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Using zarr zipstore for both transport and local caching #44

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2d6eac1
Using zarr zipstore for both transport and local caching
seboceanum Jan 28, 2026
ee45b95
Changing extensions in test
seboceanum Feb 2, 2026
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13 changes: 8 additions & 5 deletions src/oceanum/datamesh/cache.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@
import xarray as xr
import pandas as pd
import geopandas as gpd
from zarr.storage import ZipStore

from .query import Query

Expand Down Expand Up @@ -51,14 +52,15 @@ def unlock(self, query):
def _get(self, query):
cache_file = self._cachepath(query)
try:
if os.path.exists(cache_file + ".nc"):
if os.path.exists(cache_file + ".zarr.zip"):
if (
os.path.getmtime(cache_file + ".nc") + self.cache_timeout
os.path.getmtime(cache_file + ".zarr.zip") + self.cache_timeout
< time.time()
):
os.remove(cache_file + ".nc")
os.remove(cache_file + ".zarr.zip")
return None
return xr.open_dataset(cache_file + ".nc")
with ZipStore(cache_file + ".zarr.zip") as store:
return xr.open_zarr(store, consolidated=True).load()
elif os.path.exists(cache_file + ".gpq"):
if (
os.path.getmtime(cache_file + ".gpq") + self.cache_timeout
Expand Down Expand Up @@ -95,7 +97,8 @@ def copy(self, query, fname, ext):
def put(self, query, data):
cache_file = self._cachepath(query)
if isinstance(data, xr.Dataset):
data.to_netcdf(cache_file + ".nc")
with ZipStore(cache_file + ".zarr.zip") as store:
data.to_zarr(store, consolidated=True)
elif isinstance(data, gpd.GeoDataFrame):
data.to_parquet(cache_file + ".gpq")
elif isinstance(data, pd.DataFrame):
Expand Down
14 changes: 9 additions & 5 deletions src/oceanum/datamesh/connection.py
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Original file line number Diff line number Diff line change
Expand Up @@ -25,6 +25,7 @@
import numbers
import urllib3
from pydantic import ValidationError
from zarr.storage import ZipStore

from .datasource import Datasource
from .catalog import Catalog
Expand Down Expand Up @@ -354,7 +355,7 @@ def _query(self, query, use_dask=False, cache_timeout=0, retry=0):
if cache_timeout:
localcache.lock(query)
transfer_format = (
"application/x-netcdf4"
"application/zarr+zip"
if stage.container == Container.Dataset
else "application/parquet"
)
Expand Down Expand Up @@ -392,10 +393,13 @@ def _query(self, query, use_dask=False, cache_timeout=0, retry=0):
f.write(resp.content)
f.seek(0)
if stage.container == Container.Dataset:
ds = xarray.load_dataset(
f.name, decode_coords="all", mask_and_scale=True
)
ext = ".nc"
with ZipStore(f.name) as store:
ds = xarray.open_zarr(
store,
decode_coords="all",
mask_and_scale=True,
).load()
ext = ".zarr.zip"
elif stage.container == Container.GeoDataFrame:
ds = geopandas.read_parquet(f.name)
ext = ".gpq"
Expand Down
10 changes: 5 additions & 5 deletions tests/test_cache.py
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Original file line number Diff line number Diff line change
Expand Up @@ -177,7 +177,7 @@ def test_put_and_get_xarray_dataset(
):
"""Test storing and retrieving xarray Dataset."""
cache.put(sample_query, sample_xarray_dataset)
cached_file = cache._cachepath(sample_query) + ".nc"
cached_file = cache._cachepath(sample_query) + ".zarr.zip"
assert os.path.exists(cached_file)

retrieved = cache.get(sample_query)
Expand Down Expand Up @@ -260,7 +260,7 @@ def test_get_with_lock_timeout(self, cache, sample_query):

def test_get_corrupted_cache_returns_none(self, cache, sample_query):
"""Test that corrupted cache file returns None."""
cached_file = cache._cachepath(sample_query) + ".nc"
cached_file = cache._cachepath(sample_query) + ".zarr.zip"

# Create a corrupted file
with open(cached_file, "w") as f:
Expand All @@ -275,17 +275,17 @@ class TestCopy:

def test_copy_moves_file(self, cache, sample_query, temp_cache_dir):
"""Test that copy moves file to cache location."""
source_file = os.path.join(temp_cache_dir, "source.nc")
source_file = os.path.join(temp_cache_dir, "source.zarr.zip")

# Create a source file
with open(source_file, "w") as f:
f.write("test data")

assert os.path.exists(source_file)

cache.copy(sample_query, source_file, ".nc")
cache.copy(sample_query, source_file, ".zarr.zip")

cached_file = cache._cachepath(sample_query) + ".nc"
cached_file = cache._cachepath(sample_query) + ".zarr.zip"
assert os.path.exists(cached_file)
assert not os.path.exists(source_file) # Original should be moved

Expand Down
4 changes: 2 additions & 2 deletions tests/test_datamesh_query.py
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Original file line number Diff line number Diff line change
Expand Up @@ -48,7 +48,7 @@ def test_query_table(conn):
def test_query_table_cache(conn):
q = Query(**{"datasource": "oceanum-sea-level-rise"})
cache = LocalCache(cache_timeout=600)
cached_file = cache._cachepath(q) + ".nc"
cached_file = cache._cachepath(q) + ".zarr.zip"
if os.path.exists(cached_file):
os.remove(cached_file)
ds0 = conn.query(q, cache_timeout=600)
Expand Down Expand Up @@ -91,7 +91,7 @@ def test_query_dataset_cache(conn):
)

cache = LocalCache(cache_timeout=600)
cached_file = cache._cachepath(q) + ".nc"
cached_file = cache._cachepath(q) + ".zarr.zip"
if os.path.exists(cached_file):
os.remove(cached_file)
ds0 = conn.query(q, use_dask=False, cache_timeout=600)
Expand Down