Deep Research: NDJSON streaming so the connection survives long runs

Previously the endpoint returned a single JSON object at the end. Apache+
PHP-FPM buffers the entire body until PHP exits, so a 160s azure_full run
caused the browser to drop the fetch as "Failed to fetch" while the server
was still synthesising — the response then arrived to a dead socket.

Switch to application/x-ndjson with one event per line. The endpoint emits
'progress', 'start', 'step' (running/complete/warning/error), 'subq', and a
final 'final' event carrying the full result payload. Output buffering is
explicitly disabled so each line flushes through Apache as soon as the
agent emits it.

DbnDeepResearchAgent::run() now accepts an optional ?callable $emit and
fires step:running before each step + step:complete after, plus a subq
event per sub-question retrieval round.

JS reads response.body as a stream, splits on newlines, updates the
trace panel live, and renders the final result when the final event
arrives. Status pill shows live progress detail (e.g. "Synthesising with
Azure gpt-4o — this is the slowest step…").

Engine row in the form now shows expected duration per engine
(~15-45s mini, ~60-180s full, ~30-90s GPU) so users know what they're in
for before clicking Run.

api/deep-research.php

@@ -7,35 +7,72 @@ require_once __DIR__ . '/../includes/DeepResearchAgent.php';
 dbnToolsRequireMethod('POST');
 dbnToolsRequireAuth();
 
-$isMultipart = stripos((string)($_SERVER['CONTENT_TYPE'] ?? ''), 'multipart/form-data') !== false;
+// Stream-friendly response — defeat output buffering so the user's browser
+// receives progress events while the agent runs (can take 60-180s for
+// gpt-4o synthesis or multi-file ingest).
+@ini_set('output_buffering', '0');
+@ini_set('zlib.output_compression', '0');
+@ini_set('implicit_flush', '1');
+while (ob_get_level() > 0) { @ob_end_clean(); }
+ob_implicit_flush(true);
 
-if ($isMultipart) {
-    $payloadRaw = (string)($_POST['payload'] ?? '');
-    if ($payloadRaw === '') {
-        dbnToolsError('Multipart request is missing the "payload" JSON field.', 422, 'missing_payload');
+header('Content-Type: application/x-ndjson; charset=utf-8');
+header('Cache-Control: no-store');
+header('X-Accel-Buffering: no');
+
+$language = 'en';
+$startTime = microtime(true);
+
+$emit = function (string $event, array $payload = []) use ($startTime): void {
+    $payload['event'] = $event;
+    $payload['t_ms'] = (int)round((microtime(true) - $startTime) * 1000);
+    echo json_encode($payload, JSON_UNESCAPED_UNICODE | JSON_UNESCAPED_SLASHES) . "\n";
+    @flush();
+};
+
+try {
+    $isMultipart = stripos((string)($_SERVER['CONTENT_TYPE'] ?? ''), 'multipart/form-data') !== false;
+    if ($isMultipart) {
+        $payloadRaw = (string)($_POST['payload'] ?? '');
+        if ($payloadRaw === '') {
+            throw new DbnToolsHttpException('Multipart request missing payload.', 422, 'missing_payload');
+        }
+        $input = json_decode($payloadRaw, true);
+        if (!is_array($input)) {
+            throw new DbnToolsHttpException('Invalid payload JSON.', 422, 'invalid_payload_json');
+        }
+    } else {
+        $raw = file_get_contents('php://input');
+        if ($raw === false || strlen($raw) > 120000) {
+            throw new DbnToolsHttpException('Request body unreadable or too large.', 413, 'body_too_large');
+        }
+        $input = json_decode((string)$raw, true);
+        if (!is_array($input)) {
+            throw new DbnToolsHttpException('Request body must be valid JSON.', 400, 'invalid_json');
+        }
     }
-    $input = json_decode($payloadRaw, true);
-    if (!is_array($input)) {
-        dbnToolsError('Multipart "payload" field must be valid JSON.', 422, 'invalid_payload_json');
-    }
-} else {
-    $input = dbnToolsJsonInput(120000);
-}
 
