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Fix : for a added feature in weather-mv to extract specific date's data from zarr files. #400

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merged 5 commits into from
Oct 5, 2023
Merged

Fix : for a added feature in weather-mv to extract specific date's data from zarr files. #400

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b33057d
Start_date & end_date of zarr_kwargs are added.
dabhicusp Oct 3, 2023
1cc4875
Pytype checked.
dabhicusp Oct 3, 2023
c71ad86
Nit changes done.
dabhicusp Oct 3, 2023
dc51a78
Warning message added.
dabhicusp Oct 4, 2023
78f4f88
Warning.warn added in pipeline.py
dabhicusp Oct 5, 2023
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14 changes: 12 additions & 2 deletions weather_mv/loader_pipeline/bq.py
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Original file line number Diff line number Diff line change
Expand Up @@ -104,6 +104,8 @@ class ToBigQuery(ToDataSink):
skip_creating_polygon: bool = False
lat_grid_resolution: t.Optional[float] = None
lon_grid_resolution: t.Optional[float] = None
start_date: t.Optional[str] = None
end_date: t.Optional[str] = None

@classmethod
def add_parser_arguments(cls, subparser: argparse.ArgumentParser):
Expand Down Expand Up @@ -154,8 +156,10 @@ def validate_arguments(cls, known_args: argparse.Namespace, pipeline_args: t.Lis
_, uri_extension = os.path.splitext(known_args.uris)
if (uri_extension in ['.tif', '.tiff'] and not known_args.tif_metadata_for_start_time):
raise RuntimeError("'--tif_metadata_for_start_time' is required for tif files.")
elif (uri_extension not in ['.tif', '.tiff'] and (known_args.tif_metadata_for_start_time
or known_args.tif_metadata_for_end_time)):
elif uri_extension not in ['.tif', '.tiff'] and (
known_args.tif_metadata_for_start_time
or known_args.tif_metadata_for_end_time
):
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raise RuntimeError("'--tif_metadata_for_start_time' and "
"'--tif_metadata_for_end_time' can be specified only for tif files.")

Expand All @@ -171,6 +175,8 @@ def __post_init__(self):
"""Initializes Sink by creating a BigQuery table based on user input."""
if self.zarr:
self.xarray_open_dataset_kwargs = self.zarr_kwargs
self.start_date = self.zarr_kwargs.get('start_date')
self.end_date = self.zarr_kwargs.get('end_date')
with open_dataset(self.first_uri, self.xarray_open_dataset_kwargs,
self.disable_grib_schema_normalization, self.tif_metadata_for_start_time,
self.tif_metadata_for_end_time, is_zarr=self.zarr) as open_ds:
Expand Down Expand Up @@ -311,6 +317,10 @@ def expand(self, paths):
xarray_open_dataset_kwargs = self.xarray_open_dataset_kwargs.copy()
xarray_open_dataset_kwargs.pop('chunks')
ds, chunks = xbeam.open_zarr(self.first_uri, **xarray_open_dataset_kwargs)

if self.start_date is not None and self.end_date is not None:
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@alxmrs alxmrs Oct 3, 2023 •
edited
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Would this be useful for non-Zarr datasets? I'm on the fence.

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The PR: #396 is useful for the non-zarr datasets and this PR will be working on zarr datasets.

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SGTM.

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@alxmrs I found that for non-zarr datasets it isn't working so I added a issue & PR. I tested for zarr & non-zarr dataset and it's working with this new PR's code.

ds = ds.sel(time=slice(self.start_date, self.end_date))

ds.attrs[DATA_URI_COLUMN] = self.first_uri
extracted_rows = (
paths
Expand Down
6 changes: 6 additions & 0 deletions weather_mv/loader_pipeline/pipeline.py
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Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,7 @@
import json
import logging
import typing as t
import warnings

import apache_beam as beam
from apache_beam.io.filesystems import FileSystems
Expand Down Expand Up @@ -145,6 +146,11 @@ def run(argv: t.List[str]) -> t.Tuple[argparse.Namespace, t.List[str]]:
if known_args.zarr_kwargs and not known_args.zarr:
raise ValueError('`--zarr_kwargs` argument is only allowed with valid Zarr input URI.')

if known_args.zarr_kwargs:
if not known_args.zarr_kwargs.get('start_date') or not known_args.zarr_kwargs.get('end_date'):
warnings.warn('`--zarr_kwargs` not contains both `start_date` and `end_date`'
'so whole zarr-dataset will ingested.')

if known_args.zarr:
known_args.zarr_kwargs['chunks'] = known_args.zarr_kwargs.get('chunks', None)
known_args.zarr_kwargs['consolidated'] = known_args.zarr_kwargs.get('consolidated', True)
Expand Down
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