soil-report-ai/controllers/ollamaGenerate.php

<?php
/**
 * controllers/ollamaGenerate.php
 *
 * AJAX POST handler: generates AI agronomic text using Ollama, grounded
 * with relevant passages retrieved from the soil science knowledge base
 * (William A. Albrecht et al.) stored in MySQL knowledge_chunks.
 *
 * Flow:
 *  1. Load full soil record + specification ranges from DB
 *  2. Build a structured data summary covering ALL measured elements
 *  3. Embed that summary via nomic-embed-text → cosine search over knowledge_chunks
 *  4. Inject retrieved passages + data into a section-specific prompt
 *  5. Send to llama3.1 and return the generated text
 *
 * POST params:
 *   csrf_token  string
 *   rid         int     soil_records.id
 *   rand        string  soil_records.rand
 *   section     string  overview | ai_interpretation | foliar | microbial
 *
 * Note: run ingestion from Windows where Ollama is accessible:
 *   php tools/ingest_knowledge.php --test
 *   php tools/ingest_knowledge.php --file="book.pdf" --author="William A. Albrecht"
 */

if (session_status() === PHP_SESSION_NONE) {
    session_start();
}

require_once __DIR__ . '/../config/database.php';
require_once __DIR__ . '/../lib/auth.php';
require_once __DIR__ . '/../lib/csrf.php';

header('Content-Type: application/json');

// ── Config ───────────────────────────────────────────────────────────────────
define('OLLAMA_HOST',    'http://192.168.8.73:11434');
define('OLLAMA_MODEL',   'llama3.1:8b-instruct-q4_K_M');
define('EMBED_MODEL',    'nomic-embed-text');
define('RAG_TOP_K',      6);    // book passages injected per request
define('OLLAMA_TIMEOUT', 180);  // seconds — LLM can be slow

// ── Auth + CSRF ───────────────────────────────────────────────────────────────
if (!isLoggedIn()) {
    http_response_code(401);
    echo json_encode(['success' => false, 'error' => 'Not authenticated']);
    exit;
}

if ($_SERVER['REQUEST_METHOD'] !== 'POST') {
    http_response_code(405);
    echo json_encode(['success' => false, 'error' => 'Method not allowed']);
    exit;
}

if (!verifyCsrfToken($_POST['csrf_token'] ?? '')) {
    http_response_code(403);
    echo json_encode(['success' => false, 'error' => 'Invalid CSRF token']);
    exit;
}

$recordId   = (int)trim($_POST['rid']         ?? '');
$randId     = trim($_POST['rand']             ?? '');
$section    = trim($_POST['section']          ?? '');
$recordType = trim($_POST['record_type']      ?? 'soil');  // soil | plant

$validSoilSections  = ['overview', 'ai_interpretation', 'foliar', 'microbial'];
$validPlantSections = ['general', 'ai_interpretation', 'recommended', 'foliar'];
$validSections      = $recordType === 'plant' ? $validPlantSections : $validSoilSections;

if (!$recordId || $randId === '' || !in_array($section, $validSections, true)
    || !in_array($recordType, ['soil', 'plant'], true)) {
    http_response_code(400);
    echo json_encode(['success' => false, 'error' => 'Invalid parameters']);
    exit;
}

// ── Load record + spec ────────────────────────────────────────────────────────
try {
    $pdo = getDBConnection();

    if ($recordType === 'plant') {
        $stmt = $pdo->prepare('SELECT * FROM plant_records WHERE id = ? AND rand = ?');
        $stmt->execute([$recordId, $randId]);
        $row = $stmt->fetch(PDO::FETCH_ASSOC);

        if (!$row) {
            http_response_code(404);
            echo json_encode(['success' => false, 'error' => 'Record not found']);
            exit;
        }

        $spec = [];
        if (!empty($row['crop_type'])) {
            $stmtSpec = $pdo->prepare('SELECT * FROM plant_specifications WHERE plant_type = ? LIMIT 1');
            $stmtSpec->execute([$row['crop_type']]);
            $spec = $stmtSpec->fetch(PDO::FETCH_ASSOC) ?: [];
        }
    } else {
        $stmt = $pdo->prepare('SELECT * FROM soil_records WHERE id = ? AND rand = ?');
        $stmt->execute([$recordId, $randId]);
        $row = $stmt->fetch(PDO::FETCH_ASSOC);

        if (!$row) {
            http_response_code(404);
            echo json_encode(['success' => false, 'error' => 'Record not found']);
            exit;
        }

        $spec = [];
        if (!empty($row['soil_type'])) {
            $stmtSpec = $pdo->prepare('SELECT * FROM soil_specifications WHERE soil_type = ? LIMIT 1');
            $stmtSpec->execute([$row['soil_type']]);
            $spec = $stmtSpec->fetch(PDO::FETCH_ASSOC) ?: [];
        }
    }

} catch (PDOException $e) {
    error_log('DB error in ollamaGenerate.php: ' . $e->getMessage());
    http_response_code(500);
    echo json_encode(['success' => false, 'error' => 'Database error']);
    exit;
}

