diff --git a/DEPLOYMENT_PLAN.md b/DEPLOYMENT_PLAN.md new file mode 100644 index 0000000..1715acb --- /dev/null +++ b/DEPLOYMENT_PLAN.md @@ -0,0 +1,80 @@ +# Peptide News Aggregator v2.6.0 — Complete Implementation & Deployment Plan + +**Target Architecture:** +- **Shared Hosting Server**: Prepaid WordPress hosting (MySQL Database `wp_peptide_news_articles`, public WordPress frontend, Admin UI). +- **Hostinger KVM8 VPS (Coolify)**: Dedicated VPS running Coolify to execute the standalone worker (`tools/vps-worker/`) for heavy 3-step OpenRouter LLM processing, PubMed XML extraction, and Google News URL redirect unwrapping. + +--- + +## 1. Current Codebase Status (100% Implemented & Verified) +All v2.6.0 features and adversarial security hardenings have been implemented in `c:\Users\terence\Projects\peptidenews`: +- **89/89 PHPUnit tests passing** (`vendor/bin/phpunit`). +- **REST API Worker Routes (`/wp-json/peptide-news/v1/worker/*`)**: Authenticated via `X-Peptide-News-Token` (with timing-safe comparison and automatic token decryption). +- **Standalone Coolify Worker (`tools/vps-worker/`)**: Complete with `Dockerfile`, `docker-compose.yml`, and `worker.php` supporting both CLI arguments and Coolify environment variables (`WP_URL`, `VPS_TOKEN`, `OPENROUTER_KEY`, `OPENROUTER_MODEL`, `WORKER_ACTION`, `BATCH_SIZE`). +- **3-Step AI Pipeline**: + - **Step 1 (Gatekeeper)**: Assigns scientific rigor score (1–10) and classifies study type. Rejects low-quality/promotional spam (`score < 3` or `is_spam = true`) by setting `'is_active' => 0`. + - **Step 2 (Extraction)**: Extracts target peptides, mechanism, experimental model, and keywords, saving checkpoint to `ai_metadata`. + - **Step 3 (Generation)**: Creates a 300–500 word structured Markdown summary (`## Executive Summary`, `## Scientific Context & Mechanism`, etc.). + +--- + +## 2. Instructions for the Agent: Step-by-Step Execution + +### Step 1: Package as an Installable WordPress Plugin ZIP +Before deploying to WordPress, create a clean, installable ZIP archive (`peptidenews-v2.6.0.zip`) that can be uploaded directly via **WordPress Admin -> Plugins -> Add New -> Upload Plugin**: +1. From the parent directory of `peptidenews`, generate a clean zip archive containing the `peptidenews/` root folder while excluding development, test, and git files: + ```bash + # Linux / macOS / Bash: + zip -r peptidenews-v2.6.0.zip peptidenews/ \ + -x "peptidenews/.git/*" \ + -x "peptidenews/tests/*" \ + -x "peptidenews/phpunit.xml*" \ + -x "peptidenews/.phpunit*" \ + -x "peptidenews/scratch/*" \ + -x "peptidenews/*.md" + ``` + *(On Windows PowerShell, use `Compress-Archive -Path .\peptidenews -DestinationPath .\peptidenews-v2.6.0.zip` after excluding `tests` and `.git`).* +2. **Verify ZIP Archive Structure**: Ensure `peptidenews/peptide-news-plugin.php` is located at the top level inside the zip archive so WordPress correctly recognizes it as a valid plugin. + +### Step 2: Deploy & Configure WordPress on Shared Hosting +1. Upload and install `peptidenews-v2.6.0.zip` via WordPress Admin or extract it into `/wp-content/plugins/peptidenews/` on the shared WordPress server. +2. In WordPress Admin -> **Settings -> Peptide News**: + - Under **NCBI API Key**, enter an NCBI API key (optional, increases PubMed rate limit to 10 req/sec). + - Under **VPS Worker Integration**, enter a strong secret token (e.g., `coolify_secret_token_2026`) and save. +3. Verify the REST API endpoint responds correctly: + ```bash + curl -i -H "X-Peptide-News-Token: coolify_secret_token_2026" \ + "https://your-wordpress-site.com/wp-json/peptide-news/v1/worker/pending?limit=5" + ``` + +### Step 3: Deploy Worker Application to Coolify (Hostinger KVM8 VPS) +Use the Coolify UI or Coolify MCP to create and configure the standalone worker: +1. **Create Application in Coolify**: + - Add a new **Application** and point it to the repository (or upload `tools/vps-worker/`). + - Set **Build Pack** to `Dockerfile` with path `tools/vps-worker/Dockerfile`. +2. **Configure Environment Variables in Coolify**: + ```env + WP_URL=https://your-wordpress-site.com + VPS_TOKEN=coolify_secret_token_2026 + WORKER_ACTION=process-llm + OPENROUTER_KEY=sk-or-v1-your-openrouter-api-key + OPENROUTER_MODEL=google/gemini-2.0-flash-001 + BATCH_SIZE=25 + ``` +3. **Configure Scheduled Task (Coolify Cron)**: + - Under **Scheduled Tasks** / Cron Jobs for the application, create a new schedule: + - **Cron Expression**: `0 * * * *` *(runs hourly)* + - **Command**: `php /app/worker.php` + - Click **Deploy** to build and launch the Alpine PHP container. + +--- + +## 3. Automated Verification Checklist for the Agent +1. **Verify Plugin ZIP Installation**: Confirm `peptidenews-v2.6.0.zip` installs and activates cleanly in WordPress Admin without warnings or missing dependencies. +2. **Run Unit Tests Locally**: Execute `vendor/bin/phpunit` and confirm `OK (89 tests, 231 assertions)`. +3. **Test One-Off Execution in Coolify**: + - Trigger the Coolify scheduled job or run `php /app/worker.php --action="pending"` inside the container. + - Confirm it connects to WordPress without HTTP 403 or 500 errors. +4. **Check Gatekeeper Database State**: + - Confirm in WordPress Admin that legitimate scientific articles (`rigor_score >= 3`) receive structured Markdown summaries and tags. + - Confirm that rejected promotional spam (`rigor_score < 3` or `is_spam`) is automatically updated with `'is_active' => 0` and excluded from frontend widgets. diff --git a/admin/class-pn-admin-field-renderers.php b/admin/class-pn-admin-field-renderers.php index 84d4b43..10ee4b2 100644 --- a/admin/class-pn-admin-field-renderers.php +++ b/admin/class-pn-admin-field-renderers.php @@ -117,6 +117,26 @@ class Peptide_News_Admin_Field_Renderers { ); } + public static function render_ncbi_key_field(): void { + $value = get_option( 'peptide_news_ncbi_api_key', '' ); + $display_value = ! empty( $value ) ? self::mask_api_key( $value ) : ''; + printf( + '', + esc_attr( $display_value ), + esc_attr__( 'Enter NCBI API key (optional)', 'peptide-news' ) + ); + } + + public static function render_vps_token_field(): void { + $value = get_option( 'peptide_news_vps_token', '' ); + $display_value = ! empty( $value ) ? self::mask_api_key( $value ) : ''; + printf( + '', + esc_attr( $display_value ), + esc_attr__( 'Enter secret VPS token (optional)', 'peptide-news' ) + ); + } + public static function render_article_retention_field(): void { $value = get_option( 'peptide_news_article_retention', 90 ); printf( diff --git a/admin/class-pn-admin-settings.php b/admin/class-pn-admin-settings.php index f85d448..93c28c7 100644 --- a/admin/class-pn-admin-settings.php +++ b/admin/class-pn-admin-settings.php @@ -61,6 +61,30 @@ class Peptide_News_Admin_Settings { $this->add_setting( 'newsapi_enabled', __( 'Enable NewsAPI', 'peptide-news' ), 'render_newsapi_enabled_field', 'peptide_news_newsapi' ); $this->add_setting( 'newsapi_key', __( 'API Key', 'peptide-news' ), 'render_newsapi_key_field', 'peptide_news_newsapi' ); + // --- NCBI E-utilities section --- + add_settings_section( + 'peptide_news_ncbi_section', + __( 'NCBI PubMed E-utilities', 'peptide-news' ), + function () { + echo '