-$language = dbnToolsNormalizeLanguage($input['language'] ?? 'en');
-
-dbnToolsWithTelemetry('deep_research', $language, function () use ($input, $language) {
-    $seedQuery   = dbnToolsString($input, 'query', 4000, false);
-    $pastedText  = dbnToolsString($input, 'paste_text', 64000, false);
-    $sliceInput  = $input['slices'] ?? null;
+    $language    = dbnToolsNormalizeLanguage($input['language'] ?? 'en');
+    $seedQuery   = trim((string)($input['query'] ?? ''));
+    $pastedText  = trim((string)($input['paste_text'] ?? ''));
+    $sliceInput  = $input['slices'] ?? [];
     $engine      = (string)($input['engine'] ?? 'azure_mini');
     $controls    = is_array($input['controls'] ?? null) ? $input['controls'] : [];
 
+    if (mb_strlen($seedQuery, 'UTF-8') > 4000) {
+        throw new DbnToolsHttpException('Query is too long.', 422, 'query_too_long');
+    }
+    if (mb_strlen($pastedText, 'UTF-8') > 64000) {
+        throw new DbnToolsHttpException('Pasted text is too long.', 422, 'paste_too_long');
+    }
+
+    $emit('progress', ['detail' => 'Reading upload(s)…']);
+
     $uploadedFiles = [];
     if (!empty($_FILES['files']) && is_array($_FILES['files']['tmp_name'] ?? null)) {
         $count = count($_FILES['files']['tmp_name']);
         if ($count > 5) {
-            dbnToolsAbort('At most 5 files can be uploaded per request.', 413, 'too_many_files');
+            throw new DbnToolsHttpException('At most 5 files can be uploaded per request.', 413, 'too_many_files');
         }
         for ($i = 0; $i < $count; $i++) {
             $file = [
@@ -52,16 +89,67 @@ dbnToolsWithTelemetry('deep_research', $language, function () use ($input, $lang
                 'chars'     => $extracted['chars'],
                 'truncated' => $extracted['truncated'],
             ];
+            $emit('progress', [
+                'detail' => sprintf('Extracted %s (%d chars%s)',
+                    $extracted['filename'],
+                    $extracted['chars'],
+                    !empty($extracted['truncated']) ? ', truncated' : ''
+                ),
+            ]);
         }
     }
 
-    return (new DbnDeepResearchAgent())->run(
+    $emit('start', [
+        'engine' => $engine,
+        'language' => $language,
+        'upload_count' => count($uploadedFiles),
+    ]);
+
+    $result = (new DbnDeepResearchAgent())->run(
         $seedQuery,
         $pastedText,
         $uploadedFiles,
         is_array($sliceInput) ? $sliceInput : [],
         $engine,
         $language,
-        $controls
+        $controls,
+        $emit
     );
-});
+
+    $result['ok'] = true;
+    $result['latency_ms'] = (int)round((microtime(true) - $startTime) * 1000);
+
+    dbnToolsLogMetadata([
+        'tool'         => 'deep_research',
+        'language'     => $language,
+        'ok'           => true,
+        'latency_ms'   => $result['latency_ms'],
+        'chunk_count'  => (int)($result['trace_metadata']['chunk_count'] ?? 0),
+        'source_count' => (int)($result['trace_metadata']['source_count'] ?? 0),
+        'deployment'   => $result['trace_metadata']['deployment'] ?? null,
+    ]);
+
+    $emit('final', ['result' => $result]);
+
+} catch (DbnToolsHttpException $e) {
+    $latency = (int)round((microtime(true) - $startTime) * 1000);
+    dbnToolsLogMetadata([
+        'tool'       => 'deep_research',
+        'language'   => $language,
+        'ok'         => false,
+        'latency_ms' => $latency,
+        'error_code' => $e->errorCode,
+    ]);
+    $emit('error', ['code' => $e->errorCode, 'message' => $e->getMessage(), 'status' => $e->status]);
+} catch (Throwable $e) {
+    error_log('DBN deep research fatal: ' . $e->getMessage());
+    $latency = (int)round((microtime(true) - $startTime) * 1000);
+    dbnToolsLogMetadata([
+        'tool'       => 'deep_research',
+        'language'   => $language,
+        'ok'         => false,
+        'latency_ms' => $latency,
+        'error_code' => 'internal_error',
+    ]);
+    $emit('error', ['code' => 'internal_error', 'message' => 'The agent could not complete this request.']);
+}

