## Summary
`claude -p` (headless mode) gives SessionEnd hook subprocesses ~1 second before SIGTERM, regardless of work in progress. `agnes push` for a typical workspace takes 5-30s. The current synchronous SessionEnd hook (`agnes push --quiet 2>/dev/null || true`) was therefore being killed mid-first-upload — `|| true` masks the SIGTERM as exit 0, so this regression was invisible until I traced it via a wrapper script and Claude's `~/.claude/debug/<sid>.txt` log.
Fix: wrap SessionEnd push in `bash -c "( nohup agnes push --quiet </dev/null >/dev/null 2>&1 & ) ; true"`. The subshell exits immediately, orphaning the upload child to init so it survives the hook subprocess kill. Same `bash -c` pattern as the existing `refresh-marketplace` SessionStart entry (for Windows compatibility).
End-to-end verified against production: claude exited in 5s, detached child completed the upload, file `491e3a23-...jsonl` landed on the server within 30s with mtime 14:30 UTC.
## Test plan
- [x] `pytest tests/test_lib_hooks.py` — added `test_session_end_push_is_detached` regression test asserting `nohup`, `&`, `</dev/null` are all present.
- [x] `pytest tests/test_setup_hooks_template.py` — assertions loosened from `==` to `in` where necessary.
- [x] Verified end-to-end against production with the detached wrapper before opening this PR (manual probe).
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## Summary
Verified against production: `claude -p` headless mode doesn't fire SessionEnd hooks (proven via `--output-format stream-json --include-hook-events`: zero `SessionEnd` events), so any session JSONLs from `-p` invocations stay orphaned locally and never reach the server. Fix: add `agnes push --quiet` as a third SessionStart entry — symmetric self-heal alongside the existing `agnes pull` entry. Existing workspaces pick this up on their next `agnes init` via the marker-based migration already in `cli/lib/hooks.py`.
Separately: a colleague's fresh install showed `agnes diagnose` warning "uploads are not being processed", which led them to suspect their `agnes push` was broken. The warning is actually about the LLM-based `verification-detector` backlog (uploads themselves were arriving fine — confirmed by 23+3 JSONLs landed on the server while the warning was firing). Reword the warning to "verification-detector backlog" + add `last_processed` to the diagnose dict so operators don't have to grep logs to confirm.
## Test plan
- [x] `pytest tests/test_lib_hooks.py` — updated count + added `agnes push in SessionStart` assertion.
- [x] `pytest tests/test_setup_hooks_template.py` — updated.
- [x] `pytest tests/test_clean_install_integration.py` — updated.
- [x] `pytest tests/test_health_session_pipeline.py` — updated warning text + asserted `last_processed` field.
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## Summary
`agnes query "DESCRIBE unit_economics"` (where `unit_economics` is `query_mode='remote'`) previously returned DuckDB's nearest-name suggestion (`Did you mean "order_economics"`?), sending users down the wrong path. Now appends a friendly hint about remote tables.
Reproduced from a real analyst session — colleague spent ~30s diagnosing what was actually "this is a remote table, not materialized locally".
## Test plan
- [x] New test: `_query_local("DESCRIBE unit_economics", ...)` against an empty local DuckDB triggers the new hint, original DuckDB error still echoed.
- [x] Negative test: a syntax-error query does NOT trigger the hint (regex only matches "Table with name X does not exist").
- [x] `pytest tests/test_cli_query*.py` clean.
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## Summary
When `agnes query --remote` references a column that doesn't exist on the FROM table, users were seeing `Table "<id>" must be qualified with a dataset` instead of the actually-useful `Unrecognized name: <column>` from BigQuery. Surface the first-attempt diagnostic now; keep the second-attempt context as `underlying_original`.
Reproduced against production:
```
$ agnes query --remote "SELECT COUNT(*) FROM unit_economics WHERE authorize_date = DATE '2025-05-06'"
Error: remote_estimate_failed (HTTP 400)
message: Could not estimate scan size for this query.
underlying: 400 ... Table "unit_economics" must be qualified with a dataset.
```
(`unit_economics` has `authorize_timestamp`, not `authorize_date`.)
## Test plan
- [x] New `test_remote_estimate_failed_surfaces_first_error_when_attempts_differ` asserts the first-attempt message wins, second-attempt is preserved as `underlying_original`, hint points to `agnes schema`.
- [x] Existing `test_guardrail_returns_400_remote_estimate_failed_on_double_parse_error` still passes (both attempts mocked to identical error).
- [x] `pytest tests/test_api_query_guardrail.py` clean.
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Cuts the [Unreleased] section into [0.46.0] in CHANGELOG.md and
bumps pyproject.toml. The user-visible content was already on main
via PR #190 (commit 28430ced); this is the release-cut commit that
should have been the last commit on that PR — splitting it out so
the operator-facing release artifact (tag + GitHub Release) lines up
with what's already deployed at :stable.
* fix: cutover regressions + parallel Keboola legacy fallback
Bundled fixes from a fresh-deploy run on a Keboola Storage backend with
the block-shared-snowflake-access feature flag — DuckDB Keboola
extension's per-table scan can't access bucket schemas, so the legacy
kbcstorage Storage-API client is the only working path.
CUTOVER REGRESSIONS
- agnes pull hash mismatch on every Keboola local-mode table —
src/orchestrator.py:_update_sync_state stored md5(mtime+size)[:12]
while the CLI compares against full 32-char content MD5. Now stores
the same content MD5 the materialized SQL path already used.
- Trailing-slash sanitization in connectors/keboola/access.py and
extractor.py — DuckDB Keboola extension's ATTACH fails when the URL
ends in / (canonical form).
- src/profiler.py:TableInfo.description becomes optional — two call
sites instantiated without it, crashing the profiler pass.
- scripts/ops/agnes-auto-upgrade.sh: chown on UID change — older images
ran as root, current runs as agnes (uid 999). Reads target uid:gid
from /etc/passwd inside the new image and chowns ${STATE_DIR},
/data/extracts, /data/analytics when the digest moves.
- POST /api/sync/trigger is now singleton per process — two
near-simultaneous trigger calls each forked an extractor subprocess,
fought for extract.duckdb's file lock, starved uvicorn, flipped the
container to unhealthy. Trigger now returns 409
(sync_already_in_progress) when held; _run_sync acquires non-blocking.
PARALLEL LEGACY FALLBACK
- Process pool fan-out for the _extract_via_legacy queue (default 8
workers, override via AGNES_KEBOOLA_PARALLELISM). Process pool, not
thread pool, because connectors/keboola/client.py:export_table does
os.chdir(temp_dir) — process-global, so threads raced and slice files
landed in the wrong directory ("[Errno 2] No such file or directory:
'<job_id>.csv_X_Y_Z.csv'").
- Extractor subprocess timeout 1800s -> 3600s (configurable via
AGNES_EXTRACTOR_TIMEOUT_SEC). 28+ tables × multi-minute Keboola export
jobs need the headroom on telemetry-class projects.
- Process group cleanup on timeout — Popen(start_new_session=True) puts
the extractor in its own group. On timeout the parent SIGTERMs the
group (10s grace) then SIGKILLs stragglers. Without this, the pool
workers were reparented to PID 1 and continued holding open Keboola
Storage export jobs. Inline extractor script also installs a SIGTERM
-> sys.exit(143) handler so the with ProcessPoolExecutor(...) block
__exit__ runs cleanly.
Tests: existing tests that patched subprocess.run updated to patch
subprocess.Popen with a _FakePopen stand-in (same exit-code-injection
contract). Two tests that exercised the parallel path forced
AGNES_KEBOOLA_PARALLELISM=1 to keep mocks alive (mocks don't ride into
ProcessPoolExecutor subprocesses).
Squashed onto current main (was 7 commits + multi-commit CHANGELOG +
agnes-auto-upgrade.sh conflicts; squash avoids per-commit conflict
resolution against main's flat-mount STATE_DIR refactor and 0.38.0
release cut).
* feat(keboola): Storage API direct extract path; drop extension data path
The DuckDB Keboola extension's COPY routes through Keboola QueryService,
which is unreliable on linked-bucket projects (extension v0.1.6 fixes
that case but isn't yet in the community CDN, and pre-fix any project
with the block-shared-snowflake-access feature flag couldn't see bucket
schemas at all). Move the extract path off the extension entirely and
talk to the Storage API directly via signed-URL download — works on any
project, regardless of extension state.
connectors/keboola/storage_api.py (NEW)
Lightweight client built on requests.Session. Three endpoints:
- POST /v2/storage/tables/{id}/export-async (kicks off job)
- GET /v2/storage/jobs/{id} (poll until done)
- GET /v2/storage/files/{id}?federationToken=1 (signed URL detail)
- GET <signed_url> (download bytes)
Supports sliced exports (manifest + per-slice signed URLs) and gzipped
payloads. ExportFilter dataclass mirrors the Keboola filter spec
(whereFilters / columns / changedSince / limit) and handles JSON
round-trip with the registry's source_query column. Token redaction
in error messages. Bounded exponential backoff on job polling.
No cloud-SDK dependency on the data path; thread-safe.
connectors/keboola/extractor.py
- materialize_query() rewritten: takes bucket/source_table/source_query
(JSON filter spec), exports via KeboolaStorageClient, converts CSV
to parquet via DuckDB, atomic os.replace. Same return shape so
sync.py downstream code stays uniform with the BQ branch.
