nlm-memory 0.20.0 → 0.21.0

package/dist/core/ingest/reprocess.js

@@ -0,0 +1,280 @@
+/**
+ * reprocess: retroactive re-classification of prior sessions under a
+ * stronger configured lane.
+ *
+ * Selection: sessions with a non-empty body whose classifier_model is NULL,
+ * differs from the current lane model, or (when --min-confidence is given)
+ * whose stored confidence falls below the threshold even for the same model.
+ *
+ * Per session: classifyAdaptive on the stored body, then a full insertSession
+ * upsert (refreshes chunks + facts). A below-floor classification updates the
+ * session row (label, summary, markers, provenance) but preserves prior facts
+ * and their embeddings unchanged. It is counted in belowFloorOverwrites.
+ * Workstream binding (workstream_id) is NOT touched by the upsert.
+ *
+ * Resumable via a JSON state file (default ~/.nlm/reprocess.state). A lane
+ * change (different provider or model) invalidates the done-set.
+ *
+ * SQLite only. Pg variant deferred; file task against nlm#TODO in report.
+ */
+import { existsSync, mkdirSync, readFileSync, writeFileSync } from "node:fs";
+import { dirname, join } from "node:path";
+import { homedir } from "node:os";
+import { classifyAdaptive } from "../classifier/hierarchical-classify.js";
+import { extractFacts } from "../facts/extract-facts.js";
+const DEFAULT_STATE_PATH = join(homedir(), ".nlm", "reprocess.state");
+const SAVE_EVERY = 25;
+const CONFIDENCE_FLOOR = 0.4;
+function confidenceBand(conf) {
+    if (conf === null)
+        return "null";
+    if (conf < 0.4)
+        return "<0.4";
+    if (conf < 0.6)
+        return "0.4-0.6";
+    if (conf < 0.8)
+        return "0.6-0.8";
+    return ">=0.8";
+}
+function loadState(path, lane) {
+    if (!existsSync(path))
+        return new Set();
+    try {
+        const raw = JSON.parse(readFileSync(path, "utf8"));
+        if (raw.lane?.provider === lane.provider && raw.lane?.model === lane.model) {
+            return new Set(raw.done ?? []);
+        }
+        return new Set();
+    }
+    catch {
+        // Malformed state file: restart reprocessing from scratch.
+        return new Set();
+    }
+}
+function saveState(path, done, lane) {
+    mkdirSync(dirname(path), { recursive: true });
+    writeFileSync(path, JSON.stringify({ done: [...done].sort(), lane }));
+}
+export function selectReprocessCandidates(db, model, minConfidence, opts) {
+    const params = [];
+    let classifierClause;
+    if (opts?.onlyNull) {
+        classifierClause = "classifier_model IS NULL";
+    }
+    else if (minConfidence !== undefined) {
+        classifierClause = "(classifier_model IS NULL OR classifier_model != ? OR classifier_confidence < ?)";
+        params.push(model, minConfidence);
+    }
+    else {
+        classifierClause = "(classifier_model IS NULL OR classifier_model != ?)";
+        params.push(model);
+    }
+    const excludeModels = opts?.excludeModels ?? [];
+    let excludeClause = "";
+    if (excludeModels.length > 0) {
+        const placeholders = excludeModels.map(() => "?").join(", ");
+        excludeClause = ` AND (classifier_model IS NULL OR classifier_model NOT IN (${placeholders}))`;
+        params.push(...excludeModels);
+    }
+    const sql = "SELECT id, runtime, runtime_session_id, started_at, ended_at, duration_min, " +
+        "label, summary, status, transcript_kind, transcript_path, " +
+        "transcript_offset, transcript_length, " +
+        "classifier_provider, classifier_model, classifier_confidence " +
+        "FROM sessions " +
+        "WHERE body IS NOT NULL AND length(body) > 0 " +
+        "AND " +
+        classifierClause +
+        excludeClause +
+        " " +
+        "ORDER BY started_at DESC";
+    return db.prepare(sql).all(...params);
+}
+export async function reprocess(deps, opts = {}) {
+    const { db, store, factStore, embedder, classifier, classifierDescriptor } = deps;
+    const log = deps.log ?? ((m) => console.error(m));
