diff --git a/.github/dependabot.yml b/.github/dependabot.yml index a9bbdb9..d6bb65c 100644 --- a/.github/dependabot.yml +++ b/.github/dependabot.yml @@ -4,6 +4,10 @@ updates: directory: "/" schedule: interval: "monthly" + groups: + pip-dependencies: + patterns: + - "*" # Raise pull requests for version updates # to pip against the `develop` branch target-branch: "develop" @@ -11,4 +15,8 @@ updates: directory: "/" schedule: interval: "monthly" + groups: + gha-dependencies: + patterns: + - "*" target-branch: "develop" diff --git a/.github/workflows/build-pipeline.yml b/.github/workflows/build-pipeline.yml index 32218e0..6248b1a 100644 --- a/.github/workflows/build-pipeline.yml +++ b/.github/workflows/build-pipeline.yml @@ -170,7 +170,7 @@ jobs: - name: Build and push Docker image if: ${{ !startsWith(github.ref, 'refs/heads/main/') }} id: docker-push - uses: docker/build-push-action@v5 + uses: docker/build-push-action@v6 with: context: . file: Dockerfile diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml index bdb9863..e2b88e4 100644 --- a/.github/workflows/run_tests.yml +++ b/.github/workflows/run_tests.yml @@ -36,7 +36,7 @@ jobs: poetry-version: ${{ env.POETRY_VERSION }} - name: Install package - run: poetry install + run: poetry install --with=harmony --without integration - name: Run linting run: | diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index c2f5229..3f92e7e 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,4 +1,10 @@ --- +ci: + autoupdate_schedule: "monthly" # Like dependabot + autoupdate_commit_msg: "chore: update pre-commit hooks" + autoupdate_branch: "develop" + autofix_prs: false # Comment "pre-commit.ci autofix" on a PR to trigger + repos: - repo: https://github.com/pre-commit/pre-commit-hooks rev: v4.6.0 diff --git a/CHANGELOG.md b/CHANGELOG.md index d307976..316f78d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,7 +12,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [Issue #181](https://github.com/nasa/stitchee/issues/181): Add a group delimiter argument - [Issue #134](https://github.com/nasa/stitchee/issues/134): Add an integration test that runs stitchee on files first subsetted by the operational Harmony subsetter - [Issue #194](https://github.com/nasa/stitchee/issues/194): Add page about the SAMBAH service chain to the Readthedocs documentation +- [issue #193](https://github.com/nasa/stitchee/issues/193): Add autoupdate schedule for pre-commit ### Changed +- [Issue #206](https://github.com/nasa/stitchee/issues/206): Group dependabot updates into one PR +- [issue #208](https://github.com/nasa/stitchee/issues/208): Increase continuous integration/unit test coverage +- [issue #198](https://github.com/nasa/stitchee/issues/198): Use time variable instead of concat dim for ordering datasets ### Deprecated ### Removed ### Fixed diff --git a/concatenator/__init__.py b/concatenator/__init__.py index 16386c2..648914c 100644 --- a/concatenator/__init__.py +++ b/concatenator/__init__.py @@ -24,24 +24,9 @@ def __getattr__(name): # type: ignore """ global _options - if name == "__options__": - return _options if name == "group_delim": return _options.group_delim if name == "coord_delim": return _options.coord_delim else: raise AttributeError(f"module {__name__!r} has no attribute {name!r}") - - -def __setattr__(name, value): # type: ignore - """Module-level setattr to handle setting of `concatenator.options`. - - Other unhandled attributes raise as `AttributeError` as expected. - """ - if name == "group_delim": - _options.group_delim = value - elif name == "coord_delim": - _options.coord_delim = value - else: - raise AttributeError(f"module {__name__!r} has no attribute {name!r}") diff --git a/concatenator/attribute_handling.py b/concatenator/attribute_handling.py index 83425cd..3ec3e46 100644 --- a/concatenator/attribute_handling.py +++ b/concatenator/attribute_handling.py @@ -26,7 +26,7 @@ def regroup_coordinate_attribute(attribute_string: str) -> str: Examples -------- >>> coord_att = "__Time_and_Position__time __Time_and_Position__instrument_fov_latitude __Time_and_Position__instrument_fov_longitude" - >>> _flatten_coordinate_attribute(coord_att) + >>> flatten_string_with_groups(coord_att) Time_and_Position/time Time_and_Position/instrument_fov_latitude Time_and_Position/instrument_fov_longitude Parameters @@ -54,27 +54,29 @@ def regroup_coordinate_attribute(attribute_string: str) -> str: def