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Posted to commits@sdap.apache.org by rk...@apache.org on 2024/03/20 15:55:32 UTC
(incubator-sdap-nexus) branch develop updated: Merge master into develop post-1.2.0 release (#305)
This is an automated email from the ASF dual-hosted git repository.
rkk pushed a commit to branch develop
in repository https://gitbox.apache.org/repos/asf/incubator-sdap-nexus.git
The following commit(s) were added to refs/heads/develop by this push:
new 0071e43 Merge master into develop post-1.2.0 release (#305)
0071e43 is described below
commit 0071e4367f84b1f293e86e6bb6cfeb5b4a137575
Author: Riley Kuttruff <72...@users.noreply.github.com>
AuthorDate: Wed Mar 20 08:55:27 2024 -0700
Merge master into develop post-1.2.0 release (#305)
* Update .asf.yaml (#293)
Co-authored-by: rileykk <ri...@jpl.nasa.gov>
* domspurge patch (#280)
* Fix delete query to account for PK update
* Fixed mistake in domspurge readme
---------
Co-authored-by: rileykk <ri...@jpl.nasa.gov>
* Patch: Made conda dep changes accidentally omitted from geos PR
* SDAP-511 - Switch package manager to poetry (#301)
* Redid branch w/ correct base
I tried to just rebase but it didn't work properly
* Changelogs
* Delete old dockerfile
* Removed old conda install files
* Removed version.txt to just use pyproject.toml
---------
Co-authored-by: rileykk <ri...@jpl.nasa.gov>
* pyproject.toml dependency updates for Zarr
---------
Co-authored-by: rileykk <ri...@jpl.nasa.gov>
Co-authored-by: Stepheny Perez <sk...@users.noreply.github.com>
---
.gitignore | 2 +
CHANGELOG.md | 3 +-
VERSION.txt | 1 -
analysis/conda-requirements.txt | 37 -
analysis/package-list.txt | 68 -
analysis/setup.py | 82 -
analysis/webservice/webapp.py | 25 +-
data-access/requirements.txt | 31 -
data-access/setup.py | 55 -
docker/nexus-webapp/Dockerfile | 155 +-
docker/nexus-webapp/entrypoint.sh | 133 ++
docker/nexus-webapp/install_conda.sh | 42 -
docker/nexus-webapp/install_nexusproto.sh | 4 +
docker/nexus-webapp/install_python.sh | 48 +
poetry.lock | 2545 +++++++++++++++++++++++++++++
pyproject.toml | 83 +
tools/domspurge/purge.py | 10 +-
17 files changed, 2924 insertions(+), 400 deletions(-)
diff --git a/.gitignore b/.gitignore
index 23f8435..1f6290c 100644
--- a/.gitignore
+++ b/.gitignore
@@ -7,3 +7,5 @@ analysis/webservice/algorithms/doms/domsconfig.ini
data-access/nexustiles/backends/nexusproto/config/datastores.ini
data-access/nexustiles/config/datasets.ini
venv/
+
+dist/
\ No newline at end of file
diff --git a/CHANGELOG.md b/CHANGELOG.md
index ff9e717..5ad70cd 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -50,10 +50,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- Support for deploying on k8s version 1.25:
- Upgraded Cassandra Helm chart dependency version
- Bumped default Cassandra protocol version 3 -> 4 in webapp and tools
-- SDAP-507: Changes to remove `geos` sub-dependency from core image build:
+- SDAP-507: Changes to remove `geos` sub-dependency from core image build (partially superseded by SDAP-511 changes):
- Removed `gdal` and `basemap` as core dependencies
- Moved `shapely` installation in docker build from conda install to pip install
- Disabled `/domsplot` endpoint & commented out references to its source file as it depends on `basemap` and raises `ImportError`s at startup
+- SDAP-511: Switched package management to use Poetry instead of conda/mamba
### Deprecated
### Removed
- SDAP-465: Removed `climatology` directory.
diff --git a/VERSION.txt b/VERSION.txt
deleted file mode 100644
index 867e524..0000000
--- a/VERSION.txt
+++ /dev/null
@@ -1 +0,0 @@
-1.2.0
\ No newline at end of file
diff --git a/analysis/conda-requirements.txt b/analysis/conda-requirements.txt
deleted file mode 100644
index 22dff06..0000000
--- a/analysis/conda-requirements.txt
+++ /dev/null
@@ -1,37 +0,0 @@
-# Licensed to the Apache Software Foundation (ASF) under one or more
-# contributor license agreements. See the NOTICE file distributed with
-# this work for additional information regarding copyright ownership.
