This is an automated email from the ASF dual-hosted git repository.
rkk pushed a commit to branch develop
in repository https://gitbox.apache.org/repos/asf/sdap-nexus.git
The following commit(s) were added to refs/heads/develop by this push:
new 1ccbb4b data-access patch (#313)
1ccbb4b is described below
commit 1ccbb4bf15c832564d3393b66cbb95a0479f8f07
Author: Riley Kuttruff <[email protected]>
AuthorDate: Thu Jun 6 17:03:58 2024 -0700
data-access patch (#313)
* 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
* Changelog
---------
Co-authored-by: rileykk <[email protected]>
---
CHANGELOG.md | 4 +
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 +
6 files changed, 235 insertions(+), 182 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 5396c30..895931d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -22,6 +22,10 @@ and this project adheres to [Semantic
Versioning](https://semver.org/spec/v2.0.0
- SDAP-500: Improvements to SDAP Asynchronous Jobs
- SDAP-499: Added page number to default filename for matchup output
- SDAP-472: Overhauled `data-access` to support multiple backends for
simultaneous support of multiple ARD formats
+- Data access backends patches:
+ - Added `dask` dependency
+ - Code cleanup
+ - Zarr: Fixed handling of times conversion from xr/np datetimes to Unix
timestamps
### Deprecated
### Removed
- SDAP-493:
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.
[[package]]
name = "aiobotocore"
@@ -299,13 +299,13 @@ graph = ["gremlinpython (==3.4.6)"]
[[package]]
name = "certifi"
-version = "2024.2.2"
+version = "2024.6.2"
description = "Python package for providing Mozilla's CA Bundle."
optional = false
python-versions = ">=3.6"
files = [
- {file = "certifi-2024.2.2-py3-none-any.whl", hash =
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- {file = "certifi-2024.2.2.tar.gz", hash =
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+ {file = "certifi-2024.6.2-py3-none-any.whl", hash =
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+ {file = "certifi-2024.6.2.tar.gz", hash =
"sha256:3cd43f1c6fa7dedc5899d69d3ad0398fd018ad1a17fba83ddaf78aa46c747516"},
]
[[package]]
@@ -402,6 +402,17 @@ files = [
[package.dependencies]
colorama = {version = "*", markers = "platform_system == \"Windows\""}
+[[package]]
+name = "cloudpickle"
+version = "3.0.0"
+description = "Pickler class to extend the standard pickle.Pickler
functionality"
+optional = false
+python-versions = ">=3.8"
+files = [
+ {file = "cloudpickle-3.0.0-py3-none-any.whl", hash =
"sha256:246ee7d0c295602a036e86369c77fecda4ab17b506496730f2f576d9016fd9c7"},
+ {file = "cloudpickle-3.0.0.tar.gz", hash =
"sha256:996d9a482c6fb4f33c1a35335cf8afd065d2a56e973270364840712d9131a882"},
+]
+
[[package]]
name = "colorama"
version = "0.4.6"
@@ -413,17 +424,6 @@ files = [
{file = "colorama-0.4.6.tar.gz", hash =
"sha256:08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44"},
]
-[[package]]
-name = "contextlib2"
-version = "21.6.0"
-description = "Backports and enhancements for the contextlib module"
-optional = false
-python-versions = ">=3.6"
-files = [
- {file = "contextlib2-21.6.0-py2.py3-none-any.whl", hash =
"sha256:3fbdb64466afd23abaf6c977627b75b6139a5a3e8ce38405c5b413aed7a0471f"},
- {file = "contextlib2-21.6.0.tar.gz", hash =
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-]
-
[[package]]
name = "contourpy"
version = "1.1.0"
@@ -559,63 +559,63 @@ test-no-images = ["pytest", "pytest-cov", "wurlitzer"]
[[package]]
name = "coverage"
-version = "7.4.4"
+version = "7.5.3"
description = "Code coverage measurement for Python"
optional = false
python-versions = ">=3.8"
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"sha256:38b7b51f512eed9e84a22788b4bce1de17c0adb134d6becb09836e37d8654cd3"},
]
[package.extras]
docs = ["furo (>=2023.9.10)", "proselint (>=0.13)", "sphinx (>=7.2.6)",
"sphinx-autodoc-typehints (>=1.25.2)"]
test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.4.3)",
"pytest-cov (>=4.1)", "pytest-mock (>=3.12)"]
+type = ["mypy (>=1.8)"]
[[package]]
name = "pluggy"
-version = "1.4.0"
+version = "1.5.0"
description = "plugin and hook calling mechanisms for python"
optional = false
python-versions = ">=3.8"
files = [
- {file = "pluggy-1.4.0-py3-none-any.whl", hash =
"sha256:7db9f7b503d67d1c5b95f59773ebb58a8c1c288129a88665838012cfb07b8981"},
- {file = "pluggy-1.4.0.tar.gz", hash =
"sha256:8c85c2876142a764e5b7548e7d9a0e0ddb46f5185161049a79b7e974454223be"},
+ {file = "pluggy-1.5.0-py3-none-any.whl", hash =
"sha256:44e1ad92c8ca002de6377e165f3e0f1be63266ab4d554740532335b9d75ea669"},
+ {file = "pluggy-1.5.0.tar.gz", hash =
"sha256:2cffa88e94fdc978c4c574f15f9e59b7f4201d439195c3715ca9e2486f1d0cf1"},
]
[package.extras]
@@ -2029,13 +2087,13 @@ files = [
[[package]]
name = "requests"
-version = "2.31.0"
+version = "2.32.3"
description = "Python HTTP for Humans."
optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
files = [
- {file = "requests-2.31.0-py3-none-any.whl", hash =
"sha256:58cd2187c01e70e6e26505bca751777aa9f2ee0b7f4300988b709f44e013003f"},
- {file = "requests-2.31.0.tar.gz", hash =
"sha256:942c5a758f98d790eaed1a29cb6eefc7ffb0d1cf7af05c3d2791656dbd6ad1e1"},
+ {file = "requests-2.32.3-py3-none-any.whl", hash =
"sha256:70761cfe03c773ceb22aa2f671b4757976145175cdfca038c02654d061d6dcc6"},
+ {file = "requests-2.32.3.tar.gz", hash =
"sha256:55365417734eb18255590a9ff9eb97e9e1da868d4ccd6402399eaf68af20a760"},
]
[package.dependencies]
@@ -2087,18 +2145,15 @@ crt = ["botocore[crt] (>=1.20.29,<2.0a.0)"]
[[package]]
name = "schema"
-version = "0.7.5"
+version = "0.7.7"
description = "Simple data validation library"
optional = false
python-versions = "*"
files = [
- {file = "schema-0.7.5-py2.py3-none-any.whl", hash =
"sha256:f3ffdeeada09ec34bf40d7d79996d9f7175db93b7a5065de0faa7f41083c1e6c"},
- {file = "schema-0.7.5.tar.gz", hash =
"sha256:f06717112c61895cabc4707752b88716e8420a8819d71404501e114f91043197"},
+ {file = "schema-0.7.7-py2.py3-none-any.whl", hash =
"sha256:5d976a5b50f36e74e2157b47097b60002bd4d42e65425fcc9c9befadb4255dde"},
+ {file = "schema-0.7.7.tar.gz", hash =
"sha256:7da553abd2958a19dc2547c388cde53398b39196175a9be59ea1caf5ab0a1807"},
]
-[package.dependencies]
-contextlib2 = ">=0.5.5"
-
[[package]]
name = "scipy"
version = "1.6.0"
@@ -2191,13 +2246,24 @@ files = [
[[package]]
name = "tomlkit"
-version = "0.12.4"
+version = "0.12.5"
description = "Style preserving TOML library"
optional = false
python-versions = ">=3.7"
files = [
- {file = "tomlkit-0.12.4-py3-none-any.whl", hash =
"sha256:5cd82d48a3dd89dee1f9d64420aa20ae65cfbd00668d6f094d7578a78efbb77b"},
- {file = "tomlkit-0.12.4.tar.gz", hash =
"sha256:7ca1cfc12232806517a8515047ba66a19369e71edf2439d0f5824f91032b6cc3"},
+ {file = "tomlkit-0.12.5-py3-none-any.whl", hash =
"sha256:af914f5a9c59ed9d0762c7b64d3b5d5df007448eb9cd2edc8a46b1eafead172f"},
+ {file = "tomlkit-0.12.5.tar.gz", hash =
"sha256:eef34fba39834d4d6b73c9ba7f3e4d1c417a4e56f89a7e96e090dd0d24b8fb3c"},
+]
+
+[[package]]
+name = "toolz"
+version = "0.12.1"
+description = "List processing tools and functional utilities"
+optional = false
+python-versions = ">=3.7"
+files = [
+ {file = "toolz-0.12.1-py3-none-any.whl", hash =
"sha256:d22731364c07d72eea0a0ad45bafb2c2937ab6fd38a3507bf55eae8744aa7d85"},
+ {file = "toolz-0.12.1.tar.gz", hash =
"sha256:ecca342664893f177a13dac0e6b41cbd8ac25a358e5f215316d43e2100224f4d"},
]
[[package]]
@@ -2252,13 +2318,13 @@ files = [
[[package]]
name = "typing-extensions"
-version = "4.10.0"
+version = "4.12.1"
description = "Backported and Experimental Type Hints for Python 3.8+"
optional = false
python-versions = ">=3.8"
files = [
- {file = "typing_extensions-4.10.0-py3-none-any.whl", hash =
"sha256:69b1a937c3a517342112fb4c6df7e72fc39a38e7891a5730ed4985b5214b5475"},
- {file = "typing_extensions-4.10.0.tar.gz", hash =
"sha256:b0abd7c89e8fb96f98db18d86106ff1d90ab692004eb746cf6eda2682f91b3cb"},
+ {file = "typing_extensions-4.12.1-py3-none-any.whl", hash =
"sha256:6024b58b69089e5a89c347397254e35f1bf02a907728ec7fee9bf0fe837d203a"},
+ {file = "typing_extensions-4.12.1.tar.gz", hash =
"sha256:915f5e35ff76f56588223f15fdd5938f9a1cf9195c0de25130c627e4d597f6d1"},
]
[[package]]
@@ -2526,20 +2592,20 @@ jupyter = ["ipytree", "notebook"]
[[package]]
name = "zipp"
-version = "3.18.1"
+version = "3.19.2"
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"
