From 6ee2a4fc67c4d1588441ae7bb5a2e8040325b959 Mon Sep 17 00:00:00 2001 From: bahill Date: Tue, 18 Jun 2024 14:01:10 -0400 Subject: [PATCH 1/4] adding cffi to toml so that it doesn't get cleaned up during install. (it was getting removed in part due to not using virtual envs, which we don't want in a Docker image) --- orchestration/poetry.lock | 9 +++++---- orchestration/pyproject.toml | 1 + 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/orchestration/poetry.lock b/orchestration/poetry.lock index e1f0e47a..ff182272 100644 --- a/orchestration/poetry.lock +++ b/orchestration/poetry.lock @@ -168,7 +168,7 @@ python-versions = ">=3.6" name = "cffi" version = "1.16.0" description = "Foreign Function Interface for Python calling C code." -category = "dev" +category = "main" optional = false python-versions = ">=3.8" @@ -597,7 +597,7 @@ beautifulsoup4 = "*" [[package]] name = "google-api-core" -version = "2.17.1" +version = "2.19.0" description = "Google API client core library" category = "main" optional = false @@ -608,6 +608,7 @@ google-auth = ">=2.14.1,<3.0.dev0" googleapis-common-protos = ">=1.56.2,<2.0.dev0" grpcio = {version = ">=1.33.2,<2.0dev", optional = true, markers = "extra == \"grpc\""} grpcio-status = {version = ">=1.33.2,<2.0.dev0", optional = true, markers = "extra == \"grpc\""} +proto-plus = ">=1.22.3,<2.0.0dev" protobuf = ">=3.19.5,<3.20.0 || >3.20.0,<3.20.1 || >3.20.1,<4.21.0 || >4.21.0,<4.21.1 || >4.21.1,<4.21.2 || >4.21.2,<4.21.3 || >4.21.3,<4.21.4 || >4.21.4,<4.21.5 || >4.21.5,<5.0.0.dev0" requests = ">=2.18.0,<3.0.0.dev0" @@ -1455,7 +1456,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" name = "pycparser" version = "2.21" description = "C parser in Python" -category = "dev" +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" @@ -2056,7 +2057,7 @@ testing = ["coverage (>=5.0.3)", "zope.event", "zope.testing"] [metadata] lock-version = "1.1" python-versions = "3.9.16" -content-hash = "3843b5b4da4115630ff2d7fa35ec0a3b1c2ca2c3d9fa0860b81359eff735853b" +content-hash = "188d2c1e4fa7c8d434aa39e0854b49e1ff4a606096161d60ac1ecc9b43b04e95" [metadata.files] aiohttp = [] diff --git a/orchestration/pyproject.toml b/orchestration/pyproject.toml index 8ac5e380..bafabcd7 100644 --- a/orchestration/pyproject.toml +++ b/orchestration/pyproject.toml @@ -10,6 +10,7 @@ python = "3.9.16" argo-workflows = "^5.0.0" broad-dagster-utils = "0.6.7" cached-property = "^1.5.2" +cffi = "1.16.0" # TODO: we'll probably want to use just the dagster version here and not the API versions as well # https://github.com/dagster-io/dagster/blob/master/MIGRATION.md#migrating-to-10 dagster = "0.12.14" From 30fad67d1fc06fe6529df9419e9aad2eb0c48b2d Mon Sep 17 00:00:00 2001 From: bahill Date: Tue, 18 Jun 2024 17:24:33 -0400 Subject: [PATCH 2/4] attempting to install poetry in the image so we don't have to do it at run time --- Dockerfile | 2 ++ 1 file changed, 2 insertions(+) diff --git a/Dockerfile b/Dockerfile index ed4bf710..95f6e1a7 100644 --- a/Dockerfile +++ b/Dockerfile @@ -114,6 +114,8 @@ RUN mv /hca_manage /orchestration/. \ && cd /hca-ingest/ # NB sbt test and pytest require that you gcloud auth credentials, so they must be run in the container. +CMD poetry install --no-interaction --no-ansi --no-dev | tee /logs/poetry_install.log + CMD ["bin/bash"] # builds with GitHub Action "Main Validation