From 5b7c33733e7b3f8f9b1a5dee458892252f89397f Mon Sep 17 00:00:00 2001 From: Ben Galewsky Date: Sun, 5 Jan 2025 20:25:53 -0600 Subject: [PATCH] Add asset to create catalogs --- downscaled_climate_data/assets/loca2.py | 136 +- downscaled_climate_data/definitions.py | 6 +- tests/assets/loca2_esm_catalog.csv | 2107 +++++++++++++++++++++++ tests/assets/test_loca2_esm_catalog.py | 146 ++ 4 files changed, 2390 insertions(+), 5 deletions(-) create mode 100644 tests/assets/loca2_esm_catalog.csv create mode 100644 tests/assets/test_loca2_esm_catalog.py diff --git a/downscaled_climate_data/assets/loca2.py b/downscaled_climate_data/assets/loca2.py index 6b99761..b600bab 100644 --- a/downscaled_climate_data/assets/loca2.py +++ b/downscaled_climate_data/assets/loca2.py @@ -1,8 +1,11 @@ +from tempfile import TemporaryDirectory + +import intake_esm.cat import requests -from dagster import AssetExecutionContext, Config, asset, EnvVar, AssetIn -from dagster_aws.s3 import S3Resource import s3fs import xarray as xr +from dagster import AssetExecutionContext, AssetIn, Config, EnvVar, asset +from dagster_aws.s3 import S3Resource import downscaled_climate_data @@ -98,3 +101,132 @@ def loca2_zarr(context, # Close the dataset to free memory ds.close() + + +class ESMCatalogConfig(Config): + data_format: str = "netcdf" + id: str = "loca2_raw_netcdf_monthly_esm_catalog" + description: str = "LOCA2 raw data catalog" + + def is_zarr(self): + return self.data_format == "zarr" + + +def parse_key(relative_path: str, bucket: str, full_key: str) -> dict[str, str]: + # Split the relative path into parts + # Filter out empty strings that occur when there are consecutive slashes + path_parts = [part for part in relative_path.split('/') if part] + + model = path_parts[0] + scheme = path_parts[1] + + file_parts = path_parts[-1].split('.') + variable = file_parts[0] + experiment_id = file_parts[3] + time_range = file_parts[4] + + uri = f"s3://{bucket}/{full_key}" + return { + "variable": variable, + "model": model, + "scheme": scheme, + "experiment_id": experiment_id, + "time_range": time_range, + "path": uri + } + + +@asset( + name="loca2_esm_catalog", + group_name="loca2", + description="Generate an Intake-ESM Catalog for LOCA2 datasets", + code_version=downscaled_climate_data.__version__) +def loca2_esm_catalog(context: AssetExecutionContext, + config: ESMCatalogConfig, + s3: S3Resource): + + bucket = EnvVar("LOCA2_BUCKET").get_value() + + if config.is_zarr(): + prefix = EnvVar("LOCA2_ZARR_PATH_ROOT").get_value() + else: + prefix = EnvVar("LOCA2_RAW_PATH_ROOT").get_value() + + catalog_metadata = intake_esm.cat.ESMCatalogModel( + esmcat_version="0.1.0", + id=config.id, + description=config.description, + catalog_file=f"s3://{bucket}/{config.id}.csv", + attributes=[ + intake_esm.cat.Attribute(column_name="variable"), + intake_esm.cat.Attribute(column_name="model"), + intake_esm.cat.Attribute(column_name="scheme"), + intake_esm.cat.Attribute(column_name="experiment_id"), + intake_esm.cat.Attribute(column_name="time_range"), + intake_esm.cat.Attribute(column_name="path") + ], + assets=intake_esm.cat.Assets( + column_name='path', + format=intake_esm.cat.DataFormat.zarr + if config.is_zarr() else intake_esm.cat.DataFormat.netcdf, + ) + ) + context.log.info(catalog_metadata.model_dump_json()) + + s3_client = s3.get_client() + paginator = s3_client.get_paginator('list_objects_v2') + pages = paginator.paginate(Bucket=bucket, Prefix=prefix) + + # We use a set to keep track of unique keys since the zarr keys are only + # directories with many files in them, so they show up as a number of + # keys in the S3 bucket + keys = set() + + for page in pages: + if 'Contents' in page: + for obj in page['Contents']: + full_key = obj['Key'] + + # If we are cataloging Zarr stores, we need to identify the directory + # that holds all the files for a single dataset. These directories end + # with "cent.zarr" and are the base path for the dataset + if config.is_zarr(): + if "monthly.cent.zarr" in full_key: + base_path = (full_key.rsplit("monthly.cent.zarr", 1)[0] + + "monthly.cent.zarr") + elif "cent.monthly.zarr" in full_key: + base_path = (full_key.rsplit("cent.monthly.zarr", 1)[0] + + "cent.monthly.zarr") + else: + base_path = full_key + keys.add(base_path) + + context.log.info(f"Found {len(keys)} unique base paths") + + with TemporaryDirectory() as temp_dir: + collection_spec_path = f"{temp_dir}/{config.id}.json" + with open(collection_spec_path, "w") as json_file: + json_file.write(catalog_metadata.model_dump_json(indent=4)) + + catalog_path = f"{temp_dir}/{config.id}.csv" + + with open(catalog_path, 'w') as f: + f.write("variable,model,scheme,experiment_id,time_range,path\n") + + # Now that we have the unique base paths, we can write the catalog + for full_key in keys: + relative_path = full_key[len(prefix):] if full_key.startswith(prefix) \ + else full_key + try: + parsed = parse_key(relative_path, bucket, full_key) + f.write(f"{parsed['variable']},{parsed['model']},{parsed['scheme']},{parsed['experiment_id']},{parsed['time_range']},{parsed['path']}\n") # NOQA E501 + except IndexError as e: + context.log.error(f"Error processing {full_key}: {e}") + + s3_client.upload_file(Filename=catalog_path, + Bucket=bucket, + Key=f"{config.id}.csv") + + s3_client.upload_file(Filename=collection_spec_path, + Bucket=bucket, + Key=f"{config.id}.json") diff --git a/downscaled_climate_data/definitions.py b/downscaled_climate_data/definitions.py index 92fca44..5cbc8f1 100644 --- a/downscaled_climate_data/definitions.py +++ b/downscaled_climate_data/definitions.py @@ -1,8 +1,8 @@ from dagster import Definitions, EnvVar from dagster_aws.s3 import S3Resource -from downscaled_climate_data.assets.loca2 import loca2_zarr -from downscaled_climate_data.assets.loca2 import loca2_raw_netcdf +from downscaled_climate_data.assets.loca2 import loca2_zarr, loca2_raw_netcdf +from downscaled_climate_data.assets.loca2 import loca2_esm_catalog from downscaled_climate_data.sensors.loca2_models import Loca2Models from downscaled_climate_data.sensors.loca2_sensor import (loca2_sensor_monthly_pr, loca2_sensor_monthly_tasmin, @@ -13,7 +13,7 @@ loca2_sensor_tasmin) defs = Definitions( - assets=[loca2_raw_netcdf, loca2_zarr], + assets=[loca2_raw_netcdf, loca2_zarr, loca2_esm_catalog], sensors=[loca2_sensor_tasmax, loca2_sensor_tasmin, loca2_sensor_pr, diff --git a/tests/assets/loca2_esm_catalog.csv b/tests/assets/loca2_esm_catalog.csv new file mode 100644 index 0000000..b72982a --- /dev/null +++ b/tests/assets/loca2_esm_catalog.csv @@ -0,0 +1,2107 @@ +variable,model,scheme,experiment_id,time_range,path +pr,ACCESS-CM2,historical,r1i1p1f1,1950-2014,s3://ees240146/netcdf/LOCA2/monthly/ACCESS-CM2/historical/pr.ACCESS-CM2.historical.r1i1p1f1.1950-2014.LOCA_16thdeg_v20240915.cent.monthly.nc 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+import pytest +import os +from dagster import DagsterInstance, build_asset_context +import pandas as pd + +from downscaled_climate_data.assets.loca2 import (ESMCatalogConfig, + loca2_esm_catalog, parse_key) + + +@pytest.fixture +def s3(mocker): + s3 = mocker.MagicMock() + s3_client = mocker.MagicMock() + s3.get_client.return_value = s3_client + + paginator = mocker.MagicMock() + s3_client.get_paginator.return_value = paginator + return s3 + + +def set_bucket_contents(s3, keys): + contents = [{"Key": key} for key in keys] + + paginator = s3.get_client.return_value.get_paginator.return_value + paginator.paginate.return_value = [{"Contents": contents}] + + +@pytest.mark.parametrize( + "key, expected_variable, expected_model, expected_scheme, expected_experiment_id, expected_time_range, expected_path", # noqa: E501 + [ + ("ACCESS-CM2/historical/tasmin.ACCESS-CM2.historical.r3i1p1f1.1950-2014.LOCA_16thdeg_v20220413.monthly.cent.zarr", # noqa: E501 + "tasmin", "ACCESS-CM2", "historical", "r3i1p1f1", "1950-2014", + "s3://test-bucket/zarr/LOCA2/monthly/ACCESS-CM2/historical/tasmin.ACCESS-CM2.historical.r3i1p1f1.1950-2014.LOCA_16thdeg_v20220413.monthly.cent.zarr"), # noqa: E501 + ("ACCESS-ESM1-5/historical/tasmin.ACCESS-ESM1-5.historical.r5i1p1f1.1950-2014.LOCA_16thdeg_v20220413.monthly.cent.zarr", # noqa: E501 + "tasmin", "ACCESS-ESM1-5", "historical", "r5i1p1f1", "1950-2014", + "s3://test-bucket/zarr/LOCA2/monthly/ACCESS-ESM1-5/historical/tasmin.ACCESS-ESM1-5.historical.r5i1p1f1.1950-2014.LOCA_16thdeg_v20220413.monthly.cent.zarr"), # noqa: E501 + ] +) +def test_parse_key(key, expected_variable, expected_model, expected_scheme, + expected_experiment_id, expected_time_range, expected_path): + parsed = parse_key( + key, + "test-bucket", + "zarr/LOCA2/monthly/" + key + ) + assert parsed == { + "variable": expected_variable, + "model": expected_model, + "scheme": expected_scheme, + "experiment_id": expected_experiment_id, + "time_range": expected_time_range, + "path": expected_path + } + + +def test_generate_catalog_zarr(s3): + instance = DagsterInstance.ephemeral() + set_bucket_contents(s3, [ + "zarr/LOCA2/monthly/ACCESS-CM2/historical/tasmin.ACCESS-CM2.historical.r3i1p1f1.1950-2014.LOCA_16thdeg_v20220413.monthly.cent.zarr/time/0", # noqa: E501 + "zarr/LOCA2/monthly/ACCESS-CM2/historical/tasmin.ACCESS-CM2.historical.r3i1p1f1.1950-2014.LOCA_16thdeg_v20220413.monthly.cent.zarr/lon/0", # noqa: E501 + "zarr/LOCA2/monthly/MIROC6/ssp370/pr.MIROC6.ssp370.r2i1p1f1.2045-2074.LOCA_16thdeg_v20240915.cent.monthly.zarr/pr_tavg/3.0.1cent.zarr" # noqa: E501 + ]) + + os.environ['LOCA2_ZARR_PATH_ROOT'] = 'zarr/LOCA2/monthly' + os.environ['LOCA2_BUCKET'] = 'test_bucket' + with TemporaryDirectory() as tmpdir: + with patch('downscaled_climate_data.assets.loca2.TemporaryDirectory') as mock_temp: # noqa: E501 + mock_temp.return_value.