agnes-the-ai-analyst/docs/architecture.md

Architecture — Detailed Reference

Comprehensive architectural overview of the AI Data Analyst platform (v2).

Top-Level Module Map

ai-data-analyst/
├── src/                  Core engine (db, orchestrator, rbac, profiler, repositories)
├── connectors/           Pluggable data connectors (keboola, bigquery, jira, llm, openmetadata)
├── app/                  FastAPI application (API + web UI)
│   ├── api/              REST API routers
│   ├── auth/             Auth providers (JWT, Google OAuth, email magic link, password)
│   └── web/              HTML dashboard routes
├── services/             Standalone background services (scheduler, telegram_bot, ws_gateway, …)
├── cli/                  CLI tool (agnes pull, agnes query, agnes admin)
├── scripts/              Utility and migration scripts
├── config/               Instance configuration templates
├── tests/                Test suite
└── docs/                 User-facing documentation

System Overview

┌─────────────────────────────────────────────────────────────────┐
│  EXTERNAL DATA SOURCES                                          │
│  Keboola Storage  │  BigQuery  │  Jira Cloud  │  CSV/files     │
└──────────┬────────┴─────┬──────┴──────┬────────┴────────────────┘
           │              │             │
           ▼              ▼             ▼
┌─────────────────────────────────────────────────────────────────┐
│  CONNECTORS  (connectors/)                                      │
│  extractor.py per source → extract.duckdb contract             │
└──────────────────────────┬──────────────────────────────────────┘
                           │  /data/extracts/{source}/extract.duckdb
                           ▼
┌─────────────────────────────────────────────────────────────────┐
│  SYNC ORCHESTRATOR  (src/orchestrator.py)                       │
│  Scans extracts/, ATTACHes each extract.duckdb,                │
│  creates master views in analytics.duckdb (atomic swap)        │
└──────────────────────────┬──────────────────────────────────────┘
                           │
              ┌────────────┼────────────┐
              ▼            ▼            ▼
     ┌──────────────┐  ┌────────┐  ┌──────────────┐
     │  FastAPI app  │  │  CLI   │  │  Scheduler   │
     │  port 8000    │  │  `da`  │  │  sidecar     │
     └──────────────┘  └────────┘  └──────────────┘
              │
    ┌─────────┴──────────┐
    ▼                    ▼
system.duckdb       analytics.duckdb
(state/registry)    (master views)

Deployment: Docker Compose. The app service runs Uvicorn. The scheduler sidecar triggers sync jobs and the LLM pipeline (corporate-memory, verification-detector, session-collector) via the app's REST API on offset cadences. Optional full profile adds telegram-bot and ws-gateway.

docker compose up               # app + scheduler
docker compose --profile full up  # all services
docker compose --profile extract run extract  # one-shot extraction

---

extract.duckdb Contract

Every connector writes to the same directory layout:

/data/extracts/{source_name}/
├── extract.duckdb          ← _meta table + views over parquet files
└── data/                   ← parquet files (local connectors only)
    ├── table_a.parquet
    └── table_b.parquet

_meta table

Required in every extract.duckdb:

CREATE TABLE _meta (
    table_name   VARCHAR NOT NULL,
    description  TEXT,
    rows         BIGINT,
    size_bytes   BIGINT,
    extracted_at TIMESTAMP,
    query_mode   VARCHAR    -- 'local' or 'remote'
);

The orchestrator reads _meta to know which tables exist and creates a corresponding view in analytics.duckdb for each row.

_remote_attach table (optional)

Connectors whose views reference an external DuckDB extension (e.g. Keboola, BigQuery) must include this table so the orchestrator can re-ATTACH the external source at rebuild time:

CREATE TABLE _remote_attach (
    alias     VARCHAR,  -- DuckDB alias for the attached source, e.g. 'kbc'
    extension VARCHAR,  -- Extension name, e.g. 'keboola'
    url       VARCHAR,  -- Connection URL
    token_env VARCHAR   -- Name of the env var holding the auth token
);

The orchestrator installs/loads the extension, reads the token from the environment, and ATTACHes the external source so remote views resolve correctly. This mechanism is generic — any connector can use it. Auth credentials are never stored in extract.duckdb.