flatten_coordinate_attribute_paths( dataset: netCDF4.Dataset, var: netCDF4.Variable, variable_name: str ) -> None: - """Flatten the paths of variables referenced in the coordinates attribute.""" + """Flatten the paths of variables referenced in the 'coordinates' attribute.""" if "coordinates" in var.ncattrs(): coord_att = var.getncattr("coordinates") - new_coord_att = _flatten_coordinate_attribute(coord_att) + new_coord_att = flatten_string_with_groups(coord_att) dataset.variables[variable_name].setncattr("coordinates", new_coord_att) -def _flatten_coordinate_attribute(attribute_string: str) -> str: - """Converts attributes that specify group membership via "/" to use new group delimiter, even for the root level. +def flatten_string_with_groups(str_with_groups: str) -> str: + """Determine separator and flatten string specifying group membership via "/". + + Applies to variable paths or attributes, even for the root level. Examples -------- >>> coord_att = "Time_and_Position/time Time_and_Position/instrument_fov_latitude Time_and_Position/instrument_fov_longitude" - >>> _flatten_coordinate_attribute(coord_att) + >>> flatten_string_with_groups(coord_att) __Time_and_Position__time __Time_and_Position__instrument_fov_latitude __Time_and_Position__instrument_fov_longitude Parameters ---------- - attribute_string : str + str_with_groups : str Returns ------- @@ -82,8 +84,10 @@ def _flatten_coordinate_attribute(attribute_string: str) -> str: """ # Use the separator that's in the attribute string only if all separators in the string are the same. # Otherwise, we will use our own default separator. - whitespaces = re.findall(r"\s+", attribute_string) - if len(set(whitespaces)) <= 1: + whitespaces = re.findall(r"\s+", str_with_groups) + if len(set(whitespaces)) == 0: + new_sep = "" + elif len(set(whitespaces)) == 1: new_sep = whitespaces[0] else: new_sep = concatenator.coord_delim @@ -91,7 +95,7 @@ def _flatten_coordinate_attribute(attribute_string: str) -> str: # A new string is constructed. return new_sep.join( f'{concatenator.group_delim}{c.replace("/", concatenator.group_delim)}' - for c in attribute_string.split() # split on any whitespace + for c in str_with_groups.split() # split on any whitespace ) diff --git a/concatenator/dataset_and_group_handling.py b/concatenator/dataset_and_group_handling.py index 2895f1e..8e44a2a 100644 --- a/concatenator/dataset_and_group_handling.py +++ b/concatenator/dataset_and_group_handling.py @@ -8,6 +8,7 @@ from __future__ import annotations import re +from logging import Logger import netCDF4 as nc import numpy as np @@ -273,7 +274,7 @@ def _get_nested_group(dataset: nc.Dataset, group_path: str) -> nc.Group: return nested_group -def _calculate_chunks(dim_sizes: list, default_low_dim_chunksize=4000) -> tuple: +def _calculate_chunks(dim_sizes: list, default_low_dim_chunksize: int = 4000) -> tuple: """ For the given dataset, calculate if the size on any dimension is worth chunking. Any dimension larger than 4000 will be chunked. This @@ -324,8 +325,8 @@ def _get_dimension_size(dataset: nc.Dataset, dim_name: str) -> int: return dim_size -def validate_workable_files(files, logger) -> tuple[list[str], int]: - """Remove files from list that are not open-able as netCDF or that are empty.""" +def validate_workable_files(files: list[str], logger: Logger) -> tuple[list[str], int]: + """Remove files from a list that are not open-able as netCDF or that are empty.""" workable_files = [] for file in files: try: @@ -336,7 +337,7 @@ def validate_workable_files(files, logger) -> tuple[list[str], int]: except OSError: logger.debug("Error opening <%s> as a netCDF dataset. Skipping.", file) - # addressing the issue 153: propagate first empty file if all input files are empty + # addressing GitHub issue 153: propagate the first empty file if all input files are empty if (len(workable_files)) == 0 and (len(files) > 0): workable_files.append(files[0]) diff --git a/concatenator/harmony/cli.py b/concatenator/harmony/cli.py index 3329095..54db997 100644 --- a/concatenator/harmony/cli.py +++ b/concatenator/harmony/cli.py @@ -1,4 +1,5 @@ """A Harmony CLI wrapper around the concatenate-batcher""" + from argparse import ArgumentParser import harmony diff --git a/concatenator/harmony/download_worker.py b/concatenator/harmony/download_worker.py index b9cf089..4b947c9 100644 --- a/concatenator/harmony/download_worker.py +++ b/concatenator/harmony/download_worker.py @@ -113,6 +113,6 @@ def _download_worker( dest_path = path.parent.joinpath(filename) path = path.rename(dest_path) else: - logger.warning("Origin filename could not be assertained - %s", url) + logger.warning("Origin filename could not be ascertained - %s", url) path_list.append(str(path)) diff --git a/concatenator/stitchee.py b/concatenator/stitchee.py index 34a4ee0..cc2c1ee 100644 --- a/concatenator/stitchee.py +++ b/concatenator/stitchee.py @@ -15,6 +15,7 @@ import xarray as xr import concatenator +from concatenator.attribute_handling import flatten_string_with_groups from concatenator.dataset_and_group_handling import ( flatten_grouped_dataset, regroup_flattened_dataset, @@ -39,6 +40,7 @@ def stitchee( concat_method: str | None = "xarray-concat", concat_dim: str = "", concat_kwargs: dict | None = None, + time_variable: str = "geolocation/time", history_to_append: str | None = None, copy_input_files: bool = False, overwrite_output_file: bool = False, @@ -137,9 +139,11 @@ def stitchee( decode_coords=False, drop_variables=coord_vars, ) as xrds: - first_value = xrds[concatenator.group_delim + concat_dim].values.flatten()[ - 0 - ] + # Determine value for later dataset sorting. + first_value = xrds[ + flatten_string_with_groups(time_variable) + ].values.flatten()[0] + # first_value = xrds[concatenator.group_delim + concat_dim].values.flatten()[0] concat_dim_order.append(first_value) benchmark_log["flattening"] = time.time() - start_time diff --git a/poetry.lock b/poetry.lock index 48f81fc..e88a7af 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. 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python-versions = "^3.10" -content-hash = "5cc1bc065f5eff1f9524d34a1231e8656024dced0edb34ef864387e343323d03" +content-hash = "2bd1674f70981be7d7cc64c6e963f0c0fa453fff6c6ec57711ac5120db327d13" diff --git a/pyproject.toml b/pyproject.toml index cdb9af3..018a62f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "stitchee" -version = "1.3.0a12" +version = "1.4.0a0" description = "NetCDF4 Along-existing-dimension Concatenation Service" authors = ["Daniel Kaufman "] readme = "README.md" @@ -19,28 +19,29 @@ stitchee = 'concatenator.run_stitchee:main' [tool.poetry.dependencies] python = "^3.10" -netcdf4 = "^1.6.5" -xarray = "^2024.3.0" -dask = "^2024.4.1" +netcdf4 = ">=1.6.5" +xarray = ">=2024.3.0" +dask = ">=2024.4.1" +pystac = ">=0.5.6" [tool.poetry.group.dev.dependencies] -pytest = "^8.1.1" -mypy = "^1.9.0" -black = "^24.4.0" -ruff = ">=0.3.7,<0.5.0" -pytest-cov = "^5.0.0" -mkdocs = "^1.6.0" -markdown-callouts = "^0.4.0" -markdown-include = "^0.8.1" -mkdocstrings = "^0.25.1" -mkdocs-jupyter = "^0.24.7" -mkdocs-material = "^9.5.22" +pytest = ">=8.1.1" +mypy = ">=1.9.0" +black = ">=24.4.0" +ruff = ">=0.5.0,<0.6.0" +pytest-cov = ">=5.0.0" +mkdocs = ">=1.6.0" +markdown-callouts = ">=0.4.0" +markdown-include = ">=0.8.1" +mkdocstrings = ">=0.25.1" +mkdocs-jupyter = ">=0.24.7" +mkdocs-material = ">=9.5.22" [tool.poetry.group.harmony.dependencies] -harmony-service-lib = "^1.0.26" +harmony-service-lib = ">=1.0.26" [tool.poetry.group.integration.dependencies] -harmony-py = "^0.4.14" +harmony-py = ">=0.4.14" [build-system] requires = ["poetry-core"] @@ -78,3 +79,21 @@ select = [ "I", # isort "UP", # Pyupgrade ] + +[tool.coverage.run] +concurrency = ["multiprocessing"] + +[tool.coverage.report] +# Regexes for lines to exclude from consideration +exclude_lines = [ + # Have to re-enable the standard pragma + "pragma: no cover", + + # Don't complain if tests don't hit defensive assertion code: + "raise AssertionError", + "raise NotImplementedError", + + # Don't complain if non-runnable code isn't run: + "if 0:", + "if __name__ == .__main__.:" +] diff --git a/tests/conftest.py b/tests/conftest.py index 232b69e..b917654 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -19,6 +19,10 @@ class TempDirs(typing.NamedTuple): toy_data_path: Path +def path_str(dir_path: Path, filename: str) -> str: + return str(dir_path.joinpath(filename)) + + def pytest_addoption(parser): """Sets up optional argument to keep temporary testing directory.""" parser.addoption( @@ -32,7 +36,7 @@ def prep_input_files(input_dir: Path, output_dir: Path) -> list[str]: """Prepare input by copying from the original test data directory.""" input_files = [] for filepath in input_dir.iterdir(): - if Path(filepath).suffix.lower() in (".nc", ".h5", ".hdf"): + if Path(filepath).suffix.lower() in (".nc", ".nc4", ".h5", ".hdf"): copied_input_new_path = output_dir / Path(filepath).name # type: ignore shutil.copyfile(filepath, copied_input_new_path) input_files.append(str(copied_input_new_path)) diff --git a/tests/data/harmony/granule_copies_dir/.placeholder_for_dir b/tests/data/harmony/granule_copies_dir/.placeholder_for_dir new file mode 100644 index 0000000..e69de29 diff --git a/tests/data/harmony/granules/TEMPO_NO2_L2_V03_20240601T210934Z_S012G01_subsetted.nc4 b/tests/data/harmony/granules/TEMPO_NO2_L2_V03_20240601T210934Z_S012G01_subsetted.nc4 new file mode 100644 index 0000000..73084df Binary files /dev/null and b/tests/data/harmony/granules/TEMPO_NO2_L2_V03_20240601T210934Z_S012G01_subsetted.nc4 differ diff --git a/tests/data/harmony/granules/TEMPO_NO2_L2_V03_20240601T211614Z_S012G02_subsetted.nc4 b/tests/data/harmony/granules/TEMPO_NO2_L2_V03_20240601T211614Z_S012G02_subsetted.nc4 new file mode 100644 index 0000000..f21701a Binary files /dev/null and b/tests/data/harmony/granules/TEMPO_NO2_L2_V03_20240601T211614Z_S012G02_subsetted.nc4 differ diff --git a/tests/data/harmony/granules/TEMPO_NO2_L2_V03_20240601T212254Z_S012G03_subsetted.nc4 b/tests/data/harmony/granules/TEMPO_NO2_L2_V03_20240601T212254Z_S012G03_subsetted.nc4 new file mode 100644 index 0000000..28de57b Binary files /dev/null and b/tests/data/harmony/granules/TEMPO_NO2_L2_V03_20240601T212254Z_S012G03_subsetted.nc4 differ diff --git a/tests/data/harmony/message.json b/tests/data/harmony/message.json new file mode 100644 index 0000000..21eb885 --- /dev/null +++ b/tests/data/harmony/message.json @@ -0,0 +1,16 @@ +{ + "sources": [{ + "collection": "C1234088182-EEDTEST" + }], + "format": { + "mime": "application/x-netcdf4" + }, + "subset": {}, + "requestId": "00001111-2222-3333-4444-555566667777", + "user": "jdoe", + "client": "harmony-example", + "isSynchronous": false, + "stagingLocation": "s3://example-bucket/public/some-org/some-service/some-uuid/", + "callback": "http://localhost/some-path", + "version": "0.10.0" +} diff --git a/tests/data/harmony/source/catalog.json b/tests/data/harmony/source/catalog.json new file mode 100644 index 0000000..213f7a5 --- /dev/null +++ b/tests/data/harmony/source/catalog.json @@ -0,0 +1,30 @@ +{ + "stac_version": "1.0.0-beta.2", + "stac_extensions": [], + "id": "cfc32383-cfd1-4e43-8d5f-55f539b6fa59", + "links": [ + { + "rel": "harmony_source", + "href": "https://cmr.uat.earthdata.nasa.gov/search/concepts/C1234088182-EEDTEST" + }, + { + "rel": "item", + "href": "./granule_S012G01.json", + "type": "application/json", + "title": "granule_S012G01" + }, + { + "rel": "item", + "href": "./granule_S012G02.json", + "type": "application/json", + "title": "granule_S012G02" + }, + { + "rel": "item", + "href": "./granule_S012G03.json", + "type": "application/json", + "title": "granule_S012G03" + } + ], + "description": "CMR Granules for C1234088182-EEDTEST batch 1" +} diff --git a/tests/data/harmony/source/catalog0.json b/tests/data/harmony/source/catalog0.json new file mode 100644 index 0000000..f4de590 --- /dev/null +++ b/tests/data/harmony/source/catalog0.json @@ -0,0 +1,30 @@ +{ + "stac_version": "1.0.0-beta.2", + "stac_extensions": [], + "id": "cfc32383-cfd1-4e43-8d5f-55f539b6fa59", + "links": [ + { + "rel": "harmony_source", + "href": "https://cmr.uat.earthdata.nasa.gov/search/concepts/C1234088182-EEDTEST" + }, + { + "rel": "item", + "href": "./granule_S012G01.json", + "type": "application/json", + "title": "granule_S012G01" + }, + { + "rel": "item", + "href": "./granule_S012G02.json", + "type": "application/json", + "title": "granule_S012G02" + }, + { + "rel": "next", + "href": "tests/data/harmony/source/catalog1.json", + "type": "application/json", + "title": "Next page" + } + ], + "description": "CMR Granules for C1234088182-EEDTEST batch 1" +} diff --git a/tests/data/harmony/source/catalog1.json b/tests/data/harmony/source/catalog1.json new file mode 100644 index 0000000..0361054 --- /dev/null +++ b/tests/data/harmony/source/catalog1.json @@ -0,0 +1,24 @@ +{ + "stac_version": "1.0.0-beta.2", + "stac_extensions": [], + "id": "cfc32383-cfd1-4e43-8d5f-55f539b6fa59", + "links": [ + { + "rel": "harmony_source", + "href": "https://cmr.uat.earthdata.nasa.gov/search/concepts/C1234088182-EEDTEST" + }, + { + "rel": "item", + "href": "./granule_S012G03.json", + "type": "application/json", + "title": "granule_S012G03" + }, + { + "rel": "prev", + "href": "tests/data/harmony/source/catalog0.json", + "type": "application/json", + "title": "Previous