* 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.
734 lines
32 KiB
Python
734 lines
32 KiB
Python
"""Keboola extractor — produces extract.duckdb + data/*.parquet using DuckDB Keboola extension."""
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import logging
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import os
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from datetime import datetime, timezone
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from pathlib import Path
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from typing import List, Dict, Any, Optional
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import duckdb
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from src.identifier_validation import (
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is_safe_quoted_identifier,
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validate_identifier,
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validate_quoted_identifier,
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)
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logger = logging.getLogger(__name__)
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def materialize_query(
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table_id: str,
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*,
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bucket: str,
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source_table: str,
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source_query: Optional[str] = None,
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storage_client=None, # KeboolaStorageClient (avoid circular import)
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keboola_url: Optional[str] = None,
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keboola_token: Optional[str] = None,
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output_dir: Path,
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) -> dict:
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"""Materialize a Keboola Storage table to a local parquet via Storage API.
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Replaces the previous DuckDB-extension path. The extension's QueryService
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scan is unreliable on linked-bucket projects (keboola/duckdb-extension#17;
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fix shipped upstream as v0.1.6 but not yet in the community CDN, and on
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flag-restricted projects the pre-fix workspace role wouldn't have GRANTs
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on the bucket schema anyway). The Storage API export-async path always
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works regardless of project flags.
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Parallel of `connectors/bigquery/extractor.py:materialize_query` in
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surface — same return shape, same atomic write, same MD5 contract — but
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the inputs differ because Keboola's structured filter spec replaces
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BQ's free-form SQL.
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Args:
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table_id: parquet filename + sync_state key (must be a safe ident).
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bucket: Keboola bucket id, e.g. ``in.c-crm``.
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source_table: table id within the bucket, e.g. ``orders``.
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source_query: optional JSON string with a Storage API filter spec
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(see `storage_api.ExportFilter`). Empty / NULL = full table.
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storage_client: pre-built `KeboolaStorageClient` (preferred — lets
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sync.py share one across rows). When omitted, ``keboola_url``
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and ``keboola_token`` are used to construct a one-shot client.
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keboola_url, keboola_token: alternative to ``storage_client`` for
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single-call usage (tests, ad-hoc).
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output_dir: directory to write `<table_id>.parquet`.
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Returns:
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``{"table_id", "path", "rows", "bytes", "md5"}`` — same shape the
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BQ branch returns, so ``app/api/sync.py:_run_materialized_pass``
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downstream code stays uniform.
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"""
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import re
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import hashlib
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import json
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import duckdb
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if not re.fullmatch(r"[A-Za-z_][A-Za-z0-9_]*", table_id):
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raise ValueError(f"unsafe table_id for materialize: {table_id!r}")
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# Lazy import to avoid pulling `requests` at module import time when only
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# the sync trigger imports `extractor` for `run()`.
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from connectors.keboola.storage_api import (
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FILE_TYPE_CSV, FILE_TYPE_PARQUET, ExportFilter, KeboolaStorageClient,
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)
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if storage_client is None:
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if not (keboola_url and keboola_token):
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raise ValueError(
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"materialize_query requires either storage_client or "
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"(keboola_url + keboola_token)"
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)
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storage_client = KeboolaStorageClient(url=keboola_url, token=keboola_token)
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# Filter spec is optional. Admin can register a row with no
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# source_query at all (= full-table export), or with a JSON object
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# describing whereFilters / columns / changedSince / file_type.
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payload: dict = {}
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if source_query:
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try:
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payload = json.loads(source_query)
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except json.JSONDecodeError as e:
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raise ValueError(
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f"source_query for {table_id} is not valid JSON: {e}"
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) from e
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export_filter = ExportFilter.from_dict(payload)
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# Default the materialized path to parquet — Storage API serves it
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# via native Snowflake UNLOAD, the extractor renames it into place,
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# no CSV intermediate, no DuckDB COPY, no peak-memory load. Admin
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# can pin `{"file_type":"csv"}` in source_query to fall back (legacy
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# debugging, or projects whose backend can't UNLOAD parquet — none
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# known today, but the escape hatch costs nothing). Only override
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# when the admin spec didn't *explicitly* set a file_type.