- _extract_via_legacy() also moved to Storage API direct (kept the
name for caller compatibility with _legacy_worker / the parallel
batch extractor). Per-call temp directories — no os.chdir, threads
don't race.
app/api/sync.py
_run_materialized_pass for source_type='keboola' rows now constructs a
KeboolaStorageClient (replaces KeboolaAccess) and passes
bucket/source_table/source_query to materialize_query. Reuses one
client across rows for HTTP keep-alive. Sources keboola URL from env
too (KEBOOLA_STACK_URL) when instance.yaml doesn't have stack_url
configured.
cli/commands/admin.py
discover-and-register defaults Keboola rows to query_mode='materialized'
(NULL source_query = full table), matching the v26 migration's
unification of the local/materialized split for Keboola. BigQuery and
Jira keep their per-source defaults.
src/db.py
Schema bump 25 → 26. Migration: UPDATE table_registry SET
query_mode='materialized' WHERE source_type='keboola' AND
query_mode='local'. NULL source_query on those rows means "full table
export" — same effective behavior the local mode provided, but now
via Storage API instead of the extension.
pyproject.toml
kbcstorage dep stays (admin-side bucket/table list still uses the
SDK in app/api/admin.py / connectors/keboola/client.py); only the
data path is migrated off the SDK. Comment updated to reflect the
new boundary.
tests
- test_keboola_storage_api.py (NEW, 19 tests): ExportFilter parsing,
HTTP client (token redaction, retry logic, polling), download_file
(single, gzipped, sliced), end-to-end export_table_to_csv.
- test_keboola_materialize.py rewritten: mocks KeboolaStorageClient
instead of FakeAccess; same atomic-write + zero-rows + unsafe-id
contracts.
- test_sync_trigger_keboola_materialized.py: registry rows now carry
bucket+source_table+JSON-shape source_query.
114+ Keboola-impacted tests green locally.
* test: schema version assertion bumped to 26 alongside the keboola query_mode migration
* fix(keboola): cutover hot-patches surfaced on agnes-dev
Five small fixes that were applied as in-container hot-patches during
agnes-dev cutover and need to be on the source-of-truth image so a fresh
upgrade does not undo them.
- app/api/sync.py: auto-discover gate considers the WHOLE registry (any
source, any mode), not just rows where source matches and query_mode
is local. After the v25→v26 keboola materialized migration an
instance can have 30 materialized rows and zero local rows; the
previous gate kept re-firing _discover_and_register_tables every
scheduler tick, creating duplicate auto-discovered rows with the
wrong bucket prefix every time.
- app/api/admin.py: _discover_and_register_tables reassembles the
bucket as <stage>.<bucket-id> (e.g. in.c-finance) instead of
dropping the stage prefix; default query_mode for keboola is now
materialized (the v26 contract); validator allows NULL source_query
for keboola materialized rows (full-table export via Storage API
export-async, no SQL needed).
- cli/commands/admin.py: register-table mirrors the server validator
(NULL source_query allowed for source_type=keboola); --bucket help
text generalized to cover both BQ dataset and Keboola bucket id.
- connectors/keboola/extractor.py: max_line_size=64 MiB on
read_csv_auto so embedded JSON / SQL cells (kbc_component_configuration
in particular) do not trip the default 2 MiB ceiling.
- connectors/keboola/storage_api.py: GCP backend support — when the
Storage API returns a manifest whose slice URLs are gs://
references with a gcsCredentials block, rewrite to the JSON REST
download endpoint and authenticate with the issued OAuth bearer
token; redact tokens in any surfaced error string.
* test: align with new keboola materialized + auto-discover-gate contracts
- test_admin_keboola_materialized: rename
test_register_keboola_materialized_rejects_missing_source_query →
test_register_keboola_materialized_accepts_missing_source_query.
v25→v26 introduced 'keboola materialized with NULL source_query
means full-table export via Storage API export-async' as the
default registration shape; the rejection case is no longer the
contract.
- test_sync_filter: add list_all() to _StubRegistry. The auto-discover
gate in _run_sync now keys off the WHOLE registry (not just local
rows) so materialized-only Keboola instances do not re-trigger
discovery on every tick.
* feat(keboola): native parquet export — skip CSV roundtrip
Storage API export-async accepts fileType={csv,parquet}. Switching the
materialized sync to parquet eliminates the CSV → DuckDB COPY → parquet
roundtrip that pinned a single uvicorn worker over 4 GiB on multi-GB
tables (read_csv with all_varchar + max_line_size=64MB has to
materialize the whole CSV in memory before COPY can stream out a
parquet). Snowflake UNLOAD on Keboola's side already produces typed,
self-contained parquet files; the extractor downloads them and renames
into place.
Two cases:
- **Single-file** export (small table): file_info.url points at one
signed URL; download_file streams chunks straight to .parquet.tmp
and we're done. No DuckDB.
- **Sliced** export (Snowflake UNLOAD respects MAX_FILE_SIZE — 16 MiB
default — so anything larger arrives as N parquet slices): each
slice is a complete parquet file with its own footer; naive concat
would corrupt them. download_file_slices keeps the slices as
separate files in a tempdir, then DuckDB COPY (SELECT * FROM
read_parquet([slice0, slice1, ...])) merges them into one
consolidated parquet. DuckDB streams row groups during this — peak
memory bounded to one row group (~1 MiB) regardless of source size.
The legacy CSV path stays as the explicit opt-in via source_query=
'{"file_type":"csv"}' for projects whose backend can't UNLOAD
parquet (none known today; cheap escape hatch). Backward-compat alias
KeboolaStorageClient.export_table_to_csv kept.
Also fixes a latent bug in download_file's gzip detection: previous
heuristic flagged any unencrypted file as gzipped, which would have
corrupted parquet downloads at gunzip time. Name-suffix-only now.
* fix: tempdir leak cleanup, every 0m schedule, /sync/trigger body shapes
Three small self-contained fixes uncovered during agnes-dev cutover.
- connectors/keboola/extractor.py: tempfile.TemporaryDirectory now uses
ignore_cleanup_errors=True so a worker death mid-write doesn't leave
multi-GiB stale slice trees on the boot disk. (12 GiB seen after a
disk-full crash where TemporaryDirectory's own cleanup also raised
and got swallowed.)
- src/scheduler.py: is_valid_schedule accepts 'every 0m' (interval=0
= always due). Force-resync of an errored row no longer requires
waiting out the default 'every 1h' interval — admin can flip the
schedule, trigger, then flip back.
- app/api/sync.py: POST /api/sync/trigger accepts both ['table_id']
(legacy bare-array body) and {'tables': ['table_id']} (matches the
response payload shape, more discoverable for clients building
requests by hand). Malformed bodies return 422 with a structured
detail; null/missing means 'sync everything' as before.
Tests cover: tempdir cleanup on raise (sliced parquet path),
is_valid_schedule + is_table_due 'every 0m' acceptance, and trigger
body parametrized matrix (8 valid shapes + 6 rejection cases).
* fix: targeted-trigger filter in materialized pass + auto-upgrade defer
Two operational gaps observed during agnes-dev cutover, in the same
sync-routing area.
- _run_materialized_pass now takes a 'tables' arg and skips rows not in
the target set with reason='not_in_target'. POST /api/sync/trigger
with a body of tables previously only scoped the legacy extractor
subprocess — the materialized pass kept iterating every due
materialized row, so an admin asking to re-sync kbc_job re-ran
every other due materialized row alongside it. Match on registry id
OR name (admins commonly pass either form). tables=None preserves
the no-filter behavior.
- New GET /api/sync/status (public, no auth) returns {locked: bool}
off _sync_lock.locked(). agnes-auto-upgrade.sh probes this before
docker compose up -d and exits 0 with a 'deferred recreate' log
line if a sync is in flight — the next 5-min cron tick retries.
Pre-fix, an auto-upgrade triggered mid-sync would recreate the
uvicorn worker and kill the in-flight extractor / Snowflake-UNLOAD
download (observed when kbc_job's first 7-day retry got SIGKILLed).
Connection failures in the probe fall through to the upgrade —
being stuck on a wedged image is worse than interrupting a
hypothetical sync.
* fix: auto-discover protects admin overrides + surfaces drift
Two real-world incidents on agnes-dev drove this:
1. kbc_job was registered manually with the correct
(in.c-kbc_telemetry, kbc_job) coordinates. A naive auto-discover
re-run would have inserted a SECOND kbc_job row at the slugified
id 'in_c-keboola-storage_kbc_job' (where Keboola's discovery
places it) — and that row's Storage API export-async 404s.
2. An earlier auto-discover bug stripped the stage prefix from
bucket ids ('c-finance' instead of 'in.c-finance'), inserting
137 rows whose syncs all failed.
Fix:
- _discover_and_register_tables now builds a plan first
(_build_keboola_discovery_plan) classifying each discovered table
into one of new / existing_match / existing_drift / invalid, then
executes only the 'new' bucket. Drift rows are reported with both
sides of the disagreement plus drift_kind:
- same_id_diff_coords: registry has the same id but different
bucket / source_table (admin migrated coords inline).