+    const statePath = opts.statePath ?? DEFAULT_STATE_PATH;
+    const lane = {
+        provider: classifierDescriptor.provider,
+        model: classifierDescriptor.model,
+    };
+    const allCandidates = selectReprocessCandidates(db, classifierDescriptor.model, opts.minConfidence, {
+        ...(opts.onlyNull ? { onlyNull: true } : {}),
+        ...(opts.excludeModels ? { excludeModels: opts.excludeModels } : {}),
+    });
+    if (opts.dryRun) {
+        const groupMap = new Map();
+        for (const row of allCandidates) {
+            const key = `${row.classifier_provider ?? ""}\u0000${row.classifier_model ?? ""}\u0000${confidenceBand(row.classifier_confidence)}`;
+            const existing = groupMap.get(key);
+            if (existing) {
+                groupMap.set(key, { ...existing, count: existing.count + 1 });
+            }
+            else {
+                groupMap.set(key, {
+                    classifierProvider: row.classifier_provider,
+                    classifierModel: row.classifier_model,
+                    confidenceBand: confidenceBand(row.classifier_confidence),
+                    count: 1,
+                });
+            }
+        }
+        const cohort = [...groupMap.values()].sort((a, b) => b.count - a.count);
+        let stateNote;
+        if (existsSync(statePath)) {
+            const n = loadState(statePath, lane).size;
+            stateNote = `state file present, ${n} sessions already done, real run will skip them`;
+        }
+        return {
+            totalEligible: allCandidates.length,
+            processed: 0,
+            succeeded: 0,
+            failed: 0,
+            skippedAlreadyDone: 0,
+            limitSkipped: 0,
+            belowFloorOverwrites: 0,
+            meanConfidenceOld: null,
+            meanConfidenceNew: null,
+            cohort,
+            ...(stateNote !== undefined ? { stateNote } : {}),
+        };
+    }
+    if (deps.embeddingConfig && deps.embedderDescriptor) {
+        const stored = deps.embeddingConfig.getLane("prose");
+        if (stored) {
+            let dim = null;
+            try {
+                const result = await deps.embedder.embed("nlm probe", "query");
+                dim = result.vector.length;
+            }
+            catch {
+                // probe failure: pre-tracking tolerance, proceed
+            }
+            if (dim !== null) {
+                const mismatch = stored.provider !== deps.embedderDescriptor.provider ||
+                    stored.model !== deps.embedderDescriptor.model ||
+                    stored.dim !== dim;
+                if (mismatch && !opts.forceEmbed) {
+                    const msg = `reprocess: prose embedding lane mismatch: stored ${stored.provider}/${stored.model}@${stored.dim}` +
+                        ` vs runtime ${deps.embedderDescriptor.provider}/${deps.embedderDescriptor.model}@${dim}.` +
+                        ` Re-embedding under a mismatched lane writes mixed vectors. Run nlm embed-backfill first,` +
+                        ` or pass --force-embed to override.`;
+                    log(msg);
+                    throw new Error(msg);
+                }
+            }
+        }
+    }
+    const bodyStmt = db.prepare("SELECT body FROM sessions WHERE id = ?");
+    const done = loadState(statePath, lane);
+    const skippedByState = allCandidates.filter((r) => done.has(r.id)).length;
+    const candidates = allCandidates.filter((r) => !done.has(r.id));
+    const work = opts.limit !== undefined ? candidates.slice(0, opts.limit) : candidates;
+    const total = work.length;
+    let processed = 0;
+    let succeeded = 0;
+    let failed = 0;
+    let belowFloorOverwrites = 0;
+    let sumConfidenceOld = 0;
+    let countOld = 0;
+    let sumConfidenceNew = 0;
+    let countNew = 0;
+    for (let i = 0; i < work.length; i++) {
+        const row = work[i];
+        const sid = row.id;
+        const idx = i + 1;
