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/.github/workflows/build-pipeline.yml b/.github/workflows/build-pipeline.yml
new file mode 100644
index 0000000..205c39b
--- /dev/null
+++ b/.github/workflows/build-pipeline.yml
@@ -0,0 +1,135 @@
+# When code is pushed to a branch, run linting and tests, and
+# then automatically increment the version number as appropriate for the branch source.
+name: Lint and Test
+
+# Controls when the workflow will run
+on:
+ # Triggers the workflow on push events
+ push:
+ branches: [ develop, release/**, main, feature/**, issue/**, issues/** ]
+
+ # Allows you to run this workflow manually from the Actions tab
+ workflow_dispatch:
+
+jobs:
+ run_tests:
+ uses: ./.github/workflows/reusable_run_tests.yml
+
+ bump_version:
+ needs: run_tests
+ runs-on: ubuntu-latest
+
+ steps:
+ - uses: actions/checkout@v4
+
+ - uses: actions/setup-python@v4
+ with:
+ python-version: '3.10'
+
+ - name: Install Poetry
+ uses: abatilo/actions-poetry@v2.3.0
+ with:
+ poetry-version: 1.3.2
+
+ - name: Get version
+ id: get-version
+ run: |
+ echo "current_version=$(poetry version | awk '{print $2}')" >> $GITHUB_OUTPUT
+ echo "pyproject_name=$(poetry version | awk '{print $1}')" >> $GITHUB_ENV
+
+# - name: Bump pre-alpha version
+# # If triggered by push to a feature branch
+# if: |
+# ${{ startsWith(github.ref, 'refs/heads/issue') }} ||
+# ${{ startsWith(github.ref, 'refs/heads/dependabot/') }} ||
+# ${{ startsWith(github.ref, 'refs/heads/feature/') }}
+# run: |
+# new_ver="${{ steps.get-version.outputs.current_version }}+$(git rev-parse --short ${GITHUB_SHA})"
+# poetry version $new_ver
+# echo "software_version=$(poetry version | awk '{print $2}')" >> $GITHUB_ENV
+#
+# - name: Bump alpha version
+# # If triggered by push to the develop branch
+# if: ${{ github.ref == 'refs/heads/develop' }}
+# run: |
+# poetry version prerelease
+# echo "software_version=$(poetry version | awk '{print $2}')" >> $GITHUB_ENV
+# echo "venue=sit" >> $GITHUB_ENV
+#
+# - name: Bump rc version
+# # If triggered by push to a release branch
+# if: ${{ startsWith(github.ref, 'refs/heads/release/') }}
+# env:
+# # True if the version already has a 'rc' pre-release identifier
+# BUMP_RC: ${{ contains(steps.get-version.outputs.current_version, 'rc') }}
+# run: |
+# if [ "$BUMP_RC" = true ]; then
+# poetry version prerelease
+# else
+# poetry version ${GITHUB_REF#refs/heads/release/}rc1
+# fi
+# echo "software_version=$(poetry version | awk '{print $2}')" >> $GITHUB_ENV
+# echo "venue=uat" >> $GITHUB_ENV
+#
+# - name: Release version
+# # If triggered by push to the main branch
+# if: ${{ startsWith(github.ref, 'refs/heads/main') }}
+# env:
+# CURRENT_VERSION: ${{ steps.get-version.outputs.current_version }}
+# # Remove rc* from the end of version string
+# # The ${string%%substring} syntax below deletes the longest match of $substring from back of $string.