-# The ASF licenses this file to You under the Apache License, Version 2.0
-# (the "License"); you may not use this file except in compliance with
-# the License. You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-
-netcdf4==1.5.5.1
-basemap==1.2.2
-scipy==1.6.0
-pyspark==3.2.1
-pytz==2021.1
-utm==0.6.0
-shapely==1.7.1
-backports.functools_lru_cache==1.6.1
-boto3>=1.16.63
-botocore==1.24.21
-pillow==8.1.0
-mpld3=0.5.1
-tornado==6.1
-pyproj==2.6.1.post1
-pyyaml==6.0
-geos==3.8.1
-gdal==3.2.1
-mock==4.0.3
-importlib_metadata==4.11.4
-#singledispatch==3.4.0.3
-schema
diff --git a/analysis/package-list.txt b/analysis/package-list.txt
deleted file mode 100644
index fa7c30b..0000000
--- a/analysis/package-list.txt
+++ /dev/null
@@ -1,68 +0,0 @@
-# Licensed to the Apache Software Foundation (ASF) under one or more
-# contributor license agreements. See the NOTICE file distributed with
-# this work for additional information regarding copyright ownership.
-# The ASF licenses this file to You under the Apache License, Version 2.0
-# (the "License"); you may not use this file except in compliance with
-# the License. You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-
-# This file may be used to create an environment using:
-# $ conda create --name <env> --file <this file>
-# platform: osx-64
-basemap=1.0.7=np111py27_0
-configobj=5.0.6=py27_0
-curl=7.45.0=0
-cycler=0.10.0=py27_0
-freetype=2.5.5=1
-gdal=2.0.0=np111py27_3
-geos=3.4.2=0
-geotiff=1.4.1=0
-hdf4=4.2.11=0
-hdf5=1.8.16=0
-jbig=2.1=0
-jinja2=2.8=py27_1
-jpeg=8d=1
-kealib=1.4.5=2
-libgdal=2.0.0=4
-libnetcdf=4.4.0=1
-libpng=1.6.22=0
-libtiff=4.0.6=2
-markupsafe=0.23=py27_2
-matplotlib=1.5.1=np111py27_0
-mkl=11.3.3=0
-mpld3=0.2=py27_0
-netcdf4=1.2.4=np111py27_0
-numpy=1.11.2=py27_0
-openssl=1.0.2j=0
-pip=9.0.1=py27_1
-proj4=4.9.2=0
-pyface=4.5.2=py27_0
-pygments=2.1.3=py27_0
-pyparsing=2.1.4=py27_0
-pyproj=1.9.5.1=py27_0
-pyqt=4.11.4=py27_4
-python=2.7.12=1
-python-dateutil=2.5.3=py27_0
-pytz=2016.6.1=py27_0
-qt=4.8.7=4
-readline=6.2=2
-scipy=0.17.1=np111py27_0
-setuptools=27.2.0=py27_0
-sip=4.18=py27_0
-six=1.10.0=py27_0
-sqlite=3.13.0=0
-tk=8.5.18=0
-traits=4.5.0=py27_0
-traitsui=4.5.1=py27_0
-wheel=0.29.0=py27_0
-xerces-c=3.1.4=0
-xz=5.2.2=0
-zlib=1.2.8=3
diff --git a/analysis/setup.py b/analysis/setup.py
deleted file mode 100644
index 2e09815..0000000
--- a/analysis/setup.py
+++ /dev/null
@@ -1,82 +0,0 @@
-# Licensed to the Apache Software Foundation (ASF) under one or more
-# contributor license agreements. See the NOTICE file distributed with
-# this work for additional information regarding copyright ownership.
-# The ASF licenses this file to You under the Apache License, Version 2.0
-# (the "License"); you may not use this file except in compliance with
-# the License. You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-
-import setuptools
-from subprocess import check_call, CalledProcessError
-
-try:
- with open('../VERSION.txt', 'r') as f:
- __version__ = f.read()
-except:
- __version__ = None
-
-
-try:
- check_call(['mamba', 'install', '-y', '-c', 'conda-forge', '--file', 'conda-requirements.txt'])
-except (CalledProcessError, IOError) as e:
- print('Failed install with mamba; falling back to conda')
- try:
- check_call(['conda', 'install', '-y', '-c', 'conda-forge', '--file', 'conda-requirements.txt'])
- except (CalledProcessError, IOError) as e:
- raise EnvironmentError("Error installing conda packages", e)
-
-
-setuptools.setup(
- name="nexusanalysis",
- version=__version__,
- url="https://github.com/apache/incubator-sdap-nexus",
-
- author="Team Nexus",
-
- description="NEXUS API.",
- long_description=open('README.md').read(),
- packages=setuptools.find_packages(),
- #packages=[
- # 'webservice',
- # 'webservice.algorithms',
- # 'webservice.algorithms.doms',
- # 'webservice.algorithms_spark',
- # 'webservice.metrics',
- # 'webservice.webmodel',
- # 'webservice.tornado_nexus',
- # 'webservice.nexus_tornado',
- # 'webservice.nexus_tornado.request',
- # 'webservice.nexus_tornado.request.handlers',
- # 'webservice.nexus_tornado.request.renderers'
- #],
- package_data={
- 'webservice': [
- 'config/web.ini',
- 'config/algorithms.ini',
- 'apidocs/index.html',
- 'apidocs/openapi.yml',
- 'apidocs/dataset-populate.js',
- 'config/scheduler.xml'