// ── Helpers ───────────────────────────────────────────────────────────────────

function fv(mixed $v, int $dp = 2): string
{
    if ($v === null || $v === '') return 'N/A';
    return is_numeric($v) ? number_format((float)$v, $dp) : (string)$v;
}

function rangeStatus(mixed $value, mixed $min, mixed $max): string
{
    if (!is_numeric($value)) return '';
    $v  = (float)$value;
    $lo = is_numeric($min) ? (float)$min : null;
    $hi = is_numeric($max) ? (float)$max : null;
    if ($lo !== null && $v < $lo) return '[DEFICIENT]';
    if ($hi !== null && $v > $hi) return '[EXCESS]';
    if ($lo !== null || $hi !== null) return '[IDEAL]';
    return '';
}

/** Resolve a value — check spec row first, then soil record row */
function sv(array $spec, array $row, string $col): mixed
{
    if (isset($spec[$col]) && $spec[$col] !== '' && $spec[$col] !== null) return $spec[$col];
    if (isset($row[$col])  && $row[$col]  !== '' && $row[$col]  !== null) return $row[$col];
    return null;
}

$r = $row;
$s = $spec;

// ── Pre-compute all display values (heredocs don't support function calls) ────
$d_ph_h2o    = fv($r['ph_h2o'],    1);  $d_ph_h2o_st  = rangeStatus($r['ph_h2o'], 6.2, 6.8);
$d_ph_cacl2  = fv($r['ph_cacl2'],  1);
$d_ec        = fv($r['ec'],        2);
$d_colour    = $r['colour']  ?? 'N/A';
$d_texture   = $r['texture'] ?? 'N/A';
$d_gravel    = fv($r['gravel'],    1);
$d_ocarbon   = fv($r['ocarbon'],   1);
$d_omatter   = fv($r['omatter'],   1);
$d_cec       = fv($r['cec'],       2);
$d_tec       = fv($r['tec'],       2);
$d_paramag   = fv($r['paramag'],   0);
$d_no3       = fv($r['NO3_N'],     0);  $d_no3_st    = rangeStatus($r['NO3_N'], 10, 20);
$d_nh3       = fv($r['NH3_N'],     0);
$d_cn_ratio  = fv($r['c_n_ratio'], 1);
$d_p_colwell = fv($r['p_colwell'], 0);
$d_p_morgan  = fv($r['p_morgan'],  0);
$d_p_mehlick = fv($r['p_mehlick'], 0);
$d_p_bray2   = fv($r['p_bray2'],   0);

// Major cations
$d_ca_ppm    = fv($r['BS_ca_ppm'], 0);
$d_ca_min    = fv(sv($s,$r,'ca_ppm_min'), 0);  $d_ca_max = fv(sv($s,$r,'ca_ppm_max'), 0);
$d_ca_st     = rangeStatus($r['BS_ca_ppm'], sv($s,$r,'ca_ppm_min'), sv($s,$r,'ca_ppm_max'));
$d_mg_ppm    = fv($r['BS_mg_ppm'], 0);
$d_mg_min    = fv(sv($s,$r,'mg_ppm_min'), 0);  $d_mg_max = fv(sv($s,$r,'mg_ppm_max'), 0);
$d_mg_st     = rangeStatus($r['BS_mg_ppm'], sv($s,$r,'mg_ppm_min'), sv($s,$r,'mg_ppm_max'));
$d_k_ppm     = fv($r['BS_k_ppm'],  0);
$d_k_min     = fv(sv($s,$r,'k_ppm_min'),  0);  $d_k_max  = fv(sv($s,$r,'k_ppm_max'),  0);
$d_k_st      = rangeStatus($r['BS_k_ppm'],  sv($s,$r,'k_ppm_min'),  sv($s,$r,'k_ppm_max'));
$d_na_ppm    = fv($r['BS_na_ppm'], 0);
$d_na_min    = fv(sv($s,$r,'na_ppm_min'), 0);  $d_na_max = fv(sv($s,$r,'na_ppm_max'), 0);
$d_na_st     = rangeStatus($r['BS_na_ppm'], sv($s,$r,'na_ppm_min'), sv($s,$r,'na_ppm_max'));

// Base saturations
$d_ca_bs     = fv($r['BS_ca2'], 2);
$d_ca_bs_min = fv(sv($s,$r,'cabs_min'), 1);  $d_ca_bs_max = fv(sv($s,$r,'cabs_max'), 1);
$d_ca_bs_st  = rangeStatus($r['BS_ca2'], sv($s,$r,'cabs_min'), sv($s,$r,'cabs_max'));
$d_mg_bs     = fv($r['BS_mg2'], 2);
$d_mg_bs_min = fv(sv($s,$r,'mgbs_min'), 1);  $d_mg_bs_max = fv(sv($s,$r,'mgbs_max'), 1);
$d_mg_bs_st  = rangeStatus($r['BS_mg2'], sv($s,$r,'mgbs_min'), sv($s,$r,'mgbs_max'));
$d_k_bs      = fv($r['BS_k'],   2);
$d_k_bs_min  = fv(sv($s,$r,'kbs_min'),  1);  $d_k_bs_max  = fv(sv($s,$r,'kbs_max'),  1);
$d_k_bs_st   = rangeStatus($r['BS_k'],   sv($s,$r,'kbs_min'),  sv($s,$r,'kbs_max'));
$d_na_bs     = fv($r['BS_na'],  2);
$d_na_bs_min = fv(sv($s,$r,'nabs_min'), 1);  $d_na_bs_max = fv(sv($s,$r,'nabs_max'), 1);
$d_na_bs_st  = rangeStatus($r['BS_na'],  sv($s,$r,'nabs_min'), sv($s,$r,'nabs_max'));
$d_ob        = fv($r['BS_ob'],  2);  $d_ob_rec = fv(sv($s,$r,'ob_rec'), 1);
$d_h         = fv($r['BS_h'],   2);  $d_h_rec  = fv(sv($s,$r,'h_rec'),  1);
$d_al3       = fv($r['BS_al3'], 2);

