$identifier\n" . implode("\n", $ids)];
$response = Bibcode_Response_Processing($curl_opts, $adsabs_url);
if (!isset($response->docs)) {
return;
}
foreach ($response->docs as $record) { // Check for remapped bibcodes
$record = (object) $record; // Make static analysis happy
if (isset($record->bibcode) && !in_array($record->bibcode, $ids, true) && isset($record->identifier)) {
foreach ($record->identifier as $identity) {
if (in_array($identity, $ids, true)) {
$record->citation_bot_new_bibcode = $record->bibcode; // save it
$record->bibcode = $identity; // unmap it
}
}
}
}
$matched_ids = [];
foreach ($response->docs as $record) {
report_info("Found match for bibcode " . bibcode_link($record->bibcode));
$matched_ids[] = $record->bibcode;
foreach($ids as $template_key => $an_id) { // Cannot use array_search since that only returns first
if (isset($record->bibcode) && strtolower($an_id) === strtolower((string) $record->bibcode)) { // BibCodes at not case-sensitive
$this_template = $templates[$template_key];
if (isset($record->citation_bot_new_bibcode)) {
$this_template->set('bibcode', (string) $record->citation_bot_new_bibcode);
$record->bibcode = $record->citation_bot_new_bibcode;
unset($record->citation_bot_new_bibcode);
} elseif ($an_id !== (string) $record->bibcode) { // Existing one is wrong case
$this_template->set('bibcode', (string) $record->bibcode);
}
if ((stripos($an_id, 'book') === false) && (stripos($an_id, 'PhD') === false)) {
process_bibcode_data($this_template, $record);
} else {
expand_book_adsabs($this_template, $record);
}
}
}
}
$unmatched_ids = array_udiff($ids, $matched_ids, 'strcasecmp');
if (count($unmatched_ids)) {
report_warning("No match for bibcode identifier: " . echoable(implode('; ', $unmatched_ids))); // @codeCoverageIgnore
bot_debug_log("No match for bibcode identifier: " . implode('; ', $unmatched_ids)); // @codeCoverageIgnore
}
foreach ($templates as $template) {
if ($template->blank(['year', 'date']) && preg_match('~^(\d{4}).*book.*$~', $template->get('bibcode'), $matches)) {
$template->add_if_new('year', $matches[1]); // Fail safe book code to grab a year directly from the bibcode itself
}
}
return;
}
/** @param array<string> $_ids
@param array<Template> $templates */
function query_doi_api(array $_ids, array &$templates): void { // $id not used yet // Pointer to save memory
foreach ($templates as $template) {
expand_by_doi($template);
}
return;
}
function expand_by_doi(Template $template, bool $force = false): void {
set_time_limit(120);
// Because it can recover rarely used parameters such as editors, series & isbn,
// there will be few instances where it could not in principle be profitable to
// run this function, so we don't check this first.
if (!$template->verify_doi()) {
return;
}
$doi = $template->get_without_comments_and_placeholders('doi');
if ($doi === $template->last_searched_doi) {
return;
}
$template->last_searched_doi = $doi;
if (preg_match(REGEXP_DOI_ISSN_ONLY, $doi)) {
return;
}
if ($doi && preg_match('~^10\.2307/(\d+)$~', $doi)) {
$template->add_if_new('jstor', substr($doi, 8));
}
if ($doi && ($force || $template->incomplete())) {
$crossRef = query_crossref($doi);
if ($crossRef) {
if (in_array(strtolower((string) @$crossRef->article_title), BAD_ACCEPTED_MANUSCRIPT_TITLES, true)) {
return ;
}
if ($template->has('title') && trim((string) @$crossRef->article_title) && $template->get('title') !== 'none') { // Verify title of DOI matches existing data somewhat
