diff --git a/.devcontainer/README.md b/.devcontainer/README.md new file mode 100755 index 00000000..e69de29b diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json new file mode 100755 index 00000000..f2ec933d --- /dev/null +++ b/.devcontainer/devcontainer.json @@ -0,0 +1,74 @@ +// For format details, see https://aka.ms/devcontainer.json. For config options, see the README at: +// https://github.com/microsoft/vscode-dev-containers/tree/v0.245.0/containers/python-3 +{ + "name": "Pdp Compose Dev Container", + "dockerComposeFile": ["../docker/local-run/docker-compose.yaml", "./docker-compose.override.yaml"], + "service": "frontend", + "workspaceFolder": "/workspace", + // Configure tool-specific properties. + "customizations": { + // Configure properties specific to VS Code. + "vscode": { + // Set *default* container specific settings.json values on container create. + "settings": { + "terminal.integrated.defaultProfile.linux": "bash", + "terminal.integrated.profiles.linux": { "bash": { "path": "/bin/bash" } }, + "python.defaultInterpreterPath": "${workspaceFolder}/.venv/bin/python", + "python.linting.enabled": true, + "python.formatting.autopep8Path": "/usr/local/py-utils/bin/autopep8", + "python.formatting.blackPath": "/usr/local/py-utils/bin/black", + "python.formatting.yapfPath": "/usr/local/py-utils/bin/yapf", + "python.linting.banditPath": "/usr/local/py-utils/bin/bandit", + "python.linting.mypyPath": "/usr/local/py-utils/bin/mypy", + "python.linting.pycodestylePath": "/usr/local/py-utils/bin/pycodestyle", + "python.linting.pydocstylePath": "/usr/local/py-utils/bin/pydocstyle", + "python.linting.pylintPath": "/usr/local/py-utils/bin/pylint" + }, + + // VSCODE ONLY: Add the IDs of extensions you want installed when the container is created. + "extensions": [ + "ms-python.python", + "ms-python.vscode-pylance", + "tamasfe.even-better-toml", + "github.vscode-github-actions", + "ms-vscode.makefile-tools" + ] + } + }, + + // Use 'forwardPorts' to make a list of ports inside the container available locally. + //"forwardPorts": [48423], + + // Use 'postCreateCommand' to run commands after the container is created. + "postCreateCommand": "bash ./.devcontainer/post-install.sh", + "postStartCommand": "bash ./.devcontainer/post-start.sh", + + "features": { + "docker-in-docker": "latest", + //"ghcr.io/devcontainers/features/git:1": {}, + // add python to container + "ghcr.io/devcontainers/features/python:1": { + "version": "3.11" + } + }, + // Comment out to connect as root instead. More info: https://aka.ms/vscode-remote/containers/non-root. + // PDP specific: this is the default user in the pdp-base-minimal container, I can't seem to work out + // how to override. It may not be necessary but it might be nice to centralize on a standard user. + "remoteUser": "dockremap", + + "remoteEnv": { + // "PATH": "${containerEnv:PATH}:${containerEnv:HOME}/.local/bin" + }, + "mounts": [ + // Re-use local SSH keys (useful if you use SSH keys for Git repo access or other SSH work) + "source=${localEnv:HOME}/.ssh,target=/home/vscode/.ssh,type=bind,consistency=cached", + // Re-use local Git configuration + "source=${localEnv:HOME}/.gitconfig,target=/home/vscode/.gitconfig,type=bind,consistency=cached" + ], + + // "runArgs": [ + // // allow container to be treated with no network isolation + // "--network=host", + // // give a nicer name to the container + // "--name", "${localEnv:USER}_pdp_devcontainer"] + } \ No newline at end of file diff --git a/.devcontainer/docker-compose.override.yaml b/.devcontainer/docker-compose.override.yaml new file mode 100755 index 00000000..c026bc59 --- /dev/null +++ b/.devcontainer/docker-compose.override.yaml @@ -0,0 +1,6 @@ +version: '3' +services: + frontend: + entrypoint: ["/workspace/.devcontainer/entry-fe.sh"] + volumes: + - ../../:/workspace \ No newline at end of file diff --git a/.devcontainer/entry-fe.sh b/.devcontainer/entry-fe.sh new file mode 100755 index 00000000..7658ed01 --- /dev/null +++ b/.devcontainer/entry-fe.sh @@ -0,0 +1,2 @@ +#!