// Morgans
$d_ca_m = fv($r['ca_morgan'], 2);  $d_mg_m = fv($r['mg_morgan'], 2);
$d_k_m  = fv($r['k_morgan'],  2);  $d_na_m = fv($r['na_morgan'], 2);

// Mehlick-3
$d_ca_me = fv($r['ca_mehlick3'], 2);  $d_mg_me = fv($r['mg_mehlick3'], 2);
$d_k_me  = fv($r['k_mehlick3'],  2);  $d_na_me = fv($r['na_mehlick3'], 2);
$d_al_me = fv($r['al_mehlick3'], 2);

// Trace elements
$d_s  = fv($r['s_morgan'], 2);  $d_b  = fv($r['b_cacl2'],  2);
$d_mn = fv($r['mn_dtpa'],  2);  $d_cu = fv($r['cu_dtpa'],  2);
$d_zn = fv($r['zn_dtpa'],  2);  $d_fe = fv($r['fe_dtpa'],  2);
$d_fe_tot = fv($r['fe'],   2);  $d_al = fv($r['al'],       2);
$d_si = fv($r['sl_cacl2'], 2);  $d_co = fv($r['co_dtpa'],  2);
$d_mo = fv($r['m_dtpa'],   2);  $d_se = fv($r['se'],       2);

// Ratios
$_ca_me_v = is_numeric($r['ca_mehlick3']) ? (float)$r['ca_mehlick3'] : 0;
$_mg_me_v = is_numeric($r['mg_mehlick3']) ? (float)$r['mg_mehlick3'] : 0;
$d_ca_mg_ratio     = fv($_mg_me_v != 0 ? round($_ca_me_v / $_mg_me_v, 1) : null, 1);
$d_ca_mg_ratio_rec = fv(sv($s,$r,'ca_mg_ratio'), 1);

// Build comprehensive soil data block (ALL elements)
$soilData = <<<TEXT
=====================================
SOIL TEST DATA — COMPLETE ANALYSIS
=====================================
Client:       {$r['client_name']}
Location:     {$r['site_address']}, {$r['state_postcode']}
Crop:         {$r['sample_id']}
Crop Type:    {$r['crop_type']}
Soil Type:    {$r['soil_type']}
Lab No:       {$r['lab_no']}
Date Sampled: {$r['date_sampled']}

--- SOIL PHYSICAL / REACTION ---
pH (H2O):                $d_ph_h2o   [target: 6.2-6.8]  $d_ph_h2o_st
pH (CaCl2):              $d_ph_cacl2
EC (mS/cm):              $d_ec
Colour:                  $d_colour
Texture:                 $d_texture
Gravel (%):              $d_gravel

--- ORGANIC MATTER ---
Organic Carbon (%):      $d_ocarbon
Organic Matter (%):      $d_omatter

--- CATION EXCHANGE ---
CEC (meq/100g):          $d_cec
TEC (meq/100g):          $d_tec
Paramagnetic:            $d_paramag

--- NITROGEN ---
Nitrate-N (NO3-N ppm):   $d_no3   [target: 10-20 ppm]  $d_no3_st
Ammonium-N (NH3-N ppm):  $d_nh3
C:N ratio:               $d_cn_ratio

--- PHOSPHORUS ---
P Colwell (ppm):         $d_p_colwell
P Morgan (ppm):          $d_p_morgan
P Mehlick (ppm):         $d_p_mehlick
P Bray2 (ppm):           $d_p_bray2

--- MAJOR CATIONS (ppm) ---
Calcium Ca  (ppm):       $d_ca_ppm   [min: $d_ca_min, max: $d_ca_max]  $d_ca_st
Magnesium Mg (ppm):      $d_mg_ppm   [min: $d_mg_min, max: $d_mg_max]  $d_mg_st
Potassium K  (ppm):      $d_k_ppm    [min: $d_k_min,  max: $d_k_max]   $d_k_st
Sodium Na    (ppm):      $d_na_ppm   [min: $d_na_min, max: $d_na_max]  $d_na_st