- ],
- 'webservice.algorithms.doms': ['domsconfig.ini.default'],
- },
- data_files=[
- ('static', ['static/index.html'])
- ],
- platforms='any',
- python_requires='~=3.8',
- classifiers=[
- 'Development Status :: 1 - Pre-Alpha',
- 'Intended Audience :: Developers',
- 'Operating System :: OS Independent',
- 'Programming Language :: Python :: 2.7',
- ]
-)
diff --git a/analysis/webservice/webapp.py b/analysis/webservice/webapp.py
index e060d3c..0549863 100644
--- a/analysis/webservice/webapp.py
+++ b/analysis/webservice/webapp.py
@@ -27,6 +27,27 @@ from webservice.redirect import RemoteCollectionMatcher
from webservice.nexus_tornado.app_builders import NexusAppBuilder
from webservice.nexus_tornado.app_builders import RedirectAppBuilder
+try:
+ from importlib.metadata import version as _version
+ from importlib.metadata import files as _files
+except ImportError:
+ from importlib_metadata import version as _version
+
+try:
+ __version__ = _version('sdap-nexus')
+except Exception:
+ __version__ = 'Cannot be determined'
+
+banner = [
+ '',
+ ' ____ ____ _ ____ | ',
+ '/ ___|| _ \\ / \\ | _ \\ | Apache SDAP (TM)',
+ '\\___ \\| | | |/ _ \\ | |_) | | Science Data Analytics Platform',
+ f' ___) | |_| / ___ \\| __/ | Version: {__version__}',
+ '|____/|____/_/ \\_\\_| | ',
+ ''
+]
+
def inject_args_in_config(args, config):
"""
@@ -49,7 +70,6 @@ def inject_args_in_config(args, config):
def main():
-
logging.basicConfig(
level=logging.DEBUG,
format='%(asctime)s - %(name)s - %(levelname)s - %(message)s',
@@ -58,6 +78,9 @@ def main():
log = logging.getLogger(__name__)
+ for line in banner:
+ log.info(line)
+
web_config = configparser.RawConfigParser()
web_config.read_file(open(os.path.join(os.path.dirname(__file__), "config", "web.ini")))
diff --git a/data-access/requirements.txt b/data-access/requirements.txt
deleted file mode 100644
index 05b7894..0000000
--- a/data-access/requirements.txt
+++ /dev/null
@@ -1,31 +0,0 @@
-# Licensed to the Apache Software Foundation (ASF) under one or more
-# contributor license agreements. See the NOTICE file distributed with
-# this work for additional information regarding copyright ownership.
-# The ASF licenses this file to You under the Apache License, Version 2.0
-# (the "License"); you may not use this file except in compliance with
-# the License. You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-numpy==1.24.3
-cassandra-driver==3.24.0
-pysolr==3.9.0
-elasticsearch==8.3.1
-urllib3==1.26.2
-requests
-nexusproto
-Shapely
-s3fs==2022.5.0
-fsspec==2022.5.0
-botocore==1.24.21
-aiohttp==3.8.1
-xarray~=2022.3.0
-zarr>=2.11.3
-pandas<2.1.0rc0 # Temporary restriction because 2.1.0rc0 fails to build
-
diff --git a/data-access/setup.py b/data-access/setup.py
deleted file mode 100644
index e539e1e..0000000
--- a/data-access/setup.py
+++ /dev/null
@@ -1,55 +0,0 @@
-# Licensed to the Apache Software Foundation (ASF) under one or more
-# contributor license agreements. See the NOTICE file distributed with
-# this work for additional information regarding copyright ownership.
-# The ASF licenses this file to You under the Apache License, Version 2.0
-# (the "License"); you may not use this file except in compliance with
-# the License. You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-import setuptools
-from setuptools import setup
-
-try:
- with open('../VERSION.txt', 'r') as f:
- __version__ = f.read()
-except:
- __version__ = None
-
-
-with open('requirements.txt') as f:
- pip_requirements = f.readlines()
-
-setup(
- name="nexus-data-access",
- version=__version__,
- url="https://github.com/apache/incubator-sdap-nexus",
-
- author="Team Nexus",
-
- description="NEXUS API.",
- long_description=open('README.md').read(),
-
- packages=setuptools.find_packages(), # ['nexustiles', 'nexustiles.model', 'nexustiles.dao'],
- package_data={
- 'nexustiles':
- ['config/datasets.ini.default', 'config/datasets.ini'],
- 'nexustiles.backends.nexusproto':
- ['config/datastores.ini.default', 'config/datastores.ini']
- },
- platforms='any',
- python_requires='~=3.8',
- install_requires=pip_requirements,
- classifiers=[
- 'Development Status :: 1 - Pre-Alpha',
- 'Intended Audience :: Developers',
- 'Operating System :: OS Independent',
- 'Programming Language :: Python :: 2.7',
- ],
- zip_safe=False
-)