$bad_data = true;
$new = (string) $crossRef->article_title;
if (preg_match('~^(.................+)[\.\?]\s+([IVX]+)\.\s.+$~i', $new, $matches)) {
$new = $matches[1];
$new_roman = $matches[2];
} elseif (preg_match('~^([IVX]+)\.[\s\-\—]*(.................+)$~i', $new, $matches)) {
$new = $matches[2];
$new_roman = $matches[1];
} else {
$new_roman = false;
}
foreach (THINGS_THAT_ARE_TITLES as $possible) {
if ($template->has($possible)) {
$old = $template->get($possible);
if (preg_match('~^(.................+)[\.\?]\s+([IVX]+)\.\s.+$~i', $old, $matches)) {
$old = $matches[1];
$old_roman = $matches[2];
} elseif (preg_match('~^([IVX]+)\.[\s\-\—]*(.................+)$~i', $old, $matches)) {
$old = $matches[2];
$old_roman = $matches[1];
} else {
$old_roman = false;
}
if (titles_are_similar($old, $new)) {
if ($old_roman && $new_roman) {
if ($old_roman === $new_roman) { // If they got roman numeral truncted, then must match
$bad_data = false;
break;
}
} else {
$bad_data = false;
break;
}
}
}
}
if (isset($crossRef->series_title)) {
foreach (THINGS_THAT_ARE_TITLES as $possible) { // Series === series could easily be false positive
if ($template->has($possible) && titles_are_similar(preg_replace("~# # # CITATION_BOT_PLACEHOLDER_TEMPLATE \d+ # # #~i", "�", $template->get($possible)), (string) $crossRef->series_title)) {
$bad_data = false;
break;
}
}
}
if ($bad_data) {
report_warning("CrossRef title did not match existing title: doi:" . doi_link($doi));
if (isset($crossRef->series_title)) {
report_info(" Possible new title: " . str_replace("\n", "", echoable((string) $crossRef->series_title)));
}
if (isset($crossRef->article_title)) {
report_info(" Possible new title: " . echoable((string) $crossRef->article_title));
}
foreach (THINGS_THAT_ARE_TITLES as $possible) {
if ($template->has($possible)) {
report_info(" Existing old title: " . echoable(preg_replace("~# # # CITATION_BOT_PLACEHOLDER_TEMPLATE \d+ # # #~i", "�", $template->get($possible))));
}
}
return;
}
}
report_action("Querying CrossRef: doi:" . doi_link($doi));
if ((string) @$crossRef->volume_title === 'Professional Paper') {
unset($crossRef->volume_title);
}
if ((string) @$crossRef->series_title === 'Professional Paper') {
unset($crossRef->series_title);
}
if ($template->has('book-title')) {
unset($crossRef->volume_title);
}
if ($crossRef->volume_title && ($template->blank(WORK_ALIASES) || $template->wikiname() === 'cite book')) {
if (mb_strtolower($template->get('title')) === mb_strtolower((string) $crossRef->article_title)) {
$template->rename('title', 'chapter');
} else {
$new_title = CrossRefTitle($doi);
if ($new_title !== '' && $crossRef->article_title) {
$template->add_if_new('chapter', $new_title);
} else {
$template->add_if_new('chapter', restore_italics((string) $crossRef->article_title), 'crossref');
}
}
$template->add_if_new('title', restore_italics((string) $crossRef->volume_title), 'crossref'); // add_if_new will wikify title and sanitize the string
} else {
$new_title = CrossRefTitle($doi);
if ($new_title !== '' && $crossRef->article_title) {
$template->add_if_new('title', $new_title, 'crossref');
} else {
$template->add_if_new('title', restore_italics((string) $crossRef->article_title), 'crossref');
}
}
$template->add_if_new('series', (string) $crossRef->series_title, 'crossref'); // add_if_new will format the title for a series?
