peptide-repo-core v0.6.0: peptide schema backfill + Yoast-integrated Drug/MedicalWebPage/FAQ (#19)
Backfill psa_*->_pr_* meta (migration 0004 + PubChem fallback); enrich Drug node with {permalink}#drug @id + molecularFormula/Weight/alternateName; rewrite emitter into Yoast schema graph (MedicalWebPage retype + FAQPage, no duplicate nodes).
QA: APPROVE (independent) — qa-reviews/peptide-repo-core/2026-06-13-817690c1b6ec2118ddcf3b8cfe8bc5ea7f3933b3.md
Agent-Session: peptide-schema-backfill v0.6.0 merge
This commit is contained in:
peptiderepo
@@ -68,7 +68,7 @@ class PR_Core_Peptide_CPT {
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'aliases' => [
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'type' => 'string',
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'default' => '[]',
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'sanitize' => [ __CLASS__, 'sanitize_json_array' ],
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'sanitize' => [ PR_Core_Schema_Sanitizers::class, 'sanitize_json_array' ],
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],
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'molecular_formula' => [
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'type' => 'string',
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@@ -145,6 +145,28 @@ class PR_Core_Peptide_CPT {
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'default' => 'current',
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'sanitize' => [ PR_Core_Verification_Sanitizers::class, 'sanitize_status' ],
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],
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// Schema-input meta (v0.6.0): molecular data sourced from PSA psa_* keys via migration 0004.
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'_pr_molecular_formula' => [
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'type' => 'string',
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'default' => '',
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'sanitize' => [ PR_Core_Schema_Sanitizers::class, 'sanitize_molecular_formula' ],
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],
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'_pr_molecular_weight' => [
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'type' => 'string',
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'default' => '',
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'sanitize' => [ PR_Core_Schema_Sanitizers::class, 'sanitize_molecular_weight_string' ],
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],
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'_pr_aliases' => [
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'type' => 'string',
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'default' => '[]',
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'sanitize' => [ PR_Core_Schema_Sanitizers::class, 'sanitize_json_array' ],
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],
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// FAQ items (v0.6.0): [{question, answer}] JSON for FAQPage schema. Populated by CMO content sprint.
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'_pr_faq_items' => [
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'type' => 'string',
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'default' => '[]',
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'sanitize' => [ PR_Core_Schema_Sanitizers::class, 'sanitize_faq_items' ],
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],
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];
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}
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@@ -160,12 +182,7 @@ class PR_Core_Peptide_CPT {
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}
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/**
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* Register the `peptide` custom post type.
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*
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* Guarded with `post_type_exists()`: if another plugin (historically PSA)
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* has already registered the `peptide` post type, this call no-ops. This
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* makes deploy order between PR Core and PSA irrelevant during the
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* PSA v4.5.0 consolidation transition.
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* Register the `peptide` CPT. Guarded with post_type_exists() so deploy order is irrelevant.
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*
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* Side effects: registers CPT with WordPress.
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*
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@@ -218,15 +235,7 @@ class PR_Core_Peptide_CPT {
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}
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/**
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* Register the `peptide_category` taxonomy.
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*
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* Guarded with `taxonomy_exists()` for the same reason CPT registration
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* is guarded. The 8 existing terms + term_relationships stay intact —
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* they key on taxonomy name `peptide_category` in wp_term_taxonomy,
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* which is exactly what we register here.
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*
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* v0.2.0: `pr_peptide_family` taxonomy removed — never populated, never
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* surfaced in UI.
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* Register the `peptide_category` taxonomy. Guarded with taxonomy_exists().
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*
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* Side effects: registers taxonomy with WordPress.
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*
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@@ -272,20 +281,6 @@ class PR_Core_Peptide_CPT {
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}
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}
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/** Sanitize a JSON array string (e.g., aliases field). */
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public static function sanitize_json_array( $value ): string {
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if ( is_array( $value ) ) {
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$value = wp_json_encode( array_map( 'sanitize_text_field', $value ) );
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}
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$decoded = json_decode( (string) $value, true );
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if ( ! is_array( $decoded ) ) {
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return '[]';
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}
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return wp_json_encode( array_values( array_map( 'sanitize_text_field', $decoded ) ) );
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}
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/** Sanitize evidence_strength to allowed enum values. */
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public static function sanitize_evidence_strength( $value ): string {
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$value = sanitize_text_field( (string) $value );
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152
includes/cpt/class-pr-core-schema-sanitizers.php
Normal file
152
includes/cpt/class-pr-core-schema-sanitizers.php
Normal file
@@ -0,0 +1,152 @@
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<?php
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declare(strict_types=1);
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/**
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* Sanitizers for v0.6.0 schema-input meta fields.
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*
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* What: Static sanitizer methods for _pr_molecular_formula, _pr_molecular_weight,
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* and _pr_faq_items meta fields introduced in v0.6.0.
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*
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* Who calls it: PR_Core_Peptide_CPT::get_meta_fields() registers these as
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* sanitize_callback values for register_post_meta().
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*
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* Dependencies: WordPress sanitize_text_field, sanitize_textarea_field, wp_json_encode.
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*
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* @see cpt/class-pr-core-peptide-cpt.php — Meta field registration.
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* @see ARCHITECTURE.md — §v0.6.0 schema sprint.