+# run: |
+# poetry version ${CURRENT_VERSION%%rc*}
+# echo "software_version=$(poetry version | awk '{print $2}')" >> $GITHUB_ENV
+# echo "venue=ops" >> $GITHUB_ENV
+#
+# - name: Commit Version Bump
+# # If building develop, a release branch, or main then we commit the version bump back to the repo
+# if: |
+# github.ref == 'refs/heads/develop' ||
+# github.ref == 'refs/heads/main' ||
+# startsWith(github.ref, 'refs/heads/release')
+# run: |
+# git config --global user.name 'batchee bot'
+# git config --global user.email 'batchee@noreply.github.com'
+# git commit -am "/version ${{ env.software_version }}"
+# git push
+#
+# - name: Push Tag
+# if: |
+# github.ref == 'refs/heads/develop' ||
+# github.ref == 'refs/heads/main' ||
+# startsWith(github.ref, 'refs/heads/release')
+# run: |
+# git config user.name "${GITHUB_ACTOR}"
+# git config user.email "${GITHUB_ACTOR}@users.noreply.github.com"
+# git tag -a "${{ env.software_version }}" -m "Version ${{ env.software_version }}"
+# git push origin "${{ env.software_version }}"
+
+# - name: Build Python Artifact
+# run: |
+# poetry build
+#
+# - uses: actions/upload-artifact@v3
+# with:
+# name: python-artifact
+# path: dist/*
+#
+# - name: Publish to test.pypi.org
+# id: pypi-test-publish
+# if: |
+# github.ref == 'refs/heads/develop' ||
+# startsWith(github.ref, 'refs/heads/release')
+# env:
+# POETRY_PYPI_TOKEN_TESTPYPI: ${{secrets.POETRY_PYPI_TOKEN_TESTPYPI}}
+# run: |
+# poetry config repositories.testpypi https://test.pypi.org/legacy/
+# poetry publish -r testpypi
+#
+# - name: Publish to pypi.org
+# if: ${{ github.ref == 'refs/heads/main' }}
+# id: pypi-publish
+# env:
+# POETRY_PYPI_TOKEN_PYPI: ${{secrets.POETRY_PYPI_TOKEN_PYPI}}
+# run: |
+# poetry publish
diff --git a/.github/workflows/on_push.yml b/.github/workflows/on_push.yml
deleted file mode 100644
index eb942d6..0000000
--- a/.github/workflows/on_push.yml
+++ /dev/null
@@ -1,107 +0,0 @@
-name: Lint and Test
-
-# Controls when the workflow will run
-on:
- # Triggers the workflow on push events
- push:
- branches: [ develop, release/**, main, feature/**, issue/**, issues/** ]
-
- # Allows you to run this workflow manually from the Actions tab
- workflow_dispatch:
-
-jobs:
- run_tests:
- uses: ./.github/workflows/run_tests.yml
-
- bump_version:
- needs: run_tests
- runs-on: ubuntu-20.04
-
- steps:
- - name: Retrieve repository
- uses: actions/checkout@v4
-
- - name: Set up Python
- uses: actions/setup-python@v4
- with:
- python-version: '3.10'
-
- - name: Install Poetry
- uses: abatilo/actions-poetry@v2.3.0
- with:
- poetry-version: 1.3.2
-
- - name: Get version
- id: get-version
- run: |
- echo "current_version=$(poetry version | awk '{print $2}')" >> $GITHUB_OUTPUT
- echo "pyproject_name=$(poetry version | awk '{print $1}')" >> $GITHUB_ENV
-
- - name: Bump pre-alpha version
- # If triggered by push to a feature branch
- if: |
- ${{ startsWith(github.ref, 'refs/heads/issue') }} ||
- ${{ startsWith(github.ref, 'refs/heads/dependabot/') }} ||
- ${{ startsWith(github.ref, 'refs/heads/feature/') }}
- run: |
- new_ver="${{ steps.get-version.outputs.current_version }}+$(git rev-parse --short ${GITHUB_SHA})"
- poetry version $new_ver
- echo "software_version=$(poetry version | awk '{print $2}')" >> $GITHUB_ENV
-
- - name: Bump alpha version
- # If triggered by push to the develop branch
- if: ${{ github.ref == 'refs/heads/develop' }}
- run: |
- poetry version prerelease
- echo "software_version=$(poetry version | awk '{print $2}')" >> $GITHUB_ENV
- echo "venue=sit" >> $GITHUB_ENV
-
- - name: Bump rc version
- # If triggered by push to a release branch
- if: ${{ startsWith(github.ref, 'refs/heads/release/') }}
- env:
- # True if the version already has a 'rc' pre-release identifier
- BUMP_RC: ${{ contains(steps.get-version.outputs.current_version, 'rc') }}
- run: |
- if [ "$BUMP_RC" = true ]; then
- poetry version prerelease
- else
- poetry version ${GITHUB_REF#refs/heads/release/}rc1
- fi
- echo "software_version=$(poetry version | awk '{print $2}')" >> $GITHUB_ENV
- echo "venue=uat" >> $GITHUB_ENV
-
- - name: Release version
- # If triggered by push to the main branch
- if: ${{ startsWith(github.ref, 'refs/heads/main') }}
- env:
- CURRENT_VERSION: ${{ steps.get-version.outputs.current_version }}
- # Remove rc* from end of version string
- # The ${string%%substring} syntax below deletes the longest match of $substring from back of $string.