---

SyncOrchestrator

src/orchestrator.py — thread-safe via _rebuild_lock.

rebuild()

1. Open a temporary DuckDB file (analytics.duckdb.tmp).
2. Scan /data/extracts/*/extract.duckdb (sorted, skips non-directories and missing files).
3. Validate each directory name as a safe SQL identifier (^[a-zA-Z_][a-zA-Z0-9_]{0,63}$).
4. For each source: ATTACH '{db_file}' AS {source_name} (READ_ONLY).
5. Handle _remote_attach — install extension, read token from env, ATTACH external source.
6. Read _meta, validate each table_name identifier, create CREATE OR REPLACE VIEW.
7. Update sync_state in system.duckdb (mtime-based hash, no full file read).
8. CHECKPOINT and close the temp connection.
9. Atomic swap: shutil.move(tmp_path, target_path) — replaces analytics.duckdb in-place.

rebuild_source(source_name)

Convenience wrapper that calls rebuild() in full (partial rebuild is not possible because analytics.duckdb is written fresh from scratch each time). Used after Jira webhooks.

Identifier validation

Both source_name and table_name are checked against ^[a-zA-Z_][a-zA-Z0-9_]{0,63}$ before being interpolated into SQL. Invalid names are skipped with a warning.

---

Data Sources

Keboola — Batch Pull

connectors/keboola/extractor.py

• Uses the DuckDB Keboola community extension to download tables directly to parquet.
• Fallback path: connectors/keboola/client.py (Keboola Storage API wrapper).
• Sync strategies: full_refresh, incremental, partitioned.
• Writes extract.duckdb + data/*.parquet under /data/extracts/keboola/.
• For tables with query_mode='remote', populates _remote_attach so views proxy queries to Keboola rather than downloading data locally.

Sync trigger flow:

POST /api/sync/trigger (admin)
  → BackgroundTask: _run_sync()
    → Read table_registry from system.duckdb (main process)
    → Serialize configs as JSON, spawn subprocess (no DuckDB lock conflict)
    → Subprocess: connectors/keboola/extractor.run()  →  extract.duckdb
    → SyncOrchestrator().rebuild()  →  analytics.duckdb
    → Profiler: profile each synced parquet  →  table_profiles

BigQuery — Remote Attach

connectors/bigquery/extractor.py

• Uses the DuckDB BigQuery community extension via the BqAccess facade in connectors/bigquery/access.py.
• No data download — views proxy all queries directly to BigQuery.
• Auth via GOOGLE_APPLICATION_CREDENTIALS (service account JSON) or ADC.
• Populates _remote_attach with extension='bigquery' and no token_env (env-based auth).

BigQuery — Materialized SQL

connectors/bigquery/extractor.py::materialize_query (added in v0.25.0)

• Runs admin-registered SQL through the DuckDB BigQuery extension via BqAccess.duckdb_session() and writes the result to /data/extracts/bigquery/data/<id>.parquet atomically (<id>.parquet.tmp → os.replace).
• Triggered by _run_materialized_pass in app/api/sync.py between custom-connectors and orchestrator rebuild on every /api/sync/trigger. Per-table sync_schedule honored via is_table_due().
• Cost guardrail: BQ dry-run via app.api.v2_scan._bq_dry_run_bytes (single source of truth for cost-estimate logic). data_source.bigquery.max_bytes_per_materialize (default 10 GiB; 0 disables). Fail-open when dry-run errors (DuckDB three-part syntax the native BQ client can't parse) — log warning + proceed.
• Distribution: result parquet rides the same manifest + agnes pull flow as Keboola tables. Per-user RBAC unchanged (resource_grants(group, ResourceType.TABLE, table_id)).

Jira — Real-Time Push

connectors/jira/webhook.py → incremental_transform.py → extract_init.py

Jira Cloud webhook (issue created/updated/deleted)
  → POST /api/jira/webhook  (HMAC-SHA256 verification)
  → connectors/jira/webhook.py  (validate, persist raw JSON)
  → connectors/jira/incremental_transform.py  (update monthly parquet shards)
  → extract_init.py  (update _meta)
  → SyncOrchestrator().rebuild_source('jira')

Output tables (6): issues, comments, attachments, changelog, issuelinks, remote_links.

