<?php

namespace app\common;

use think\Env;
use Smalot\PdfParser\Parser as PdfParser;

/**
 * 参考文献内容抓取（cma.j.cn 优先中文源 → Europe PMC → PubMed → PMC全文 → Unpaywall PDF → Crossref）
 */
class ReferenceLiteratureFetchService
{
    /** @var EuropePmcService */
    private $epmc;
    /** @var PubmedService */
    private $pubmed;
    /** @var CrossrefService */
    private $crossref;
    /** @var UnpaywallService */
    private $unpaywall;
    /** @var CmaJournalLiteratureService */
    private $cmaJournal;
    /** @var ReferenceCheckService */
    private $refUtil;
    /** @var \app\common\service\BibliographicMetaService */
    private $bibMeta;

    /** @var bool 预抓取阶段暂不调用 Yiigle 机构 API */
    private $skipYiigle = false;

    public function __construct()
    {
        $this->epmc = new EuropePmcService();
        $this->pubmed = new PubmedService([
            'email' => trim((string)Env::get('pubmed_email', '')),
            'tool'  => trim((string)Env::get('pubmed_tool', 'tmrjournals')),
        ]);
        $this->crossref = new CrossrefService([
            'mailto' => trim((string)Env::get('crossref_mailto', '')),
        ]);
        $this->unpaywall = new UnpaywallService();
        $this->cmaJournal = new CmaJournalLiteratureService();
        $this->refUtil = new ReferenceCheckService();
        $this->bibMeta = new \app\common\service\BibliographicMetaService();
    }

    public function setSkipYiigle($skip = true)
    {
        $this->skipYiigle = (bool)$skip;

        return $this;
    }

    /**
     * @return array{
     *   doi:string,pmid:string,pmcid:string,title:string,journal:string,year:string,
     *   abstract:string,raw_content:string,pdf_url:string,mesh_terms:array,sources:array,fetch_log:string
     * }
     */
    public function fetchForRefer(array $refer)
    {
        DbReconnectHelper::release();

        // 图书/ISBN 类参考文献不走 DOI 管道（书上的 DOI 常为错误挂接的期刊文章）
        if ($this->shouldSkipDoiFetchForRefer($refer)) {
            return $this->emptyResult('book_skip_doi_fetch');
        }

        $dois = $this->resolveDoiCandidatesForFetch($refer);
        foreach ($dois as $doi) {
            $result = $this->fetchByDoiPipeline($doi, $refer);
            if ($this->fetchedResultMatchesRefer($result, $refer)) {
                return $result;
            }
        }

        $title = trim((string)($refer['title'] ?? ''));
        $author = trim((string)($refer['author'] ?? ''));
        $year = $this->extractYearFromRefer($refer);
        if ($title === '') {
            $title = $this->guessTitleFromReferContent($refer);
        }

        $resolvedDoi = '';
        $meta = null;
        if ($title !== '') {
            $meta = $this->epmc->searchByBibliographic($title, $author, $year);
            if (is_array($meta) && trim((string)($meta['doi'] ?? '')) !== '') {
                $resolvedDoi = trim((string)$meta['doi']);
            }
            if ($resolvedDoi === '') {
                $pub = $this->pubmed->searchByBibliographic($title, $author, $year);
                if (is_array($pub)) {
                    $resolvedDoi = trim((string)($pub['doi'] ?? ''));
                    if ($meta === null) {
                        $meta = $pub;
                    }
                }
            }
        }

        if ($resolvedDoi !== '') {
            $result = $this->fetchByDoiPipeline($resolvedDoi, $refer);
            if (is_array($meta)) {
                if ($result['title'] === '' && trim((string)($meta['title'] ?? '')) !== '') {
                    $result['title'] = trim((string)$meta['title']);
                }
            }
            if ($this->fetchedResultMatchesRefer($result, $refer)) {
                $result['fetch_log'] = 'no_doi_in_refer; resolved_doi=' . $resolvedDoi . '; ' . $result['fetch_log'];
                return $result;
            }
        }

        return $this->emptyResult('no_doi_and_bibliographic_search_failed');
    }

    /**
     * 判断已入库/已清洗内容与 refer 元数据是否明显错配（用于跳过错误缓存、触发重抓）。
     */
    public function storedContentMatchesRefer(array $refer, $abstract, $cleaned)
    {
        $text = trim((string)$abstract . "\n" . (string)$cleaned);
        if ($text === '') {
            return true;
        }