- name_collision: discovery's slugified id differs from any
registry id, but the discovered .name matches an existing row's
.name (case-insensitive). Catches the kbc_job case.
- Bucket detection now prefers the API's authoritative bucket_id
field (separate field on the Keboola tables.list response,
normalised by KeboolaClient.discover_all_tables). Falls back to
id-string parsing only when bucket_id is missing (older fallback
path inside discover_all_tables).
- Endpoint POST /api/admin/discover-and-register?dry_run=true
returns the plan without writing — would_register, drift,
invalid lists. Lets an operator audit before merging discovery
with a registry that has admin overrides.
Removed 'every 0m' from test_register_request_rejects_malformed_sync_schedule
— the runtime started accepting it in the previous commit (force-resync
override) and the validator follows suit.
* feat(keboola): AGNES_TEMP_DIR routes tempfiles off overlayfs /tmp
The container's /tmp lives on the boot disk's overlayfs (29 GiB on
agnes-dev, shared with /var). Snowflake UNLOAD of a wide table writes
slices into per-call /tmp tempdirs that fill multi-GiB / many-slice
exports long before the dedicated data disk fills. agnes-dev hit
100% boot-disk while the 20 GiB data disk had 15 GiB free.
connectors.keboola.storage_api.get_temp_root() reads AGNES_TEMP_DIR;
mkdirs the target on first use; unset / empty / unwritable falls
back to None (system tempdir, OSS-pre-fix behaviour). Both
materialize_query (parquet path) and _extract_via_legacy (CSV
fallback) and the sliced-CSV concat path in storage_api use the
helper now.
docker-compose.yml defaults AGNES_TEMP_DIR=/data/tmp on app, scheduler,
and extract services. The data volume is the dedicated disk in
production layouts and a plain docker volume in single-disk
dev/laptop setups — same blast radius as the previous /tmp default
on the latter, no regression.
Operator-and-analyst quality bundle: a security fix for the optional
Telegram bot, two CLI gaps closed, and three rounds of UX polish on
`agnes diagnose` and `agnes pull` so non-TTY consumers (CI runners,
Claude Code SessionStart hooks, sub-agent watchdogs) get readable,
actionable signal.
- Pairing-code RNG: random.choices -> secrets.choice (CSPRNG).
- Telegram script runner: refuse out-of-shape usernames before sudo -u.
CLAUDE.md.bak.<ISO-timestamp> before regenerating.
- agnes admin unregister-table <id> -> DELETE /api/admin/registry/{id}
- agnes admin update-table <id> --field=value ... -> PUT /api/admin/registry/{id}
response but never promotes the headline. BQ billing-equals-data check
downgraded warning -> info.
default (5 s / 1 MiB vs 30 s / 10%) so sub-agent watchdogs don't kill
the pull as a hung process. New env knobs:
AGNES_PULL_PROGRESS_INTERVAL_{SECONDS,BYTES}.
--include-schema (or ?include=schema) to opt back in.
Tests: 120 passed across the touched modules, including new tests for
each fix. Pre-existing failures on main (DB migration v1->v9, binary
rename) are unrelated and not introduced here.
See CHANGELOG.md for the full entry. (Bumped from 0.42.0 to 0.43.0 since
0.42.0 was taken by PR #208's backtick-rewriter fix during this branch's
review cycle.)
0.40.0 added _persist_materialized_inner_view in materialize_query, which
tried to open extract.duckdb from a fresh DuckDB handle to write the _meta
row + inner view. In production this conflicts with the same uvicorn
process's existing read-only ATTACH (orchestrator's analytics conn holds
extract.duckdb ATTACHed as <source_name> alias), and DuckDB single-process
file-handle uniqueness rejects with:
Binder Error: Unique file handle conflict: Cannot attach "extract"
— already attached by database "<source>"
The helper logs WARNING fail-soft, parquet stays canonical, but the
master view never appears via the meta path.
Fix: at the end of _attach_and_create_views, scan
<extract_dir>/data/*.parquet and CREATE OR REPLACE VIEW <id> AS
SELECT * FROM read_parquet('<path>') for any parquet whose <id> is not
already in the per-source tables list (= meta path didn't pick it up).
Decoupled from materialize_query open-handle race. Honors the same
view_ownership cross-connector collision rules as the meta path
(first-come-first-served via view_repo.claim).
Tests:
- filesystem-fallback fires when _meta row missing
- skipped when meta path already created the view (no shadow)
- skips invalid identifiers (e.g. parquet stem starting with a digit)
- doesn't crash when source has no data/ subdir
Pre-fix flow:
1. extractor subprocess writes _meta with N remote rows + creates N inner
views in extract.duckdb (rebuild_from_registry skips materialized rows
per design — explicit `continue` at line 389)
2. _run_materialized_pass calls materialize_query, which writes parquet
atomically + returns stats — but never updates _meta
3. orchestrator.rebuild scans _meta, finds only the N remote rows, creates
master views only for them. Materialized parquet is on disk but
invisible to /api/query → 400 'not yet materialized'
Symptom appears after every container recreate (the previous run's _meta
state is wiped because docker compose down nukes the named volume that
backs extract.duckdb on some compose layouts; even on volumes that
persist, the next extractor pass calls _create_meta_table which DROPs
+ CREATEs _meta cleanly).
Fix: after os.replace(tmp_path, parquet_path) in materialize_query, open
extract.duckdb (read-write), DELETE existing _meta row for table_id,
INSERT new one with query_mode='materialized', and CREATE OR REPLACE
VIEW <table_id> AS SELECT * FROM read_parquet(<path>). All inside a
single transaction so concurrent reads see either old or new state, not
torn rows. Fail-soft on lock contention or schema drift — parquet
remains canonical, next sync pass recovers.
Tests: 3 new in test_bq_materialize.py covering:
- meta + inner view registered after materialize, alongside existing
remote rows
- re-run replaces (not duplicates) the meta row
- skips inner-view registration when extract.duckdb doesn't exist yet
(fresh BQ-only deployment edge case)
Pool the httpx.Client used by `stream_download` so N parquet downloads
share a single TLS handshake instead of one handshake each. With the
optional `h2` package installed, HTTP/2 multiplexing further lets all
chunk Range requests share a single TCP connection — synergizes with
the range-chunked download path added in the previous commit.
The shared client is created lazily on first stream-download call, kept
alive for the duration of the process via a module-level slot, and
closed at exit via `atexit.register`. Construction wraps in a
try/except: when `h2` is unavailable (slim install), httpx raises
ImportError on `http2=True` and we transparently fall back to an
HTTP/1.1 client — pooling alone still amortizes TLS handshakes.
`agnes pull` must never crash on a missing optional package, so the
fallback path is non-negotiable. `h2>=4.1.0` is added to the core
dependency set; downstream slim installs that drop it lose the HTTP/2
benefit but keep correctness.
Renames the [Unreleased] section to [0.36.0] in CHANGELOG, adds the
top-level summary, drops a fresh empty [Unreleased] above, and bumps
pyproject from 0.35.1.
Also fixes the third Devin Review finding on this PR: the CLI
ReadTimeout message hardcoded QUERY_TIMEOUT_S (300s) so a 30s-default
call (agnes catalog, agnes auth, …) reported a wait window that
didn't match reality. _translate_transport_error now takes the actual
httpx timeout from the calling helper; the BQ-job advisory only
appears for calls where the timeout was set ≥ 60s.
Three first-try-failure-surface fixes from Pavel's #185 trace + the
template guidance question, all under PR #188's umbrella so they land
together with the file_server / parallel pull / Tier 1 work.
1. CLI clean-error wrapper — new AgnesTransportError raised by the
api_*/stream_download helpers when httpx times out / drops /
refuses, plus a top-level Typer wrapper (cli/main.py) that prints
one-line "Error: …" + actionable hint and exits non-zero. Full
traceback goes to ~/.config/agnes/last-error.log for support
forwarding. Unhandled Exceptions are caught at the same boundary
so no Python traceback ever leaks to the analyst's terminal.
Pavel's #185 Phase 3B: a 30-frame httpx traceback from a slow BQ
--remote query made it look like a CLI bug. Now: clean message +
hint pointing at `agnes snapshot create` / partition-column
guidance.
Entry point in pyproject.toml flipped from `cli.main:app` →
`cli.main:_run_with_clean_errors` so the wrapper actually runs
under the installed `agnes` binary.
2. agnes init / agnes pull --skip-materialize + progress bar.
--skip-materialize omits query_mode='materialized' rows from the
download set so a first init doesn't spend 44 minutes silently
pulling a single 6 GB parquet (Pavel's #185 Phase 1). Rich-driven
per-file progress bar with label/bytes/rate/ETA renders to stderr
when not --quiet and not --json. Aggregates across the parallel
ThreadPoolExecutor workers added earlier in this PR.
3. config/claude_md_template.txt: explicit one-line snippet pointing
at `agnes catalog --json | jq '.tables[] | select(.id=="<id>")'`
for per-table descriptions + restated invariant: "the description
field on each catalog row is the authoritative business-rules
text — re-read live, never copy into this file." Resolves the
regression-or-feature debate between Pavel (wants annotations)
and the user feedback that landed in the prior commit (don't
embed table-specific content; tables change). Catalog command
stays the source of truth.