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if "file_type" not in payload and "fileType" not in payload:
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export_filter.file_type = FILE_TYPE_PARQUET
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output_dir = Path(output_dir)
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output_dir.mkdir(parents=True, exist_ok=True)
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parquet_path = output_dir / f"{table_id}.parquet"
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tmp_parquet = output_dir / f"{table_id}.parquet.tmp"
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if tmp_parquet.exists():
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tmp_parquet.unlink()
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# Per-call temp dir for the intermediate file (CSV or parquet) —
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# separates concurrent exports cleanly without the os.chdir() race
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# the kbcstorage SDK has. ``ignore_cleanup_errors=True`` keeps
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# disk-full / permission errors from masking the original
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# exception, and prevents a half-cleaned dir from sitting around
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# forever (a 12 GiB stale slice tree was seen after a worker died
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# mid-write on a saturated boot disk). ``dir=get_temp_root()``
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# routes to ``AGNES_TEMP_DIR`` when the operator has steered
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# tempfiles off the overlayfs (e.g. onto the data disk) — see
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# storage_api.get_temp_root for the rationale.
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import tempfile
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from connectors.keboola.storage_api import get_temp_root
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with tempfile.TemporaryDirectory(
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prefix=f"kbc-export-{table_id}-",
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dir=get_temp_root(),
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ignore_cleanup_errors=True,
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) as tmpdir:
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full_table_id = f"{bucket}.{source_table}"
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if export_filter.file_type == FILE_TYPE_PARQUET:
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# Native parquet path. Storage API serves Snowflake UNLOAD
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# output directly. Two shapes to handle:
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#
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# 1. **Single file** (small exports): file_info.url points at
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# one signed URL; download to tmp_parquet and we're done.
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# 2. **Sliced** (large exports — Snowflake UNLOAD respects
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# MAX_FILE_SIZE, default 16 MiB, so anything past that
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# arrives as a manifest of N parquet slices). Each slice
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# is itself a complete parquet file with its own footer;
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# naively concatenating them like CSV would be invalid.
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# We download all slices into the per-call tempdir, then
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# DuckDB-COPY across `read_parquet([slice1, slice2, ...])`
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# into one consolidated tmp_parquet. DuckDB streams row
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# groups during this consolidation — peak memory is one
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# row group (~1 MiB), not the full table.
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stats = storage_client.prepare_export(
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full_table_id, export_filter=export_filter,
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)
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file_info = stats["file_info"]
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if file_info.get("isSliced"):
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slice_dir = Path(tmpdir) / "slices"
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slice_paths = storage_client.download_file_slices(
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file_info, slice_dir
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)
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if not slice_paths:
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raise RuntimeError(
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f"sliced parquet export for {full_table_id} "
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f"yielded no slices"
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)
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quoted = ", ".join(
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"'" + str(p).replace("'", "''") + "'" for p in slice_paths
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)
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safe_tmp = str(tmp_parquet).replace("'", "''")
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conv = duckdb.connect()
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try:
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conv.execute(
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f"COPY (SELECT * FROM read_parquet([{quoted}])) "
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f"TO '{safe_tmp}' (FORMAT PARQUET)"
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)
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finally:
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conv.close()
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else:
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storage_client.download_file(file_info, tmp_parquet)
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stats["bytes"] = (
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tmp_parquet.stat().st_size if tmp_parquet.exists() else 0
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)
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if not tmp_parquet.exists() or tmp_parquet.stat().st_size == 0:
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logger.warning(
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"Storage API parquet export for %s returned no data "
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"(filter may be too restrictive)",
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full_table_id,
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)
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# Empty placeholder parquet so the orchestrator doesn't
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# choke on a missing file.
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duckdb.connect().execute(
|
|
f"COPY (SELECT 1 AS _empty WHERE FALSE) TO '{tmp_parquet}' (FORMAT PARQUET)"
|
|
).close()
|
|
else:
