diff --git a/.dockerignore b/.dockerignore new file mode 100644 index 0000000..3c94215 --- /dev/null +++ b/.dockerignore @@ -0,0 +1,103 @@ +TEMPO_*.nc +tests/ +pytest.ini +.git +.gitignore +.travis.yaml +.swagger-codegen-ignore +tox.ini + +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] +*$py.class + +# C extensions +*.so + +# Distribution / packaging +.Python +env/ +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +*.egg-info/ +.installed.cfg +*.egg + +# PyInstaller +# Usually these files are written by a python script from a template +# before PyInstaller builds the exe, so as to inject date/other infos into it. +*.manifest +*.spec + +# Installer logs +pip-log.txt +pip-delete-this-directory.txt + +# Unit test / coverage reports +htmlcov/ +.tox/ +.coverage +.coverage.* +.cache +nosetests.xml +coverage.xml +*,cover +.hypothesis/ +venv/ +.python-version + +# Translations +*.mo +*.pot + +# Django stuff: +*.log + +# Sphinx documentation +docs/_build/ + +# PyBuilder +target/ + +#Ipython Notebook +.ipynb_checkpoints + +# Intellij project settings +.idea + +# VSCode project settings +.vscode + +# mkdocs documentation +/site + +# mypy +.mypy_cache/ +.dmypy.json +dmypy.json + +# ruff +.ruff_cache/ +# pytest +.pytest_cache/ + +# Pyre type checker +.pyre/ + +# Github integration settings +.github + +# .dockerignore and builder script themselves are not needed by +# docker build. +.dockerignore +build-service diff --git a/.github/dependabot.yml b/.github/dependabot.yml index 5a488df..c2c98d6 100644 --- a/.github/dependabot.yml +++ b/.github/dependabot.yml @@ -3,15 +3,12 @@ updates: - package-ecosystem: pip directory: "/" schedule: - interval: daily + interval: "weekly" # Raise pull requests for version updates # to pip against the `develop` branch target-branch: "develop" - package-ecosystem: "github-actions" directory: "/" schedule: - # Check for updates to GitHub Actions every weekday - interval: "daily" - # Raise pull requests for version updates - # to pip against the `develop` branch + interval: "weekly" target-branch: "develop" diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 2aa0f30..ba7dee6 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -38,9 +38,3 @@ repos: - id: yamllint args: ["-d {extends: relaxed, rules: {line-length: {max: 120}}}"] stages: [commit, push] - - - repo: https://github.com/pryorda/dockerfilelint-precommit-hooks - rev: v0.1.0 - hooks: - - id: dockerfilelint - stages: [commit, push] diff --git a/CHANGELOG.md b/CHANGELOG.md index a69d564..9fde59f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,9 +8,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Added - [PR #1](https://github.com/danielfromearth/stitchee/pull/1): An initial GitHub Actions workflow + - [Issue #8](https://github.com/danielfromearth/stitchee/issues/8): Create working Docker image + - [Issue #10](https://github.com/danielfromearth/stitchee/issues/10): Add code necessary to communicate with Harmony + - [Issue #49](https://github.com/danielfromearth/stitchee/issues/49): More CLI arguments for finer control of concatenation method ### Changed - [PR #12](https://github.com/danielfromearth/stitchee/pull/12): Changed name to "stitchee" - [PR #15](https://github.com/danielfromearth/stitchee/pull/15): Use ruff+black chain for pre-commit lint & format + - [Issue #45](https://github.com/danielfromearth/stitchee/issues/45): Rename CLI argument to clarify temporary copying behavior + - [Issue #44](https://github.com/danielfromearth/stitchee/issues/44): Concatenation dimension CLI argument is required but isn't listed as such in the help message ### Deprecated ### Removed ### Fixed diff --git a/Dockerfile b/Dockerfile new file mode 100644 index 0000000..eedcd8a --- /dev/null +++ b/Dockerfile @@ -0,0 +1,47 @@ + +FROM python:3.10-slim + +RUN apt-get update \ + && DEBIAN_FRONTEND=noninteractive apt-get upgrade -y \ + gcc \ + libnetcdf-dev \ + #libhdf5-dev \ + #hdf5-helpers \ + && pip3 install --upgrade pip \ + && pip3 install cython \ + && pip3 install poetry \ + && apt-get clean && rm -rf /var/lib/apt/lists/* + + +# 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 PATH="/home/dockeruser/.local/bin:${PATH}" + +# The 'SOURCE' argument is what will be used in 'pip install'. +ARG SOURCE + +# Set this argument if running the pip install on a local directory, so +# the local dist files are copied into the container. +ARG DIST_PATH + +USER root +RUN mkdir -p /worker && chown dockeruser /worker +COPY pyproject.toml /worker + +WORKDIR /worker +# ENV PYTHONPATH=${PYTHONPATH}:${PWD} +COPY --chown=dockeruser $DIST_PATH $DIST_PATH +#RUN pip3 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 + +#install poetry as root +RUN poetry config virtualenvs.create false +RUN poetry install --only main + +USER dockeruser +COPY --chown=dockeruser ./docker-entrypoint.sh docker-entrypoint.sh +# Run the service +ENTRYPOINT ["./docker-entrypoint.sh"] diff --git a/README.md b/README.md index 6b87d96..1e823d9 100644 --- a/README.md +++ b/README.md @@ -25,35 +25,45 @@ poetry run pytest tests/ ```shell $ poetry run stitchee --help -usage: stitchee [-h] -o output_path [--concat_dim concat_dim] [--make_dir_copy] [--keep_tmp_files] [-O] [-v] +usage: stitchee [-h] -o OUTPUT_PATH [--no_input_file_copies] [--keep_tmp_files] [--concat_method {xarray-concat,xarray-combine}] [--concat_dim CONCAT_DIM] + [--xarray_arg_compat XARRAY_ARG_COMPAT] [--xarray_arg_combine_attrs XARRAY_ARG_COMBINE_ATTRS] [--xarray_arg_join XARRAY_ARG_JOIN] [-O] + [-v] path/directory or path list [path/directory or path list ...] Run the along-existing-dimension concatenator. options: -h, --help show this help message and exit - --concat_dim concat_dim - Dimension to concatenate along, if possible. - --make_dir_copy Make a duplicate of the input directory to avoid modification of input files. This is useful for testing, but - uses more disk space. - --keep_tmp_files Prevents removal, after successful execution, of (1) the flattened concatenated file and (2) the input - directory copy if created by '--make_dir_copy'. + --no_input_file_copies + By default, input files are copied into a temporary directory to avoid modification of input files. This is useful for testing, + but uses more disk space. By specifying this argument, no copying is performed. + --keep_tmp_files Prevents removal, after successful execution, of (1) the flattened concatenated file and (2) the input directory copy if created + by '--make_dir_copy'. + --concat_method {xarray-concat,xarray-combine} + Whether to use the xarray concat method or the combine-by-coords method. + --concat_dim CONCAT_DIM + Dimension to concatenate along, if possible. This is required if using the 'xarray-concat' method + --xarray_arg_compat XARRAY_ARG_COMPAT + 'compat' argument passed to xarray.concat() or xarray.combine_by_coords(). + --xarray_arg_combine_attrs XARRAY_ARG_COMBINE_ATTRS + 'combine_attrs' argument passed to xarray.concat() or xarray.combine_by_coords(). + --xarray_arg_join XARRAY_ARG_JOIN + 'join' argument passed to xarray.concat() or xarray.combine_by_coords(). -O, --overwrite Overwrite output file if it already exists. -v, --verbose Enable verbose output to stdout; useful for debugging Required: path/directory or path list - Files to be concatenated, specified via a (1) single directory containing the files to be concatenated, (2) - single text file containing linebreak-separated paths of the files to be concatenated, or (3) multiple - filepaths of the files to be concatenated. - -o output_path, --output_path output_path + Files to be concatenated, specified via a (1) single directory containing the files to be concatenated, (2) single text file + containing linebreak-separated paths of the files to be concatenated, or (3) multiple filepaths of the files to be concatenated. + -o OUTPUT_PATH, --output_path OUTPUT_PATH The output filename for the merged output. ``` For example: ```shell -poetry run stitchee /path/to/netcdf/directory/ /path/to/output.nc +poetry run stitchee /path/to/netcdf/directory/ -o /path/to/output.nc ``` ## Roadmap diff --git a/build-service b/build-service new file mode 100755 index 0000000..1026e26 --- /dev/null +++ b/build-service @@ -0,0 +1,3 @@ +#!/bin/bash + +docker build -t "asdc-trade/stitchee:${VERSION-latest}" . diff --git a/concatenator/group_handling.py b/concatenator/group_handling.py index 2cc3193..277011c 100644 --- a/concatenator/group_handling.py +++ b/concatenator/group_handling.py @@ -174,7 +174,6 @@ def regroup_flattened_dataset( output_file : str Name of the output file to write the resulting NetCDF file to. """ - with nc.Dataset(output_file, mode="w", format="NETCDF4") as base_dataset: # Copy global attributes base_dataset.setncatts(dataset.attrs) diff --git a/concatenator/harmony/__init__.py b/concatenator/harmony/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/concatenator/harmony/cli.py b/concatenator/harmony/cli.py new file mode 100644 index 0000000..3329095 --- /dev/null +++ b/concatenator/harmony/cli.py @@ -0,0 +1,33 @@ +"""A Harmony CLI wrapper around the concatenate-batcher""" +from argparse import ArgumentParser + +import harmony + +from concatenator.harmony.service_adapter import StitcheeAdapter as HarmonyAdapter + + +def main(config: harmony.util.Config = None) -> None: + """Parse command line arguments and invoke the service to respond to them. + + Parameters + ---------- + config : harmony.util.Config + harmony.util.Config is injectable for tests + + Returns + ------- + None + """ + parser = ArgumentParser( + prog="Stitchee", description="Run the STITCH by Extending a dimEnsion service" + ) + harmony.setup_cli(parser) + args = parser.parse_args() + if harmony.is_harmony_cli(args): + harmony.run_cli(parser, args, HarmonyAdapter, cfg=config) + else: + parser.error("Only --harmony CLIs are supported") + + +if __name__ == "__main__": + main() diff --git a/concatenator/harmony/download_worker.py b/concatenator/harmony/download_worker.py new file mode 100644 index 0000000..3f502e3 --- /dev/null +++ b/concatenator/harmony/download_worker.py @@ -0,0 +1,119 @@ +"""A utility for downloading multiple granules simultaneously""" + +import queue +import re +from copy import deepcopy +from multiprocessing import Manager, Process +from os import cpu_count +from pathlib import Path +from urllib.parse import urlparse + +from harmony.logging import build_logger +from harmony.util import download + + +def multi_core_download( + urls: list, destination_dir: str, access_token: str, cfg: dict, process_count: int | None = None +) -> list[Path]: + """ + A method which automagically scales downloads to the number of CPU + cores. For further explaination, see documentation on "multi-track + drifting" + + Parameters + ---------- + urls : list + list of urls to download + destination_dir : str + output path for downloaded files + access_token : str + access token as provided in Harmony input + cfg : dict + Harmony configuration information + process_count : int, optional + Number of worker processes to run (expected >= 1) + + Returns + ------- + list + list of downloaded files as pathlib.Path objects + """ + + if process_count is None: + process_count = cpu_count() + if process_count is None: + raise RuntimeError("cannot determine number of cpus") + + with Manager() as manager: + url_queue = manager.Queue(len(urls)) + path_list = manager.list() + + for url in urls: + url_queue.put(url) + + # Spawn worker processes + processes = [] + for _ in range(process_count): + download_process = Process( + target=_download_worker, + args=(url_queue, path_list, destination_dir, access_token, cfg), + ) + processes.append(download_process) + download_process.start() + + # Ensure worker processes exit successfully + for process in processes: + process.join() + if process.exitcode != 0: + raise RuntimeError(f"Download failed - exit code: {process.exitcode}") + + process.close() + + path_list = deepcopy(path_list) # ensure GC can cleanup multiprocessing + + return [Path(path) for path in path_list] + + +def _download_worker( + url_queue: queue.Queue, path_list: list, destination_dir: str, access_token: str, cfg: dict +) -> None: + """ + A method to be executed in a separate process which processes the url_queue + and places paths to completed downloads into the path_list. Downloads are + handled by harmony.util.download + + Parameters + ---------- + url_queue : queue.Queue + URLs to process - should be filled from start and only decreases + path_list : list + paths to completed file downloads + destination_dir : str + output path for downloaded files + access_token : str + access token as provided in Harmony input + cfg : dict + Harmony configuration information + """ + + logger = build_logger(cfg) + + while not url_queue.empty(): + try: + url = url_queue.get_nowait() + except queue.Empty: + break + + path = Path( + download(url, destination_dir, logger=logger, access_token=access_token, cfg=cfg) + ) + filename_match = re.match(r".*\/(.+\..+)", urlparse(url).path) + + if filename_match is not None: + filename = filename_match.group(1) + dest_path = path.parent.joinpath(filename) + path = path.rename(dest_path) + else: + logger.warning("Origin filename could not be assertained - %s", url) + + path_list.append(str(path)) diff --git a/concatenator/harmony/service_adapter.py b/concatenator/harmony/service_adapter.py new file mode 100644 index 0000000..f3eb3ec --- /dev/null +++ b/concatenator/harmony/service_adapter.py @@ -0,0 +1,179 @@ +from pathlib import Path +from shutil import copyfile +from tempfile import TemporaryDirectory +from urllib.parse import urlsplit +from uuid import uuid4 + +import pystac +from harmony.adapter import BaseHarmonyAdapter +from harmony.util import bbox_to_geometry, stage +from pystac import Item +from pystac.item import Asset + +from concatenator.harmony.download_worker import multi_core_download +from concatenator.harmony.util import ( + _get_netcdf_urls, + _get_output_bounding_box, + _get_output_date_range, + sizeof_fmt, +) +from concatenator.stitchee import stitchee + + +class StitcheeAdapter(BaseHarmonyAdapter): + """ + A harmony-service-lib wrapper around the concatenate-batcher module. + This wrapper does not support Harmony calls that do not have STAC catalogs + as support for this behavior is being depreciated in harmony-service-lib + """ + + def __init__(self, message, catalog=None, config=None): + """ + Constructs the adapter + + Parameters + ---------- + message : harmony.Message + The Harmony input which needs acting upon + catalog : pystac.Catalog + A STAC catalog containing the files on which to act + config : harmony.util.Config + The configuration values for this runtime environment. + """ + super().