diff --git a/.github/workflows/build-pipeline.yml b/.github/workflows/build-pipeline.yml index 3eb9022..535b15f 100644 --- a/.github/workflows/build-pipeline.yml +++ b/.github/workflows/build-pipeline.yml @@ -162,7 +162,7 @@ jobs: -Dsonar.tests=tests/ -Dsonar.projectName=${{ github.repository }} -Dsonar.projectVersion=${{ env.software_version }} - -Dsonar.python.version=3.9,3.10 + -Dsonar.python.version=3.10,3.11 - name: Run Snyk as a blocking step uses: snyk/actions/python-3.10@master env: diff --git a/.github/workflows/release-created.yml b/.github/workflows/release-created.yml index 738f1da..929872c 100644 --- a/.github/workflows/release-created.yml +++ b/.github/workflows/release-created.yml @@ -26,6 +26,7 @@ jobs: with: repository: ${{ github.repository }} token: ${{ steps.podaac-cicd.outputs.token }} + ref: 'refs/heads/develop' - uses: actions/setup-python@v5 with: python-version: '3.10' diff --git a/CHANGELOG.md b/CHANGELOG.md index 53d0952..19cefa2 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,6 +5,12 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). ## [Unreleased] +### Changed + +## [0.4.0] +### Changed +- [issues/25](https://github.com/podaac/net2cog/issues/25): Converted harmony adapter to operate on STAC catalog +- [issues/3](https://github.com/podaac/net2cog/issues/3): Improved error handling and updated test cases to use new-style harmony execution ## [0.3.0] ### Changed @@ -30,5 +36,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Setup process for deploying the netcdf reformatter to SIT using Terraform deployment via Jenkins. In order to accomplish this I setup unique terraform naming conventions for the netcdf converter while maintaining the same terraform config as l2ss. Updated the jenkins logic to allow for SIT deployment testing. -[Unreleased]: https://github.com/podaac/net2cog/compare/v0.3.0...HEAD +[Unreleased]: https://github.com/podaac/net2cog/compare/v0.4.0...HEAD +[0.4.0]: https://github.com/podaac/net2cog/compare/v0.3.0...v0.4.0 [0.3.0]: https://github.com/podaac/net2cog/compare/eabb00704a6fc693aa4d79536dc5c5354c6de4d9...v0.3.0 \ No newline at end of file diff --git a/cmr/netcdf_cmr_umm_s.json b/cmr/netcdf_cmr_umm_s.json index f6603b3..e26ba7e 100755 --- a/cmr/netcdf_cmr_umm_s.json +++ b/cmr/netcdf_cmr_umm_s.json @@ -25,8 +25,18 @@ ], "SupportedInputFormat": "NETCDF-4" } - ] + ], + "Subset": { + "VariableSubset": { + "AllowMultipleValues": false + } + } }, + "OperationMetadata": [ + { + "OperationName": "VARIABLE_SUBSETTING" + } + ], "AccessConstraints": "None", "ServiceKeywords": [ { @@ -69,4 +79,4 @@ "Name": "UMM-S", "Version": "1.5.2" } -} \ No newline at end of file +} diff --git a/cmr/ops_associations.txt b/cmr/ops_associations.txt index c953e06..36f985b 100644 --- a/cmr/ops_associations.txt +++ b/cmr/ops_associations.txt @@ -1 +1 @@ -C1234410736-POCLOUD \ No newline at end of file +C1940468263-POCLOUD \ No newline at end of file diff --git a/cmr/uat_associations.txt b/cmr/uat_associations.txt index b43cb58..1a8d1cb 100644 --- a/cmr/uat_associations.txt +++ b/cmr/uat_associations.txt @@ -1 +1,2 @@ -C1247485690-LARC_CLOUD \ No newline at end of file +C1247485690-LARC_CLOUD +C1234410736-POCLOUD \ No newline at end of file diff --git a/docker/Dockerfile b/docker/Dockerfile index bb4f480..4e1b083 100644 --- a/docker/Dockerfile +++ b/docker/Dockerfile @@ -15,9 +15,11 @@ FROM python:3.10-slim RUN apt-get update \ && DEBIAN_FRONTEND=noninteractive apt-get upgrade -y \ gcc \ + g++ \ libnetcdf-dev \ libhdf5-dev \ hdf5-helpers \ + libgdal-dev \ && pip3 