--- BASE SATURATIONS (%) ---
Calcium  Ca (%):         $d_ca_bs%   [min: $d_ca_bs_min, max: $d_ca_bs_max]  $d_ca_bs_st
Magnesium Mg (%):        $d_mg_bs%   [min: $d_mg_bs_min, max: $d_mg_bs_max]  $d_mg_bs_st
Potassium  K  (%):       $d_k_bs%    [min: $d_k_bs_min,  max: $d_k_bs_max]   $d_k_bs_st
Sodium     Na (%):       $d_na_bs%   [min: $d_na_bs_min, max: $d_na_bs_max]  $d_na_bs_st
Other Bases (%):         $d_ob%   [recommended: $d_ob_rec]
Hydrogen    (%):         $d_h%    [recommended: $d_h_rec]
Aluminium  Al3 (%):      $d_al3%

--- MORGANS EXTRACT (ppm) ---
Ca Morgan:               $d_ca_m
Mg Morgan:               $d_mg_m
K  Morgan:               $d_k_m
Na Morgan:               $d_na_m

--- MEHLICK-3 EXTRACT (ppm) ---
Ca Mehlick3:             $d_ca_me
Mg Mehlick3:             $d_mg_me
K  Mehlick3:             $d_k_me
Na Mehlick3:             $d_na_me
Al Mehlick3:             $d_al_me

--- TRACE ELEMENTS (ppm) ---
Sulfur    S  (ppm):      $d_s
Boron     B  (ppm):      $d_b
Manganese Mn (ppm):      $d_mn
Copper    Cu (ppm):      $d_cu
Zinc      Zn (ppm):      $d_zn
Iron      Fe (ppm):      $d_fe
Iron      Fe (total):    $d_fe_tot
Aluminium Al (ppm):      $d_al
Silicon   Si (ppm):      $d_si
Cobalt    Co (ppm):      $d_co
Molybdenum Mo (ppm):     $d_mo
Selenium  Se (ppm):      $d_se

--- RATIOS ---
Ca:Mg ratio:             $d_ca_mg_ratio   [recommended: $d_ca_mg_ratio_rec]
C:N  ratio:              $d_cn_ratio

TEXT;

// Append quick deficiency/excess summary
$deficiencies = [];
$excesses     = [];

$checkElements = [
    ['pH (H2O)',        $r['ph_h2o'],    6.2,  6.8],
    ['Nitrate-N',       $r['NO3_N'],     10,   20],
    ['Calcium (ppm)',   $r['BS_ca_ppm'], sv($s,$r,'ca_ppm_min'), sv($s,$r,'ca_ppm_max')],
    ['Magnesium (ppm)', $r['BS_mg_ppm'], sv($s,$r,'mg_ppm_min'), sv($s,$r,'mg_ppm_max')],
    ['Potassium (ppm)', $r['BS_k_ppm'],  sv($s,$r,'k_ppm_min'),  sv($s,$r,'k_ppm_max')],
    ['Sodium (ppm)',    $r['BS_na_ppm'], sv($s,$r,'na_ppm_min'), sv($s,$r,'na_ppm_max')],
    ['Ca sat (%)',      $r['BS_ca2'],    sv($s,$r,'cabs_min'),   sv($s,$r,'cabs_max')],
    ['Mg sat (%)',      $r['BS_mg2'],    sv($s,$r,'mgbs_min'),   sv($s,$r,'mgbs_max')],
    ['K sat (%)',       $r['BS_k'],      sv($s,$r,'kbs_min'),    sv($s,$r,'kbs_max')],
    ['Na sat (%)',      $r['BS_na'],     sv($s,$r,'nabs_min'),   sv($s,$r,'nabs_max')],
];

foreach ($checkElements as [$label, $val, $lo, $hi]) {
    if (!is_numeric($val)) continue;
    $v = (float)$val;
    if (is_numeric($lo) && $v < (float)$lo) $deficiencies[] = $label;
    if (is_numeric($hi) && $v > (float)$hi) $excesses[]     = $label;
}

$soilData .= "Deficient: " . (empty($deficiencies) ? 'None detected' : implode(', ', $deficiencies)) . "\n";
$soilData .= "In Excess: " . (empty($excesses)     ? 'None detected' : implode(', ', $excesses))     . "\n";
$soilData .= "=====================================\n";

// ── System prompt per record type ────────────────────────────────────────────
$systemPrompts = [
    'soil' =>
        "You are a certified agronomist and soil scientist specialising in mineral soil balancing, "
        . "trained in the Albrecht method of base saturation and cation exchange chemistry. "
        . "You have deep knowledge of soil chemistry, soil biology, and the relationship between "
        . "soil mineral balance and crop productivity, livestock health, and human nutrition. "
        . "You understand Australian soil types — Vertosols, Chromosols, Sodosols, Tenosols, "
        . "Dermosols and others — and how climate and rainfall influence nutrient behaviour. "
        . "Always ground your recommendations in the measured data. "
        . "Write in a professional but accessible tone suitable for a farmer-facing report. "
        . "When knowledge passages from the Albrecht literature are provided, "
        . "prefer them over your general training — they are the authoritative reference.",

