diff --git a/.flake8 b/.flake8 deleted file mode 100644 index 38ffcd9b..00000000 --- a/.flake8 +++ /dev/null @@ -1,3 +0,0 @@ -[flake8] -max-line-length = 120 -exclude = mypy-stubs,stubs,typeshed diff --git a/.github/dependabot.yml b/.github/dependabot.yml index ae038bd6..19eec96f 100644 --- a/.github/dependabot.yml +++ b/.github/dependabot.yml @@ -10,6 +10,14 @@ updates: schedule: interval: "monthly" groups: - all-dependencies: + pip-dependencies: + patterns: + - "*" + - package-ecosystem: "github-actions" + directory: "/" + schedule: + interval: "monthly" + groups: + gha-dependencies: patterns: - "*" diff --git a/.github/workflows/binder-badge.yml b/.github/workflows/binder-badge.yml deleted file mode 100644 index 22e7195e..00000000 --- a/.github/workflows/binder-badge.yml +++ /dev/null @@ -1,11 +0,0 @@ -name: AddBinderBadge -on: - pull_request_target: - -jobs: - badge: - runs-on: ubuntu-latest - steps: - - uses: manics/action-binderbadge@main - with: - githubToken: ${{ secrets.GITHUB_TOKEN }} diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml deleted file mode 100644 index 975ae16b..00000000 --- a/.github/workflows/documentation.yml +++ /dev/null @@ -1,67 +0,0 @@ -name: Documentation - -on: - push: - branches: - - main - - documentation - paths: - - earthaccess/** - - tests/** - - docs/** - - notebooks/** - - .github/workflows/documentation.yml - pull_request: - paths: - - earthaccess/** - - tests/** - - docs/** - - notebooks/** - - .github/workflows/documentation.yml - types: [opened, synchronize] - -jobs: - documentation: - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v3 - - name: Set up Python - id: setup-python - uses: actions/setup-python@v2 - with: - python-version: 3.9 - - name: Install and configure Poetry - uses: snok/install-poetry@v1 - with: - version: 1.5.1 - virtualenvs-create: true - virtualenvs-in-project: false - virtualenvs-path: .venv - installer-parallel: true - - name: Set up cache - uses: actions/cache@v1 - id: cache - with: - path: .venv - key: venv-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/poetry.lock') }} - - name: Ensure cache is healthy - if: steps.cache.outputs.cache-hit == 'true' - run: poetry run pip --version >/dev/null 2>&1 || rm -rf .venv - - name: Install Dependencies - if: steps.cache.outputs.cache-hit != 'true' - run: poetry install --no-interaction - - name: Build docs - run: poetry run bash scripts/build-docs.sh - env: - EARTHDATA_USERNAME: ${{ secrets.EDL_USERNAME }} - EARTHDATA_PASSWORD: ${{ secrets.EDL_PASSWORD }} - - - name: Deploy - if: | - github.event_name == 'push' - && (github.ref == 'refs/heads/main' || github.ref == 'ref/heads/documentation') - && github.repository == 'nsidc/earthaccess' - uses: peaceiris/actions-gh-pages@v3 - with: - GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - publish_dir: ./site diff --git a/.github/workflows/integration-test.yml b/.github/workflows/integration-test.yml index 8b6352c6..d416449e 100644 --- a/.github/workflows/integration-test.yml +++ b/.github/workflows/integration-test.yml @@ -15,13 +15,13 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: [3.8, 3.9, '3.10', '3.11'] + python-version: [3.8, 3.9, "3.10", "3.11"] fail-fast: false steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 - name: Set up Python - uses: actions/setup-python@v1 + uses: actions/setup-python@v4 with: python-version: ${{ matrix.python-version }} - name: Get full python version @@ -34,7 +34,7 @@ jobs: - name: Configure poetry run: poetry config virtualenvs.in-project true - name: Set up cache - uses: actions/cache@v1 + uses: actions/cache@v3 id: cache with: path: .venv @@ -52,4 +52,4 @@ jobs: EARTHACCESS_TEST_PASSWORD: ${{ secrets.EDL_PASSWORD }} run: poetry run bash scripts/integration-test.sh - name: Upload coverage - uses: codecov/codecov-action@v1 + uses: codecov/codecov-action@v3 diff --git a/.github/workflows/issue-manager.yml b/.github/workflows/issue-manager.yml index 46c544b2..2ddeab30 100644 --- a/.github/workflows/issue-manager.yml +++ b/.github/workflows/issue-manager.yml @@ -2,20 +2,28 @@ name: "Issue Manager" on: schedule: - - cron: "0 0 * * *" + - cron: "0 0 * * *" + issue_comment: + types: + - "created" + issues: + types: + - "labeled" + pull_request_target: + types: + - "labeled" jobs: issue-manager: - runs-on: ubuntu-latest + runs-on: "ubuntu-latest" steps: - - uses: tiangolo/issue-manager@master - with: - token: ${{ secrets.GITHUB_TOKEN }} - config: > + - uses: "tiangolo/issue-manager@0.4.0" + with: + token: "${{ secrets.GITHUB_TOKEN }}" + config: > { - "answered": { - "users": ["betolink"], + "feedback requested": { "delay": 864000, - "message": "Assuming the original issue was solved, it will be automatically closed now. But feel free to add more comments or create new issues." + "message": "Closing after 10 days of waiting for feedback. If you feel this was in error, please re-open, `@` a maintainer, or create new issues." } } diff --git a/.github/workflows/pr-rtd-link.yml b/.github/workflows/pr-rtd-link.yml new file mode 100644 index 00000000..b4e9efc7 --- /dev/null +++ b/.github/workflows/pr-rtd-link.yml @@ -0,0 +1,21 @@ +# The ReadTheDocs preview link is "hidden" within the GitHub "Checks" +# interface. For users who don't know this, finding the preview link may be +# very difficult or frustrating. This workflow makes the link more +# findable by updating PR descriptions to include it. +name: "Add ReadTheDocs preview link to PR descriptions" + +on: + pull_request_target: + types: + - opened + +permissions: + pull-requests: "write" + +jobs: + autolink-rtd-previews: + runs-on: "ubuntu-latest" + steps: + - uses: "readthedocs/actions/preview@v1" + with: + project-slug: "earthaccess" diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml index b2c2bd64..5f031432 100644 --- a/.github/workflows/publish.yml +++ b/.github/workflows/publish.yml @@ -7,11 +7,11 @@ jobs: build: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 - name: verify version matches git tag run: scripts/verify_tag.sh - name: Build and publish to pypi - uses: JRubics/poetry-publish@v1.8 + uses: JRubics/poetry-publish@v1.17 with: python_version: "3.9" pypi_token: ${{ secrets.PYPI_TOKEN }} diff --git a/.github/workflows/static-analysis.yml b/.github/workflows/static-analysis.yml new file mode 100644 index 00000000..826982aa --- /dev/null +++ b/.github/workflows/static-analysis.yml @@ -0,0 +1,27 @@ +name: Lint and Format with Ruff + +on: push + +jobs: + check-with-ruff: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + + - name: Install Python + uses: actions/setup-python@v4 + with: + python-version: 3.x + + - name: Install dependencies + run: | + python -m pip install --upgrade pip + pip install ruff + + - name: Ruff linting check + run: | + ruff check --output-format=github . + + - name: Ruff format check + run: | + ruff format --diff . diff --git a/.github/workflows/test-mindeps.yml b/.github/workflows/test-mindeps.yml new file mode 100644 index 00000000..21035cf6 --- /dev/null +++ b/.github/workflows/test-mindeps.yml @@ -0,0 +1,49 @@ +name: Test minimum dependencies + +on: + push: + pull_request: + workflow_dispatch: + +# When this workflow is queued, automatically cancel any previous running +# or pending jobs from the same branch +concurrency: + group: ${{ github.ref }} + cancel-in-progress: true + +# Required shell entrypoint to have properly activated conda environments +defaults: + run: + shell: bash -l {0} + +jobs: + test: + runs-on: ubuntu-latest + strategy: + fail-fast: false + + steps: + - name: Checkout source + uses: actions/checkout@v4.1.1 + - name: Setup