* 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.
231 lines
9.6 KiB
Python
231 lines
9.6 KiB
Python
"""Pure-function tests for the Keboola auto-discovery planner.
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The planner walks the discovered table list and the live registry,
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classifying each entry as ``new`` / ``existing_match`` /
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``existing_drift`` / ``invalid`` so the caller can decide whether
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to write. The endpoint and CLI compose on top of this; the planner
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itself touches no external services.
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Two real-world incidents drove this split:
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- kbc_job arrived with the wrong bucket from a manual registration
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(``in.c-keboola-storage`` instead of ``in.c-kbc_telemetry``); a
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naive auto-discover re-run would have overwritten the admin's
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correction. The planner now classifies that as ``existing_drift``
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and the writer skips it, surfacing the divergence in the response.
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- Earlier auto-discover bug stripped the stage prefix off bucket ids
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(e.g. ``c-finance`` instead of ``in.c-finance``), inserting 137
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rows whose Storage API export-async calls all 404'd. The planner
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now uses the Keboola API's authoritative ``bucket_id`` field
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directly, falling back to id-string parsing only when the field
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isn't present.
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"""
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from __future__ import annotations
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from unittest.mock import MagicMock
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import pytest
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from app.api.admin import _build_keboola_discovery_plan, _split_keboola_table_id
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# ---- _split_keboola_table_id (id parser fallback) --------------------------
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class TestSplitKeboolaTableId:
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def test_three_segment_canonical(self):
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# in.c-finance.orders → bucket=in.c-finance, table=orders
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assert _split_keboola_table_id("in.c-finance.orders") == (
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"in.c-finance", "orders",
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)
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def test_three_segment_with_dotted_table_name(self):
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# Bucket-id always c-<word>; treat anything trailing as table.
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# 4-segment id → bucket = first three joined, table = last.
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assert _split_keboola_table_id("in.c-x.foo.bar") == (
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"in.c-x.foo", "bar",
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)
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def test_two_segment_no_stage(self):
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# Defensive: id missing the stage prefix → use what we have.
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assert _split_keboola_table_id("c-foo.events") == (
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"c-foo", "events",
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)
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def test_one_segment_falls_back_to_name(self):
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bucket, table = _split_keboola_table_id("orphan", fallback_name="orphan_t")
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assert bucket == ""
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assert table == "orphan_t"
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def test_empty_string_safe(self):
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bucket, table = _split_keboola_table_id("", fallback_name="x")
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assert bucket == ""
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assert table == "x"
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# ---- _build_keboola_discovery_plan -----------------------------------------
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def _make_repo(rows: dict[str, dict]):
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"""Build a stub repo whose `.get(table_id)` returns the row in `rows`
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(or None). Mirror of TableRegistryRepository's lookup-by-id surface."""
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repo = MagicMock()
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repo.get.side_effect = lambda tid: rows.get(tid)
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return repo
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@pytest.fixture(autouse=True)
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def stub_table_registry(monkeypatch):
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"""The planner instantiates `TableRegistryRepository(conn)` itself.
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Patch the class to return whatever fixture-provided repo we set up
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via ``request.param``-style indirection — but here a simpler
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pattern: per-test setup attaches the rows dict to a module-level
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cache that the fake reads."""
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state = {"rows": {}}
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class _FakeRepo:
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def __init__(self, conn): pass
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def get(self, tid): return state["rows"].get(tid)
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def list_all(self):
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# The planner uses list_all() once at the top to build the
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# name→row index for collision detection. Stamp `source_type`
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# on every row so the planner's keboola filter accepts them.
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return [
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{**v, "id": k, "source_type": v.get("source_type", "keboola")}
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for k, v in state["rows"].items()
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]
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monkeypatch.setattr("app.api.admin.TableRegistryRepository", _FakeRepo)
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return state
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def test_plan_buckets_new_existing_match_drift_and_invalid(stub_table_registry):
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"""Single test exercising the four buckets at once — easier to read
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than four separate tests; failures here surface the exact bucket
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that misclassified.
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Drift here is the **same-id, different-coords** flavour: registry
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has a row at id `kbc_organization` with stale bucket; discovery
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would write a different bucket under the same id. (The
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name-collision flavour gets its own test below.)"""
