From 21eac2b85c1e58db50ae55cf89ef58b700b206d6 Mon Sep 17 00:00:00 2001 From: EliseCastle23 Date: Mon, 17 Jul 2023 08:52:19 -0600 Subject: [PATCH 01/54] adding gunicorn instead of uwsgi and modifying the base image to use the new python 3.9 --- Dockerfile | 40 ++++++++++++++---------------- deployment/uwsgi/uwsgi.ini | 36 --------------------------- deployment/wsgi/gunicorn.conf.py | 3 +++ deployment/{uwsgi => wsgi}/wsgi.py | 0 poetry.lock | 6 ++--- pyproject.toml | 1 + 6 files changed, 25 insertions(+), 61 deletions(-) delete mode 100644 deployment/uwsgi/uwsgi.ini create mode 100644 deployment/wsgi/gunicorn.conf.py rename deployment/{uwsgi => wsgi}/wsgi.py (100%) diff --git a/Dockerfile b/Dockerfile index 7f2f4b00..9c1a1f5c 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,22 +1,19 @@ # To run: docker run -v /path/to/wsgi.py:/var/www/indexd/wsgi.py --name=indexd -p 81:80 indexd # To check running container: docker exec -it indexd /bin/bash -FROM quay.io/cdis/python:python3.9-buster-2.0.0 +FROM python3.9-gpe-979 + +USER root ENV appname=indexd -RUN pip install --upgrade pip poetry -RUN apt-get update && apt-get install -y --no-install-recommends \ - build-essential libffi-dev musl-dev gcc libxml2-dev libxslt-dev \ - curl bash git vim +# This one is causing an issue +RUN pip3 install --upgrade poetry + +RUN yum update -y && yum install -y \ + gcc gcc-c++ kernel-devel make libffi-devel libxml2-devel libxslt-devel postgresql-devel python3-devel \ + bash git vim -RUN mkdir -p /var/www/$appname \ - && mkdir -p /var/www/.cache/Python-Eggs/ \ - && mkdir /run/nginx/ \ - && ln -sf /dev/stdout /var/log/nginx/access.log \ - && ln -sf /dev/stderr /var/log/nginx/error.log \ - && chown nginx -R /var/www/.cache/Python-Eggs/ \ - && chown nginx /var/www/$appname EXPOSE 80 @@ -25,25 +22,24 @@ WORKDIR /$appname # copy ONLY poetry artifact, install the dependencies but not indexd # this will make sure than the dependencies is cached COPY poetry.lock pyproject.toml /$appname/ -RUN poetry config virtualenvs.create false \ +RUN poetry config \ && poetry install -vv --no-root --no-dev --no-interaction \ - && poetry show -v + && poetry show -v \ + && poetry add gunicorn # copy source code ONLY after installing dependencies COPY . /$appname -COPY ./deployment/uwsgi/uwsgi.ini /etc/uwsgi/uwsgi.ini -COPY ./deployment/uwsgi/wsgi.py /$appname/wsgi.py -COPY clear_prometheus_multiproc /$appname/clear_prometheus_multiproc +COPY ./deployment/wsgi/wsgi.py /$appname/wsgi.py # install indexd -RUN poetry config virtualenvs.create false \ +RUN poetry config \ && poetry install -vv --no-dev --no-interaction \ && poetry show -v RUN COMMIT=`git rev-parse HEAD` && echo "COMMIT=\"${COMMIT}\"" >$appname/index/version_data.py \ && VERSION=`git describe --always --tags` && echo "VERSION=\"${VERSION}\"" >>$appname/index/version_data.py -# directory where the app can find Alembic files -WORKDIR /indexd - -CMD /dockerrun.sh +# USER nobody +RUN poetry config \ + && poetry add gunicorn +CMD ["poetry run gunicorn -c deployment/uwsgi/gunicorn.conf.py"] diff --git a/deployment/uwsgi/uwsgi.ini b/deployment/uwsgi/uwsgi.ini deleted file mode 100644 index 7e2d7969..00000000 --- a/deployment/uwsgi/uwsgi.ini +++ /dev/null @@ -1,36 +0,0 @@ -[uwsgi] -protocol = uwsgi -socket = /var/run/gen3/uwsgi.sock -buffer-size = 32768 -uid = nginx -gid = nginx -chown-socket = nginx:nginx -chmod-socket = 666 -master = true -harakiri-verbose = true -# No global HARAKIRI, using only user HARAKIRI, because export overwrites it -# Cannot overwrite global HARAKIRI with user's: https://git.io/fjYuD -# harakiri = 45 -; If VIRTUAL_ENV is set then use its value to specify the virtualenv directory -if-env = VIRTUAL_ENV -virtualenv = %(_) -endif = -http-timeout = 45 -socket-timeout = 45 -worker-reload-mercy = 45 -reload-mercy = 45 -mule-reload-mercy = 45 -disable-logging = true -wsgi-file=/indexd/wsgi.py -plugins = python3 -vacuum = true -pythonpath = /indexd/ -stats = 127.0.0.1:9191 -stats-http = true -env = prometheus_multiproc_dir=/var/tmp/uwsgi_flask_metrics -exec-asap = /indexd/clear_prometheus_multiproc /var/tmp/uwsgi_flask_metrics -# Initialize application in worker processes, not master. This prevents the -# workers from all trying to open the same database connections at startup. -lazy = true -lazy-apps = true -listen = 4096 diff --git a/deployment/wsgi/gunicorn.conf.py b/deployment/wsgi/gunicorn.conf.py new file mode 100644 index 00000000..290fbfcd --- /dev/null +++ b/deployment/wsgi/gunicorn.conf.py @@ -0,0 +1,3 @@ +wsgi_app = "deployment.wsgi.wsgi:application" +bind = "0.0.0.0:8000" +workers = 4 diff --git a/deployment/uwsgi/wsgi.py b/deployment/wsgi/wsgi.py similarity index 100% rename from deployment/uwsgi/wsgi.py rename to deployment/wsgi/wsgi.py diff --git a/poetry.lock b/poetry.lock index b70402ba..98afeb91 100644 --- a/poetry.lock +++ b/poetry.lock @@ -181,14 +181,14 @@ resolved_reference = "bdfdeb05e45407e839fd954ce6d195d847cd8024" [[package]] name = "certifi" -version = "2022.12.7" +version = "2023.5.7" description = "Python package for providing Mozilla's CA Bundle." category = "main" optional = false python-versions = ">=3.6" files = [ - {file = "certifi-2022.12.7-py3-none-any.whl", hash = "sha256:4ad3232f5e926d6718ec31cfc1fcadfde020920e278684144551c91769c7bc18"}, - {file = "certifi-2022.12.7.tar.gz", hash = "sha256:35824b4c3a97115964b408844d64aa14db1cc518f6562e8d7261699d1350a9e3"}, + {file = "certifi-2023.5.7-py3-none-any.whl", hash = "sha256:c6c2e98f5c7869efca1f8916fed228dd91539f9f1b444c314c06eef02980c716"}, + {file = "certifi-2023.5.7.tar.gz", hash = "sha256:0f0d56dc5a6ad56fd4ba36484d6cc34451e1c6548c61daad8c320169f91eddc7"}, ] [[package]] diff --git a/pyproject.toml b/pyproject.toml index 49bc2005..59138308 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -15,6 +15,7 @@ alembic = "^1.9.4" authutils = "^6.0.0" cdislogging = "^1.0.0" cdiserrors = "^1.0.0" +certifi = "2023.5.7" doiclient = {git = "https://github.com/uc-cdis/doiclient", rev = "1.0.0"} dosclient = {git = "https://github.com/uc-cdis/dosclient", rev = "1.1.0"} gen3authz = "^1.0.4" From a306bbe891c2611b4e6425fc28fd158dddbbfc78 Mon Sep 17 00:00:00 2001 From: EliseCastle23 Date: Mon, 17 Jul 2023 09:03:33 -0600 Subject: [PATCH 02/54] resetting the lock and toml files as I changed to try an resolve a poetry error --- poetry.lock | 6 +++--- pyproject.toml | 1 - 2 files changed, 3 insertions(+), 4 deletions(-) diff --git a/poetry.lock b/poetry.lock index 98afeb91..b70402ba 100644 --- a/poetry.lock +++ b/poetry.lock @@ -181,14 +181,14 @@ resolved_reference = "bdfdeb05e45407e839fd954ce6d195d847cd8024" [[package]] name = "certifi" -version = "2023.5.7" +version = "2022.12.7" description = "Python package for providing Mozilla's CA Bundle." category = "main" optional = false python-versions = ">=3.6" files = [ - {file = "certifi-2023.5.7-py3-none-any.whl", hash = "sha256:c6c2e98f5c7869efca1f8916fed228dd91539f9f1b444c314c06eef02980c716"}, - {file = "certifi-2023.5.7.tar.gz", hash = "sha256:0f0d56dc5a6ad56fd4ba36484d6cc34451e1c6548c61daad8c320169f91eddc7"}, + {file = "certifi-2022.12.7-py3-none-any.whl", hash = "sha256:4ad3232f5e926d6718ec31cfc1fcadfde020920e278684144551c91769c7bc18"}, + {file = "certifi-2022.12.7.tar.gz", hash = "sha256:35824b4c3a97115964b408844d64aa14db1cc518f6562e8d7261699d1350a9e3"}, ] [[package]] diff --git a/pyproject.toml b/pyproject.toml index 59138308..49bc2005 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -15,7 +15,6 @@ alembic = "^1.9.4" authutils = "^6.0.0" cdislogging = "^1.0.0" cdiserrors = "^1.0.0" -certifi = "2023.5.7" doiclient = {git = "https://github.com/uc-cdis/doiclient", rev = "1.0.0"} dosclient = {git = "https://github.com/uc-cdis/dosclient", rev = "1.1.0"} gen3authz = "^1.0.4" From d436084befa8fea508fff961ca766161eafb992a Mon Sep 17 00:00:00 2001 From: EliseCastle23 Date: Mon, 17 Jul 2023 14:44:35 -0600 Subject: [PATCH 03/54] changing workers to 1 and adding the Docker cmd --- Dockerfile | 4 +++- deployment/wsgi/gunicorn.conf.py | 2 +- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index 9c1a1f5c..bb27973f 100644 --- a/Dockerfile +++ b/Dockerfile @@ -42,4 +42,6 @@ RUN COMMIT=`git rev-parse HEAD` && echo "COMMIT=\"${COMMIT}\"" >$appname/index/v # USER nobody RUN poetry config \ && poetry add gunicorn -CMD ["poetry run gunicorn -c deployment/uwsgi/gunicorn.conf.py"] + + +CMD ["poetry run gunicorn -c deployment/wsgi/gunicorn.conf.py"] diff --git a/deployment/wsgi/gunicorn.conf.py b/deployment/wsgi/gunicorn.conf.py index 290fbfcd..045d3619 100644 --- a/deployment/wsgi/gunicorn.conf.py +++ b/deployment/wsgi/gunicorn.conf.py @@ -1,3 +1,3 @@ wsgi_app = "deployment.wsgi.wsgi:application" bind = "0.0.0.0:8000" -workers = 4 +workers = 1 From e76088f9b50a865bbc201ccf016ceefbe7db194b Mon Sep 17 00:00:00 2001 From: EliseCastle23 Date: Tue, 18 Jul 2023 11:45:16 -0600 Subject: [PATCH 04/54] changed the format of the CMD in the Dockerfile, changed the port from 8000 to 80, and changed the base image to point to the "quay" repo --- Dockerfile | 9 ++++----- deployment/wsgi/gunicorn.conf.py | 2 +- 2 files changed, 5 insertions(+), 6 deletions(-) diff --git a/Dockerfile b/Dockerfile index bb27973f..25f256f6 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,7 +1,7 @@ # To run: docker run -v /path/to/wsgi.py:/var/www/indexd/wsgi.py --name=indexd -p 81:80 indexd # To check running container: docker exec -it indexd /bin/bash -FROM python3.9-gpe-979 +FROM quay.io/cdis/python:python3.9-buster-GPE-788 USER root @@ -23,7 +23,7 @@ WORKDIR /$appname # this will make sure than the dependencies is cached COPY poetry.lock pyproject.toml /$appname/ RUN poetry config \ - && poetry install -vv --no-root --no-dev --no-interaction \ + && poetry install -vv --no-root --only main --no-interaction \ && poetry show -v \ && poetry add gunicorn @@ -33,7 +33,7 @@ COPY ./deployment/wsgi/wsgi.py /$appname/wsgi.py # install indexd RUN poetry config \ - && poetry install -vv --no-dev --no-interaction \ + && poetry install -vv --only main --no-interaction \ && poetry show -v RUN COMMIT=`git rev-parse HEAD` && echo "COMMIT=\"${COMMIT}\"" >$appname/index/version_data.py \ @@ -43,5 +43,4 @@ RUN COMMIT=`git rev-parse HEAD` && echo "COMMIT=\"${COMMIT}\"" >$appname/index/v RUN poetry config \ && poetry add gunicorn - -CMD ["poetry run gunicorn -c deployment/wsgi/gunicorn.conf.py"] +CMD ["poetry", "run", "gunicorn", "-c", "deployment/wsgi/gunicorn.conf.py"] diff --git a/deployment/wsgi/gunicorn.conf.py b/deployment/wsgi/gunicorn.conf.py index 045d3619..8be62107 100644 --- a/deployment/wsgi/gunicorn.conf.py +++ b/deployment/wsgi/gunicorn.conf.py @@ -1,3 +1,3 @@ wsgi_app = "deployment.wsgi.wsgi:application" -bind = "0.0.0.0:8000" +bind = "0.0.0.0:80" workers = 1 From a441e9aef15aa86868cc9ec4270afc1e558540ad Mon Sep 17 00:00:00 2001 From: EliseCastle23 Date: Tue, 25 Jul 2023 09:39:43 -0600 Subject: [PATCH 05/54] removing comment and re-building image --- Dockerfile | 1 - 1 file changed, 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 25f256f6..11bcd94c 100644 --- a/Dockerfile +++ b/Dockerfile @@ -7,7 +7,6 @@ USER root ENV appname=indexd -# This one is causing an issue RUN pip3 install --upgrade poetry RUN yum update -y && yum install -y \ From c121d94a99975ff512e9cca068d8d49f08f0a541 Mon Sep 17 00:00:00 2001 From: EliseCastle23 Date: Wed, 26 Jul 2023 14:00:45 -0600 Subject: [PATCH 06/54] Changing the user to "nobody" so the container doesn't run as root. Always set gunicorn to run as user "nobody" --- Dockerfile | 2 ++ deployment/wsgi/gunicorn.conf.py | 2 ++ 2 files changed, 4 insertions(+) diff --git a/Dockerfile b/Dockerfile index 11bcd94c..06f18699 100644 --- a/Dockerfile +++ b/Dockerfile @@ -42,4 +42,6 @@ RUN COMMIT=`git rev-parse HEAD` && echo "COMMIT=\"${COMMIT}\"" >$appname/index/v RUN poetry config \ && poetry add gunicorn +USER nobody + CMD ["poetry", "run", "gunicorn", "-c", "deployment/wsgi/gunicorn.conf.py"] diff --git a/deployment/wsgi/gunicorn.conf.py b/deployment/wsgi/gunicorn.conf.py index 8be62107..ec08941b 100644 --- a/deployment/wsgi/gunicorn.conf.py +++ b/deployment/wsgi/gunicorn.conf.py @@ -1,3 +1,5 @@ wsgi_app = "deployment.wsgi.wsgi:application" bind = "0.0.0.0:80" workers = 1 +user = "nobody" +group = "nobody" From ffc63f84fa34dfc522d764204bec3107d1f2b290 Mon Sep 17 00:00:00 2001 From: EliseCastle23 Date: Mon, 7 Aug 2023 11:12:02 -0600 Subject: [PATCH 07/54] changing the Dockerfile to use user "appuser" instead of "nobody" as it was causing issue. Also, changing the base image. --- Dockerfile | 28 ++++++++++++++-------------- deployment/wsgi/gunicorn.conf.py | 4 ++-- 2 files changed, 16 insertions(+), 16 deletions(-) diff --git a/Dockerfile b/Dockerfile index 06f18699..303a70c4 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,7 +1,7 @@ # To run: docker run -v /path/to/wsgi.py:/var/www/indexd/wsgi.py --name=indexd -p 81:80 indexd # To check running container: docker exec -it indexd /bin/bash -FROM quay.io/cdis/python:python3.9-buster-GPE-788 +FROM quay.io/cdis/python:python3.9-GPE-788 USER root @@ -10,9 +10,8 @@ ENV appname=indexd RUN pip3 install --upgrade poetry RUN yum update -y && yum install -y \ - gcc gcc-c++ kernel-devel make libffi-devel libxml2-devel libxslt-devel postgresql-devel python3-devel \ - bash git vim - + gcc gcc-c++ make kernel-devel libffi-devel libxml2-devel libxslt-devel postgresql-devel python3-devel \ + bash git EXPOSE 80 @@ -21,7 +20,7 @@ WORKDIR /$appname # copy ONLY poetry artifact, install the dependencies but not indexd # this will make sure than the dependencies is cached COPY poetry.lock pyproject.toml /$appname/ -RUN poetry config \ +RUN poetry config virtualenvs.in-project true \ && poetry install -vv --no-root --only main --no-interaction \ && poetry show -v \ && poetry add gunicorn @@ -30,18 +29,19 @@ RUN poetry config \ COPY . /$appname COPY ./deployment/wsgi/wsgi.py /$appname/wsgi.py -# install indexd -RUN poetry config \ - && poetry install -vv --only main --no-interaction \ - && poetry show -v - RUN COMMIT=`git rev-parse HEAD` && echo "COMMIT=\"${COMMIT}\"" >$appname/index/version_data.py \ && VERSION=`git describe --always --tags` && echo "VERSION=\"${VERSION}\"" >>$appname/index/version_data.py -# USER nobody -RUN poetry config \ - && poetry add gunicorn +RUN useradd -ms /bin/bash appuser -USER nobody +RUN chown -R appuser:appuser /$appname +# RUN chown -R appuser:appuser /deployment + +USER appuser + +# install indexd +RUN poetry config virtualenvs.in-project true \ + && poetry install -vv --no-root --only main --no-interaction \ + && poetry show -v CMD ["poetry", "run", "gunicorn", "-c", "deployment/wsgi/gunicorn.conf.py"] diff --git a/deployment/wsgi/gunicorn.conf.py b/deployment/wsgi/gunicorn.conf.py index ec08941b..778ad6d0 100644 --- a/deployment/wsgi/gunicorn.conf.py +++ b/deployment/wsgi/gunicorn.conf.py @@ -1,5 +1,5 @@ wsgi_app = "deployment.wsgi.wsgi:application" bind = "0.0.0.0:80" workers = 1 -user = "nobody" -group = "nobody" +user = "appuser" +group = "appuser" From 03ecf41296a8d7c8f254db780eb663d3acc0d8c1 Mon Sep 17 00:00:00 2001 From: EliseCastle23 Date: Tue, 8 Aug 2023 10:39:43 -0600 Subject: [PATCH 08/54] did a mutli-stage Dockerbuild to reduce image size --- Dockerfile | 46 ++++++++++++++++++++++++++++++---------------- 1 file changed, 30 insertions(+), 16 deletions(-) diff --git a/Dockerfile b/Dockerfile index 303a70c4..aa4c19fb 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,7 +1,7 @@ # To run: docker run -v /path/to/wsgi.py:/var/www/indexd/wsgi.py --name=indexd -p 81:80 indexd # To check running container: docker exec -it indexd /bin/bash -FROM quay.io/cdis/python:python3.9-GPE-788 +FROM quay.io/cdis/python:python3.9-GPE-788 as build-deps USER root @@ -9,21 +9,18 @@ ENV appname=indexd RUN pip3 install --upgrade poetry -RUN yum update -y && yum install -y \ - gcc gcc-c++ make kernel-devel libffi-devel libxml2-devel libxslt-devel postgresql-devel python3-devel \ - bash git - -EXPOSE 80 +RUN yum update -y && yum install -y --setopt install_weak_deps=0 \ + kernel-devel libffi-devel libxml2-devel libxslt-devel postgresql-devel python3-devel shadow-utils \ + git WORKDIR /$appname # copy ONLY poetry artifact, install the dependencies but not indexd -# this will make sure than the dependencies is cached +# this will make sure that the dependencies is cached COPY poetry.lock pyproject.toml /$appname/ RUN poetry config virtualenvs.in-project true \ - && poetry install -vv --no-root --only main --no-interaction \ - && poetry show -v \ - && poetry add gunicorn + && poetry install -vv --no-root --only main --no-interaction\ + && poetry show -v # copy source code ONLY after installing dependencies COPY . /$appname @@ -32,16 +29,33 @@ COPY ./deployment/wsgi/wsgi.py /$appname/wsgi.py RUN COMMIT=`git rev-parse HEAD` && echo "COMMIT=\"${COMMIT}\"" >$appname/index/version_data.py \ && VERSION=`git describe --always --tags` && echo "VERSION=\"${VERSION}\"" >>$appname/index/version_data.py +# install indexd +RUN poetry config virtualenvs.in-project true \ + && poetry install -vv --no-root --only main --no-interaction \ + && poetry show -v + + +#Creating the runtime image +FROM quay.io/cdis/python:python3.9-GPE-788 + +ENV appname=indexd + +USER root + +EXPOSE 80 + +RUN pip3 install --upgrade poetry + +RUN yum update -y && yum install -y bash shadow-utils + RUN useradd -ms /bin/bash appuser -RUN chown -R appuser:appuser /$appname -# RUN chown -R appuser:appuser /deployment +COPY --from=build-deps --chown=appuser:appuser /$appname /$appname + +WORKDIR /$appname USER appuser -# install indexd -RUN poetry config virtualenvs.in-project true \ - && poetry install -vv --no-root --only main --no-interaction \ - && poetry show -v +RUN poetry add gunicorn CMD ["poetry", "run", "gunicorn", "-c", "deployment/wsgi/gunicorn.conf.py"] From f2d7006f81fd80e9e362c90ad7bcf919c69ddfb7 Mon Sep 17 00:00:00 2001 From: EliseCastle23 Date: Wed, 9 Aug 2023 15:10:16 -0600 Subject: [PATCH 09/54] changing to port 8000 for testing --- deployment/wsgi/gunicorn.conf.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/deployment/wsgi/gunicorn.conf.py b/deployment/wsgi/gunicorn.conf.py index 778ad6d0..6044e973 100644 --- a/deployment/wsgi/gunicorn.conf.py +++ b/deployment/wsgi/gunicorn.conf.py @@ -1,5 +1,5 @@ wsgi_app = "deployment.wsgi.wsgi:application" -bind = "0.0.0.0:80" +bind = "0.0.0.0:8000" workers = 1 user = "appuser" group = "appuser" From 03223c2d3aee59f654d33e2e1b1b2f7ccad7bf8c Mon Sep 17 00:00:00 2001 From: EliseCastle23 Date: Fri, 11 Aug 2023 10:15:07 -0600 Subject: [PATCH 10/54] changing back to port 80 for Jenkins testing --- deployment/wsgi/gunicorn.conf.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/deployment/wsgi/gunicorn.conf.py b/deployment/wsgi/gunicorn.conf.py index 6044e973..778ad6d0 100644 --- a/deployment/wsgi/gunicorn.conf.py +++ b/deployment/wsgi/gunicorn.conf.py @@ -1,5 +1,5 @@ wsgi_app = "deployment.wsgi.wsgi:application" -bind = "0.0.0.0:8000" +bind = "0.0.0.0:80" workers = 1 user = "appuser" group = "appuser" From 3751d38b6847315cd934cabad198f663bae8948b Mon Sep 17 00:00:00 2001 From: EliseCastle23 Date: Fri, 11 Aug 2023 12:46:33 -0600 Subject: [PATCH 11/54] changing back to port 8000 and will modify the indexd service --- deployment/wsgi/gunicorn.conf.