' . esc_html__( 'Optional. An NCBI API key raises PubMed rate limits from 3 req/sec to 10 req/sec.', 'peptide-news' ) . '

'; + }, + 'peptide-news-settings' + ); + + $this->add_setting( 'ncbi_api_key', __( 'NCBI API Key', 'peptide-news' ), 'render_ncbi_key_field', 'peptide_news_ncbi_section' ); + + // --- VPS Worker section --- + add_settings_section( + 'peptide_news_vps_section', + __( 'VPS Worker Integration', 'peptide-news' ), + function () { + echo '

' . esc_html__( 'Optional. Set a secret token to allow an external VPS worker to sync articles via REST API without admin login.', 'peptide-news' ) . '

'; + }, + 'peptide-news-settings' + ); + + $this->add_setting( 'vps_token', __( 'VPS Worker Token', 'peptide-news' ), 'render_vps_token_field', 'peptide_news_vps_section' ); + // --- Analytics section --- add_settings_section( 'peptide_news_analytics_section', @@ -201,6 +225,12 @@ class Peptide_News_Admin_Settings { 'newsapi_key' => function ( $value ) { return $this->sanitize_api_key( $value, 'peptide_news_newsapi_key' ); }, + 'ncbi_api_key' => function ( $value ) { + return $this->sanitize_api_key( $value, 'peptide_news_ncbi_api_key' ); + }, + 'vps_token' => function ( $value ) { + return $this->sanitize_api_key( $value, 'peptide_news_vps_token' ); + }, 'article_retention' => 'absint', 'analytics_retention' => 'absint', 'anonymize_ip' => 'absint', diff --git a/composer.lock b/composer.lock new file mode 100644 index 0000000..600ce9c --- /dev/null +++ b/composer.lock @@ -0,0 +1,2540 @@ +{ + "_readme": [ + "This file locks the dependencies of your project to a known state", + "Read 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b/includes/class-peptide-news-activator.php @@ -57,11 +57,16 @@ class Peptide_News_Activator { ai_summary TEXT NOT NULL, hash VARCHAR(64) NOT NULL DEFAULT '', is_active TINYINT(1) NOT NULL DEFAULT 1, + rigor_score TINYINT(1) UNSIGNED DEFAULT NULL, + study_type VARCHAR(50) DEFAULT NULL, + ai_metadata LONGTEXT DEFAULT NULL, PRIMARY KEY (id), UNIQUE KEY hash (hash), KEY idx_published (published_at), KEY idx_source (source), - KEY idx_active_published (is_active, published_at) + KEY idx_active_published (is_active, published_at), + KEY idx_rigor_score (rigor_score), + KEY idx_study_type (study_type) ) {$charset_collate};"; // Click analytics table — one row per click event. @@ -120,11 +125,23 @@ class Peptide_News_Activator { 'newsapi_key' => '', 'newsapi_enabled' => 0, 'rss_feeds' => implode( "\n", array( - 'https://news.google.com/rss/search?q=peptide+research&hl=en-US&gl=US&ceid=US:en', - 'https://pubmed.ncbi.nlm.nih.gov/rss/search/1sUlVGjEXm1YN9QiGPblv_-bwB51JCtyLwVX85CVGDKCHFFR9Q/?limit=20&utm_campaign=pubmed-2&fc=20220101000000', + 'https://news.google.com/rss/search?q=(%22peptide+research%22+OR+%22peptide+therapeutics%22+OR+%22peptide+drug+discovery%22+OR+%22macrocyclic+peptides%22+OR+%22GLP-1+receptor%22)+-prnewswire+-businesswire+-globenewswire+-accesswire+-openpr+-cision+-einpresswire+-newswire+-newsfilecorp+-gossip+-celebrity+-kardashian+-hollywood+-supplement+-vendor+-clinic+-%22press+release%22+-%22sponsored+post%22+-%22market+report%22+-cagr&hl=en-US&gl=US&ceid=US:en', + 'https://pubmed.ncbi.nlm.nih.gov/rss/search/1sUlVGjEXm1YN9QiGPblv_-bwB51JCtyLwVX85CVGDKCHFFR9Q/?limit=50&utm_campaign=pubmed-2&fc=20240101000000', + 'https://connect.biorxiv.org/biorxiv_xml.php?subject=biochemistry+pharmacology_and_toxicology+bioengineering+synthetic_biology', + 'https://connect.medrxiv.org/medrxiv_xml.php?subject=endocrinology+pharmacology_and_therapeutics', + 