751 lines
27 KiB
PHP
751 lines
27 KiB
PHP
<?php
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namespace app\common;
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use think\Db;
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use think\Queue;
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use GuzzleHttp\Client;
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use think\Env;
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class ExpertFinderService
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{
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private $httpClient;
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private $ncbiBaseUrl = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/';
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private $logFile;
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public function __construct()
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{
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$this->httpClient = new Client([
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'timeout' => 180,
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'connect_timeout' => 15,
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'verify' => false,
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]);
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$this->logFile = ROOT_PATH . 'runtime' . DS . 'expert_finder.log';
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}
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public function doFetchForField($field, $source = 'pubmed', $perPage = 100, $minYear = null)
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{
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if ($minYear === null) {
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$minYear = date('Y') - 3;
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}
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$fetchLog = $this->getFetchLog($field, $source);
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$page = $fetchLog['last_page'] + 1;
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if ($source === 'pmc') {
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$result = $this->searchViaPMC($field, $perPage, $minYear, $page);
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} else {
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$result = $this->searchViaPubMed($field, $perPage, $minYear, $page);
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}
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if(!isset($result['total'])){
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return [
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"has_more"=>"no"
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];
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}
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$saveResult = $this->saveExperts($result['experts'], $field, $source);
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$nextPage = $result['has_more'] ? $page : $fetchLog['last_page'];
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$totalPages = $result['total_pages'] ?? $fetchLog['total_pages'];
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$this->updateFetchLog($field, $source, $nextPage, $totalPages);
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return [
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'keyword' => $field,
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'page' => $page,
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'experts_found' => $result['total'],
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'saved_new' => $saveResult['inserted'],
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'saved_exist' => $saveResult['existing'],
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'list' => $result['experts'],
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'field_enriched' => $saveResult['field_enriched'],
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'has_more' => $result['has_more'],
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];
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}
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public function searchExperts($keyword, $perPage, $minYear, $page, $source)
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{
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if ($source === 'pmc') {
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return $this->searchViaPMC($keyword, $perPage, $minYear, $page);
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}
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return $this->searchViaPubMed($keyword, $perPage, $minYear, $page);
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}
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public function saveExperts($experts, $field, $source)
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{
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$inserted = 0;
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$existing = 0;
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$fieldEnrich = 0;
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foreach ($experts as $expert) {
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$email = strtolower(trim($expert['email']));
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if (empty($email)) {
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continue;
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}
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$exists = Db::name('expert')->where('email', $email)->find();
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$expertId = null;
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if ($exists) {
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$existing++;
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$expertId = intval($exists['expert_id']);
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} else {
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try {
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$expertId = Db::name('expert')->insertGetId([
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'name' => mb_substr($expert['name'], 0, 255),
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'email' => mb_substr($email, 0, 128),
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'affiliation' => mb_substr($expert['affiliation'], 0, 128),
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'source' => mb_substr($source, 0, 128),
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'ctime' => time(),
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'ltime' => 0,
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'state' => 0,
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]);
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$inserted++;
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} catch (\Exception $e) {
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$existing++;
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continue;
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}
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}