Background supplements:

• jira-sla-poll — refreshes SLA fields for open tickets every 5 min.
• jira-consistency — detects and backfills missing issues every 6 h.

Files NOT to modify: connectors/jira/file_lock.py, connectors/jira/transform.py.

---

DuckDB Schema

system.duckdb — {DATA_DIR}/state/system.duckdb

Current schema version: 59 (auto-migrated from any earlier version on startup — see src/db.py).

Table	Purpose
schema_version	Tracks applied migration version
users	Registered users: id, email, name, password_hash, setup/reset tokens, active flag
user_groups	Named groups (Admin, Everyone seeded as is_system=TRUE; admin-managed and Google-synced groups)
user_group_members	(user_id, group_id, source) — source ∈ {admin, google_sync, system_seed}
resource_grants	Generic per-(group, resource_type, resource_id) grants (replaces dataset_permissions + plugin_access)
sync_state	Per-table sync status: last_sync, rows, file_size_bytes, hash, status
sync_history	Historical sync runs with duration and error
user_sync_settings	Per-user dataset enable/disable preferences
table_registry	Registered tables: source_type, bucket, source_table, query_mode, sync_schedule
table_profiles	JSON data profiles (stats, nulls, cardinality) per table
knowledge_items	Corporate memory knowledge entries (confidence, entities, source_type, source_ref, valid_from/valid_until, supersedes, sensitivity, is_personal, is_required — v49 dropped the scalar domain column; relations live in knowledge_item_domains)
knowledge_votes	Up/down votes on knowledge items
knowledge_contradictions	Pairs of items the LLM judge flagged as contradictory; carries severity and suggested_resolution (JSON-encoded structured action — see ADR Decision 4)
verification_evidence	One row per detected verification — persists user_quote, detection_type, and source_ref so future Bayesian re-calibration has raw signal (ADR Decision 3)
session_extraction_state	Tracks which /data/user_sessions/*.jsonl files have been processed by the verification detector
audit_log	API action log: user, action, resource, duration
telegram_links	Telegram chat_id linked to user_id
pending_codes	Telegram link confirmation codes
script_registry	Deployed Python notification scripts
data_packages	Admin-curated bundles of tables (id, slug, name, icon, color). Distributed as a single "stack" unit; tables M:N via data_package_tables.
data_package_tables	M:N junction between data_packages and table_registry.
memory_domains	First-class memory domain rows (id, slug, name, icon, color). Replaces the scalar knowledge_items.domain column dropped in v49.
knowledge_item_domains	M:N junction between knowledge_items and memory_domains. One item can live in multiple domains.
user_stack_subscriptions	Per-user opt-in for available-tier Data Packages + Memory Domains ((user_id, resource_type, resource_id)). Marketplace plugins keep their legacy user_plugin_optouts table.

Connections: get_system_db() returns a cursor on a single shared connection per DATA_DIR (protected by threading.Lock). Callers close() the cursor, not the underlying connection. This avoids DuckDB write-lock conflicts in the multi-threaded FastAPI process.

analytics.duckdb — {DATA_DIR}/analytics/server.duckdb

Read-only views over all ATTACHed extract.duckdb sources. Rebuilt atomically by SyncOrchestrator.rebuild(). Query endpoints open this file via get_analytics_db_readonly() which ATTACHes all extract.duckdb files in read-only mode so remote views resolve correctly.

---

Authentication

All auth flows issue a JWT (app/auth/jwt.py) stored as a cookie (access_token) or passed as a Bearer token in the Authorization header. The get_current_user dependency validates the JWT and loads the user from users in system.duckdb.

Providers (app/auth/providers/)

Provider	Available when	Flow
google.py	GOOGLE_CLIENT_ID + GOOGLE_CLIENT_SECRET set	Google OAuth 2.0 / OIDC (Authlib). Domain restriction via allowed_domains in instance.yaml. Callback issues JWT cookie.
email.py	SMTP_HOST or SENDGRID_API_KEY set	Magic link: POST /auth/email/send-link generates a token stored in users.setup_token; POST /auth/email/verify exchanges it for a JWT.
password.py	Always registered	Email + password with hashed credentials.