diff --git a/docker/nexus-webapp/Dockerfile b/docker/nexus-webapp/Dockerfile
index c38c5f2..99c7acc 100644
--- a/docker/nexus-webapp/Dockerfile
+++ b/docker/nexus-webapp/Dockerfile
@@ -13,98 +13,95 @@
# See the License for the specific language governing permissions and
# limitations under the License.
-FROM nexusjpl/alpine-pyspark:3.1.1
+FROM eclipse-temurin:8
+COPY --chmod=755 docker/nexus-webapp/install_python.sh /tmp/install_python.sh
-MAINTAINER Apache SDAP "dev@sdap.apache.org"
+# Install python
+RUN /tmp/install_python.sh
+RUN ln -s /opt/python/3.9.7/bin/python3.9 /opt/python/3.9.7/bin/python
+ENV PATH="/opt/python/3.9.7/bin:$PATH"
-ARG CONDA_VERSION="4.7.12.1"
-ARG CONDA_MD5="81c773ff87af5cfac79ab862942ab6b3"
-ARG CONDA_DIR="/opt/conda"
-
-ENV \
- PYTHONPATH=/opt/conda/share/py4j/py4j0.10.9.2.jar \
- NEXUS_SRC=/tmp/incubator-sdap-nexus \
- PROJ_LIB=/opt/conda/lib/python3.8/site-packages/pyproj/data \
- PATH="$CONDA_DIR/bin:$PATH" \
+# Python & Poetry env vars
+ENV PYTHONUNBUFFERED=1 \
+ # prevents python creating .pyc files
PYTHONDONTWRITEBYTECODE=1 \
- SPARK_HOME=/opt/spark \
- PYSPARK_DRIVER_PYTHON=/opt/conda/bin/python3.8 \
- PYSPARK_PYTHON=/opt/conda/bin/python3.8 \
- LD_LIBRARY_PATH=/usr/lib \
- REQUESTS_CA_BUNDLE=/etc/ssl/certs/ca-certificates.crt
-
-RUN apk add --update --no-cache \
- bzip2 \
- gcc \
- git \
- mesa-gl \
- wget \
- curl \
- which \
- python3 \
- bash==4.4.19-r1 \
- libc-dev \
- libressl2.7-libcrypto
-
-RUN apk upgrade musl
-
-WORKDIR /tmp
-
-RUN apk del libc6-compat
-RUN apk --no-cache add wget zlib && \
- wget -q -O /etc/apk/keys/sgerrand.rsa.pub https://alpine-pkgs.sgerrand.com/sgerrand.rsa.pub && \
- wget https://github.com/sgerrand/alpine-pkg-glibc/releases/download/2.30-r0/glibc-2.30-r0.apk && \
- apk add glibc-2.30-r0.apk && \
- ln -s /lib/libz.so.1 /usr/glibc-compat/lib/ && \
- ln -s /lib/libc.musl-x86_64.so.1 /usr/glibc-compat/lib && \
- ln -s /usr/lib/libgcc_s.so.1 /usr/glibc-compat/lib
-
-COPY docker/nexus-webapp/install_conda.sh ./install_conda.sh
-RUN /tmp/install_conda.sh
-
-RUN conda install -c conda-forge python=3.8.15=h257c98d_0_cpython tqdm=4.64.1=py38h06a4308_0 mamba && conda clean -afy
-
-RUN cd /usr/lib && ln -s libcom_err.so.2 libcom_err.so.3 && \
- cd /opt/conda/lib && \
- ln -s libnetcdf.so.11 libnetcdf.so.7 && \
- ln -s libkea.so.1.4.6 libkea.so.1.4.5 && \
- ln -s libhdf5_cpp.so.12 libhdf5_cpp.so.10 && \
- ln -s libjpeg.so.9 libjpeg.so.8
-
-# Change REBUILD_CODE if you want tell Docker not to use cached layers from this line on
+ \
+ # pip
+ PIP_NO_CACHE_DIR=off \
+ PIP_DISABLE_PIP_VERSION_CHECK=on \
+ PIP_DEFAULT_TIMEOUT=100 \
+ \
+ # poetry
+ # https://python-poetry.org/docs/configuration/#using-environment-variables
+ POETRY_VERSION=1.8.1 \
+ # make poetry install to this location
+ POETRY_HOME="/opt/poetry" \
+ # make poetry create the virtual environment in the project's root
+ # it gets named `.venv`
+ POETRY_VIRTUALENVS_IN_PROJECT=true \
+ # do not ask any interactive question
+ POETRY_NO_INTERACTION=1 \
+ PYSETUP_PATH="/opt/pysetup" \
+ \
+ VENV_PATH="/incubator-sdap-nexus/.venv" \
+ POETRY_CACHE_DIR="/opt/.cache/poetry"
+
+# Edit this to rebuild everything from this point
ARG REBUILD_CODE=0
-ARG BUILD_NEXUSPROTO
-
-ARG APACHE_NEXUSPROTO=https://github.com/apache/incubator-sdap-nexusproto.git
-ARG APACHE_NEXUSPROTO_BRANCH=master
-
-COPY docker/nexus-webapp/install_nexusproto.sh ./install_nexusproto.sh