- run: |
- poetry version ${CURRENT_VERSION%%rc*}
- echo "software_version=$(poetry version | awk '{print $2}')" >> $GITHUB_ENV
- echo "venue=ops" >> $GITHUB_ENV
-
-# - name: Commit Version Bump
-# # If building develop, a release branch, or main then we commit the version bump back to the repo
-# if: |
-# github.ref == 'refs/heads/develop' ||
-# github.ref == 'refs/heads/main' ||
-# startsWith(github.ref, 'refs/heads/release')
-# run: |
-# git config --global user.name 'batchee bot'
-# git config --global user.email 'batchee@noreply.github.com'
-# git commit -am "/version ${{ env.software_version }}"
-# git push
-#
-# - name: Push Tag
-# if: |
-# github.ref == 'refs/heads/develop' ||
-# github.ref == 'refs/heads/main' ||
-# startsWith(github.ref, 'refs/heads/release')
-# run: |
-# git config user.name "${GITHUB_ACTOR}"
-# git config user.email "${GITHUB_ACTOR}@users.noreply.github.com"
-# git tag -a "${{ env.software_version }}" -m "Version ${{ env.software_version }}"
-# git push origin "${{ env.software_version }}"
diff --git a/.github/workflows/run_tests_on_pull_requests.yml b/.github/workflows/pull-request-received.yml
similarity index 50%
rename from .github/workflows/run_tests_on_pull_requests.yml
rename to .github/workflows/pull-request-received.yml
index 3a0b4c1..fbfe8c5 100644
--- a/.github/workflows/run_tests_on_pull_requests.yml
+++ b/.github/workflows/pull-request-received.yml
@@ -1,3 +1,4 @@
+# When a pull request is opened, run linting and tests.
name: Receive PR
# read-only repo token
@@ -5,11 +6,8 @@ name: Receive PR
on:
pull_request:
# Sequence of patterns matched against refs/heads
- branches:
- - feature/**
- - issue/**
- - issues/**
+ branches: [ feature/**, issue/**, issues/** ]
jobs:
build_and_test:
- uses: ./.github/workflows/run_tests.yml
+ uses: ./.github/workflows/reusable_run_tests.yml
diff --git a/.github/workflows/release-created.yml b/.github/workflows/release-created.yml
new file mode 100644
index 0000000..62a79d7
--- /dev/null
+++ b/.github/workflows/release-created.yml
@@ -0,0 +1,40 @@
+# As soon as a release branch is pushed, the minor version on develop is bumped automatically.
+# This allows further development to continue on develop for ‘the next’ release.
