492 lines
16 KiB
PHP
492 lines
16 KiB
PHP
<?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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// NCBI 限流：无 key 时 3 次/秒，配 key 后 10 次/秒。多 worker 并行处理参考文献时必须配。
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private $apiKey = '';
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private $maxRetry = 3;
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public function __construct(array $config = [])
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{
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$this->email = (string)$this->envGet('pubmed_email', '');
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$this->apiKey = (string)$this->envGet('pubmed_api_key', '');
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$tool = trim((string)$this->envGet('pubmed_tool', ''));
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if ($tool !== '') $this->tool = $tool;
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if (isset($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 (!empty($config['tool'])) $this->tool = (string)$config['tool'];
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if (!empty($config['email'])) $this->email = (string)$config['email'];
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if (!empty($config['api_key'])) $this->apiKey = (string)$config['api_key'];
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if (isset($config['max_retry'])) $this->maxRetry = max(1, intval($config['max_retry']));
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}
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private function envGet($key, $default = '')
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{
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if (!class_exists('\think\Env')) {
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return $default;
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}
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return \think\Env::get($key, $default);
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}
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/**
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* tool/email/api_key 是 NCBI 要求的调用方标识，缺失会被更严格限流
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*/
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private function commonParams(): array
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{
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$params = ['tool' => $this->tool, 'email' => $this->email];
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if ($this->apiKey !== '') {
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$params['api_key'] = $this->apiKey;
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}
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return $params;
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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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// v3：解析结果新增 authors / volume / issue / pages / doi，换 key 避免命中旧缓存
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$cacheKey = 'pmid_v3_' . $pmid;
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$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(array_merge([
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'db' => 'pubmed',
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'id' => $pmid,
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'retmode' => 'xml',
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], $this->commonParams()));
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$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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/**
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* DOI -> 期刊规范缩写（NLM/ISO 形式，如 "J Clin Oncol"）
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* 优先 ISOAbbreviation，回退 MedlineTA；查不到返回 null。
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*/
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public function journalAbbrByDoi(string $doi): ?string
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{
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$info = $this->fetchByDoi($doi);
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if (!is_array($info)) return null;
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$abbr = trim((string)($info['journal_iso_abbr'] ?? ''));
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if ($abbr === '') {
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$abbr = trim((string)($info['journal_medline_ta'] ?? ''));
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}
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return $abbr !== '' ? $abbr : null;
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}
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/**
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* 按书目信息检索 PubMed（标题 + 第一作者 + 年份）
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*/
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public function searchByBibliographic($title, $author = '', $year = ''): ?array
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{
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$title = trim((string)$title);
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if ($title === '') {
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return null;
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}
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$terms = ['(' . $this->quoteTerm($title) . '[Title])'];
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$author = trim((string)$author);
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if ($author !== '') {
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$parts = preg_split('/[,;]/', $author);
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$first = trim((string)($parts[0] ?? ''));
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if ($first !== '') {
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$terms[] = '(' . $this->quoteTerm($first) . '[Author])';
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}
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}
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$year = trim((string)$year);
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if ($year !== '' && preg_match('/^(19|20)\d{2}$/', $year)) {
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$terms[] = '(' . $year . '[pdat])';
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}
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$pmid = $this->esearch(implode(' AND ', $terms));
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if (!$pmid) {
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return null;
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}
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$info = $this->fetchByPmid($pmid);
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if (!$info) {
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return null;
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}
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$info['pmid'] = $pmid;
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$info['doi'] = $this->extractDoiFromPmidRecord($pmid);
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return $info;
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}
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private function quoteTerm($text)
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{
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return str_replace('"', '', trim((string)$text));
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}
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private function extractDoiFromPmidRecord($pmid)
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{
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$url = $this->base . 'efetch.fcgi?' . http_build_query(array_merge([
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'db' => 'pubmed',
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'id' => $pmid,
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'retmode' => 'xml',
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], $this->commonParams()));
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$xml = $this->httpGet($url);
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if ($xml === '') {
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return '';
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}
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if (preg_match('/<ArticleId IdType="doi">([^<]+)<\/ArticleId>/i', $xml, $m)) {
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return trim($m[1]);
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}
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return '';
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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(array_merge([
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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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], $this->commonParams()));
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$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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// 期刊规范缩写：ISOAbbreviation（Journal 下）与 MedlineTA（MedlineJournalInfo 下）
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$journalIsoAbbr = $this->xpText($xp, '//PubmedArticle//Journal//ISOAbbreviation');
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$journalMedlineTa = $this->xpText($xp, '//PubmedArticle//MedlineJournalInfo//MedlineTA');
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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 === '' && $abstract === '') {
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return null;
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}
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$doi = $this->xpText($xp, '//PubmedArticle//ArticleIdList/ArticleId[@IdType="doi"]');
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if ($doi === '') {
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$doi = $this->xpText($xp, '//PubmedArticle//ELocationID[@EIdType="doi"]');
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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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'journal_iso_abbr' => $journalIsoAbbr,
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'journal_medline_ta' => $journalMedlineTa,
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'year' => $year,