if (strpos($doi, '10.7817/jameroriesoci') === false || (string) $crossRef->year !== '2021') { // 10.7817/jameroriesoci "re-published" everything in 2021
$template->add_if_new("year", (string) $crossRef->year, 'crossref');
}
if ( $template->blank(['editor', 'editor1', 'editor-last', 'editor1-last', 'editor-last1']) // If editors present, authors may not be desired
&& $crossRef->contributors->contributor
) {
$au_i = 0;
$ed_i = 0;
// Check to see whether a single author is already set
// This might be, for example, a collaboration
$existing_author = $template->first_author();
$add_authors = $existing_author === '' || author_is_human($existing_author);
foreach ($crossRef->contributors->contributor as $author) {
if (strtoupper((string) $author->surname) === '&NA;') {
break; // No Author, leave loop now! Have only seen upper-case in the wild
}
if ((string) $author["contributor_role"] === 'editor') {
++$ed_i;
if ($ed_i < 31 && !isset($crossRef->journal_title)) {
$template->add_if_new("editor-last$ed_i", format_surname((string) $author->surname), 'crossref');
$template->add_if_new("editor-first$ed_i", format_forename((string) $author->given_name), 'crossref');
}
} elseif ((string) $author['contributor_role'] === 'author' && $add_authors) {
++$au_i;
$template->add_if_new("last$au_i", format_surname((string) $author->surname), 'crossref');
$template->add_if_new("first$au_i", format_forename((string) $author->given_name), 'crossref');
}
}
}
$template->add_if_new('isbn', (string) $crossRef->isbn, 'crossref');
$template->add_if_new('journal', (string) $crossRef->journal_title); // add_if_new will format the title
if ((int)$crossRef->volume > 0) {
$template->add_if_new('volume', (string) $crossRef->volume, 'crossref');
}
if (((strpos((string) $crossRef->issue, '-') > 0 || (int) $crossRef->issue > 1))) {
// "1" may refer to a journal without issue numbers,
// e.g. 10.1146/annurev.fl.23.010191.001111, as well as a genuine issue 1. Best ignore.
$template->add_if_new('issue', (string) $crossRef->issue, 'crossref');
}
if ($template->blank("page")) {
if ($crossRef->last_page && (strcmp((string) $crossRef->first_page, (string) $crossRef->last_page) !== 0)) {
if (strpos((string) $crossRef->first_page . (string) $crossRef->last_page, '-') === false) { // Very rarely get stuff like volume/issue/year added to pages
$template->add_if_new("pages", $crossRef->first_page . "-" . $crossRef->last_page, 'crossref'); //replaced by an endash later in script
}
} else {
if (strpos((string) $crossRef->first_page, '-') === false) { // Very rarely get stuff like volume/issue/year added to pages
$template->add_if_new("pages", (string) $crossRef->first_page, 'crossref');
}
}
}
} else {
report_info("No CrossRef record found for doi '" . echoable($doi) ."'");
expand_doi_with_dx($template, $doi);
}
}
return;
}
function query_crossref(string $doi): ?object {
static $ch = null;
if ($ch === null) {
$ch = bot_curl_init(1.0, []);
}
if (strpos($doi, '10.2307') === 0) {
return null; // jstor API is better
}
set_time_limit(120);
$doi = str_replace(DOI_URL_DECODE, DOI_URL_ENCODE, $doi);
/** @psalm-taint-escape ssrf */
$url = "https://www.crossref.org/openurl/?pid=" . CROSSREFUSERNAME . "&id=doi:$doi&noredirect=TRUE";
curl_setopt($ch, CURLOPT_URL, $url);
for ($i = 0; $i < 2; $i++) {
$raw_xml = bot_curl_exec($ch);
if (!$raw_xml) {
sleep(1); // @codeCoverageIgnore
continue; // @codeCoverageIgnore
// Keep trying...
}
$raw_xml = preg_replace(
'~(\<year media_type=\"online\"\>\d{4}\<\/year\>\<year media_type=\"print\"\>)~',
'<year media_type="print">',
$raw_xml);
$xml = @simplexml_load_string($raw_xml);
unset($raw_xml);
if (is_object($xml) && isset($xml->query_result->body->query)) {
$result = $xml->query_result->body->query;
if ((string) @$result["status"] === "resolved") {
if (stripos($doi, '10.1515/crll') === 0) {
$volume = intval(trim((string) @$result->volume));
if ($volume > 1820) {
if (isset($result->issue)) {
$result->volume = $result->issue;
unset($result->issue);
} else {
unset($result->volume);
}
}
}
if (stripos($doi, '10.3897/ab.') === 0) {
unset($result->volume);
unset($result->page);
unset($result->issue);
}
return $result;
} else {
return null;
}
} else {
sleep(1); // @codeCoverageIgnore
// Keep trying...