|
|
# Legacy CSV path. Kept for the explicit `{"file_type":"csv"}`
|
|
# opt-in. Slower (CSV parse + parquet rewrite) and
|
|
# memory-heavier (DuckDB pulls the CSV into a buffer with
|
|
# max_line_size headroom), but doesn't depend on Storage
|
|
# API parquet support if a future project backend lacks it.
|
|
csv_path = Path(tmpdir) / f"{table_id}.csv"
|
|
stats = storage_client.export_table(
|
|
full_table_id, csv_path, export_filter=export_filter,
|
|
)
|
|
if not csv_path.exists() or csv_path.stat().st_size == 0:
|
|
logger.warning(
|
|
"Storage API CSV export for %s returned no data "
|
|
"(filter may be too restrictive)",
|
|
full_table_id,
|
|
)
|
|
duckdb.connect().execute(
|
|
f"COPY (SELECT 1 AS _empty WHERE FALSE) TO '{tmp_parquet}' (FORMAT PARQUET)"
|
|
).close()
|
|
else:
|
|
# CSV → parquet via DuckDB. `all_varchar=True` matches the
|
|
# legacy client's behavior — preserves the source's exact
|
|
# character data without DuckDB's type inference rewriting
|
|
# numeric-looking strings (e.g. "Non-Manager") as NULL.
|
|
#
|
|
# `max_line_size=64MB` overrides DuckDB's default 2 MB cap
|
|
# on any single CSV line. Keboola tables that store
|
|
# embedded JSON / SQL transformation bodies routinely
|
|
# have multi-MB cells (e.g. `kbc_component_configuration`
|
|
# rows ship full Snowflake transformation SQL inline as
|
|
# a JSON column value); the default 2 MB ceiling rejects
|
|
# them with `Maximum line size of 2000000 bytes
|
|
# exceeded`. 64 MB is generous enough to absorb any
|
|
# reasonable embedded blob; DuckDB allocates a single
|
|
# buffer of this size per worker thread.
|
|
safe_csv = str(csv_path).replace("'", "''")
|
|
safe_tmp = str(tmp_parquet).replace("'", "''")
|
|
try:
|
|
conv = duckdb.connect()
|
|
conv.execute(
|
|
f"COPY (SELECT * FROM read_csv('{safe_csv}', "
|
|
f"all_varchar=true, max_line_size=67108864)) "
|
|
f"TO '{safe_tmp}' (FORMAT PARQUET)"
|
|
)
|
|
conv.close()
|
|
except Exception:
|
|
if tmp_parquet.exists():
|
|
tmp_parquet.unlink()
|
|
raise
|
|
|
|
# Row count from the parquet, not from `stats["rows"]` — Storage API
|
|
# sometimes omits totalRowsCount on small results, and the parquet is
|
|
# the authoritative count we'll be serving downstream anyway.
|
|
safe_tmp = str(tmp_parquet).replace("'", "''")
|
|
cnt_conn = duckdb.connect()
|
|
try:
|
|
row_count = cnt_conn.execute(
|
|
f"SELECT COUNT(*) FROM read_parquet('{safe_tmp}')"
|
|
).fetchone()[0]
|
|
finally:
|
|
cnt_conn.close()
|
|
|
|
# Streaming MD5 — bounded memory regardless of parquet size.
|
|
h = hashlib.md5()
|
|
with open(tmp_parquet, "rb") as f:
|
|
for chunk in iter(lambda: f.read(8192), b""):
|
|
h.update(chunk)
|
|
md5 = h.hexdigest()
|
|
size = tmp_parquet.stat().st_size
|
|
|
|
os.replace(tmp_parquet, parquet_path)
|
|
|
|
if row_count == 0:
|
|
logger.warning(
|
|
"Materialized Keboola export for %s wrote 0 rows — verify the "
|
|
"filter and that the source bucket has data.",
|
|
table_id,
|
|
)
|
|
|
|
return {
|
|
"table_id": table_id,
|
|
"path": str(parquet_path),
|
|
"rows": row_count,
|
|
"bytes": size,
|
|
"md5": md5,
|
|
}
|
|
|
|
|
|
def _create_meta_table(conn: duckdb.DuckDBPyConnection) -> None:
|
|
"""Create the _meta table required by the extract.duckdb contract."""
|
|
conn.execute("DROP TABLE IF EXISTS _meta")
|
|
conn.execute("""CREATE TABLE _meta (
|
|
table_name VARCHAR NOT NULL,
|
|
description VARCHAR,
|
|
rows BIGINT,
|
|
size_bytes BIGINT,
|
|
extracted_at TIMESTAMP,
|
|
query_mode VARCHAR DEFAULT 'local'
|
|
)""")
|
|
|
|
|
|
def _create_remote_attach_table(conn: duckdb.DuckDBPyConnection, keboola_url: str) -> None:
|
|
"""Write _remote_attach so orchestrator can re-ATTACH the Keboola extension."""