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stub_table_registry["rows"] = {
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# existing_match: registry agrees with discovery
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"in_c-sales_orders": {
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"name": "orders", "bucket": "in.c-sales", "source_table": "orders",
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},
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# existing_drift (same id): admin migrated bucket post-registration
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"in_c-kbc_telemetry_kbc_organization": {
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"name": "kbc_organization",
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"bucket": "in.c-OLD-bucket", "source_table": "kbc_organization",
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},
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}
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discovered = [
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# new
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{"id": "in.c-sales.invoices", "name": "invoices",
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"bucket_id": "in.c-sales"},
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# existing_match
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{"id": "in.c-sales.orders", "name": "orders",
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"bucket_id": "in.c-sales"},
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# existing_drift (same id, different bucket)
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{"id": "in.c-kbc_telemetry.kbc_organization", "name": "kbc_organization",
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"bucket_id": "in.c-kbc_telemetry"},
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# invalid — empty id
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{"id": "", "name": "broken",
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"bucket_id": ""},
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]
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plan = _build_keboola_discovery_plan(MagicMock(), discovered)
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assert [e["table_id"] for e in plan["new"]] == ["in_c-sales_invoices"]
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assert [e["table_id"] for e in plan["existing_match"]] == ["in_c-sales_orders"]
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assert len(plan["existing_drift"]) == 1
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drift = plan["existing_drift"][0]
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assert drift["drift_kind"] == "same_id_diff_coords"
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assert drift["table_id"] == "in_c-kbc_telemetry_kbc_organization"
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assert drift["bucket"] == "in.c-kbc_telemetry"
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assert drift["registry_bucket"] == "in.c-OLD-bucket"
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assert len(plan["invalid"]) == 1
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assert plan["invalid"][0]["full_id"] == ""
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def test_plan_drift_via_name_collision_kbc_job_real_world(stub_table_registry):
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"""Real-world incident: kbc_job was registered manually as
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``id='kbc_job', name='kbc_job', bucket='in.c-kbc_telemetry'``;
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Keboola's auto-discovery exposes the same logical table at
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``id='in.c-keboola-storage.job', name='job'``. Without
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name-collision detection, the planner would have classified the
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discovered row as `new` and inserted a duplicate whose Storage
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API export-async 404s.
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With the fix, planner detects the **discovered.name == registry.name**
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(case-insensitive) collision, classifies as drift, surfaces the
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`registry_id` so an operator can reconcile."""
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stub_table_registry["rows"] = {
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"kbc_job": {
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"name": "kbc_job",
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"bucket": "in.c-kbc_telemetry", "source_table": "kbc_job",
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},
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}
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discovered = [
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{"id": "in.c-keboola-storage.kbc_job", "name": "kbc_job",
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"bucket_id": "in.c-keboola-storage"},
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]
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plan = _build_keboola_discovery_plan(MagicMock(), discovered)
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assert plan["new"] == [], (
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"duplicate kbc_job must NOT be in new bucket — would 404 at "
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"next sync and clobber operator alerting"
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)
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assert len(plan["existing_drift"]) == 1
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drift = plan["existing_drift"][0]
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assert drift["drift_kind"] == "name_collision"
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assert drift["table_id"] == "in_c-keboola-storage_kbc_job"
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assert drift["registry_id"] == "kbc_job"
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assert drift["bucket"] == "in.c-keboola-storage"
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assert drift["registry_bucket"] == "in.c-kbc_telemetry"
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def test_plan_prefers_api_bucket_id_over_id_parse(stub_table_registry):
|
|
"""Authoritative source for bucket is the API's `bucket_id` field
|
|
(when present). Pre-fix, the parser stripped the stage prefix and
|
|
inserted 137 broken rows — using `bucket_id` directly avoids that
|
|
class of bug entirely."""
|
|
discovered = [
|
|
# bucket_id explicit + present, full id agrees: trivial
|
|
{"id": "in.c-x.t1", "name": "t1", "bucket_id": "in.c-x"},
|
|
# bucket_id present, full id messy / unreliable — bucket_id wins
|
|
{"id": "weird-id-without-dots", "name": "t2", "bucket_id": "in.c-y"},
|
|
]
|
|
plan = _build_keboola_discovery_plan(MagicMock(), discovered)
|
|
by_id = {e["table_id"]: e for e in plan["new"]}
|
|
assert by_id["in_c-x_t1"]["bucket"] == "in.c-x"
|
|
assert by_id["weird-id-without-dots"]["bucket"] == "in.c-y"
|
|
assert by_id["weird-id-without-dots"]["source_table"] == "t2"
|
|
|
|
|
|
def test_plan_falls_back_to_parser_when_bucket_id_missing(stub_table_registry):
|
|
"""Older Keboola SDK fallback path doesn't return `bucket_id`.
|
|
Plan must still produce a usable bucket via the id parser."""
|
|
discovered = [
|
|
{"id": "in.c-z.events", "name": "events"}, # no bucket_id field
|
|
]
|
|
plan = _build_keboola_discovery_plan(MagicMock(), discovered)
|
|
assert plan["new"][0]["bucket"] == "in.c-z"
|
|
assert plan["new"][0]["source_table"] == "events"
|
|
|
|
|
|
def test_plan_drift_skips_overwrite(stub_table_registry):
|
|
"""The plan classifies drift; the writer's contract (separate test
|
|
in test_admin_configure_api.py against the endpoint) is to NOT
|
|
overwrite. Verify here that drifted rows are NOT in the `new`
|
|
bucket (which is the only bucket the writer iterates)."""
|
|
stub_table_registry["rows"] = {
|
|
"in_c-sales_orders": {
|
|
"bucket": "in.c-OLD", "source_table": "orders_renamed",
|
|
},
|
|
}
|
|
discovered = [
|
|
{"id": "in.c-sales.orders", "name": "orders",
|
|
"bucket_id": "in.c-sales"},
|
|
]
|
|
plan = _build_keboola_discovery_plan(MagicMock(), discovered)
|
|
assert plan["new"] == []
|
|
assert len(plan["existing_drift"]) == 1
|