__enter__.return_value = str(tmpdir) + ctx = build_asset_context(instance=instance, + resources={ + "s3": s3 + }) + + config = ESMCatalogConfig( + data_format="zarr", + id="loca2_zarr_monthly_esm_catalog", + description="LOCA2 zarr data catalog" + ) + + loca2_esm_catalog(ctx, config) + + with open(f"{tmpdir}/loca2_zarr_monthly_esm_catalog.json", "r") as json_file: + collection_config = json.load(json_file) + assert collection_config['id'] == "loca2_zarr_monthly_esm_catalog" + + with open(f"{tmpdir}/loca2_zarr_monthly_esm_catalog.csv", 'r') as csv_file: + cat = pd.read_csv(csv_file) + assert cat.shape == (2, 6) + + filtered_df = cat[cat["experiment_id"] == "r3i1p1f1"] + r31_series = filtered_df.iloc[0] + assert r31_series['variable'] == "tasmin" + assert r31_series['model'] == "ACCESS-CM2" + assert r31_series['scheme'] == "historical" + assert r31_series['experiment_id'] == "r3i1p1f1" + assert r31_series['time_range'] == "1950-2014" + assert r31_series['path'] == "s3://test_bucket/zarr/LOCA2/monthly/ACCESS-CM2/historical/tasmin.ACCESS-CM2.historical.r3i1p1f1.1950-2014.LOCA_16thdeg_v20220413.monthly.cent.zarr" # noqa: E501 + print(cat) + + +def test_generate_catalog_netcdf(s3): + instance = DagsterInstance.ephemeral() + set_bucket_contents(s3, [ + "netcdf/LOCA2/monthly/ACCESS-CM2/ssp585/tasmin.ACCESS-CM2.ssp585.r3i1p1f1.2075-2100.LOCA_16thdeg_v20220413.monthly.cent.nc", # noqa: E501 + "netcdf/LOCA2/monthly/ACCESS-ESM1-5/historical/tasmin.ACCESS-ESM1-5.historical.r5i1p1f1.1950-2014.LOCA_16thdeg_v20220413.monthly.cent.nc" # noqa: E501 + ]) + + os.environ['LOCA2_RAW_PATH_ROOT'] = 'netcdf/LOCA2/monthly' + os.environ['LOCA2_BUCKET'] = 'test_bucket' + with TemporaryDirectory() as tmpdir: + with patch('downscaled_climate_data.assets.loca2.TemporaryDirectory') as mock_temp: # noqa: E501 + mock_temp.return_value.__enter__.return_value = str(tmpdir) + ctx = build_asset_context(instance=instance, + resources={ + "s3": s3 + }) + + config = ESMCatalogConfig( + data_format="netcdf", + id="loca2_raw_monthly_esm_catalog", + description="LOCA2 raw data catalog" + ) + + loca2_esm_catalog(ctx, config) + + with open(f"{tmpdir}/loca2_raw_monthly_esm_catalog.json", "r") as json_file: + collection_config = json.load(json_file) + assert collection_config['id'] == "loca2_raw_monthly_esm_catalog" + + with open(f"{tmpdir}/loca2_raw_monthly_esm_catalog.csv", 'r') as csv_file: + cat = pd.read_csv(csv_file) + assert cat.shape == (2, 6) + + filtered_df = cat[cat["experiment_id"] == "r3i1p1f1"] + r31_series = filtered_df.iloc[0] + assert r31_series['variable'] == "tasmin" + assert r31_series['model'] == "ACCESS-CM2" + assert r31_series['scheme'] == "ssp585" + assert r31_series['experiment_id'] == "r3i1p1f1" + assert r31_series['time_range'] == "2075-2100" + assert r31_series['path'] == "s3://test_bucket/netcdf/LOCA2/monthly/ACCESS-CM2/ssp585/tasmin.ACCESS-CM2.ssp585.r3i1p1f1.2075-2100.LOCA_16thdeg_v20220413.monthly.cent.nc" # noqa: E501 + print(cat)