'https://onlinelibrary.wiley.com/feed/10991387/most-recent', + 'https://www.nature.com/nchembio.rss', + 'https://www.nature.com/nrd.rss', + 'https://www.nature.com/natbiomedeng.rss', + 'https://www.sciencedaily.com/rss/matter_energy/biochemistry.xml', + 'https://www.sciencedaily.com/rss/health_medicine/pharmacology.xml', + 'https://www.biospace.com/rss/', + 'https://www.statnews.com/feed/', + 'https://endpts.com/feed/', + 'https://www.fiercebiotech.com/rss/Fierce%20Biotech%20Homepage/xml', ) ), 'rss_enabled' => 1, - 'search_keywords' => 'peptide, peptides, peptide therapy, peptide research, BPC-157, Thymosin, GHK-Cu', + 'search_keywords' => '("peptide research" OR "peptide therapeutics" OR "peptide drug discovery" OR "macrocyclic peptides" OR "GLP-1 receptor" OR "BPC-157" OR "GHK-Cu") NOT (prnewswire OR businesswire OR globenewswire OR accesswire OR openpr OR "press release" OR "market report" OR "sponsored post" OR celebrity OR gossip OR kardashian OR supplement OR vendor)', 'thumbnail_fallback' => PEPTIDE_NEWS_PLUGIN_URL . 'public/images/default-thumb.png', 'article_retention' => 90, 'analytics_retention' => 365, @@ -144,6 +161,19 @@ class Peptide_News_Activator { add_option( "peptide_news_{$key}", $value ); } } + + // Upgrade legacy default feeds and keywords to high-signal scientific defaults. + $current_feeds = (string) get_option( 'peptide_news_rss_feeds', '' ); + $legacy_feeds = 'https://news.google.com/rss/search?q=peptide+research&hl=en-US&gl=US&ceid=US:en' . "\n" . + 'https://pubmed.ncbi.nlm.nih.gov/rss/search/1sUlVGjEXm1YN9QiGPblv_-bwB51JCtyLwVX85CVGDKCHFFR9Q/?limit=20&utm_campaign=pubmed-2&fc=20220101000000'; + if ( $legacy_feeds === $current_feeds ) { + update_option( 'peptide_news_rss_feeds', $defaults['rss_feeds'] ); + } + + $current_kw = (string) get_option( 'peptide_news_search_keywords', '' ); + if ( 'peptide, peptides, peptide therapy, peptide research, BPC-157, Thymosin, GHK-Cu' === $current_kw ) { + update_option( 'peptide_news_search_keywords', $defaults['search_keywords'] ); + } } /** diff --git a/includes/class-peptide-news-cli.php b/includes/class-peptide-news-cli.php new file mode 100644 index 0000000..dfc4eb1 --- /dev/null +++ b/includes/class-peptide-news-cli.php @@ -0,0 +1,119 @@ +] + * : Number of articles to process. Defaults to 15 in CLI mode. + * + * [--force] + * : Ignore the admin max articles per cycle limit. + * + * ## EXAMPLES + * + * wp peptide-news process-llm --batch=20 --force + * + * @when after_wp_load + */ + public function process_llm( array $args = array(), array $assoc_args = array() ): void { + if ( ! Peptide_News_LLM::is_enabled() ) { + if ( class_exists( 'WP_CLI' ) && method_exists( 'WP_CLI', 'error' ) ) { + WP_CLI::error( 'LLM processing is disabled or missing an API key.' ); + } + return; + } + + $batch_size = isset( $assoc_args['batch'] ) ? absint( $assoc_args['batch'] ) : 15; + if ( $batch_size < 1 ) { + $batch_size = 15; + } + $force = isset( $assoc_args['force'] ); + + if ( class_exists( 'WP_CLI' ) && method_exists( 'WP_CLI', 'log' ) ) { + WP_CLI::log( sprintf( 'Processing up to %d unanalyzed articles through 3-Step AI Pipeline...', $batch_size ) ); + } + $start = microtime( true ); + $processed = Peptide_News_LLM::process_unanalyzed( $batch_size, $force ); + $duration = round( microtime( true ) - $start, 2 ); + + if ( class_exists( 'WP_CLI' ) && method_exists( 'WP_CLI', 'success' ) ) { + WP_CLI::success( sprintf( 'Successfully generated AI summaries for %d articles in %s seconds.', $processed, $duration ) ); + } + } + + /** + * Resolve Google News redirect URLs and update database sources. + * + * ## OPTIONS + * + * [--limit=] + * : Maximum number of unresolved URLs to resolve. Default 20. + * + * ## EXAMPLES + * + * wp peptide-news backfill-sources --limit=50 + * + * @when after_wp_load + */ + public function backfill_sources( array $args = array(), array $assoc_args = array() ): void { + $limit = isset( $assoc_args['limit'] ) ? absint( $assoc_args['limit'] ) : 20; + if ( $limit < 1 ) { + $limit = 20; + } + + if ( class_exists( 'WP_CLI' ) && method_exists( 'WP_CLI', 'log' ) ) { + WP_CLI::log( sprintf( 'Resolving up to %d redirect URLs...', $limit ) ); + } + $start = microtime( true ); + $resolved = Peptide_News_Source_Resolver::backfill( $limit ); + $duration = round( microtime( true ) - $start, 2 ); + + if ( class_exists( 'WP_CLI' ) && method_exists( 'WP_CLI', 'success' ) ) { + WP_CLI::success( sprintf( 'Resolved %d URLs in %s seconds.', $resolved, $duration ) ); + } + } +} diff --git a/includes/class-peptide-news-content-extractor.php b/includes/class-peptide-news-content-extractor.php new file mode 100644 index 0000000..f422fa6 --- /dev/null +++ b/includes/class-peptide-news-content-extractor.php @@ -0,0 +1,264 @@ + Extracted data array with 'title', 'content', 'author', 'journal'. + */ + public static function extract( string $html = '', string $url = '' ): array { + if ( empty( $html ) && ! empty( $url ) ) { + $response = wp_remote_get( + $url, + array( + 'timeout' => 15, + 'user-agent' => 'Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/123.0.0.0 Safari/537.36', + ) + ); + if ( is_wp_error( $response ) || 200 !== (int) wp_remote_retrieve_response_code( $response ) ) { + return array( + 'title' => '', + 'content' => '', + 'author' => '', + 'journal' => '', + ); + } + $html = (string) wp_remote_retrieve_body( $response ); + } + + if ( empty( $html ) ) { + return array( + 'title' => '', + 'content' => '', + 'author' => '', + 'journal' => '', + ); + } + + // Enforce 500 KB size cap safely for multi-byte UTF-8 characters. + if ( strlen( $html ) > self::MAX_HTML_SIZE ) { + $html = function_exists( 'mb_strcut' ) ? mb_strcut( $html, 0, self::MAX_HTML_SIZE, 'UTF-8' ) : substr( $html, 0, self::MAX_HTML_SIZE ); + } + + // Strip scripts, styles, svgs, and base64 data URIs before DOM parsing. + $html = preg_replace( '/<(script|style|svg|noscript|iframe)[^>]*>.*?<\/\1>/is', '', $html ); + $html = preg_replace( '/data:image\/[a-z0-9+-]+;base64,[a-z0-9+\/=_]+/i', '', (string) $html ); + + // Enforce UTF-8 pre-encoding normalization without deprecated mb_convert_encoding. + $html_encoded = '' . (string) $html; + + $libxml_prev = libxml_use_internal_errors( true ); + $dom = new DOMDocument(); + $dom->loadHTML( $html_encoded, LIBXML_NOERROR | LIBXML_NOWARNING | LIBXML_NONET ); + libxml_clear_errors(); + libxml_use_internal_errors( $libxml_prev ); + + $xpath = new DOMXPath( $dom ); + + // 1. Try JSON-LD Schema.org Article / ScholarlyArticle + $jsonld_data = self::extract_from_jsonld( $xpath ); + if ( ! empty( $jsonld_data['content'] ) && strlen( $jsonld_data['content'] ) > 100 ) { + return $jsonld_data; + } + + // 2. Try Highwire Press / Citation Meta Tags + $highwire_data = self::extract_from_highwire( $xpath ); + if ( ! empty( $highwire_data['content'] ) && strlen( $highwire_data['content'] ) > 100 ) { + return $highwire_data; + } + + // 3. Fallback: DOMXPath Paragraph Density Scoring + return self::extract_from_paragraphs( $xpath, $jsonld_data, $highwire_data ); + } + + /** + * Extract data from JSON-LD `