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$papers = (isset($expert['papers']) && is_array($expert['papers'])) ? $expert['papers'] : [];
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$fieldEnrich += $this->saveFieldWithPapers($expertId, $field, $source, $papers);
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}
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return ['inserted' => $inserted, 'existing' => $existing, 'field_enriched' => $fieldEnrich];
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}
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/**
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* 保存领域与论文的关联。
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* 有论文时：每篇论文一行（expert_id + field + source + paper_article_id 去重）。
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* 无论文时：只存一条领域行（expert_id + field 去重）。
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*/
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private function saveFieldWithPapers($expertId, $field, $source, $papers)
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{
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$field = trim($field);
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if (empty($field)) return 0;
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$added = 0;
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if (empty($papers)) {
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$exists = Db::name('expert_field')
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->where('expert_id', $expertId)
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->where('field', $field)
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->where('state', 0)
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->find();
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if (!$exists) {
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Db::name('expert_field')->insert([
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'expert_id' => $expertId,
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'source' => mb_substr((string)$source, 0, 64),
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'field' => mb_substr($field, 0, 128),
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'paper_title' => '',
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'paper_article_id' => '',
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'paper_journal' => '',
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'state' => 0,
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]);
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$added = 1;
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}
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} else {
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foreach ($papers as $paper) {
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$articleId = isset($paper['article_id']) ? (string)$paper['article_id'] : '';
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if ($articleId === '' || $articleId === '0') {
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continue;
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}
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$check = Db::name('expert_field')
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->where('expert_id', $expertId)
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->where('field', $field)
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->where('source', $source)
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->where('paper_article_id', $articleId)
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->where('state', 0)
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->find();
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if ($check) {
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continue;
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}
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Db::name('expert_field')->insert([
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'expert_id' => $expertId,
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'source' => mb_substr((string)$source, 0, 64),
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'paper_title' => isset($paper['title']) ? mb_substr((string)$paper['title'], 0, 255) : '',
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'paper_article_id' => mb_substr($articleId, 0, 64),
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'paper_journal' => isset($paper['journal']) ? mb_substr((string)$paper['journal'], 0, 255) : '',
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'field' => mb_substr($field, 0, 128),
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'state' => 0,
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]);
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$added++;
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}
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}
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return $added;
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}
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public function getFetchLog($field, $source)
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{
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$log = Db::name('expert_fetch')
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->where('field', $field)
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->where('source', $source)
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->find();
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if (!$log) {
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return ['last_page' => 0, 'total_pages' => 0, 'last_time' => 0];
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}
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return $log;
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}
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public function updateFetchLog($field, $source, $lastPage, $totalPages)
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{
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$exists = Db::name('expert_fetch')
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->where('field', $field)
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->where('source', $source)
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->find();
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if ($exists) {
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Db::name('expert_fetch')
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->where('expert_fetch_id', $exists['expert_fetch_id'])
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->update([
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'last_page' => $lastPage,
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'total_pages' => $totalPages,
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'last_time' => time(),
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]);
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} else {
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Db::name('expert_fetch')->insert([
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'field' => mb_substr($field, 0, 128),