Conda Environment + uses: conda-incubator/setup-miniconda@v2.2.0 + with: + miniforge-variant: Mambaforge + miniforge-version: latest + use-mamba: true + channel-priority: strict + environment-file: ci/environment-mindeps.yaml + activate-environment: test-environment + auto-activate-base: false + + - name: Install + run: python -m pip install --no-deps -e . + + - name: mamba list + run: mamba list + + - name: Test + run: bash scripts/test.sh + + - name: Upload coverage + uses: codecov/codecov-action@v1 diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 684764df..a5ee57cb 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -14,9 +14,9 @@ jobs: fail-fast: false steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 - name: Set up Python - uses: actions/setup-python@v2 + uses: actions/setup-python@v4 with: python-version: ${{ matrix.python-version }} - name: Get full python version @@ -29,7 +29,7 @@ jobs: - name: Configure poetry run: poetry config virtualenvs.in-project true - name: Set up cache - uses: actions/cache@v1 + uses: actions/cache@v3 id: cache with: path: .venv @@ -42,4 +42,4 @@ jobs: - name: Test run: poetry run bash scripts/test.sh - name: Upload coverage - uses: codecov/codecov-action@v1 + uses: codecov/codecov-action@v3 diff --git a/.gitignore b/.gitignore index 86a27a3f..ea6fc19e 100644 --- a/.gitignore +++ b/.gitignore @@ -18,6 +18,7 @@ build/ *.egg-info/ docs/tutorials/data tests/integration/data +.ruff_cache # OS X .DS_Store diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index fffe4a1d..891d4132 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,17 +1,30 @@ ci: - autoupdate_schedule: "monthly" # Like dependabot + autoupdate_schedule: "monthly" # Like dependabot autoupdate_commit_msg: "chore: update pre-commit hooks" - autofix_prs: false # Comment "pre-commit.ci autofix" on a PR to trigger + autofix_prs: false # Comment "pre-commit.ci autofix" on a PR to trigger repos: -- repo: https://github.com/pre-commit/pre-commit-hooks - rev: v2.3.0 - hooks: - - id: check-yaml - - id: trailing-whitespace - - id: check-toml - - id: check-json -- repo: https://github.com/psf/black - rev: 23.10.1 - hooks: - - id: black + - repo: https://github.com/pre-commit/pre-commit-hooks + rev: v4.5.0 + hooks: + - id: check-yaml + - id: trailing-whitespace + - id: check-toml + - id: check-json + - repo: https://github.com/astral-sh/ruff-pre-commit + rev: v0.1.6 + hooks: + - id: ruff + args: ["--fix", "--exit-non-zero-on-fix"] + - id: ruff-format + - repo: https://github.com/pre-commit/mirrors-prettier + rev: "v3.1.0" + hooks: + - id: prettier + types_or: [yaml] + - repo: https://github.com/citation-file-format/cffconvert + rev: "054bda51dbe278b3e86f27c890e3f3ac877d616c" + hooks: + - id: "validate-cff" + args: + - "--verbose" diff --git a/CHANGELOG.md b/CHANGELOG.md index d7fd3a1e..3b83fcdc 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,35 @@ # Changelog +## [v0.8.2] 2023-12-06 +* Bug fixes: + * Enable AWS check with IMDSv2 + * Add region to running in AWS check + * Handle opening multi-file granules +* Maintenance: + * Add CI tests with minimum supported versions + * Update poetry lockfile + * Add `python-dateutil` as a direct dependency + * Remove binder PR comments + * Add YAML formatting (prettier) + +## [v0.8.1] 2023-12-01 +* New Features: + * Add `kerchunk` metadata consolidation utility. +* Enhancements: + * Handle S3 credential expiration more gracefully. +* Maintenanece: + * Use dependabot to update Github Actions. + * Consolidate dependabot updates. + * Switch to `ruff` for formatting. + +## [v0.8.0] 2023-11-29 +* Bug fixes: + * Fix zero granules being reported for restricted datasets. +* Enhancements: + * earthaccess will `raise` errors instead of `print`ing them in more cases. + * `daac` and `provider` parameters are now normalized to uppercase, since lowercase + characters are never valid. + ## [v0.7.1] 2023-11-08 * Bug Fixes: * Treat granules without `RelatedUrls` as not cloud-hosted. diff --git a/CITATION.cff b/CITATION.cff index aea82a41..dac47250 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -4,7 +4,7 @@ message: | Authors are listed in alphabetical order. title: "earthaccess" -doi: "https://doi.org/10.5281/zenodo.8365009" +doi: "10.5281/zenodo.8365009" abstract: "Python Library for NASA Earthdata APIs" contact: - name: "The earthaccess community" @@ -12,7 +12,10 @@ contact: - name: "NSIDC" email: "nsidc@nsidc.org" type: "software" -license: ["MIT"] +# NOTE: The CFF spec says `license` can be a list, but Zenodo is currently not +# accepting lists for this key: +# https://github.com/zenodo/zenodo/issues/2515 +license: "MIT" keywords: - "data" - "Remote sensing" @@ -23,51 +26,65 @@ keywords: url: "https://earthaccess.readthedocs.io" repository-code: "https://github.com/nsidc/earthaccess" -version: "0.7.1" -date-released: "2023-11-08" +version: "0.8.2" +date-released: "2023-12-06" authors: -- family-names: "Barrett" - given-names: "Andrew" - orcid: "https://orcid.org/0000-0003-4394-5445" - website: "https://github.com/andypbarrett" -- family-names: "Battisto" - given-names: "Chris" - orcid: "https://orcid.org//0000-0002-9608-3634" - website: "https://github.com/battistowx" -- family-names: "Bourbeau" - given-names: "James" - orcid: "https://orcid.org/0000-0003-2164-7789" - website: "https://github.com/jrbourbeau" -- family-names: "Fisher" - given-names: "Matt" - orcid: "https://orcid.org/0000-0003-3260-5445" - website: "https://mfisher87.github.io/" -- family-names: "Kennedy" - given-names: "Joseph" - orcid: "https://orcid.org/0000-0002-9348-693X" - website: "https://github.com/jhkennedy" -- family-names: "Lopez" - given-names: "Luis" - orcid: "https://orcid.org/0000-0003-4896-3263" - website: "https://github.com/betolink" -- family-names: "Lowndes" - given-names: "Julia" - orcid: "https://orcid.org/0000-0003-1682-3872" - website: "https://github.com/jules32" -- family-names: "Scheick" - given-names: "Jessica" - orcid: "https://orcid.org/0000-0002-3421-4459" - website: "https://github.com/JessicaS11" -- family-names: "Steiker" - given-names: "Amy" - orcid: "https://orcid.org/0000-0002-3039-0260" - website: "https://github.com/asteiker" + - family-names: "Barrett" + given-names: "Andrew" + orcid: "https://orcid.org/0000-0003-4394-5445" + website: "https://github.com/andypbarrett" + - family-names: "Battisto" + given-names: "Chris" + orcid: "https://orcid.org/0000-0002-9608-3634" + website: "https://github.com/battistowx" + - family-names: "Bourbeau" + given-names: "James" + orcid: "https://orcid.org/0000-0003-2164-7789" + website: "https://github.com/jrbourbeau" + - family-names: "Fisher" + given-names: "Matt" + orcid: "https://orcid.org/0000-0003-3260-5445" + website: "https://mfisher87.github.io/" + - family-names: "Kaufman" + given-names: "Daniel" + orcid: "https://orcid.org/0000-0002-1487-7298" + website: "https://github.com/danielfromearth" + - family-names: "Kennedy" + given-names: "Joseph" + orcid: "https://orcid.org/0000-0002-9348-693X" + website: "https://github.com/jhkennedy" + - family-names: "Lopez" + given-names: "Luis" + orcid: "https://orcid.org/0000-0003-4896-3263" + website: "https://github.com/betolink" + - family-names: "Lowndes" + given-names: "Julia" + orcid: "https://orcid.org/0000-0003-1682-3872" + website: "https://github.com/jules32" + - family-names: "Scheick" + given-names: "Jessica" + orcid: "https://orcid.org/0000-0002-3421-4459" + website: "https://github.com/JessicaS11" + - family-names: "Steiker" + given-names: "Amy" + orcid: "https://orcid.org/0000-0002-3039-0260" + website: "https://github.com/asteiker" references: -- type: "grant" - institution: - name: "National Aeronautics and Space Administration" - number: "20-TWSC20-2-0003" + - type: "grant" + title: "Openscapes: Supporting better science for future us" + institution: + name: "National Aeronautics and Space Administration" + number: "20-TWSC20-2-0003" + authors: + - family-names: "Lowndes" + given-names: "Julia" + orcid: "https://orcid.org/0000-0003-1682-3872" + website: "https://github.com/jules32" + - family-names: "Robinson" + given-names: "Erin" + orcid: "https://orcid.org/0000-0001-9998-0114" + website: "https://erinrobinson.info/" diff --git a/binder/environment-dev.yml b/binder/environment-dev.yml index 82e7eb22..202d825b 100644 --- a/binder/environment-dev.yml +++ b/binder/environment-dev.yml @@ -1,15 +1,15 @@ name: earthaccess-dev channels: -- conda-forge + - conda-forge dependencies: -# This environment bootstraps poetry, the actual dev environment -# is installed and managed with poetry -- python=3.9 -- jupyterlab=3 -- xarray>=0.19 -- ipyleaflet>=0.13 -- h5netcdf>=0.11 -- cartopy -- pip -- pip: - - poetry + # This environment bootstraps poetry, the actual dev environment + # is installed and managed with poetry + - python=3.9 + - jupyterlab=3 + - xarray>=0.19 + - ipyleaflet>=0.13 + - h5netcdf>=0.11 + - cartopy + - pip + - pip: + - poetry diff --git a/binder/environment.yml b/binder/environment.yml index cf0d2be4..2bc59969 100644 --- a/binder/environment.yml +++ b/binder/environment.yml @@ -1,20 +1,20 @@ name: earthaccess channels: -- conda-forge + - conda-forge dependencies: -- python=3.9 -- xarray>=0.19 -- dask>=2022.1 -- rioxarray>=0.3 -- matplotlib-base>=3.3 -- cartopy>=0.18.0 -- ipyleaflet>=0.15 -- netcdf4>=1.5 -- h5netcdf>=0.11 -- h5py>=3.2 -- geopandas>=0.9 -- zarr>=2.9.5 -- jupyterlab>=3 -- hvplot -- holoviews -- panel + - python=3.9 + - xarray>=0.19 + - dask>=2022.1 + - rioxarray>=0.3 + - matplotlib-base>=3.3 + - cartopy>=0.18.0 + - ipyleaflet>=0.15 + - netcdf4>=1.5 + - h5netcdf>=0.11 + - h5py>=3.2 + - geopandas>=0.9 + - zarr>=2.9.5 + - jupyterlab>=3 + - hvplot + - holoviews + - panel diff --git a/ci/environment-mindeps.yaml b/ci/environment-mindeps.yaml new file mode 100644 index 00000000..90c6c5d0 --- /dev/null +++ b/ci/environment-mindeps.yaml @@ -0,0 +1,26 @@ +# NOTE: Minimum dependencies are defined in `pyproject.toml`. +# This file is only used for testing purposes. +# When making changes to minimum dependencies, make sure both this file +# and `pyproject.toml` are consistent with each other. +name: test-environment +channels: + - conda-forge +dependencies: + # required dependencies + - python=3.8 + - python-cmr=0.9.0 + - pqdm=0.1 + - requests=2.26 + - s3fs=2022.11 + - fsspec=2022.11 + - tinynetrc=1.3.1 + - multimethod=1.8 + - python-dateutil=2.8.2 + # test dependencies + - responses + - pytest + - pytest-cov + - mypy + - types-requests + - types-setuptools + - ruff diff --git a/earthaccess/__init__.py b/earthaccess/__init__.py index 4e71e69d..4977bf38 100644 --- a/earthaccess/__init__.py +++ b/earthaccess/__init__.py @@ -1,7 +1,6 @@ import logging import threading from importlib.metadata import version -from typing import Any from .api import ( auth_environ, @@ -18,6 +17,7 @@ search_datasets, ) from .auth import Auth +from .kerchunk import consolidate_metadata from .search import DataCollections, DataGranules from .store import Store @@ -40,6 +40,7 @@ "Auth", "Store", "auth_environ", + "consolidate_metadata", ] __version__ = version("earthaccess") diff --git a/earthaccess/api.py b/earthaccess/api.py index 4ef8598d..8e518912 100644 --- a/earthaccess/api.py +++ b/earthaccess/api.py @@ -1,10 +1,11 @@ from typing import Any, Dict, List, Optional, Type, Union -import earthaccess import requests import s3fs from fsspec import AbstractFileSystem +import earthaccess + from .auth import Auth from .results import DataGranule from .search import CollectionQuery, DataCollections, DataGranules, GranuleQuery @@ -12,6 +13,21 @@ from .utils import _validation as validate +def _normalize_location(location: Union[str, None]) -> Union[str, None]: + """Handle user-provided `daac` and `provider` values + + These values must have a capital letter as the first character + followed by capital letters, numbers, or an underscore. Here we + uppercase all strings to handle the case when users provide + lowercase values (e.g. "pocloud" instead of "POCLOUD"). + + https://wiki.earthdata.nasa.gov/display/ED/CMR+Data+Partner+User+Guide?src=contextnavpagetreemode + """ + if location is not None: + location = location.upper() + return location + + def search_datasets( count: int = -1, **kwargs: Any ) -> List[earthaccess.results.DataCollection]: @@ -151,7 +167,7 @@ def login(strategy: str = "all", persist: bool = False) -> Auth: def download( - granules: Union[DataGranule, List[DataGranule], List[str]], + granules: Union[DataGranule, List[DataGranule], str, List[str]], local_path: Union[str, None], provider: Optional[str] = None, threads: int = 8, @@ -162,7 +178,7 @@ def download( * If we run it outside AWS (us-west-2 region) and the dataset is cloud hostes we'll use HTTP links Parameters: - granules: a granule, list of granules, or a list of granule links (HTTP) + granules: a granule, list of granules, a granule link (HTTP), or a list of granule links (HTTP) local_path: local directory to store the remote data granules provider: if we download a list of URLs we need to specify the provider. threads: parallel number of threads to use to download the files, adjust as necessary, default = 8 @@ -170,8 +186,11 @@ def download( Returns: List of downloaded files """ + provider = _normalize_location(provider) if isinstance(granules, DataGranule): granules = [granules] + elif isinstance(granules, str): + granules = [granules] try: results = earthaccess.__store__.get(granules, local_path, provider, threads) except AttributeError as err: @@ -194,6 +213,7 @@ def open( Returns: a list of s3fs "file pointers" to s3 files. """ + provider = _normalize_location(provider) results = earthaccess.__store__.open(granules=granules, provider=provider) return results @@ -215,10 +235,8 @@ def get_s3_credentials( Returns: a dictionary with S3 credentials for the DAAC or provider """ - if daac is not None: - daac = daac.upper() - if provider is not None: - provider = provider.upper() + daac = _normalize_location(daac) + provider = _normalize_location(provider) if results is not None: endpoint = results[0].get_s3_credentials_endpoint() return earthaccess.