jonathanvajda · jonathanvajda · Apr 23, 2026 · Mar 24, 2026 · Mar 24, 2026 · Mar 24, 2026
diff --git a/LICENSE b/LICENSE
diff --git a/public/analyst-workflow.html b/public/analyst-workflow.html
@@ -0,0 +1,153 @@
+<!doctype html>
+<html lang="en">
+<head>
+<meta charset="utf-8" />
+<meta name="viewport" content="width=device-width, initial-scale=1" />
+<title>Analytic Workflow Builder – Clean Layout</title>
+<style>
+:root {
+  --bg:#f5f7fa; --panel:#fff; --border:#d0d7e2; --text:#1f2937; --muted:#6b7280;
+  --accent:#3b5b86; --accent-soft:#eaf0f8; --radius:12px; --gap:14px;
+}
+body { margin:0; font-family:system-ui, sans-serif; background:var(--bg); color:var(--text);} 
+.page { max-width:1400px; margin:auto; padding:16px; }
+.header { display:flex; justify-content:space-between; align-items:center; margin-bottom:12px; }
+.tabs { display:flex; gap:8px; margin-bottom:12px; }
+.tab { padding:8px 12px; border:1px solid var(--border); border-radius:8px; cursor:pointer; background:var(--panel);} 
+.tab.active { background:var(--accent); color:#fff; }
+.layout { display:grid; grid-template-columns:240px 1fr 320px; gap:var(--gap); }
+.panel { background:var(--panel); border:1px solid var(--border); border-radius:var(--radius); padding:12px; }
+.hidden { display:none; }
+.step { border:1px dashed var(--border); padding:10px; border-radius:8px; margin-bottom:10px; }
+.bottom-drawer { margin-top:12px; border:1px solid var(--border); border-radius:var(--radius); padding:12px; background:var(--panel);} 
+button { padding:6px 10px; border-radius:6px; border:1px solid var(--border); cursor:pointer; }
+.primary { background:var(--accent); color:white; border-color:var(--accent);} 
+</style>
+</head>
+<body>
+<div class="page">
+
+<div class="header">
+  <div>
+    <h2 style="margin:0;">Analytic Workflow Builder</h2>
+    <small class="muted">Build, manage, and run conditional query pipelines</small>
+  </div>
+  <div>
+    <button>Save</button>
+    <button>Export</button>
+    <button class="primary">Run</button>
+  </div>
+</div>
+
+<div class="tabs">
+  <div class="tab active" onclick="showTab('pipelines')">Pipelines</div>
+  <div class="tab" onclick="showTab('data')">Data</div>
+  <div class="tab" onclick="showTab('queries')">Queries</div>
+  <div class="tab" onclick="showTab('run')">Run</div>
+</div>
+
+<!-- PIPELINES -->
+<div id="pipelines" class="tab-content">
+  <div class="layout">
+
+    <!-- LEFT: Pipeline list -->
+    <div class="panel">
+      <strong>Pipelines</strong>
+      <div class="step">QA Review</div>
+      <div class="step">Lead Expansion</div>
+      <div class="step">Data Transformation</div>
+      <button style="margin-top:8px;">+ New</button>
+    </div>
+
+    <!-- CENTER: Steps -->
+    <div class="panel">
+      <div style="display:flex; justify-content:space-between;">
+        <strong>Workflow Steps</strong>
+        <button onclick="addStep()">+ Add Step</button>
+      </div>
+
+      <div class="step" onclick="selectStep(this)">
+        step_1 · ASK → true/false
+      </div>
+      <div class="step" onclick="selectStep(this)">
+        step_2 · SELECT → rows/no rows
+      </div>
+
+    </div>
+
+    <!-- RIGHT: Inspector -->
+    <div id="inspector" class="panel hidden">
+      <strong>Step Inspector</strong>
+      <div style="margin-top:10px;">
+        <label>Step ID</label>
+        <div class="panel">step_1</div>
+      </div>
+      <div style="margin-top:10px;">
+        <label>Query</label>
+        <div class="panel">qa_has_version_iri</div>
+      </div>
+      <div style="margin-top:10px;">
+        <label>Branching</label>
+        <div class="panel">true → step_2<br>false → step_3</div>
+      </div>
+    </div>
+
+  </div>
+</div>
+
+<!-- DATA -->
+<div id="data" class="tab-content hidden">
+  <div class="panel">
+    <strong>Data Management</strong>
+    <p class="muted">Load RDF into IndexedDB and inspect graphs.</p>
+    <button>Upload RDF</button>
+    <button>View Graphs</button>
+  </div>
+</div>
+
+<!-- QUERIES -->
+<div id="queries" class="tab-content hidden">
+  <div class="panel">
+    <strong>Query Registry</strong>
+    <div class="step">qa_has_version_iri (ASK)</div>
+    <div class="step">select_associates (SELECT)</div>
+    <div class="step">construct_roles (CONSTRUCT)</div>
+  </div>
+</div>
+
+<!-- RUN -->
+<div id="run" class="tab-content hidden">
+  <div class="panel">
+    <strong>Run Pipeline</strong>
+    <p>Select dataset and execute pipeline.</p>
+    <button class="primary">Run</button>
+  </div>
+
+  <div class="bottom-drawer">
+    <strong>Execution Trace</strong>
+    <p class="muted">Appears after run</p>
+  </div>
+</div>
+
+</div>
+
+<script>
+function showTab(id) {
+  document.querySelectorAll('.tab-content').forEach(el => el.classList.add('hidden'));
+  document.getElementById(id).classList.remove('hidden');
+
+  document.querySelectorAll('.tab').forEach(t => t.classList.remove('active'));
+  event.target.classList.add('active');
+}
+
+function selectStep(el) {
+  document.getElementById('inspector').classList.remove('hidden');
+}
+
+function addStep() {
+  alert('Add step UI goes here');
+}
+</script>
+
+</body>
+</html>
diff --git a/public/app/axiolotl-inference.js b/public/app/axiolotl-inference.js
@@ -116,6 +116,36 @@ function quadKey(q) {
   ].join('¦');
 }
 