    'plant' =>
        "You are a certified agronomist specialising in plant tissue analysis and crop nutrition. "
        . "You have deep knowledge of plant physiology, nutrient uptake mechanisms, and the "
        . "relationship between tissue nutrient levels and crop yield, quality, and disease resistance. "
        . "You are familiar with the CSIRO Plant Analysis Handbook, Hill Laboratories guidelines, "
        . "and PIRSA soil and plant analysis standards used in Australia. "
        . "You understand how soil mineral imbalances, pH, and antagonisms (e.g. Ca/Mg, Zn/P, "
        . "K/Mg) translate into plant deficiency or excess symptoms. "
        . "Always base your interpretation on the measured tissue values and specified ranges. "
        . "Write in a professional but accessible tone suitable for a farmer-facing report.",

    'water' =>
        "You are a certified irrigation agronomist and water quality specialist. "
        . "You have deep knowledge of water chemistry, salinity, sodicity, and the effects of "
        . "irrigation water quality on soil structure, nutrient availability, and crop health. "
        . "You are familiar with Australian irrigation guidelines (ANZECC/ARMCANZ), SAR and "
        . "EC thresholds for different soil types and crops, and bicarbonate/carbonate effects "
        . "on calcium and magnesium availability. "
        . "Always base your interpretation on the measured water analysis values. "
        . "Write in a professional but accessible tone suitable for a farmer-facing report.",

    'animal' =>
        "You are a certified animal nutritionist and ruminant dietitian with expertise in "
        . "livestock dietary mineral balance for Australian conditions. "
        . "You have deep knowledge of macro and trace mineral requirements for cattle, sheep, "
        . "and other livestock — including the relationship between pasture/feed mineral levels "
        . "and animal health, reproduction, and production outcomes. "
        . "You understand antagonisms such as Cu/Mo/S, Se/S, Zn/Fe, and the role of "
        . "Albrecht-balanced soils in producing nutritionally complete feed. "
        . "Always base your interpretation on the measured dietary analysis values. "
        . "Write in a professional but accessible tone suitable for a farmer or veterinarian.",

    'compost' =>
        "You are a certified agronomist and composting specialist with expertise in organic "
        . "matter management, compost maturity assessment, and the use of compost to restore "
        . "soil biology and mineral balance. "
        . "You have deep knowledge of C:N ratios, microbial succession, humus formation, "
        . "and how compost inputs interact with existing soil chemistry. "
        . "You are familiar with the Elaine Ingham and Arden Anderson's compost guidelines, "
        . "You understand Australian composting standards and the role of biologically active "
        . "compost in supporting the Albrecht soil balancing philosophy. "
        . "Always base your interpretation on the measured compost analysis values. "
        . "Write in a professional but accessible tone suitable for a farmer-facing report.",
];

$system = $systemPrompts[$recordType] ?? $systemPrompts['soil'];

// ── Build analysis data block + prompts depending on record type ──────────────
$ragChunks = [];  // initialised here; populated only for soil path

if ($recordType === 'plant') {

    // ── Plant data summary ────────────────────────────────────────────────────
    $p = $row;
    $ps = $spec;

    // Spec column map (matches plant_specifications DB schema)
    $pSpecCols = [
        'n'  => ['n_min',  'n_max'],
        'p'  => ['P_Min',  'P_Max'],
        'k'  => ['K_Min',  'K_Max'],
        's'  => ['S_Min',  'S_Max'],
        'mg' => ['Mg_Min', 'Mg_Max'],
        'ca' => ['Ca_Min', 'Ca_Max'],
        'na' => ['Na_Min', 'Na_Max'],
        'fe' => ['Fe_Min', 'Fe_Max'],
        'mn' => ['Mn_Min', 'Mn_Max'],
        'zn' => ['Zn_Min', 'Zn_Max'],
        'cu' => ['Cu_Min', 'Cu_Max'],
        'b'  => ['B_Min',  'B_Max'],
        'm'  => ['M_Min',  'M_Max'],
        'co' => ['Co_min', 'Co_max'],
        'se' => ['se_min', 'se_max'],
        'cl' => ['cl_min', 'cl_max'],
        'c'  => ['c_min',  'c_max'],
    ];

    $plantElements = [
        ['n',  'Nitrogen',   '%'],
        ['p',  'Phosphorus', '%'],
        ['k',  'Potassium',  '%'],
        ['s',  'Sulfur',     '%'],
        ['mg', 'Magnesium',  '%'],
        ['ca', 'Calcium',    '%'],
        ['na', 'Sodium',     '%'],
        ['fe', 'Iron',      'ppm'],
        ['mn', 'Manganese', 'ppm'],
        ['zn', 'Zinc',      'ppm'],
        ['cu', 'Copper',    'ppm'],
        ['b',  'Boron',     'ppm'],
        ['m',  'Molybdenum','ppm'],
        ['co', 'Cobalt',    'ppm'],
        ['se', 'Selenium',  'ppm'],
        ['cl', 'Chloride',  'ppm'],
        ['c',  'Carbon',    '%'],
    ];