__auth__.get_s3_credentials(endpoint=endpoint) @@ -315,6 +333,8 @@ def get_s3fs_session( Returns: class s3fs.S3FileSystem: an authenticated s3fs session valid for 1 hour """ + daac = _normalize_location(daac) + provider = _normalize_location(provider) if results is not None: endpoint = results[0].get_s3_credentials_endpoint() if endpoint is not None: diff --git a/earthaccess/daac.py b/earthaccess/daac.py index 5581f2c5..a15972c1 100644 --- a/earthaccess/daac.py +++ b/earthaccess/daac.py @@ -110,23 +110,11 @@ # Some testing urls behind EDL DAAC_TEST_URLS = [ - ( - "https://archive.podaac.earthdata.nasa.gov/podaac-ops-cumulus-protected/" - "JASON_CS_S6A_L2_ALT_LR_STD_OST_NRT_F/" - ), - ( - "https://data.nsidc.earthdatacloud.nasa.gov/nsidc-cumulus-prod-protected/ATLAS/" - "ATL03/005/2018/10/14/dummy.nc" - ), - ( - "https://n5eil01u.ecs.nsidc.org/DP7/ATLAS/ATL06.005/2018.10.14/" - "ATL06_20181014045341_02380102_005_01.iso.xml" - ), - ("https://hydro1.gesdisc.eosdis.nasa.gov/data/GLDAS/GLDAS_NOAH10_M.2.0/1948/"), - ( - "https://e4ftl01.cr.usgs.gov//DP114/MOTA/MCD43A3.006/2000.02.24/" - "MCD43A3.A2000055.h15v07.006.2016101151720.hdf.xml" - ), + "https://archive.podaac.earthdata.nasa.gov/podaac-ops-cumulus-protected/JASON_CS_S6A_L2_ALT_LR_STD_OST_NRT_F/", + "https://data.nsidc.earthdatacloud.nasa.gov/nsidc-cumulus-prod-protected/ATLAS/ATL03/005/2018/10/14/dummy.nc", + "https://n5eil01u.ecs.nsidc.org/DP7/ATLAS/ATL06.005/2018.10.14/ATL06_20181014045341_02380102_005_01.iso.xml", + "https://hydro1.gesdisc.eosdis.nasa.gov/data/GLDAS/GLDAS_NOAH10_M.2.0/1948/", + "https://e4ftl01.cr.usgs.gov//DP114/MOTA/MCD43A3.006/2000.02.24/MCD43A3.A2000055.h15v07.006.2016101151720.hdf.xml", "https://daac.ornl.gov/daacdata/npp/grassland/NPP_BCN/data/bcn_cli.txt", ] diff --git a/earthaccess/kerchunk.py b/earthaccess/kerchunk.py new file mode 100644 index 00000000..eb3f4cae --- /dev/null +++ b/earthaccess/kerchunk.py @@ -0,0 +1,58 @@ +from __future__ import annotations + +import fsspec +import s3fs + +import earthaccess + + +def _get_chunk_metadata( + granuale: earthaccess.results.DataGranule, + fs: fsspec.AbstractFileSystem | s3fs.S3FileSystem, +) -> list[dict]: + from kerchunk.hdf import SingleHdf5ToZarr + + metadata = [] + access = "direct" if isinstance(fs, s3fs.S3FileSystem) else "indirect" + for url in granuale.data_links(access=access): + with fs.open(url) as inf: + h5chunks = SingleHdf5ToZarr(inf, url) + m = h5chunks.translate() + metadata.append(m) + return metadata + + +def consolidate_metadata( + granuales: list[earthaccess.results.DataGranule], + kerchunk_options: dict | None = None, + access: str = "direct", + outfile: str | None = None, + storage_options: dict | None = None, +) -> str | dict: + try: + import dask + + from kerchunk.combine import MultiZarrToZarr + except ImportError as e: + raise ImportError( + "`earthaccess.consolidate_metadata` requires `dask` and `kerchunk` to be be installed" + ) from e + + if access == "direct": + fs = earthaccess.get_s3fs_session(provider=granuales[0]["meta"]["provider-id"]) + else: + fs = earthaccess.get_fsspec_https_session() + + # Get metadata for each granuale + get_chunk_metadata = dask.delayed(_get_chunk_metadata) + chunks = dask.compute(*[get_chunk_metadata(g, fs) for g in granuales]) + chunks = sum(chunks, start=[]) + + # Get combined metadata object + mzz = MultiZarrToZarr(chunks, **(kerchunk_options or {})) + if outfile is not None: + output = fsspec.utils.stringify_path(outfile) + mzz.translate(outfile, storage_options=storage_options or {}) + return output + else: + return mzz.translate() diff --git a/earthaccess/results.py b/earthaccess/results.py index f0bb2167..a466e1c3 100644 --- a/earthaccess/results.py +++ b/earthaccess/results.py @@ -228,9 +228,7 @@ def __repr__(self) -> str: Temporal coverage: {self['umm']['TemporalExtent']} Size(MB): {self.size()} Data: {data_links}\n\n - """.strip().replace( - " ", "" - ) + """.strip().replace(" ", "") return rep_str def _repr_html_(self) -> str: diff --git a/earthaccess/search.py b/earthaccess/search.py index 3fd70684..8392ca51 100644 --- a/earthaccess/search.py +++ b/earthaccess/search.py @@ -58,7 +58,7 @@ def hits(self) -> int: Returns: - number of results reproted by CMR + number of results reported by CMR """ return super().hits() @@ -238,7 +238,10 @@ def get(self, limit: int = 2000) -> list: try: response.raise_for_status() except exceptions.HTTPError as ex: - raise RuntimeError(ex.response.text) + if ex.response is not None: + raise RuntimeError(ex.response.text) from ex + else: + raise RuntimeError(str(ex)) from ex if self._format == "json": latest = response.json()["feed"]["entry"] @@ -318,6 +321,28 @@ def __init__(self, auth: Any = None, *args: Any, **kwargs: Any) -> None: self._debug = False + def hits(self) -> int: + """ + Returns the number of hits the current query will return. This is done by + making a lightweight query to CMR and inspecting the returned headers. + + :returns: number of results reported by CMR + """ + + url = self._build_url() + + response = self.session.get(url, headers=self.headers, params={"page_size": 0}) + + try: + response.raise_for_status() + except exceptions.HTTPError as ex: + if ex.response is not None: + raise RuntimeError(ex.response.text) from ex + else: + raise RuntimeError(str(ex)) from ex + + return int(response.headers["CMR-Hits"]) + def parameters(self, **kwargs: Any) -> Type[CollectionQuery]: """Provide query parameters as keyword arguments. The keyword needs to match the name of the method, and the value should either be the value or a tuple of values. @@ -542,7 +567,10 @@ def get(self, limit: int = 2000) -> list: try: response.raise_for_status() except exceptions.HTTPError as ex: - raise RuntimeError(ex.response.text) + if ex.response is not None: + raise RuntimeError(ex.response.text) from ex + else: + raise RuntimeError(str(ex)) from ex if self._format == "json": latest = response.json()["feed"]["entry"] diff --git a/earthaccess/store.py b/earthaccess/store.py index cfe7bc79..645721ad 100644 --- a/earthaccess/store.py +++ b/earthaccess/store.py @@ -2,21 +2,21 @@ import os import shutil import traceback -from copy import deepcopy from functools import lru_cache from itertools import chain from pathlib import Path from pickle import dumps, loads -from typing import Any, Dict, List, Optional, Union +from typing import Any, Dict, List, Mapping, Optional, Tuple, Union from uuid import uuid4 -import earthaccess import fsspec import requests import s3fs from multimethod import multimethod as singledispatchmethod from pqdm.threads import pqdm +import earthaccess + from .auth import Auth from .daac import DAAC_TEST_URLS, find_provider from .results import DataGranule @@ -44,23 +44,15 @@ def __repr__(self) -> str: def _open_files( - data_links: List[str], - granules: Union[List[str], List[DataGranule]], + url_mapping: Mapping[str, Union[DataGranule, None]], fs: fsspec.AbstractFileSystem, threads: Optional[int] = 8, ) -> List[fsspec.AbstractFileSystem]: def multi_thread_open(data: tuple) -> EarthAccessFile: urls, granule = data - if type(granule) is not str: - if len(granule.data_links()) > 1: - print( - "Warning: This collection contains more than one file per granule. " - "earthaccess will only open the first data link, " - "try filtering the links before opening them." - ) return EarthAccessFile(fs.open(urls), granule) - fileset = pqdm(zip(data_links, granules), multi_thread_open, n_jobs=threads) + fileset = pqdm(url_mapping.items(), multi_thread_open, n_jobs=threads) return fileset @@ -74,8 +66,8 @@ def make_instance( # When sending EarthAccessFiles between processes, it's possible that # we will need to switch between s3 <--> https protocols. - if (earthaccess.__store__.running_in_aws and cls is not s3fs.S3File) or ( - not earthaccess.__store__.running_in_aws and cls is s3fs.S3File + if (earthaccess.__store__.in_region and cls is not s3fs.S3File) or ( + not earthaccess.