assets/js/deep-research.js

@@ -232,27 +232,38 @@
       return;
     }
 
-    setStatus('Running deep research…', 'busy');
-    els.runButton.disabled = true;
-    els.results.innerHTML = `<div class="empty-state"><h3>Working…</h3><p>The agent is expanding the question, retrieving from the corpus, and synthesising the brief. This usually takes 6–15 seconds.</p></div>`;
+    const engine = getEngine();
+    const expectedDuration = engine === 'azure_full'
+      ? '60–180 seconds with Azure gpt-4o'
+      : (engine === 'gpu' ? '30–90 seconds on GPU' : '15–45 seconds with Azure gpt-4o-mini');
 
-    // Render placeholder trace with first step running
-    const placeholder = STEP_LABELS.map((label, i) => ({
-      label,
-      detail: i === 0 ? 'Running…' : 'Queued',
-      status: i === 0 ? 'running' : 'idle',
-    }));
-    renderTrace(placeholder);
+    setStatus(`Running deep research… (${expectedDuration})`, 'busy');
+    els.runButton.disabled = true;
+    els.results.innerHTML = `<div class="empty-state"><h3>Working…</h3><p>The agent is expanding your question and researching the corpus. Live progress in the right-hand panel. Expect ${expectedDuration}.</p></div>`;
+
+    // Initialise the trace with all 7 steps as 'idle'
+    const stepState = STEP_LABELS.map((label) => ({ label, detail: 'Queued', status: 'idle' }));
+    renderTrace(stepState);
 
     const payload = {
       query,
       paste_text: '',
       slices,
-      engine: getEngine(),
+      engine,
       language: lang,
       controls: getControls(),
     };
 
+    const stepKeyToIndex = {
+      interpretation: 0,
+      expansion: 1,
+      slice_resolution: 2,
+      upload_indexing: 3,
+      retrieval: 4,
+      synthesis: 5,
+      confidence: 6,
+    };
+
     let response;
     try {
       if (uploadFiles.length > 0) {
@@ -271,25 +282,113 @@
     } catch (err) {
       setStatus(`Network error: ${err.message || err}`, 'error');
       els.runButton.disabled = false;
+      stepState[0] = { ...stepState[0], status: 'error', detail: String(err) };
+      renderTrace(stepState);
       return;
     }
 
-    let data = null;
-    try { data = await response.json(); } catch (_) {}
-
-    if (!response.ok || !data || data.ok === false) {
-      const msg = (data && data.error && data.error.message) || `Request failed (${response.status}).`;
-      setStatus(msg, 'error');
+    if (!response.ok || !response.body) {
+      setStatus(`Request failed (${response.status}).`, 'error');
       els.runButton.disabled = false;
-      renderTrace(placeholder.map((s, i) => i === 0 ? { ...s, status: 'error', detail: msg } : s));
       return;
     }
 
