<?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 = '';
    // 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。
    private $apiKey = '';
    private $maxRetry = 3;

    public function __construct(array $config = [])
    {
        $this->email = (string)$this->envGet('pubmed_email', '');
        $this->apiKey = (string)$this->envGet('pubmed_api_key', '');
        $tool = trim((string)$this->envGet('pubmed_tool', ''));
        if ($tool !== '') $this->tool = $tool;

        if (isset($config['base'])) $this->base = rtrim((string)$config['base'], '/') . '/';
        if (isset($config['timeout'])) $this->timeout = max(5, intval($config['timeout']));
        if (!empty($config['tool'])) $this->tool = (string)$config['tool'];
        if (!empty($config['email'])) $this->email = (string)$config['email'];
        if (!empty($config['api_key'])) $this->apiKey = (string)$config['api_key'];
        if (isset($config['max_retry'])) $this->maxRetry = max(1, intval($config['max_retry']));
    }

    private function envGet($key, $default = '')
    {
        if (!class_exists('\think\Env')) {
            return $default;
        }
        return \think\Env::get($key, $default);
    }

    /**
     * tool/email/api_key 是 NCBI 要求的调用方标识，缺失会被更严格限流
     */
    private function commonParams(): array
    {
        $params = ['tool' => $this->tool, 'email' => $this->email];
        if ($this->apiKey !== '') {
            $params['api_key'] = $this->apiKey;
        }
        return $params;
    }

    /**
     * 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;

        // v3：解析结果新增 authors / volume / issue / pages / doi，换 key 避免命中旧缓存
        $cacheKey = 'pmid_v3_' . $pmid;
        $cached = $this->cacheGet($cacheKey, 30 * 86400);
        if (is_array($cached)) return $cached;

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

        $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;
    }

    /**
     * DOI -> 期刊规范缩写（NLM/ISO 形式，如 "J Clin Oncol"）
     * 优先 ISOAbbreviation，回退 MedlineTA；查不到返回 null。
     */
    public function journalAbbrByDoi(string $doi): ?string
    {
        $info = $this->fetchByDoi($doi);
        if (!is_array($info)) return null;

        $abbr = trim((string)($info['journal_iso_abbr'] ?? ''));
        if ($abbr === '') {
            $abbr = trim((string)($info['journal_medline_ta'] ?? ''));
        }
        return $abbr !== '' ? $abbr : null;
    }

    /**
     * 按书目信息检索 PubMed（标题 + 第一作者 + 年份）
     */
    public function searchByBibliographic($title, $author = '', $year = ''): ?array
    {
        $title = trim((string)$title);
        if ($title === '') {
            return null;
        }

        $terms = ['(' . $this->quoteTerm($title) . '[Title])'];
        $author = trim((string)$author);
        if ($author !== '') {
            $parts = preg_split('/[,;]/', $author);
            $first = trim((string)($parts[0] ?? ''));
            if ($first !== '') {
                $terms[] = '(' . $this->quoteTerm($first) . '[Author])';
            }
        }
        $year = trim((string)$year);
        if ($year !== '' && preg_match('/^(19|20)\d{2}$/', $year)) {
            $terms[] = '(' . $year . '[pdat])';
        }

        $pmid = $this->esearch(implode(' AND ', $terms));
        if (!$pmid) {
            return null;
        }

        $info = $this->fetchByPmid($pmid);
        if (!$info) {
            return null;
        }
        $info['pmid'] = $pmid;
        $info['doi'] = $this->extractDoiFromPmidRecord($pmid);
        return $info;
    }

    private function quoteTerm($text)
    {
        return str_replace('"', '', trim((string)$text));
    }

    private function extractDoiFromPmidRecord($pmid)
    {
        $url = $this->base . 'efetch.fcgi?' . http_build_query(array_merge([
            'db' => 'pubmed',
            'id' => $pmid,
            'retmode' => 'xml',
        ], $this->commonParams()));
        $xml = $this->httpGet($url);
        if ($xml === '') {
            return '';
        }
        if (preg_match('/<ArticleId IdType="doi">([^<]+)<\/ArticleId>/i', $xml, $m)) {
            return trim($m[1]);
        }
        return '';
    }

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

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

        $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');
        // 期刊规范缩写：ISOAbbreviation（Journal 下）与 MedlineTA（MedlineJournalInfo 下）
        $journalIsoAbbr = $this->xpText($xp, '//PubmedArticle//Journal//ISOAbbreviation');
        $journalMedlineTa = $this->xpText($xp, '//PubmedArticle//MedlineJournalInfo//MedlineTA');