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'source' => mb_substr($source, 0, 128),
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'last_page' => $lastPage,
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'total_pages' => $totalPages,
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'last_time' => time(),
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]);
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}
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}
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// ==================== PubMed Search ====================
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private function searchViaPubMed($keyword, $perPage, $minYear, $page = 1)
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{
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set_time_limit(600);
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$searchResult = $this->esearch('pubmed', $keyword, $perPage, $minYear, $page);
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$ids = $searchResult['ids'];
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$totalArticles = $searchResult['total'];
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if (empty($ids)) {
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return $this->buildPagedResult([], 0, 0, $totalArticles, $page, $perPage, 'pubmed');
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}
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$allAuthors = [];
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$batches = array_chunk($ids, 50);
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foreach ($batches as $batch) {
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$xml = $this->efetchWithRetry('pubmed', $batch);
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if ($xml) {
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$authors = $this->parsePubMedXml($xml);
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$allAuthors = array_merge($allAuthors, $authors);
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}
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usleep(400000);
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}
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$experts = $this->aggregateExperts($allAuthors);
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return $this->buildPagedResult($experts, count($experts), count($ids), $totalArticles, $page, $perPage, 'pubmed');
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}
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// ==================== PMC Search ====================
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private function searchViaPMC($keyword, $perPage, $minYear, $page = 1)
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{
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set_time_limit(600);
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$searchResult = $this->esearch('pmc', $keyword, $perPage, $minYear, $page);
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$ids = $searchResult['ids'];
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$totalArticles = $searchResult['total'];
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if (empty($ids)) {
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return $this->buildPagedResult([], 0, 0, $totalArticles, $page, $perPage, 'pmc');
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}
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$allAuthors = [];
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$batches = array_chunk($ids, 5);
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foreach ($batches as $batch) {
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$xml = $this->efetchWithRetry('pmc', $batch);
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if ($xml) {
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$authors = $this->parsePMCXml($xml);
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$allAuthors = array_merge($allAuthors, $authors);
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}
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usleep(500000);
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}
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$experts = $this->aggregateExperts($allAuthors);
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return $this->buildPagedResult($experts, count($experts), count($ids), $totalArticles, $page, $perPage, 'pmc');
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}
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// ==================== NCBI API ====================
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private function esearch($db, $keyword, $perPage, $minYear, $page = 1)
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{
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$term = $keyword . ' AND ' . $minYear . ':' . date('Y') . '[pdat]';
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$retstart = ($page - 1) * $perPage;
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$response = $this->httpClient->get($this->ncbiBaseUrl . 'esearch.fcgi', [
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'query' => [
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'db' => $db,
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'term' => $term,
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'retstart' => $retstart,
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'retmax' => $perPage,
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'retmode' => 'json',
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'sort' => 'relevance',
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],
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]);
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$data = json_decode($response->getBody()->getContents(), true);
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$ids = $data['esearchresult']['idlist'] ?? [];
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$total = intval($data['esearchresult']['count'] ?? 0);
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return ['ids' => $ids, 'total' => $total];
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}
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private function efetch($db, $ids)
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{
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$response = $this->httpClient->post($this->ncbiBaseUrl . 'efetch.fcgi', [
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'form_params' => [
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'db' => $db,
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'id' => implode(',', $ids),
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'retmode' => 'xml',
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],
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]);
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return $response->getBody()->getContents();
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}
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private function efetchWithRetry($db, $ids, $maxRetries = 3)
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{