        // 子表内容已按 p_refer_id 绑定；用 refer 标题锚定，避免中文摘要因不含英文作者姓氏被误判为错配
        $expectedTitle = trim((string)($refer['title'] ?? ''));

        return $this->fetchedResultMatchesRefer([
            'title'       => $expectedTitle,
            'abstract'    => $text,
            'raw_content' => $text,
        ], $refer);
    }

    /**
     * 图书类参考文献：refer_type=book 或带 ISBN 且呈教材/专著特征时，不通过 DOI 抓外部摘要。
     */
    private function shouldSkipDoiFetchForRefer(array $refer)
    {
        if (strtolower(trim((string)($refer['refer_type'] ?? ''))) === 'book') {
            return true;
        }
        $isbn = trim((string)($refer['isbn'] ?? ''));
        if ($isbn === '') {
            return false;
        }
        $blob = strtolower(
            trim((string)($refer['joura'] ?? '')) . ' '
            . trim((string)($refer['dateno'] ?? '')) . ' '
            . trim((string)($refer['title'] ?? ''))
        );

        return preg_match('/\bed\.?|edition|publishing|press|lippincott|elsevier|springer|wiley|company|图书|教材|专著/u', $blob);
    }

    /**
     * 相关性校对抓取：优先 refer_doi/doilink（结构化字段），再 refer_content（原始文本，可能错链）。
     *
     * @return string[]
     */
    private function resolveDoiCandidatesForFetch(array $refer)
    {
        $result = [];
        foreach (['refer_doi', 'doilink', 'doi', 'refer_content', 'refer_frag'] as $field) {
            $slice = array_merge($refer, ['refer_content' => (string)($refer[$field] ?? '')]);
            foreach ($this->refUtil->extractAllDoiCandidatesFromRefer($slice) as $doi) {
                if (!in_array($doi, $result, true)) {
                    $result[] = $doi;
                }
            }
        }

        return $result;
    }

    /**
     * 校验抓取结果标题/作者是否与 refer 行一致，防止 refer_content 错链到另一篇文献。
     */
    private function fetchedResultMatchesRefer(array $result, array $refer)
    {
        $expectedTitle = trim((string)($refer['title'] ?? ''));
        $fetchedTitle = trim((string)($result['title'] ?? ''));
        $blob = strtolower(
            $fetchedTitle . ' '
            . trim((string)($result['abstract'] ?? '')) . ' '
            . trim((string)($result['raw_content'] ?? ''))
        );

        $titleConfirmed = false;
        if ($expectedTitle !== '' && $fetchedTitle !== '') {
            if (!$this->titlesLikelyMatch($expectedTitle, $fetchedTitle)) {
                return false;
            }
            $titleConfirmed = true;
        }

        $author = trim((string)($refer['author'] ?? ''));
        // 标题已能确认同一文献时，不再要求摘要/正文里出现作者姓氏（PubMed 摘要通常不含作者）
        if ($author !== '' && !$titleConfirmed) {
            $needles = $this->extractAuthorNeedles($author);
            $matched = 0;
            foreach ($needles as $needle) {
                if ($needle !== '' && strpos($blob, $needle) !== false) {
                    $matched++;
                }
            }
            if (!empty($needles) && $matched === 0) {
                return false;
            }
        }

        return true;
    }

    private function titlesLikelyMatch($expected, $fetched)
    {
        $a = $this->normalizeTitleForMatch($expected);
        $b = $this->normalizeTitleForMatch($fetched);
        if ($a === '' || $b === '') {
            return true;
        }
        if ($a === $b || strpos($a, $b) !== false || strpos($b, $a) !== false) {
            return true;
        }
        similar_text($a, $b, $pct);

        return $pct >= 38;
    }

    private function normalizeTitleForMatch($title)
    {
        $title = strtolower(trim((string)$title));
        $title = preg_replace('/[^a-z0-9\s]+/u', ' ', $title);

        return trim(preg_replace('/\s+/u', ' ', $title));
    }

    /**
     * @return string[]
     */
    private function extractAuthorNeedles($author)
    {
        $author = trim((string)$author);
        if ($author === '') {
            return [];
        }
        $needles = [];
        if (preg_match_all('/[A-Za-z]{3,}/', $author, $m)) {
            foreach ($m[0] as $part) {
                $needles[] = strtolower($part);
            }
        }

        return array_values(array_unique($needles));
    }

    /**
     * 抓取 + LLM 清洗（校对执行时调用）
     *
     * @return array 含 abstract_final, content_cleaned
     */
    public function fetchAndCleanForRefer(array $refer)
    {
        $fetched = $this->fetchForRefer($refer);
        DbReconnectHelper::ensure();