* fix(keboola): per-table fallback to legacy Storage-API client
The DuckDB Keboola extension's per-table COPY fails with
`Schema '..."in.c-..."' does not exist or not authorized` on
projects whose Snowflake backend doesn't expose bucket schemas
to the storage-token-derived QueryService role
(keboola/duckdb-extension#17). ATTACH itself succeeds, so the
existing extension-level fallback in `_try_attach_extension`
never triggers — the table is just marked failed.
- Promote `kbcstorage>=0.9.0` from optional to core dep so the
legacy client import in `_extract_via_legacy` doesn't crash
default installs with `ModuleNotFoundError`.
- Wrap `_extract_via_extension` in a per-table try/except so a
scan failure retries via `_extract_via_legacy` instead of
recording `tables_failed` and moving on.
Slower than the extension path, but produces correct parquets
on affected projects while the upstream extension fix lands.
* test(keboola): cover per-table extension→legacy fallback
Two existing tests mocked _extract_via_extension to throw and asserted
the original message survived in result["errors"]. With per-table
fallback, the new flow retries via _extract_via_legacy — which on the
mock URLs would throw a different (404 / DNS-fail) error, replacing the
asserted message.
- Mock _extract_via_legacy alongside _extract_via_extension in
test_network_timeout_during_extraction +
test_partial_failure_continues +
test_all_tables_fail_returns_full_failure_stats so the assertion
observes the final propagated error from the fallback chain.
- Add test_extension_per_table_failure_falls_back_to_legacy that
exercises the new behavior directly: extension scan fails with the
QueryService schema-not-authorized message
(keboola/duckdb-extension#17), legacy succeeds, parquet ends up
queryable.
Patch release bundling the only Unreleased change: bump httpx client
timeout for agnes query --remote from 30s to 300s (configurable via
AGNES_QUERY_TIMEOUT). Renames CHANGELOG [Unreleased] section to
[0.35.1] and bumps pyproject version to match.
Five compounding defects on default `docker compose up` deploys made the
session pipeline silently broken: sessions uploaded by analysts via
`agnes push` landed on /data/user_sessions/<user>/*.jsonl but nothing
ever processed them. Fix is one PR: promote anthropic + openai to core
deps, wire all three LLM-pipeline jobs into scheduler-v2 with offset
cadences (10m/15m/17m), drop the side-car services from compose, seed a
default ai: block on first-time setup with an env-var fallback in code,
surface the pending review queue to admins, and expose a health check
that warns when uploaded jsonls aren't being processed.
**BREAKING** for operators on COMPOSE_PROFILES=full or with custom
Compose overrides referencing the corporate-memory or session-collector
service stanzas — drop them. The scheduler is now the sole driver.
LLM provider SDKs are imported by services/corporate_memory and
services/verification_detector — both production code paths. Listing
them only in [project.optional-dependencies].dev caused the scheduler
container to boot-loop with ModuleNotFoundError on default
`docker compose up` deploys, because the Dockerfile installs core
deps only (`uv pip install --system --no-cache .`).
Adds tests/test_packaging.py to lock the contract: anthropic + openai
must live in [project].dependencies, not in dev extras.
CHANGELOG: rename [Unreleased] → [0.32.0] — 2026-05-04, prepend a new
empty [Unreleased] for next-PR landing zone.
pyproject.toml: version 0.31.0 → 0.32.0.
Per repo discipline (memory: feedback_release_cut_with_pr.md), the
release-cut commit lands as the FINAL commit of the PR that contained
the user-visible behavior change — it does not get a separate PR.
After merge: tag v0.32.0 on the merge commit + create a GitHub Release
(memory: feedback_github_release_per_tag.md — the tag alone isn't
enough; the Release prose is the operator-visible artifact).
Headline: closes#160. da query --remote now resolves query_mode='remote'
BQ rows whose entity is VIEW or MATERIALIZED_VIEW (the bug Pavel hit).
Plus 4 reinforcing fixes — server-side cost guardrail (bq_max_scan_bytes,
default 5 GiB), registry-gating of direct bq.* paths, bigquery_query()
function-call backdoor closed, structured CLI render of typed BQ errors —
and one operator-side admin convenience (BQ test-connection endpoint +
billing_project placeholder UI).
14 issues caught and addressed across 6 iterations of Devin Review.
E2E verified on agnes-zsrotyr.groupondev.com (commit 7f743d03):
- VIEW path resolves (count=23 from active_inventory_view)
- VIEW aggregate parity vs filtered BASE TABLE
- cost guardrail rejects with structured 400 detail
- bq_path_not_registered 403 (incl. quoted "bq" variant)
- bigquery_query() blocklist 400
- test-connection endpoint 200 with elapsed_ms
* security(auth): per-IP rate limit on auth endpoints + generalize last-admin guard
Closes#45 and #151.
#45 — every auth endpoint was unthrottled (login, magic-link, token,
bootstrap), leaving us open to password brute-force and SMTP
email-bombing. Wires slowapi (new dep) into the middleware chain with
per-route limits: 10/min on login + token, 5/min on send-link, 3/min on
bootstrap. Returns 429 with Retry-After: 60 once exceeded. Per-IP key
respects the leftmost X-Forwarded-For hop (Caddy in front of the app
strips client-supplied XFF). Operator escape hatch:
AGNES_AUTH_RATELIMIT_ENABLED=0. Test suite disables the limiter via
autouse conftest fixture so existing auth tests that hammer endpoints
in tight loops are unaffected.
#151 — DELETE /api/admin/users/{id}/memberships/{group_id} and the
mirror DELETE /api/admin/groups/{group_id}/members/{user_id} only
guarded against self-removal as last admin. Generalizes to refuse
removing anyone from the seeded Admin group when they are the only
remaining active admin (mirrors the existing
count_admins(active_only=True) <= 1 check on delete_user / update_user).
Recovery from zero admins requires direct DB access, so this closes
a path where a scheduler/bootstrap actor that bypasses normal admin
checks could otherwise empty the group.
* security(auth): throttle remaining email-bombing + token-confirm endpoints
Address code-review gap on PR #165 — the first commit covered /send-link
but missed two endpoints with the IDENTICAL email-bombing surface:
- POST /auth/password/reset — sends reset mail, anti-enum response
- POST /auth/password/setup/request — sends setup mail, anti-enum response
Both now share the 5/min limit with /send-link.
Also add 10/min to the token-confirm surfaces — high-entropy tokens but
partial leaks via logs / referer have surfaced before, and unbounded
guess rate would let an attacker exhaust the keyspace adjacent to a
leaked prefix:
- POST /auth/email/verify
- GET /auth/email/verify — closes the click-through bypass
- POST /auth/password/reset/confirm
- POST /auth/password/setup/confirm
Doc fix: rate_limit.py module docstring + CHANGELOG entry no longer
claim "disable without a redeploy" (misleading). The Limiter constructor
freezes `enabled` from env at import time, matching every other Agnes
env knob — operators set the flag and bounce the container.
Tests: 4 new cases in test_auth_rate_limit.py covering
/reset, /setup/request, /reset/confirm, GET /verify. Full suite:
2583 passed, 32 skipped, 0 failed.
* security(auth): throttle JSON /auth/password/setup — closes form-throttle bypass
Second code-review pass on PR #165 caught a fifth gap: POST /auth/password/setup
(JSON variant, kept for backward compat) consumes the same setup_token as
the web form /setup/confirm but was unthrottled — an attacker brute-forcing
the token just switches from the form path to the JSON path and resumes
at unbounded RPS. Apply the same 10/min limit and signature shape used
on /setup/confirm.
Also extend CHANGELOG note about the JSON-variant bypass for future
operators reading the security entry.
Test: 1 new case (test_password_setup_json_rate_limited_after_10_requests),
9 rate-limit tests + 28 password-flow tests + 41 auth-provider tests pass,
no regressions.
* chore(release): cut 0.30.1 — auth security hardening (rate limit + last-admin guard)
* fix(tls-rotate): self-signed fallback sets basicConstraints=critical,CA:FALSE
OpenSSL's default '[v3_ca]' config marks CA:TRUE on 'req -x509', which
causes strict TLS stacks (rustls / webpki, used by uv, cargo, and
future versions of pip) to reject the cert with
'invalid peer certificate: CaUsedAsEndEntity' per RFC 5280 §4.2.1.9.
Browsers, curl, and OpenSSL-based clients tolerated the violation,
hiding the bug until a uv user hit it.
Affects every VM running on the self-signed fallback while the corp
PKI hasn't published the real chain yet. Fix lands on the next
agnes-tls-rotate.timer tick (or 'systemctl start
agnes-tls-rotate.service' for an immediate refresh). Existing CSR /
real-cert paths unaffected; only the bring-up fallback regenerates.
* chore(release): cut 0.29.0
---------
Co-authored-by: ZdenekSrotyr <zdenek.srotyr@keboola.com>
* fix(analyst): document BigQuery remote-query capability in bootstrap CLAUDE.md template
Closes#153.
The CLAUDE.md template generated by `da analyst bootstrap` (config/claude_md_template.txt)
covered metrics, sync, corporate memory, and directory layout — but had ZERO
mention of query_mode: "remote", da fetch, da query --remote, or --register-bq.