-    lastResult = data;
-    setStatus(`Done in ${data.latency_ms || 0} ms · ${data.trace_metadata?.source_count || 0} sources · confidence ${data.trace_metadata?.citation_confidence || '?'}`, 'ok');
+    // Read the NDJSON stream
+    const reader = response.body.getReader();
+    const decoder = new TextDecoder('utf-8');
+    let buffer = '';
+    let finalResult = null;
+    let errorEvent = null;
+    let progressDetail = '';
+
+    while (true) {
+      let chunk;
+      try {
+        chunk = await reader.read();
+      } catch (err) {
+        setStatus(`Stream error: ${err.message || err}`, 'error');
+        els.runButton.disabled = false;
+        return;
+      }
+      const { done, value } = chunk;
+      if (value) {
+        buffer += decoder.decode(value, { stream: true });
+        const lines = buffer.split('\n');
+        buffer = lines.pop();
+        for (const line of lines) {
+          const trimmed = line.trim();
+          if (!trimmed) continue;
+          let evt;
+          try { evt = JSON.parse(trimmed); } catch (_) { continue; }
+          handleStreamEvent(evt);
+        }
+      }
+      if (done) break;
+    }
+
+    if (errorEvent) {
+      setStatus(`${errorEvent.code}: ${errorEvent.message}`, 'error');
+      els.runButton.disabled = false;
+      // Mark the currently-running step as error
+      const runningIdx = stepState.findIndex((s) => s.status === 'running');
+      if (runningIdx >= 0) {
+        stepState[runningIdx] = { ...stepState[runningIdx], status: 'error', detail: errorEvent.message };
+        renderTrace(stepState);
+      }
+      return;
+    }
+
+    if (!finalResult) {
+      setStatus('Stream ended without a final result.', 'error');
+      els.runButton.disabled = false;
+      return;
+    }
+
+    lastResult = finalResult;
+    const meta = finalResult.trace_metadata || {};
+    setStatus(
+      `Done in ${Math.round((finalResult.latency_ms || 0) / 1000)} s · ${meta.source_count || 0} sources · confidence ${meta.citation_confidence || '?'}`,
+      'ok'
+    );
     els.runButton.disabled = false;
-    renderTrace(data.trace || []);
-    renderResults(data);
+    renderTrace(finalResult.trace || []);
+    renderResults(finalResult);
+
+    function handleStreamEvent(evt) {
+      if (!evt || !evt.event) return;
+      if (evt.event === 'progress') {
+        progressDetail = evt.detail || '';
+        if (progressDetail) setStatus(progressDetail, 'busy');
+        return;
+      }
+      if (evt.event === 'start') {
+        setStatus(`Running… engine=${evt.engine}, uploads=${evt.upload_count || 0}`, 'busy');
+        return;
+      }
+      if (evt.event === 'step') {
+        const idx = stepKeyToIndex[evt.step];
+        if (idx === undefined) return;
+        stepState[idx] = {
+          label: evt.label || stepState[idx].label,
+          detail: evt.detail || stepState[idx].detail,
+          status: evt.status || stepState[idx].status,
+        };
+        renderTrace(stepState);
+        return;
+      }
+      if (evt.event === 'subq') {
+        setStatus(`Retrieving sub-question ${evt.index}/${evt.total}: ${evt.question.slice(0, 80)}${evt.question.length > 80 ? '…' : ''}`, 'busy');
+        return;
+      }
+      if (evt.event === 'final') {
+        finalResult = evt.result;
+        return;
+      }
+      if (evt.event === 'error') {
+        errorEvent = evt;
+        return;
+      }
+    }
   }
 
   function setStatus(message, kind) {

deep-research.php

@@ -16,11 +16,11 @@ require_once __DIR__ . '/includes/layout.php';
 
                     <div class="control-row" id="drEngineControl">
                         <span class="control-label">Engine</span>
-                        <label><input type="radio" name="drEngine" value="azure_mini" checked> Azure gpt-4o-mini &#9733; <small class="control-hint">(fast)</small></label>
-                        <label><input type="radio" name="drEngine" value="azure_full"> Azure gpt-4o <small class="control-hint">(best)</small></label>
-                        <label><input type="radio" name="drEngine" value="gpu"> GPU (cuttlefish) <small class="control-hint">(local)</small></label>
+                        <label><input type="radio" name="drEngine" value="azure_mini" checked> Azure gpt-4o-mini &#9733; <small class="control-hint">(~15-45s)</small></label>
+                        <label><input type="radio" name="drEngine" value="azure_full"> Azure gpt-4o <small class="control-hint">(best · ~60-180s)</small></label>
+                        <label><input type="radio" name="drEngine" value="gpu"> GPU (cuttlefish) <small class="control-hint">(local · ~30-90s)</small></label>
                     </div>
-                    <p class="upload-hint">Azure engines use your BNL Azure credits. GPU runs qwen2.5:14b via LiteLLM on cuttlefish.</p>
+                    <p class="upload-hint">Azure mini is the default and finishes fastest. Azure full is the most thorough but can take 1-3 minutes. GPU keeps everything inside the BNL fleet. Live progress shown in the right-hand reasoning panel.</p>
 