}
}
report_warning("Error loading CrossRef file from DOI " . echoable($doi) . "!"); // @codeCoverageIgnore
return null; // @codeCoverageIgnore
}
function expand_doi_with_dx(Template $template, string $doi): void {
// See https://crosscite.org/docs.html for discussion of API we are using -- not all agencies resolve the same way
// https://api.crossref.org/works/$doi can be used to find out the agency
// https://www.doi.org/registration_agencies.html https://www.doi.org/RA_Coverage.html List of all ten doi granting agencies - many do not do journals
// Examples of DOI usage https://www.doi.org/demos.html
// This basically does this:
// curl -LH "Accept: application/vnd.citationstyles.csl+json" https://dx.doi.org/10.5524/100077
static $ch = null;
if ($ch === null) {
$ch = bot_curl_init(1.5, // can take a long time when nothing to be found
[CURLOPT_HTTPHEADER => ["Accept: application/vnd.citationstyles.csl+json"]]);
}
if (strpos($doi, '10.2307') === 0 || // jstor API is better
strpos($doi, '10.24436') === 0 || // They have horrible meta-data
strpos($doi, '10.5284/1028203') === 0) { // database
return;
}
set_time_limit(120);
/** @param array|string|null|int $data */
$try_to_add_it = function(string $name, $data) use($template): void {
if ($template->has($name)) {
return; // Not worth updating based upon DX
}
if (is_null($data)) {
return;
}
while (is_array($data)) {
if (!isset($data['0']) || isset($data['1'])) {
return;
}
$data = $data['0'];
}
$data = (string) $data;
if ($data === '') {
return;
}
$template->add_if_new($name, $data, 'dx');
return;
};
if (!$doi) {
return;
}
/** @psalm-taint-escape ssrf */
$doi = trim($doi);
curl_setopt($ch, CURLOPT_URL, 'https://doi.org/' . $doi);
report_action("Querying dx.doi.org: doi:" . doi_link($doi));
try {
$data = bot_curl_exec($ch);
} catch (Exception $e) { // @codeCoverageIgnoreStart
$template->mark_inactive_doi();
return;
} // @codeCoverageIgnoreEnd
if ($data === "" || stripos($data, 'DOI Not Found') !== false || stripos($data, 'DOI prefix') !== false) {
$template->mark_inactive_doi();
return;
}
$json = @json_decode($data, true);
unset($data);
if($json === false || $json === null) {
return;
}
// BE WARNED: this code uses the "@$var" method.
// If the variable is not set, then PHP just passes null, then that is interpreted as a empty string
if ($template->blank(['date', 'year'])) {
$try_to_add_it('year', @$json['issued']['date-parts']['0']['0']);
$try_to_add_it('year', @$json['created']['date-parts']['0']['0']);
$try_to_add_it('year', @$json['published-print']['date-parts']['0']['0']);
}
$try_to_add_it('issue', @$json['issue']);
$try_to_add_it('pages', @$json['pages']);
$try_to_add_it('volume', @$json['volume']);
$try_to_add_it('isbn', @$json['ISBN']['0']);
$try_to_add_it('isbn', @$json['isbn-type']['0']['value']);
if (isset($json['author'])) {
$i = 0;
foreach ($json['author'] as $auth) {
$i += 1;
$full_name = mb_strtolower(trim((string) @$auth['given'] . ' ' . (string) @$auth['family'] . (string) @$auth['literal']));
if (in_array($full_name, BAD_AUTHORS, true)) {
break;
}
if (((string) @$auth['family'] === '') && ((string) @$auth['given'] !== '')) {
$try_to_add_it('author' . (string) $i, @$auth['given']); // First name without last name. Probably an organization or chinese/korean/japanese name
} else {
$try_to_add_it('last' . (string) $i, @$auth['family']);
$try_to_add_it('first' . (string) $i, @$auth['given']);
$try_to_add_it('author' . (string) $i, @$auth['literal']);
}
}
}
// Publisher hiding as journal name - defective data
if (isset($json['container-title']) && isset($json['publisher']) && ($json['publisher'] === $json['container-title'])) {
unset($json['container-title']); // @codeCoverageIgnore
}