/bin/sh +/bin/sh -c "while sleep 1000; do :; done" \ No newline at end of file diff --git a/.devcontainer/post-install.sh b/.devcontainer/post-install.sh new file mode 100755 index 00000000..ceee53e3 --- /dev/null +++ b/.devcontainer/post-install.sh @@ -0,0 +1,19 @@ +#!/bin/bash +set -ex + +## +## Create some aliases +## +echo 'alias ll="ls -alF"' >> $HOME/.bashrc +echo 'alias la="ls -A"' >> $HOME/.bashrc +echo 'alias l="ls -CF"' >> $HOME/.bashrc + +# Convenience workspace directory for later use +WORKSPACE_DIR=$(pwd) + +# Set current workspace as safe for git +git config --global --add safe.directory ${WORKSPACE_DIR} + +poetry install + +echo "Done!" \ No newline at end of file diff --git a/.devcontainer/post-start.sh b/.devcontainer/post-start.sh new file mode 100755 index 00000000..16b727b2 --- /dev/null +++ b/.devcontainer/post-start.sh @@ -0,0 +1,5 @@ +#!/bin/bash +set -ex + +# Convenience workspace directory for later use +WORKSPACE_DIR=$(pwd) diff --git a/.env b/.env new file mode 100644 index 00000000..5ea4cc1c --- /dev/null +++ b/.env @@ -0,0 +1,3 @@ +DSN=postgresql://********:********@pgbouncer-dev:5432/pcic_meta +PCDS_DSN=postgresql://********:********@pgbouncer-dev:5432/crmp +ORCA_ROOT=https://services.pacificclimate.org/dev/orca \ No newline at end of file diff --git a/.gitignore b/.gitignore index 8e4d3297..8ce903e7 100644 --- a/.gitignore +++ b/.gitignore @@ -65,3 +65,6 @@ target/ # Passwords *password* +.venv +.cache +.env.test diff --git a/.vscode/launch.json b/.vscode/launch.json new file mode 100755 index 00000000..22edee08 --- /dev/null +++ b/.vscode/launch.json @@ -0,0 +1,23 @@ +{ + // Use IntelliSense to learn about possible attributes. + // Hover to view descriptions of existing attributes. + // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387 + "version": "0.2.0", + "configurations": [ + { + "name": "Pytest: Current File", + "type": "debugpy", + "request": "launch", + "module": "pytest", + "console": "integratedTerminal", + "cwd": "${workspaceFolder}", + "justMyCode": false, + "envFile": "${workspaceFolder}/.env.test", + "args": [ + "${file}", + "-k", + "test_nc_raster_response" + ] + } + ] +} \ No newline at end of file diff --git a/docker/local-run/Dockerfile b/docker/local-run/Dockerfile old mode 100644 new mode 100755 index 8bd84aea..9855d1f9 --- a/docker/local-run/Dockerfile +++ b/docker/local-run/Dockerfile @@ -1,21 +1,64 @@ -FROM pcic/pdp-base-minimal:pdp-python3 -LABEL Maintainer="Rod Glover " +FROM ubuntu:20.04 -USER root +ARG USERNAME=dockremap +ARG USER_UID=1000 +ARG USER_GID=$USER_UID +ARG CODEBASE_DIR=/codebase -# TODO: Move into pdp-base-minimal? -RUN apt-get update && apt-get install -yq wget -# Create directory for supervisord logs -RUN mkdir etc/ +# from https://code.visualstudio.com/remote/advancedcontainers/add-nonroot-user +# Create the user +RUN groupadd --gid $USER_GID $USERNAME \ + && useradd --uid $USER_UID --gid $USER_GID -m $USERNAME \ + # + # [Optional] Add sudo support. Omit if you don't need to install software after connecting. + && apt-get update \ + && apt-get install -y sudo \ + && echo $USERNAME ALL=\(root\) NOPASSWD:ALL > /etc/sudoers.d/$USERNAME \ + && chmod 0440 /etc/sudoers.d/$USERNAME -EXPOSE 8000 +RUN apt-get update && \ + DEBIAN_FRONTEND=noninteractive apt-get install -yq \ + build-essential \ + libhdf5-dev \ + libgdal-dev \ + libnetcdf-dev \ + python3 \ + python3-dev \ + python3-pip \ + git \ + curl \ + && \ + rm -rf /var/lib/apt/lists/* + +# [Optional] Set the default user. Omit if you want to keep the default as root. +USER $USERNAME -USER ${USERNAME} +# Install poetry +RUN curl -sSL https://install.python-poetry.org | python3 - +ENV PATH="/home/$USERNAME/.local/bin:$PATH" # You must mount the local codebase to /codebase -WORKDIR /codebase -ADD *requirements.txt /codebase/ +WORKDIR $CODEBASE_DIR + +# Change some Poetry settings to better deal with working in a container +RUN poetry config cache-dir $CODEBASE_DIR/.cache +RUN poetry config virtualenvs.in-project true + +# Apply gdal environment variables +ENV CPLUS_INCLUDE_PATH /usr/include/gdal +ENV C_INCLUDE_PATH /usr/include/gdal -RUN pip3 install -r requirements.txt -r test_requirements.txt -r deploy_requirements.txt -ENTRYPOINT ./docker/local-run/entrypoint.sh \ No newline at end of file +# Copy project files into /codebase +ADD --chown=${USERNAME}:${GROUPNAME} ../.. . + +# Pre-install initial packages (pip, setuptools, numpy) +# RUN poetry install --only initial +# # Install gdal using pip3 into the Poetry virtualenv +# RUN poetry run pip3 install gdal==3.0.4 +# # Install rest of project +# RUN poetry install + +EXPOSE 8000 +ENTRYPOINT [ "poetry", "run", "gunicorn"] +CMD ["--config", "docker/local-run/gunicorn.conf", "--log-config", "docker/local-run/logging.conf", "pdp.wsgi:frontend"] diff --git a/docker/local-run/docker-compose.yaml b/docker/local-run/docker-compose.yaml index 218e7627..9a58e0a2 100755 --- a/docker/local-run/docker-compose.yaml +++ b/docker/local-run/docker-compose.yaml @@ -1,14 +1,53 @@ -version: '3.2' +version: '3.8' services: - image: - # This service only builds the image common to both frontend and backend. + #image: pcic/pdp-local-run + backend: build: context: ../.. dockerfile: ./docker/local-run/Dockerfile image: pcic/pdp-local-run + container_name: pdp-local-run-be + stdin_open: true + tty: true + env_file: + - common-with-passwords.env + environment: + # Specific to backend + - ORCA_ROOT=http://pdp.localhost:5000/orca + - APP_MODULE=pdp.wsgi:backend + - GUNICORN_WORKER_CLASS=gevent + entrypoint: /codebase/docker/local-run/entrypoint-be.sh +# ports: +# - "30446:8000" # backend + volumes: + # This is to enable installing local versions of other packages from + # your own filesystem. You'll need to update this. Source and target + # could probably be made environment variables. Or it could be + # a relative source path and an impersonal target path such as + # `/local-packages`. + # - type: bind + # source: /home/rglover/code + # target: /home/rglover/code + - type: bind + source: ../.. + target: /codebase + # These bindings are for testing the solution but I've had problems with them when attempting + # to use them in a docker desktop context (They seem to cause the container to hang on startup) + # Alternatively to binding, if using the .devcontainer you can nfs mount them directly. + # - /storage/data/climate/downscale:/storage/data/climate/downscale:ro + # - /storage/data/climate/hydrology:/storage/data/climate/hydrology:ro + # - /storage/data/climate/observations:/storage/data/climate/observations:ro + # - /storage/data/climate/PRISM:/storage/data/climate/PRISM:ro + # - /storage/data/projects/dataportal:/storage/data/projects/dataportal:ro + # - /storage/data/projects/hydrology:/storage/data/projects/hydrology:ro + # - /storage/data/projects/PRISM:/storage/data/projects/PRISM:ro + + frontend: image: pcic/pdp-local-run + depends_on: + - backend container_name: pdp-local-run-fe stdin_open: true tty: true @@ -35,9 +74,9 @@ services: # could probably be made environment variables. Or it could be # a relative source path and an impersonal target path such as # `/local-packages`. - - type: bind - source: /home/rglover/code - target: /home/rglover/code + # - type: bind + # source: /home/rglover/code + # target: /home/rglover/code - type: bind source: ../.. target: /codebase @@ -45,41 +84,6 @@ services: source: ./prism_demo_config.js target: /codebase/pdp/static/js/prism_demo_config.js - backend: - image: pcic/pdp-local-run - container_name: pdp-local-run-be - stdin_open: true - tty: true - env_file: - - common-with-passwords.env - environment: - # Specific to backend - - ORCA_ROOT=http://pdp.localhost:5000/orca - - APP_MODULE=pdp.wsgi:backend - - GUNICORN_WORKER_CLASS=gevent - entrypoint: /codebase/docker/local-run/entrypoint-be.sh -# ports: -# - "30446:8000" # backend - volumes: - # This is to enable installing local versions of other packages from - # your own filesystem. You'll need to update this. Source and target - # could probably be made environment variables. Or it could be - # a relative source path and an impersonal target path such as - # `/local-packages`. - - type: bind - source: /home/rglover/code - target: /home/rglover/code - - type: bind - source: ../.. - target: /codebase - - /storage/data/climate/downscale:/storage/data/climate/downscale:ro - - /storage/data/climate/hydrology:/storage/data/climate/hydrology:ro - - /storage/data/climate/observations:/storage/data/climate/observations:ro - - /storage/data/climate/PRISM:/storage/data/climate/PRISM:ro - - /storage/data/projects/dataportal:/storage/data/projects/dataportal:ro - - /storage/data/projects/hydrology:/storage/data/projects/hydrology:ro - - /storage/data/projects/PRISM:/storage/data/projects/PRISM:ro - pgbouncer: image: edoburu/pgbouncer container_name: pgbouncer-dev diff --git a/docker/local-run/pgbouncer.ini b/docker/local-run/pgbouncer.ini index ca9daeb3..92b137f6 100755 --- a/docker/local-run/pgbouncer.ini +++ b/docker/local-run/pgbouncer.ini @@ -1,5 +1,5 @@ [databases] 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+[build-system] +requires = ["poetry-core"] +build-backend = "poetry.core.masonry.api" + +[tool.poetry] +name = "pdp" +version = "4.4.0" +description = "PCIC's Data Portal (pdp): the server software to run the entire web application" +keywords = [ + "opendap", + "dods", + "dap", + "open", + "data", + "science", + "climate", + "meteorology", + "downscaling", + "modelling", +] +#packages=["pdp", "pdp.portals"] // TODO: work this out +license = "GNU General Public License v3 (GPLv3)" +authors = ["James Hiebert ", "Rod Glover "] +readme = "README.md" +homepage = "http://www.pacificclimate.org/" +repository = "https://github.com/pacificclimate/pdp" +classifiers = [ + "Development Status :: 5 - Production/Stable", + "Environment :: Console", + "Environment :: Web Environment", + "Framework :: Flask", + "Natural Language :: English", + "Intended Audience :: Developers", + "Intended Audience :: Science/Research", + "License :: OSI Approved :: GNU General Public License (GPL)", + "Operating System :: OS Independent", + "Programming Language :: Python", + "Programming Language :: Python :: 2.7", + "Topic :: Internet", + "Topic :: Internet :: WWW/HTTP :: WSGI", + "Topic :: Internet :: WWW/HTTP :: WSGI :: Application", + "Topic :: Scientific/Engineering", + "Topic :: Scientific/Engineering :: Atmospheric Science", + "Topic :: Scientific/Engineering :: GIS", + "Topic :: Software Development :: Libraries :: Python Modules", +] + +# TODO: really? should this just be gunicorn/flask now? +# [tool.poetry.scripts] +# serve = "scripts/rast_serve" + +[[tool.poetry.source]] +name = "pcic-pypi" +url = "https://pypi.pacificclimate.org/simple/" +priority = "supplemental" + +[tool.poetry.group.initial.dependencies] +# These dependencies must be installed