    $plantDeficiencies = [];
    $plantExcesses     = [];
    $elementLines      = '';

    foreach ($plantElements as [$el, $name, $unit]) {
        $val = (float)($p[$el] ?? 0);
        [$minCol, $maxCol] = $pSpecCols[$el];
        $min = (float)($ps[$minCol] ?? 0);
        $max = (float)($ps[$maxCol] ?? 0);
        $range = ($min > 0 || $max > 0)
            ? number_format($min, 3) . '–' . number_format($max, 3)
            : 'N/A';
        $found = $val > 0 ? number_format($val, 3) : 'N/A';
        $status = '';
        if ($val > 0 && ($min > 0 || $max > 0)) {
            if ($min > 0 && $val < $min) { $status = '[DEFICIENT]'; $plantDeficiencies[] = $name; }
            elseif ($max > 0 && $val > $max) { $status = '[EXCESS]'; $plantExcesses[] = $name; }
            else { $status = '[IDEAL]'; }
        }
        $elementLines .= sprintf("%-20s %s  found: %-8s  range: %-15s %s\n",
            "$name ($unit):", '', $found, $range, $status);
    }

    $plantData = "=====================================\n"
        . "PLANT TISSUE ANALYSIS — COMPLETE\n"
        . "=====================================\n"
        . "Client:       {$p['client_name']}\n"
        . "Crop Type:    {$p['crop_type']}\n"
        . "Sample ID:    {$p['sample_id']}\n"
        . "Site ID:      {$p['site_id']}\n"
        . "Lab No:       {$p['lab_no']}\n"
        . "Date Sampled: {$p['date_sampled']}\n\n"
        . "--- ELEMENT RESULTS ---\n"
        . $elementLines . "\n"
        . "Deficient: " . (empty($plantDeficiencies) ? 'None detected' : implode(', ', $plantDeficiencies)) . "\n"
        . "In Excess: " . (empty($plantExcesses)     ? 'None detected' : implode(', ', $plantExcesses))     . "\n"
        . "=====================================\n";

    $ragChunks        = retrieveRelevantChunks($pdo, $plantData, $section, RAG_TOP_K);
    $knowledgeContext = '';
    if (!empty($ragChunks)) {
        $knowledgeContext = "\n\n===================================================\n"
                          . "RELEVANT PASSAGES FROM SOIL & PLANT SCIENCE LITERATURE\n"
                          . "===================================================\n";
        foreach ($ragChunks as $i => $chunk) {
            $knowledgeContext .= sprintf("\n[%d] \"%s\" — %s (p.%d)\n%s\n",
                $i + 1, $chunk['source'], $chunk['author'], $chunk['page'], $chunk['chunk_text']);
        }
    }

    $ctx = $plantData . $knowledgeContext;

    $prompts = [
        'general' =>
            "{$system}\n\n{$ctx}\n\n"
            . "TASK: Write a concise general comment on these plant tissue analysis results (2–3 paragraphs). "
            . "Cover: (1) the overall nutritional status of the crop, "
            . "(2) the most significant deficiencies or excesses and their likely effect on crop yield and quality, "
            . "(3) any elements in good balance. Do not recommend specific product names.",

        'ai_interpretation' =>
            "{$system}\n\n{$ctx}\n\n"
            . "TASK: Write a detailed technical interpretation with these headings:\n"
            . "1. MAJOR ELEMENTS (N, P, K, S, Mg, Ca, Na)\n"
            . "2. TRACE ELEMENTS (Fe, Mn, Zn, Cu, B)\n"
            . "3. OTHER ELEMENTS (Mo, Co, Se, Cl, C)\n"
            . "4. NUTRIENT INTERACTIONS & ANTAGONISMS\n"
            . "5. OVERALL NUTRITIONAL ASSESSMENT\n"
            . "For each element marked [DEFICIENT] or [EXCESS], explain the agronomic significance, "
            . "likely causes, and interactions with other nutrients.",

        'recommended' =>
            "{$system}\n\n{$ctx}\n\n"
            . "TASK: Design a recommended remedial soil and fertiliser program to correct the deficiencies shown. "
            . "Format as a numbered list or table: "
            . "Element | Current Status | Recommended Action | Product Type (generic) | Rate | Timing. "
            . "Prioritise elements marked [DEFICIENT]. "
            . "Note any nutrient antagonisms that may be limiting uptake.",

        'foliar' =>
            "{$system}\n\n{$ctx}\n\n"
            . "TASK: Design a foliar spray program to rapidly correct deficiencies shown in the tissue test. "
            . "Format as a numbered list or table: "
            . "Growth Stage | Product Type (generic) | Active Element | Rate (L or kg/ha) | Timing. "
            . "Prioritise elements marked [DEFICIENT]. "
            . "Note carrier water pH requirements and any tank-mix incompatibilities.",
    ];

} else {

    // ── Soil: RAG + prompts ───────────────────────────────────────────────────
    $ragChunks        = retrieveRelevantChunks($pdo, $soilData, $section, RAG_TOP_K);
    $knowledgeContext = '';
    if (!empty($ragChunks)) {
        $knowledgeContext = "\n\n===================================================\n"
                          . "RELEVANT PASSAGES FROM SOIL SCIENCE LITERATURE\n"
                          . "(William A. Albrecht and other authorities)\n"
                          . "===================================================\n";
        foreach ($ragChunks as $i => $chunk) {
            $knowledgeContext .= sprintf("\n[%d] \"%s\" — %s (p.%d)\n%s\n",
                $i + 1, $chunk['source'], $chunk['author'], $chunk['page'], $chunk['chunk_text']);
        }
    }