+        const bodyRow = bodyStmt.get(sid);
+        if (!bodyRow?.body) {
+            failed++;
+            processed++;
+            log(`[reprocess] empty body ${sid}: skipping`);
+            opts.onProgress?.(idx, total, sid, "empty_body");
+            continue;
+        }
+        const body = bodyRow.body;
+        let classification;
+        try {
+            classification = await classifyAdaptive(body, classifier, {
+                ...(opts.classifyTimeoutMs ? { perCallTimeoutMs: opts.classifyTimeoutMs } : {}),
+            });
+        }
+        catch (e) {
+            failed++;
+            processed++;
+            log(`[reprocess] classify failed ${sid}: ${e instanceof Error ? e.message : String(e)}`);
+            opts.onProgress?.(idx, total, sid, "classify_failed");
+            continue;
+        }
+        if (row.classifier_confidence !== null) {
+            sumConfidenceOld += row.classifier_confidence;
+            countOld++;
+        }
+        sumConfidenceNew += classification.confidence;
+        countNew++;
+        const belowFloor = classification.confidence < CONFIDENCE_FLOOR;
+        if (belowFloor) {
+            belowFloorOverwrites++;
+            if (opts.verbose) {
+                log(`[reprocess] below-floor ${sid}: old=${row.classifier_confidence ?? "null"} new=${classification.confidence}`);
+            }
+        }
+        else if (opts.verbose) {
+            log(`[reprocess] ${sid}: old=${row.classifier_confidence ?? "null"} new=${classification.confidence}`);
+        }
+        const record = {
+            id: sid,
+            runtime: row.runtime,
+            runtimeSessionId: row.runtime_session_id,
+            startedAt: row.started_at,
+            endedAt: row.ended_at,
+            durationMin: row.duration_min,
+            label: classification.label,
+            summary: classification.summary,
+            body,
+            status: row.status,
+            transcriptKind: row.transcript_kind,
+            transcriptPath: row.transcript_path,
+            transcriptOffset: row.transcript_offset,
+            transcriptLength: row.transcript_length,
+            entities: classification.entities,
+            decisions: classification.decisions,
+            openQuestions: classification.open,
+            // Reprocess rebuilds from the stored row, which carries no project
+            // directory evidence; the scope backfill command re-derives from the
+            // transcript, so a NULL here is recoverable.
+            scope: null,
+            classifier: { ...classifierDescriptor, confidence: classification.confidence },
+        };
+        try {
+            const factSinkArg = belowFloor
+                ? null
+                : { factStore, facts: extractFacts(classification, sid, row.started_at) };
+            await store.insertSession(record, embedder, null, factSinkArg);
+            done.add(sid);
+            succeeded++;
+            processed++;
+            opts.onProgress?.(idx, total, sid, "ok");
+            if (succeeded % SAVE_EVERY === 0)
+                saveState(statePath, done, lane);
+        }
+        catch (e) {
+            failed++;
+            processed++;
+            log(`[reprocess] ingest failed ${sid}: ${e instanceof Error ? e.message : String(e)}`);
+            opts.onProgress?.(idx, total, sid, "ingest_failed");
+        }
+    }
+    saveState(statePath, done, lane);
+    const limitSkipped = opts.limit !== undefined ? candidates.length - work.length : 0;
+    return {
+        totalEligible: allCandidates.length,
+        processed,
+        succeeded,
+        failed,
+        skippedAlreadyDone: skippedByState,
+        limitSkipped,
+        belowFloorOverwrites,
+        meanConfidenceOld: countOld > 0 ? sumConfidenceOld / countOld : null,
+        meanConfidenceNew: countNew > 0 ? sumConfidenceNew / countNew : null,
+    };
+}
+//# sourceMappingURL=reprocess.js.map