|
|
conn.execute("DROP TABLE IF EXISTS _remote_attach")
|
|
conn.execute("""CREATE TABLE _remote_attach (
|
|
alias VARCHAR,
|
|
extension VARCHAR,
|
|
url VARCHAR,
|
|
token_env VARCHAR
|
|
)""")
|
|
conn.execute(
|
|
"INSERT INTO _remote_attach VALUES (?, ?, ?, ?)",
|
|
["kbc", "keboola", keboola_url, "KEBOOLA_STORAGE_TOKEN"],
|
|
)
|
|
|
|
|
|
def _try_attach_extension(conn: duckdb.DuckDBPyConnection, keboola_url: str, keboola_token: str) -> bool:
|
|
"""Try to install and attach the Keboola DuckDB extension. Returns True on success."""
|
|
try:
|
|
conn.execute("INSTALL keboola FROM community; LOAD keboola;")
|
|
escaped_token = keboola_token.replace("'", "''")
|
|
# Strip trailing slash — the Keboola DuckDB extension's ATTACH fails
|
|
# with a network error when the URL ends in `/` (e.g. the canonical
|
|
# `https://connection.us-east4.gcp.keboola.com/` form). Bare host
|
|
# works.
|
|
attach_url = keboola_url.rstrip("/")
|
|
conn.execute(f"ATTACH '{attach_url}' AS kbc (TYPE keboola, TOKEN '{escaped_token}')")
|
|
logger.info("Using DuckDB Keboola extension")
|
|
return True
|
|
except Exception as e:
|
|
logger.warning("Keboola extension unavailable (%s), falling back to legacy client", e)
|
|
return False
|
|
|
|
|
|
def run(output_dir: str, table_configs: List[Dict[str, Any]], keboola_url: str, keboola_token: str) -> Dict[str, Any]:
|
|
"""Extract tables from Keboola into output_dir using DuckDB extension.
|
|
|
|
Args:
|
|
output_dir: Path to write extract.duckdb + data/
|
|
table_configs: List of table config dicts from table_registry
|
|
keboola_url: Keboola stack URL
|
|
keboola_token: Keboola Storage API token
|
|
|
|
Returns:
|
|
Dict with extraction stats: {tables_extracted: int, tables_failed: int, errors: list}
|
|
"""
|
|
output_path = Path(output_dir)
|
|
data_dir = output_path / "data"
|
|
data_dir.mkdir(parents=True, exist_ok=True)
|
|
|
|
# Write to temp file then rename — avoids lock conflict with orchestrator
|
|
# which may hold a read lock on the existing extract.duckdb
|
|
db_path = output_path / "extract.duckdb"
|
|
tmp_db_path = output_path / "extract.duckdb.tmp"
|
|
if tmp_db_path.exists():
|
|
tmp_db_path.unlink()
|
|
conn = duckdb.connect(str(tmp_db_path))
|
|
|
|
stats = {"tables_extracted": 0, "tables_failed": 0, "errors": []}
|
|
now = datetime.now(timezone.utc)
|
|
|
|
# Per-table workitems whose extension scan failed and need the legacy
|
|
# Storage-API fallback. Drained in a parallel pool below the per-table
|
|
# serial loop. Items are `(tc, pq_path)` tuples.
|
|
legacy_queue: List[tuple] = []
|
|
|
|
try:
|
|
# Try DuckDB Keboola extension
|
|
use_extension = _try_attach_extension(conn, keboola_url, keboola_token)
|
|
|
|
_create_meta_table(conn)
|
|
|
|
has_remote = any(tc.get("query_mode") == "remote" for tc in table_configs)
|
|
if has_remote and use_extension:
|
|
_create_remote_attach_table(conn, keboola_url)
|
|
|
|
for tc in table_configs:
|
|
table_name = tc["name"]
|
|
query_mode = tc.get("query_mode", "local")