+name: Release Branch Created
+
+# Run whenever a ref is created https://docs.github.com/en/actions/reference/events-that-trigger-workflows#create
+on:
+ create
+
+jobs:
+ # First job in the workflow builds and verifies the software artifacts
+ bump:
+ name: Bump minor version on develop
+ # The type of runner that the job will run on
+ runs-on: ubuntu-latest
+ # Only run if ref created was a release branch
+ if:
+ ${{ startsWith(github.ref, 'refs/heads/release/') }}
+ steps:
+ # Checks-out the develop branch
+ - uses: actions/checkout@v4
+ with:
+ ref: 'refs/heads/develop'
+# - uses: actions/setup-python@v4
+# with:
+# python-version: '3.10'
+# - name: Install Poetry
+# uses: abatilo/actions-poetry@v2.3.0
+# with:
+# poetry-version: 1.3.2
+## - name: Bump minor version
+## run: |
+## poetry version ${GITHUB_REF#refs/heads/release/}
+## poetry version preminor
+## echo "software_version=$(poetry version | awk '{print $2}')" >> $GITHUB_ENV
+## - name: Commit Version Bump
+## run: |
+## git config --global user.name 'batchee bot'
+## git config --global user.email 'batchee@noreply.github.com'
+## git commit -am "/version ${{ env.software_version }}"
+## git push
diff --git a/.github/workflows/reusable_run_tests.yml b/.github/workflows/reusable_run_tests.yml
new file mode 100644
index 0000000..7337a29
--- /dev/null
+++ b/.github/workflows/reusable_run_tests.yml
@@ -0,0 +1,56 @@
+# This workflow will install Python dependencies, run tests,
+# and report test results and code coverage as artifacts. It will
+# be called by the workflow that runs tests against new PRs and as
+# a first step in the workflow that publishes new Docker images.
+
+name: A reusable workflow to build and run the unit test suite
+
+on:
+ workflow_call:
+ workflow_dispatch:
+
+jobs:
+ build_and_test:
+ runs-on: ubuntu-latest
+ strategy:
+ matrix:
+ python-version: [ '3.10' ]
+
+ name: Python ${{ matrix.python-version }} tests
+ steps:
+ - uses: actions/checkout@v4
+
+ - name: Set up Python
+ uses: actions/setup-python@v4
+ with:
+ python-version: ${{ matrix.python-version }}
+
+ - name: Set up Poetry
+ uses: abatilo/actions-poetry@v2.3.0
+ with:
+ poetry-version: 1.3.2
+
+ - name: Install package
+ run: poetry install
+
+ - name: Lint
+ run: |
+ poetry run ruff batcher
+
+ - name: Run tests with coverage
+ run: |
+ poetry run pytest --cov=batcher --cov-report=xml:build/reports/coverage.xml --cov-report=html:build/reports/coverage.html tests/
+
+ - name: Archive code coverage report (xml)
+ if: ${{ always() }}
+ uses: actions/upload-artifact@v3
+ with:
+ name: code coverage report (xml)
+ path: build/reports/coverage.xml
+
+ - name: Archive code coverage report (HTML)
+ if: ${{ always() }}
+ uses: actions/upload-artifact@v3
+ with:
+ name: code coverage report (HTML)
+ path: build/reports/coverage.html
diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml
deleted file mode 100644
index 64733a9..0000000
--- a/.github/workflows/run_tests.yml
+++ /dev/null
@@ -1,68 +0,0 @@
-# This workflow will install Python dependencies, run tests,
-# and report test results and code coverage as artifacts. It will
-# be called by the workflow that run tests against new PRs and as
-# a first step in the workflow that publishes new Docker images.
-
-name: A reusable workflow to build and run the unit test suite
-
-on:
- workflow_call:
- workflow_dispatch:
-
-jobs:
- build_and_test:
- runs-on: ubuntu-latest
-
- steps:
- - name: Retrieve repository
- uses: actions/checkout@v4
-
- - name: Set up Python
- uses: actions/setup-python@v4
- with:
- python-version: '3.10'
-
- - name: Set up Poetry
- uses: abatilo/actions-poetry@v2.3.0
- with:
- poetry-version: 1.3.2
-
- - name: Install package
- run: poetry install
-
- - name: Run linting
- run: |
- poetry run ruff batcher
-
- - name: Run tests with coverage
- run: |
- poetry run coverage run -m pytest >& test_results.txt
- # poetry run pytest tests/test_filename_grouping.py >& test_results.txt