package/dist/core/ingest/reprocess.js.map

@@ -0,0 +1 @@
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package/dist/core/ingest/transcript-derivables.d.ts

@@ -0,0 +1,27 @@
+/**
+ * transcript-derivables — post-classify scan of the raw transcript file for
+ * primary_model/total_tokens/skill (#352 phase 2, Task 5). Complements
+ * deriveSubagentMeta (Task 2), which derives persona/parent from the chunk's
+ * already-parsed runtimeSessionId + label; this scan needs the per-message
+ * `model` + `usage` + `tool_use` blocks the chunk parser summarizes away, so
+ * it re-reads the transcript file directly.
+ *
+ * v1 supports claude-code-jsonl only: assistant events carry `message.model`
+ * and `message.usage.{input,output}_tokens` (same fields
+ * claude-code.ts's parseSession already reads for `lastModel`); a Skill-tool
+ * invocation is a `content` block with `type: "tool_use"`, `name: "Skill"`,
+ * and `input.skill` holding the slug (e.g. "superpowers:brainstorming").
+ * Every other transcript kind returns all-null — no per-runtime scanner
+ * exists yet.
+ *
+ * Streamed line-by-line (readline over a ReadStream), never readFileSync:
+ * transcripts reach tens of MB and this runs on the ingest write path, not
+ * just backfill. A missing, unreadable, or rotated-away file resolves nulls
+ * rather than rejecting — never throws.
+ */
+export interface TranscriptDerivables {
+    readonly primaryModel: string | null;
+    readonly totalTokens: number | null;
+    readonly skill: string | null;
+}
+export declare function scanTranscriptDerivables(path: string, kind: string): Promise<TranscriptDerivables>;