+function quadHasBlankNode(q) {
+  return q.subject.termType === 'BlankNode' ||
+         q.object.termType === 'BlankNode' ||
+         q.graph.termType === 'BlankNode';
+}
+
+function looseQuadKey(q) {
+  const subj =
+    q.subject.termType === 'BlankNode'
+      ? 'BlankNode:_'
+      : `${q.subject.termType}:${q.subject.value}`;
+
+  const obj =
+    q.object.termType === 'BlankNode'
+      ? 'BlankNode:_'
+      : `${q.object.termType}:${q.object.value}:${q.object.language || ''}:${q.object.datatype?.value || ''}`;
+
+  const graph =
+    q.graph.termType === 'BlankNode'
+      ? 'BlankNode:_'
+      : `${q.graph.termType}:${q.graph.value || ''}`;
+
+  return [
+    subj,
+    `${q.predicate.termType}:${q.predicate.value}`,
+    obj,
+    graph
+  ].join('¦');
+}
+
 function canBeSubject(term) {
   return !!term && (term.termType === 'NamedNode' || term.termType === 'BlankNode');
 }
@@ -412,7 +442,7 @@ async function inferUntilStable(rules) {
   // ---- 3) Seed closures from existing dataset ----
   let totalAdded = 0;
   let pass = 0;
-  const MAX_PASSES = 100;
+  const MAX_PASSES = 30;
 
   const seedSeenBefore = seen.size;
   processQueues();
@@ -421,6 +451,11 @@ async function inferUntilStable(rules) {
 
   inferenceInfo(`[inferUntilStable] Seed closures added ${seedAdded} triples.`);
 