- # TODO: expand tests to include full concatenation runs, i.e., don't just run test_group_handling.py
-
- - name: Generate coverage report
- if: ${{ always() }}
- run: |
- poetry run coverage report -m >& coverage_report.txt
- poetry run coverage html --dir htmlcov
-
- - name: Archive test results
- if: ${{ always() }}
- uses: actions/upload-artifact@v3
- with:
- name: test result
- path: test_results.txt
-
- - name: Archive code coverage report (plain text)
- if: ${{ always() }}
- uses: actions/upload-artifact@v3
- with:
- name: code coverage report (plain text)
- path: coverage_report.txt
-
- - name: Archive code coverage report (HTML)
- if: ${{ always() }}
- uses: actions/upload-artifact@v3
- with:
- name: code coverage report (HTML)
- path: htmlcov/*
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 1468387..f8b85f1 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,9 +7,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
## [Unreleased]
### Added
+- [issue/6](https://github.com/danielfromearth/batchee/issues/6): Create Adapter code that processes a Harmony Message and STAC Catalog
+- [issue/7](https://github.com/danielfromearth/batchee/issues/7): Create working Docker image
- [issue/13](https://github.com/danielfromearth/batchee/issues/13): Add simple command line interface for testing
+- [issue/16](https://github.com/danielfromearth/batchee/issues/16): Add a logo
### Changed
- [issue/11](https://github.com/danielfromearth/batchee/issues/11): Rename from concat_batcher to batchee
+- [issue/21](https://github.com/danielfromearth/batchee/issues/21): Improve CICD workflows
### Deprecated
### Removed
### Fixed
diff --git a/docker/Dockerfile b/Dockerfile
similarity index 59%
rename from docker/Dockerfile
rename to Dockerfile
index 353fea4..96036d1 100644
--- a/docker/Dockerfile
+++ b/Dockerfile
@@ -5,12 +5,14 @@ RUN apt-get update \
&& DEBIAN_FRONTEND=noninteractive apt-get upgrade -y \
gcc \
libnetcdf-dev \
- libhdf5-dev \
- hdf5-helpers \
+ #libhdf5-dev \
+ #hdf5-helpers \
&& pip3 install --upgrade pip \
&& pip3 install cython \
+ && pip3 install poetry \
&& apt-get clean
+
# Create a new user
RUN adduser --quiet --disabled-password --shell /bin/sh --home /home/dockeruser --gecos "" --uid 1000 dockeruser
USER dockeruser
@@ -27,13 +29,25 @@ ARG DIST_PATH
USER root
RUN mkdir -p /worker && chown dockeruser /worker
+COPY pyproject.toml /worker
+# COPY ../pyproject.toml /worker
USER dockeruser
+
WORKDIR /worker
+# ENV PYTHONPATH=${PYTHONPATH}:${PWD}
+
COPY --chown=dockeruser $DIST_PATH $DIST_PATH
USER dockeruser
-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
+#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
-# Run the Batchee Harmony service
-ENTRYPOINT ["batchee_harmony"]
\ No newline at end of file
+#install poetry as root
+USER root
+RUN poetry config virtualenvs.create false
+RUN poetry install --no-dev
+
+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 9d5373b..0811fa8 100644
--- a/README.md
+++ b/README.md
@@ -1,5 +1,40 @@
+[
](stitchee_9_hex)
+
+
# Overview
_____
-_Batchee_ is used to group together filenames so that concatenation operations can be performed on
-batches.
+_Batchee_ groups together filenames so that further operations (such as concatenation) can be performed separately on each group of files.
+
+## Installing
+_____
+
+For local development, one can clone the repository and then use poetry or pip from the local directory:
+
+```shell
+git clone
+```
+
+###### (Option A) using poetry:
+i) Follow the instructions for installing `poetry` [here](https://python-poetry.org/docs/).
+
+ii) Run ```poetry install``` from the repository directory.
+
+###### (Option B) using pip: Run ```pip install .``` from the repository directory.
+
+## Usage
+_____
+
+```shell
+batchee [file_names ...]
+```
+
+###### Or, If installed using a `poetry` environment:
+```shell
+poetry run batchee [file_names ...]