-RUN /tmp/install_nexusproto.sh $APACHE_NEXUSPROTO $APACHE_NEXUSPROTO_BRANCH
-
-COPY VERSION.txt /incubator-sdap-nexus/VERSION.txt
+WORKDIR /incubator-sdap-nexus
+COPY poetry.lock pyproject.toml ./
COPY data-access /incubator-sdap-nexus/data-access
COPY analysis /incubator-sdap-nexus/analysis
COPY tools /incubator-sdap-nexus/tools
+COPY docker/nexus-webapp/install_nexusproto.sh /tmp/install_nexusproto.sh
+COPY docker/nexus-webapp/entrypoint.sh /opt/entrypoint.sh
-WORKDIR /incubator-sdap-nexus/data-access
-RUN python3 setup.py install clean
+# Copy readme + ASF legal files
+COPY README.md README DISCLAIMER LICENSE NOTICE ./
-WORKDIR /incubator-sdap-nexus/analysis
-RUN python3 setup.py install clean && mamba clean -afy
+ENV PATH="$POETRY_HOME/bin:$VENV_PATH/bin:$PATH"
-RUN pip install shapely==1.7.1
+# Install additional dependencies for image
+RUN apt-get update && \
+ apt-get install --no-install-recommends -y proj-bin tini && \
+ apt-get clean && \
+ rm -rf /var/lib/apt/lists/*
-WORKDIR /incubator-sdap-nexus/tools/deletebyquery
-ARG CASS_DRIVER_BUILD_CONCURRENCY=8
-RUN pip3 install cassandra-driver==3.20.1 pyspark py4j
-RUN pip3 install -r requirements.txt
-RUN pip3 install cython
+# Install poetry, install project, cleanup, and remove poetry install from layer
+RUN curl -sSL https://install.python-poetry.org -o /tmp/install_poetry.py && \
+ python /tmp/install_poetry.py && \
+ poetry install --no-dev && \
+ rm -rf $POETRY_CACHE_DIR && \
+ python /tmp/install_poetry.py --uninstall && \
+ rm /tmp/install_poetry.py
-WORKDIR /incubator-sdap-nexus
+ARG REBUILD_CODE=1
+
+ARG BUILD_NEXUSPROTO
+
+ARG APACHE_NEXUSPROTO=https://github.com/apache/incubator-sdap-nexusproto.git
+ARG APACHE_NEXUSPROTO_BRANCH=master
+
+RUN /tmp/install_nexusproto.sh $APACHE_NEXUSPROTO $APACHE_NEXUSPROTO_BRANCH
+
+# Spark, Nexus, etc env vars
+ENV \
+ PYTHONPATH=/incubator-sdap-nexus/.venv/share/py4j/py4j0.10.9.3.jar \
+ NEXUS_SRC=/tmp/incubator-sdap-nexus \
+ \
+# PROJ_LIB=/opt/conda/lib/python3.8/site-packages/pyproj/data \
+ PATH="$POETRY_HOME/bin:$VENV_PATH/bin:/opt/python/3.9.7/bin:$PATH" \
+ SPARK_HOME=/incubator-sdap-nexus/.venv/lib/python3.9/site-packages/pyspark \
+ PYSPARK_DRIVER_PYTHON=/incubator-sdap-nexus/.venv/bin/python3.9 \
+ PYSPARK_PYTHON=/incubator-sdap-nexus/.venv/bin/python3.9 \
+ LD_LIBRARY_PATH=/usr/lib \
+ REQUESTS_CA_BUNDLE=/etc/ssl/certs/ca-certificates.crt
+
+# This image has k8s client jar version 5.4.1, idk if we should force-install 4.12.0 or if it's even needed anymore...
+#RUN rm $SPARK_HOME/jars/kubernetes-client-4.12.0.jar
+#ADD https://repo1.maven.org/maven2/io/fabric8/kubernetes-client/4.12.0/kubernetes-client-4.12.0.jar $SPARK_HOME/jars
-# Upgrade kubernetes client jar from the default version
-RUN rm /opt/spark/jars/kubernetes-client-4.12.0.jar
-ADD https://repo1.maven.org/maven2/io/fabric8/kubernetes-client/4.12.0/kubernetes-client-4.12.0.jar /opt/spark/jars
+ENTRYPOINT ["/opt/entrypoint.sh"]
diff --git a/docker/nexus-webapp/entrypoint.sh b/docker/nexus-webapp/entrypoint.sh
new file mode 100755
index 0000000..ba5d17b
--- /dev/null
+++ b/docker/nexus-webapp/entrypoint.sh
@@ -0,0 +1,133 @@
+#!/bin/bash
+#
+# Licensed to the Apache Software Foundation (ASF) under one or more
+# contributor license agreements. See the NOTICE file distributed with
+# this work for additional information regarding copyright ownership.