Result: the AI analyst running in a freshly-bootstrapped workspace had no
idea BigQuery-backed tables existed, no path to fetch unsynced data, and no
fallback for tables not in the catalog.
Validated against /Users/<user>/foundry-ai/foundryai-data-analyst/CLAUDE.md
on 2026-05-01: section confirmed missing. Workspace-level (parent-dir)
CLAUDE.md carried legacy SSH-heredoc instructions but the analyst-level
file (which Claude reads as primary project context) had nothing.
## Changes
### config/claude_md_template.txt (+83)
Added a `## Remote Queries (BigQuery)` section covering:
- Discovery first — `da catalog --json | jq '...'` to see all tables
with their query_mode, then `da schema` and `da describe` for shape.
- Three query patterns:
- `da fetch` (preferred) — materialize a filtered subset locally,
query the snapshot, drop when done.
- `da query --remote` — one-shot server-side execution (cheap probes).
- `da query --register-bq` — hybrid joins between local + ad-hoc BQ.
- `da fetch` estimate-first discipline — rules of thumb on
--select / --where / --estimate / snapshot reuse.
- BigQuery SQL flavor cheat sheet for `--where` (DATE literal,
DATE_SUB, REGEXP_CONTAINS, CAST AS INT64).
- Unknown-table fallback: when a table isn't in `da catalog` at all,
use ad-hoc `--register-bq` if the agnes server SA has BQ access, or
ask admin to register with `query_mode: "remote"` for ongoing use.
- Pointer to `da skills show agnes-data-querying` for deeper guidance.
### docs/setup/claude_md_template.txt (deleted)
Stale 359-line template that documented the deprecated SSH-heredoc
remote_query.sh protocol. No code references it (verified via grep
across .py / .sh / .yml / .md). Removing eliminates two failure
modes:
1. A future refactor accidentally pulling it into a workspace and
shipping deprecated guidance to analyst Claude sessions.
2. Reviewer confusion over which template is canonical.
### CHANGELOG.md
`### Fixed` and `### Removed` entries under [Unreleased].
## Tested
- Manually walked the diff against `da skills show agnes-data-querying`
output on a live VM (foundryai-development) — patterns + flags
match the modern CLI exactly.
- Re-bootstrap test deferred: requires network round-trip; pattern
is identical to existing template substitution path so render is
not at risk.
## Out of scope
- The companion gap that data_description.md often only enumerates
query_mode: "local" tables (no signal that other modes exist) —
separate concern, fix likely belongs in the metadata generator
on the server side, not in the analyst template.
- Encouraging admins to register frequently-queried BQ tables as
`query_mode: "remote"` in the registry — workflow improvement, not
a code bug.
* chore(release): cut 0.28.0
---------
Co-authored-by: ZdenekSrotyr <zdenek.srotyr@keboola.com>
* feat(rbac): drop dataset_permissions + access_requests + users.role + is_public; v19 migration
BREAKING. Sjednocení datové RBAC vrstvy do per-group resource_grants modelu.
Před PR byla legacy data RBAC vrstva (dataset_permissions + is_public bypass)
de-facto neaktivní — is_public neměl API/UI/CLI surface, default true znamenal
že can_access_table vždycky bypassl. Dnes každý non-admin přístup vyžaduje
explicitní resource_grants(group, "table", id) řádek.
Schema v18 → v19 (src/db.py:_v18_to_v19_finalize):
- DROP TABLE dataset_permissions, access_requests
- DROP COLUMN users.role (NULL artifact since v13)
- DROP COLUMN table_registry.is_public
- Drops přes table-rebuild idiom (rename → create new → INSERT … SELECT
→ drop old) kvůli DuckDB ALTER DROP COLUMN limitacím na tabulkách
s historic FK constraints. INSERT picks intersection sloupců, takže
test fixtures s minimal pre-v19 schemou migrate cleanly.
Runtime:
- src/rbac.py:can_access_table → deleguje na app.auth.access.can_access
- DatasetPermissionRepository, AccessRequestRepository smazány
- AGNES_ENABLE_TABLE_GRANTS env-gate v app/resource_types.py odstraněn
(TABLE je unconditionally enabled)
API drop:
- app/api/permissions.py, app/api/access_requests.py celé soubory
- /admin/permissions web route + admin_permissions.html
- "Request Access" modal v catalog.html + locked-row UI
- ~10 if user.get("role") != "admin" checků nahrazeno (admin shortcut
je uvnitř can_access_table)
- /api/settings: drop permissions field z GET; PUT /api/settings/dataset
gate přepnut na can_access(user_id, "table", dataset, conn)
Auth:
- app/auth/jwt.py:create_access_token: drop role parametr (claim zmizí
z nově vydávaných JWT; staré tokeny zůstávají valid, claim ignored)
- app/api/users.py: drop role z CreateUserRequest / UpdateUserRequest
(admin promotion = explicit add to Admin group via memberships API)
- src/repositories/users.py: drop role z create() / update()
CLI:
- da admin set-role smazán → hard-fail s replacement command
- da admin add-user --role flag pryč
- da auth import-token --role flag pryč
- da auth whoami: drop "Role:" výpis
- cli/config.py:save_token: role parametr now optional, no longer written
(back-compat se starými token.json soubory zachována — pole se ignoruje)
Tests:
- DELETE: test_permissions.py, test_permissions_api.py, test_access_requests_api.py
- REWRITE: test_access_control.py (resource_grants flow), test_rbac.py
(can_access_table over resource_grants), test_journey_rbac.py
(drop access-request flow), test_resource_types.py (drop env-gate
tests, drop is_public from helpers), test_v2_*.py (drop role-based
user dicts in favor of id-based + Admin group membership),
test_settings_api.py (no permissions field, can_access gate)
- TRIVIAL: ~30 souborů — drop role="admin" arg z UserRepository.create
a 3rd positional role z create_access_token
- NEW: test_v18_to_v19 migration test (test_db.py),
test_can_access_table_no_implicit_public (test_rbac.py),
test_admin_set_role_returns_hardfail (test_cli_admin.py)
- OpenAPI snapshot regenerated
Docs:
- CHANGELOG: BREAKING entry pod [Unreleased]
- CLAUDE.md: schema v18 → v19
- docs/architecture.md: schema table + RBAC sekce přepsána
- docs/auth-google-oauth.md: admin promotion přes da admin break-glass
- cli/skills/security.md: kompletně přepsáno na group-based model
- docs/TODO-rbac-data-enforcement.md: smazáno (TODO splněn)
Test results: 2363 passed, 19 failed. Zbývající failures jsou pre-existing
Windows-specific issues (fcntl, charset) nesouvisející s tímto PR —
ověřeno git stash pop.
Plan: ~/.claude/plans/floofy-coalescing-parnas.md
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
* chore(release): cut 0.27.0
---------
Co-authored-by: Minas Arustamyan <arustamyan.minas@gmail.com>
Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Co-authored-by: ZdenekSrotyr <zdenek.srotyr@keboola.com>
* refactor(ops): bake all host artifacts into image, drop every curl-from-main
Replaces the curl-from-main pattern (originally introduced in 0.25.0 for
agnes-auto-upgrade.sh; older for the compose files + Caddyfile) with image-
bundled host artifacts. Same-tag delivery for everything the host runs,
version-pinned by AGNES_TAG, atomically rolled back by reverting the image.
## Motivation
The customer-instance startup template was curling 6 files from
raw.githubusercontent.com on every VM boot:
docker-compose.yml
docker-compose.prod.yml
docker-compose.host-mount.yml
docker-compose.tls.yml
Caddyfile
scripts/ops/agnes-auto-upgrade.sh (added in 0.25.0)
Every one of them already lives inside the image (`COPY . .` copies the
whole repo to /app/). Curling them from the public internet duplicates
content the image already carries and introduces three problems:
1. **Split-brain version pinning.** image_tag pins the docker image to an
immutable digest. The compose files + script bypassed that pinning by
tracking `main` (or the rarely-set compose_ref). A customer pinned to
stable-2026.04.516 could wake up tomorrow with their host artifacts
floating on whatever shipped to main overnight — even though they're
explicitly pinned for stability.
2. **No rollback knob.** Reverting a bad host artifact meant reverting
the upstream PR globally — affects every customer that reboots after
the bad commit. No "rollback for me only" path; tag-pinning gave no
protection.
3. **Public-internet dependency on every boot.** The image is already
pulled from a private registry on the same boot. Reusing that channel
is strictly cheaper than adding a second one. Customers with restricted
egress (no raw.githubusercontent.com reachability) silently broke on
every boot.
## Changes
### Dockerfile (+19 -8)
After `COPY . .` and before the wheel build, an explicit `cp` lifts every
host-side artifact into a stable contract path /opt/agnes-host/:
agnes-auto-upgrade.sh (mode 0755 — host cron driver)
docker-compose.{yml,prod,host-mount,tls}.yml
Caddyfile (mode 0644)
Why a copy instead of pointing at /app directly: /app is owned by uid 999
(USER agnes); /opt/agnes-host is root-owned, mode 0755 across the board,
stable path that won't shift if /app structure refactors.