page" + } + ], + "description": "CMR Granules for C1234088182-EEDTEST batch 2" +} diff --git a/tests/data/harmony/source/granule_S012G01.json b/tests/data/harmony/source/granule_S012G01.json new file mode 100644 index 0000000..8220f5e --- /dev/null +++ b/tests/data/harmony/source/granule_S012G01.json @@ -0,0 +1,49 @@ +{ + "stac_version": "1.0.0-beta.2", + "stac_extensions": [], + "id": "51d02b24-d00e-4640-9887-05f98f6b96d8", + "type": "Feature", + "links": [], + "properties": { + "start_datetime": "2020-01-02T00:00:00.000Z", + "end_datetime": "2020-01-02T23:59:59.000Z" + }, + "bbox": [1, 3, 1, 3], + "geometry": { + "type": "Polygon", + "coordinates": [ + [ + [ + -179.95, + -89.95 + ], + [ + -179.95, + 89.95 + ], + [ + 179.95, + 89.95 + ], + [ + 179.95, + -89.95 + ], + [ + -179.95, + -89.95 + ] + ] + ] + }, + "assets": { + "data": { + "href": "file://tests/data/harmony/granule_copies_dir/TEMPO_NO2_L2_V03_20240601T210934Z_S012G01_subsetted.nc4", + "title": "TEMPO_NO2_L2_V03_20240601T210934Z_S012G01_subsetted.nc4", + "type": "application/x-netcdf4", + "roles": [ + "data" + ] + } + } +} diff --git a/tests/data/harmony/source/granule_S012G02.json b/tests/data/harmony/source/granule_S012G02.json new file mode 100644 index 0000000..091f46e --- /dev/null +++ b/tests/data/harmony/source/granule_S012G02.json @@ -0,0 +1,49 @@ +{ + "stac_version": "1.0.0-beta.2", + "stac_extensions": [], + "id": "21eb7dc5-7a9d-4374-9a88-12451ba653ef", + "type": "Feature", + "links": [], + "properties": { + "start_datetime": "2020-01-03T00:00:00.000Z", + "end_datetime": "2020-01-03T23:59:59.000Z" + }, + "bbox": [-1, -3, -1, -3], + "geometry": { + "type": "Polygon", + "coordinates": [ + [ + [ + -179.95, + -89.95 + ], + [ + -179.95, + 89.95 + ], + [ + 179.95, + 89.95 + ], + [ + 179.95, + -89.95 + ], + [ + -179.95, + -89.95 + ] + ] + ] + }, + "assets": { + "data": { + "href": "file://tests/data/harmony/granule_copies_dir/TEMPO_NO2_L2_V03_20240601T211614Z_S012G02_subsetted.nc4", + "title": "TEMPO_NO2_L2_V03_20240601T211614Z_S012G02_subsetted.nc4", + "type": "application/x-netcdf4", + "roles": [ + "data" + ] + } + } +} diff --git a/tests/data/harmony/source/granule_S012G03.json b/tests/data/harmony/source/granule_S012G03.json new file mode 100644 index 0000000..383a427 --- /dev/null +++ b/tests/data/harmony/source/granule_S012G03.json @@ -0,0 +1,49 @@ +{ + "stac_version": "1.0.0-beta.2", + "stac_extensions": [], + "id": "dc07a25a-54bd-4389-97b6-c1d68cf0d586", + "type": "Feature", + "links": [], + "properties": { + "start_datetime": "2020-01-05T00:00:00.000Z", + "end_datetime": "2020-01-05T23:59:59.000Z" + }, + "bbox": [-4, -2, -4, 2], + "geometry": { + "type": "Polygon", + "coordinates": [ + [ + [ + -179.95, + -89.95 + ], + [ + -179.95, + 89.95 + ], + [ + 179.95, + 89.95 + ], + [ + 179.95, + -89.95 + ], + [ + -179.95, + -89.95 + ] + ] + ] + }, + "assets": { + "data": { + "href": "file://tests/data/harmony/granule_copies_dir/TEMPO_NO2_L2_V03_20240601T212254Z_S012G03_subsetted.nc4", + "title": "TEMPO_NO2_L2_V03_20240601T212254Z_S012G03_subsetted.nc4", + "type": "application/x-netcdf4", + "roles": [ + "data" + ] + } + } +} diff --git a/tests/data/harmony/source/granule_S012G04.json b/tests/data/harmony/source/granule_S012G04.json new file mode 100644 index 0000000..6f4b460 --- /dev/null +++ b/tests/data/harmony/source/granule_S012G04.json @@ -0,0 +1,49 @@ +{ + "stac_version": "1.0.0-beta.2", + "stac_extensions": [], + "id": "53cdf09b-4004-4405-9363-f93455a11c2f", + "type": "Feature", + "links": [], + "properties": { + "start_datetime": "2020-01-04T00:00:00.000Z", + "end_datetime": "2020-01-04T23:59:59.000Z" + }, + "bbox": [4, 2, 4, 2], + "geometry": { + "type": "Polygon", + "coordinates": [ + [ + [ + -179.95, + -89.95 + ], + [ + -179.95, + 89.95 + ], + [ + 179.95, + 89.95 + ], + [ + 179.95, + -89.95 + ], + [ + -179.95, + -89.95 + ] + ] + ] + }, + "assets": { + "data": { + "href": "file://tests/data/harmony/granules/TEMPO_NO2_L2_V03_20240601T120121Z_S012G04.nc", + "title": "TEMPO_NO2_L2_V03_20240601T120121Z_S012G04.nc", + "type": "application/x-netcdf4", + "roles": [ + "data" + ] + } + } +} diff --git a/tests/data/harmony/source/granule_S012G05.json b/tests/data/harmony/source/granule_S012G05.json new file mode 100644 index 0000000..1766751 --- /dev/null +++ b/tests/data/harmony/source/granule_S012G05.json @@ -0,0 +1,49 @@ +{ + "stac_version": "1.0.0-beta.2", + "stac_extensions": [], + "id": "349b5f4a-34ab-4b0d-ae00-b55fe3d166fb", + "type": "Feature", + "links": [], + "properties": { + "start_datetime": "2020-01-05T00:00:00.000Z", + "end_datetime": "2020-01-05T23:59:59.000Z" + }, + "bbox": [-5, -3, -5, 3], + "geometry": { + "type": "Polygon", + "coordinates": [ + [ + [ + -179.95, + -89.95 + ], + [ + -179.95, + 89.95 + ], + [ + 179.95, + 89.95 + ], + [ + 179.95, + -89.95 + ], + [ + -179.95, + -89.95 + ] + ] + ] + }, + "assets": { + "data": { + "href": "file://tests/data/harmony/granules/TEMPO_NO2_L2_V03_20240601T120128Z_S012G05.nc", + "title": "TEMPO_NO2_L2_V03_20240601T120128Z_S012G05.nc", + "type": "application/x-netcdf4", + "roles": [ + "data" + ] + } + } +} diff --git a/tests/data/harmony/source/granule_S012G06.json b/tests/data/harmony/source/granule_S012G06.json new file mode 100644 index 0000000..94135f2 --- /dev/null +++ b/tests/data/harmony/source/granule_S012G06.json @@ -0,0 +1,49 @@ +{ + "stac_version": "1.0.0-beta.2", + "stac_extensions": [], + "id": "cb0271ad-05a9-4138-8bfb-fa6b83fbe6fa", + "type": "Feature", + "links": [], + "properties": { + "start_datetime": "2020-01-05T00:00:00.000Z", + "end_datetime": "2020-01-05T23:59:59.000Z" + }, + "bbox": [5, 3, 5, 3], + "geometry": { + "type": "Polygon", + "coordinates": [ + [ + [ + -179.95, + -89.95 + ], + [ + -179.95, + 89.95 + ], + [ + 179.95, + 89.95 + ], + [ + 179.95, + -89.95 + ], + [ + -179.95, + -89.95 + ] + ] + ] + }, + "assets": { + "data": { + "href": "file://tests/data/harmony/granules/TEMPO_NO2_L2_V03_20240601T120135Z_S012G06.nc", + "title": "TEMPO_NO2_L2_V03_20240601T120135Z_S012G06.nc", + "type": "application/x-netcdf4", + "roles": [ + "data" + ] + } + } +} diff --git a/tests/integration/test_history_construction.py b/tests/integration/test_history_construction.py index 064f033..034e6de 100644 --- a/tests/integration/test_history_construction.py +++ b/tests/integration/test_history_construction.py @@ -28,6 +28,7 @@ def test_construct_and_append_history_for_sample_concatenation( concat_method="xarray-concat", history_to_append=new_history_json, concat_dim="step", + time_variable="step", ) stitcheed_dataset = xr.open_dataset(output_path) diff --git a/tests/unit/test_attribute_handling.py b/tests/unit/test_attribute_handling.py index 26af9b1..817682a 100644 --- a/tests/unit/test_attribute_handling.py +++ b/tests/unit/test_attribute_handling.py @@ -1,5 +1,8 @@ +import pytest + +import concatenator from concatenator.attribute_handling import ( - _flatten_coordinate_attribute, + flatten_string_with_groups, regroup_coordinate_attribute, ) @@ -7,7 +10,7 @@ def test_coordinate_attribute_flattening(): # Case with groups present and double spaces. assert ( - _flatten_coordinate_attribute( + flatten_string_with_groups( "Time_and_Position/time Time_and_Position/instrument_fov_latitude Time_and_Position/instrument_fov_longitude" ) == "__Time_and_Position__time __Time_and_Position__instrument_fov_latitude __Time_and_Position__instrument_fov_longitude" @@ -15,13 +18,21 @@ def test_coordinate_attribute_flattening(): # Case with NO groups present and single spaces. assert ( - _flatten_coordinate_attribute( + flatten_string_with_groups( "time longitude latitude ozone_profile_pressure ozone_profile_altitude" ) == "__time __longitude __latitude __ozone_profile_pressure __ozone_profile_altitude" ) +def test_variable_path_flattening(): + # Case with group present. + assert flatten_string_with_groups("geolocation/time") == "__geolocation__time" + + # Case with NO groups present. + assert flatten_string_with_groups("time") == "__time" + + def test_coordinate_attribute_regrouping(): # Case with groups present and double spaces. assert ( @@ -38,3 +49,30 @@ def test_coordinate_attribute_regrouping(): ) == "time longitude latitude ozone_profile_pressure ozone_profile_altitude" ) + + +def test_concatenator_options_getting_and_setting(): + """Test setting attributes for the concatenator module. + + Note that currently, new attributes can be defined dynamically. + Note also, that attributes must be reset before further testing because they are global. + """ + default_group_delim = "__" + assert concatenator.group_delim == default_group_delim + concatenator.group_delim = "%" + assert concatenator.group_delim == "%" + concatenator.group_delim = default_group_delim + assert concatenator.group_delim == default_group_delim + + default_coord_delim = " " + assert concatenator.coord_delim == default_coord_delim + concatenator.coord_delim = "---" + assert concatenator.coord_delim == "---" + concatenator.coord_delim = default_coord_delim + assert concatenator.coord_delim == default_coord_delim + + concatenator.nonexistent_attribute = "---" + assert concatenator.nonexistent_attribute == "---" + del concatenator.nonexistent_attribute + with pytest.raises(AttributeError): + _ = concatenator.nonexistent_attribute diff --git a/tests/unit/test_cli.py b/tests/unit/test_cli.py deleted file mode 100644 index ab911be..0000000 --- a/tests/unit/test_cli.py +++ /dev/null @@ -1,13 +0,0 @@ -from concatenator.run_stitchee import parse_args - - -def test_parser(): - parsed = parse_args( - ["ncfile1", "ncfile2", "ncfile3", "-o", "outfile", "--concat_dim", "mirror_step"] - ) - - assert parsed.input == ["ncfile1", "ncfile2", "ncfile3"] - assert parsed.output_path == "outfile" - assert parsed.concat_dim == "mirror_step" - assert parsed.concat_method == "xarray-concat" - assert parsed.verbose is False diff --git a/tests/unit/test_group_handling.py b/tests/unit/test_group_handling.py index 89a51a1..53cb094 100644 --- a/tests/unit/test_group_handling.py +++ b/tests/unit/test_group_handling.py @@ -1,44 +1,36 @@ """Tests for manipulating netCDF groups.""" # pylint: disable=C0116, C0301 +import logging +from pathlib import Path -from concatenator.attribute_handling import ( - _flatten_coordinate_attribute, - regroup_coordinate_attribute, -) - - -def test_coordinate_attribute_flattening(): - # Case with groups present and double spaces. - assert ( - _flatten_coordinate_attribute( - "Time_and_Position/time Time_and_Position/instrument_fov_latitude Time_and_Position/instrument_fov_longitude" - ) - == "__Time_and_Position__time __Time_and_Position__instrument_fov_latitude __Time_and_Position__instrument_fov_longitude" - ) - - # Case with NO groups present and single spaces. - assert ( - _flatten_coordinate_attribute( - "time longitude latitude ozone_profile_pressure ozone_profile_altitude" - ) - == "__time __longitude __latitude __ozone_profile_pressure __ozone_profile_altitude" - ) - - -def test_coordinate_attribute_regrouping(): - # Case with groups present and double spaces. - assert ( - regroup_coordinate_attribute( - "__Time_and_Position__time __Time_and_Position__instrument_fov_latitude __Time_and_Position__instrument_fov_longitude" - ) - == "Time_and_Position/time Time_and_Position/instrument_fov_latitude Time_and_Position/instrument_fov_longitude" - ) - - # Case with NO groups present and single spaces. - assert ( - regroup_coordinate_attribute( - "__time __longitude __latitude __ozone_profile_pressure __ozone_profile_altitude" - ) - == "time longitude latitude ozone_profile_pressure ozone_profile_altitude" - ) +import pytest + +from concatenator.dataset_and_group_handling import validate_workable_files + +from ..conftest import path_str + +logger = logging.getLogger(__name__) + + +@pytest.mark.usefixtures("pass_options") +class TestGroupHandling: + __test_path = Path(__file__).parents[1].resolve() + __data_path = __test_path.joinpath("data") + __harmony_path = __data_path.joinpath("harmony") + __granules_path = __harmony_path.joinpath("granules") + + def test_workable_files_validation(self, temp_output_dir): + filepaths = [ + path_str( + self.__granules_path, "TEMPO_NO2_L2_V03_20240601T210934Z_S012G01_subsetted.nc4" + ), + path_str( + self.__granules_path, "TEMPO_NO2_L2_V03_20240601T211614Z_S012G02_subsetted.nc4" + ), + path_str( + self.__granules_path, "TEMPO_NO2_L2_V03_20240601T212254Z_S012G03_subsetted.nc4" + ), + ] + + assert validate_workable_files(filepaths, logger)[1] == 3 diff --git a/tests/unit/test_harmony_adapter.py b/tests/unit/test_harmony_adapter.py new file mode 100644 index 0000000..5526506 --- /dev/null +++ b/tests/unit/test_harmony_adapter.py @@ -0,0 +1,91 @@ +import json +import sys +from os import environ +from pathlib import Path +from unittest.mock import patch +from urllib.parse import urlsplit + +import pytest +from netCDF4 import Dataset + +import concatenator.harmony.cli +from tests.conftest import prep_input_files + + +@pytest.mark.usefixtures("pass_options") +class TestBatching: + __test_path = Path(__file__).parents[1].resolve() + __data_path = __test_path.joinpath("data") + __harmony_path = __data_path.joinpath("harmony") + __granule_copies_path = __harmony_path.joinpath("granule_copies_dir") + __granules_path = __harmony_path.joinpath("granules") + + def test_service_invoke(self, temp_output_dir): + in_message_path = self.