                     <div class="dr-slice-section">
                         <p class="control-label">Corpus slices</p>

includes/DeepResearchAgent.php

@@ -30,7 +30,8 @@ final class DbnDeepResearchAgent
         array  $sliceSelection,
         string $engine,
         string $language,
-        array  $controls
+        array  $controls,
+        ?callable $emit = null
     ): array {
         $seedQuery   = trim($seedQuery);
         $pastedText  = trim($pastedText);
@@ -58,31 +59,49 @@ final class DbnDeepResearchAgent
         $trace = [];
         $seedDescription = $this->buildSeedDescription($seedQuery, $pastedText, $uploadedFiles);
 
-        // STEP 1: Query interpretation — build research brief
+        $emitStep = function (string $stepId, string $label, string $detail, string $status) use (&$trace, $emit): void {
+            $trace[] = $this->trace($label, $detail, $status);
+            if ($emit) {
+                $emit('step', [
+                    'step'   => $stepId,
+                    'label'  => $label,
+                    'detail' => $detail,
+                    'status' => $status,
+                ]);
+            }
+        };
+        $emitRunning = function (string $stepId, string $label, string $detail = 'Running…') use ($emit): void {
+            if ($emit) {
+                $emit('step', [
+                    'step'   => $stepId,
+                    'label'  => $label,
+                    'detail' => $detail,
+                    'status' => 'running',
+                ]);
+            }
+        };
+
+        // STEP 1: Query interpretation
+        $emitRunning('interpretation', 'Query interpretation', 'Summarising the seed input…');
         $stepStart = microtime(true);
         $interpretation = $this->interpretSeed($seedDescription, $language);
         $this->stepTimings['interpretation'] = $this->elapsedMs($stepStart);
-        $trace[] = $this->trace(
-            'Query interpretation',
-            $interpretation['detail'],
-            'complete'
-        );
+        $emitStep('interpretation', 'Query interpretation', $interpretation['detail'], 'complete');
 
         // STEP 2: Query expansion
+        $emitRunning('expansion', 'Query expansion', 'Generating sub-questions…');
         $stepStart = microtime(true);
         $expansion = $this->expandQueries($seedDescription, $interpretation['brief'], $controls['sub_q_count'], $language);
         $this->stepTimings['expansion'] = $this->elapsedMs($stepStart);
         $subQuestions = $expansion['questions'];
         $expansionStatus = $expansion['fallback'] ? 'warning' : 'complete';
-        $trace[] = $this->trace(
-            'Query expansion',
-            $expansion['fallback']
-                ? 'Could not parse sub-questions; falling back to retrieving on the seed query alone.'
-                : sprintf('Generated %d sub-questions to research the corpus from multiple angles.', count($subQuestions)),
-            $expansionStatus
-        );
+        $expansionDetail = $expansion['fallback']
+            ? 'Could not parse sub-questions; falling back to retrieving on the seed query alone.'
+            : sprintf('Generated %d sub-questions to research the corpus from multiple angles.', count($subQuestions));
+        $emitStep('expansion', 'Query expansion', $expansionDetail, $expansionStatus);
 
         // STEP 3: Slice resolution
+        $emitRunning('slice_resolution', 'Slice resolution', 'Resolving slice toggles to document IDs…');
         $stepStart = microtime(true);
         $sliceSelectionNormalized = dbnV6NormalizeSliceSelection($sliceSelection);
         if (!array_filter($sliceSelectionNormalized)) {
@@ -104,9 +123,12 @@ final class DbnDeepResearchAgent
             $sliceDetail = 'Slice resolution failed; corpus search will run unconstrained.';
         }
         $this->stepTimings['slice_resolution'] = $this->elapsedMs($stepStart);
-        $trace[] = $this->trace('Slice resolution', $sliceDetail, $sliceStatus);
+        $emitStep('slice_resolution', 'Slice resolution', $sliceDetail, $sliceStatus);
 
         // STEP 4: Upload indexing (in-memory, ephemeral)
+        $emitRunning('upload_indexing', 'Upload indexing', empty($uploadedFiles)
+            ? 'No uploads; skipping…'
+            : sprintf('Chunking + embedding %d file(s) in memory…', count($uploadedFiles)));
         $stepStart = microtime(true);
         $uploadChunks = [];
         foreach ($uploadedFiles as $idx => $file) {
@@ -141,15 +163,16 @@ final class DbnDeepResearchAgent
             $uploadDetail = 'No files uploaded; agent will research the corpus only.';
         }
         $this->stepTimings['upload_indexing'] = $this->elapsedMs($stepStart);
-        $trace[] = $this->trace('Upload indexing', $uploadDetail, $uploadStatus);
+        $emitStep('upload_indexing', 'Upload indexing', $uploadDetail, $uploadStatus);
 