+```
+
+#### Options
+
+- `-h`, `--help` show this help message and exit
+- `-v`, `--verbose` Enable verbose output to stdout; useful for debugging
diff --git a/batcher/harmony/__init__.py b/batcher/harmony/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/batcher/harmony_cli.py b/batcher/harmony/cli.py
similarity index 54%
rename from batcher/harmony_cli.py
rename to batcher/harmony/cli.py
index cec149e..802d373 100644
--- a/batcher/harmony_cli.py
+++ b/batcher/harmony/cli.py
@@ -1,33 +1,28 @@
"""A Harmony CLI wrapper around the concatenate-batcher"""
-import sys
from argparse import ArgumentParser
import harmony
-from .harmony_adapter import ConcatBatching as HarmonyAdapter
+from batcher.harmony.service_adapter import ConcatBatching as HarmonyAdapter
-def main(argv, **kwargs):
- """Main Harmony CLI entrypoint
+def main(config: harmony.util.Config = None) -> None:
+ """Parse command line arguments and invoke the service to respond to them.
- Parses command line arguments and invokes the appropriate method to respond to them
+ Parameters
+ ----------
+ config : harmony.util.Config
+ harmony.util.Config is injectable for tests
Returns
-------
None
"""
-
- config = None
- # Optional: harmony.util.Config is injectable for tests
- if "config" in kwargs:
- config = kwargs.get("config")
-
parser = ArgumentParser(
prog="Pre-concatenate-batching", description="Run the pre-concatenate-batching service"
)
harmony.setup_cli(parser)
-
- args = parser.parse_args(argv[1:])
+ args = parser.parse_args()
if harmony.is_harmony_cli(args):
harmony.run_cli(parser, args, HarmonyAdapter, cfg=config)
else:
@@ -35,4 +30,4 @@ def main(argv, **kwargs):
if __name__ == "__main__":
- main(sys.argv)
+ main()
diff --git a/batcher/harmony/service_adapter.py b/batcher/harmony/service_adapter.py
new file mode 100644
index 0000000..31bff4b
--- /dev/null
+++ b/batcher/harmony/service_adapter.py
@@ -0,0 +1,117 @@
+from uuid import uuid4
+
+import pystac
+from harmony.adapter import BaseHarmonyAdapter
+from harmony.util import bbox_to_geometry
+from pystac import Item
+from pystac.item import Asset
+
+from batcher.harmony.util import (
+ _get_netcdf_urls,
+ _get_output_bounding_box,
+ _get_output_date_range,
+)
+from batcher.tempo_filename_parser import get_batch_indices
+
+
+class ConcatBatching(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):
+ """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}.")
+
+ # --- Map each granule to an index representing the batch to which it belongs ---
+ batch_indices: list[int] = get_batch_indices(netcdf_urls, self.logger)
+ sorted(set(batch_indices), key=batch_indices.index)
+ self.logger.info(f"batch_indices==={batch_indices}.")
+
+ # --- Construct a dictionary with a separate key for each batch ---
+ grouped: dict[int, list[Item]] = {}
+ for k, v in zip(batch_indices, items):
+ grouped.setdefault(k, []).append(v)
+
+ # --- Construct a STAC Catalog that holds multiple Items (which represent each TEMPO scan),
+ # and each Item holds multiple Assets (which represent each granule).
+ result.clear_items()
+
+ for batch_id, batch_items in grouped.items():
+ batch_urls: list[str] = _get_netcdf_urls(batch_items)
+ bounding_box = _get_output_bounding_box(batch_items)
+ properties = _get_output_date_range(batch_items)
+
+ self.logger.info(f"constructing new pystac.Item for batch_id==={batch_id}.")
+
+ # Construct a new pystac.Item with every granule in the batch as a pystac.Asset
+ output_item = Item(
+ str(uuid4()), bbox_to_geometry(bounding_box), bounding_box, None, properties
+ )
+
+ for idx, item in enumerate(batch_items):
+ output_item.add_asset(
+ f"data_{idx}",
+ Asset(
+ batch_urls[idx],
+ title=batch_urls[idx],
+ media_type="application/x-netcdf4",
+ roles=["data"],
+ ),
+ )
+
+ result.add_item(output_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
diff --git a/batcher/harmony/util.py b/batcher/harmony/util.py
new file mode 100644
index 0000000..f77aeb9
--- /dev/null
+++ b/batcher/harmony/util.py
@@ -0,0 +1,98 @@
+"""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
diff --git a/batcher/harmony_adapter.py b/batcher/harmony_adapter.py
deleted file mode 100644
index 80c1976..0000000
--- a/batcher/harmony_adapter.py
+++ /dev/null
@@ -1,104 +0,0 @@
-from harmony.adapter import BaseHarmonyAdapter
-from pystac import Catalog, Item
-from pystac.item import Asset
-
-from batcher.tempo_filename_parser import get_unique_day_scan_categories
-
-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]
-
-
-class ConcatBatching(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 Batcher without a STAC catalog is not supported")
-
- return self.message, self.process_items_many_to_one()
-
- def process_items_many_to_one(self):
- """Converts a list of STAC catalogs into a list of lists of STAC catalogs."""