    $ctx = $soilData . $knowledgeContext;

    $prompts = [
        'overview' =>
            "{$system}\n\n{$ctx}\n\n"
            . "TASK: Write an executive overview of these soil test results (3–4 paragraphs). "
            . "Cover: (1) overall soil health and fertility level, "
            . "(2) the most significant deficiencies or imbalances and their likely effect on crop performance, "
            . "(3) any positive attributes. "
            . "Use the Albrecht philosophy as a framework. Do not recommend specific product names.",

        'ai_interpretation' =>
            "{$system}\n\n{$ctx}\n\n"
            . "TASK: Write a detailed technical interpretation structured with these headings:\n"
            . "1. SOIL REACTION (pH, EC, Paramagnetic)\n"
            . "2. ORGANIC MATTER & BIOLOGY (C, N, C:N ratio)\n"
            . "3. CATION EXCHANGE CAPACITY & BASE SATURATIONS\n"
            . "4. MAJOR ELEMENTS (Ca, Mg, K, Na, P — ppm and saturation %)\n"
            . "5. TRACE ELEMENTS (S, B, Mn, Cu, Zn, Fe, Al, Si, Co, Mo, Se)\n"
            . "6. ELEMENTAL RATIOS & INTERACTIONS (Ca:Mg, C:N, K:Mg antagonisms)\n"
            . "7. OVERALL SOIL BALANCE ASSESSMENT\n"
            . "For each element marked [DEFICIENT] or [EXCESS], explain agronomic significance "
            . "and interactions with other elements. Reference the Albrecht literature where relevant.",

        'foliar' =>
            "{$system}\n\n{$ctx}\n\n"
            . "TASK: Design a foliar nutrition program to address the deficiencies shown. "
            . "Format as a numbered list or table: "
            . "Growth Stage | Product Type (generic) | Active Element | Rate (L or kg/ha) | Timing. "
            . "Prioritise elements marked [DEFICIENT]. "
            . "Note antagonisms (e.g. Ca/Mg competition, Zn/P, K/Mg lockout). "
            . "Add a note on carrier water pH and adjuvant recommendations.",

        'microbial' =>
            "{$system}\n\n{$ctx}\n\n"
            . "TASK: Design a biological/microbial soil improvement program. "
            . "Structure your response:\n"
            . "1. CURRENT BIOLOGY ASSESSMENT (based on OM%, C:N ratio, pH)\n"
            . "2. RECOMMENDED INOCULANTS (mycorrhizae, rhizobia, EM, compost tea etc.)\n"
            . "3. CARBON FEEDING STRATEGY (humates, fish hydrolysate, molasses, cover crops)\n"
            . "4. TIMING & INTEGRATION with the mineral balancing program\n"
            . "Reference Albrecht's work on the relationship between mineral balance and soil biology.",
    ];

}

// ── Call Ollama ───────────────────────────────────────────────────────────────
$payload = json_encode([
    'model'  => OLLAMA_MODEL,
    'prompt' => $prompts[$section],
    'stream' => false,
    'options' => [
        'temperature'    => 0.3,
        'num_predict'    => 2048,
        'num_ctx'        => 6144,
        'repeat_penalty' => 1.1,
        'keep_alive'     => -1,   // keep model resident between requests
    ],
]);

$ch = curl_init(OLLAMA_HOST . '/api/generate');
curl_setopt_array($ch, [
    CURLOPT_POST           => true,
    CURLOPT_POSTFIELDS     => $payload,
    CURLOPT_HTTPHEADER     => ['Content-Type: application/json'],
    CURLOPT_RETURNTRANSFER => true,
    CURLOPT_TIMEOUT        => OLLAMA_TIMEOUT,
    CURLOPT_CONNECTTIMEOUT => 5,
]);

$response = curl_exec($ch);
$httpCode = curl_getinfo($ch, CURLINFO_HTTP_CODE);
$curlErr  = curl_error($ch);
curl_close($ch);

if ($curlErr || $response === false) {
    http_response_code(502);
    echo json_encode(['success' => false, 'error' => 'Could not connect to Ollama: ' . ($curlErr ?: 'no response')]);
    exit;
}

if ($httpCode !== 200) {
    http_response_code(502);
    echo json_encode(['success' => false, 'error' => 'Ollama returned HTTP ' . $httpCode]);
    exit;
}

$ollamaData = json_decode($response, true);
$text = trim($ollamaData['response'] ?? '');

if ($text === '') {
    http_response_code(502);
    echo json_encode(['success' => false, 'error' => 'Ollama returned an empty response']);
    exit;
}

echo json_encode([
    'success'          => true,
    'text'             => $text,
    'rag_chunks_used'  => count($ragChunks),
]);
exit;