        $raw = trim((string)($fetched['raw_content'] ?? ''));
        if ($raw === '') {
            return array_merge($fetched, [
                'abstract_final'    => trim((string)($fetched['abstract'] ?? '')),
                'content_cleaned'   => '',
                'content_clean_skip'=> true,
            ]);
        }

        DbReconnectHelper::release();
        $fetchedForClean = $fetched;
        $clean = (new \app\common\service\ReferenceContentCleanLlmService())->clean($raw, $fetchedForClean);
        DbReconnectHelper::ensure();

        $abstractFinal = trim((string)($clean['abstract'] ?? ''));
        if ($abstractFinal === '') {
            $abstractFinal = trim((string)($fetched['abstract'] ?? ''));
        }

        return array_merge($fetched, [
            'abstract_final'     => $abstractFinal,
            'content_cleaned'    => trim((string)($clean['cleaned'] ?? '')),
            'content_clean_skip' => !empty($clean['skipped']),
        ]);
    }

    private function fetchByDoiPipeline($doi, array $refer)
    {
        $doi = trim((string)$doi);
        $blocks = [];
        $sources = [];
        $abstract = '';
        $title = trim((string)($refer['title'] ?? ''));
        $pmid = '';
        $pmcid = '';
        $journal = '';
        $year = $this->extractYearFromRefer($refer);
        $fetchLogs = [];
        $pdfUrl = '';
        $meshTerms = [];
        $language = '';
        $country = '';

        // 0) 中华医学会期刊 DOI：OpenAlex 中文摘要（可选 Yiigle 机构 API）
        if (CmaJournalLiteratureService::isCmaJournalDoi($doi)) {
            $cmaSvc = $this->cmaJournal;
            if ($this->skipYiigle) {
                $cmaSvc = new CmaJournalLiteratureService(['skip_yiigle' => true]);
            }
            $cma = $cmaSvc->fetchByDoi($doi);
            if (is_array($cma)) {
                $sources = array_merge($sources, (array)($cma['sources'] ?? []));
                if ($title === '' && trim((string)($cma['title'] ?? '')) !== '') {
                    $title = trim((string)$cma['title']);
                }
                if ($journal === '' && trim((string)($cma['journal'] ?? '')) !== '') {
                    $journal = trim((string)$cma['journal']);
                }
                if ($year === '' && trim((string)($cma['year'] ?? '')) !== '') {
                    $year = trim((string)$cma['year']);
                }
                if ($pmid === '' && trim((string)($cma['pmid'] ?? '')) !== '') {
                    $pmid = trim((string)$cma['pmid']);
                }
                if (trim((string)($cma['abstract'] ?? '')) !== '') {
                    $abstract = trim((string)$cma['abstract']);
                }
                foreach ((array)($cma['blocks'] ?? []) as $block) {
                    $block = trim((string)$block);
                    if ($block !== '') {
                        $blocks[] = $block;
                    }
                }
                $cmaContent = trim((string)($cma['content'] ?? ''));
                if ($cmaContent !== '') {
                    $blocks[] = "=== 中华医学期刊全文 ===\n" . $this->truncate($cmaContent, 20000);
                }
                if (trim((string)($cma['fetch_log'] ?? '')) !== '') {
                    $fetchLogs[] = (string)$cma['fetch_log'];
                }
            }
        }

        // 1) Europe PMC by DOI
        $epmc = $this->epmc->searchByDoi($doi);
        if (is_array($epmc)) {
            $sources[] = 'europe_pmc';
            if ($title === '') {
                $title = trim((string)($epmc['title'] ?? ''));
            }
            if (trim((string)($epmc['abstract'] ?? '')) !== '') {
                $abstract = trim((string)$epmc['abstract']);
                $blocks[] = "=== Europe PMC ===\n" . $abstract;
            }
            $pmid = trim((string)($epmc['pmid'] ?? ''));
            $pmcid = trim((string)($epmc['pmcid'] ?? ''));
            $journal = trim((string)($epmc['journal'] ?? ''));
            if ($year === '' && trim((string)($epmc['year'] ?? '')) !== '') {
                $year = trim((string)$epmc['year']);
            }
        }