before those in any other groups, +# including the main dependencies. This is required to install GDAL 3.0.4. +pip = "22.3.1" +setuptools = "<58" +numpy = "<=1.21" # Required by GDAL 3.0.4, but not declared in that package + +[tool.poetry.dependencies] +python = "~3.8" +pdp-util = { git = "https://github.com/pacificclimate/pdp_util", rev = "generate-metadata" } +Beaker = "^1.9.0" +Flask = "^2.0.3" +Genshi = "0.7.5" +netCDF4 = "1.6.5" +static = "1.1.1" +xlrd = "^1.1.0" +jsmin = "^3.0.1" + +[tool.poetry.group.deploy.dependencies] +gunicorn = "^19.9.0" +GitPython = "^2.1.15" +Sphinx = "^1.8.5" +wheel = "^0.43.0" +twine = "^5.0.0" + +[tool.poetry.group.test.dependencies] +pytest = ">=4.1.1" +"testing.postgresql" = "*" + +[tool.poetry.group.black.dependencies] +black = ">=23.11.0" + +[tool.pytest.ini_options] +markers = [ + "bulk_data: marks tests that use bulk_data set from storage server (deselect with '-m \"not bulk_data\"')", + "crmpdb: marks tests that use a crmp database (deselect with '-m \"not crmpdb\"')", + "local_only: marks tests that will only work on local machines and not in github actions (deselect with '-m \"not local_only\"')", + "slow: marks tests that are slow (deselect with '-m \"not slow\"')", + "veryslow: marks tests that are very slow (deselect with '-m \"not veryslow\"')", +] diff --git a/pytest.ini b/pytest.ini deleted file mode 100644 index 7c44853f..00000000 --- a/pytest.ini +++ /dev/null @@ -1,7 +0,0 @@ -[pytest] -markers = - bulk_data: marks tests that use bulk_data set from storage server (deselect with '-m "not bulk_data"') - crmpdb: marks tests that use a crmp database (deselect with '-m "not crmpdb"') - local_only: marks tests that will only work on local machines and not in github actions (deselect with '-m "not local_only"') - slow: marks tests that are slow (deselect with '-m "not slow"') - veryslow: marks tests that are very slow (deselect with '-m "not veryslow"') diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index c8e9243b..00000000 --- a/requirements.txt +++ /dev/null @@ -1,66 +0,0 @@ -alembic==1.6.5 -asn1crypto==0.24.0 -Beaker==1.9.0 -cached-property==1.5.2 -certifi==2021.5.30 -cftime==1.3.1 -chardet==3.0.4 -click==7.1.2 -coards==1.0.5 -cryptography==3.3.2 -enum34==1.1.6 -Flask==2.0.3 -funcsigs==1.0.2 -# GDAL==3.0.4 -Genshi==0.7.5 -GeoAlchemy==0.7.3 -GeoAlchemy2==0.9.1 -gitdb2==2.0.6 -GitPython==2.1.15 -# h5py==2.7.1 - pre-installed in docker -idna==2.6 -ipaddress==1.0.17 -itsdangerous==2.1.2 -Jinja2==3.0.3 -keyring==10.6.0 -keyrings.alt==3.0 -Mako==1.1.4 -MarkupSafe==2.0 -modelmeta==0.3.0 -nchelpers==5.5.7 -netCDF4==1.3.0 -# numpy==1.16.6 - pre-installed in docker -olefile==0.46 -openid2rp==1.12 -Paste==2.0.3 -git+https://github.com/pacificclimate/pdp_util@generate-metadata # actually using a custom version, will be changed when new release is created -Pillow==4.3.0 -ply==3.10 -psycopg2==2.9.1 -pupynere-pdp==2.0.1 -PyCDS==2.2.1 -PyCRS==1.0.2 -pycrypto==2.6.1 -Pydap==3.2.2 -pydap_extras -# pygobject==3.26.1 - not available, lack doesn't seem to matter -pystache==0.5.4 -python-dateutil==2.6.1 -python-editor==1.0.4 -pytz==2017.3 -PyYAML==5.4.1 -requests==2.25.1 -SecretStorage==2.3.1 -simplejson==3.12.0 -six==1.11.0 -slimit==0.8.1 -smmap==3.0.5 -smmap2==3.0.1 -SQLAlchemy==1.4.3 #added for pydap-extras -sqlparse==0.3.1 -static==1.1.1 -urllib3==1.26.5 -WebOb==1.8.7 -Werkzeug==2.0.1 -XlsxWriter==1.3.8 -xlwt==1.3.0 diff --git a/test_requirements.txt b/test_requirements.txt deleted file mode 100644 index 9f9db413..00000000 --- a/test_requirements.txt +++ /dev/null @@ -1,9 +0,0 @@ -beautifulsoup4==4.6.0 -configparser==4.0.2 -flake8==3.5.0 -mccabe==0.6.1 -py==1.10.0 -pycodestyle==2.3.1 -pyflakes==1.6.0 -pytest==3.2.5 -xlrd==1.1.0