__store__.in_region and cls is s3fs.S3File ): # NOTE: This uses the first data_link listed in the granule. That's not # guaranteed to be the right one. @@ -84,6 +76,17 @@ def make_instance( return EarthAccessFile(loads(data), granule) +def _get_url_granule_mapping( + granules: List[DataGranule], access: str +) -> Mapping[str, DataGranule]: + """Construct a mapping between file urls and granules""" + url_mapping = {} + for granule in granules: + for url in granule.data_links(access=access): + url_mapping[url] = granule + return url_mapping + + class Store(object): """ Store class to access granules on-prem or in the cloud. @@ -97,8 +100,9 @@ def __init__(self, auth: Any, pre_authorize: bool = False) -> None: """ if auth.authenticated is True: self.auth = auth - self.s3_fs = None - self.initial_ts = datetime.datetime.now() + self._s3_credentials: Dict[ + Tuple, Tuple[datetime.datetime, Dict[str, str]] + ] = {} oauth_profile = "https://urs.earthdata.nasa.gov/profile" # sets the initial URS cookie self._requests_cookies: Dict[str, Any] = {} @@ -111,7 +115,7 @@ def __init__(self, auth: Any, pre_authorize: bool = False) -> None: else: print("Warning: the current session is not authenticated with NASA") self.auth = None - self.running_in_aws = self._am_i_in_aws() + self.in_region = self._running_in_us_west_2() def _derive_concept_provider(self, concept_id: Optional[str] = None) -> str: if concept_id is not None: @@ -135,16 +139,25 @@ def _own_s3_credentials(self, links: List[Dict[str, Any]]) -> Union[str, None]: return link["URL"] return None - def _am_i_in_aws(self) -> bool: + def _running_in_us_west_2(self) -> bool: session = self.auth.get_session() try: # https://docs.aws.amazon.com/AWSEC2/latest/UserGuide/instancedata-data-retrieval.html + token_ = session.put( + "http://169.254.169.254/latest/api/token", + headers={"X-aws-ec2-metadata-token-ttl-seconds": "21600"}, + timeout=1, + ) resp = session.get( - "http://169.254.169.254/latest/meta-data/public-ipv4", timeout=1 + "http://169.254.169.254/latest/meta-data/placement/region", + timeout=1, + headers={"X-aws-ec2-metadata-token": token_.text}, ) except Exception: return False - if resp.status_code == 200: + + if resp.status_code == 200 and b"us-west-2" == resp.content: + # On AWS in region us-west-2 return True return False @@ -182,7 +195,6 @@ def set_requests_session( elif resp.status_code >= 500: resp.raise_for_status() - @lru_cache def get_s3fs_session( self, daac: Optional[str] = None, @@ -200,40 +212,54 @@ def get_s3fs_session( Returns: a s3fs file instance """ - if self.auth is not None: - if not any([concept_id, daac, provider, endpoint]): - raise ValueError( - "At least one of the concept_id, daac, provider or endpoint" - "parameters must be specified. " - ) + if self.auth is None: + raise ValueError( + "A valid Earthdata login instance is required to retrieve S3 credentials" + ) + if not any([concept_id, daac, provider, endpoint]): + raise ValueError( + "At least one of the concept_id, daac, provider or endpoint" + "parameters must be specified. " + ) + + if concept_id is not None: + provider = self._derive_concept_provider(concept_id) + + # Get existing S3 credentials if we already have them + location = ( + daac, + provider, + endpoint, + ) # Identifier for where to get S3 credentials from + need_new_creds = False + try: + dt_init, creds = self._s3_credentials[location] + except KeyError: + need_new_creds = True + else: + # If cached credentials are expired, invalidate the cache + delta = datetime.datetime.now() - dt_init + if round(delta.seconds / 60, 2) > 55: + need_new_creds = True + self._s3_credentials.pop(location) + + if need_new_creds: + # Don't have existing valid S3 credentials, so get new ones + now = datetime.datetime.now() if endpoint is not None: - s3_credentials = self.auth.get_s3_credentials(endpoint=endpoint) - elif concept_id is not None: - provider = self._derive_concept_provider(concept_id) - s3_credentials = self.auth.get_s3_credentials(provider=provider) + creds = self.auth.get_s3_credentials(endpoint=endpoint) elif daac is not None: - s3_credentials = self.auth.get_s3_credentials(daac=daac) + creds = self.auth.get_s3_credentials(daac=daac) elif provider is not None: - s3_credentials = self.auth.get_s3_credentials(provider=provider) - now = datetime.datetime.now() - delta_minutes = now - self.initial_ts - # TODO: test this mocking the time or use https://github.com/dbader/schedule - # if we exceed 1 hour - if ( - self.s3_fs is None or round(delta_minutes.seconds / 60, 2) > 59 - ) and s3_credentials is not None: - self.s3_fs = s3fs.S3FileSystem( - key=s3_credentials["accessKeyId"], - secret=s3_credentials["secretAccessKey"], - token=s3_credentials["sessionToken"], - ) - self.initial_ts = datetime.datetime.now() - return deepcopy(self.s3_fs) - else: - print( - "A valid Earthdata login instance is required to retrieve S3 credentials" - ) - return None + creds = self.auth.get_s3_credentials(provider=provider) + # Include new credentials in the cache + self._s3_credentials[location] = now, creds + + return s3fs.S3FileSystem( + key=creds["accessKeyId"], + secret=creds["secretAccessKey"], + token=creds["sessionToken"], + ) @lru_cache def get_fsspec_session(self) -> fsspec.AbstractFileSystem: @@ -269,7 +295,7 @@ def open( self, granules: Union[List[str], List[DataGranule]], provider: Optional[str] = None, - ) -> Union[List[Any], None]: + ) -> List[Any]: """Returns a list of fsspec file-like objects that can be used to access files hosted on S3 or HTTPS by third party libraries like xarray. @@ -280,15 +306,14 @@ def open( """ if len(granules): return self._open(granules, provider) - print("The granules list is empty, moving on...") - return None + return [] @singledispatchmethod def _open( self, granules: Union[List[str], List[DataGranule]], provider: Optional[str] = None, - ) -> Union[List[Any], None]: + ) -> List[Any]: """Returns a list of fsspec file-like objects that can be used to access files hosted on S3 or HTTPS by third party libraries like xarray. @@ -305,21 +330,19 @@ def _open_granules( granules: List[DataGranule], provider: Optional[str] = None, threads: Optional[int] = 8, - ) -> Union[List[Any], None]: + ) -> List[Any]: fileset: List = [] - data_links: List = [] total_size = round(sum([granule.size() for granule in granules]) / 1024, 2) - print(f" Opening {len(granules)} granules, approx size: {total_size} GB") + print(f"Opening {len(granules)} granules, approx size: {total_size} GB") if self.auth is None: - print( + raise ValueError( "A valid Earthdata login instance is required to retrieve credentials" ) - return None - if self.running_in_aws: + if self.in_region: if granules[0].cloud_hosted: - access_method = "direct" + access = "direct" provider = granules[0]["meta"]["provider-id"] # if the data has its own S3 credentials endpoint we'll use it endpoint = self._own_s3_credentials(granules[0]["umm"]["RelatedUrls"]) @@ -330,41 +353,29 @@ def _open_granules( print(f"using provider: {provider}") s3_fs = self.get_s3fs_session(provider=provider) else: - access_method = "on_prem" + access = "on_prem" s3_fs = None - data_links = list( - chain.from_iterable( - granule.data_links(access=access_method) for granule in granules - ) - ) - + url_mapping = _get_url_granule_mapping(granules, access) if s3_fs is not None: try: fileset = _open_files( - data_links=data_links, - granules=granules, + url_mapping, fs=s3_fs, threads=threads, ) - except Exception: - print( - "An exception occurred while trying to access remote files on S3: " - "This may be caused by trying to access the data outside the us-west-2 region" + except Exception as e: + raise RuntimeError( + "An exception occurred while trying to access remote files on S3. " + "This may be caused by trying to access the data outside the us-west-2 region." f"Exception: {traceback.format_exc()}" - ) - return None + ) from e else: - fileset = self._open_urls_https(data_links, granules, threads=threads) + fileset = self._open_urls_https(url_mapping, threads=threads) return fileset else: - access_method = "on_prem" - data_links = list( - chain.from_iterable( - granule.data_links(access=access_method) for granule in granules - ) - ) - fileset = self._open_urls_https(data_links, granules, threads=threads) + url_mapping = _get_url_granule_mapping(granules, access="on_prem") + fileset = self._open_urls_https(url_mapping, threads=threads) return fileset @_open.register @@ -373,60 +384,53 @@ def _open_urls( granules: List[str], provider: Optional[str] = None, threads: Optional[int] = 8, - ) -> Union[List[Any], None]: + ) -> List[Any]: fileset: List = [] - data_links: List = [] if isinstance(granules[0], str) and ( granules[0].startswith("s3") or granules[0].startswith("http") ): # TODO: method to derive the DAAC from url? provider = provider - data_links = granules else: - print( + raise ValueError( f"Schema for {granules[0]} is not recognized, must be an HTTP or S3 URL" ) - return None if self.auth is None: - print( + raise ValueError( "A valid Earthdata login instance is required to retrieve S3 credentials" ) - return None - if self.running_in_aws and granules[0].startswith("s3"): + url_mapping: Mapping[str, None] = {url: None for url in granules} + if self.in_region and granules[0].startswith("s3"): if provider is not None: s3_fs = self.get_s3fs_session(provider=provider) if s3_fs is not None: try: fileset = _open_files( - data_links=data_links, - granules=granules, + url_mapping, fs=s3_fs, threads=threads, ) - except Exception: - print( - "An exception occurred while trying to access remote files on S3: " - "This may be caused by trying to access the data outside the us-west-2 region" + except Exception as e: + raise RuntimeError( + "An exception occurred while trying to access remote files on S3. " + "This may be caused by trying to access the data outside the us-west-2 region." f"Exception: {traceback.format_exc()}" - ) - return None + ) from e else: print(f"Provider {provider} has no valid cloud credentials") return fileset else: - print( + raise ValueError( "earthaccess cannot derive the DAAC provider from URLs only, a provider is needed e.g. POCLOUD" ) - return None else: if granules[0].startswith("s3"): - print( + raise ValueError( "We cannot open S3 links when we are not in-region, try using HTTPS links" ) - return None - fileset = self._open_urls_https(data_links, granules, threads) + fileset = self._open_urls_https(url_mapping, threads) return fileset def get( @@ -435,7 +439,7 @@ def get( local_path: Optional[str] = None, provider: Optional[str] = None, threads: int = 8, - ) -> Union[None, List[str]]: + ) -> List[str]: """Retrieves data granules from a remote storage system. * If we run this in the cloud we are moving data from S3 to a cloud compute instance (EC2, AWS Lambda) @@ -463,8 +467,7 @@ def get( files = self._get(granules, local_path, provider, threads) return files else: - print("List of URLs or DataGranule isntances expected") - return None + raise ValueError("List of URLs or DataGranule isntances expected") @singledispatchmethod def _get( @@ -473,7 +476,7 @@ def _get( local_path: str, provider: Optional[str] = None, threads: int = 8, - ) -> Union[None, List[str]]: + ) -> List[str]: """Retrieves data granules from a remote storage system. * If we run this in the cloud we are moving data from S3 to a cloud compute instance (EC2, AWS Lambda) @@ -491,8 +494,7 @@ def _get( Returns: None """ - print("List of URLs or DataGranule isntances expected") - return None + raise NotImplementedError(f"Cannot _get {granules}") @_get.register def _get_urls( @@ -501,16 +503,15 @@ def _get_urls( local_path: str, provider: Optional[str] = None, threads: int = 8, - ) -> Union[None, List[str]]: + ) -> List[str]: data_links = granules downloaded_files: List = [] - if provider is None and self.running_in_aws and "cumulus" in data_links[0]: - print( + if provider is None and self.in_region and "cumulus" in data_links[0]: + raise ValueError( "earthaccess can't yet guess the provider for cloud collections, " "we need to use one from earthaccess.list_cloud_providers()" ) - return None - if self.running_in_aws and data_links[0].startswith("s3"): + if self.in_region and data_links[0].startswith("s3"): print(f"Accessing cloud dataset using provider: {provider}") s3_fs = self.get_s3fs_session(provider=provider) # TODO: make this parallel or concurrent @@ -532,17 +533,17 @@ def _get_granules( local_path: str, provider: Optional[str] = None, threads: int = 8, - ) -> Union[None, List[str]]: + ) -> List[str]: data_links: List = [] downloaded_files: List = [] provider = granules[0]["meta"]["provider-id"] endpoint = self._own_s3_credentials(granules[0]["umm"]["RelatedUrls"]) cloud_hosted = granules[0].cloud_hosted - access = "direct" if (cloud_hosted and self.running_in_aws) else "external" + access = "direct" if (cloud_hosted and self.in_region) else "external" data_links = list( # we are not in region chain.from_iterable( - granule.data_links(access=access, in_region=self.running_in_aws) + granule.data_links(access=access, in_region=self.in_region) for granule in granules ) ) @@ -615,13 +616,11 @@ def _download_onprem_granules( :returns: None """ if urls is None: - print("The granules didn't provide a valid GET DATA link") - return None + raise ValueError("The granules didn't provide a valid GET DATA link") if self.auth is None: - print( + raise ValueError( "We need to be logged into NASA EDL in order to download data granules" ) - return [] if not os.path.exists(directory): os.makedirs(directory) @@ -636,14 +635,13 @@ def _download_onprem_granules( def _open_urls_https( self, - urls: List[str], - granules: Union[List[str], List[DataGranule]], + url_mapping: Mapping[str, Union[DataGranule, None]], threads: Optional[int] = 8, ) -> List[fsspec.AbstractFileSystem]: https_fs = self.get_fsspec_session() if https_fs is not None: try: - fileset = _open_files(urls, granules, https_fs, threads) + fileset = _open_files(url_mapping, https_fs, threads) except Exception: print( "An exception occurred while trying to access remote files via HTTPS: " diff --git a/mkdocs.yml b/mkdocs.yml index 5b31db1a..c1905ba3 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -3,7 +3,7 @@ site_description: Client library for NASA Earthdata APIs site_url: https://github.com/nsidc/earthaccess theme: - name: 'material' + name: "material" logo: earth.png favicon: earth.png palette: @@ -19,7 +19,7 @@ theme: repo_name: nsidc/earthaccess repo_url: https://github.com/nsidc/earthaccess -edit_uri: '' +edit_uri: "" extra_css: - css/styles.css @@ -42,45 +42,45 @@ plugins: - mkdocs-jupyter: execute: True ignore: - - "tutorials/dask.ipynb" - - "**/.ipynb_checkpoints/*" + - "tutorials/dask.ipynb" + - "**/.ipynb_checkpoints/*" nav: - OVERVIEW: - - 'Readme': 'index.md' - - 'Getting started': 'tutorials/getting-started.ipynb' - - 'Resources' : 'resources.md' + - "Readme": "index.md" + - "Getting started": "tutorials/getting-started.ipynb" + - "Resources": "resources.md" - HOW-TO: - - 'Authenticate with Earthdata Login': 'howto/authenticate.md' - - 'Search NASA datasets using filters': 'howto/search-collections.md' - - 'Search for data using filters': 'howto/search-granules.md' - - 'Determine if a dataset is available in the cloud': 'howto/storage-location.md' - - 'Using authenticated sessions to access data': 'howto/edl.ipynb' - - 'Download data from on-prem location': 'howto/onprem.md' - - 'Direct S3 access - Open/stream files in the cloud': 'howto/cloud.md' + - "Authenticate with Earthdata Login": "howto/authenticate.md" + - "Search NASA datasets using filters": "howto/search-collections.md" + - "Search for data using filters": "howto/search-granules.md" + - "Determine if a dataset is available in the cloud": "howto/storage-location.md" + - "Using authenticated sessions to access data": "howto/edl.ipynb" + - "Download data from on-prem location": "howto/onprem.md" + - "Direct S3 access - Open/stream