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for ($attempt = 1; $attempt <= $maxRetries; $attempt++) {
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try {
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return $this->efetch($db, $ids);
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} catch (\Exception $e) {
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if ($attempt === $maxRetries) {
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if (count($ids) > 1) {
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$half = ceil(count($ids) / 2);
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$firstHalf = array_slice($ids, 0, $half);
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$secondHalf = array_slice($ids, $half);
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$xml1 = $this->efetchWithRetry($db, $firstHalf, 2);
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$xml2 = $this->efetchWithRetry($db, $secondHalf, 2);
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return $this->mergeXml($xml1, $xml2);
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}
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return null;
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}
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sleep($attempt * 2);
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}
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}
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return null;
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}
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private function mergeXml($xml1, $xml2)
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{
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if (empty($xml1)) return $xml2;
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if (empty($xml2)) return $xml1;
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return $xml1 . "\n" . $xml2;
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}
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// ==================== PubMed XML Parsing ====================
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private function parsePubMedXml($xmlString)
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{
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$results = [];
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libxml_use_internal_errors(true);
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$xml = simplexml_load_string($xmlString);
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if ($xml === false) {
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return $results;
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}
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foreach ($xml->PubmedArticle as $article) {
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$citation = $article->MedlineCitation;
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$articleData = $citation->Article;
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$title = $this->xmlNodeToString($articleData->ArticleTitle);
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$pmid = (string) $citation->PMID;
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$journal = '';
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if (isset($articleData->Journal->Title)) {
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$journal = (string) $articleData->Journal->Title;
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}
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if (!isset($articleData->AuthorList->Author)) {
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continue;
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}
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foreach ($articleData->AuthorList->Author as $author) {
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$lastName = (string) ($author->LastName ?? '');
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$foreName = (string) ($author->ForeName ?? '');
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$fullName = trim($foreName . ' ' . $lastName);
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if (empty($fullName)) continue;
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$email = '';
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$affiliation = '';
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if (isset($author->AffiliationInfo)) {
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foreach ($author->AffiliationInfo as $affInfo) {
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$affText = (string) $affInfo->Affiliation;
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if (empty($affiliation)) $affiliation = $affText;
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if (empty($email)) $email = $this->extractEmailFromText($affText);
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}
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}
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if (empty($email)) continue;
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$results[] = [
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'name' => $fullName,
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'email' => strtolower($email),
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'affiliation' => $this->cleanAffiliation($affiliation),
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'article_title' => $title,
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'article_id' => $pmid,
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'journal' => $journal,
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];
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}
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}
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return $results;
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}
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// ==================== PMC XML Parsing ====================
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private function parsePMCXml($xmlString)
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{
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$results = [];
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libxml_use_internal_errors(true);
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$xml = simplexml_load_string($xmlString);
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if ($xml === false) {
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return $results;
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}
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$articles = $xml->article ?? $xml->children();
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foreach ($articles as $article) {
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if ($article->getName() !== 'article') continue;
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$front = $article->front;
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if (!$front) continue;
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$articleMeta = $front->{'article-meta'};
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if (!$articleMeta) continue;