- try:
- items: list[Catalog] = list(self.get_all_catalog_items(self.catalog))
- netcdf_urls: list[str] = _get_netcdf_urls(items)
-
- batch_indices: list[int] = get_unique_day_scan_categories(netcdf_urls)
- unique_category_indices: list[int] = sorted(set(batch_indices), key=batch_indices.index)
-
- grouped: dict[int, list[Catalog]] = {}
- for k, v in zip(batch_indices, items):
- grouped.setdefault(k, []).append(v)
- catalogs: list[list[Catalog]] = [grouped[k] for k in unique_category_indices]
-
- return catalogs
-
- except Exception as service_exception:
- self.logger.error(service_exception, exc_info=1)
- raise service_exception
diff --git a/batcher/tempo_filename_parser.py b/batcher/tempo_filename_parser.py
index c75e04e..06488d4 100644
--- a/batcher/tempo_filename_parser.py
+++ b/batcher/tempo_filename_parser.py
@@ -4,6 +4,8 @@
from argparse import ArgumentParser
from pathlib import Path
+default_logger = logging.getLogger(__name__)
+
tempo_granule_filename_pattern = re.compile(
r"^.*TEMPO_"
r"(?P[1-9A-Z]+)"
@@ -17,13 +19,15 @@
)
-def get_unique_day_scan_categories(filenames: list) -> list[int]:
+def get_batch_indices(filenames: list, logger: logging.Logger = default_logger) -> list[int]:
"""
Returns
-------
list[int]
- category integer for each filename in the original list, e.g. [0, 0, 0, 1, 1, 1, ...]
+ batch index for each filename in the original list, e.g. [0, 0, 0, 1, 1, 1, ...]
"""
+ logger.info(f"get_batch_indices() starting --- with {len(filenames)} filenames")
+
# Make a new list with days and scans, e.g. [('20130701', 'S009'), ('20130701', 'S009'), ...]
day_and_scans: list[tuple[str, str]] = []
for name in filenames:
@@ -32,19 +36,21 @@ def get_unique_day_scan_categories(filenames: list) -> list[int]:
match_dict = matches.groupdict()
day_and_scans.append((match_dict["day_in_granule"], match_dict["daily_scan_id"]))
- # Unique categories are determined, while keeping the same order
+ # Unique day-scans are determined (while keeping the same order). Each will be its own batch.
unique_day_scans: list[tuple[str, str]] = sorted(set(day_and_scans), key=day_and_scans.index)
+ logger.info(f"unique_day_scans==={unique_day_scans}.")