        $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;
        }

        $doi = $this->xpText($xp, '//PubmedArticle//ArticleIdList/ArticleId[@IdType="doi"]');
        if ($doi === '') {
            $doi = $this->xpText($xp, '//PubmedArticle//ELocationID[@EIdType="doi"]');
        }

        return [
            'title' => $title,
            'abstract' => $abstract,
            'mesh_terms' => $mesh,
            'publication_types' => $pubTypes,
            'journal' => $journal,
            'journal_iso_abbr' => $journalIsoAbbr,
            'journal_medline_ta' => $journalMedlineTa,
            'year' => $year,
            'authors' => $this->parseAuthors($xp),
            'volume' => $this->xpText($xp, '//PubmedArticle//JournalIssue//Volume'),
            'issue' => $this->xpText($xp, '//PubmedArticle//JournalIssue//Issue'),
            'pages' => $this->parsePagination($xp),
            'doi' => $doi,
        ];
    }

    /**
     * 作者列表：LastName/ForeName/Initials，机构作者用 CollectiveName
     */
    private function parseAuthors(\DOMXPath $xp): array
    {
        $out = [];
        $nodes = $xp->query('//PubmedArticle//AuthorList/Author');
        if (!$nodes) {
            return $out;
        }

        foreach ($nodes as $n) {
            $family = $given = $initials = $collective = '';
            foreach ($n->childNodes as $c) {
                switch ($c->nodeName) {
                    case 'LastName':
                        $family = trim($c->textContent);
                        break;
                    case 'ForeName':
                        $given = trim($c->textContent);
                        break;
                    case 'Initials':
                        $initials = trim($c->textContent);
                        break;
                    case 'CollectiveName':
                        $collective = trim($c->textContent);
                        break;
                }
            }
            if ($family === '' && $given === '' && $collective === '') {
                continue;
            }
            $out[] = [
                'family' => $family,
                'given' => $given,
                'initials' => $initials,
                'collective' => $collective,
            ];
        }

        return $out;
    }

    /**
     * 页码：StartPage/EndPage → MedlinePgn → 电子刊文章号（ELocationID pii）
     *
     * MedlinePgn 用 NLM 缩写式尾页（210-8 表示 210–218），展开逻辑由调用方处理。
     */
    private function parsePagination(\DOMXPath $xp): string
    {
        $start = $this->xpText($xp, '//PubmedArticle//Pagination//StartPage');
        if ($start !== '') {
            $end = $this->xpText($xp, '//PubmedArticle//Pagination//EndPage');
            return $end !== '' ? $start . '-' . $end : $start;
        }

        $medlinePgn = $this->xpText($xp, '//PubmedArticle//Pagination//MedlinePgn');
        if ($medlinePgn !== '') {
            return $medlinePgn;
        }

        // 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
        $pii = $this->xpText($xp, '//PubmedArticle//ELocationID[@EIdType="pii"]');
        return preg_match('/^e?\d+$/i', $pii) === 1 ? $pii : '';
    }

    /**
     * 引用格式作者串：姓全写 + 名首字母，超过 $maxAuthors 个取前 N 个 + et al
     * 例：Smith JA, Jones B, Lee C, et al
     */
    public function authorsCitation(array $authors, int $maxAuthors = 3): string
    {
        $list = [];
        foreach ($authors as $a) {
            $collective = trim((string)($a['collective'] ?? ''));
            if ($collective !== '') {
                $list[] = $collective;
                continue;
            }

            $family = trim((string)($a['family'] ?? ''));
            if ($family === '') {
                continue;
            }
            $initials = trim((string)($a['initials'] ?? ''));
            if ($initials === '') {
                $initials = $this->givenToInitials((string)($a['given'] ?? ''));
            }
            $list[] = $initials !== '' ? $family . ' ' . $initials : $family;
        }

        if (empty($list)) {
            return '';
        }

        $maxAuthors = max(1, $maxAuthors);
        if (count($list) > $maxAuthors) {
            return implode(', ', array_slice($list, 0, $maxAuthors)) . ', et al';
        }
        return implode(', ', $list);
    }

    private function givenToInitials($given): string
    {
        $given = trim((string)$given);
        if ($given === '') {
            return '';
        }
        $parts = preg_split('/[\s\-\.]+/u', $given, -1, PREG_SPLIT_NO_EMPTY);
        $initials = '';
        foreach ($parts as $p) {
            $first = mb_substr($p, 0, 1);
            if ($first !== '') {
                $initials .= mb_strtoupper($first);
            }
        }
        return $initials;
    }

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

    /**
     * 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
     */
    private function httpGet(string $url): string
    {
        for ($attempt = 0; $attempt < $this->maxRetry; $attempt++) {
            $ch = curl_init();
            curl_setopt($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);
            $httpCode = (int)curl_getinfo($ch, CURLINFO_HTTP_CODE);
            curl_close($ch);

            if ($httpCode === 200 && is_string($res) && trim($res) !== '') {
                return $res;
            }

            if ($httpCode !== 429 && $httpCode < 500 && $httpCode !== 0) {
                return '';
            }

            usleep((int)(($attempt + 1) * 400000));
        }

        return '';
    }

    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));
    }
}