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/deployment/wsgi/gunicorn.conf.py b/deployment/wsgi/gunicorn.conf.py index 778ad6d0..6044e973 100644 --- a/deployment/wsgi/gunicorn.conf.py +++ b/deployment/wsgi/gunicorn.conf.py @@ -1,5 +1,5 @@ wsgi_app = "deployment.wsgi.wsgi:application" -bind = "0.0.0.0:80" +bind = "0.0.0.0:8000" workers = 1 user = "appuser" group = "appuser" From 56fdfba98b3e31815fa3d83f0a51cb5a22cf2e50 Mon Sep 17 00:00:00 2001 From: EliseCastle23 Date: Tue, 15 Aug 2023 13:53:31 -0600 Subject: [PATCH 12/54] made changes to the Dockerfile to fix error with indexd being installed by changing where the "git" command runs. I also had to install postgresql-devel in the runtime image so "local_settings" can be imported. --- Dockerfile | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/Dockerfile b/Dockerfile index aa4c19fb..73ad97ec 100644 --- a/Dockerfile +++ b/Dockerfile @@ -10,7 +10,7 @@ ENV appname=indexd RUN pip3 install --upgrade poetry RUN yum update -y && yum install -y --setopt install_weak_deps=0 \ - kernel-devel libffi-devel libxml2-devel libxslt-devel postgresql-devel python3-devel shadow-utils \ + kernel-devel libffi-devel libxml2-devel libxslt-devel postgresql-devel python3-devel \ git WORKDIR /$appname @@ -19,21 +19,20 @@ WORKDIR /$appname # this will make sure that the dependencies is cached COPY poetry.lock pyproject.toml /$appname/ RUN poetry config virtualenvs.in-project true \ - && poetry install -vv --no-root --only main --no-interaction\ + && poetry install -vv --no-root --only main --no-interaction \ && poetry show -v # copy source code ONLY after installing dependencies COPY . /$appname COPY ./deployment/wsgi/wsgi.py /$appname/wsgi.py -RUN COMMIT=`git rev-parse HEAD` && echo "COMMIT=\"${COMMIT}\"" >$appname/index/version_data.py \ - && VERSION=`git describe --always --tags` && echo "VERSION=\"${VERSION}\"" >>$appname/index/version_data.py - # install indexd RUN poetry config virtualenvs.in-project true \ - && poetry install -vv --no-root --only main --no-interaction \ + && poetry install -vv --no-dev --no-interaction \ && poetry show -v +RUN COMMIT=`git rev-parse HEAD` && echo "COMMIT=\"${COMMIT}\"" >$appname/index/version_data.py \ + && VERSION=`git describe --always --tags` && echo "VERSION=\"${VERSION}\"" >>$appname/index/version_data.py #Creating the runtime image FROM quay.io/cdis/python:python3.9-GPE-788 @@ -46,7 +45,9 @@ EXPOSE 80 RUN pip3 install --upgrade poetry -RUN yum update -y && yum install -y bash shadow-utils +RUN yum update -y && yum install -y --setopt install_weak_deps=0 \ + postgresql-devel shadow-utils \ + bash RUN useradd -ms /bin/bash appuser From e8eff0036d39e38ec7a8a3a26e5a1b36fe7f8d9e Mon Sep 17 00:00:00 2001 From: EliseCastle23 Date: Tue, 15 Aug 2023 13:53:58 -0600 Subject: [PATCH 13/54] removing the dockerrun from the indexd_setup script --- deployment/scripts/indexd/indexd_setup.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/deployment/scripts/indexd/indexd_setup.sh b/deployment/scripts/indexd/indexd_setup.sh index e6d02cd7..74582ea9 100644 --- a/deployment/scripts/indexd/indexd_setup.sh +++ b/deployment/scripts/indexd/indexd_setup.sh @@ -11,4 +11,4 @@ poetry install -vv --no-dev --no-interaction && poetry show -v python3 -m pip install cdispyutils popd -/dockerrun.sh \ No newline at end of file +# /dockerrun.sh From 8deb1bc14eb92eb3f6da066bcc3cd3c3d25c8303 Mon Sep 17 00:00:00 2001 From: EliseCastle23 Date: Tue, 19 Sep 2023 16:13:12 -0600 Subject: [PATCH 14/54] increasing timeouts for testing --- deployment/wsgi/gunicorn.conf.py | 1 + 1 file changed, 1 insertion(+) diff --git a/deployment/wsgi/gunicorn.conf.py b/deployment/wsgi/gunicorn.conf.py index 6044e973..ebf5eca6 100644 --- a/deployment/wsgi/gunicorn.conf.py +++ b/deployment/wsgi/gunicorn.conf.py @@ -3,3 +3,4 @@ workers = 1 user = "appuser" group = "appuser" +timeout = 600 # Increase the timeout to 600 seconds (10 minutes) From 72e163efe1f92ed6ace2bb3266aa73d070c3711e Mon Sep 17 00:00:00 2001 From: EliseCastle23 Date: Wed, 20 Sep 2023 08:42:56 -0600 Subject: [PATCH 15/54] adding a worker class for better concurrency --- deployment/wsgi/gunicorn.conf.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/deployment/wsgi/gunicorn.conf.py b/deployment/wsgi/gunicorn.conf.py index ebf5eca6..f868249b 100644 --- a/deployment/wsgi/gunicorn.conf.py +++ b/deployment/wsgi/gunicorn.conf.py @@ -3,4 +3,5 @@ workers = 1 user = "appuser" group = "appuser" -timeout = 600 # Increase the timeout to 600 seconds (10 minutes) +timeout = 300 +worker_class = "gevent" From d97fe2b3b6b77175ade600f14683e34831db9de5 Mon Sep 17 00:00:00 2001 From: EliseCastle23 Date: Wed, 20 Sep 2023 13:54:26 -0600 Subject: [PATCH 16/54] testing gevent --- Dockerfile | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 73ad97ec..19a96278 100644 --- a/Dockerfile +++ b/Dockerfile @@ -46,9 +46,12 @@ EXPOSE 80 RUN pip3 install --upgrade poetry RUN yum update -y && yum install -y --setopt install_weak_deps=0 \ - postgresql-devel shadow-utils \ + postgresql-devel shadow-utils\ bash +RUN yum install python3-devel gcc -y +#RUN poetry run pip install python3-devel gcc + RUN useradd -ms /bin/bash appuser COPY --from=build-deps --chown=appuser:appuser /$appname /$appname @@ -58,5 +61,6 @@ WORKDIR /$appname USER appuser RUN poetry add gunicorn +RUN poetry add gevent CMD ["poetry", "run", "gunicorn", "-c", "deployment/wsgi/gunicorn.conf.py"] From 453c8615c3c0017777404daa18c75bfa00bfd857 Mon Sep 17 00:00:00 2001 From: EliseCastle23 Date: Thu, 21 Sep 2023 11:29:00 -0600 Subject: [PATCH 17/54] removing gevent as it is no longer needed. --- Dockerfile | 4 ---- deployment/wsgi/gunicorn.conf.py | 1 - 2 files changed, 5 deletions(-) diff --git a/Dockerfile b/Dockerfile index 19a96278..09dde1d0 100644 --- a/Dockerfile +++ b/Dockerfile @@ -49,9 +49,6 @@ RUN yum update -y && yum install -y --setopt install_weak_deps=0 \ postgresql-devel shadow-utils\ bash -RUN yum install python3-devel gcc -y -#RUN poetry run pip install python3-devel gcc - RUN useradd -ms /bin/bash appuser COPY --from=build-deps --chown=appuser:appuser /$appname /$appname @@ -61,6 +58,5 @@ WORKDIR /$appname USER appuser RUN poetry add gunicorn -RUN poetry add gevent CMD ["poetry", "run", "gunicorn", "-c", "deployment/wsgi/gunicorn.conf.py"] diff --git a/deployment/wsgi/gunicorn.conf.py b/deployment/wsgi/gunicorn.conf.py index f868249b..baa208a4 100644 --- a/deployment/wsgi/gunicorn.conf.py +++ b/deployment/wsgi/gunicorn.conf.py @@ -4,4 +4,3 @@ user = "appuser" group = "appuser" timeout = 300 -worker_class = "gevent" From d3f403e76b364a43a5db16e9215942faf25926fc Mon Sep 17 00:00:00 2001 From: EliseCastle23 Date: Fri, 22 Sep 2023 10:16:14 -0600 Subject: [PATCH 18/54] changing the base image for indexd as I moved the python3.9 image to the "base-repo" --- Dockerfile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index 09dde1d0..394edb03 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,7 +1,7 @@ # To run: docker run -v /path/to/wsgi.py:/var/www/indexd/wsgi.py --name=indexd -p 81:80 indexd # To check running container: docker exec -it indexd /bin/bash -FROM quay.io/cdis/python:python3.9-GPE-788 as build-deps +FROM quay.io/cdis/amazonlinux:python3.9-feat_GPE-979 as build-deps USER root @@ -35,7 +35,7 @@ RUN COMMIT=`git rev-parse HEAD` && echo "COMMIT=\"${COMMIT}\"" >$appname/index/v && VERSION=`git describe --always --tags` && echo "VERSION=\"${VERSION}\"" >>$appname/index/version_data.py #Creating the runtime image -FROM quay.io/cdis/python:python3.9-GPE-788 +FROM quay.io/cdis/amazonlinux:python3.9-feat_GPE-979 ENV appname=indexd From cfe4742e2581784345df79d98afcd47ca54d2c4e Mon Sep 17 00:00:00 2001 From: EliseCastle23 Date: Tue, 26 Sep 2023 15:58:40 -0600 Subject: [PATCH 19/54] changing the image indexd is based on --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 394edb03..e58da7bc 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,7 +1,7 @@ # To run: docker run -v /path/to/wsgi.py:/var/www/indexd/wsgi.py --name=indexd -p 81:80 indexd # To check running container: docker exec -it indexd /bin/bash -FROM quay.io/cdis/amazonlinux:python3.9-feat_GPE-979 as build-deps +FROM quay.io/cdis/amazonlinux:python3.9-master as build-deps USER root From 86ff8ddfc8b37cd470be4363dfeef26322b0d2f9 Mon Sep 17 00:00:00 2001 From: EliseCastle23 Date: Thu, 5 Oct 2023 08:23:19 -0600 Subject: [PATCH 20/54] updating the image that the runtime iamge is based on --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index e58da7bc..0dbde0fb 100644 --- a/Dockerfile +++ b/Dockerfile @@ -35,7 +35,7 @@ RUN COMMIT=`git rev-parse HEAD` && echo "COMMIT=\"${COMMIT}\"" >$appname/index/v && VERSION=`git describe --always --tags` && echo "VERSION=\"${VERSION}\"" >>$appname/index/version_data.py #Creating the runtime image -FROM quay.io/cdis/amazonlinux:python3.9-feat_GPE-979 +FROM quay.io/cdis/amazonlinux:python3.9-master ENV appname=indexd From 7092eec9562180c2784b51ed515e1246bb7f159e Mon Sep 17 00:00:00 2001 From: Andrew Prokhorenkov Date: Fri, 6 Oct 2023 16:13:52 -0500 Subject: [PATCH 21/54] feat: update to new base image --- Dockerfile | 59 +--- poetry.lock | 901 +++++++++++++++++++++++++------------------------ pyproject.toml | 2 +- 3 files changed, 477 insertions(+), 485 deletions(-) diff --git a/Dockerfile b/Dockerfile index 0dbde0fb..b4f96fa7 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,62 +1,39 @@ -# To run: docker run -v /path/to/wsgi.py:/var/www/indexd/wsgi.py --name=indexd -p 81:80 indexd -# To check running container: docker exec -it indexd /bin/bash +ARG AZLINUX_BASE_VERSION=master -FROM quay.io/cdis/amazonlinux:python3.9-master as build-deps - -USER root +FROM 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/python-build-base:${AZLINUX_BASE_VERSION} as base +# FROM quay.io/cdis/python-build-base:${AZLINUX_BASE_VERSION} as base ENV appname=indexd +ENV POETRY_NO_INTERACTION=1 \ + POETRY_VIRTUALENVS_IN_PROJECT=1 \ + POETRY_VIRTUALENVS_CREATE=1 -RUN pip3 install --upgrade poetry +FROM base as builder -RUN yum update -y && yum install -y --setopt install_weak_deps=0 \ - kernel-devel libffi-devel libxml2-devel libxslt-devel postgresql-devel python3-devel \ - git +RUN source /venv/bin/activate WORKDIR /$appname -# copy ONLY poetry artifact, install the dependencies