if (str_ends_with((string) @$json['title'], '.PDF') ||
str_ends_with((string) @$json['title'], '.pdf')) {
unset($json['title']);
}
$type = (string) @$json['type'];
if ($type === 'article-journal' ||
$type === 'journal-article' ||
$type === 'article' ||
$type === 'proceedings-article' ||
$type === 'conference-paper' ||
$type === 'entry' ||
($type === '' && (isset($json['container-title']) || isset($json['issn']['0'])))) {
$try_to_add_it('journal', @$json['container-title']);
$try_to_add_it('title', @$json['title']);
$try_to_add_it('issn', @$json['issn']); // Will not add if journal is set
} elseif ($type === 'journal-issue') { // Very rare: Do not add "title": should be blank anyway. Got this once from DOI:10.7592/fejf2015.62
$try_to_add_it('journal', @$json['container-title']); // @codeCoverageIgnore
$try_to_add_it('issn', @$json['issn']); // @codeCoverageIgnore
} elseif ($type === 'journal') { // Very rare: Do not add "title": should be blank anyway. Got this once from DOI:10.1007/13539.2190-6009 and DOI:10.14296/rih/issn.1749.8155
$try_to_add_it('issn', @$json['issn']); // @codeCoverageIgnore
} elseif ($type === 'reference-entry') { // Very rare: Got this once from DOI:10.1002/14356007.a02_115.pub2
$try_to_add_it('work', @$json['container-title']); // @codeCoverageIgnore
$try_to_add_it('title', @$json['title']); // @codeCoverageIgnore
} elseif ($type === 'monograph' || $type === 'book' || $type === 'edited-book') {
$try_to_add_it('title', @$json['title']);
$try_to_add_it('title', @$json['container-title']);// Usually not set, but just in case this instead of title is set
$try_to_add_it('location', @$json['publisher-location']);
$try_to_add_it('publisher', @$json['publisher']);
} elseif ($type === 'reference-book') { // VERY rare
$try_to_add_it('title', @$json['title']); // @codeCoverageIgnore
$try_to_add_it('title', @$json['container-title']); // @codeCoverageIgnore
$try_to_add_it('chapter', @$json['original-title']); // @codeCoverageIgnore
$try_to_add_it('location', @$json['publisher-location']); // @codeCoverageIgnore
$try_to_add_it('publisher', @$json['publisher']); // @codeCoverageIgnore
} elseif ($type === 'chapter' ||
$type === 'book-chapter') {
$try_to_add_it('title', @$json['container-title']);
$try_to_add_it('chapter', @$json['title']);
$try_to_add_it('location', @$json['publisher-location']);
$try_to_add_it('publisher', @$json['publisher']);
} elseif ($type === 'other') {
if (isset($json['container-title'])) {
$try_to_add_it('title', @$json['container-title']);
$try_to_add_it('chapter', @$json['title']);
} else {
$try_to_add_it('title', @$json['title']);
}
$try_to_add_it('location', @$json['publisher-location']);
$try_to_add_it('publisher', @$json['publisher']);
} elseif ($type === 'dataset') {
$try_to_add_it('type', 'Data Set');
$try_to_add_it('title', @$json['title']);
$try_to_add_it('location', @$json['publisher-location']);
$try_to_add_it('publisher', @$json['publisher']);
if (!isset($json['categories']['1']) &&
(($template->wikiname() === 'cite book') || $template->blank(WORK_ALIASES))) { // No journal/magazine set and can convert to book
$try_to_add_it('chapter', @$json['categories']['0']); // Not really right, but there is no cite data set template
}
} elseif ($type === '' || $type === 'graphic' || $type === 'report' || $type === 'report-component') { // Add what we can where we can
$try_to_add_it('title', @$json['title']);
$try_to_add_it('location', @$json['publisher-location']);
$try_to_add_it('publisher', @$json['publisher']);
} elseif ($type === 'thesis' || $type === 'dissertation' || $type === 'dissertation-thesis') {
$template->change_name_to('cite thesis');
$try_to_add_it('title', @$json['title']);
$try_to_add_it('location', @$json['publisher-location']);
