<?php

namespace app\common;

/**
 * PubMed 工具类（E-utilities）
 *
 * 功能：
 * - DOI -> PMID
 * - PMID -> 文章结构化信息（title/abstract/mesh/publication_types/year/journal）
 *
 * 说明：
 * - 默认使用 runtime 文件缓存，避免重复请求 NCBI
 */
class PubmedService
{
    private $base = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/';
    private $timeout = 20;
    private $tool = 'tmrjournals';
    private $email = '';

    public function __construct(array $config = [])
    {
        if (isset($config['base'])) $this->base = rtrim((string)$config['base'], '/') . '/';
        if (isset($config['timeout'])) $this->timeout = max(5, intval($config['timeout']));
        if (isset($config['tool'])) $this->tool = (string)$config['tool'];
        if (isset($config['email'])) $this->email = (string)$config['email'];
    }

    /**
     * DOI -> PMID（优先用 [DOI]，命中不到再用 [AID]）
     */
    public function doiToPmid(string $doi): ?string
    {
        $doi = trim($doi);
        if ($doi === '') return null;

        $cacheKey = 'doi2pmid_' . sha1(strtolower($doi));
        $cached = $this->cacheGet($cacheKey, 30 * 86400);
        if (is_string($cached) && $cached !== '') {
            return $cached;
        }

        $pmid = $this->esearch($doi . '[DOI]');
        if (!$pmid) {
            $pmid = $this->esearch($doi . '[AID]');
        }
        if ($pmid) {
            $this->cacheSet($cacheKey, $pmid);
            return $pmid;
        }
        return null;
    }

    /**
     * PMID -> 文章信息（title/abstract/mesh/publication_types/year/journal）
     */
    public function fetchByPmid(string $pmid): ?array
    {
        $pmid = trim($pmid);
        if ($pmid === '') return null;

        $cacheKey = 'pmid_' . $pmid;
        $cached = $this->cacheGet($cacheKey, 30 * 86400);
        if (is_array($cached)) return $cached;

        $url = $this->base . 'efetch.fcgi?' . http_build_query([
            'db' => 'pubmed',
            'id' => $pmid,
            'retmode' => 'xml',
            'tool' => $this->tool,
            'email' => $this->email,
        ]);

        $xml = $this->httpGet($url);
        if (!is_string($xml) || trim($xml) === '') return null;

        $data = $this->parseEfetchXml($xml);
        if (!$data) return null;

        $this->cacheSet($cacheKey, $data);
        return $data;
    }

    /**
     * DOI -> PubMed 信息（含 abstract/mesh）
     */
    public function fetchByDoi(string $doi): ?array
    {
        $pmid = $this->doiToPmid($doi);
        if (!$pmid) return null;
        $info = $this->fetchByPmid($pmid);
        if (!$info) return null;
        $info['pmid'] = $pmid;
        $info['doi'] = $doi;
        return $info;
    }

    // ----------------- Internals -----------------

    private function esearch(string $term): ?string
    {
        $url = $this->base . 'esearch.fcgi?' . http_build_query([
            'db' => 'pubmed',
            'retmode' => 'json',
            'retmax' => 1,
            'term' => $term,
            'tool' => $this->tool,
            'email' => $this->email,
        ]);

        $res = $this->httpGet($url);
        $json = json_decode((string)$res, true);
        $ids = $json['esearchresult']['idlist'] ?? [];
        if (!empty($ids[0])) return (string)$ids[0];
        return null;
    }

    private function parseEfetchXml(string $xml): ?array
    {
        libxml_use_internal_errors(true);
        $doc = new \DOMDocument();
        if (!$doc->loadXML($xml)) {
            return null;
        }
        $xp = new \DOMXPath($doc);

        $title = $this->xpText($xp, '//PubmedArticle//ArticleTitle');

        $abstractParts = [];
        $absNodes = $xp->query('//PubmedArticle//Abstract//AbstractText');
        if ($absNodes) {
            foreach ($absNodes as $n) {
                $label = $n->attributes && $n->attributes->getNamedItem('Label')
                    ? trim($n->attributes->getNamedItem('Label')->nodeValue)
                    : '';
                $txt = trim($n->textContent);
                if ($txt === '') continue;
                $abstractParts[] = $label ? ($label . ': ' . $txt) : $txt;
            }
        }
        $abstract = trim(implode("\n", $abstractParts));

        $mesh = [];
        $meshNodes = $xp->query('//PubmedArticle//MeshHeadingList//MeshHeading//DescriptorName');
        if ($meshNodes) {
            foreach ($meshNodes as $n) {
                $t = trim($n->textContent);
                if ($t !== '') $mesh[] = $t;
            }
        }
        $mesh = array_values(array_unique($mesh));

        $pubTypes = [];
        $ptNodes = $xp->query('//PubmedArticle//PublicationTypeList//PublicationType');
        if ($ptNodes) {
            foreach ($ptNodes as $n) {
                $t = trim($n->textContent);
                if ($t !== '') $pubTypes[] = $t;
            }
        }
        $pubTypes = array_values(array_unique($pubTypes));

        $journal = $this->xpText($xp, '//PubmedArticle//Journal//Title');

        $year = '';
        $year = $this->xpText($xp, '//PubmedArticle//JournalIssue//PubDate//Year');
        if ($year === '') {
            $medlineDate = $this->xpText($xp, '//PubmedArticle//JournalIssue//PubDate//MedlineDate');
            if (preg_match('/(19\\d{2}|20\\d{2})/', $medlineDate, $m)) {
                $year = $m[1];
            }
        }

        if ($title === '' && $abstract === '') {
            return null;
        }

        return [
            'title' => $title,
            'abstract' => $abstract,
            'mesh_terms' => $mesh,
            'publication_types' => $pubTypes,
            'journal' => $journal,
            'year' => $year,
        ];
    }

    private function xpText(\DOMXPath $xp, string $query): string
    {
        $n = $xp->query($query);
        if ($n && $n->length > 0) {
            return trim($n->item(0)->textContent);
        }
        return '';
    }

    private function httpGet(string $url): string
    {
        $ch = curl_init();
        curl_setopt($ch, CURLOPT_URL, $url);
        curl_setopt($ch, CURLOPT_RETURNTRANSFER, true);
        curl_setopt($ch, CURLOPT_TIMEOUT, $this->timeout);
        curl_setopt($ch, CURLOPT_SSL_VERIFYPEER, false);
        curl_setopt($ch, CURLOPT_HTTPHEADER, [
            'User-Agent: TMRjournals-PubMed/1.0'
        ]);
        $res = curl_exec($ch);
        curl_close($ch);
        return is_string($res) ? $res : '';
    }

    private function cacheDir(): string
    {
        return rtrim(ROOT_PATH, '/') . '/runtime/pubmed_cache';
    }

    private function cacheGet(string $key, int $ttlSeconds)
    {
        $file = $this->cacheDir() . '/' . $key . '.json';
        if (!is_file($file)) return null;
        $mtime = filemtime($file);
        if (!$mtime || (time() - $mtime) > $ttlSeconds) return null;
        $raw = @file_get_contents($file);
        $decoded = json_decode((string)$raw, true);
        return $decoded;
    }

    private function cacheSet(string $key, $value): void
    {
        $dir = $this->cacheDir();
        if (!is_dir($dir)) @mkdir($dir, 0777, true);
        $file = $dir . '/' . $key . '.json';
        @file_put_contents($file, json_encode($value, JSON_UNESCAPED_UNICODE));
    }
}