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$title = $this->xmlNodeToString($articleMeta->{'title-group'}->{'article-title'} ?? null);
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$pmcId = '';
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if (isset($articleMeta->{'article-id'})) {
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foreach ($articleMeta->{'article-id'} as $idNode) {
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if ((string) $idNode['pub-id-type'] === 'pmc') {
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$pmcId = (string) $idNode;
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}
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}
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}
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$journal = '';
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if (isset($front->{'journal-meta'}->{'journal-title'})) {
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$journal = (string) $front->{'journal-meta'}->{'journal-title'};
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} elseif (isset($front->{'journal-meta'}->{'journal-title-group'}->{'journal-title'})) {
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$journal = (string) $front->{'journal-meta'}->{'journal-title-group'}->{'journal-title'};
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}
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$correspEmails = [];
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if (isset($articleMeta->{'author-notes'})) {
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$this->extractEmailsFromNode($articleMeta->{'author-notes'}, $correspEmails);
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}
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$affiliationMap = [];
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if (isset($articleMeta->{'contrib-group'})) {
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foreach ($articleMeta->{'contrib-group'}->children() as $child) {
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if ($child->getName() === 'aff') {
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$affId = (string) ($child['id'] ?? '');
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$affText = $this->xmlNodeToString($child);
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if ($affId) $affiliationMap[$affId] = $affText;
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}
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}
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}
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if (isset($front->{'article-meta'}->{'aff'})) {
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foreach ($front->{'article-meta'}->{'aff'} as $aff) {
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$affId = (string) ($aff['id'] ?? '');
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$affText = $this->xmlNodeToString($aff);
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if ($affId) $affiliationMap[$affId] = $affText;
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}
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}
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if (!isset($articleMeta->{'contrib-group'})) continue;
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foreach ($articleMeta->{'contrib-group'}->contrib as $contrib) {
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if ((string) ($contrib['contrib-type'] ?? '') !== 'author') continue;
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$nameNode = $contrib->name;
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if (!$nameNode) continue;
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$surname = (string) ($nameNode->surname ?? '');
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$givenNames = (string) ($nameNode->{'given-names'} ?? '');
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$fullName = trim($givenNames . ' ' . $surname);
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if (empty($fullName)) continue;
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$email = '';
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if (isset($contrib->email)) {
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$email = strtolower(trim((string) $contrib->email));
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}
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$affiliation = '';
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if (isset($contrib->xref)) {
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foreach ($contrib->xref as $xref) {
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if ((string) $xref['ref-type'] === 'aff') {
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$rid = (string) $xref['rid'];
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if (isset($affiliationMap[$rid])) {
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$affiliation = $affiliationMap[$rid];
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break;
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}
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}
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}
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}
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if (empty($affiliation) && isset($contrib->aff)) {
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$affiliation = $this->xmlNodeToString($contrib->aff);
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}
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$isCorresponding = false;
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if (isset($contrib->xref)) {
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foreach ($contrib->xref as $xref) {
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if ((string) $xref['ref-type'] === 'corresp') $isCorresponding = true;
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}
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}
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if ((string) ($contrib['corresp'] ?? '') === 'yes') $isCorresponding = true;
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if (empty($email) && $isCorresponding && !empty($correspEmails)) {
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$email = $correspEmails[0];
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}
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if (empty($email)) {
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$extracted = $this->extractEmailFromText($affiliation);
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if ($extracted) $email = $extracted;
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}
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if (empty($email)) continue;
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$results[] = [
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'name' => $fullName,
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'email' => strtolower($email),
|
||
'affiliation' => $this->cleanAffiliation($affiliation),
|
||
'article_title' => $title,
|
||
'article_id' => $pmcId,
|
||
'journal' => $journal,
|
||
];
|
||
}
|
||
}
|
||
|
||
return $results;
|
||
}
|
||
|
||