// ── RAG: retrieve relevant knowledge chunks from MySQL ────────────────────────

function retrieveRelevantChunks(PDO $pdo, string $queryText, string $section, int $topK): array
{
    try {
        $count = (int)$pdo->query('SELECT COUNT(*) FROM knowledge_chunks')->fetchColumn();
    } catch (PDOException $e) {
        return [];  // Table doesn't exist yet
    }

    if ($count === 0) {
        return [];  // Knowledge base not yet populated — run ingest_knowledge.php
    }

    // Try vector similarity first
    $queryEmbedding = getQueryEmbedding($queryText);
    if ($queryEmbedding !== null) {
        return vectorSearch($pdo, $queryEmbedding, $topK);
    }

    // Fallback: MySQL FULLTEXT search
    return fulltextSearch($pdo, $section, $topK);
}

function getQueryEmbedding(string $text): ?array
{
    $queryText = substr($text, 0, 2000);

    // Try new /api/embed (Ollama >= 0.1.26) first
    $ch = curl_init(OLLAMA_HOST . '/api/embed');
    curl_setopt_array($ch, [
        CURLOPT_POST           => true,
        CURLOPT_POSTFIELDS     => json_encode(['model' => EMBED_MODEL, 'input' => $queryText]),
        CURLOPT_HTTPHEADER     => ['Content-Type: application/json'],
        CURLOPT_RETURNTRANSFER => true,
        CURLOPT_TIMEOUT        => 15,
        CURLOPT_CONNECTTIMEOUT => 3,
    ]);
    $resp = curl_exec($ch);
    $code = curl_getinfo($ch, CURLINFO_HTTP_CODE);
    curl_close($ch);

    if ($resp && $code === 200) {
        $data = json_decode($resp, true);
        $emb  = $data['embeddings'][0] ?? null;
        if (is_array($emb) && count($emb) > 0) return $emb;
    }

    // Fallback: legacy /api/embeddings
    $ch = curl_init(OLLAMA_HOST . '/api/embeddings');
    curl_setopt_array($ch, [
        CURLOPT_POST           => true,
        CURLOPT_POSTFIELDS     => json_encode(['model' => EMBED_MODEL, 'prompt' => $queryText]),
        CURLOPT_HTTPHEADER     => ['Content-Type: application/json'],
        CURLOPT_RETURNTRANSFER => true,
        CURLOPT_TIMEOUT        => 15,
        CURLOPT_CONNECTTIMEOUT => 3,
    ]);
    $resp2 = curl_exec($ch);
    $code2 = curl_getinfo($ch, CURLINFO_HTTP_CODE);
    curl_close($ch);

    if ($resp2 && $code2 === 200) {
        $data2 = json_decode($resp2, true);
        $emb2  = $data2['embedding'] ?? null;
        if (is_array($emb2) && count($emb2) > 0) return $emb2;
    }

    return null;
}

function vectorSearch(PDO $pdo, array $queryVec, int $topK): array
{
    $stmt   = $pdo->query('SELECT id, source, author, page, chunk_text, embedding FROM knowledge_chunks');
    $scores = [];

    while ($row = $stmt->fetch(PDO::FETCH_ASSOC)) {
        $chunkVec = json_decode($row['embedding'], true);
        if (!is_array($chunkVec)) continue;
        $scores[] = [
            'score'      => cosineSimilarity($queryVec, $chunkVec),
            'source'     => $row['source'],
            'author'     => $row['author'],
            'page'       => $row['page'],
            'chunk_text' => $row['chunk_text'],
        ];
    }

    usort($scores, fn($a, $b) => $b['score'] <=> $a['score']);
    return array_slice($scores, 0, $topK);
}

function fulltextSearch(PDO $pdo, string $section, int $topK): array
{
    $keywords = [
        'overview'          => 'soil fertility mineral balance calcium magnesium albrecht',
        'ai_interpretation' => 'base saturation calcium magnesium potassium pH organic matter',
        'foliar'            => 'foliar nutrition trace elements deficiency correction spray',
        'microbial'         => 'soil biology microbial organic matter carbon nitrogen humus',
    ];
    $query = $keywords[$section] ?? 'soil fertility mineral nutrition';

    try {
        $stmt = $pdo->prepare(
            'SELECT source, author, page, chunk_text,
                    MATCH(chunk_text) AGAINST(? IN NATURAL LANGUAGE MODE) AS score
             FROM knowledge_chunks
             WHERE MATCH(chunk_text) AGAINST(? IN NATURAL LANGUAGE MODE)
             ORDER BY score DESC
             LIMIT ?'
        );
        $stmt->execute([$query, $query, $topK]);
        return $stmt->fetchAll(PDO::FETCH_ASSOC);
    } catch (PDOException $e) {
        error_log('RAG fulltext search failed: ' . $e->getMessage());
        return [];
    }
}

function cosineSimilarity(array $a, array $b): float
{
    $dot = $normA = $normB = 0.0;
    $len = min(count($a), count($b));
    for ($i = 0; $i < $len; $i++) {
        $dot   += $a[$i] * $b[$i];
        $normA += $a[$i] * $a[$i];
        $normB += $b[$i] * $b[$i];
    }
    $denom = sqrt($normA) * sqrt($normB);
    return $denom > 0 ? $dot / $denom : 0.0;
}