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*/
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class PR_Core_Schema_Sanitizers {
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/**
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* Regex token for a single element symbol + optional count (e.g., "C10", "Na", "O").
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*
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* Matches: one uppercase letter, optionally followed by one lowercase letter,
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* optionally followed by one or more digits.
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*
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* @var string
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*/
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const FORMULA_TOKEN = '[A-Z][a-z]?\d*';
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/**
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* Regex character class for allowed group-separator / structural characters.
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*
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* Covers: parentheses, square brackets, interpunct (·, U+00B7), period, digits.
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* These may appear between element tokens in complex or hydrated formulas.
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*
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* @var string
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*/
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const FORMULA_SEP = '[().\[\]\xB7\d]';
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/**
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* Sanitize a molecular formula string (for _pr_molecular_formula).
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*
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* Strips HTML tags and control characters, then validates the value against
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* an element-formula grammar. Returns the longest leading run of valid
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* formula tokens and separators; returns '' when nothing valid is found.
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*
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* Grammar (per token): [A-Z][a-z]?\d* — an element symbol plus optional count.
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* Separators: ( ) [ ] · . and standalone digits (for hydrated formulas).
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* Input is treated as UNTRUSTED; downstream JSON escaping is unchanged.
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*
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* Examples:
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* "C62H98N16O22" → "C62H98N16O22" (valid, unchanged)
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* "C10H12\ninjection" → "C10H12" (injection stripped)
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* "C2H5(OH)" → "C2H5(OH)" (parenthesised formula preserved)
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* "<script>alert(1)</script>" → "" (no valid leading token)
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* "" → "" (empty input)
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*
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* @param mixed $value Raw input value.
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* @return string Sanitized formula string, or '' when no valid formula found.
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*/
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public static function sanitize_molecular_formula( $value ): string {
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// 1. Strip control characters (including newlines, tabs, null bytes).
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$value = preg_replace( '/[\x00-\x1F\x7F]/', '', (string) $value ) ?? '';
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// 2. Strip HTML tags; then strip remaining unsafe text characters.
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$value = sanitize_text_field( wp_strip_all_tags( $value ) );
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if ( '' === $value ) {
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return '';
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}
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// 3. Extract the maximal leading run of valid element tokens and separators.
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// A valid run must start with an element token ([A-Z][a-z]?\d*), not a separator.
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$pattern = '/^((?:' . self::FORMULA_TOKEN . '|' . self::FORMULA_SEP . ')+)/u';
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if ( preg_match( $pattern, $value, $m ) ) {
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return $m[1];
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}
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return '';
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}
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/**
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* Sanitize a molecular weight stored as a float string (for _pr_molecular_weight).
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*
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* Strips any trailing "Da" unit suffix, returns a float string.
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* Stored as string in post_meta to avoid float precision issues.
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* Returns empty string for invalid/zero inputs.
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*
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* @param mixed $value Raw input value (e.g., "1419.5" or "1419.5 Da").
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* @return string Float string (e.g., "1419.5"), or "" on invalid input.
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*/
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public static function sanitize_molecular_weight_string( $value ): string {
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$clean = trim( preg_replace( '/\s*[Dd][Aa]\s*$/', '', trim( (string) $value ) ) ?? '' );
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$f = (float) $clean;
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return $f > 0.0 ? (string) $f : '';
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}
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/**
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* Sanitize a JSON array string (e.g., for legacy aliases field or _pr_aliases).
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*
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* Accepts a JSON string or PHP array. Sanitizes each element individually.
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* Input is UNTRUSTED.
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*
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* @param mixed $value Raw input (JSON string or array).
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* @return string JSON array of sanitized strings, or '[]'.
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*/
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public static function sanitize_json_array( $value ): string {
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if ( is_array( $value ) ) {
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$value = wp_json_encode( array_map( 'sanitize_text_field', $value ) );
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}
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$decoded = json_decode( (string) $value, true );
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if ( ! is_array( $decoded ) ) {
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return '[]';
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}
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return wp_json_encode( array_values( array_map( 'sanitize_text_field', $decoded ) ) );
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}
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/**
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* Sanitize FAQ items JSON (for _pr_faq_items).
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*
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* Expects a JSON array of {question: string, answer: string} objects.
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* Sanitizes each question and answer individually.
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* Input is UNTRUSTED — malformed entries are silently dropped.
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*
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* @param mixed $value Raw input (JSON string or PHP array).
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* @return string JSON array of sanitized FAQ item objects, or '[]'.
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*/
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public static function sanitize_faq_items( $value ): string {
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if ( is_string( $value ) ) {
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$value = json_decode( $value, true );
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}
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if ( ! is_array( $value ) ) {
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return '[]';
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}
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$clean = [];
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foreach ( $value as $item ) {
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if ( ! is_array( $item ) ) {
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continue;
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}
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$question = sanitize_text_field( (string) ( $item['question'] ?? '' ) );
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$answer = sanitize_textarea_field( (string) ( $item['answer'] ?? '' ) );
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if ( '' !== $question && '' !== $answer ) {
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$clean[] = [
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'question' => $question,
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'answer' => $answer,
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];
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}
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}
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return wp_json_encode( $clean, JSON_UNESCAPED_UNICODE ) ?: '[]';
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}
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}
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