### infra/modules/customer-instance/startup-script.sh.tpl (+22 -36)
Replaced six curls and the standalone agnes-auto-upgrade.sh extract block
(introduced earlier in this PR) with one extract sequence in section 3:
docker pull "$${IMAGE_REPO}:$${IMAGE_TAG}"
EXTRACT_CONTAINER=$(docker create "$${IMAGE_REPO}:$${IMAGE_TAG}")
trap "docker rm '$EXTRACT_CONTAINER' >/dev/null 2>&1 || true" EXIT
docker cp "$EXTRACT_CONTAINER:/opt/agnes-host/." "$APP_DIR/"
docker cp "$EXTRACT_CONTAINER:/opt/agnes-host/agnes-auto-upgrade.sh" /usr/local/bin/agnes-auto-upgrade.sh
chmod +x /usr/local/bin/agnes-auto-upgrade.sh
The auto-upgrade section (#6) is now a no-op — script is already in place.
### infra/modules/customer-instance/variables.tf (+1 -1)
`compose_ref` marked DEPRECATED in description. Default unchanged for
one release cycle to avoid breaking existing terraform plans. Will be
removed in a future major bump.
### CHANGELOG.md
`### Changed` entry under [Unreleased] — supersedes the narrower entry
this PR previously had (which only covered the script).
## Out of scope (filed as follow-ups)
1. **agnes-the-ai-analyst-infra/startup.sh (operator deploy)** still
curls the same artifacts from main. Symmetric fix needed there.
Will file as a separate PR against the infra repo.
2. **Self-update inside agnes-auto-upgrade.sh** after a successful
`docker compose pull` of a new digest. Otherwise the running cron
keeps using the OLD baked-in script for one tick after image upgrade.
~10 LOC. Deferred to keep this PR scoped.
3. **scripts/ops/agnes-tls-rotate.sh** has the same shape — host-side
bash currently sourced via the infra repo. Should follow the same
bake-into-image pattern.
## Tested
- Local: `docker build .` succeeds with the new RUN block.
- `docker create` + `docker cp /opt/agnes-host/.` round-trips all 6
artifacts; sha matches each source file.
- Not yet tested on a live VM bring-up — that requires a CI image with
this Dockerfile change. **Recommend reviewer trigger CI build, then
do a single VM-recreate against a dev VM (e.g. foundryai-development)
to confirm the extract path works end-to-end before merge.**
## Compatibility
- Existing VMs running 0.25.0 are unaffected — they have host artifacts
in place from `curl from main` already; this PR doesn't touch them.
They pick up the new pattern only on next VM recreate.
- VMs pinned to an image_tag *older* than this PR (no /opt/agnes-host
in the image) would FAIL the docker cp. Current diff fails-loud (no
fallback). Recommend operators upgrade to a fresh-enough image_tag
alongside the template upgrade — same coupling as any compose-flag bump.
* docs(infra): document image_tag >= v0.26.0 minimum on prod/dev_instances
The new startup script extracts host artifacts from /opt/agnes-host/
inside the image — a directory added in this PR (will ship as v0.26.0).
Pinning image_tag to an older tag would fail-loud at first boot with
'docker cp: No such file or directory'. Existing VMs are unaffected
because the module ignores metadata_startup_script changes.
Devin ANALYSIS_0004 on PR #149.
* fix(changelog): mark BREAKING + drop private-repo reference
Per CLAUDE.md, breaking changes start with **BREAKING** so operators
can grep before bumping the pin. The image_tag minimum constraint
introduced here qualifies — older tags fail-loud at first boot.
Also drop the explicit 'agnes-the-ai-analyst-infra' name from the
entry; the OSS distribution shouldn't reference operator-side
deploy templates by their private-repo names. Generic 'consumer-
side deploy templates' wording instead.
Devin BUG_0001 + WARN_0001 on PR #149.
* chore(release): cut 0.26.0
---------
Co-authored-by: ZdenekSrotyr <zdenek.srotyr@keboola.com>
* fix(ops): fail-fast guard in agnes-auto-upgrade — refuse to start containers if config disk not mounted
Companion to keboola/agnes-the-ai-analyst-infra#62. Same incident:
foundryai-development 2026-04-30, marketplaces / DuckDB / session secret
written to /data (sdb) instead of the config disk (sdc), wiped on next
container recreate.
## Why an app-side guard
agnes-auto-upgrade.sh fires every 5 min on every VM. If `/data/state` is
not on the config disk (because of the propagation regression fixed by the
infra PR, or the boot-time udev race fixed by infra #58, or any future
mount-loss path), this script previously ran `docker compose up -d`
anyway — and the app silently wrote state onto the wrong disk. Next
recreate, that state was gone.
The boot-time fixes in infra are preventive. This is the runtime backstop.
## Behavior
Before the existing pull/up logic, when /dev/disk/by-id/google-config-disk
exists on the VM:
1. Up to 3 mount-and-verify attempts with backoff (2s, 4s, 6s).
- Mount the config disk if /data/state is not a mountpoint.
- Detect mismatch: if /data/state is mounted from the wrong source,
umount and retry.
2. After the loop, assert findmnt source matches the config disk.
- On mismatch: `logger -t agnes-auto-upgrade FATAL` + exit 1. systemd
marks the service failed; no docker compose action runs; existing
containers (if any) keep running on stale state, but no new write
lands on the wrong disk.
3. Once verified mounted: re-apply `mount --make-rprivate /data /data/state`
on every run. Idempotent. Guards against propagation regressions
sneaking back in via future docker / kernel changes.
VMs without a config disk (foundryai-poc, single-disk legacy) skip the
whole block — the `if [ -e $CONFIG_DEVICE ]` guard.
## Tested
Patched script installed on foundryai-development as a hotfix; manual run
post-migration was a no-op (digest unchanged); /data/state stayed on sdc
across a full `docker compose down + up -d` cycle.
## Rollout
- This file is fetched by infra startup.sh from
raw.githubusercontent.com/keboola/agnes-the-ai-analyst/main on every
boot. Once merged to main, all VMs pick up the new script on their
next boot — no infra recreate needed.
- For immediate rollout to running VMs without waiting for next boot:
`scp scripts/ops/agnes-auto-upgrade.sh <vm>:/tmp/ &&
ssh <vm> sudo install -m755 -o root -g root /tmp/agnes-auto-upgrade.sh
/usr/local/bin/agnes-auto-upgrade.sh` (already done on
foundryai-development).
* chore: vendor-agnostic comment + changelog text
Drop customer-specific VM names from the script comment and
CHANGELOG entry. The OSS distribution should not name a particular
operator's hosts; the technical description already conveys why
the guard exists.
* fix(ops): suppress mount stderr in retry loop
Match the rest of the script's error-tolerant idiom (2>/dev/null).
Mount failures in the cold-boot udev race the loop is designed
to handle gracefully should not flow to stdout — cron would mail
on every transient retry.
Devin BUG_0001 on PR #146.
* fix(changelog): move auto-upgrade entry to [Unreleased]
Entry landed under v0.20.0 because that section was [Unreleased]
when this branch first opened — releases v0.21–v0.24 cut in the
meantime stranded it inside an already-released section. Move it
back where new entries belong.
Devin BUG_0001 on PR #146.
* fix(infra): single-source agnes-auto-upgrade.sh via curl from main
Replace the inline heredoc copy of the auto-upgrade script in the
customer-instance Terraform startup template with a curl fetch from
raw.githubusercontent.com on every boot. The inline copy had drifted
several iterations behind canonical scripts/ops/agnes-auto-upgrade.sh
(missing TLS overlay detection, array-form COMPOSE_FILES, and now
the config-disk fail-fast guard from this PR).
Devin ANALYSIS_0001 on PR #146.
* fix(infra): fetch docker-compose.tls.yml unconditionally + document coupling
The canonical agnes-auto-upgrade.sh from main detects TLS at runtime
via cert files on disk, regardless of the TLS_MODE Terraform variable.
Certs can appear after boot via agnes-tls-rotate.sh or manual
provisioning, and the cron job would then fail every 5 min under
'set -euo pipefail' because docker-compose.tls.yml was never fetched.
Also document the main-vs-COMPOSE_REF coupling: when the canonical
script references a new compose file, the fetch list above must be
updated to match — pinned-ref VMs would otherwise break.
Devin BUG_0001 + ANALYSIS_0001 on PR #146.
* fix(ops,infra): unconditional Caddyfile + skip tls overlay if missing
Caddyfile fetch now matches docker-compose.tls.yml: unconditional in
startup-script.sh.tpl. Without it, Docker would auto-create an empty
directory at the bind-mount target and Caddy would crash-loop while
the tls overlay has already closed :8000 — making the app
unreachable on any non-caddy VM where certs land via rotate or
manual provisioning.
Defensive layer: agnes-auto-upgrade.sh now also requires Caddyfile
to exist (size > 0) before activating the tls profile, with a
WARN log if it's missing. Belt-and-suspenders so the failure mode
is contained even when the script is deployed by some other path
(not just the customer-instance TF module).
Devin BUG_0001 on PR #146.