|
|
|
|
# Materialized rows are written by the sync trigger pass via
|
|
# `materialize_query()` — they live as parquets in
|
|
# /data/extracts/keboola/data/, picked up by the orchestrator's
|
|
# standard local-parquet discovery. Don't extract here (would
|
|
# double-write data via the source bucket reference and confuse
|
|
# sync_state bookkeeping). Mirror of the BQ extractor's skip at
|
|
# connectors/bigquery/extractor.py:190.
|
|
if query_mode == "materialized":
|
|
logger.info(
|
|
"Skipping legacy extract for %s — query_mode='materialized', "
|
|
"handled by _run_materialized_pass instead",
|
|
tc.get("id") or tc.get("name"),
|
|
)
|
|
continue
|
|
|
|
# #81 Group D — refuse rows whose identifiers don't pass the
|
|
# whitelist. The registry is admin-controlled but anyone with
|
|
# write access can otherwise inject SQL via the CREATE VIEW /
|
|
# COPY / SELECT interpolation below. Skip-and-continue rather
|
|
# than crashing the whole extraction; valid rows still process.
|
|
#
|
|
# `table_name` is the DuckDB view name in the master
|
|
# analytics DB. The orchestrator uses the STRICT validator
|
|
# (`^[a-zA-Z_][a-zA-Z0-9_]{0,63}$`) when re-creating views,
|
|
# so any name with `-` or `.` would pass extraction here
|
|
# but be silently dropped at orchestrator-rebuild time.
|
|
# Use the strict validator here too so the failure is
|
|
# caught early and visible in tables_failed.
|
|
if not validate_identifier(table_name, "Keboola table_name"):
|
|
stats["tables_failed"] += 1
|
|
stats["errors"].append({"table": table_name, "error": "unsafe identifier"})
|
|
continue
|
|
|
|
if query_mode == "remote":
|
|
# Create view pointing to kbc extension (requires re-ATTACH at query time)
|
|
bucket = tc.get("bucket", "")
|
|
source_table = tc.get("source_table", table_name)
|
|
if not (
|
|
validate_quoted_identifier(bucket, "Keboola bucket")
|
|
and validate_quoted_identifier(source_table, "Keboola source_table")
|
|
):
|
|
stats["tables_failed"] += 1
|
|
stats["errors"].append({"table": table_name, "error": "unsafe bucket/source_table"})
|
|
continue
|
|
if use_extension and bucket:
|
|
conn.execute(
|
|
f'CREATE OR REPLACE VIEW "{table_name}" AS SELECT * FROM kbc."{bucket}"."{source_table}"'
|
|
)
|
|
conn.execute(
|
|
"INSERT INTO _meta VALUES (?, ?, 0, 0, ?, 'remote')",
|
|
[table_name, tc.get("description", ""), now],
|
|
)
|
|
stats["tables_extracted"] += 1
|
|
continue
|
|
|
|
try:
|
|
pq_path = str(data_dir / f"{table_name}.parquet")
|
|
|
|
if use_extension:
|
|
try:
|
|
_extract_via_extension(conn, tc, pq_path)
|
|
except Exception as ext_err:
|
|
# ATTACH succeeded but the per-table COPY failed —
|
|
# most commonly a Keboola QueryService permission error
|
|
# (`Schema '..."in.c-..."' does not exist or not
|
|
# authorized`, see keboola/duckdb-extension#17). The
|
|
# legacy Storage-API client doesn't go through
|
|
# QueryService at all, so queue for the parallel
|
|
# legacy fallback below.
|
|
logger.warning(
|
|
"Keboola extension scan failed for %s (%s); queued for legacy Storage-API fallback",
|
|
table_name, ext_err,
|
|
)
|
|
legacy_queue.append((tc, pq_path))
|
|
continue
|
|
else:
|
|
legacy_queue.append((tc, pq_path))
|
|
continue
|
|
|
|
# Extension path succeeded — register _meta synchronously.
|
|
_register_local_meta(conn, tc, pq_path, now)
|
|
stats["tables_extracted"] += 1
|
|
rows_log = conn.execute(
|
|
f"SELECT count(*) FROM read_parquet('{pq_path.replace(chr(39), chr(39)*2)}')"
|
|
).fetchone()[0]
|
|
logger.info("Extracted %s via extension: %d rows", table_name, rows_log)
|
|
|
|
except Exception as e:
|
|
logger.error("Failed to extract %s: %s", table_name, e)
|
|
stats["tables_failed"] += 1
|
|
stats["errors"].append({"table": table_name, "error": str(e)})
|
|
|
|
# Detach Keboola if extension was used
|
|
if use_extension:
|
|
try:
|
|
conn.execute("DETACH kbc")
|
|
except Exception:
|
|
pass
|
|
|
|
# Phase 2: legacy fallback in parallel. Keboola Storage API export
|
|
# jobs are independent per table — a worker pool of N workers fans
|
|
# out the per-table HTTP roundtrips (export job submit + poll +
|
|
# CSV download) instead of stacking them sequentially. Project-level
|
|
# concurrency is bounded by the storage.jobsParallelism limit
|
|
# (typically 10); default to 4 to leave headroom for other clients.
|
|
# Override via AGNES_KEBOOLA_PARALLELISM env var.
|
|
#
|
|
# Workers are PROCESSES, not threads — `connectors/keboola/client.py:
|
|
# export_table` does `os.chdir(temp_dir)` to redirect kbcstorage's
|
|
# slice-file downloads into a per-call temp directory, and `os.chdir`
|
|
# is process-global. With threads, two parallel exports race on CWD
|
|
# and slice files end up in the wrong directory; the merge step then
|
|
# fails with `[Errno 2] No such file or directory:
|
|
# '<job_id>.csv_X_Y_Z.csv'`. ProcessPoolExecutor gives each worker
|
|
# its own process and therefore its own CWD.
|
|
if legacy_queue:
|
|
parallelism = max(1, int(os.environ.get("AGNES_KEBOOLA_PARALLELISM", "8")))
|
|
workers = min(parallelism, len(legacy_queue))
|
|
logger.info(
|
|
"Running legacy Storage-API fallback for %d tables across %d worker processes",
|
|
len(legacy_queue), workers,
|
|
)
|
|
|
|
if workers == 1:
|
|
legacy_results = [_legacy_worker(item, keboola_url, keboola_token) for item in legacy_queue]
|
|
else:
|
|
from concurrent.futures import ProcessPoolExecutor
|
|
|
|
with ProcessPoolExecutor(max_workers=workers) as ex:
|
|
futures = [ex.submit(_legacy_worker, item, keboola_url, keboola_token) for item in legacy_queue]
|
|
legacy_results = [f.result() for f in futures]
|
|
|
|
# Phase 3: serial _meta insert for legacy results. DuckDB conn
|
|
# isn't thread-safe, so we collect parallel work and only touch
|
|
# `conn` (and `stats`) here on the main thread.
|
|
for tc_, pq_, err in legacy_results:
|
|
tn = tc_["name"]
|
|
if err is not None:
|
|
logger.error("Failed to extract %s via legacy: %s", tn, err)
|
|
stats["tables_failed"] += 1
|
|
stats["errors"].append({"table": tn, "error": err})
|
|
continue
|
|
try:
|
|
_register_local_meta(conn, tc_, pq_, now)
|
|
stats["tables_extracted"] += 1
|
|
rows_log = conn.execute(
|
|
f"SELECT count(*) FROM read_parquet('{pq_.replace(chr(39), chr(39)*2)}')"
|
|
).fetchone()[0]
|
|
logger.info("Extracted %s via legacy: %d rows", tn, rows_log)
|
|
except Exception as e:
|
|
logger.error("Failed to register _meta for %s: %s", tn, e)
|
|
stats["tables_failed"] += 1
|
|
stats["errors"].append({"table": tn, "error": str(e)})
|
|
|
|
finally:
|
|
conn.execute("CHECKPOINT")
|
|
conn.close()
|
|
|
|
# Atomic replace: swap temp DB into place, cleaning up any WAL files
|
|
import shutil
|
|
|
|
old_wal = Path(str(db_path) + ".wal")
|
|
if old_wal.exists():
|
|
old_wal.unlink()
|
|
|
|
if tmp_db_path.exists():
|
|
shutil.move(str(tmp_db_path), str(db_path))
|
|
|
|
tmp_wal = Path(str(tmp_db_path) + ".wal")
|
|
if tmp_wal.exists():
|
|
tmp_wal.unlink()
|
|
|
|
return stats
|
|
|
|
|
|
def _register_local_meta(
|
|
conn: duckdb.DuckDBPyConnection,
|
|
tc: Dict[str, Any],
|
|
pq_path: str,
|
|
extracted_at: datetime,
|
|
) -> None:
|
|
"""After a parquet has been written for a local-mode table, create the
|
|
DuckDB view and register the row in `_meta`. Hoisted out of the run()
|
|
body so both the serial extension-success path and the parallel
|
|
legacy-result path share one implementation."""