and Release" ../.github/workflows/build-and-publish-main.yaml From 942eaa6862ebc374717e9da2d7c66c9d80f9ed77 Mon Sep 17 00:00:00 2001 From: bahill Date: Tue, 18 Jun 2024 17:45:06 -0400 Subject: [PATCH 3/4] nevermind - this requires more thought and it only takes a minute to poetry install when you start up the container. Tech_debt for another time. --- Dockerfile | 2 -- 1 file changed, 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index 95f6e1a7..ed4bf710 100644 --- a/Dockerfile +++ b/Dockerfile @@ -114,8 +114,6 @@ RUN mv /hca_manage /orchestration/. \ && cd /hca-ingest/ # NB sbt test and pytest require that you gcloud auth credentials, so they must be run in the container. -CMD poetry install --no-interaction --no-ansi --no-dev | tee /logs/poetry_install.log - CMD ["bin/bash"] # builds with GitHub Action "Main Validation and Release" ../.github/workflows/build-and-publish-main.yaml From 8b7a3de827955bf42a38685ac39c9767fb22e807 Mon Sep 17 00:00:00 2001 From: dsp-fieldeng-bot Date: Wed, 19 Jun 2024 15:31:21 +0000 Subject: [PATCH 4/4] Update requirements.txt --- orchestration/requirements.txt | 2 ++ 1 file changed, 2 insertions(+) diff --git a/orchestration/requirements.txt b/orchestration/requirements.txt index c0f2571a..544c4e4c 100644 --- a/orchestration/requirements.txt +++ b/orchestration/requirements.txt @@ -9,6 +9,7 @@ broad-dagster-utils==0.6.7; python_version >= "3.9" and python_version < "3.10" cached-property==1.5.2 cachetools==5.3.2; python_version >= "3.9" and python_full_version < "3.0.0" and python_version < "3.10" or python_full_version >= "3.6.0" and python_version >= "3.9" and python_version < "3.10" certifi==2023.7.22; python_version >= "3.9" and python_version < "3.10" +cffi==1.16.0; python_version >= "3.8" charset-normalizer==3.3.1; python_version >= "3.9" and python_version < "3.10" and python_full_version >= "3.7.0" click==7.1.2; python_version >= "3.9" and python_full_version < "3.0.0" and python_version < "3.10" or python_version >= "3.9" and python_version < "3.10" and python_full_version >= "3.5.0" colorama==0.4.6; python_version >= "3.9" and python_full_version < "3.0.0" and python_version < "3.10" and platform_system == "Windows" or python_version >= "3.9" and python_version < "3.10" and platform_system == "Windows" and python_full_version >= "3.7.0" @@ -65,6 +66,7 @@ psutil==5.9.6; python_version >= "3.9" and python_full_version < "3.0.0" and pyt psycopg2-binary==2.9.9; python_version >= "3.7" pyasn1-modules==0.3.0; python_version >= "3.9" and python_full_version < "3.0.0" and python_version < "3.10" or python_full_version >= "3.6.0" and python_version >= "3.9" and python_version < "3.10" pyasn1==0.5.0; python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "4" or python_version >= "3.6" and python_version < "4" and python_full_version >= "3.6.0" +pycparser==2.21; python_version >= "3.8" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.8" pyparsing==3.1.1; python_full_version >= "3.6.8" and python_version > "3.0" pyreadline3==3.4.1; sys_platform == "win32" and python_version >= "3.8" and (python_version >= "3.9" and python_full_version < "3.0.0" and python_version < "3.10" or python_version >= "3.9" and python_version < "3.10" and python_full_version >= "3.5.0") python-dateutil==2.8.2; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.3.0")