* chore(release): cut 0.25.0
---------
Co-authored-by: ZdenekSrotyr <zdenek.srotyr@keboola.com>
* docs(spec): #134 unify BigQuery access behind BqAccess facade
Brainstorm output for issue #134. Captures:
- root cause (incl. correction of the issue's hypothesis about commit 33a9964)
- BqAccess facade API + project resolution rules
- error contract — typed BqAccessError mapped to HTTP 502 for upstream
BQ failures, 500 for deployment/config bugs
- migration plan for v2_scan, v2_sample, RemoteQueryEngine
- test rewrite eliminating _bq_client_factory injection point
- E2E verification protocol on agnes-development as success criterion
* docs(spec): #134 revise after first review
Incorporates code-reviewer findings:
Must-fix:
- Add v2_schema (2 copies of INSTALL/LOAD/SECRET dance) to migration scope.
- Reframe v2_scan headline: missing try/except around BQ calls is the
actual cause of bare 500s, not project resolution (which 33a9964 fixed).
- List two more deferred call sites (extractor.py, register_bq_table)
with explicit rationale.
Important:
- Drop billing != data clause from cross_project_forbidden heuristic;
rely only on 'serviceusage' substring. billing != data is normal
for cross-project setup, was over-classifying.
- Split bq_bad_request into _user (400) and _server (502) variants;
add sql_origin parameter to translate_bq_error so call sites declare
whether SQL contains user input.
- Add @functools.cache to BqAccess.from_config; document tests bypass
via dependency_overrides.
- Replace monkey-patched-classmethod test pattern with
BqAccess(client_factory=...) injection at construction time. Cleaner
than today's _bq_client_factory and 1:1 migration shape.
- Keep BqProjects.data (reviewer assumed registry has source_project;
it doesn't). Multi-project explicitly listed as non-goal with note.
Nice-to-have:
- Add 'Implementation strategy' section: 2 staged commits (bug fix
alone is revertable; refactor follows).
- Extend E2E protocol to cover all three endpoints, not just /sample.
- Note removal of stale docstring at src/remote_query.py:204.
* docs(spec): #134 revision 3 — incorporates second-round review
Must-fix from second review:
- v2_schema split into two migration cases: _fetch_bq_schema translates
errors via translate_bq_error; _fetch_bq_table_options preserves its
swallow-all 'except Exception → return {}' so /schema doesn't 502 on
partition-info failures.
- RemoteQueryEngine.__init__ now resolves BqAccess lazily (in
_get_bq_client, not in __init__). Without this, ~7 DuckDB-only tests
in test_remote_query.py would suddenly fail with not_configured.
- translate_bq_error pass-through for BqAccessError is now load-bearing
(clause 1, before any Google-API branch). bq.client() raises BqAccessError
for bq_lib_missing/auth_failed; without explicit pass-through those
fall to 'unknown' and re-raise as bare 500.
- Commit 1 now emits the SAME structured response shape as commit 2 to
avoid contract churn between commits.
- BIGQUERY_PROJECT env-var precedence is BREAKING for env-only deployments
— flagged in CHANGELOG ### Changed.
Editorial:
- sql_origin renamed to bad_request_status with values 'client_error' /
'upstream_error' (clearer about what the parameter actually decides).
bq_bad_request_user/_server kinds collapsed to bq_bad_request (400)
and bq_upstream_error (502).
- CLI (cli/commands/query.py) noted as external RemoteQueryEngine caller;
unaffected because new bq_access kwarg has default None.
- Added unit/integration tests for the new contracts:
test_translate_passes_through_BqAccessError,
test_v2_scan_returns_500_on_bq_lib_missing,
test_v2_schema_returns_200_with_empty_partition_on_bq_failure,
test_resolve_succeeds_after_config_set.
- E2E protocol now covers /schema as the fourth endpoint.
- Documented functools.cache-doesn't-cache-exceptions semantics and
fixture nullcontext-doesn't-close caveat for nested sessions.
* docs(spec): #134 revision 4 — incorporates third-round review
Third reviewer verdict: 'implementation-ready with two trivial edits';
explicitly noted prior rounds did the heavy lifting.
Edits:
1. get_bq_access() module-level function instead of @classmethod
@functools.cache from_config. Removes the classmethod-cache stacking
footgun (different Python versions wrap differently) and gives FastAPI's
dependency introspection a clean function signature. Drops the
'Do not subclass BqAccess' caveat that no longer applies.
2. Commit 1 strategy explicitly: wrap _fetch_bq_sample (v2_sample),
_bq_dry_run_bytes + _run_bq_scan (v2_scan), and _fetch_bq_schema
(v2_schema strict block). Do NOT touch _fetch_bq_table_options swallow-all
in commit 1 — preserved as-is, then migrated (still preserved) in commit 2.
All three endpoints emit the same structured body shape so client parsers
see one consistent contract throughout the staged rollout. No more
half-rolled-out window where /sample is bare 500 while /scan is
structured 502.
* docs(plan): #134 implementation plan — Phase 1 (atomic bug fix) + Phase 2 (BqAccess refactor) + Phase 3 (verification)
Bite-sized TDD tasks. 3 phases, 16 tasks total:
Phase 1 (Commit 1) — atomic bug fix across all four v2 endpoints:
Tasks 1.1-1.5 wrap _fetch_bq_sample, _bq_dry_run_bytes, _run_bq_scan,
_fetch_bq_schema with structured 502/400 try/except. _fetch_bq_table_options
preserved untouched. CHANGELOG Fixed entries.
Phase 2 (Commit 2) — BqAccess facade extraction + migration:
Tasks 2.1-2.5 build connectors/bigquery/access.py bottom-up
(BqProjects, BqAccessError, translate_bq_error, default factories,
BqAccess class, get_bq_access module-level cached). Task 2.6 adds
conftest.py fixture. Tasks 2.7-2.9 migrate v2_scan, v2_sample, v2_schema
to BqAccess. Tasks 2.10-2.11 migrate RemoteQueryEngine + tests
(lazy bq_access, drop _bq_client_factory). Task 2.12 CHANGELOG
Changed BREAKING + Internal.
Phase 3 — Verification:
3.1 full pytest. 3.2 squash into two PR-shape commits. 3.3 manual
E2E on agnes-development per spec protocol → close#134.
Self-review table maps spec sections to implementing tasks; no gaps.
* fix(v2): #134 structured 502/400 on BQ errors across /scan, /scan/estimate, /sample, /schema
Wraps the BigQuery call sites in v2_scan, v2_sample, and v2_schema (strict
block only) with try/except for google.api_core exceptions, translating to
HTTPException with a structured body shape: {error, message, details}.
Fixes Pavel's report (#134) where these endpoints returned bare HTTP 500
with no body when the SA on agnes-development hit cross-project Forbidden
on serviceusage.services.use.
Also fixes /sample's missing billing_project fallback (the bug 33a9964
fixed for /scan never landed here).
Status code split:
- /scan, /scan/estimate: BadRequest -> 400 (bq_bad_request) since SQL is
user-derived from req.select/where/order_by.
- /sample, /schema: BadRequest -> 502 (bq_upstream_error) since SQL is
server-constructed from validated identifiers.
- All Forbidden -> 502 with cross_project_forbidden if 'serviceusage' in
error message (with hint pointing at data_source.bigquery.billing_project),
else bq_forbidden.
Body shape matches what the upcoming BqAccess refactor (next commit) will
produce, so client-side parsers see one consistent contract throughout
the staged rollout.
_fetch_bq_table_options preserved exactly as-is — its swallow-all-and-return-empty
contract is intentional and survives into the refactor; /schema continues to
return 200 with empty partition info when partition queries fail.
Outer wraps in scan_endpoint, scan_estimate_endpoint, sample, and schema
endpoints exist only to make the test pattern (monkeypatching whole
_fetch_* functions) work, and are tagged TODO(#134 Phase 2) for removal
once BqAccess centralizes translation.
* refactor(bq): #134 BqAccess facade — unify v2_scan, v2_sample, v2_schema, RemoteQueryEngine
Extracts the duplicated BigQuery-access pattern (project resolution +
client construction + DuckDB-extension session + Google-API error
translation) into connectors/bigquery/access.py. Migrates four
call sites to use it:
- app/api/v2_scan.py — _bq_dry_run_bytes, _run_bq_scan
- app/api/v2_sample.py — _fetch_bq_sample
- app/api/v2_schema.py — _fetch_bq_schema (strict translation),
_fetch_bq_table_options (preserves swallow-all best-effort contract)
- src/remote_query.py — RemoteQueryEngine, lazy bq_access kwarg
The new module exposes:
- BqProjects (frozen dataclass: billing + data project IDs)
- BqAccessError (typed exception with HTTP_STATUS class mapping)
- BqAccess (facade with injectable client_factory/duckdb_session_factory
for tests; defaults call the real google-cloud-bigquery + DuckDB extension)
- get_bq_access (module-level @functools.cache; FastAPI Depends target)
- translate_bq_error (Google API exception → BqAccessError mapper, with
BqAccessError pass-through, 'serviceusage'-substring heuristic for
cross_project_forbidden, and bad_request_status param distinguishing
user-derived (400) from server-constructed (502) SQL)
- _default_client_factory, _default_duckdb_session_factory
RemoteQueryEngine.__init__ no longer accepts _bq_client_factory; tests
migrate to bq_access=BqAccess(projects, client_factory=...). DuckDB-only
RemoteQueryEngine tests need no changes — bq_access defaults to None and
get_bq_access() is only invoked on first BQ call (lazy resolution).