+# The ASF licenses this file to You under the Apache License, Version 2.0
+# (the "License"); you may not use this file except in compliance with
+# the License. You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
+# echo commands to the terminal output
+set -ex
+
+# Check whether there is a passwd entry for the container UID
+myuid=$(id -u)
+mygid=$(id -g)
+# turn off -e for getent because it will return error code in anonymous uid case
+set +e
+uidentry=$(getent passwd $myuid)
+set -e
+
+# If there is no passwd entry for the container UID, attempt to create one
+if [ -z "$uidentry" ] ; then
+ if [ -w /etc/passwd ] ; then
+ echo "$myuid:x:$myuid:$mygid:anonymous uid:$SPARK_HOME:/bin/false" >> /etc/passwd
+ else
+ echo "Container ENTRYPOINT failed to add passwd entry for anonymous UID"
+ fi
+fi
+
+SPARK_K8S_CMD="$1"
+case "$SPARK_K8S_CMD" in
+ driver | driver-py | driver-r | executor)
+ shift 1
+ ;;
+ "")
+ ;;
+ *)
+ echo "Non-spark-on-k8s command provided, proceeding in pass-through mode..."
+ exec /usr/bin/tini -s -- "$@"
+ ;;
+esac
+
+SPARK_CLASSPATH="$SPARK_CLASSPATH:${SPARK_HOME}/jars/*"
+env | grep SPARK_JAVA_OPT_ | sort -t_ -k4 -n | sed 's/[^=]*=\(.*\)/\1/g' > /tmp/java_opts.txt
+readarray -t SPARK_EXECUTOR_JAVA_OPTS < /tmp/java_opts.txt
+
+if [ -n "$SPARK_EXTRA_CLASSPATH" ]; then
+ SPARK_CLASSPATH="$SPARK_CLASSPATH:$SPARK_EXTRA_CLASSPATH"
+fi
+
+if [ -n "$PYSPARK_FILES" ]; then
+ PYTHONPATH="$PYTHONPATH:$PYSPARK_FILES"
+fi
+
+PYSPARK_ARGS=""
+if [ -n "$PYSPARK_APP_ARGS" ]; then
+ PYSPARK_ARGS="$PYSPARK_APP_ARGS"
+fi
+
+R_ARGS=""
+if [ -n "$R_APP_ARGS" ]; then
+ R_ARGS="$R_APP_ARGS"
+fi
+
+if [ "$PYSPARK_MAJOR_PYTHON_VERSION" == "2" ]; then
+ pyv="$(python -V 2>&1)"
+ export PYTHON_VERSION="${pyv:7}"
+ export PYSPARK_PYTHON="python"
+ export PYSPARK_DRIVER_PYTHON="python"
+elif [ "$PYSPARK_MAJOR_PYTHON_VERSION" == "3" ]; then
+ pyv3="$(python3 -V 2>&1)"
+ export PYTHON_VERSION="${pyv3:7}"
+ export PYSPARK_PYTHON="python3"
+ export PYSPARK_DRIVER_PYTHON="python3"
+fi
+
+case "$SPARK_K8S_CMD" in
+ driver)
+ CMD=(
+ "$SPARK_HOME/bin/spark-submit"
+ --conf "spark.driver.bindAddress=$SPARK_DRIVER_BIND_ADDRESS"
+ --deploy-mode client
+ "$@"
+ )
+ ;;
+ driver-py)
+ CMD=(
+ "$SPARK_HOME/bin/spark-submit"
+ --conf "spark.driver.bindAddress=$SPARK_DRIVER_BIND_ADDRESS"
+ --deploy-mode client
+ "$@" $PYSPARK_PRIMARY $PYSPARK_ARGS
+ )
+ ;;
+ driver-r)
+ CMD=(
+ "$SPARK_HOME/bin/spark-submit"
+ --conf "spark.driver.bindAddress=$SPARK_DRIVER_BIND_ADDRESS"
+ --deploy-mode client
+ "$@" $R_PRIMARY $R_ARGS
+ )
+ ;;
+ executor)
+ CMD=(
+ ${JAVA_HOME}/bin/java
+ "${SPARK_EXECUTOR_JAVA_OPTS[@]}"
+ -Xms$SPARK_EXECUTOR_MEMORY
+ -Xmx$SPARK_EXECUTOR_MEMORY
+ -cp "$SPARK_CLASSPATH"
+ org.apache.spark.executor.CoarseGrainedExecutorBackend
+ --driver-url $SPARK_DRIVER_URL
+ --executor-id $SPARK_EXECUTOR_ID
+ --cores $SPARK_EXECUTOR_CORES
+ --app-id $SPARK_APPLICATION_ID
+ --hostname $SPARK_EXECUTOR_POD_IP
+ )
+ ;;
+
+ *)
+ echo "Unknown command: $SPARK_K8S_CMD" 1>&2
+ exit 1
+esac
+
+# Execute the container CMD under tini for better hygiene
+exec /usr/bin/tini -s -- "${CMD[@]}"
diff --git a/docker/nexus-webapp/install_conda.sh b/docker/nexus-webapp/install_conda.sh
deleted file mode 100755
index 2c2ad37..0000000
--- a/docker/nexus-webapp/install_conda.sh
+++ /dev/null
@@ -1,42 +0,0 @@
-#!/usr/bin/env bash
-# Licensed to the Apache Software Foundation (ASF) under one or more
-# contributor license agreements. See the NOTICE file distributed with
-# this work for additional information regarding copyright ownership.