+
# Map each day/scan to an integer
- category_mapper: dict[tuple[str, str], int] = {
+ batch_mapper: dict[tuple[str, str], int] = {
day_scan: idx for idx, day_scan in enumerate(unique_day_scans)
}
# Generate a new list with the integer representation for each entry in the original list
- return [category_mapper[day_scan] for day_scan in day_and_scans]
+ return [batch_mapper[day_scan] for day_scan in day_and_scans]
-def main():
+def main() -> list[list[str]]:
"""Main CLI entrypoint"""
parser = ArgumentParser(
@@ -69,7 +75,7 @@ def main():
input_filenames = [str(Path(f).resolve()) for f in args.file_names]
- batch_indices = get_unique_day_scan_categories(input_filenames)
+ batch_indices = get_batch_indices(input_filenames)
unique_category_indices: list[int] = sorted(set(batch_indices), key=batch_indices.index)
logging.info(f"batch_indices = {batch_indices}")
diff --git a/docker-entrypoint.sh b/docker-entrypoint.sh
new file mode 100755
index 0000000..9ce02d6
--- /dev/null
+++ b/docker-entrypoint.sh
@@ -0,0 +1,10 @@
+#!/bin/bash
+set -e
+
+if [ "$1" = 'batchee' ]; then
+ exec batchee "$@"
+elif [ "$1" = 'batchee_harmony' ]; then
+ exec batchee_harmony "$@"
+else
+ exec batchee_harmony "$@"
+fi
diff --git a/docker/Readme.md b/docker/Readme.md
deleted file mode 100644
index 5f05138..0000000
--- a/docker/Readme.md
+++ /dev/null
@@ -1,8 +0,0 @@
-# Batchee Service Docker Image
-
-This directory contains the `Dockerfile` used to build the Docker image capable of running the Batchee service.
-
-## Building
-
-The docker image is setup to install the Batchee project into userspace using pip. It will look
-in both PyPi and TestPyPi indexes unless building from a local wheel file.
\ No newline at end of file
diff --git a/poetry.lock b/poetry.lock
index 1872cb6..a2af622 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -2,33 +2,28 @@
[[package]]
name = "black"
-version = "23.9.1"
+version = "23.10.1"
description = "The uncompromising code formatter."
optional = false
python-versions = ">=3.8"
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[[package]]
name = "boto3"
-version = "1.28.58"
+version = "1.28.73"
description = "The AWS SDK for Python"
optional = false
python-versions = ">= 3.7"
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jmespath = ">=0.7.1,<2.0.0"
s3transfer = ">=0.7.0,<0.8.0"
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[[package]]
name = "botocore"
-version = "1.31.58"
+version = "1.31.73"
description = "Low-level, data-driven core of boto 3."
optional = false
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crt = ["awscrt (==0.16.26)"]
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]
[[package]]
@@ -754,4 +770,4 @@ socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"]
[metadata]
lock-version = "2.0"
python-versions = "^3.10"
-content-hash = "2eddcedad9f6e921f2e1b770870a16780915ca6765fc63cc2c0a8130744fe001"
+content-hash = "13d72d5e93ac5ddb6bd054b98d9cf04ed920d251e91e623fb0a48a17b777cf2e"
diff --git a/pyproject.toml b/pyproject.toml
index 3399aed..1c090dd 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -15,17 +15,18 @@ packages = [
python = "^3.10"
harmony-service-lib = "^1.0.23"
-[tool.poetry.group.dev.dependencies]
-pytest = "^7.4.2"
-black = "^23.9.1"
-mypy = "^1.5.1"
-ruff = "^0.0.292"
-coverage = "^7.3.2"
-
[tool.poetry.scripts]
-batchee_harmony = 'batcher.harmony_cli:main'
+batchee_harmony = 'batcher.harmony.cli:main'
batchee = 'batcher.tempo_filename_parser:main'
+[tool.poetry.group.dev.dependencies]
+coverage = "^7.3.2"
+ruff = "^0.1.3"
+pytest = "^7.4.3"
+black = "^23.10.1"
+mypy = "^1.6.1"
+pytest-cov = "^4.1.0"
+
[build-system]
requires = ["poetry-core"]
build-backend = "poetry.core.masonry.api"
diff --git a/tests/test_filename_grouping.py b/tests/test_filename_grouping.py
index 945a79a..83ae365 100644
--- a/tests/test_filename_grouping.py
+++ b/tests/test_filename_grouping.py
@@ -1,4 +1,4 @@
-from batcher.tempo_filename_parser import get_unique_day_scan_categories
+from batcher.tempo_filename_parser import get_batch_indices
example_filenames = [
"TEMPO_HCHO_L2_V01_20130701T212354Z_S009G05.nc",
@@ -11,6 +11,6 @@
def test_grouping():
- results = get_unique_day_scan_categories(example_filenames)
+ results = get_batch_indices(example_filenames)
assert results == [0, 0, 0, 1, 1, 1]