install --upgrade pip \ && pip3 install cython \ && apt-get clean @@ -25,8 +27,8 @@ RUN apt-get update \ # Create a new user RUN adduser --quiet --disabled-password --shell /bin/sh --home /home/dockeruser --gecos "" --uid 1000 dockeruser USER dockeruser -ENV HOME /home/dockeruser -ENV PYTHONPATH "${PYTHONPATH}:/home/dockeruser/.local/bin" +ENV HOME=/home/dockeruser +ENV PYTHONPATH="${PYTHONPATH}:/home/dockeruser/.local/bin" ENV PATH="/home/dockeruser/.local/bin:${PATH}" # The 'SOURCE' argument is what will be used in 'pip install'. @@ -43,7 +45,7 @@ WORKDIR /worker COPY --chown=dockeruser $DIST_PATH $DIST_PATH USER dockeruser -RUN pip3 install --no-cache-dir --force --user --index-url https://pypi.org/simple/ --extra-index-url https://test.pypi.org/simple/ $SOURCE \ +RUN pip install --no-cache-dir --force --user --index-url https://pypi.org/simple/ --extra-index-url https://test.pypi.org/simple/ $SOURCE \ && rm -rf $DIST_PATH COPY --chown=dockeruser ./docker/docker-entrypoint.sh docker-entrypoint.sh diff --git a/net2cog/netcdf_convert.py b/net2cog/netcdf_convert.py index 90798b8..586b1ab 100644 --- a/net2cog/netcdf_convert.py +++ b/net2cog/netcdf_convert.py @@ -7,30 +7,36 @@ Functions related to converting a NetCDF file to other formats. """ +import logging import os import pathlib -from os.path import join as pjoin, basename, dirname, exists, splitext import subprocess -from subprocess import check_call - -import logging import tempfile +from os.path import join as pjoin, basename, dirname, exists, splitext +from subprocess import check_call from typing import List -import xarray as xr import rasterio +import rioxarray # noqa +import xarray as xr from rasterio import CRS - from rio_cogeo.cogeo import cog_translate from rio_cogeo.profiles import cog_profiles - -import rioxarray # noqa from rioxarray.exceptions import DimensionError LOGGER = logging.getLogger(__name__) EXCLUDE_VARS = ['lon', 'lat', 'longitude', 'latitude', 'time'] +class Net2CogError(Exception): + """ + Exception raised when an error occurs while converting a NetCDF file to COG + """ + + def __init__(self, msg): + super().__init__(msg) + + def run_command(command, work_dir): """ A simple utility to execute a subprocess command. @@ -188,7 +194,10 @@ def netcdf_converter(input_nc_file: pathlib.Path, output_cog_pathname: pathlib.P # xds_reversed = xds.reindex(lat=xds.lat[::-1]) LOGGER.info("Writing COG to %s", basename(gtiff_fname)) if var_list: - xds = xds[var_list] + try: + xds = xds[var_list] + except KeyError as error: + raise Net2CogError(f"Variable {error} not found in dataset") from error return _write_cogtiff(gtiff_fname, xds) LOGGER.error("%s: NetCDF file does not contain spatial dimensions such as lat / lon " "or x / y", netcdf_file) diff --git a/net2cog/netcdf_convert_harmony.py b/net2cog/netcdf_convert_harmony.py index d5028fb..fb43c5f 100644 --- a/net2cog/netcdf_convert_harmony.py +++ b/net2cog/netcdf_convert_harmony.py @@ -9,12 +9,19 @@ Implementation of harmony-service-lib that invokes the netcdf converter. """ import argparse +import json import os import pathlib +import shutil +import tempfile import harmony +import pystac +from harmony.exceptions import HarmonyException +from pystac import Asset from net2cog import netcdf_convert +from net2cog.netcdf_convert import Net2CogError DATA_DIRECTORY_ENV = "DATA_DIRECTORY" @@ -25,70 +32,99 @@ class NetcdfConverterService(harmony.BaseHarmonyAdapter): for documentation and examples. """ - def __init__(self, message): - super().__init__(message) + def __init__(self, message, catalog=None, config=None): + super().