-# The ASF licenses this file to You under the Apache License, Version 2.0
-# (the "License"); you may not use this file except in compliance with
-# the License. You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-echo "**** install dev packages ****"
-apk add --no-cache --virtual .build-dependencies bash wget
-
-echo "**** get Miniconda ****"
-mkdir -p "$CONDA_DIR"
-wget "http://repo.continuum.io/miniconda/Miniconda3-${CONDA_VERSION}-Linux-x86_64.sh" -O miniconda.sh
-echo "$CONDA_MD5 miniconda.sh" | md5sum -c
-
-echo "**** install Miniconda ****"
-bash miniconda.sh -f -b -p "$CONDA_DIR"
-echo "export PATH=$CONDA_DIR/bin:\$PATH" > /etc/profile.d/conda.sh
-
-echo "**** setup Miniconda ****"
-conda update --all --yes
-conda config --set auto_update_conda False
-
-echo "**** cleanup ****"
-apk del --purge .build-dependencies
-rm -f miniconda.sh
-conda clean --all --force-pkgs-dirs --yes
-find "$CONDA_DIR" -follow -type f \( -iname '*.a' -o -iname '*.pyc' -o -iname '*.js.map' \) -delete
-
-echo "**** finalize ****"
-mkdir -p "$CONDA_DIR/locks"
-chmod 777 "$CONDA_DIR/locks"
-conda update -n base conda
\ No newline at end of file
diff --git a/docker/nexus-webapp/install_nexusproto.sh b/docker/nexus-webapp/install_nexusproto.sh
index 08d1894..a4253fd 100755
--- a/docker/nexus-webapp/install_nexusproto.sh
+++ b/docker/nexus-webapp/install_nexusproto.sh
@@ -37,6 +37,10 @@ if [ ! -z ${BUILD_NEXUSPROTO+x} ]; then
rm -rf /root/.gradle
popd
rm -rf nexusproto
+elif [ ! -z ${POETRY_BUILD+x} ]; then
+ poetry add nexusproto
+ echo "Deleting poetry cache"
+ rm -rf $POETRY_CACHE_DIR
else
pip install nexusproto
fi
diff --git a/docker/nexus-webapp/install_python.sh b/docker/nexus-webapp/install_python.sh
new file mode 100755
index 0000000..5b7d842
--- /dev/null
+++ b/docker/nexus-webapp/install_python.sh
@@ -0,0 +1,48 @@
+#!/usr/bin/env bash
+# Licensed to the Apache Software Foundation (ASF) under one or more
+# contributor license agreements. See the NOTICE file distributed with
+# this work for additional information regarding copyright ownership.
+# The ASF licenses this file to You under the Apache License, Version 2.0
+# (the "License"); you may not use this file except in compliance with
+# the License. You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+set -e
+
+echo "Installing build dependencies"
+
+apt-get update
+apt-get upgrade -y
+apt-get install --no-install-recommends -y make build-essential libssl-dev zlib1g-dev libbz2-dev libreadline-dev libsqlite3-dev wget curl llvm libncurses5-dev libncursesw5-dev xz-utils tk-dev liblzma-dev tk-dev libffi-dev
+apt-get clean
+rm -rf /var/lib/apt/lists/*
+
+echo "Downloading & extracting source tarball"
+
+cd /tmp/
+wget https://www.python.org/ftp/python/3.9.7/Python-3.9.7.tgz
+tar xzf Python-3.9.7.tgz
+cd Python-3.9.7
+
+echo "Running install"
+
+./configure --prefix=/opt/python/3.9.7/ --enable-optimizations --with-lto --with-computed-gotos --with-system-ffi
+make -j "$(nproc)"
+make altinstall
+
+echo "Cleaning up install dir"
+
+rm /tmp/Python-3.9.7.tgz
+cd /tmp/
+rm -rf Python-3.9.7
+
+echo "Final steps..."
+
+/opt/python/3.9.7/bin/python3.9 -m pip install --upgrade pip setuptools wheel
diff --git a/poetry.lock b/poetry.lock
new file mode 100644
index 0000000..82d44a3
--- /dev/null
+++ b/poetry.lock
@@ -0,0 +1,2545 @@
+# This file is automatically @generated by Poetry 1.8.1 and should not be changed by hand.