// ==================== Aggregation / Pagination ====================
|
||
|
||
private function aggregateExperts($authorRecords)
|
||
{
|
||
$map = [];
|
||
foreach ($authorRecords as $record) {
|
||
$key = strtolower(trim($record['email']));
|
||
if (empty($key)) continue;
|
||
|
||
if (!isset($map[$key])) {
|
||
$map[$key] = [
|
||
'name' => $record['name'],
|
||
'email' => $record['email'],
|
||
'affiliation' => $record['affiliation'],
|
||
'paper_count' => 0,
|
||
'papers' => [],
|
||
];
|
||
}
|
||
$map[$key]['paper_count']++;
|
||
if (count($map[$key]['papers']) < 10) {
|
||
$map[$key]['papers'][] = [
|
||
'title' => $record['article_title'],
|
||
'article_id' => $record['article_id'],
|
||
'journal' => $record['journal'],
|
||
];
|
||
}
|
||
if (empty($map[$key]['affiliation']) && !empty($record['affiliation'])) {
|
||
$map[$key]['affiliation'] = $record['affiliation'];
|
||
}
|
||
}
|
||
|
||
$experts = array_values($map);
|
||
usort($experts, function ($a, $b) {
|
||
return $b['paper_count'] - $a['paper_count'];
|
||
});
|
||
return $experts;
|
||
}
|
||
|
||
private function buildPagedResult($experts, $expertCount, $articlesScanned, $totalArticles, $page, $perPage, $source)
|
||
{
|
||
$totalPages = $totalArticles > 0 ? ceil($totalArticles / $perPage) : 0;
|
||
return [
|
||
'experts' => $experts,
|
||
'total' => $expertCount,
|
||
'articles_scanned' => $articlesScanned,
|
||
'total_articles' => $totalArticles,
|
||
'page' => $page,
|
||
'per_page' => $perPage,
|
||
'total_pages' => $totalPages,
|
||
'has_more' => $page < $totalPages,
|
||
'source' => $source,
|
||
];
|
||
}
|
||
|
||
// ==================== Country Resolution ====================
|
||
|
||
/**
|
||
* 启动国家解析链：找到下一个缺国家的专家推入队列。
|
||
* 队列 Job 处理完一个后会再调此方法，自动找下一个，直到全部处理完。
|
||
* 控制器只需调一次即可。
|
||
*
|
||
* @param int $delay 延迟秒数（防止打满模型，默认1秒）
|
||
* @return bool 是否成功推入了一条
|
||
*/
|
||
/**
|
||
* 启动国家解析链：找到下一个缺国家的专家推入指定队列。
|
||
*
|
||
* @param int $delay 延迟秒数
|
||
* @param string $queue 队列名（不同队列跑不同 worker，互不阻塞）
|
||
* @param string $chatUrl 该链使用的模型地址（为空则用默认）
|
||
* @return bool
|
||
*/
|
||
public function enqueueNextCountryFill($delay = 1, $queue = 'FetchExperts', $chatUrl = '')
|
||
{
|
||
$row = Db::name('expert')
|
||
->where('affiliation', '<>', '')
|
||
->where('country_id', 0)
|
||
->where('state', '<>', 5)
|
||
->field('expert_id, affiliation')
|
||
->order('expert_id asc')
|
||
->find();
|
||
|
||
if (!$row) {
|
||
$this->log('[CountryFill] no more pending experts, queue=' . $queue);
|
||
return false;
|
||
}
|
||
|
||
$data = [
|
||
'expert_id' => intval($row['expert_id']),
|
||
'affiliation' => trim((string)$row['affiliation']),
|
||
'queue' => $queue,
|
||
'chat_url' => $chatUrl,
|
||
];
|
||
|
||
$jobClass = 'app\api\job\FillExpertCountry@fire';
|
||
if ($delay > 0) {
|
||
Queue::later($delay, $jobClass, $data, $queue);
|
||
} else {
|
||
Queue::push($jobClass, $data, $queue);
|
||
}
|
||
|
||
return true;
|
||
}
|
||
|
||
/**
|
||
* 对单个专家执行国家解析（同步），由队列 Job FillExpertCountry 调用，也可直接调用测试。
|
||
*/
|
||
public function fillExpertCountry($expertId, $affiliation, $chatUrl = '')
|
||
{
|
||
$affiliation = trim((string)$affiliation);
|
||
if ($affiliation === '') {
|
||
Db::name('expert')->where('expert_id', intval($expertId))->update(['country_id' => -1]);
|
||
return;
|
||
}
|
||
|
||
$defaultUrl = trim((string)Env::get('expert_country_chat_url', Env::get('citation_chat_url', 'http://chat.taimed.cn/v1/chat/completions')));
|
||
$url = ($chatUrl !== '') ? $chatUrl : $defaultUrl;
|
||
|
||
$resolver = new CountryResolverService([
|
||
'chat_url' => $url,
|
||
'chat_model' => trim((string)Env::get('expert_country_chat_model', Env::get('citation_chat_model', 'gpt-4.1'))),
|
||
'api_key' => trim((string)Env::get('expert_country_chat_api_key', Env::get('citation_chat_api_key', ''))),
|
||
'timeout' => max(20, intval(Env::get('expert_country_chat_timeout', 60))),
|
||
]);
|
||
|
||
$result = $resolver->resolve($affiliation);
|
||
|
||
$countryId = 0;
|
||
$enName = '';
|
||
|
||
if (!empty($result['code'])) {
|
||
$row = Db::name('country')->where('code', strtoupper(trim((string)$result['code'])))->find();
|
||
if ($row) {
|
||
$countryId = intval($row['country_id']);
|
||
$enName = (string)$row['en_name'];
|
||
}
|
||
}
|
||
|
||
if ($countryId === 0 && !empty($result['en_name'])) {
|
||
$row = Db::name('country')
|
||
->whereRaw("LOWER(en_name) = ?", [strtolower(trim((string)$result['en_name']))])
|
||
->find();
|
||
if ($row) {
|
||
$countryId = intval($row['country_id']);
|
||
$enName = (string)$row['en_name'];
|
||
}
|
||
}
|
||
|
||
if ($countryId > 0 && $enName !== '') {
|
||
Db::name('expert')->where('expert_id', intval($expertId))->update([
|
||
'country_id' => $countryId,
|
||
'country' => $enName,
|
||
]);
|
||
} else {
|
||
// country_id = -1 表示「已尝试但未识别」，避免链式执行时反复卡在同一条
|
||
Db::name('expert')->where('expert_id', intval($expertId))->update([
|
||
'country_id' => -1,
|
||
]);
|
||
$this->log('[CountryFill] expert_id=' . $expertId . ' unresolved, code=' . ($result['code'] ?? '') . ' en_name=' . ($result['en_name'] ?? ''));
|
||
}
|
||
}
|
||
|
||
// ==================== Text Helpers ====================
|
||
|
||
private function extractEmailFromText($text)
|
||
{
|
||
if (empty($text)) return '';
|
||
if (preg_match('/[Ee]lectronic address:\s*([^\s;,]+@[^\s;,]+)/', $text, $m)) {
|
||
return strtolower(trim($m[1], '.'));
|
||
}
|
||
if (preg_match('/[Ee]-?mail:\s*([^\s;,]+@[^\s;,]+)/', $text, $m)) {
|
||
return strtolower(trim($m[1], '.'));
|
||
}
|
||
if (preg_match('/\b([a-zA-Z0-9._%+\-]+@[a-zA-Z0-9.\-]+\.[a-zA-Z]{2,})\b/', $text, $m)) {
|
||
return strtolower(trim($m[1], '.'));
|
||
}
|
||
return '';
|
||
}
|
||
|
||
private function extractEmailsFromNode($node, &$emails)
|
||
{
|
||
if ($node === null) return;
|
||
foreach ($node->children() as $child) {
|
||
if ($child->getName() === 'email') {
|
||
$email = strtolower(trim((string) $child));
|
||
if (!empty($email) && !in_array($email, $emails)) $emails[] = $email;
|
||
}
|
||
$this->extractEmailsFromNode($child, $emails);
|
||
}
|
||
$text = (string) $node;
|
||
if (preg_match_all('/\b([a-zA-Z0-9._%+\-]+@[a-zA-Z0-9.\-]+\.[a-zA-Z]{2,})\b/', $text, $matches)) {
|
||
foreach ($matches[1] as $email) {
|
||
$email = strtolower(trim($email, '.'));
|
||
if (!in_array($email, $emails)) $emails[] = $email;
|
||
}
|
||
}
|
||
}
|
||
|
||
private function cleanAffiliation($text)
|
||
{
|
||
$text = preg_replace('/\s*[Ee]lectronic address:\s*[^\s;,]+@[^\s;,]+/', '', $text);
|
||
$text = preg_replace('/\s*[Ee]-?mail:\s*[^\s;,]+@[^\s;,]+/', '', $text);
|
||
$text = preg_replace('/\s*\b[a-zA-Z0-9._%+\-]+@[a-zA-Z0-9.\-]+\.[a-zA-Z]{2,}\b/', '', $text);
|
||
return trim($text, " \t\n\r\0\x0B.,;");
|
||
}
|
||
|
||
private function xmlNodeToString($node)
|
||
{
|
||
if ($node === null) return '';
|
||
$xml = $node->asXML();
|
||
$text = strip_tags($xml);
|
||
$text = html_entity_decode($text, ENT_QUOTES | ENT_XML1, 'UTF-8');
|
||
return trim(preg_replace('/\s+/', ' ', $text));
|
||
}
|
||
|
||
// ==================== Logging ====================
|
||
|
||
public function log($msg)
|
||
{
|
||
$line = date('Y-m-d H:i:s') . ' ' . $msg . PHP_EOL;
|
||
@file_put_contents($this->logFile, $line, FILE_APPEND);
|
||
}
|
||
}
|