BqAccessError raised internally is translated to RemoteQueryError(
error_type="bq_error") in _get_bq_client to preserve the engine's
existing public contract — CLI and /api/query/hybrid callers see no change.
Endpoint tests (test_v2_scan, test_v2_scan_estimate, test_v2_sample,
test_v2_schema) migrate from monkey-patching whole _fetch_* functions
to using the new bq_access fixture in tests/conftest.py — which
exercises the REAL translation path through BqAccess + translate_bq_error,
closing the test gap flagged in Task 1.1's review.
Side-effect behavior change: v2_sample's FROM clause now uses the data
project (instance.yaml data_source.bigquery.project), not the conflated
billing_project from Phase 1. Documented in CHANGELOG ### Internal.
BREAKING for deployments combining BIGQUERY_PROJECT env var with
data_source.bigquery.project in instance.yaml — env var now overrides
data project too. See CHANGELOG ### Changed.
Two known-duplicate BQ-access sites (connectors/bigquery/extractor.py,
scripts/duckdb_manager.register_bq_table) explicitly out of scope;
tracked as follow-up.
Removed stale docstring at the previous src/remote_query.py:204
that referenced scripts.duckdb_manager._create_bq_client as the default
BQ client factory (RemoteQueryEngine never actually used that function).
Test counts: tests/test_bq_access.py +27 (new), tests/test_v2_*.py +
tests/test_remote_query.py migrated to bq_access fixture (counts unchanged
or +1-2 per file). Full suite: 2086 passed, 8 pre-existing failures
(DB migration tests with unrelated internal_roles DependencyException —
not introduced by this PR).
* fix(bq_access): translate DefaultCredentialsError to BqAccessError(auth_failed)
CI on PR #138 caught: bigquery.Client(...) resolves Application Default
Credentials at construction time; without ADC (CI without SA key, dev
laptop without 'gcloud auth application-default login') it raises
google.auth.exceptions.DefaultCredentialsError synchronously.
Pre-fix _default_client_factory only caught ImportError, so DefaultCredentialsError
propagated as raw exception — and from production endpoints would surface
as bare 500 (the exact failure mode #134 sets out to fix).
Now translates to BqAccessError(kind='auth_failed', details.hint='Run
gcloud auth application-default login...'). Endpoint catch chain returns
HTTP 502 with structured body. Adds unit test
test_raises_auth_failed_on_default_credentials_error.
Third-round spec review flagged this case in passing; the fix didn't land.
CI's auth-less environment surfaced it.
* fix(bq_access): get_bq_access() returns sentinel instead of raising when not configured
Devin BUG_0001 on PR #138 review: 'get_bq_access() as FastAPI Depends
breaks all v2 endpoints for non-BigQuery instances'.
Pre-fix: get_bq_access() raised BqAccessError(not_configured) when
neither BIGQUERY_PROJECT env nor data_source.bigquery.project was set.
Because FastAPI resolves Depends() BEFORE the endpoint body runs, this
exception fires during dep-injection — the endpoint's try/except
BqAccessError clause never gets a chance to catch it. Result: every
v2 request on Keboola-only or CSV-only instances returned bare HTTP
500, even for local-source tables that never touch BigQuery.
Fix: get_bq_access() now returns a sentinel BqAccess with empty
BqProjects and factories that raise BqAccessError(not_configured)
on actual use. Construction succeeds, FastAPI's dep-injection cleanly
yields the sentinel, the endpoint runs. The local-source code path
in build_sample / build_schema / etc. never calls bq.client() or
bq.duckdb_session() (it reads parquet directly), so non-BQ tables
return 200 as before. Only when an endpoint actually tries to query
BQ (source_type == 'bigquery') does the sentinel raise — and the
endpoint's existing except BqAccessError catches it normally,
returning structured 502 with hint.
Test get_bq_access::test_raises_not_configured_when_neither_set
renamed and rewritten to test_returns_sentinel_when_neither_set:
asserts BqAccess is returned, then asserts client() and
duckdb_session() each raise BqAccessError(not_configured) on call.
Test test_does_not_cache_exceptions removed (no longer applicable)
and replaced with test_sentinel_is_cached_per_process documenting
the operator-restart-on-config-change contract.
* docs(spec+plan): #134 genericize customer-specific tokens (CLAUDE.md OSS rule)
Devin BUG_0001/0002 round 3 on PR #138: spec and plan docs contained
customer-specific deployment hostnames, deployment names, and a GCP
project ID that violated CLAUDE.md's vendor-agnostic OSS rule
('Nothing customer-specific belongs in code, configuration defaults,
comments, docs, commit messages, PR titles, or PR bodies').
Replacements:
agnes-development.groupondev.com -> <your-agnes-host>
agnes-development -> <your-dev-instance>
prj-grp-dataview-prod-1ff9 -> <your-data-project>
s1_session_landings -> <bq_table_id>
E2E verification semantics unchanged — operators still run the same
four curls + config flip + retry, just substituting their own host /
deployment name / project / table.
* fix(bq_access): hook get_bq_access.cache_clear into instance_config.reset_cache
Devin ANALYSIS_0004 on PR #138: get_bq_access is @functools.cache'd at
process level, so it captures BigQuery project IDs at first call and
ignores subsequent instance.yaml changes. Pre-Phase-2 the v2 endpoints
re-read get_value() on every request, so admin /api/admin/server-config
saves (which call instance_config.reset_cache()) hot-reloaded the BQ
project. Without this fix, my refactor silently regresses that contract
— operators editing instance.yaml via the admin UI would see no effect
on v2 endpoints until container restart.
instance_config.reset_cache() now also calls
connectors.bigquery.access.get_bq_access.cache_clear() (lazy import,
swallowed if connectors module isn't loaded — keeps instance_config
usable in isolated unit tests).
Adds test_instance_config_reset_cache_invalidates_get_bq_access as
regression guard. Updates CHANGELOG Internal entry to mention the
hot-reload contract + the not-configured sentinel behavior (round-3
fix from Devin BUG_0001 was previously only in commit message).
* fix(bq_access): surface not_configured before identifier validation + plan path genericize
Devin BUG_0001 + BUG_0002 round 5 on PR #138.
BUG_0001 (plan doc): personal filesystem path violated CLAUDE.md
vendor-agnostic rule. Replaced with '<worktree-root>' placeholder.
BUG_0002 (sentinel error path): when get_bq_access() returns the sentinel
BqAccess (BQ not configured), the empty bq.projects.data was reaching
validate_quoted_identifier first and raising ValueError -> endpoint
mapped to HTTP 400 'unsafe_identifier' instead of structured 500
'not_configured' with hint.
Each fetch helper now checks 'if not bq.projects.data: bq.client()' as
the first step, which triggers the sentinel's BqAccessError(not_configured).
Endpoint catches the typed error and returns HTTP 500 with hint pointing
at data_source.bigquery.project. Best-effort _fetch_bq_table_options
returns {} silently in this case (preserves the swallow-all contract).
* fix(bq_access): classify DuckDB-native exceptions from bigquery_query() via string match
Devin ANALYSIS on PR #138 review (latest round). The DuckDB bigquery
extension is a C++ plugin making its own HTTP calls — when BQ returns
403, it throws duckdb.IOException with the BQ error embedded as text,
not gax.Forbidden. translate_bq_error's isinstance checks would miss
these, falling to case 7 → bare 500 in production for v2_scan, v2_sample,
and v2_schema (the bigquery_query() paths).
Fix: last-resort string-match heuristic before the re-raise. 'Forbidden'
/ '403' / 'Bad Request' / '400' in the lowercased message classifies via
the same kind hierarchy. The 'serviceusage' substring still distinguishes
cross_project_forbidden from bq_forbidden. Specific enough that random
exceptions without HTTP-error keywords still re-raise.
Adds 4 unit tests covering the new heuristic + the 'don't swallow random
exceptions' invariant.
* chore(release): cut 0.22.0
PR #138 contains issue #134 user-visible behavior changes:
- BREAKING: BIGQUERY_PROJECT env var now overrides instance.yaml
data_source.bigquery.project for v2 endpoints (previously
RemoteQueryEngine billing only).
- Fixed: structured 502/400 on /api/v2/sample, /scan, /scan/estimate,
/schema when BigQuery raises Forbidden/BadRequest (was bare 500).
- Internal: BqAccess facade refactor unifying four duplicate BQ-access
call sites; instance_config.reset_cache() now invalidates BqAccess
cache too so admin server-config saves hot-reload BQ project IDs.
Bumps to 0.22.0 because PR #137 merged first and took 0.21.0.
Bootstraps the Agnes Claude Code marketplace + RBAC-allowed plugins from
the dashboard CTA, and inlines the server's TLS cert when the chain isn't
publicly trusted (self-signed / private CA). Cross-platform setup prompt
covers Windows Git Bash, macOS, Linux. Includes Bun-compiled `claude` fix
(macOS goes via git-clone fallback, same as Windows), PAT stripping after
clone, explicit error handling, and four rounds of Devin Review fixes
(phantom step references, $PLATFORM re-detection, heredoc/awk line-count
sync). Cuts 0.21.0.
See CHANGELOG.md [0.21.0] section for details.
