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wangjinlei
237
application/common/PubmedService.php
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237
application/common/PubmedService.php
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<?php
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namespace app\common;
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/**
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* PubMed 工具类（E-utilities）
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*
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* 功能：
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* - DOI -> PMID
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* - PMID -> 文章结构化信息（title/abstract/mesh/publication_types/year/journal）
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*
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* 说明：
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* - 默认使用 runtime 文件缓存，避免重复请求 NCBI
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*/
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class PubmedService
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{
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private $base = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/';
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private $timeout = 20;
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private $tool = 'tmrjournals';
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private $email = '';
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public function __construct(array $config = [])
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{
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if (isset($config['base'])) $this->base = rtrim((string)$config['base'], '/') . '/';
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if (isset($config['timeout'])) $this->timeout = max(5, intval($config['timeout']));
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if (isset($config['tool'])) $this->tool = (string)$config['tool'];
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if (isset($config['email'])) $this->email = (string)$config['email'];
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}
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/**
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* DOI -> PMID（优先用 [DOI]，命中不到再用 [AID]）
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*/
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public function doiToPmid(string $doi): ?string
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{
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$doi = trim($doi);
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if ($doi === '') return null;
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$cacheKey = 'doi2pmid_' . sha1(strtolower($doi));
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$cached = $this->cacheGet($cacheKey, 30 * 86400);
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if (is_string($cached) && $cached !== '') {
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return $cached;
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}
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$pmid = $this->esearch($doi . '[DOI]');
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if (!$pmid) {
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$pmid = $this->esearch($doi . '[AID]');
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}
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if ($pmid) {
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$this->cacheSet($cacheKey, $pmid);
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return $pmid;
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}
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return null;
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}
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/**
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* PMID -> 文章信息（title/abstract/mesh/publication_types/year/journal）
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*/
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public function fetchByPmid(string $pmid): ?array
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{
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$pmid = trim($pmid);
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if ($pmid === '') return null;
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$cacheKey = 'pmid_' . $pmid;
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$cached = $this->cacheGet($cacheKey, 30 * 86400);
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if (is_array($cached)) return $cached;
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$url = $this->base . 'efetch.fcgi?' . http_build_query([
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'db' => 'pubmed',
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'id' => $pmid,
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'retmode' => 'xml',
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'tool' => $this->tool,
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'email' => $this->email,
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]);
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$xml = $this->httpGet($url);
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if (!is_string($xml) || trim($xml) === '') return null;
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$data = $this->parseEfetchXml($xml);
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if (!$data) return null;
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$this->cacheSet($cacheKey, $data);
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return $data;
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}
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/**
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* DOI -> PubMed 信息（含 abstract/mesh）
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*/
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public function fetchByDoi(string $doi): ?array
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{
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$pmid = $this->doiToPmid($doi);
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if (!$pmid) return null;
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$info = $this->fetchByPmid($pmid);
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if (!$info) return null;
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$info['pmid'] = $pmid;
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$info['doi'] = $doi;
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return $info;
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}
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// ----------------- Internals -----------------
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private function esearch(string $term): ?string
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{
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$url = $this->base . 'esearch.fcgi?' . http_build_query([
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'db' => 'pubmed',
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'retmode' => 'json',
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'retmax' => 1,
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'term' => $term,
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'tool' => $this->tool,
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'email' => $this->email,
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]);
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$res = $this->httpGet($url);
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$json = json_decode((string)$res, true);
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$ids = $json['esearchresult']['idlist'] ?? [];
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if (!empty($ids[0])) return (string)$ids[0];
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return null;
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}
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private function parseEfetchXml(string $xml): ?array
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{
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libxml_use_internal_errors(true);
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$doc = new \DOMDocument();
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if (!$doc->loadXML($xml)) {
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return null;
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}
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$xp = new \DOMXPath($doc);
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$title = $this->xpText($xp, '//PubmedArticle//ArticleTitle');
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$abstractParts = [];
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$absNodes = $xp->query('//PubmedArticle//Abstract//AbstractText');
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if ($absNodes) {
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foreach ($absNodes as $n) {
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$label = $n->attributes && $n->attributes->getNamedItem('Label')
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? trim($n->attributes->getNamedItem('Label')->nodeValue)
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: '';
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$txt = trim($n->textContent);
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if ($txt === '') continue;
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$abstractParts[] = $label ? ($label . ': ' . $txt) : $txt;
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}
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}
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$abstract = trim(implode("\n", $abstractParts));
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$mesh = [];
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$meshNodes = $xp->query('//PubmedArticle//MeshHeadingList//MeshHeading//DescriptorName');
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if ($meshNodes) {
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foreach ($meshNodes as $n) {
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$t = trim($n->textContent);
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if ($t !== '') $mesh[] = $t;
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}
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}
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$mesh = array_values(array_unique($mesh));
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$pubTypes = [];
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$ptNodes = $xp->query('//PubmedArticle//PublicationTypeList//PublicationType');
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if ($ptNodes) {
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foreach ($ptNodes as $n) {
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$t = trim($n->textContent);
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if ($t !== '') $pubTypes[] = $t;
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}
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}
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$pubTypes = array_values(array_unique($pubTypes));
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$journal = $this->xpText($xp, '//PubmedArticle//Journal//Title');
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$year = '';
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$year = $this->xpText($xp, '//PubmedArticle//JournalIssue//PubDate//Year');
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if ($year === '') {
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$medlineDate = $this->xpText($xp, '//PubmedArticle//JournalIssue//PubDate//MedlineDate');
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if (preg_match('/(19\\d{2}|20\\d{2})/', $medlineDate, $m)) {
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$year = $m[1];
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}
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}
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if ($title === '' && $abstract === '') {
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return null;
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}
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return [
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'title' => $title,
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'abstract' => $abstract,
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'mesh_terms' => $mesh,
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'publication_types' => $pubTypes,
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'journal' => $journal,
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'year' => $year,
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];
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}
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private function xpText(\DOMXPath $xp, string $query): string
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{
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$n = $xp->query($query);
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if ($n && $n->length > 0) {
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return trim($n->item(0)->textContent);
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}
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return '';
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}
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private function httpGet(string $url): string
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{
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$ch = curl_init();
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curl_setopt($ch, CURLOPT_URL, $url);
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curl_setopt($ch, CURLOPT_RETURNTRANSFER, true);
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curl_setopt($ch, CURLOPT_TIMEOUT, $this->timeout);
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curl_setopt($ch, CURLOPT_SSL_VERIFYPEER, false);
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curl_setopt($ch, CURLOPT_HTTPHEADER, [
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'User-Agent: TMRjournals-PubMed/1.0'
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]);
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$res = curl_exec($ch);
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curl_close($ch);
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return is_string($res) ? $res : '';
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}
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private function cacheDir(): string
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{
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return rtrim(ROOT_PATH, '/') . '/runtime/pubmed_cache';
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}
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private function cacheGet(string $key, int $ttlSeconds)
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{
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$file = $this->cacheDir() . '/' . $key . '.json';
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if (!is_file($file)) return null;
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$mtime = filemtime($file);
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if (!$mtime || (time() - $mtime) > $ttlSeconds) return null;
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$raw = @file_get_contents($file);
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$decoded = json_decode((string)$raw, true);
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return $decoded;
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}
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private function cacheSet(string $key, $value): void
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{
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$dir = $this->cacheDir();
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if (!is_dir($dir)) @mkdir($dir, 0777, true);
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$file = $dir . '/' . $key . '.json';
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@file_put_contents($file, json_encode($value, JSON_UNESCAPED_UNICODE));
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}
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}
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