RBAC

Two layers, no role hierarchy (see docs/RBAC.md for the full reference):

• App-level access: membership in the Admin system group. The require_admin FastAPI dependency in app.auth.access gates admin endpoints (admin UI, user management, settings, …).
• Resource-level access: per-(group, resource_type, resource_id) grants in resource_grants. The require_resource_access(rt, path_template) dependency factory gates entity-scoped endpoints.

Table access (src/rbac.py:can_access_table) is a thin wrapper over app.auth.access.can_access(user_id, "table", table_id, conn). Admin group members short-circuit; everyone else needs an explicit resource_grants(group, "table", table_id) row via any group they belong to. There is no is_public shortcut and no implicit "Everyone can read" fallback — the legacy dataset_permissions + is_public mechanism was dropped in v19.

---

API Layer

All routes are FastAPI APIRouter instances registered in app/main.py.

REST API (app/api/)

Router	Prefix	Key endpoints
sync	/api/sync	GET /manifest (hash manifest, per-user filtered), POST /trigger (admin), GET/POST /settings, GET/POST /table-subscriptions
data	/api/data	Download parquet files for synced tables
query	/api/query	POST / — execute a SELECT against analytics.duckdb (sandbox enforced)
admin	/api/admin	GET /discover-tables, GET /registry, POST /register-table, PUT /registry/{id}, DELETE /registry/{id}
catalog	/api/catalog	Data catalog: table list, profiles, metric definitions
users	/api/users	User CRUD (admin), self-service profile
permissions	/api/permissions	Dataset permission grants (admin)
access_requests	/api/access-requests	Request + review workflow
scripts	/api/scripts	Deploy, list, run, delete Python notification scripts
settings	/api/settings	Instance and user settings
memory	/api/memory	Corporate memory CRUD and voting
upload	/api/upload	File upload (CSV, parquet)
telegram	/api/telegram	Telegram account link/unlink
jira_webhooks	/api/jira	Jira webhook receiver (HMAC-SHA256 verified)
health	/api/health	Service health, sync status, disk

Auth routes (app/auth/)

POST /auth/token, GET /auth/me, POST /auth/logout, GET /auth/google/login, GET /auth/google/callback, POST /auth/email/send-link, POST /auth/email/verify, POST /auth/password/login

Web UI (app/web/)

HTML dashboard routes served by Jinja2 templates. Registered last (catch-all).

---

Services

Each service is a self-contained Python package (services/<name>/__main__.py) run as a Docker Compose service.

Service	Profile	Schedule / Mode	Description
scheduler	default	Always-on; polls every N seconds	Lightweight sidecar that triggers jobs via the app's REST API: POST /api/sync/trigger every 15 min, GET /api/health every 5 min, POST /api/admin/run-session-collector every 10 min, POST /api/admin/run-verification-detector every 15 min, POST /api/admin/run-corporate-memory every 17 min, POST /api/marketplaces/sync-all daily 03:00. Auth via SCHEDULER_API_TOKEN or auto-fetch from /auth/token.
telegram_bot	full	Always-on (long-poll)	Telegram bot: polling + HTTP dispatch, /status command, notification script execution.
ws_gateway	full	Always-on	WebSocket gateway (TCP 8765) + HTTP dispatch socket. JWT auth. Per-user connection limit (5). Heartbeat ping/pong.
corporate_memory	(driven by scheduler)	Every 17 min	Scans CLAUDE.local.md files, extracts knowledge via LLM (Claude Haiku), writes to knowledge_items in system.duckdb. Inline contradiction detection runs after each new item: one batched Haiku structured-output call returns judgments + structured resolution suggestions for every same-domain candidate (no SQL keyword pre-filter — see ADR Decision 4). Driven by scheduler-v2 since #176.
verification_detector	(driven by scheduler)	Every 15 min	Scans unprocessed analyst session JSONLs, extracts corrections / confirmations / unprompted definitions via Haiku structured outputs. Confidence is computed in code from (source_type, detection_type) — never trusted from the LLM. Each verification persists a verification_evidence row carrying user_quote + detection_type (ADR Decision 3). Driven by scheduler-v2 since #176.
session_collector	(driven by scheduler)	Every 10 min	Copies Claude Code .jsonl session transcripts to central storage. Driven by scheduler-v2 since #176.

Files NOT to modify: services/ws_gateway/ (stable WebSocket infrastructure).