__init__(message, catalog, config) self.data_dir = os.getenv(DATA_DIRECTORY_ENV, '/home/dockeruser/data') - self.job_data_dir = os.path.join(self.data_dir, message.requestId) + pathlib.Path(self.data_dir).mkdir(parents=True, exist_ok=True) + # Create temp directory - pathlib.Path(self.job_data_dir).mkdir(parents=True, exist_ok=True) + self.job_data_dir = tempfile.mkdtemp(prefix=message.requestId, dir=self.data_dir) - def invoke(self): - """Run the service on the message contained in `self.message`. - Fetches data, runs the service, puts the result in a file, - calls back to Harmony, and cleans up after itself. + def process_item(self, item: pystac.Item, source: harmony.message.Source) -> pystac.Item: """ - - logger = self.logger - message = self.message - - logger.info("Received message %s", message) - + Performs net2cog on input STAC Item's data, returning + an output STAC item + + Parameters + ---------- + item : pystac.Item + the item that should be coggified + source : harmony.message.Source + the input source defining the item + + Returns + ------- + pystac.Item + a STAC item describing the output + """ + result = item.clone() + result.assets = {} + output_dir = self.job_data_dir try: - # Limit to the first granule. See note in method documentation - granules = message.granules - if message.isSynchronous: - granules = granules[:1] - - for i, granule in enumerate(granules): - self.download_granules([granule]) - - self.logger.info('local_filename = %s', granule.local_filename) - directory_name = os.path.splitext(os.path.basename(granule.local_filename))[0] - output_file_directory = os.path.join(self.job_data_dir, - f'converted_{directory_name}') - output_filename = pathlib.Path(f'{output_file_directory}').joinpath(os.path.basename(granule.name)) - self.logger.debug('output: %s', output_filename) - - # Run the netcdf converter for the complete netcdf granule - cogs_generated = netcdf_convert.netcdf_converter( - granule.local_filename, output_filename - ) - current_progress = int(100 * i / len(granules)) - next_progress = int(100 * (i + 1) / len(granules)) - for cog in cogs_generated: - if message.isSynchronous: - self.completed_with_local_file( - cog, - remote_filename=os.path.basename(cog), - mime="tiff" - ) - else: - self.async_add_local_file_partial_result( - cog, - remote_filename=os.path.basename(cog), - title=granule.id, - progress=current_progress if cog != cogs_generated[-1] else next_progress, - mime="tiff" - ) - if not message.isSynchronous: - self.async_completed_successfully() - - except Exception as ex: # pylint: disable=W0703 - logger.exception(ex) - self.completed_with_error('An unexpected error occurred') + self.logger.info('Input item: %s', json.dumps(item.to_dict())) + self.logger.info('Input source: %s', source) + # Get the data file + asset = next(v for k, v in item.assets.items() if 'data' in (v.roles or [])) + self.logger.info('Downloading %s to %s', asset.href, output_dir) + input_filename = harmony.adapter.util.download(asset.href, + output_dir, + logger=self.logger, + access_token=self.message.accessToken, + cfg=self.config) + + # Generate output filename + output_filename, output_file_ext = os.path.splitext( + harmony.adapter.util.generate_output_filename(asset.href, ext='tif')) + output_filename = f'{output_filename}_converted{output_file_ext}' + + # Determine variables that need processing + self.logger.info('Generating COG(s) for %s output will be saved to %s', input_filename, output_filename) + var_list = source.process('variables') + if