__init__(message, catalog=catalog, config=config) + + def invoke(self): + """ + Primary entrypoint into the service wrapper. Overrides BaseHarmonyAdapter.invoke + """ + if not self.catalog: + # Message-only support is being depreciated in Harmony, so we should expect to + # only see requests with catalogs when invoked with a newer Harmony instance + # https://github.com/nasa/harmony-service-lib-py/blob/21bcfbda17caf626fb14d2ac4f8673be9726b549/harmony/adapter.py#L71 + raise RuntimeError("Invoking Batchee without a STAC catalog is not supported") + + return self.message, self.process_catalog(self.catalog) + + def process_catalog(self, catalog: pystac.Catalog) -> pystac.Catalog: + """Converts a list of STAC catalogs into a list of lists of STAC catalogs.""" + self.logger.info("process_catalog() started.") + try: + result = catalog.clone() + result.id = str(uuid4()) + result.clear_children() + + # Get all the items from the catalog, including from child or linked catalogs + items = list(self.get_all_catalog_items(catalog)) + + self.logger.info(f"length of items==={len(items)}.") + + # Quick return if catalog contains no items + if len(items) == 0: + return result + + # # --- Get granule filepaths (urls) --- + netcdf_urls: list[str] = _get_netcdf_urls(items) + self.logger.info(f"netcdf_urls==={netcdf_urls}.") + + # -- Process metadata -- + bounding_box: list | None = _get_output_bounding_box(items) + datetimes = _get_output_date_range(items) + + # Items did not have a bbox; valid under spec + if bounding_box and len(bounding_box) == 0: + bounding_box = None + + # -- Perform merging -- + collection = self._get_item_source(items[0]).collection + filename = f"{collection}_merged.nc4" + self.logger.info(f"Merged filename will be === {filename}.") + + with TemporaryDirectory() as temp_dir: + self.logger.info("Starting granule downloads") + input_files = multi_core_download( + netcdf_urls, temp_dir, self.message.accessToken, self.config + ) + self.logger.info("Finished granule downloads.") + + for file_count, file in enumerate(input_files): + file_size = sizeof_fmt(file.stat().st_size) + self.logger.info(f"File {file_count} is size <{file_size}>. Path={file}") + + self.logger.info("Running Stitchee..") + output_path = str(Path(temp_dir).joinpath(filename).resolve()) + + # # --- Run STITCHEE --- + stitchee( + input_files, + output_path, + write_tmp_flat_concatenated=False, + keep_tmp_files=False, + concat_dim="mirror_step", # This is currently set only for TEMPO + logger=self.logger, + ) + self.logger.info("Stitchee completed.") + staged_url = self._stage(output_path, filename, "application/x-netcdf4") + self.logger.info("Staging completed.") + + # -- Output to STAC catalog -- + result.clear_items() + properties = dict( + start_datetime=datetimes["start_datetime"], end_datetime=datetimes["end_datetime"] + ) + + item = Item( + str(uuid4()), bbox_to_geometry(bounding_box), bounding_box, None, properties + ) + asset = Asset( + staged_url, title=filename, media_type="application/x-netcdf4", roles=["data"] + ) + item.add_asset("data", asset) + result.add_item(item) + + self.logger.info("STAC catalog creation complete.") + + return result + + except Exception as service_exception: + self.logger.error(service_exception, exc_info=1) + raise service_exception + + def _stage(self, local_filename: str, remote_filename: str, mime: str) -> str: + """ + Stages a local file to either to S3 (utilizing harmony.util.stage) or to + the local filesystem by performing a file copy. Staging location is + determined by message.stagingLocation or the --harmony-data-location + CLI argument override + + Parameters + ---------- + local_filename : string + A path and filename to the local file that should be staged + remote_filename : string + The basename to give to the remote file + mime : string + The mime type to apply to the staged file for use when it is served, e.g. "application/x-netcdf4" + + Returns + ------- + url : string + A URL to the staged file + """ + url_components = urlsplit(self.message.stagingLocation) + scheme = url_components.scheme + + if scheme == "file": + dest_path = Path(url_components.path).joinpath(remote_filename) + self.logger.info("Staging to local filesystem: '%s'", str(dest_path)) + + copyfile(local_filename, dest_path) + return dest_path.as_uri() + + return stage( + local_filename, + remote_filename, + mime, + logger=self.logger, + location=self.message.stagingLocation, + cfg=self.config, + ) diff --git a/concatenator/harmony/util.py b/concatenator/harmony/util.py new file mode 100644 index 0000000..a972aaf --- /dev/null +++ b/concatenator/harmony/util.py @@ -0,0 +1,110 @@ +"""Misc utility functions""" +from datetime import datetime + +from pystac import Asset, Item + +VALID_EXTENSIONS = (".nc4", ".nc") +VALID_MEDIA_TYPES = ["application/x-netcdf", "application/x-netcdf4"] + + +def _is_netcdf_asset(asset: Asset) -> bool: + """Check that a `pystac.Asset` is a valid NetCDF-4 granule. This can be + ascertained via either the media type or by checking the extension of + granule itself if that media type is absent. + + """ + return asset.media_type in VALID_MEDIA_TYPES or ( + asset.media_type is None and asset.href.lower().endswith(VALID_EXTENSIONS) + ) + + +def _get_item_url(item: Item) -> str | None: + """Check the `pystac.Item` for the first asset with the `data` role and a + valid input format. If there are no matching assets, return None + + """ + return next( + ( + asset.href + for asset in item.assets.values() + if "data" in (asset.roles or []) and _is_netcdf_asset(asset) + ), + None, + ) + + +def _get_netcdf_urls(items: list[Item]) -> list[str]: + """Iterate through a list of `pystac.Item` instances, from the input + `pystac.Catalog`. Extract the `pystac.Asset.href` for the first asset + of