From 31fc921e0c44b5a47426c9483e4b3ee976954552 Mon Sep 17 00:00:00 2001 From: danielfromearth Date: Tue, 31 Oct 2023 15:24:06 -0400 Subject: [PATCH 01/16] add build-service script --- build-service | 3 +++ 1 file changed, 3 insertions(+) create mode 100755 build-service diff --git a/build-service b/build-service new file mode 100755 index 0000000..e41115b --- /dev/null +++ b/build-service @@ -0,0 +1,3 @@ +#!/bin/bash + +docker build -t "asdc-trade/batchee:${VERSION-latest}" . From c610db363f0dc90b33561ba860b871e3bd0e7e75 Mon Sep 17 00:00:00 2001 From: danielfromearth Date: Tue, 31 Oct 2023 17:13:39 -0400 Subject: [PATCH 02/16] add .dockerignore --- .dockerignore | 102 ++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 102 insertions(+) create mode 100644 .dockerignore diff --git a/.dockerignore b/.dockerignore new file mode 100644 index 0000000..3207eef --- /dev/null +++ b/.dockerignore @@ -0,0 +1,102 @@ +TEMPO_*.nc +tests/*data*/ +.git +.gitignore +.travis.yaml +.swagger-codegen-ignore +tox.ini + +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] +*$py.class + +# C extensions +*.so + +# Distribution / packaging +.Python +env/ +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +*.egg-info/ +.installed.cfg +*.egg + +# PyInstaller +# Usually these files are written by a python script from a template +# before PyInstaller builds the exe, so as to inject date/other infos into it. +*.manifest +*.spec + +# Installer logs +pip-log.txt +pip-delete-this-directory.txt + +# Unit test / coverage reports +htmlcov/ +.tox/ +.coverage +.coverage.* +.cache +nosetests.xml +coverage.xml +*,cover +.hypothesis/ +venv/ +.python-version + +# Translations +*.mo +*.pot + +# Django stuff: +*.log + +# Sphinx documentation +docs/_build/ + +# PyBuilder +target/ + +#Ipython Notebook +.ipynb_checkpoints + +# Intellij project settings +.idea + +# VSCode project settings +.vscode + +# mkdocs documentation +/site + +# mypy +.mypy_cache/ +.dmypy.json +dmypy.json + +# ruff +.ruff_cache/ +# pytest +.pytest_cache/ + +# Pyre type checker +.pyre/ + +# Github integration settings +.github + +# .dockerignore and builder script themselves are not needed by +# docker build. +.dockerignore +build-service From 90a70b1742d61d7598b3750dac466d7db4830d46 Mon Sep 17 00:00:00 2001 From: danielfromearth Date: Tue, 31 Oct 2023 17:15:09 -0400 Subject: [PATCH 03/16] use updated poetry install argument --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 96036d1..9f3398e 100644 --- a/Dockerfile +++ b/Dockerfile @@ -45,7 +45,7 @@ USER dockeruser #install poetry as root USER root RUN poetry config virtualenvs.create false -RUN poetry install --no-dev +RUN poetry install --only main USER dockeruser COPY --chown=dockeruser ./docker-entrypoint.sh docker-entrypoint.sh From 261f0e30f767dcc27d3a5fdeb6f212f0e7510be9 Mon Sep 17 00:00:00 2001 From: danielfromearth Date: Tue, 31 Oct 2023 17:15:23 -0400 Subject: [PATCH 04/16] perform additional apt-get cleanup --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 9f3398e..0dd2850 100644 --- a/Dockerfile +++ b/Dockerfile @@ -10,7 +10,7 @@ RUN apt-get update \ && pip3 install --upgrade pip \ && pip3 install cython \ && pip3 install poetry \ - && apt-get clean + && apt-get clean && rm -rf /var/lib/apt/lists/* # Create a new user From 6e812a12693d5c419d8bfcc68c3a2e35007ca455 Mon Sep 17 00:00:00 2001 From: danielfromearth Date: Tue, 31 Oct 2023 17:15:42 -0400 Subject: [PATCH 05/16] remove extra user switching from Dockerfile --- Dockerfile | 5 ----- 1 file changed, 5 deletions(-) diff --git a/Dockerfile b/Dockerfile index 0dd2850..b2a3501 100644 --- a/Dockerfile +++ b/Dockerfile @@ -31,19 +31,14 @@ 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 $DIST_PATH #install poetry as root -USER root RUN poetry config virtualenvs.create false RUN poetry install --only main From d9a8ae931989d8cbfe4909754d4c5073f5d3d6e0 Mon Sep 17 00:00:00 2001 From: danielfromearth Date: Wed, 1 Nov 2023 12:07:43 -0400 Subject: [PATCH 06/16] exclude all tests from docker build --- .dockerignore | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.dockerignore b/.dockerignore index 3207eef..90570c8 100644 --- a/.dockerignore +++ b/.dockerignore @@ -1,5 +1,5 @@ TEMPO_*.nc -tests/*data*/ +tests/ .git .gitignore .travis.yaml From 3325b977c4d8a35feb57a51bb07806ebbbd97fec Mon Sep 17 00:00:00 2001 From: danielfromearth Date: Wed, 1 Nov 2023 12:07:52 -0400 Subject: [PATCH 07/16] remove comment --- Dockerfile | 1 - 1 file changed, 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index b2a3501..eedcd8a 100644 --- a/Dockerfile +++ b/Dockerfile @@ -30,7 +30,6 @@ ARG DIST_PATH USER root RUN mkdir -p /worker && chown dockeruser /worker COPY pyproject.toml /worker -# COPY ../pyproject.toml /worker WORKDIR /worker # ENV PYTHONPATH=${PYTHONPATH}:${PWD} From 4c32719784fc3761a89d36b21cec454da81d97f9 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 6 Nov 2023 10:48:08 +0000 Subject: [PATCH 08/16] Bump ruff from 0.1.3 to 0.1.4 Bumps [ruff](https://github.com/astral-sh/ruff) from 0.1.3 to 0.1.4. - [Release notes](https://github.com/astral-sh/ruff/releases) - [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md) - [Commits](https://github.com/astral-sh/ruff/compare/v0.1.3...v0.1.4) --- updated-dependencies: - dependency-name: ruff dependency-type: direct:development update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- poetry.lock | 43 ++++++++++++++++++++++--------------------- pyproject.toml | 2 +- 2 files changed, 23 insertions(+), 22 deletions(-) diff --git a/poetry.lock b/poetry.lock index f53d2bd..4d19a24 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. 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+ _get_item_url, _get_netcdf_urls, - _get_output_bounding_box, _get_output_date_range, ) from batcher.tempo_filename_parser import get_batch_indices @@ -48,14 +48,10 @@ def invoke(self): return self.message, self.process_catalog(self.catalog) - def process_catalog(self, catalog: pystac.Catalog): + def process_catalog(self, catalog: pystac.Catalog) -> list[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)) @@ -63,6 +59,9 @@ def process_catalog(self, catalog: pystac.Catalog): # Quick return if catalog contains no items if len(items) == 0: + result = catalog.clone() + result.id = str(uuid4()) + result.clear_children() return result # # --- Get granule filepaths (urls) --- @@ -79,38 +78,43 @@ def process_catalog(self, catalog: pystac.Catalog): 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() - + # --- Construct a list of STAC Catalogs (which represent each TEMPO scan), + # and each Catalog holds multiple Items (which represent each granule). + catalogs = [] 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 - ) + self.logger.info(f"constructing new pystac.Catalog for batch_id==={batch_id}.") + # Initialize a new, empty Catalog + batch_catalog = catalog.clone() + batch_catalog.id = str(uuid4()) + batch_catalog.clear_children() + batch_catalog.clear_items() for idx, item in enumerate(batch_items): + # Construct a new pystac.Item for each granule in the batch + output_item = Item( + str(uuid4()), + bbox_to_geometry(item.bbox), + item.bbox, + None, + _get_output_date_range([item]), + ) output_item.add_asset( f"data_{idx}", Asset( - batch_urls[idx], - title=batch_urls[idx], + _get_item_url(item), + title=_get_item_url(item), media_type="application/x-netcdf4", roles=["data"], ), ) + batch_catalog.add_item(output_item) - result.add_item(output_item) + self.logger.info("STAC catalog creation for batch_id==={batch_id} complete.") + catalogs.append(batch_catalog) - self.logger.info("STAC catalog creation complete.") + self.logger.info("All STAC catalogs are complete.") - return result + return catalogs except Exception as 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2b5ea7d..dda3535 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -24,7 +24,7 @@ coverage = "^7.3.2" ruff = "^0.1.4" pytest = "^7.4.3" black = "^23.10.1" -mypy = "^1.6.1" +mypy = "^1.7.0" pytest-cov = "^4.1.0" [build-system] From d9574e228a4ad27648e58c33d36837bb4c9ac442 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 13 Nov 2023 13:54:21 +0000 Subject: [PATCH 12/16] Bump ruff from 0.1.4 to 0.1.5 Bumps [ruff](https://github.com/astral-sh/ruff) from 0.1.4 to 0.1.5. - [Release notes](https://github.com/astral-sh/ruff/releases) - [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md) - [Commits](https://github.com/astral-sh/ruff/compare/v0.1.4...v0.1.5) --- updated-dependencies: - dependency-name: ruff dependency-type: direct:development update-type: version-update:semver-patch ... 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[Release notes](https://github.com/psf/black/releases) - [Changelog](https://github.com/psf/black/blob/main/CHANGES.md) - [Commits](https://github.com/psf/black/compare/23.10.1...23.11.0) --- updated-dependencies: - dependency-name: black dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- poetry.lock | 40 ++++++++++++++++++++-------------------- pyproject.toml | 2 +- 2 files changed, 21 insertions(+), 21 deletions(-) diff --git a/poetry.lock b/poetry.lock index 9aec8de..995729b 100644 --- a/poetry.lock +++ b/poetry.lock @@ -2,29 +2,29 @@ [[package]] name = "black" -version = "23.10.1" +version = "23.11.0" description = "The uncompromising code formatter." optional = false python-versions = ">=3.8" files = [ - {file = "black-23.10.1-cp310-cp310-macosx_10_16_arm64.whl", hash = "sha256:ec3f8e6234c4e46ff9e16d9ae96f4ef69fa328bb4ad08198c8cee45bb1f08c69"}, - {file = "black-23.10.1-cp310-cp310-macosx_10_16_x86_64.whl", hash = "sha256:1b917a2aa020ca600483a7b340c165970b26e9029067f019e3755b56e8dd5916"}, - {file = "black-23.10.