not isinstance(var_list, list): + var_list = [var_list] + if len(var_list) != 1: + raise HarmonyException( + 'net2cog harmony adapter currently only supports processing one variable at a time. ' + 'Please specify a single variable in your Harmony request.') + var_list = list(map(lambda var: var.name, var_list)) + self.logger.info('Processing variables %s', var_list) + + # Run the netcdf converter for the complete netcdf granule + try: + cog_generated = next(iter(netcdf_convert.netcdf_converter(pathlib.Path(input_filename), + pathlib.Path(output_dir).joinpath( + output_filename), + var_list=var_list)), []) + except Net2CogError as error: + raise HarmonyException( + f'net2cog failed to convert {asset.title}: {error}') from error + except Exception as uncaught_exception: + raise HarmonyException(str(f'Uncaught error in net2cog. ' + f'Notify net2cog service provider. ' + f'Message: {uncaught_exception}')) from uncaught_exception + + # Stage the output file with a conventional filename + self.logger.info('Generated COG %s', cog_generated) + staged_filename = os.path.basename(cog_generated) + url = harmony.adapter.util.stage(cog_generated, + staged_filename, + pystac.MediaType.COG, + location=self.message.stagingLocation, + logger=self.logger, + cfg=self.config) + self.logger.info('Staged %s to %s', cog_generated, url) + + # Update the STAC record + result.assets['visual'] = Asset(url, title=staged_filename, media_type=pystac.MediaType.COG, + roles=['visual']) + + # Return the STAC record + self.logger.info('Processed item %s', json.dumps(result.to_dict())) + return result finally: - self.cleanup() + # Clean up any intermediate resources + shutil.rmtree(self.job_data_dir) def main(): @@ -100,7 +136,7 @@ def main(): None """ - parser = argparse.ArgumentParser(prog='podaac-netcdf-converter', + parser = argparse.ArgumentParser(prog='net2cog_harmony', description='Run the netcdf converter service') harmony.setup_cli(parser) args = parser.parse_args() diff --git a/poetry.lock b/poetry.lock index 8ec7706..fdc0a0f 100644 --- a/poetry.lock +++ b/poetry.lock @@ -58,32 +58,32 @@ wrapt = [ [[package]] name = "attrs" -version = "23.2.0" +version = "24.2.0" description = "Classes Without Boilerplate" optional = false python-versions = ">=3.7" files = [ - {file = "attrs-23.2.0-py3-none-any.whl", hash = "sha256:99b87a485a5820b23b879f04c2305b44b951b502fd64be915879d77a7e8fc6f1"}, - {file = "attrs-23.2.0.tar.gz", hash = "sha256:935dc3b529c262f6cf76e50877d35a4bd3c1de194fd41f47a2b7ae8f19971f30"}, + {file = "attrs-24.2.0-py3-none-any.whl", hash = "sha256:81921eb96de3191c8258c199618104dd27ac608d9366f5e35d011eae1867ede2"}, + {file = "attrs-24.2.0.tar.gz", hash = "sha256:5cfb1b9148b5b086569baec03f20d7b6bf3bcacc9a42bebf87ffaaca362f6346"}, ] [package.extras] -cov = ["attrs[tests]", "coverage[toml] (>=5.3)"] -dev = ["attrs[tests]", "pre-commit"] -docs = 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"pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"] +tests-mypy = ["mypy (>=1.11.1)", "pytest-mypy-plugins"] [[package]] name = "babel" -version = "2.15.0" +version = "2.16.0" description = "Internationalization utilities" optional = false python-versions = ">=3.8" files = [ - {file = "Babel-2.15.0-py3-none-any.whl", hash = "sha256:08706bdad8d0a3413266ab61bd6c34d0c28d6e1e7badf40a2cebe67644e2e1fb"}, - {file = "babel-2.15.0.tar.gz", hash = "sha256:8daf0e265d05768bc6c7a314cf1321e9a123afc328cc635c18622a2f30a04413"}, + {file = "babel-2.16.0-py3-none-any.whl", hash = "sha256:368b5b98b37c06b7daf6696391c3240c938b37767d4584413e8438c5c435fa8b"}, + {file = "babel-2.16.0.tar.gz", hash = "sha256:d1f3554ca26605fe173f3de0c65f750f5a42f924499bf134de6423582298e316"}, ] [package.extras] @@ -91,17 +91,17 @@ dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"] [[package]] name = "boto3" -version = "1.34.148" +version = "1.34.159" description = "The AWS SDK for Python" 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">=3.9" files = [ - {file = "xarray-2024.6.0-py3-none-any.whl", hash = "sha256:721a7394e8ec3d592b2d8ebe21eed074ac077dc1bb1bd777ce00e41700b4866c"}, - {file = "xarray-2024.6.0.tar.gz", hash = "sha256:0b91e0bc4dc0296947947640fe31ec6e867ce258d2f7cbc10bedf4a6d68340c7"}, + {file = "xarray-2024.7.0-py3-none-any.whl", hash = "sha256:1b0fd51ec408474aa1f4a355d75c00cc1c02bd425d97b2c2e551fd21810e7f64"}, + {file = "xarray-2024.7.0.tar.gz", hash = "sha256:4cae512d121a8522d41e66d942fb06c526bc1fd32c2c181d5fe62fe65b671638"}, ] [package.dependencies] @@ -1851,4 +1886,4 @@ harmony = ["harmony-service-lib"] [metadata] lock-version = "2.0" python-versions = ">=3.10,<4.0" -content-hash = "e76670fbfec14267dd53bbbc004c945cf708f2e5d9a9ffbcacacb248356145b2" +content-hash = "161a76b2c499c39fc7442a582053b5d0c191c376362b26c6edbb68902dc54fa8" diff --git a/pyproject.toml b/pyproject.toml index 3e493c8..d8303b0 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "net2cog" -version = "0.3.0" +version = "0.4.0rc3" description = "NetCDF to COG Conversion Service" authors = ["podaac "] license = "Apache-2.0" @@ -19,7 +19,7 @@ python = ">=3.10,<4.0" boto3 = "^1.28.3" requests = "^2.31.0" netcdf4 = "^1.6.4" -xarray = "^2024.6.0" +xarray = "^2024.7.0" rio-cogeo = "^5.3.3" rasterio = "^1.3.8" rioxarray = "^0.17.0" @@ -39,6 +39,10 @@ harmony = ["harmony-service-lib"] [tool.poetry.scripts] net2cog_harmony = 'net2cog.netcdf_convert_harmony:main' +[tool.coverage.run] +source = ['net2cog'] +relative_files = true + [build-system] requires = ["poetry-core>=1.0.0"] build-backend = "poetry.core.masonry.api" diff --git a/tests/data/RSS_smap_SSS_L3_8day_running_2020_005_FNL_v04.0.nc b/tests/data/SMAP_RSS_L3_SSS_SMI_8DAY-RUNNINGMEAN_V4/RSS_smap_SSS_L3_8day_running_2020_005_FNL_v04.0.nc similarity index 100% rename from tests/data/RSS_smap_SSS_L3_8day_running_2020_005_FNL_v04.0.nc rename to tests/data/SMAP_RSS_L3_SSS_SMI_8DAY-RUNNINGMEAN_V4/RSS_smap_SSS_L3_8day_running_2020_005_FNL_v04.0.nc diff --git a/tests/data/SMAP_RSS_L3_SSS_SMI_8DAY-RUNNINGMEAN_V4/RSS_smap_SSS_L3_8day_running_2020_005_FNL_v04.0/RSS_smap_SSS_L3_8day_running_2020_005_FNL_v04.0.json b/tests/data/SMAP_RSS_L3_SSS_SMI_8DAY-RUNNINGMEAN_V4/RSS_smap_SSS_L3_8day_running_2020_005_FNL_v04.0/RSS_smap_SSS_L3_8day_running_2020_005_FNL_v04.0.json new file mode 100644 index 0000000..69e4bac --- /dev/null +++ b/tests/data/SMAP_RSS_L3_SSS_SMI_8DAY-RUNNINGMEAN_V4/RSS_smap_SSS_L3_8day_running_2020_005_FNL_v04.0/RSS_smap_SSS_L3_8day_running_2020_005_FNL_v04.0.json @@ -0,0 +1,38 @@ +{ + "type": "Feature", + "stac_version": "1.0.0-beta.2", + "id": "RSS_smap_SSS_L3_8day_running_2020_005_FNL_v04.0", + "properties": { + "start_datetime": "2001-01-01T01:01:01Z", + "end_datetime": "2002-02-02T02:02:02Z", + "datetime": null + }, + "geometry": null, + "links": [ + { + "rel": "root", + "href": "../catalog.json", + "type": "application/json" + }, + { + "rel": "parent", + "href": "../catalog.json", + "type": "application/json" + } + ], + "assets": { + "data": { + "href": "!!REPLACED IN TEST CASE!!", + "title": "Example2", + "roles": [ + "data" + ] + } + }, + "bbox": [ + -1, + -2, + 3, + 4 + ] +} \ No