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'authors' => $this->parseAuthors($xp),
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'volume' => $this->xpText($xp, '//PubmedArticle//JournalIssue//Volume'),
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'issue' => $this->xpText($xp, '//PubmedArticle//JournalIssue//Issue'),
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'pages' => $this->parsePagination($xp),
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'doi' => $doi,
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];
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}
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/**
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* 作者列表：LastName/ForeName/Initials，机构作者用 CollectiveName
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*/
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private function parseAuthors(\DOMXPath $xp): array
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{
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$out = [];
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$nodes = $xp->query('//PubmedArticle//AuthorList/Author');
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if (!$nodes) {
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return $out;
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}
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foreach ($nodes as $n) {
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$family = $given = $initials = $collective = '';
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foreach ($n->childNodes as $c) {
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switch ($c->nodeName) {
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case 'LastName':
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$family = trim($c->textContent);
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break;
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case 'ForeName':
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$given = trim($c->textContent);
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break;
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case 'Initials':
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$initials = trim($c->textContent);
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break;
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case 'CollectiveName':
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$collective = trim($c->textContent);
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break;
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}
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}
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if ($family === '' && $given === '' && $collective === '') {
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continue;
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}
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$out[] = [
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'family' => $family,
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'given' => $given,
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'initials' => $initials,
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'collective' => $collective,
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];
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}
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return $out;
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}
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/**
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* 页码：StartPage/EndPage → MedlinePgn → 电子刊文章号（ELocationID pii）
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*
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* MedlinePgn 用 NLM 缩写式尾页（210-8 表示 210–218），展开逻辑由调用方处理。
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*/
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private function parsePagination(\DOMXPath $xp): string
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{
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$start = $this->xpText($xp, '//PubmedArticle//Pagination//StartPage');
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if ($start !== '') {
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$end = $this->xpText($xp, '//PubmedArticle//Pagination//EndPage');
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return $end !== '' ? $start . '-' . $end : $start;
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}
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$medlinePgn = $this->xpText($xp, '//PubmedArticle//Pagination//MedlinePgn');
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if ($medlinePgn !== '') {
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return $medlinePgn;
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}
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// 无连续页码的电子刊（PLOS 等）以文章号著录；pii 也可能是出版社流水号，故只认 e12345/12345
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$pii = $this->xpText($xp, '//PubmedArticle//ELocationID[@EIdType="pii"]');
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return preg_match('/^e?\d+$/i', $pii) === 1 ? $pii : '';
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}
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/**
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* 引用格式作者串：姓全写 + 名首字母，超过 $maxAuthors 个取前 N 个 + et al
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* 例：Smith JA, Jones B, Lee C, et al
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*/
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public function authorsCitation(array $authors, int $maxAuthors = 3): string
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{
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$list = [];
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foreach ($authors as $a) {
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$collective = trim((string)($a['collective'] ?? ''));
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if ($collective !== '') {
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$list[] = $collective;
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continue;
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}
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$family = trim((string)($a['family'] ?? ''));
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if ($family === '') {
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continue;
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}
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$initials = trim((string)($a['initials'] ?? ''));
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if ($initials === '') {
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$initials = $this->givenToInitials((string)($a['given'] ?? ''));
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}
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$list[] = $initials !== '' ? $family . ' ' . $initials : $family;
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}
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if (empty($list)) {
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return '';
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}
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$maxAuthors = max(1, $maxAuthors);
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if (count($list) > $maxAuthors) {
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return implode(', ', array_slice($list, 0, $maxAuthors)) . ', et al';
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}
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return implode(', ', $list);
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}
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private function givenToInitials($given): string
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{
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$given = trim((string)$given);
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if ($given === '') {
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return '';
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}
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$parts = preg_split('/[\s\-\.]+/u', $given, -1, PREG_SPLIT_NO_EMPTY);
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$initials = '';
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foreach ($parts as $p) {
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$first = mb_substr($p, 0, 1);
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if ($first !== '') {
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$initials .= mb_strtoupper($first);
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}
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}
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return $initials;
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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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/**
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* 限流(429)与服务端错误退避重试；耗尽重试返回空串，由调用方回落到 Crossref
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*/
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private function httpGet(string $url): string
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{
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for ($attempt = 0; $attempt < $this->maxRetry; $attempt++) {
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$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($ch);
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$httpCode = (int)curl_getinfo($ch, CURLINFO_HTTP_CODE);
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curl_close($ch);
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if ($httpCode === 200 && is_string($res) && trim($res) !== '') {
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return $res;
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}
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if ($httpCode !== 429 && $httpCode < 500 && $httpCode !== 0) {
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return '';
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}
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usleep((int)(($attempt + 1) * 400000));
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}
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return '';
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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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