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:9c74de4c77b849e6359c6f01987e94873c707098322b91490d24296f66d067dc"}, - {file = "black-23.10.1-cp310-cp310-win_amd64.whl", hash = "sha256:7b4d10b0f016616a0d93d24a448100adf1699712fb7a4efd0e2c32bbb219b173"}, - 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[Release notes](https://github.com/nasa/harmony-service-lib-py/releases) - [Commits](https://github.com/nasa/harmony-service-lib-py/compare/v1.0.23...v1.0.24) --- updated-dependencies: - dependency-name: harmony-service-lib dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- poetry.lock | 8 ++++---- pyproject.toml | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/poetry.lock b/poetry.lock index 995729b..e9cae77 100644 --- a/poetry.lock +++ b/poetry.lock @@ -376,13 +376,13 @@ test = ["pytest (>=6)"] [[package]] name = "harmony-service-lib" -version = "1.0.23" +version = "1.0.24" description = "A library for Python-based Harmony services to parse incoming messages, fetch data, stage data, and call back to Harmony" optional = false python-versions = ">=3.8" files = [ - {file = "harmony-service-lib-1.0.23.tar.gz", hash = "sha256:f3c3887a02218f8e2c6cf45d2d730d2a6bf65ea1b7b2ca10533b1562bd74cb17"}, - {file = "harmony_service_lib-1.0.23-py3-none-any.whl", hash = "sha256:4ec97200dd0a03851d17278df73c39b655b273ba5a5da6dbeb267daaa617dd33"}, + {file = "harmony-service-lib-1.0.24.tar.gz", hash = "sha256:5b12456c14b530aaa9b878714bb9754f7403e2f536e98c8649f4379465c8f1e9"}, + {file = "harmony_service_lib-1.0.24-py3-none-any.whl", hash = "sha256:af7ea2ea83e5f1a629940682ffee13249615298c0bade2f2c328bb56c28bb926"}, ] [package.dependencies] @@ -772,4 +772,4 @@ socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"] [metadata] lock-version = "2.0" python-versions = "^3.10" -content-hash = "c01bd08e60d512b7c231dcf3b89031bab2766dcf451f26752e46dd4c3e373dca" +content-hash = "3ce6ddcb59c894f812594bc5e665fb9a3c1edb17e7d5676878658082a4f9c81e" diff --git a/pyproject.toml b/pyproject.toml index 6fd3a27..60c10df 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -13,7 +13,7 @@ packages = [ [tool.poetry.dependencies] python = "^3.10" -harmony-service-lib = "^1.0.23" +harmony-service-lib = "^1.0.24" [tool.poetry.scripts] batchee_harmony = 'batcher.harmony.cli:main' From e80fbc487a97d45f4b5b0e70903541675b00f8e9 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 20 Nov 2023 10:42:28 +0000 Subject: [PATCH 15/16] Bump ruff from 0.1.5 to 0.1.6 Bumps [ruff](https://github.com/astral-sh/ruff) from 0.1.5 to 0.1.6. - [Release notes](https://github.com/astral-sh/ruff/releases) - [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md) - [Commits](https://github.com/astral-sh/ruff/compare/v0.1.5...v0.1.6) --- updated-dependencies: - dependency-name: ruff dependency-type: direct:development update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- poetry.lock | 38 +++++++++++++++++++------------------- pyproject.toml | 2 +- 2 files changed, 20 insertions(+), 20 deletions(-) diff --git a/poetry.lock b/poetry.lock index e9cae77..2f2b01e 100644 --- a/poetry.lock +++ b/poetry.lock @@ -679,28 +679,28 @@ use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"] [[package]] name = "ruff" -version = "0.1.5" +version = "0.1.6" description = "An extremely fast Python linter and code formatter, written in Rust." optional = false python-versions = ">=3.7" files = [ - {file = "ruff-0.1.5-py3-none-macosx_10_7_x86_64.whl", hash = "sha256:32d47fc69261c21a4c48916f16ca272bf2f273eb635d91c65d5cd548bf1f3d96"}, - {file = "ruff-0.1.5-py3-none-macosx_10_9_x86_64.macosx_11_0_arm64.macosx_10_9_universal2.whl", hash = "sha256:171276c1df6c07fa0597fb946139ced1c2978f4f0b8254f201281729981f3c17"}, - {file = "ruff-0.1.5-py3-none-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:17ef33cd0bb7316ca65649fc748acc1406dfa4da96a3d0cde6d52f2e866c7b39"}, - 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[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 +- [issue/41](https://github.com/danielfromearth/batchee/issues/41): Change Adapter output from single to multiple STAC Catalogs ### Deprecated ### Removed ### Fixed