each item that has a role of "data". If there are any items that do + not have a data asset, then raise an exception. + + """ + catalog_urls = [_get_item_url(item) for item in items] + + if None in catalog_urls: + raise RuntimeError("Some input granules do not have NetCDF-4 assets.") + + return catalog_urls # type: ignore[return-value] + + +def _get_output_bounding_box(input_items: list[Item]) -> list[float]: + """Create a bounding box that is the maximum combined extent of all input + `pystac.Item` bounding box extents. + + """ + bounding_box = input_items[0].bbox + + for item in input_items: + bounding_box[0] = min(bounding_box[0], item.bbox[0]) + bounding_box[1] = min(bounding_box[1], item.bbox[1]) + bounding_box[2] = max(bounding_box[2], item.bbox[2]) + bounding_box[3] = max(bounding_box[3], item.bbox[3]) + + return bounding_box + + +def _get_output_date_range(input_items: list[Item]) -> dict[str, str]: + """Create a dictionary of start and end datetime, which encompasses the + full temporal range of all input `pystac.Item` instances. This output + dictionary will be used for the `properties` of the output Zarr store + `pystac.Item`. + + """ + start_datetime, end_datetime = _get_item_date_range(input_items[0]) + + for item in input_items: + new_start_datetime, new_end_datetime = _get_item_date_range(item) + start_datetime = min(start_datetime, new_start_datetime) + end_datetime = max(end_datetime, new_end_datetime) + + return {"start_datetime": start_datetime.isoformat(), "end_datetime": end_datetime.isoformat()} + + +def _get_item_date_range(item: Item) -> tuple[datetime, datetime]: + """A helper function to retrieve the temporal range from a `pystac.Item` + instance. If the `pystac.Item.datetime` property exists, there is a + single datetime associated with the granule, otherwise there will be a + start and end time contained within the `pystac.Item` metadata. + + """ + if item.datetime is None: + start_datetime = item.common_metadata.start_datetime + end_datetime = item.common_metadata.end_datetime + else: + start_datetime = item.datetime + end_datetime = item.datetime + + return start_datetime, end_datetime + + +def sizeof_fmt(num: float, suffix="B") -> str: + """Get a human-readable version of file size + + From: https://stackoverflow.com/a/1094933 + """ + for unit in ("", "Ki", "Mi", "Gi", "Ti", "Pi", "Ei", "Zi"): + if abs(num) < 1024.0: + return f"{num:3.1f}{unit}{suffix}" + num /= 1024.0 + return f"{num:.1f}Yi{suffix}" diff --git a/concatenator/run_stitchee.py b/concatenator/run_stitchee.py index 580df22..5b1ef79 100644 --- a/concatenator/run_stitchee.py +++ b/concatenator/run_stitchee.py @@ -11,7 +11,7 @@ from concatenator.stitchee import stitchee -def parse_args(args: list) -> tuple[list[str], str, str, bool, str | None]: +def parse_args(args: list) -> tuple[list[str], str, str, bool, str | None, str, dict]: """ Parse args for this script. @@ -37,23 +37,17 @@ def parse_args(args: list) -> tuple[list[str], str, str, bool, str | None]: req_grp.add_argument( "-o", "--output_path", - metavar="output_path", required=True, help="The output filename for the merged output.", ) # Optional arguments parser.add_argument( - "--concat_dim", - metavar="concat_dim", - nargs=1, - help="Dimension to concatenate along, if possible.", - ) - parser.add_argument( - "--make_dir_copy", + "--no_input_file_copies", action="store_true", - help="Make a duplicate of the input directory to avoid modification of input files. " - "This is useful for testing, but uses more disk space.", + help="By default, input files are copied into a temporary directory to avoid modification " + "of input files. This is useful for testing, but uses more disk space. " + "By specifying this argument, no copying is performed.", ) parser.add_argument( "--keep_tmp_files", @@ -62,6 +56,29 @@ def parse_args(args: list) -> tuple[list[str], str, str, bool, str | None]: "(1) the flattened concatenated file and " "(2) the input directory copy if created by '--make_dir_copy'.", ) + parser.add_argument( + "--concat_method", + choices=["xarray-concat", "xarray-combine"], + default="xarray-concat", + help="Whether to use the xarray concat method or the combine-by-coords method.", + ) + parser.add_argument( + "--concat_dim", + help="Dimension to concatenate along, if possible. " + "This is required if using the 'xarray-concat' method", + ) + parser.add_argument( + "--xarray_arg_compat", + help="'compat' argument passed to xarray.concat() or xarray.combine_by_coords().", + ) + parser.add_argument( + "--xarray_arg_combine_attrs", + help="'combine_attrs' argument passed to xarray.concat() or xarray.combine_by_coords().", + ) + parser.add_argument( + "--xarray_arg_join", + help="'join' argument passed to xarray.concat() or xarray.combine_by_coords().", + ) parser.add_argument( "-O", "--overwrite", action="store_true", help="Overwrite output file if it already exists." ) @@ -77,6 +94,71 @@ def parse_args(args: list) -> tuple[list[str], str, str, bool, str | None]: if parsed.verbose: logging.basicConfig(level=logging.DEBUG) + # Validate the input and output paths + output_path = _validate_output_path(parsed) + input_files = _validate_input_path(parsed) + + print(f"CONCAT METHOD === {parsed.concat_method}") + print(f"CONCAT DIM === {parsed.concat_dim}") + if parsed.concat_method == "xarray-concat": + if not parsed.concat_dim: + raise ValueError( + "If using the xarray-concat method, then 'concat_dim' must be specified." + ) + elif parsed.concat_method == "xarray-combine": + if parsed.concat_dim: + raise ValueError( + "If using the xarray-combine method, then 'concat_dim' cannot be specified." + ) + + # Gather the concatenation arguments that will be passed to xarray. + concat_kwargs = {} + if parsed.xarray_arg_compat: + concat_kwargs["compat"] = parsed.xarray_arg_compat + if parsed.xarray_arg_combine_attrs: + concat_kwargs["combine_attrs"] = parsed.xarray_arg_combine_attrs + if parsed.xarray_arg_join: + concat_kwargs["join"] = parsed.xarray_arg_join + + # If requested, make a temporary directory with new copies of the original input files + temporary_dir_to_remove = None + if not parsed.no_input_file_copies: + input_files, temporary_dir_to_remove = _make_temp_dir_with_input_file_copies( + input_files, output_path + ) + + return ( + input_files, + str(output_path), + parsed.concat_dim, + bool(parsed.keep_tmp_files), + temporary_dir_to_remove, + parsed.concat_method, + concat_kwargs, + ) + + +def _make_temp_dir_with_input_file_copies(input_files, output_path): + new_data_dir = Path( + add_label_to_path(str(output_path.parent / "temp_copy"), label=str(uuid.uuid4())) + ).resolve() + os.makedirs(new_data_dir, exist_ok=True) + print("Created temporary directory: %s", str(new_data_dir)) + + new_input_files = [] + for file in input_files: + new_path = new_data_dir / Path(file).name + shutil.copyfile(file, new_path) + new_input_files.append(str(new_path)) + + input_files = new_input_files + print("Copied files to temporary directory: %s", new_data_dir) + temporary_dir_to_remove = str(new_data_dir) + + return input_files, temporary_dir_to_remove + + +def _validate_output_path(parsed): # The output file path is validated. output_path = Path(parsed.output_path).resolve() if output_path.is_file(): # the file already exists @@ -86,7 +168,12 @@ def parse_args(args: list) -> tuple[list[str], str, str, bool, str | None]: raise FileExistsError( f"File already exists at <{output_path}>. Run again with option '-O' to overwrite." ) + if output_path.is_dir(): # the specified path is an existing directory + raise TypeError("Output path cannot be a directory. Please specify a new filepath.") + return output_path + +def _validate_input_path(parsed): # The input directory or file is validated. print(f"parsed_input === {parsed.input}") if len(parsed.input) > 1: @@ -99,38 +186,12 @@ def parse_args(args: list) -> tuple[list[str], str, str, bool, str | None]: input_files = _get_list_of_filepaths_from_file(directory_or_path) else: raise TypeError( - "if one path is provided for 'data_dir_or_file_or_filepaths', " + "If one path is provided for 'data_dir_or_file_or_filepaths', " "then it must be an existing directory or file." ) else: raise TypeError("input argument must be one path/directory or a list of paths.") - - # If requested, make a temporary directory with copies of the original input files - temporary_dir_to_remove = None - if parsed.make_dir_copy: - new_data_dir = Path( - add_label_to_path(str(output_path.parent / "temp_copy"), label=str(uuid.uuid4())) - ).resolve() - os.makedirs(new_data_dir, exist_ok=True) - print("Created temporary directory: %s", str(new_data_dir)) - - new_input_files = [] - for file in input_files: - new_path = new_data_dir / Path(file).name - shutil.copyfile(file, new_path) - new_input_files.append(str(new_path)) - - input_files = new_input_files - print("Copied files to temporary directory: %s", new_data_dir) - temporary_dir_to_remove = str(new_data_dir) - - return ( - input_files, - str(output_path), - parsed.concat_dim[0], - bool(parsed.keep_tmp_files), - temporary_dir_to_remove, - ) + return input_files def _get_list_of_filepaths_from_file(file_with_paths: Path): @@ -144,7 +205,7 @@ def _get_list_of_filepaths_from_file(file_with_paths: Path): def _get_list_of_filepaths_from_dir(data_dir: Path): - # Get list of files (ignoring hidden files) in directory. + # Get a list of files (ignoring hidden files) in directory. input_files = [str(f) for f in data_dir.iterdir() if not f.name.startswith(".")] return input_files @@ -153,7 +214,15 @@ def run_stitchee(args: list) -> None: """ Parse arguments and run subsetter on the specified input file """ - input_files, output_path, concat_dim, keep_tmp_files, temporary_dir_to_remove = parse_args(args) + ( + input_files, + output_path, + concat_dim, + keep_tmp_files, + temporary_dir_to_remove, + concat_method, + concat_kwargs, + ) = parse_args(args) num_inputs = len(input_files) logging.info("Executing stitchee concatenation on %d files...", num_inputs) @@ -162,7 +231,9 @@ def run_stitchee(args: list) -> None: output_path, write_tmp_flat_concatenated=keep_tmp_files, keep_tmp_files=keep_tmp_files, + concat_method=concat_method, concat_dim=concat_dim, + concat_kwargs=concat_kwargs, ) logging.info("STITCHEE