        // 2) PubMed metadata
        $pub = $this->pubmed->fetchByDoi($doi);
        if (is_array($pub)) {
            $sources[] = 'pubmed';
            if ($pmid === '' && trim((string)($pub['pmid'] ?? '')) !== '') {
                $pmid = trim((string)$pub['pmid']);
            }
            if ($title === '' && trim((string)($pub['title'] ?? '')) !== '') {
                $title = trim((string)$pub['title']);
            }
            if ($abstract === '' && trim((string)($pub['abstract'] ?? '')) !== '') {
                $abstract = trim((string)$pub['abstract']);
            }
            if (!empty($pub['mesh_terms']) && is_array($pub['mesh_terms'])) {
                $meshTerms = array_values(array_unique(array_merge($meshTerms, $pub['mesh_terms'])));
            }
            if ($language === '' && trim((string)($pub['language'] ?? '')) !== '') {
                $language = strtolower(trim((string)$pub['language']));
            }
            if ($country === '') {
                // 研究开展国以作者单位为准，期刊出版国只作兜底
                $country = $this->bibMeta->detectCountry((array)($pub['affiliations'] ?? []));
                if ($country === '' && trim((string)($pub['journal_country'] ?? '')) !== '') {
                    $country = $this->bibMeta->detectCountry((string)$pub['journal_country']);
                }
            }
            $pubBlock = $this->formatPubmedBlock($pub, $doi);
            if ($pubBlock !== '' && $abstract === '') {
                $blocks[] = $pubBlock;
            } elseif ($pubBlock !== '' && !CmaJournalLiteratureService::isCmaJournalDoi($doi)) {
                $blocks[] = $pubBlock;
            }
        }

        // 3) PMC full text
        if ($pmcid !== '') {
            $full = $this->epmc->fetchFullTextByPmcid($pmcid);
            if ($full !== '') {
                $sources[] = 'pmc_fulltext';
                $blocks[] = "=== PMC Full Text ({$pmcid}) ===\n" . $this->truncate($full, 20000);
            }
        }

        // 4) Unpaywall OA PDF + PDF parse
        $oaPdfUrl = $this->unpaywall->findOaPdfUrl($doi);
        if ($oaPdfUrl !== '') {
            $pdfUrl = $oaPdfUrl;
            $pdfText = $this->downloadAndExtractPdf($oaPdfUrl);
            if ($pdfText !== '') {
                $sources[] = 'unpaywall_pdf';
                $blocks[] = "=== OA PDF Extract ===\nSource: {$oaPdfUrl}\n" . $this->truncate($pdfText, 25000);
            }
        }

        if ($pdfUrl === '' && $pmcid !== '') {
            $pdfUrl = $this->buildPmcPdfUrl($pmcid);
        }

        // 5) Crossref supplement（已有实质性摘要或全文时跳过，避免与 PubMed 等重复）
        if (!$this->shouldSkipCrossrefSupplement($abstract, $sources, $blocks)) {
            $cr = $this->refUtil->fetchCrossrefAbstractByReferDoi(['refer_doi' => $doi, 'doi' => $doi]);
            if (is_array($cr) && trim((string)($cr['text'] ?? '')) !== '') {
                $sources[] = 'crossref';
                $blocks[] = trim((string)$cr['text']);
                if ($abstract === '' && !empty($cr['has_abstract'])) {
                    if (preg_match('/Abstract:\s*(.+)/uis', (string)$cr['text'], $m)) {
                        $abstract = trim($m[1]);
                    }
                }
            }
        } else {
            $fetchLogs[] = 'crossref=skipped_has_abstract_or_fulltext';
        }

        $raw = trim(implode("\n\n", array_filter($blocks)));
        if ($raw === '' && $abstract !== '') {
            $raw = $abstract;
        }

        return [
            'doi'         => $doi,
            'pmid'        => $pmid,
            'pmcid'       => $pmcid,
            'title'       => $title,
            'journal'     => $journal,
            'year'        => $year,
            'abstract'    => $abstract,
            'raw_content' => $raw,
            'pdf_url'     => $pdfUrl,
            'mesh_terms'  => $meshTerms,
            'language'    => $language,
            'country'     => $country,
            'sources'     => array_values(array_unique($sources)),
            'fetch_log'   => trim('doi=' . $doi . '; sources=' . implode(',', $sources) . ($fetchLogs ? '; ' . implode('; ', $fetchLogs) : '')),
        ];
    }

    private function shouldSkipCrossrefSupplement($abstract, array $sources, array $blocks)
    {
        if (mb_strlen(trim((string)$abstract)) >= 40) {
            return true;
        }
        if (!empty(array_intersect($sources, ['pmc_fulltext', 'unpaywall_pdf', 'cma_yiigle']))) {
            return true;
        }
        foreach ($blocks as $block) {
            if (preg_match('/===\s*(PMC Full Text|OA PDF Extract|中华医学期刊全文)/u', (string)$block)) {
                return true;
            }
        }

        return false;
    }

    private function buildPmcPdfUrl($pmcid)
    {
        $pmcid = strtoupper(trim((string)$pmcid));
        if ($pmcid === '') {
            return '';
        }
        if (strpos($pmcid, 'PMC') !== 0) {
            $pmcid = 'PMC' . preg_replace('/\D/', '', $pmcid);
        }