files in the cloud": "howto/cloud.md" - TUTORIALS: - - 'Accesing remote NASA data with fsspec': 'tutorials/file-access.ipynb' - - 'Search and access of restricted datasets': 'tutorials/restricted-datasets.ipynb' - - 'Reproducing NASA sea level rise infographic': 'tutorials/SSL.ipynb' - - 'Accessing and visualizing EMIT data with a few lines of code': 'tutorials/emit-earthaccess.ipynb' + - "Accesing remote NASA data with fsspec": "tutorials/file-access.ipynb" + - "Search and access of restricted datasets": "tutorials/restricted-datasets.ipynb" + - "Reproducing NASA sea level rise infographic": "tutorials/SSL.ipynb" + - "Accessing and visualizing EMIT data with a few lines of code": "tutorials/emit-earthaccess.ipynb" # - 'Distributing workloads with Dask clusters': 'tutorials/dask.ipynb' - USER REFERENCE: - API: - - 'Search and Access': 'user-reference/api/api.md' + - "Search and Access": "user-reference/api/api.md" - Modules: - - Collections: - - 'Collection Queries': 'user-reference/collections/collections-query.md' - - 'Collection Results': 'user-reference/collections/collections.md' - - Granules: - - 'Granule Queries': 'user-reference/granules/granules-query.md' - - 'Granule Results': 'user-reference/granules/granules.md' - - Store: - - 'Store': 'user-reference/store/store.md' - - Auth: - - 'Auth': 'user-reference/auth/auth.md' + - Collections: + - "Collection Queries": "user-reference/collections/collections-query.md" + - "Collection Results": "user-reference/collections/collections.md" + - Granules: + - "Granule Queries": "user-reference/granules/granules-query.md" + - "Granule Results": "user-reference/granules/granules.md" + - Store: + - "Store": "user-reference/store/store.md" + - Auth: + - "Auth": "user-reference/auth/auth.md" - Glossary: - - 'NASA Glossary': 'user-reference/glossary/nasa-glossary.md' - - 'Cloud Computing Terminology': 'user-reference/glossary/cloud-glossary.md' + - "NASA Glossary": "user-reference/glossary/nasa-glossary.md" + - "Cloud Computing Terminology": "user-reference/glossary/cloud-glossary.md" markdown_extensions: - admonition diff --git a/poetry.lock b/poetry.lock index a843ad59..bbef7c55 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,133 +1,121 @@ -# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. 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"sphinx (>=3.5)", "sphinx-lint"] testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"] +[extras] +kerchunk = ["dask", "kerchunk"] + [metadata] lock-version = "2.0" python-versions = ">=3.8,<4.0" -content-hash = "0a1997946e1e0a3050c5d40459b0220493a8ede99ad08e7b69476ed9f004821a" +content-hash = "8c6dfb95442e8a609cae73163a9ff06ba02cb2971da057703c348c5844b5b9f9" diff --git a/pyproject.toml b/pyproject.toml index 6b6fb68a..a211b43a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "earthaccess" -version = "0.7.1" +version = "0.8.2" homepage = "https://github.com/nsidc/earthaccess" description = "Client library for NASA Earthdata APIs" authors = ["earthaccess contributors"] @@ -29,24 +29,28 @@ classifiers = [ "License :: OSI Approved :: MIT License", ] +# NOTE: Minimum dependencies are tested with the packages defined in the +# `ci/environment-mindeps.yaml` conda environment. When updating minimum dependencies +# here, make sure to also update `ci/environment-mindeps.yaml`. [tool.poetry.dependencies] python = ">=3.8,<4.0" -python-cmr = ">=0.7" +python-cmr = ">=0.9.0" pqdm = ">=0.1" requests = ">=2.26,<3.0.0" -s3fs = ">=2021.11, <2024" -fsspec = ">=2022.1" +s3fs = ">=2022.11, <2024" +fsspec = ">=2022.11" tinynetrc = "^1.3.1" multimethod = ">=1.8" +python-dateutil = ">=2.8.2" +kerchunk = { version = ">=0.1.2", optional = true } +dask = { version = ">=2022.1.0", optional = true } +[tool.poetry.extras] +kerchunk = ["kerchunk", "dask"] [tool.poetry.dev-dependencies] python-magic = ">=0.4" mypy = ">=0.812" -black = ">=21.11b0" -isort = ">=5" -autoflake = ">=1.3" -flake8 = ">=3.7" jupyterlab = ">=3" pre-commit = ">=2.4" pytest = ">=6.0" @@ -61,6 +65,7 @@ mkdocs-jupyter = ">=0.19.0" pymdown-extensions = ">=9.2" pygments = ">=2.11.1" responses = ">=0.14" +ruff = "^0.1.6" types-requests = ">=0.1" types-setuptools = ">=0.1" ipywidgets = ">=7.7.0" @@ -74,9 +79,8 @@ pyproj = ">=3.5.0" bump-my-version = ">=0.10.0" [build-system] -requires = ["poetry>=0.12"] -build-backend = "poetry.masonry.api" - +requires = ["poetry-core>=1.0.0"] +build-backend = "poetry.core.masonry.api" [tool.pytest] filterwarnings = ["error::UserWarning"] @@ -93,8 +97,20 @@ module = [ ignore_errors = true +[tool.ruff] +line-length = 88 +src = ["earthaccess", "tests"] +exclude = ["mypy-stubs", "stubs", "typeshed"] + +[tool.ruff.lint] +extend-select = ["I"] + +[tool.ruff.lint.isort] +combine-as-imports = true + + [tool.bumpversion] -current_version = "0.7.1" +current_version = "0.8.2" commit = false tag = false diff --git a/scripts/format.sh b/scripts/format.sh index 6a23d027..631d46b5 100755 --- a/scripts/format.sh +++ b/scripts/format.sh @@ -1,6 +1,5 @@ #!/bin/sh -e set -x -autoflake --remove-all-unused-imports --recursive --remove-unused-variables --in-place earthaccess tests --exclude=__init__.py -black earthaccess tests -isort --multi-line=3 --trailing-comma --force-grid-wrap=0 --combine-as --line-width 88 --recursive --thirdparty earthaccess --apply earthaccess tests +ruff check --fix . +ruff format . diff --git a/scripts/lint.sh b/scripts/lint.sh index 53e22c21..3a528811 100755 --- a/scripts/lint.sh +++ b/scripts/lint.sh @@ -4,5 +4,4 @@ set -e set -x mypy earthaccess --disallow-untyped-defs -black earthaccess tests --check -isort --multi-line=3 --trailing-comma --force-grid-wrap=0 --combine-as --line-width 88 --check-only --thirdparty earthaccess tests +ruff check . diff --git a/setup.py b/setup.py deleted file mode 100644 index 4e19ec70..00000000 --- a/setup.py +++ /dev/null @@ -1,8 +0,0 @@ -#!/usr/bin/env python - -# This is a shim to hopefully allow Github to detect the package, build is done with poetry - -import setuptools - -if __name__ == "__main__": - setuptools.setup(name="earthaccess") diff --git a/tests/integration/test_api.py b/tests/integration/test_api.py index bde37b05..6fa1ccea 100644 --- a/tests/integration/test_api.py +++ b/tests/integration/test_api.py @@ -69,13 +69,18 @@ def test_granules_search_returns_valid_results(kwargs): @pytest.mark.parametrize("selection", [0, slice(None)]) -def test_earthaccess_api_can_download_granules(tmp_path, selection): +@pytest.mark.parametrize("use_url", [True, False]) +def test_download(tmp_path, selection, use_url): results = earthaccess.search_data( count=2, short_name="ATL08", cloud_hosted=True, bounding_box=(-92.86, 16.26, -91.58, 16.97), ) + if use_url: + # Download via file URL string instead of DataGranule object + results = [r.data_links(access="indirect") for r in results] + results = sum(results, start=[]) # flatten to a list of strings result = results[selection] files = earthaccess.download(result, str(tmp_path)) assertions.assertIsInstance(files, list) diff --git a/tests/integration/test_auth.py b/tests/integration/test_auth.py index a61f3513..d1bfae1e 100644 --- a/tests/integration/test_auth.py +++ b/tests/integration/test_auth.py @@ -6,6 +6,7 @@ import earthaccess import pytest +import s3fs logger = logging.getLogger(__name__) assertions = unittest.TestCase("__init__") @@ -94,3 +95,24 @@ def test_auth_can_fetch_s3_credentials(): print( f"An error occured while trying to fetch S3 credentials for {daac['short-name']}: {e}" ) + + +@pytest.mark.parametrize("location", ({"daac": "podaac"}, {"provider": "pocloud"})) +def