+
+[[package]]
+name = "aiobotocore"
+version = "2.3.4"
+description = "Async client for aws services using botocore and aiohttp"
+optional = false
+python-versions = ">=3.6"
+files = [
+ {file = "aiobotocore-2.3.4-py3-none-any.whl", hash = "sha256:eae059eb51726cee4de2027cfc72bfccc76cf0c229d6b2b08f640e53a568f657"},
+ {file = "aiobotocore-2.3.4.tar.gz", hash = "sha256:6554ebea5764f66f4be544a4fcaa0953ee80e600dd7bd818ba4893d72bf12bfb"},
+]
+
+[package.dependencies]
+aiohttp = ">=3.3.1"
+aioitertools = ">=0.5.1"
+botocore = ">=1.24.21,<1.24.22"
+wrapt = ">=1.10.10"
+
+[package.extras]
+awscli = ["awscli (>=1.22.76,<1.22.77)"]
+boto3 = ["boto3 (>=1.21.21,<1.21.22)"]
+
+[[package]]
+name = "aiohttp"
+version = "3.8.1"
+description = "Async http client/server framework (asyncio)"
+optional = false
+python-versions = ">=3.6"
+files = [
+ {file = "aiohttp-3.8.1-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:1ed0b6477896559f17b9eaeb6d38e07f7f9ffe40b9f0f9627ae8b9926ae260a8"},
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+python-versions = ">=3.8"
+files = [
+ {file = "zipp-3.18.1-py3-none-any.whl", hash = "sha256:206f5a15f2af3dbaee80769fb7dc6f249695e940acca08dfb2a4769fe61e538b"},
+ {file = "zipp-3.18.1.tar.gz", hash = "sha256:2884ed22e7d8961de1c9a05142eb69a247f120291bc0206a00a7642f09b5b715"},
+]
+
+[package.extras]
+docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"]
+
+[metadata]
+lock-version = "2.0"
+python-versions = "~=3.8"
+content-hash = "d19daaa356c410276a8cb00f1ab395b777986d146f61abd345fc1e62a0b8747b"
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000..03b02e0
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,83 @@
+# Licensed to the Apache Software Foundation (ASF) under one or more
+# contributor license agreements. See the NOTICE file distributed with
+# this work for additional information regarding copyright ownership.
+# The ASF licenses this file to You under the Apache License, Version 2.0
+# (the "License"); you may not use this file except in compliance with
+# the License. You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+[tool.poetry]
+name = "sdap-nexus"
+version = "1.2.0"
+description = "Nexus component for Apache SDAP"
+authors = ["SDAP PPMC <de...@sdap.apache.org>"]
+license = "Apache-2.0"
+readme = "README.md"
+packages = [
+ { include = "webservice", from = "analysis" },
+ { include = "nexustiles", from = "data-access" }
+]
+repository = "https://github.com/apache/incubator-sdap-nexus"
+exclude = ["docs", "tests"]
+classifiers=[
+ 'Development Status :: 6 - Mature',
+ 'Intended Audience :: Science/Research',
+ 'Operating System :: OS Independent',
+ 'Programming Language :: Python :: 3.8',
+ "License :: OSI Approved :: Apache Software License"
+]
+
+
+[tool.poetry.dependencies]
+python = "~=3.8"
+netcdf4 = "1.5.5.1"
+scipy = "1.6.0"
+pyspark = "3.2.1"
+py4j = "*"
+pytz = "2021.1"
+utm = "0.6.0"
+shapely = "1.7.1"
+backports-functools-lru-cache = "1.6.1"
+boto3 = ">=1.16.63"
+botocore = "1.24.21"
+pillow = "8.1.0"
+mpld3 = "0.5.1"
+tornado = "6.1"
+pyproj = "^3"
+pyyaml = "6.0"
+importlib_metadata = "4.11.4"
+numpy = "1.24.3"
+cassandra-driver = "3.24.0"
+pysolr = "3.9.0"
+elasticsearch = "8.3.1"
+urllib3 = "1.26.2"
+requests = "*"
+schema = "^0.7.5"
+s3fs = "2022.5.0"
+fsspec = "2022.5.0"
+aiohttp = "3.8.1"
+xarray = "^2022.3.0"
+zarr = "2.11.3"
+pandas = "<2.1.0rc0"
+
+
+[tool.poetry.dev-dependencies]
+mock = "^4.0.3"
+pytest = "^7.1.2"
+pytest-cov = "^3.0.0"
+pytest-integration-mark = "*"
+pytest-json-report = "^1.5.0"
+pytest-metadata = "^2.0.2"
+pylint = "^2.14.5"
+
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"
diff --git a/tools/domspurge/purge.py b/tools/domspurge/purge.py
index d4bb15a..8b13d2d 100644
--- a/tools/domspurge/purge.py
+++ b/tools/domspurge/purge.py
@@ -131,8 +131,11 @@ def main(args, before, keep_completed, keep_failed, purge_all, recreate):
def delete_execution(session, row_id):
- cql_data = session.prepare("""
- DELETE FROM doms_data WHERE execution_id=?;
+ cql_data_primary = session.prepare("""
+ DELETE FROM doms_data WHERE execution_id=? AND is_primary = true;
+ """)
+ cql_data_secondary = session.prepare("""
+ DELETE FROM doms_data WHERE execution_id=? AND is_primary = false;
""")
cql_execution_stats = session.prepare("""
DELETE FROM doms_execution_stats WHERE execution_id=?;
@@ -144,7 +147,8 @@ def delete_execution(session, row_id):
DELETE FROM doms_executions WHERE id=?;
""")
- session.execute(cql_data, (row_id,))
+ session.execute(cql_data_primary, (row_id,))
+ session.execute(cql_data_secondary, (row_id,))
session.execute(cql_execution_stats, (row_id,))
session.execute(cql_params, (row_id,))
session.execute(cql_executions, (row_id,))