Corporate-memory privacy boundary

is_personal on knowledge_items is enforced as an authorization rule at every read site, not a UI hint:

• GET /api/memory and GET /api/memory?search=… silently coerce exclude_personal=True for any caller whose role is below km_admin.
• GET /api/memory/{id}/provenance and POST /api/memory/{id}/vote use the shared _can_view_item(user, item) helper (not is_personal OR contributor OR km_admin/admin) and return 404 (not 403) on denial to avoid existence-leak.
• Contributors reach their own personal items via /api/memory/my-contributions.

See ADR Decision 1 for the full reasoning.

---

Security

Query Sandbox (app/api/query.py)

The /api/query endpoint enforces a strict SQL allowlist:

• Only SELECT and WITH queries accepted.
• Blocklist of ~30 keywords/functions: DROP, DELETE, INSERT, UPDATE, ALTER, CREATE, ATTACH, DETACH, LOAD, INSTALL, COPY, PRAGMA, file functions (read_parquet, read_csv, glob, etc.), URL schemes (s3://, gcs://, http://), and multi-statement separator (;).
• Table-level RBAC: forbidden views are detected by word-boundary regex match against the SQL text. Query is rejected if user lacks access to any referenced table.
• Analytics DB opened in read_only=True mode per request.

Script Sandbox (app/api/scripts.py)

Deployed and ad-hoc Python scripts are checked against a pattern blocklist before execution:

• Blocked: subprocess, shutil, ctypes, importlib, socket, requests, httpx, urllib, os, sys, signal, open(, pathlib, exec(, eval(, compile(, __import__, and others.
• Scripts run in a subprocess with a configurable timeout (SCRIPT_TIMEOUT, default 300 s) and capped output (SCRIPT_MAX_OUTPUT, default 64 KB).

Identifier Validation (src/orchestrator.py, src/db.py)

All dynamic SQL identifiers (source names, table names, extension aliases) are validated against ^[a-zA-Z_][a-zA-Z0-9_]{0,63}$ before interpolation. Invalid identifiers are skipped with a log warning, never executed.

Authentication Layers

Layer	Mechanism
Web UI / API	JWT Bearer token or access_token cookie
Google OAuth	Authlib OIDC + domain allowlist
Email magic link	secrets.token_urlsafe(32) stored in users.setup_token, 1-hour expiry
Jira webhook	HMAC-SHA256 signature verification
Inter-service (scheduler)	SCHEDULER_API_TOKEN env var or auto-fetched JWT

---

Configuration

config/instance.yaml             (instance-specific, not committed)
    │ loaded by config/loader.py
    │ ${ENV_VAR} references resolved from .env
    ▼
app/instance_config.py           (exposes get_data_source_type(), get_allowed_domains(), get_value())
    ▼
FastAPI dependency injection     (passed to API routers as needed)

Table configuration lives in table_registry inside system.duckdb, not in static files. Use POST /api/admin/register-table or the web UI admin panel to register tables.

Required env vars: DATA_DIR, JWT_SECRET_KEY. Source-specific vars (KEBOOLA_STORAGE_TOKEN, GOOGLE_CLIENT_ID, GOOGLE_CLIENT_SECRET, SMTP_HOST / SENDGRID_API_KEY, etc.) are optional and gate the relevant connectors/providers.

---

Data Filesystem Layout

/data/
├── state/
│   └── system.duckdb          user registry, sync state, table_registry, audit log
├── analytics/
│   └── server.duckdb          master analytics DB (views over all extracts)
└── extracts/
    ├── keboola/
    │   ├── extract.duckdb     _meta + views
    │   └── data/*.parquet
    ├── bigquery/
    │   └── extract.duckdb     _meta + _remote_attach + remote views
    └── jira/
        ├── extract.duckdb     _meta + views
        └── data/*.parquet

---

Extending the Platform

New Data Source

1. Create connectors/<name>/extractor.py.
2. Write extract.duckdb with _meta table and views/tables.
3. Add data/*.parquet for local sources.
4. Add _remote_attach row if views reference an external DuckDB extension.
5. SyncOrchestrator picks it up automatically on next rebuild().

New Auth Provider

1. Add app/auth/providers/<name>.py exporting a FastAPI APIRouter.
2. Register the router in app/main.py.
3. All providers must issue a JWT and set the access_token cookie on success.