newline at end of file diff --git a/tests/data/SMAP_RSS_L3_SSS_SMI_8DAY-RUNNINGMEAN_V4/catalog.json b/tests/data/SMAP_RSS_L3_SSS_SMI_8DAY-RUNNINGMEAN_V4/catalog.json new file mode 100644 index 0000000..899b1cf --- /dev/null +++ b/tests/data/SMAP_RSS_L3_SSS_SMI_8DAY-RUNNINGMEAN_V4/catalog.json @@ -0,0 +1,17 @@ +{ + "id": "test", + "stac_version": "1.0.0-beta.2", + "description": "test", + "links": [ + { + "rel": "root", + "href": "./catalog.json", + "type": "application/json" + }, + { + "rel": "item", + "href": "./RSS_smap_SSS_L3_8day_running_2020_005_FNL_v04.0/RSS_smap_SSS_L3_8day_running_2020_005_FNL_v04.0.json", + "type": "application/json" + } + ] +} \ No newline at end of file diff --git a/tests/data/test_netcdf_convert_harmony/test_service_invoke.input.json b/tests/data/SMAP_RSS_L3_SSS_SMI_8DAY-RUNNINGMEAN_V4/data_operation_message.json similarity index 68% rename from tests/data/test_netcdf_convert_harmony/test_service_invoke.input.json rename to tests/data/SMAP_RSS_L3_SSS_SMI_8DAY-RUNNINGMEAN_V4/data_operation_message.json index 7fe6fbb..8c7753b 100644 --- a/tests/data/test_netcdf_convert_harmony/test_service_invoke.input.json +++ b/tests/data/SMAP_RSS_L3_SSS_SMI_8DAY-RUNNINGMEAN_V4/data_operation_message.json @@ -9,19 +9,24 @@ "requestId": "0001111-2222-3333-4444-5555666677777", "sources": [ { - "collection": "C0001-EXAMPLE", + "collection": "C1940468263-POCLOUD", "variables": [ { - "id": "V0001-EXAMPLE", - "name": "ExampleVar", - "fullPath": "example/group/path/ExampleVar" + "id": "V2093907958-POCLOUD", + "name": "sss_smap", + "fullPath": "sss_smap" } ], "granules": [ { "id": "RSS_smap_SSS_L3_8day_running_2020_005_FNL_v04.0", "name": "Example2", - "url": "file:///home/tests/data/RSS_smap_SSS_L3_8day_running_2020_005_FNL_v04.0.nc" + "url": "!!REPLACED IN TEST CASE!!", + "temporal": { + "start": "2001-01-01T01:01:01Z", + "end": "2002-02-02T02:02:02Z" + }, + "bbox": [-1, -2, 3, 4] } ] } diff --git a/tests/test_netcdf_convert.py b/tests/test_netcdf_convert.py index 13a049d..d1ea551 100644 --- a/tests/test_netcdf_convert.py +++ b/tests/test_netcdf_convert.py @@ -14,6 +14,7 @@ import pytest from net2cog import netcdf_convert +from net2cog.netcdf_convert import Net2CogError @pytest.fixture(scope='session') @@ -29,63 +30,70 @@ def output_basedir(tmp_path): @pytest.mark.parametrize('data_file', [ - 'RSS_smap_SSS_L3_8day_running_2020_005_FNL_v04.0.nc' + 'SMAP_RSS_L3_SSS_SMI_8DAY-RUNNINGMEAN_V4/RSS_smap_SSS_L3_8day_running_2020_005_FNL_v04.0.nc' ]) def test_cog_generation(data_file, data_dir, output_basedir): """ Test that the conversion works and the output is a valid cloud optimized geotiff """ test_file = pathlib.Path(data_dir, data_file) - output_dir = pathlib.Path(output_basedir, pathlib.Path(data_file).stem) - netcdf_convert.netcdf_converter(test_file, pathlib.Path(output_basedir, data_file), []) + results = netcdf_convert.netcdf_converter(test_file, pathlib.Path(output_basedir, data_file), []) - assert os.path.isdir(output_dir) - output_files = os.listdir(output_dir) - assert len(output_files) > 0 + assert len(results) > 0 - with os.scandir(output_dir) as outdir: - for entry in outdir: - if entry.is_file(): + for entry in results: + if pathlib.Path(entry).is_file(): + cogtif_val = [ + 'rio', + 'cogeo', + 'validate', + entry + ] - cogtif_val = [ - 'rio', - 'cogeo', - 'validate', - entry.path - ] + process = subprocess.run(cogtif_val, check=True, stdout=subprocess.PIPE, universal_newlines=True) + cog_test = process.stdout + cog_test = cog_test.replace("\n", "") - process = subprocess.run(cogtif_val, check=True, stdout=subprocess.PIPE, universal_newlines=True) - cog_test = process.stdout - cog_test = cog_test.replace("\n", "") + valid_cog = entry + " is a valid cloud optimized GeoTIFF" + assert cog_test == valid_cog - valid_cog = entry.path + " is a valid cloud optimized GeoTIFF" - assert cog_test == valid_cog - -def test_band_selection(data_dir, output_basedir): +@pytest.mark.parametrize(['data_file', 'in_bands'], [ + ['SMAP_RSS_L3_SSS_SMI_8DAY-RUNNINGMEAN_V4/RSS_smap_SSS_L3_8day_running_2020_005_FNL_v04.0.nc', ['gland', 'fland', 'sss_smap']] +]) +def test_band_selection(data_file, in_bands, data_dir, output_basedir): """ Verify the correct bands asked for by the user are being converted """ - in_bands = sorted(['gland', 'fland', 'sss_smap']) - data_file = 'RSS_smap_SSS_L3_8day_running_2020_005_FNL_v04.0.nc' + in_bands = sorted(in_bands) test_file = pathlib.Path(data_dir, data_file) - output_dir = pathlib.Path(output_basedir, pathlib.Path(data_file).stem) results = netcdf_convert.netcdf_converter(test_file, pathlib.Path(output_basedir, data_file), in_bands) - assert os.path.isdir(output_dir) - output_files = os.listdir(output_dir) - assert len(output_files) == 3 assert len(results) == 3 out_bands = [] - with os.scandir(output_dir) as outdir: - for entry in outdir: - if entry.is_file(): - band_completed = entry.name.split("4.0_")[-1].replace(".tif", "") - out_bands.append(band_completed) + for entry in results: + if pathlib.Path(entry).is_file(): + band_completed = entry.split("4.0_")[-1].replace(".tif", "") + out_bands.append(band_completed) out_bands.sort() assert in_bands == out_bands + + +@pytest.mark.parametrize(['data_file', 'in_bands'], [ + ['SMAP_RSS_L3_SSS_SMI_8DAY-RUNNINGMEAN_V4/RSS_smap_SSS_L3_8day_running_2020_005_FNL_v04.0.nc', ['waldo']] +]) +def test_unknown_band_selection(data_file, in_bands, data_dir, output_basedir): + """ + Verify an incorrect band asked for by the user raises an exception + """ + + in_bands = sorted(in_bands) + test_file = pathlib.Path(data_dir, data_file) + + with pytest.raises(Net2CogError): + netcdf_convert.netcdf_converter(test_file, pathlib.Path(output_basedir, data_file), in_bands) diff --git a/tests/test_netcdf_convert_harmony.py b/tests/test_netcdf_convert_harmony.py index e058d6d..2906d90 100644 --- a/tests/test_netcdf_convert_harmony.py +++ b/tests/test_netcdf_convert_harmony.py @@ -7,10 +7,14 @@ """ import json import os.path +import pathlib +import shutil import sys from unittest.mock import patch import pytest +from harmony.exceptions import HarmonyException +from pystac import Catalog import net2cog.netcdf_convert_harmony @@ -46,18 +50,81 @@ def mock_environ(tmp_path): os.environ = old_env -def test_service_invoke(mock_environ): - test_dir = os.path.dirname(os.path.realpath(__file__)) - input_json = json.load( - open(os.path.join(test_dir, 'data', 'test_netcdf_convert_harmony', 'test_service_invoke.input.json'))) - test_granule = os.path.join(test_dir, 'data', 'RSS_smap_SSS_L3_8day_running_2020_005_FNL_v04.0.nc') - input_json['sources'][0]['granules'][0]['url'] = f'file://{test_granule}' +def test_service_invoke(mock_environ, tmp_path): + test_dir = pathlib.Path(os.path.dirname(os.path.realpath(__file__))) + data_operation_message = pathlib.Path('data', 'SMAP_RSS_L3_SSS_SMI_8DAY-RUNNINGMEAN_V4', + 'data_operation_message.json') + stac_catalog = pathlib.Path('data', 'SMAP_RSS_L3_SSS_SMI_8DAY-RUNNINGMEAN_V4', 'catalog.json') + stac_item = pathlib.Path('data', 'SMAP_RSS_L3_SSS_SMI_8DAY-RUNNINGMEAN_V4', + 'RSS_smap_SSS_L3_8day_running_2020_005_FNL_v04.0', + 