        return 'https://pmc.ncbi.nlm.nih.gov/articles/' . rawurlencode($pmcid) . '/pdf/';
    }

    private function formatPubmedBlock(array $pub, $doi)
    {
        $lines = ['=== PubMed (DOI ' . $doi . ') ==='];
        foreach (['title', 'journal', 'year'] as $k) {
            if (!empty($pub[$k])) {
                $lines[] = ucfirst($k) . ': ' . trim((string)$pub[$k]);
            }
        }
        if (!empty($pub['publication_types'])) {
            $lines[] = 'Publication Types: ' . implode('; ', (array)$pub['publication_types']);
        }
        if (!empty($pub['mesh_terms'])) {
            $lines[] = 'MeSH: ' . implode('; ', (array)$pub['mesh_terms']);
        }
        if (!empty($pub['abstract'])) {
            $lines[] = 'Abstract: ' . trim((string)$pub['abstract']);
        }
        return implode("\n", $lines);
    }

    private function downloadAndExtractPdf($url)
    {
        $url = trim((string)$url);
        if ($url === '') {
            return '';
        }

        $dir = ROOT_PATH . 'runtime' . DS . 'ref_literature_pdf';
        if (!is_dir($dir)) {
            @mkdir($dir, 0755, true);
        }
        $path = $dir . DS . date('YmdHis') . '_' . uniqid('', true) . '.pdf';

        $ch = curl_init($url);
        curl_setopt_array($ch, [
            CURLOPT_RETURNTRANSFER => true,
            CURLOPT_FOLLOWLOCATION => true,
            CURLOPT_CONNECTTIMEOUT => 15,
            CURLOPT_TIMEOUT        => 90,
            CURLOPT_SSL_VERIFYPEER => false,
            CURLOPT_HTTPHEADER     => ['User-Agent: TMRjournals-RefFetch/1.0'],
        ]);
        $body = curl_exec($ch);
        $code = (int)curl_getinfo($ch, CURLINFO_HTTP_CODE);
        curl_close($ch);

        if ($body === false || $code < 200 || $code >= 300 || strlen($body) < 1000) {
            return '';
        }
        if (strlen($body) > 15 * 1024 * 1024) {
            return '';
        }
        if (@file_put_contents($path, $body) === false) {
            return '';
        }

        try {
            $text = $this->extractPdfText($path);
        } finally {
            @unlink($path);
        }

        return $text;
    }

    private function extractPdfText($path)
    {
        if (!class_exists(PdfParser::class)) {
            return $this->extractPdfTextByPython($path);
        }
        try {
            $parser = new PdfParser();
            $pdf = $parser->parseFile($path);
            $text = $pdf->getText();
            return is_string($text) ? trim($text) : '';
        } catch (\Throwable $e) {
            return $this->extractPdfTextByPython($path);
        }
    }

    private function extractPdfTextByPython($path)
    {
        $script = ROOT_PATH . 'scripts' . DS . 'extract_pdf_text.py';
        if (!is_file($script)) {
            return '';
        }
        $cmd = 'python ' . escapeshellarg($script) . ' ' . escapeshellarg($path) . ' 2>nul';
        $out = shell_exec($cmd);
        return is_string($out) ? trim($out) : '';
    }

    private function extractYearFromRefer(array $refer)
    {
        $dateno = trim((string)($refer['dateno'] ?? ''));
        if (preg_match('/(19|20)\d{2}/', $dateno, $m)) {
            return $m[0];
        }
        return '';
    }

    private function guessTitleFromReferContent(array $refer)
    {
        $content = trim((string)($refer['refer_content'] ?? ''));
        if ($content === '') {
            return '';
        }
        $line = preg_split('/\n/', $content)[0] ?? $content;
        $line = preg_replace('/^\[\d+\]\s*/', '', trim($line));
        return mb_substr($line, 0, 300);
    }

    private function truncate($text, $max)
    {
        $text = trim((string)$text);
        if ($text === '') {
            return '';
        }
        if (mb_strlen($text) <= $max) {
            return $text;
        }
        return mb_substr($text, 0, $max) . "\n...(truncated)";
    }

    private function emptyResult($reason)
    {
        return [
            'doi'         => '',
            'pmid'        => '',
            'pmcid'       => '',
            'title'       => '',
            'journal'     => '',
            'year'        => '',
            'abstract'    => '',
            'raw_content' => '',
            'pdf_url'     => '',
            'mesh_terms'  => [],
            'language'    => '',
            'country'     => '',
            'sources'     => [],
            'fetch_log'   => (string)$reason,
        ];
    }
}