__harmony_path.joinpath("message.json") + in_message_data = in_message_path.read_text() + + # test with both paged catalogs and un-paged catalogs + for in_catalog_name in ["catalog.json", "catalog0.json"]: + + # Copy granule files, because stitchee modifies the Dataset's variable names during flattening. + # If stitchee is run two times on the same file, it will likely fail the second time. + _ = prep_input_files(self.__granules_path, self.__granule_copies_path) + + in_catalog_path = self.__harmony_path.joinpath("source", in_catalog_name) + + test_args = [ + concatenator.harmony.cli.__file__, + "--harmony-action", + "invoke", + "--harmony-input", + in_message_data, + "--harmony-source", + str(in_catalog_path), + "--harmony-metadata-dir", + str(temp_output_dir), + "--harmony-data-location", + temp_output_dir.as_uri(), + ] + + test_env = { + "ENV": "dev", + "OAUTH_CLIENT_ID": "", + "OAUTH_UID": "", + "OAUTH_PASSWORD": "", + "OAUTH_REDIRECT_URI": "", + "STAGING_PATH": "", + "STAGING_BUCKET": "", + } + + with patch.object(sys, "argv", test_args), patch.dict(environ, test_env): + concatenator.harmony.cli.main() + + # Open the outputs + out_catalog_path = temp_output_dir.joinpath("catalog.json") + out_catalog = json.loads(out_catalog_path.read_text()) + + item_meta = next(item for item in out_catalog["links"] if item["rel"] == "item") + item_href = item_meta["href"] + item_path = temp_output_dir.joinpath(item_href).resolve() + + # -- Item Verification -- + item = json.loads(item_path.read_text()) + properties = item["properties"] + + # Accumulation method checks + assert item["bbox"] == [-4, -3, 1, 3] + assert properties["start_datetime"] == "2020-01-02T00:00:00+00:00" + assert properties["end_datetime"] == "2020-01-05T23:59:59+00:00" + + # -- Asset Verification -- + data = item["assets"]["data"] + + # Sanity checks on metadata + assert data["href"].endswith("_stitched.nc4") + assert data["title"].endswith("_stitched.nc4") + assert data["type"] == "application/x-netcdf4" + assert data["roles"] == ["data"] + + path = urlsplit(data["href"]).path + dataset = Dataset(path) + assert len(dataset["mirror_step"]) == 395 diff --git a/tests/unit/test_run_stitchee.py b/tests/unit/test_run_stitchee.py new file mode 100644 index 0000000..11e58d1 --- /dev/null +++ b/tests/unit/test_run_stitchee.py @@ -0,0 +1,72 @@ +import sys +from pathlib import Path +from unittest.mock import patch + +import pytest + +import concatenator +from concatenator.run_stitchee import parse_args + +from ..conftest import path_str + + +def test_parser(): + parsed = parse_args( + ["ncfile1", "ncfile2", "ncfile3", "-o", "outfile", "--concat_dim", "mirror_step"] + ) + + assert parsed.input == ["ncfile1", "ncfile2", "ncfile3"] + assert parsed.output_path == "outfile" + assert parsed.concat_dim == "mirror_step" + assert parsed.concat_method == "xarray-concat" + assert parsed.verbose is False + + +@pytest.mark.usefixtures("pass_options") +class TestBatching: + __test_path = Path(__file__).parents[1].resolve() + __data_path = __test_path.joinpath("data") + __harmony_path = __data_path.joinpath("harmony") + __granules_path = __harmony_path.joinpath("granules") + + def test_run_stitchee_cli_with_three_filepaths(self, temp_output_dir): + test_args = [ + concatenator.run_stitchee.__file__, + path_str( + self.__granules_path, "TEMPO_NO2_L2_V03_20240601T210934Z_S012G01_subsetted.nc4" + ), + path_str( + self.__granules_path, "TEMPO_NO2_L2_V03_20240601T211614Z_S012G02_subsetted.nc4" + ), + path_str( + self.__granules_path, "TEMPO_NO2_L2_V03_20240601T212254Z_S012G03_subsetted.nc4" + ), + "--copy_input_files", + "--verbose", + "-o", + path_str(temp_output_dir, "test_run_stitchee_output.nc"), + "--concat_method", + "xarray-concat", + "--concat_dim", + "mirror_step", + ] + + with patch.object(sys, "argv", test_args): + concatenator.run_stitchee.main() + + def test_run_stitchee_cli_with_one_directorypath(self, temp_output_dir): + test_args = [ + concatenator.run_stitchee.__file__, + str(self.__granules_path), + "--copy_input_files", + "--verbose", + "-o", + path_str(temp_output_dir, "test_run_stitchee_output.nc"), + "--concat_method", + "xarray-concat", + "--concat_dim", + "mirror_step", + ] + + with patch.object(sys, "argv", test_args): + concatenator.run_stitchee.main()