+  const rulesFiltered = rules.filter(r => r !== 'subclassof' && r !== 'subpropertyof');
+  if (rules.length !== rulesFiltered.length) {
+    inferenceInfo('[inferUntilStable] SPARQL disabled for subclassof/subpropertyof; using JS closures instead.');
+  }
+
   let changed = true;
 
   while (changed) {
@@ -434,17 +469,19 @@ async function inferUntilStable(rules) {
 
     inferenceInfo(`[inferUntilStable] Starting pass ${pass}...`);
 
-    const rulesFiltered = rules.filter(r => r !== 'subclassof' && r !== 'subpropertyof');
-    if (rules.length !== rulesFiltered.length) {
-      inferenceInfo('[inferUntilStable] Skipping SPARQL for subclassof/subpropertyof (handled by JS closures)');
-    }
-
     for (const rule of rulesFiltered) {
       const constructQuery = getConstructQueryForRule(rule);
       if (!constructQuery) continue;
 
       const newQuads = await runRuleOnce(rule, rdfjsStore);
 
+      const blankCount = newQuads.filter(quadHasBlankNode).length;
+      const looseCount = new Set(newQuads.map(looseQuadKey)).size;
+
+      inferenceInfo(
+        `[inferUntilStable] Pass ${pass}, rule "${rule}": raw=${newQuads.length}, withBlank=${blankCount}, looseUnique=${looseCount}`
+      );
+
       const batch = [];
       const batchSeen = new Set();
       for (const q of newQuads) {
@@ -460,26 +497,30 @@ async function inferUntilStable(rules) {
 
       const beforeClosure = seen.size;
       processQueues();
-      const closureAdded = seen.size - beforeClosure;
+      const propagatedAdded = seen.size - beforeClosure;
 
-      const ruleAdded = directAdded + closureAdded;
-      passAdded += ruleAdded;
+      const totalRuleAdded = directAdded + propagatedAdded;
 
       inferenceInfo(
-        `[inferUntilStable] Pass ${pass}, rule "${rule}": direct=${directAdded}, propagated=${closureAdded}, total=${ruleAdded}`
+        `[inferUntilStable] Pass ${pass}, rule "${rule}": direct=${directAdded}, propagated=${propagatedAdded}, total=${totalRuleAdded}`
       );
+
+      if (totalRuleAdded > 0) {
+        passAdded += totalRuleAdded;
+        totalAdded += totalRuleAdded;
+        changed = true;
+      }
     }
 
     if (passAdded > 0) {
-      totalAdded += passAdded;
-      changed = true;
       inferenceInfo(`[inferUntilStable] Completed pass ${pass}: added ${passAdded} triples.`);
     } else {
       inferenceInfo(`[inferUntilStable] Completed pass ${pass}: no new triples. Stable.`);
     }
   }
 
   const overlayCount = overlayStore.getQuads(null, null, null, null).length;
+
   inferenceInfo(
     `[inferUntilStable] Completed inference. Passes=${pass}, total new triples=${totalAdded}, overlay triples=${overlayCount}`
   );

diff --git a/public/app/axiolotl-query.js b/public/app/axiolotl-query.js
@@ -22,8 +22,6 @@
     //  toastSuccess
     //  toastError
     //  commonSPARQLPrefixes
-    //  commonMIMEType
-    //  getSelectedOutputMime (depends on commonMIMEType)
     //  downloadText
 
 
@@ -279,9 +277,17 @@ function handleDownloadPreview(format = 'text/turtle') {
 // Get user choice of where to save inferred triples
 function getSaveTarget() {
   const isNamed = document.getElementById('save-target-named')?.checked;
+
   if (isNamed) {
-    return { mode: 'named', graphIRI: makeNamedGraphIRI('http://example.org/inferred') };
+    const iriForOverlay = document.getElementById('iri-for-save-target')?.value;
+
+    return {
+      mode: 'named',
+      // Uses iriForOverlay if it has a value, otherwise generates one
+      graphIRI: iriForOverlay?.trim() ? iriForOverlay : makeNamedGraphIRI('http://example.org/inferred')
+    };
   }
+
   return { mode: 'default', graphIRI: null };
 }
 