$try_to_add_it('publisher', @$json['publisher']);
if (stripos(@$json['URL'], 'hdl.handle.net')) {
$template->get_identifiers_from_url($json['URL']);
}
} elseif ($type === 'posted-content' || $type === 'grant' || $type === 'song' || $type === 'motion_picture') { // posted-content is from bioRxiv
$try_to_add_it('title', @$json['title']);
} else {
$try_to_add_it('title', @$json['title']); // @codeCoverageIgnore
if (!HTML_OUTPUT) {
print_r($json); // @codeCoverageIgnore
}
report_minor_error('dx.doi.org returned unexpected data type ' . echoable($type) . ' for ' . doi_link($doi)); // @codeCoverageIgnore
}
return;
}
function expand_by_jstor(Template $template): void {
static $ch = null;
if ($ch === null) {
$ch = bot_curl_init(1.0, []);
}
set_time_limit(120);
if ($template->incomplete() === false) {
return;
}
if ($template->has('jstor')) {
$jstor = trim($template->get('jstor'));
} elseif(preg_match('~^https?://(?:www\.|)jstor\.org/stable/(.*)$~', $template->get('url'), $match)) {
$jstor = $match[1];
} else {
return;
}
if (preg_match('~^(.*)(?:\?.*)$~', $jstor, $match)) {
$jstor = $match[1]; // remove ?seq= stuff
}
/** @psalm-taint-escape ssrf */
$jstor = trim($jstor);
if (strpos($jstor, ' ') !== false) {
return ; // Comment/template found
}
if (substr($jstor, 0, 1) === 'i') {
return ; // We do not want i12342 kind
}
curl_setopt($ch, CURLOPT_URL, 'https://www.jstor.org/citation/ris/' . $jstor);
$dat = bot_curl_exec($ch);
if ($dat === '') {
report_info("JSTOR API returned nothing for ". jstor_link($jstor)); // @codeCoverageIgnore
return; // @codeCoverageIgnore
}
if (stripos($dat, 'No RIS data found for') !== false) {
report_info("JSTOR API found nothing for ". jstor_link($jstor)); // @codeCoverageIgnore
return; // @codeCoverageIgnore
}
if (stripos($dat, 'Block Reference') !== false) {
report_info("JSTOR API blocked bot for ". jstor_link($jstor)); // @codeCoverageIgnore
return; // @codeCoverageIgnore
}
if (stripos($dat, 'A problem occurred trying to deliver RIS data') !== false) {
report_info("JSTOR API had a problem for ". jstor_link($jstor));
return;
}
if ($template->has('title')) {
$bad_data = true;
$ris = explode("\n", html_entity_decode($dat, ENT_COMPAT | ENT_HTML401, 'UTF-8'));
foreach ($ris as $ris_line) {
$ris_part = explode(" - ", $ris_line . " ", 2);
if (!isset($ris_part[1])) {
$ris_part[0] = ""; // Ignore
}
switch (trim($ris_part[0])) {
case "T1":
case "TI":
case "T2":
case "BT":
$new_title = trim($ris_part[1]);
foreach (THINGS_THAT_ARE_TITLES as $possible) {
if ($template->has($possible) && titles_are_similar($template->get($possible), $new_title)) {
$bad_data = false;
}
}
break;
default:
break;
}
}
if ($bad_data) { // Now for TI: T1 existing titles (title followed by sub-title)
$got_count = 0;
$new_title = ': ';
foreach ($ris as $ris_line) {
$ris_part = explode(" - ", $ris_line . " ", 2);
if (!isset($ris_part[1])) {
$ris_part[0] = ""; // Ignore
}
switch (trim($ris_part[0])) {
case "T1":
$new_title .= trim($ris_part[1]);
$got_count += 10;
break;
case "TI":
$new_title = trim($ris_part[1]) . $new_title;
$got_count += 100;
break;
default:
break;
}
}
if ($got_count === 110) { // Exactly one of each
foreach (THINGS_THAT_ARE_TITLES as $possible) {
if ($template->has($possible) && titles_are_similar(preg_replace("~# # # CITATION_BOT_PLACEHOLDER_TEMPLATE \d+ # # #~i", "�", $template->get($possible)), $new_title)) {
$bad_data = false;
}
}
}
}
if ($bad_data) {
report_info('Old title did not match for ' . jstor_link($jstor));
foreach ($ris as $ris_line) {
if (!isset($ris_part[1])) {
$ris_part[0] = ""; // Ignore
}
$ris_part = explode(" - ", $ris_line . " ", 2);
switch (trim($ris_part[0])) {
case "T1":
case "TI":
case "T2":
case "BT":
$new_title = trim($ris_part[1]);