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40 changes: 24 additions & 16 deletions pysus/management/sync.py
Original file line number Diff line number Diff line change
Expand Up @@ -21,6 +21,7 @@
import asyncio
import shutil
from collections.abc import Callable
from dataclasses import dataclass
from datetime import datetime
from logging import error, info, warning
from pathlib import Path
Expand Down Expand Up @@ -89,6 +90,15 @@
_CONCURRENCY_BUDGET: int = 2500 * 1024 * 1024 # 2.5 GB


@dataclass
class CatalogCursors:
"""Bundles cursors for the three metadata catalogs."""

central: Any
dataset: Any
columns: Any


class _WeightGate:
"""Bound how many pipeline slots are in use by byte weight.

Expand Down Expand Up @@ -423,9 +433,9 @@ async def upload_file(
"parquet_digest": parquet_digest,
}
self._catalog_rows(
central_cursor,
dataset_cursor,
columns_cursor,
CatalogCursors(
central_cursor, dataset_cursor, columns_cursor
),
file,
payload,
)
Expand Down Expand Up @@ -1162,9 +1172,9 @@ def _catalog_write_entry(
with adapter.transaction() as (conn, dataset_cursor):
self.writer._ensure_management_columns(dataset_cursor)
self._catalog_rows(
central_cursor,
dataset_cursor,
columns_cursor,
CatalogCursors(
central_cursor, dataset_cursor, columns_cursor
),
file,
payload,
)
Expand All @@ -1175,16 +1185,14 @@ def _catalog_write_entry(

def _catalog_rows(
self,
central_cursor,
dataset_cursor,
columns_cursor,
cursors: CatalogCursors,
file: BaseRemoteFile,
payload: dict,
) -> None:
"""Write dataset/group/file/column rows for an uploaded artifact."""
writer = self.writer
dataset_id = writer.ensure_dataset(
central_cursor,
cursors.central,
file.dataset.name,
file.dataset.long_name,
getattr(file.dataset, "description", None),
Expand All @@ -1194,15 +1202,15 @@ def _catalog_rows(
group_name = getattr(group, "name", None) if group is not None else None
group_name = str(group_name) if group_name else None
group_id = writer.ensure_group(
dataset_cursor,
cursors.dataset,
dataset_id,
group_name,
getattr(group, "long_name", None) if group else None,
getattr(group, "description", None) if group else None,
)

writer.upsert_file(
dataset_cursor,
cursors.dataset,
dataset_id=dataset_id,
group_id=group_id,
path=payload["s3_key"],
Expand All @@ -1222,12 +1230,12 @@ def _catalog_rows(
file_type="PARQUET",
)

inserted = writer.get_file(dataset_cursor, payload["s3_key"])
inserted = writer.get_file(cursors.dataset, payload["s3_key"])
assert inserted is not None
file_id, _ = inserted
writer.link_columns(
dataset_cursor,
columns_cursor,
cursors.dataset,
cursors.columns,
file_id,
payload["schema"],
dataset_id,
Expand All @@ -1237,7 +1245,7 @@ def _catalog_rows(
from pysus.api.saude.schemas import apply_column_descriptions

apply_column_descriptions(
columns_cursor,
cursors.columns,
dataset_id,
dataset=file.dataset.name.lower(),
endpoint=file.basename.rsplit(".", 1)[0],
Expand Down
6 changes: 4 additions & 2 deletions pysus/tests/management/test_sync_internal.py
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@

import pytest
from pysus.management.records import FileComparison, FileRecord
from pysus.management.sync import SyncEngine
from pysus.management.sync import CatalogCursors, SyncEngine


@pytest.fixture
Expand Down Expand Up @@ -285,7 +285,9 @@ def test_catalog_rows(self, engine):
) as mock_writer_prop:
mock_writer_prop.return_value = writer
engine._catalog_rows(
central_cursor, dataset_cursor, columns_cursor, file, payload
CatalogCursors(central_cursor, dataset_cursor, columns_cursor),
file,
payload,
)

writer.ensure_dataset.assert_called_once()
Expand Down