|
|
table_name = tc["name"]
|
|
safe_pq_lit = pq_path.replace("'", "''")
|
|
rows = conn.execute(f"SELECT count(*) FROM read_parquet('{safe_pq_lit}')").fetchone()[0]
|
|
size = os.path.getsize(pq_path)
|
|
conn.execute(
|
|
f'CREATE OR REPLACE VIEW "{table_name}" AS SELECT * FROM read_parquet(\'{safe_pq_lit}\')'
|
|
)
|
|
conn.execute(
|
|
"INSERT INTO _meta VALUES (?, ?, ?, ?, ?, 'local')",
|
|
[table_name, tc.get("description", ""), rows, size, extracted_at],
|
|
)
|
|
|
|
|
|
def _extract_via_extension(conn: duckdb.DuckDBPyConnection, tc: Dict[str, Any], pq_path: str) -> None:
|
|
"""Extract a table using the DuckDB Keboola extension."""
|
|
bucket = tc.get("bucket", "")
|
|
source_table = tc.get("source_table", tc["name"])
|
|
# #81 Group D — defense-in-depth. The caller already validates these;
|
|
# refuse here too in case a future caller forgets. Use the relaxed
|
|
# quoted-identifier check that accepts Keboola's `in.c-foo` form.
|
|
if not (is_safe_quoted_identifier(bucket) and is_safe_quoted_identifier(source_table)):
|
|
raise ValueError(f"unsafe bucket/source_table: {bucket!r}/{source_table!r}")
|
|
safe_pq_lit = pq_path.replace("'", "''")
|
|
conn.execute(f'COPY (SELECT * FROM kbc."{bucket}"."{source_table}") TO \'{safe_pq_lit}\' (FORMAT PARQUET)')
|
|
|
|
|
|
def _legacy_worker(tc_pq, keboola_url: str, keboola_token: str):
|
|
"""Module-level wrapper for ProcessPoolExecutor — must be picklable.
|
|
|
|
Returns `(tc, pq_path, error_str_or_None)` so the main process can
|
|
aggregate results and update _meta serially on its DuckDB connection.
|
|
"""
|
|
tc_, pq_ = tc_pq
|
|
try:
|
|
_extract_via_legacy(tc_, pq_, keboola_url, keboola_token)
|
|
return (tc_, pq_, None)
|
|
except Exception as exc:
|
|
return (tc_, pq_, str(exc))
|
|
|
|
|
|
def _extract_via_legacy(tc: Dict[str, Any], pq_path: str, keboola_url: str, keboola_token: str) -> None:
|
|
"""Per-table extract via the Storage API export-async path.
|
|
|
|
Despite the name (kept for caller compatibility with `_legacy_worker`),
|
|
this no longer goes through the `kbcstorage` SDK — it talks to the
|
|
Storage API directly via `connectors/keboola/storage_api.py`. The old
|
|
SDK path had a thread-unsafe `os.chdir(temp_dir)` that broke parallel
|
|
execution; the direct path uses per-call temp directories and signed-URL
|
|
downloads, so threads / processes don't trip on each other.
|
|
|
|
Same surface as before — `(tc, pq_path, url, token) → writes parquet at
|
|
pq_path` — so callers (including the parallel `_legacy_worker`) don't
|
|
need to change.
|
|
"""
|
|
import tempfile
|
|
from connectors.keboola.storage_api import KeboolaStorageClient, get_temp_root
|
|
|
|
bucket = tc.get("bucket", "")
|
|
source_table = tc.get("source_table", tc["name"])
|
|
table_id = f"{bucket}.{source_table}" if bucket else tc.get("id", tc["name"])
|
|
|
|
with tempfile.TemporaryDirectory(
|
|
prefix=f"kbc-export-{tc['name']}-",
|
|
dir=get_temp_root(),
|
|
ignore_cleanup_errors=True,
|
|
) as tmpdir:
|
|
csv_path = Path(tmpdir) / f"{tc['name']}.csv"
|
|
client = KeboolaStorageClient(url=keboola_url, token=keboola_token)
|
|
client.export_table_to_csv(table_id, csv_path)
|
|
|
|
if not csv_path.exists() or csv_path.stat().st_size == 0:
|
|
# Storage API succeeded but produced no rows. Emit an empty
|
|
# parquet rather than crashing — same defensive behavior as
|
|
# `materialize_query`.
|
|
duckdb.connect().execute(
|
|
f"COPY (SELECT 1 AS _empty WHERE FALSE) TO '{pq_path}' (FORMAT PARQUET)"
|
|
).close()
|
|
return
|
|
|
|
# all_varchar=true preserves the source's exact character data —
|
|
# matches what the kbcstorage path used to do, prevents DuckDB
|
|
# type inference from rewriting numeric-looking strings as NULL.
|
|
# max_line_size=64MB overrides DuckDB's 2MB default; matches the
|
|
# materialize_query path. See comment there for rationale.
|
|
safe_csv = str(csv_path).replace("'", "''")
|
|
safe_pq = pq_path.replace("'", "''")
|
|
conv = duckdb.connect()
|
|
try:
|
|
conv.execute(
|
|
f"COPY (SELECT * FROM read_csv('{safe_csv}', "
|
|
f"all_varchar=true, max_line_size=67108864)) "
|
|
f"TO '{safe_pq}' (FORMAT PARQUET)"
|
|
)
|
|
finally:
|
|
conv.close()
|
|
|
|
|
|
def compute_exit_code(stats: Dict[str, Any], total: int) -> int:
|
|
"""Map an extraction `stats` dict to a process exit code.
|
|
|
|
Issue #81 Group B: distinguish full success from partial failure so
|
|
the sync API and CLI consumers can alert on partial vs. full failure
|
|
rather than treating any non-zero as one bucket.
|
|
|
|
- ``0`` — every table succeeded (or no tables registered).
|
|
- ``1`` — every table failed (full failure).
|
|
- ``2`` — at least one succeeded and at least one failed (partial).
|
|
|
|
`total` is the count of tables the extractor was asked to process.
|
|
`stats["tables_failed"]` is the count it actually failed.
|
|
"""
|
|
failed = stats.get("tables_failed", 0)
|
|
if total == 0:
|
|
return 0
|
|
if failed == 0:
|
|
return 0
|
|
if failed >= total:
|
|
return 1
|
|
return 2
|
|
|
|
|
|
if __name__ == "__main__":
|
|
"""Standalone: reads config from env + table_registry, runs extraction.
|
|
|
|
Used by sync trigger subprocess. Reads KEBOOLA_STORAGE_TOKEN and
|
|
KEBOOLA_STACK_URL from environment, table list from DuckDB registry.
|
|
"""
|
|
from app.logging_config import setup_logging
|
|
|
|
setup_logging(__name__)
|
|
|
|
# Read Keboola credentials — env first, then instance.yaml fallback
|
|
url = os.environ.get("KEBOOLA_STACK_URL", "")
|
|
token = os.environ.get("KEBOOLA_STORAGE_TOKEN", "")
|
|
|
|
if not url or not token:
|
|
try:
|
|
from config.loader import load_instance_config
|
|
|
|
config = load_instance_config()
|
|
kbc_config = config.get("keboola", {})
|
|
url = url or kbc_config.get("url", "")
|
|
token_env = kbc_config.get("token_env", "KEBOOLA_STORAGE_TOKEN")
|
|
token = token or os.environ.get(token_env, "")
|
|
except Exception:
|
|
pass
|
|
|
|
if not url or not token:
|
|
logger.error("Missing KEBOOLA_STACK_URL or KEBOOLA_STORAGE_TOKEN")
|
|
exit(1)
|
|
|
|
# Read table list from registry
|
|
from src.db import get_system_db
|
|
from src.repositories.table_registry import TableRegistryRepository
|
|
|
|
sys_conn = get_system_db()
|
|
try:
|
|
repo = TableRegistryRepository(sys_conn)
|
|
tables = repo.list_by_source("keboola")
|
|
finally:
|
|
sys_conn.close()
|
|
|
|
if not tables:
|
|
logger.warning("No Keboola tables registered in table_registry")
|
|
exit(0)
|
|
|
|
logger.info("Extracting %d tables from %s", len(tables), url)
|
|
data_dir = Path(os.environ.get("DATA_DIR", "./data"))
|
|
result = run(str(data_dir / "extracts" / "keboola"), tables, url, token)
|
|
logger.info("Extraction complete: %s", result)
|
|
|
|
code = compute_exit_code(result, len(tables))
|
|
if code == 2:
|
|
logger.error("Partial failure: %d of %d tables failed", result.get("tables_failed", 0), len(tables))
|
|
elif code == 1:
|
|
logger.error("All %d tables failed", len(tables))
|
|
exit(code)
|