complete. Result in %s", output_path) diff --git a/concatenator/stitchee.py b/concatenator/stitchee.py index 103e3b6..d1f2c8d 100644 --- a/concatenator/stitchee.py +++ b/concatenator/stitchee.py @@ -3,6 +3,7 @@ import os import time from logging import Logger +from warnings import warn import netCDF4 as nc import xarray as xr @@ -23,6 +24,7 @@ def stitchee( output_file: str, write_tmp_flat_concatenated: bool = False, keep_tmp_files: bool = True, + concat_method: str = "xarray-concat", concat_dim: str = "", concat_kwargs: dict | None = None, logger: Logger = default_logger, @@ -52,84 +54,108 @@ def stitchee( logger.info("No non-empty netCDF files found. Exiting.") return "" - logger.debug("Flattening all input files...") - xrdataset_list = [] - for i, filepath in enumerate(input_files): - # The group structure is flattened. - start_time = time.time() - logger.debug(" ..file %03d/%03d <%s>..", i + 1, num_input_files, filepath) - flat_dataset, coord_vars, _ = flatten_grouped_dataset( - nc.Dataset(filepath, "r"), filepath, ensure_all_dims_are_coords=True + if concat_dim and (concat_method == "xarray-combine"): + warn( + "'concat_dim' was specified, but will not be used because xarray-combine method was selected." ) - flat_dataset = remove_duplicate_dims(flat_dataset) - - xrds = xr.open_dataset( - xr.backends.NetCDF4DataStore(flat_dataset), - decode_times=False, - decode_coords=False, - drop_variables=coord_vars, - ) + logger.info("Flattening all input files...") + xrdataset_list = [] - benchmark_log["flattening"] = time.time() - start_time - - # The flattened file is written to disk. - # flat_file_path = add_label_to_path(filepath, label="_flat_intermediate") - # xrds.to_netcdf(flat_file_path, encoding={v_name: {'dtype': 'str'} for v_name in string_vars}) - # intermediate_flat_filepaths.append(flat_file_path) - # xrdataset_list.append(xr.open_dataset(flat_file_path)) - xrdataset_list.append(xrds) - - # Flattened files are concatenated together (Using XARRAY). - start_time = time.time() - logger.debug("Concatenating flattened files...") - # combined_ds = xr.open_mfdataset(intermediate_flat_filepaths, - # decode_times=False, - # decode_coords=False, - # data_vars='minimal', - # coords='minimal', - # compat='override') - - if concat_kwargs is None: - concat_kwargs = {} - - combined_ds = xr.concat( - xrdataset_list, - dim=GROUP_DELIM + concat_dim, - data_vars="minimal", - coords="minimal", - **concat_kwargs, - ) - - benchmark_log["concatenating"] = time.time() - start_time - - if write_tmp_flat_concatenated: - logger.debug("Writing concatenated flattened temporary file to disk...") - # Concatenated, yet still flat, file is written to disk for debugging. - tmp_flat_concatenated_path = add_label_to_path(output_file, label="_flat_intermediate") - combined_ds.to_netcdf(tmp_flat_concatenated_path, format="NETCDF4") - else: - tmp_flat_concatenated_path = None - - # The group hierarchy of the concatenated file is reconstructed (using XARRAY). - start_time = time.time() - logger.debug("Reconstructing groups within concatenated file...") - regroup_flattened_dataset(combined_ds, output_file) - benchmark_log["reconstructing_groups"] = time.time() - start_time - - logger.info("--- Benchmark results ---") - total_time = 0.0 - for k, v in benchmark_log.items(): - logger.info("%s: %f", k, v) - total_time += v - logger.info("-- total processing time: %f", total_time) - - # If requested, remove temporary intermediate files. - if not keep_tmp_files: - for file in intermediate_flat_filepaths: - os.remove(file) - if tmp_flat_concatenated_path: - os.remove(tmp_flat_concatenated_path) + try: + for i, filepath in enumerate(input_files): + # The group structure is flattened. + start_time = time.time() + logger.info(" ..file %03d/%03d <%s>..", i + 1, num_input_files, filepath) + flat_dataset, coord_vars, _ = flatten_grouped_dataset( + nc.Dataset(filepath, "r"), filepath, ensure_all_dims_are_coords=True + ) + + logger.info("Removing duplicate dimensions") + flat_dataset = remove_duplicate_dims(flat_dataset) + + logger.info("Opening flattened file with xarray.") + xrds = xr.open_dataset( + xr.backends.NetCDF4DataStore(flat_dataset), + decode_times=False, + decode_coords=False, + drop_variables=coord_vars, + ) + + benchmark_log["flattening"] = time.time() - start_time + + # The flattened file is written to disk. + # flat_file_path = add_label_to_path(filepath, label="_flat_intermediate") + # xrds.to_netcdf(flat_file_path, encoding={v_name: {'dtype': 'str'} for v_name in string_vars}) + # intermediate_flat_filepaths.append(flat_file_path) + # xrdataset_list.append(xr.open_dataset(flat_file_path)) + xrdataset_list.append(xrds) + + # Flattened files are concatenated together (Using XARRAY). + start_time = time.time() + logger.info("Concatenating flattened files...") + # combined_ds = xr.open_mfdataset(intermediate_flat_filepaths, + # decode_times=False, + # decode_coords=False, + # data_vars='minimal', + # coords='minimal', + # compat='override') + + if concat_kwargs is None: + concat_kwargs = {} + + if concat_method == "xarray-concat": + combined_ds = xr.concat( + xrdataset_list, + dim=GROUP_DELIM + concat_dim, + data_vars="minimal", + coords="minimal", + **concat_kwargs, + ) + elif concat_method == "xarray-combine": + combined_ds = xr.combine_by_coords( + xrdataset_list, + data_vars="minimal", + coords="minimal", + **concat_kwargs, + ) + else: + raise ValueError("Unexpected concatenation method, <%s>." % concat_method) + + benchmark_log["concatenating"] = time.time() - start_time + + if write_tmp_flat_concatenated: + logger.info("Writing concatenated flattened temporary file to disk...") + # Concatenated, yet still flat, file is written to disk for debugging. + tmp_flat_concatenated_path = add_label_to_path(output_file, label="_flat_intermediate") + combined_ds.to_netcdf(tmp_flat_concatenated_path, format="NETCDF4") + else: + tmp_flat_concatenated_path = None + + # The group hierarchy of the concatenated file is reconstructed (using XARRAY). + start_time = time.time() + logger.info("Reconstructing groups within concatenated file...") + regroup_flattened_dataset(combined_ds, output_file) + benchmark_log["reconstructing_groups"] = time.time() - start_time + + logger.info("--- Benchmark results ---") + total_time = 0.0 + for k, v in benchmark_log.items(): + logger.info("%s: %f", k, v) + total_time += v + logger.info("-- total processing time: %f", total_time) + + # If requested, remove temporary intermediate files. + if not keep_tmp_files: + for file in intermediate_flat_filepaths: + os.remove(file) + if tmp_flat_concatenated_path: + os.remove(tmp_flat_concatenated_path) + + except Exception as err: + logger.info("Stitchee encountered an error!") + logger.error(err) + raise err return output_file diff --git a/docker-entrypoint.sh b/docker-entrypoint.sh new file mode 100755 index 0000000..000ebbe --- /dev/null +++ b/docker-entrypoint.sh @@ -0,0 +1,10 @@ +#!/bin/bash +set -e + +if [ "$1" = 'stitchee' ]; then + exec stitchee "$@" +elif [ "$1" = 'stitchee_harmony' ]; then + exec stitchee_harmony "$@" +else + exec stitchee_harmony "$@" +fi diff --git a/poetry.lock b/poetry.lock index 370225b..170ea00 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,34 +1,30 @@ -# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. 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-black = "^23.9.1" -ruff = "^0.0.292" +pytest = "^7.4.3" +mypy = "^1.6.1" +black = "^23.10.1" +ruff = "^0.1.4" coverage = "^7.3.2" [tool.poetry.group.extras.dependencies] nco = "^1.1.0" [tool.poetry.scripts] +stitchee_harmony = 'concatenator.harmony.cli:main' stitchee = 'concatenator.run_stitchee:main' [build-system] diff --git a/tests/test_concat.py b/tests/test_concat.py index 24511f1..2ec0f82 100644 --- a/tests/test_concat.py +++ b/tests/test_concat.py @@ -34,6 +34,7 @@ def run_verification_with_stitchee( self, data_dir, output_name, + concat_method: str = "xarray-concat", record_dim_name: str = "mirror_step", concat_kwargs: dict | None = None, ): @@ -55,6 +56,7 @@ def run_verification_with_stitchee( output_file=output_path, write_tmp_flat_concatenated=True, keep_tmp_files=True, + concat_method=concat_method, concat_dim=record_dim_name, concat_kwargs=concat_kwargs, ) @@ -93,16 +95,24 @@ def run_verification_with_nco(self, data_dir, output_name, record_dim_name="mirr assert length_sum == len(merged_dataset.variables[record_dim_name]) def test_tempo_no2_concat_with_stitchee(self): - self.run_verification_with_stitchee("tempo/no2", "tempo_no2_bee_concatenated.nc") + self.run_verification_with_stitchee( + "tempo/no2", "tempo_no2_bee_concatenated.nc", concat_method="xarray-concat" + ) def test_tempo_hcho_concat_with_stitchee(self): - self.run_verification_with_stitchee("tempo/hcho", "tempo_hcho_bee_concatenated.nc") + self.run_verification_with_stitchee( + "tempo/hcho", "tempo_hcho_bee_concatenated.nc", concat_method="xarray-concat" + ) def test_tempo_cld04_concat_with_stitchee(self): - self.run_verification_with_stitchee("tempo/cld04", "tempo_cld04_bee_concatenated.nc") + self.run_verification_with_stitchee( + "tempo/cld04", "tempo_cld04_bee_concatenated.nc", concat_method="xarray-concat" + ) def test_tempo_o3prof_concat_with_stitchee(self): - self.run_verification_with_stitchee("tempo/o3prof", "tempo_o3prof_bee_concatenated.nc") + self.run_verification_with_stitchee( + "tempo/o3prof", "tempo_o3prof_bee_concatenated.nc", concat_method="xarray-concat" + ) # def test_icesat_concat_with_stitchee(self): # self.run_verification_with_stitchee('icesat', 'icesat_concat_with_stitchee.nc') @@ -111,15 +121,18 @@ def test_ceres_concat_with_stitchee(self): self.run_verification_with_stitchee( "ceres-subsetter-output", "ceres_bee_concatenated.nc", + concat_method="xarray-combine", record_dim_name="time", - concat_kwargs={"compat": "override"}, + concat_kwargs={"compat": "override", "combine_attrs": "override"}, ) def test_ceres_flash_concat_with_stitchee(self): self.run_verification_with_stitchee( "ceres_flash-subsetter-output", "ceres_flash_bee_concatenated.nc", + concat_method="xarray-combine", record_dim_name="time", + concat_kwargs={"compat": "override", "combine_attrs": "override"}, ) # def test_ceres_flash_concat_with_stitchee(self):