         // STEP 5: Retrieval (per sub-question)
-        $stepStart = microtime(true);
         $retrievalQueries = $subQuestions ?: [[
             'id'        => 'q1',
             'question'  => $seedQuery !== '' ? $seedQuery : ($interpretation['brief'] ?: 'legal research'),
             'rationale' => 'Seed query (no sub-question expansion).',
         ]];
+        $emitRunning('retrieval', 'Retrieval', sprintf('Hybrid vector + keyword + rerank across %d sub-question(s)…', count($retrievalQueries)));
+        $stepStart = microtime(true);
 
         try {
             $rag = new ClientRagPipeline((int)$client['id'], 'http://10.0.1.10:4000', 60);
@@ -159,7 +182,15 @@ final class DbnDeepResearchAgent
 
         $rawPool = [];
         $retrievalWarnings = 0;
-        foreach ($retrievalQueries as $sq) {
+        foreach ($retrievalQueries as $idx => $sq) {
+            if ($emit) {
+                $emit('subq', [
+                    'index'    => $idx + 1,
+                    'total'    => count($retrievalQueries),
+                    'id'       => $sq['id'],
+                    'question' => $sq['question'],
+                ]);
+            }
             try {
                 $corpusChunks = $rag->searchAll(
                     $sq['question'],
@@ -197,22 +228,21 @@ final class DbnDeepResearchAgent
         $merged = $this->mergeAndDedupe($rawPool, self::POOL_CAP);
         $this->stepTimings['retrieval'] = $this->elapsedMs($stepStart);
         $retrievalStatus = $retrievalWarnings > 0 ? 'warning' : 'complete';
-        $trace[] = $this->trace(
-            'Retrieval',
-            sprintf(
-                '%d sub-question(s) × hybrid + RRF + rerank → %d raw chunks → %d unique after dedupe.',
-                count($retrievalQueries),
-                count($rawPool),
-                count($merged)
-            ),
-            $retrievalStatus
+        $retrievalDetail = sprintf(
+            '%d sub-question(s) × hybrid + RRF + rerank → %d raw chunks → %d unique after dedupe.',
+            count($retrievalQueries),
+            count($rawPool),
+            count($merged)
         );
+        $emitStep('retrieval', 'Retrieval', $retrievalDetail, $retrievalStatus);
 
         // Cap pool to reranker top-K for synthesis
         $synthesisPool = array_slice($merged, 0, $controls['reranker_top_k']);
         $numberedSources = $this->numberSources($synthesisPool);
 
         // STEP 6: Synthesis
+        $synthesisEngineLabel = $engine === 'azure_full' ? 'Azure gpt-4o' : ($engine === 'gpu' ? 'GPU qwen2.5:14b' : 'Azure gpt-4o-mini');
+        $emitRunning('synthesis', 'Synthesis', sprintf('Synthesising cited brief with %s — this is the slowest step…', $synthesisEngineLabel));
         $stepStart = microtime(true);
         $synthesis = $this->synthesise(
             $seedDescription,
@@ -224,7 +254,8 @@ final class DbnDeepResearchAgent
             $controls['temperature']
         );
         $this->stepTimings['synthesis'] = $this->elapsedMs($stepStart);
-        $trace[] = $this->trace(
+        $emitStep(
+            'synthesis',
             'Synthesis',
             sprintf('%s synthesised the brief using %d grounded source(s).', $synthesis['deploy_label'], count($numberedSources)),
             'complete'
@@ -232,7 +263,8 @@ final class DbnDeepResearchAgent
 
         // STEP 7: Confidence
         $confidence = $this->citationConfidence($numberedSources);
-        $trace[] = $this->trace(
+        $emitStep(
+            'confidence',
             'Citation confidence',
             sprintf('%s confidence based on %d source(s) and reranker score distribution.', ucfirst($confidence), count($numberedSources)),
             $confidence === 'low' ? 'warning' : 'complete'