package/dist/core/ingest/transcript-derivables.js

@@ -0,0 +1,138 @@
+/**
+ * transcript-derivables — post-classify scan of the raw transcript file for
+ * primary_model/total_tokens/skill (#352 phase 2, Task 5). Complements
+ * deriveSubagentMeta (Task 2), which derives persona/parent from the chunk's
+ * already-parsed runtimeSessionId + label; this scan needs the per-message
+ * `model` + `usage` + `tool_use` blocks the chunk parser summarizes away, so
+ * it re-reads the transcript file directly.
+ *
+ * v1 supports claude-code-jsonl only: assistant events carry `message.model`
+ * and `message.usage.{input,output}_tokens` (same fields
+ * claude-code.ts's parseSession already reads for `lastModel`); a Skill-tool
+ * invocation is a `content` block with `type: "tool_use"`, `name: "Skill"`,
+ * and `input.skill` holding the slug (e.g. "superpowers:brainstorming").
+ * Every other transcript kind returns all-null — no per-runtime scanner
+ * exists yet.
+ *
+ * Streamed line-by-line (readline over a ReadStream), never readFileSync:
+ * transcripts reach tens of MB and this runs on the ingest write path, not
+ * just backfill. A missing, unreadable, or rotated-away file resolves nulls
+ * rather than rejecting — never throws.
+ */
+import { createReadStream } from "node:fs";
+import { createInterface } from "node:readline";
+const CLAUDE_CODE_JSONL_KIND = "claude-code-jsonl";
+const NULL_DERIVABLES = {
+    primaryModel: null,
+    totalTokens: null,
+    skill: null,
+};
+export function scanTranscriptDerivables(path, kind) {
+    if (kind !== CLAUDE_CODE_JSONL_KIND)
+        return Promise.resolve(NULL_DERIVABLES);
+    return new Promise((resolve) => {
+        const modelCounts = new Map();
+        const modelLastSeenAt = new Map();
+        let lineNumber = 0;
+        let inputTokens = 0;
+        let outputTokens = 0;
+        let sawUsage = false;
+        let skill = null;
+        let settled = false;
+        const finish = (result) => {
+            if (settled)
+                return;
+            settled = true;
+            resolve(result);
+        };
+        let stream;
+        try {
+            stream = createReadStream(path, { encoding: "utf8" });
+        }
+        catch {
+            // Synchronous throw (e.g. malformed path) — most fs errors surface via
+            // the 'error' event below instead.
+            finish(NULL_DERIVABLES);
+            return;
+        }
+        // Missing/unreadable/rotated-away file — resolve nulls, never throw.
+        stream.on("error", () => finish(NULL_DERIVABLES));
+        const rl = createInterface({ input: stream, crlfDelay: Infinity });
+        rl.on("error", () => finish(NULL_DERIVABLES));
+        rl.on("line", (line) => {
+            const trimmed = line.trim();
+            if (!trimmed)
+                return;
+            lineNumber += 1;
+            let evt;
+            try {
+                evt = JSON.parse(trimmed);
+            }
+            catch {
+                return;
+            }
+            if (evt["type"] !== "assistant")
+                return;
+            const msg = evt["message"] ?? {};
+            const model = msg["model"];
+            if (typeof model === "string" && model) {
+                modelCounts.set(model, (modelCounts.get(model) ?? 0) + 1);
+                modelLastSeenAt.set(model, lineNumber);
+            }
+            const usage = msg["usage"];
+            if (usage && typeof usage === "object") {
+                const input = usage["input_tokens"];
+                const output = usage["output_tokens"];
+                if (typeof input === "number") {
+                    inputTokens += input;
+                    sawUsage = true;
+                }
+                if (typeof output === "number") {
+                    outputTokens += output;
+                    sawUsage = true;
+                }
+            }
+            if (skill === null) {
+                const content = msg["content"];
+                if (Array.isArray(content)) {
+                    for (const block of content) {
+                        if (!block || typeof block !== "object")
+                            continue;
+                        const b = block;
+                        if (b["type"] === "tool_use" && b["name"] === "Skill") {
+                            const toolInput = b["input"];
+                            const slug = toolInput?.["skill"];
+                            if (typeof slug === "string" && slug)
+                                skill = slug;
+                            break;
+                        }
+                    }
+                }
+            }
+        });
+        rl.on("close", () => {
+            finish({
+                primaryModel: majorityModel(modelCounts, modelLastSeenAt),
+                totalTokens: sawUsage ? inputTokens + outputTokens : null,
+                skill,
+            });
+        });
+    });
+}
+/** Majority wins by occurrence count; ties break to whichever model's last
+ *  occurrence is chronologically latest in the transcript. */
+function majorityModel(counts, lastSeenAt) {
+    let best = null;
+    let bestCount = -1;
+    let bestLastSeenAt = -1;
+    for (const [model, count] of counts) {
+        const lastSeen = lastSeenAt.get(model) ?? -1;
+        if (count > bestCount || (count === bestCount && lastSeen > bestLastSeenAt)) {
+            best = model;
+            bestCount = count;
+            bestLastSeenAt = lastSeen;
+        }
+    }
+    return best;
+}
+//# sourceMappingURL=transcript-derivables.js.map

package/dist/core/ingest/transcript-derivables.js.map

@@ -0,0 +1 @@
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package/dist/core/integrity/check-invariants.d.ts

@@ -13,8 +13,12 @@
  *       'replaces' edges (BFS, depth-capped at 100)
  *   I4  every session_edges endpoint exists in sessions
  *   I5  at most one active fact per (subject, predicate); every superseded_by
- *       references an existing facts.id
+ *       references an existing facts.id; superseded_by forms no cycle (I5c)
  *   I6  every non-null adapter_state.session_id references a sessions.id
+ *   I7  every fact_embeddings row has a live (active, non-retired) parent fact
+ *   I7b chunk-level ghost: every session_embedding_chunks row has a map entry
+ *       (I7b-1); every session_chunk_map row references an existing session
+ *       (I7b-2)
  */
 import type Database from "better-sqlite3";
 import type { Pool } from "pg";
@@ -36,6 +40,7 @@ export declare function runCheapChecksOnPg(pool: Pool): Promise<ReadonlyArray<Vi
 export interface FixReport {
     readonly deletedSelfLoops: number;
     readonly restoredToClosed: number;
+    readonly deletedGhostEmbeddings: number;
 }
 export declare function applyFixOnSqlite(db: Database.Database): FixReport;
 export declare function applyFixOnPg(pool: Pool): Promise<FixReport>;