'RSS_smap_SSS_L3_8day_running_2020_005_FNL_v04.0.json') + test_granule = pathlib.Path('data', 'SMAP_RSS_L3_SSS_SMI_8DAY-RUNNINGMEAN_V4', + 'RSS_smap_SSS_L3_8day_running_2020_005_FNL_v04.0.nc') + + data_operation_message_json = json.load(open(test_dir.joinpath(data_operation_message))) + data_operation_message_json['sources'][0]['granules'][0]['url'] = f'file://{test_dir.joinpath(test_granule)}' + tmp_path.joinpath(data_operation_message).parent.mkdir(parents=True, exist_ok=True) + tmp_path.joinpath(data_operation_message).touch() + with open(tmp_path.joinpath(data_operation_message), 'w') as f: + f.write(json.dumps(data_operation_message_json)) + + stac_item_json = json.load(open(test_dir.joinpath(stac_item))) + stac_item_json['assets']['data']['href'] = f'file://{test_dir.joinpath(test_granule)}' + tmp_path.joinpath(stac_item).parent.mkdir(parents=True, exist_ok=True) + tmp_path.joinpath(stac_item).touch() + with open(tmp_path.joinpath(stac_item), 'w') as f: + f.write(json.dumps(stac_item_json)) + + shutil.copy(test_dir.joinpath(stac_catalog), tmp_path.joinpath(stac_catalog)) test_args = [ net2cog.netcdf_convert_harmony.__file__, "--harmony-action", "invoke", - "--harmony-input", json.dumps(input_json) + "--harmony-input-file", f"{tmp_path.joinpath(data_operation_message)}", + "--harmony-sources", f"{tmp_path.joinpath(stac_catalog)}", + "--harmony-metadata-dir", str(tmp_path), ] with patch.object(sys, 'argv', test_args): net2cog.netcdf_convert_harmony.main() + + +def test_service_error(mock_environ, tmp_path): + test_dir = pathlib.Path(os.path.dirname(os.path.realpath(__file__))) + data_operation_message = pathlib.Path('data', 'SMAP_RSS_L3_SSS_SMI_8DAY-RUNNINGMEAN_V4', + 'data_operation_message.json') + stac_catalog = pathlib.Path('data', 'SMAP_RSS_L3_SSS_SMI_8DAY-RUNNINGMEAN_V4', 'catalog.json') + stac_item = pathlib.Path('data', 'SMAP_RSS_L3_SSS_SMI_8DAY-RUNNINGMEAN_V4', + 'RSS_smap_SSS_L3_8day_running_2020_005_FNL_v04.0', + 'RSS_smap_SSS_L3_8day_running_2020_005_FNL_v04.0.json') + test_granule = pathlib.Path('data', 'SMAP_RSS_L3_SSS_SMI_8DAY-RUNNINGMEAN_V4', + 'RSS_smap_SSS_L3_8day_running_2020_005_FNL_v04.0.nc') + + data_operation_message_json = json.load(open(test_dir.joinpath(data_operation_message))) + data_operation_message_json['sources'][0]['granules'][0]['url'] = f'file://{test_dir.joinpath(test_granule)}' + data_operation_message_json['sources'][0]['variables'][0]['name'] = 'thor' + tmp_path.joinpath(data_operation_message).parent.mkdir(parents=True, exist_ok=True) + tmp_path.joinpath(data_operation_message).touch() + with open(tmp_path.joinpath(data_operation_message), 'w') as f: + f.write(json.dumps(data_operation_message_json)) + + stac_item_json = json.load(open(test_dir.joinpath(stac_item))) + stac_item_json['assets']['data']['href'] = f'file://{test_dir.joinpath(test_granule)}' + tmp_path.joinpath(stac_item).parent.mkdir(parents=True, exist_ok=True) + tmp_path.joinpath(stac_item).touch() + with open(tmp_path.joinpath(stac_item), 'w') as f: + f.write(json.dumps(stac_item_json)) + + shutil.copy(test_dir.joinpath(stac_catalog), tmp_path.joinpath(stac_catalog)) + + test_args = [ + net2cog.netcdf_convert_harmony.__file__, + "--harmony-action", "invoke", + "--harmony-input-file", f"{tmp_path.joinpath(data_operation_message)}", + "--harmony-sources", f"{tmp_path.joinpath(stac_catalog)}", + "--harmony-metadata-dir", str(tmp_path), + ] + + with patch.object(sys, 'argv', test_args): + with pytest.raises(HarmonyException): + net2cog.netcdf_convert_harmony.main()