test_get_s3_credentials_lowercase_location(location): + activate_environment() + earthaccess.login(strategy="environment") + creds = earthaccess.get_s3_credentials(**location) + assert creds + assert all( + creds[key] + for key in ["accessKeyId", "secretAccessKey", "sessionToken", "expiration"] + ) + + +@pytest.mark.parametrize("location", ({"daac": "podaac"}, {"provider": "pocloud"})) +def test_get_s3fs_session_lowercase_location(location): + activate_environment() + earthaccess.login(strategy="environment") + fs = earthaccess.get_s3fs_session(**location) + assert isinstance(fs, s3fs.S3FileSystem) + assert all(fs.storage_options[key] for key in ["key", "secret", "token"]) diff --git a/tests/integration/test_cloud_download.py b/tests/integration/test_cloud_download.py index 4c76dc23..63a05b93 100644 --- a/tests/integration/test_cloud_download.py +++ b/tests/integration/test_cloud_download.py @@ -120,7 +120,7 @@ def test_earthaccess_can_download_cloud_collection_granules(daac): granule_query = DataGranules().concept_id(concept_id) total_granules = granule_query.hits() granules = granule_query.get(granules_count) - assert type(granules) is list and len(granules) > 0 + assert isinstance(granules, list) and len(granules) > 0 assert isinstance(granules[0], earthaccess.results.DataGranule) local_path = f"./tests/integration/data/{concept_id}" granules_to_download, total_size_cmr = get_sample_granules( @@ -157,3 +157,13 @@ def test_earthaccess_can_download_cloud_collection_granules(daac): f"Warning: {concept_id} downloaded size {total_mb_downloaded}MB is " f"different from the size reported by CMR: {total_size_cmr}MB" ) + + +def test_multi_file_granule(tmp_path): + # Ensure granules that contain multiple files are handled correctly + granules = earthaccess.search_data(short_name="HLSL30", count=1) + assert len(granules) == 1 + urls = granules[0].data_links() + assert len(urls) > 1 + files = earthaccess.download(granules, str(tmp_path)) + assert set(map(os.path.basename, urls)) == set(map(os.path.basename, files)) diff --git a/tests/integration/test_cloud_open.py b/tests/integration/test_cloud_open.py index d9d8fdea..78050f22 100644 --- a/tests/integration/test_cloud_open.py +++ b/tests/integration/test_cloud_open.py @@ -157,3 +157,13 @@ def test_earthaccess_can_open_onprem_collection_granules(daac): logger.info(f"File type: {magic.from_buffer(file.read(2048))}") else: logger.warning(f"File could not be open: {file}") + + +def test_multi_file_granule(): + # Ensure granules that contain multiple files are handled correctly + granules = earthaccess.search_data(short_name="HLSL30", count=1) + assert len(granules) == 1 + urls = granules[0].data_links() + assert len(urls) > 1 + files = earthaccess.open(granules) + assert set(urls) == set(f.path for f in files) diff --git a/tests/integration/test_kerchunk.py b/tests/integration/test_kerchunk.py new file mode 100644 index 00000000..39c95e99 --- /dev/null +++ b/tests/integration/test_kerchunk.py @@ -0,0 +1,86 @@ +import logging +import os +import unittest + +import earthaccess +import pytest +from fsspec.core import strip_protocol + +kerchunk = pytest.importorskip("kerchunk") +pytest.importorskip("dask") + +logger = logging.getLogger(__name__) +assertions = unittest.TestCase("__init__") + +assertions.assertTrue("EARTHDATA_USERNAME" in os.environ) +assertions.assertTrue("EARTHDATA_PASSWORD" in os.environ) + +logger.info(f"Current username: {os.environ['EARTHDATA_USERNAME']}") +logger.info(f"earthaccess version: {earthaccess.__version__}") + + +@pytest.fixture(scope="module") +def granuales(): + granuales = earthaccess.search_data( + count=2, + short_name="SEA_SURFACE_HEIGHT_ALT_GRIDS_L4_2SATS_5DAY_6THDEG_V_JPL2205", + cloud_hosted=True, + ) + return granuales + + +@pytest.mark.parametrize("protocol", ["", "file://"]) +def test_consolidate_metadata_outfile(tmp_path, granuales, protocol): + outfile = f"{protocol}{tmp_path / 'metadata.json'}" + assert not os.path.exists(outfile) + result = earthaccess.consolidate_metadata( + granuales, + outfile=outfile, + access="indirect", + kerchunk_options={"concat_dims": "Time"}, + ) + assert os.path.exists(strip_protocol(outfile)) + assert result == outfile + + +def test_consolidate_metadata_memory(tmp_path, granuales): + result = earthaccess.consolidate_metadata( + granuales, + access="indirect", + kerchunk_options={"concat_dims": "Time"}, + ) + assert isinstance(result, dict) + assert "refs" in result + + +@pytest.mark.parametrize("output", ["file", "memory"]) +def test_consolidate_metadata(tmp_path, granuales, output): + xr = pytest.importorskip("xarray") + # Open directly with `earthaccess.open` + expected = xr.open_mfdataset(earthaccess.open(granuales)) + + # Open with kerchunk consolidated metadata file + if output == "file": + kwargs = {"outfile": tmp_path / "metadata.json"} + else: + kwargs = {} + metadata = earthaccess.consolidate_metadata( + granuales, access="indirect", kerchunk_options={"concat_dims": "Time"}, **kwargs + ) + + fs = earthaccess.get_fsspec_https_session() + result = xr.open_dataset( + "reference://", + engine="zarr", + chunks={}, + backend_kwargs={ + "consolidated": False, + "storage_options": { + "fo": metadata, + "remote_protocol": "https", + "remote_options": fs.storage_options, + }, + }, + ) + + xr.testing.assert_equal(result, expected) diff --git a/tests/unit/test_store.py b/tests/unit/test_store.py index 388cb5af..2faed5b8 100644 --- a/tests/unit/test_store.py +++ b/tests/unit/test_store.py @@ -5,6 +5,7 @@ import fsspec import pytest import responses +import s3fs from earthaccess import Auth, Store @@ -60,12 +61,22 @@ def test_store_can_create_s3_fsspec_session(self): "https://api.giovanni.earthdata.nasa.gov/s3credentials", "https://data.laadsdaac.earthdatacloud.nasa.gov/s3credentials", ] + mock_creds = { + "accessKeyId": "sure", + "secretAccessKey": "correct", + "sessionToken": "whynot", + } + expected_storage_options = { + "key": mock_creds["accessKeyId"], + "secret": mock_creds["secretAccessKey"], + "token": mock_creds["sessionToken"], + } for endpoint in custom_endpoints: responses.add( responses.GET, endpoint, - json={}, + json=mock_creds, status=200, ) @@ -74,17 +85,13 @@ def test_store_can_create_s3_fsspec_session(self): responses.add( responses.GET, daac["s3-credentials"], - json={ - "accessKeyId": "sure", - "secretAccessKey": "correct", - "sessionToken": "whynot", - }, + json=mock_creds, status=200, ) responses.add( responses.GET, "https://urs.earthdata.nasa.gov/profile", - json={}, + json=mock_creds, status=200, ) @@ -92,22 +99,25 @@ def test_store_can_create_s3_fsspec_session(self): self.assertTrue(isinstance(store.auth, Auth)) for daac in ["NSIDC", "PODAAC", "LPDAAC", "ORNLDAAC", "GES_DISC", "ASF"]: s3_fs = store.get_s3fs_session(daac=daac) - self.assertEqual(type(s3_fs), type(fsspec.filesystem("s3"))) + assert isinstance(s3_fs, s3fs.S3FileSystem) + assert s3_fs.storage_options == expected_storage_options for endpoint in custom_endpoints: s3_fs = store.get_s3fs_session(endpoint=endpoint) - self.assertEqual(type(s3_fs), type(fsspec.filesystem("s3"))) + assert isinstance(s3_fs, s3fs.S3FileSystem) + assert s3_fs.storage_options == expected_storage_options for provider in [ "NSIDC_CPRD", "POCLOUD", "LPCLOUD", - "ORNLCLOUD", + "ORNL_CLOUD", "GES_DISC", "ASF", ]: s3_fs = store.get_s3fs_session(provider=provider) - assert isinstance(s3_fs, fsspec.AbstractFileSystem) + assert isinstance(s3_fs, s3fs.S3FileSystem) + assert s3_fs.storage_options == expected_storage_options # Ensure informative error is raised with pytest.raises(ValueError, match="parameters must be specified"):