@@ -366,7 +372,10 @@ async function exportInferredOverlay() {
     const ext = ({
       'text/turtle': 'ttl',
       'application/n-triples': 'nt',
-      'application/n-quads': 'nq'
+      'application/n-quads': 'nq',
+      'application/trig': 'trig',
+      'application/ld+json': 'jsonld',
+      'application/rdf+xml': 'rdf'
     })[mime] || 'ttl';
 
     downloadText(`inferred-${timestampUTC()}.${ext}`, text, mime);
@@ -417,9 +426,7 @@ function addNewFileRow() {
 function toggleReasonerButtons() {
   const useDB = document.getElementById('reasoner-source-indexeddb')?.checked;
   const saveBtn = document.getElementById('save-inferred-to-db');
-  const insertBtn = document.getElementById('insert-inferred-to-endpoint');
   if (saveBtn)   saveBtn.style.display   = useDB ? '' : 'none';
-  if (insertBtn) insertBtn.style.display = useDB ? 'none' : '';
 }
 // run at load + when radios change
 ['reasoner-source-indexeddb','reasoner-source-endpoint'].forEach(id=>{
@@ -430,7 +437,6 @@ toggleReasonerButtons();
 // Event handlers
 document.getElementById('run-inference')?.addEventListener('click', runInference);
 document.getElementById('save-inferred-to-db')?.addEventListener('click', saveInferredTriplesToDB);
-document.getElementById('insert-inferred-to-endpoint')?.addEventListener('click', insertInferredTriplesIntoEndpoint);
 document.getElementById('export-inferred')?.addEventListener('click', async () => {
   await exportInferredOverlay();
 });
@@ -655,6 +661,17 @@ const $writeOpts = document.getElementById('write-options');
   });
 });
 
+const stashInferenceDefaultGraphMode = document.getElementById('save-target-default');
+const stashInferenceNamedGraphMode = document.getElementById('save-target-named');
+const nameSaveTargetEl = document.getElementById('name-save-target');
+
+[stashInferenceDefaultGraphMode, stashInferenceNamedGraphMode].forEach(el=>{
+  el?.addEventListener('change', ()=>{
+    const namedGraphOptionChosen = stashInferenceNamedGraphMode?.checked;
+    if (nameSaveTargetEl) nameSaveTargetEl.style.display = namedGraphOptionChosen ? 'block' : 'none';
+  });
+});
+
 /**
  * Validate that query kind matches UI mode. Returns {ok:boolean,reason?:string}
  * Pure; logs for developer visibility.
@@ -1329,6 +1346,27 @@ function renderQueryError(err) {
   resultsDiv.innerHTML = html;
 }
 
+// Drop-down id="output-format" has values: Turtle, n-Triples, JSON-LD, RDF/XML
+const commonMIMEType = {
+  'Turtle':    'text/turtle',
+  'n-Triples': 'application/n-triples',
+  'JSON-LD':   'application/ld+json',
+  'RDF/XML':   'application/rdf+xml',
+  'N-Quads':   'application/n-quads',
+  'TriG':      'application/trig',
+  'SPARQL Results JSON': 'application/sparql-results+json',
+  'SPARQL Results XML':  'application/sparql-results+xml',
+  'SPARQL Update':      'application/sparql-update',
+  'SPARQL Query':       'application/sparql-query',
+};
+
+// Utility to get selected output MIME type from dropdown
+function getSelectedOutputMime() {
+  const sel = document.getElementById('output-format');
+  const label = sel?.value || 'Turtle';
+  return commonMIMEType[label] || 'text/turtle';
+}
+
 // Make callable from other modules if they need it
 window.renderQueryError = renderQueryError;