This is an automated email from the ASF dual-hosted git repository. rkk pushed a commit to branch backends-patch in repository https://gitbox.apache.org/repos/asf/sdap-nexus.git
commit 8e5823e244e01d7a6ffa4e78ce0e12f43a450f6d Author: rileykk <[email protected]> AuthorDate: Thu Jun 6 09:48:00 2024 -0700 Patches to backend mgmt and zarr backend - Code cleanup - Added dask as dependency, so it will be leveraged with Zarr datasets - Fixed creation of tile times array from Zarr data to ensure its in seconds from 1970-01-01. Original method has been seen to produce incorrect results from bad assumptions --- data-access/nexustiles/AbstractTileService.py | 9 - data-access/nexustiles/backends/zarr/backend.py | 14 +- data-access/nexustiles/nexustiles.py | 9 - poetry.lock | 380 ++++++++++++++---------- pyproject.toml | 1 + 5 files changed, 231 insertions(+), 182 deletions(-) diff --git a/data-access/nexustiles/AbstractTileService.py b/data-access/nexustiles/AbstractTileService.py index 2046778..1e04f69 100644 --- a/data-access/nexustiles/AbstractTileService.py +++ b/data-access/nexustiles/AbstractTileService.py @@ -21,15 +21,6 @@ import numpy.ma as ma class AbstractTileService(ABC): - # @staticmethod - # @abstractmethod - # def open_dataset(dataset_s, **kwargs): - # pass - - # @abstractmethod - # def try_connect(self) -> bool: - # raise NotImplementedError() - def __init__(self, dataset_name): self._name = dataset_name diff --git a/data-access/nexustiles/backends/zarr/backend.py b/data-access/nexustiles/backends/zarr/backend.py index e1d0a0c..c4df96b 100644 --- a/data-access/nexustiles/backends/zarr/backend.py +++ b/data-access/nexustiles/backends/zarr/backend.py @@ -42,7 +42,8 @@ logger = logging.getLogger(__name__) class ZarrBackend(AbstractTileService): def __init__(self, dataset_name, path, config=None): AbstractTileService.__init__(self, dataset_name) - self.__config = config if config is not None else {} + config = config if config is not None else {} + self.__config = config logger.info(f'Opening zarr backend at {path} for dataset {self._name}') @@ -153,7 +154,7 @@ class ZarrBackend(AbstractTileService): times = self.__ds.sel(sel)[self.__time].to_numpy() if np.issubdtype(times.dtype, np.datetime64): - times = ((times - np.datetime64(EPOCH)) / 1e9).astype(int) + times = (times - np.datetime64(EPOCH)).astype('timedelta64[s]').astype(int) times = sorted(times.tolist()) @@ -325,10 +326,10 @@ class ZarrBackend(AbstractTileService): max_date = self.__ds[self.__time].max().to_numpy() if np.issubdtype(min_date.dtype, np.datetime64): - min_date = ((min_date - np.datetime64(EPOCH)) / 1e9).astype(int).item() + min_date = (min_date - np.datetime64(EPOCH)).astype('timedelta64[s]').astype(int).item() if np.issubdtype(max_date.dtype, np.datetime64): - max_date = ((max_date - np.datetime64(EPOCH)) / 1e9).astype(int).item() + max_date = (max_date - np.datetime64(EPOCH)).astype('timedelta64[s]').astype(int).item() return min_date, max_date @@ -435,7 +436,7 @@ class ZarrBackend(AbstractTileService): TileVariable(v, v) for v in self.__variables ] - matched = self.__ds.sel(sel_g) #.sel(sel_t, method=method) + matched = self.__ds.sel(sel_g) if sel_t is not None: matched = matched.sel(sel_t, method=method) @@ -446,7 +447,7 @@ class ZarrBackend(AbstractTileService): times = matched[self.__time].to_numpy() if np.issubdtype(times.dtype, np.datetime64): - times = ((times - np.datetime64(EPOCH)) / 1e9).astype(int) + times = (times - np.datetime64(EPOCH)).astype('timedelta64[s]').astype(int) tile.times = ma.masked_invalid(times) @@ -459,7 +460,6 @@ class ZarrBackend(AbstractTileService): tile.data = ma.masked_invalid(var_data[0]) tile.is_multi = False - def _metadata_store_docs_to_tiles(self, *store_docs): return [ZarrBackend.__nts_url_to_tile(d) for d in store_docs] diff --git a/data-access/nexustiles/nexustiles.py b/data-access/nexustiles/nexustiles.py index b4fd6bb..51046f8 100644 --- a/data-access/nexustiles/nexustiles.py +++ b/data-access/nexustiles/nexustiles.py @@ -179,14 +179,6 @@ class NexusTileService: b = NexusTileService.backends[dataset_s] - # if not b['up']: - # success = b['backend'].try_connect() - # - # if not success: - # raise NexusProcessingException(reason=f'Dataset {dataset_s} is currently unavailable') - # else: - # NexusTileService.backends[dataset_s]['up'] = True - return b['backend'] @@ -243,7 +235,6 @@ class NexusTileService: if d_id in NexusTileService.backends: continue - # is_up = NexusTileService.backends[d_id]['backend'].try_connect() added_datasets += 1 diff --git a/poetry.lock b/poetry.lock index 82d44a3..b48e064 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.8.1 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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description = "Backport of pathlib-compatible object wrapper for zip files" optional = false python-versions = ">=3.8" files = [ - {file = "zipp-3.18.1-py3-none-any.whl", hash = "sha256:206f5a15f2af3dbaee80769fb7dc6f249695e940acca08dfb2a4769fe61e538b"}, - {file = "zipp-3.18.1.tar.gz", hash = "sha256:2884ed22e7d8961de1c9a05142eb69a247f120291bc0206a00a7642f09b5b715"}, + {file = "zipp-3.19.2-py3-none-any.whl", hash = "sha256:f091755f667055f2d02b32c53771a7a6c8b47e1fdbc4b72a8b9072b3eef8015c"}, + {file = "zipp-3.19.2.tar.gz", hash = "sha256:bf1dcf6450f873a13e952a29504887c89e6de7506209e5b1bcc3460135d4de19"}, ] [package.extras] -docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] -testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"] +doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] +test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"] [metadata] lock-version = "2.0" python-versions = "~=3.8" -content-hash = "d19daaa356c410276a8cb00f1ab395b777986d146f61abd345fc1e62a0b8747b" +content-hash = "392c80ca8973c4868a1d3aefa7b836be85ae433de6464dd889a72cb320a6701e" diff --git a/pyproject.toml b/pyproject.toml index 03b02e0..a03d4e8 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -64,6 +64,7 @@ s3fs = "2022.5.0" fsspec = "2022.5.0" aiohttp = "3.8.1" xarray = "^2022.3.0" +dask = "*" zarr = "2.11.3" pandas = "<2.1.0rc0"