but not indexd -# this will make sure that the dependencies is cached COPY poetry.lock pyproject.toml /$appname/ -RUN poetry config virtualenvs.in-project true \ - && poetry install -vv --no-root --only main --no-interaction \ - && poetry show -v +RUN pip install --upgrade poetry \ + && poetry install --without dev --no-interaction -# copy source code ONLY after installing dependencies COPY . /$appname COPY ./deployment/wsgi/wsgi.py /$appname/wsgi.py - -# install indexd -RUN poetry config virtualenvs.in-project true \ - && poetry install -vv --no-dev --no-interaction \ - && poetry show -v +RUN poetry install --without dev --no-interaction RUN COMMIT=`git rev-parse HEAD` && echo "COMMIT=\"${COMMIT}\"" >$appname/index/version_data.py \ && VERSION=`git describe --always --tags` && echo "VERSION=\"${VERSION}\"" >>$appname/index/version_data.py -#Creating the runtime image -FROM quay.io/cdis/amazonlinux:python3.9-master - -ENV appname=indexd - -USER root +FROM base -EXPOSE 80 +RUN source /venv/bin/activate -RUN pip3 install --upgrade poetry - -RUN yum update -y && yum install -y --setopt install_weak_deps=0 \ - postgresql-devel shadow-utils\ - bash - -RUN useradd -ms /bin/bash appuser - -COPY --from=build-deps --chown=appuser:appuser /$appname /$appname +COPY --from=builder /venv /venv +COPY --from=builder /$appname /$appname WORKDIR /$appname -USER appuser - -RUN poetry add gunicorn - -CMD ["poetry", "run", "gunicorn", "-c", "deployment/wsgi/gunicorn.conf.py"] +ENV PYTHONUNBUFFERED=1 \ + PYTHONIOENCODING=UTF-8 +CMD ["gunicorn", "-c", "deployment/wsgi/gunicorn.conf.py"] diff --git a/poetry.lock b/poetry.lock index b70402ba..b5262db2 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,50 +1,49 @@ -# This file is automatically @generated by Poetry and should not be changed by hand. +# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. [[package]] name = "alembic" -version = "1.9.4" +version = "1.12.0" description = "A database migration tool for SQLAlchemy." -category = "main" optional = false python-versions = ">=3.7" files = [ - {file = "alembic-1.9.4-py3-none-any.whl", hash = "sha256:6f1c2207369bf4f49f952057a33bb017fbe5c148c2a773b46906b806ea6e825f"}, - {file = "alembic-1.9.4.tar.gz", hash = "sha256:4d3bd32ecdbb7bbfb48a9fe9e6d6fd6a831a1b59d03e26e292210237373e7db5"}, + {file = "alembic-1.12.0-py3-none-any.whl", hash = "sha256:03226222f1cf943deee6c85d9464261a6c710cd19b4fe867a3ad1f25afda610f"}, + {file = "alembic-1.12.0.tar.gz", hash = "sha256:8e7645c32e4f200675e69f0745415335eb59a3663f5feb487abfa0b30c45888b"}, ] [package.dependencies] Mako = "*" SQLAlchemy = ">=1.3.0" +typing-extensions = ">=4" [package.extras] tz = ["python-dateutil"] [[package]] name = "anyio" -version = "3.6.2" +version = "4.0.0" description = "High level compatibility layer for multiple asynchronous event loop implementations" -category = "main" optional = false -python-versions = ">=3.6.2" +python-versions = ">=3.8" files = [ - {file = "anyio-3.6.2-py3-none-any.whl", hash = "sha256:fbbe32bd270d2a2ef3ed1c5d45041250284e31fc0a4df4a5a6071842051a51e3"}, - {file = "anyio-3.6.2.tar.gz", hash = "sha256:25ea0d673ae30af41a0c442f81cf3b38c7e79fdc7b60335a4c14e05eb0947421"}, + {file = "anyio-4.0.0-py3-none-any.whl", hash = "sha256:cfdb2b588b9fc25ede96d8db56ed50848b0b649dca3dd1df0b11f683bb9e0b5f"}, + {file = "anyio-4.0.0.tar.gz", hash = "sha256:f7ed51751b2c2add651e5747c891b47e26d2a21be5d32d9311dfe9692f3e5d7a"}, ] [package.dependencies] +exceptiongroup = {version = ">=1.0.2", markers = "python_version < \"3.11\""} idna = ">=2.8" sniffio = ">=1.1" [package.extras] -doc = ["packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme"] -test = ["contextlib2", "coverage[toml] (>=4.5)", "hypothesis (>=4.0)", "mock (>=4)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (<0.15)", "uvloop (>=0.15)"] -trio = ["trio (>=0.16,<0.22)"] +doc = ["Sphinx (>=7)", "packaging", "sphinx-autodoc-typehints (>=1.2.0)"] +test = ["anyio[trio]", "coverage[toml] (>=7)", "hypothesis (>=4.0)", "psutil (>=5.9)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (>=0.17)"] +trio = ["trio (>=0.22)"] [[package]] name = "atomicwrites" version = "1.4.1" description = "Atomic file writes." -category = "dev" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ @@ -53,28 +52,26 @@ files = [ [[package]] name = "attrs" -version = "22.2.0" +version = "23.1.0" description = "Classes Without Boilerplate" -category = "main" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" files = [ - {file = "attrs-22.2.0-py3-none-any.whl", hash = "sha256:29e95c7f6778868dbd49170f98f8818f78f3dc5e0e37c0b1f474e3561b240836"}, - {file = "attrs-22.2.0.tar.gz", hash = "sha256:c9227bfc2f01993c03f68db37d1d15c9690188323c067c641f1a35ca58185f99"}, + {file = "attrs-23.1.0-py3-none-any.whl", hash = "sha256:1f28b4522cdc2fb4256ac1a020c78acf9cba2c6b461ccd2c126f3aa8e8335d04"}, + {file = "attrs-23.1.0.tar.gz", hash = "sha256:6279836d581513a26f1bf235f9acd333bc9115683f14f7e8fae46c98fc50e015"}, ] [package.extras] -cov = ["attrs[tests]", "coverage-enable-subprocess", "coverage[toml] (>=5.3)"] -dev = ["attrs[docs,tests]"] -docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope.interface"] -tests = ["attrs[tests-no-zope]", "zope.interface"] -tests-no-zope = ["cloudpickle", "cloudpickle", "hypothesis", "hypothesis", "mypy (>=0.971,<0.990)", "mypy (>=0.971,<0.990)", "pympler", "pympler", "pytest (>=4.3.0)", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-mypy-plugins", "pytest-xdist[psutil]", "pytest-xdist[psutil]"] +cov = ["attrs[tests]", "coverage[toml] (>=5.3)"] +dev = ["attrs[docs,tests]", "pre-commit"] +docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope-interface"] +tests = ["attrs[tests-no-zope]", "zope-interface"] +tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"] [[package]] name = "authlib" version = "0.11" description = "The ultimate Python library in building OAuth and OpenID Connect servers." -category = "main" optional = false python-versions = "*" files = [ @@ -88,33 +85,31 @@ requests = "*" [[package]] name = "authutils" -version = "6.2.2" +version = "6.1.2" description = "Gen3 auth utility functions" -category = "main" optional = false -python-versions = ">=3.9,<4.0" +python-versions = ">=3.6,<4.0" files = [ - {file = "authutils-6.2.2-py3-none-any.whl", hash = "sha256:df9b551b4ab561452f0f4b50edaddccc443905b4d77ee69ea7eea78938e7caed"}, - {file = "authutils-6.2.2.tar.gz", hash = "sha256:ded3e5c0e35160eab83bfb217976920396441e19ed977acacbb769e988323850"}, + {file = "authutils-6.1.2-py3-none-any.whl", hash = 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+python-versions = ">=3.8" files = [ - {file = "urllib3-2.0.6-py3-none-any.whl", hash = "sha256:7a7c7003b000adf9e7ca2a377c9688bbc54ed41b985789ed576570342a375cd2"}, - {file = "urllib3-2.0.6.tar.gz", hash = "sha256:b19e1a85d206b56d7df1d5e683df4a7725252a964e3993648dd0fb5a1c157564"}, + {file = "urllib3-2.1.0-py3-none-any.whl", hash = "sha256:55901e917a5896a349ff771be919f8bd99aff50b79fe58fec595eb37bbc56bb3"}, + {file = "urllib3-2.1.0.tar.gz", hash = "sha256:df7aa8afb0148fa78488e7899b2c59b5f4ffcfa82e6c54ccb9dd37c1d7b52d54"}, ] [package.extras] brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)"] -secure = ["certifi", "cryptography (>=1.9)", "idna (>=2.0.0)", "pyopenssl (>=17.1.0)", "urllib3-secure-extra"] socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"] zstd = ["zstandard (>=0.18.0)"] [[package]] name = "werkzeug" -version = "3.0.0" +version = "3.0.1" description = "The comprehensive WSGI web application library." optional = false python-versions = ">=3.8" files = [ - {file = "werkzeug-3.0.0-py3-none-any.whl", hash = "sha256:cbb2600f7eabe51dbc0502f58be0b3e1b96b893b05695ea2b35b43d4de2d9962"}, - {file = "werkzeug-3.0.0.tar.gz", hash = "sha256:3ffff4dcc32db52ef3cc94dff3000a3c2846890f3a5a51800a27b909c5e770f0"}, + {file = "werkzeug-3.0.1-py3-none-any.whl", hash = "sha256:90a285dc0e42ad56b34e696398b8122ee4c681833fb35b8334a095d82c56da10"}, + {file = "werkzeug-3.0.1.tar.gz", hash = "sha256:507e811ecea72b18a404947aded4b3390e1db8f826b494d76550ef45bb3b1dcc"}, ] [package.dependencies] @@ -1430,4 +1458,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p [metadata] lock-version = "2.0" python-versions = "3.9.*" -content-hash = "98c02bf5896ed49374900d1e0d17035b11db43729cd89aba92d328d3b4963940" +content-hash = "4a91f82d5fa70b91cf93bb29cdc1d3d275e32d8a2c83555a152d04b1e9408292" diff --git a/pyproject.toml b/pyproject.toml index f5921f64..82da8ac4 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -26,7 +26,7 @@ psycopg2-binary = "^2.7" sqlalchemy = "~1.3.3" sqlalchemy-utils = "^0.37.3" PyYAML = "^5.4" - +gunicorn = "^21.2.0" [tool.poetry.dev-dependencies] cdisutilstest = {git = "https://github.com/uc-cdis/cdisutils-test", rev = "1.0.0"} From 45efbe28143373a3494498bab6b800399d0342e0 Mon Sep 17 00:00:00 2001 From: Jawad Qureshi Date: Tue, 28 Nov 2023 18:02:53 -0600 Subject: [PATCH 23/54] Change Dockerfile to use gen3 user --- Dockerfile | 50 ++++++++++++++++++++++++++++++++++++-------------- 1 file changed, 36 insertions(+), 14 deletions(-) diff --git a/Dockerfile b/Dockerfile index b4f96fa7..ed075f6a 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,39 +1,61 @@ ARG AZLINUX_BASE_VERSION=master -FROM 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/python-build-base:${AZLINUX_BASE_VERSION} as base -# FROM quay.io/cdis/python-build-base:${AZLINUX_BASE_VERSION} as base +# Base stage with python-build-base +FROM quay.io/cdis/python-build-base:${AZLINUX_BASE_VERSION} as base + +# Comment this in, and comment out the line above, if quay is down +# FROM 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/python-build-base:${AZLINUX_BASE_VERSION} as base ENV appname=indexd ENV POETRY_NO_INTERACTION=1 \ POETRY_VIRTUALENVS_IN_PROJECT=1 \ POETRY_VIRTUALENVS_CREATE=1 +WORKDIR /${appname} + +# create gen3 user +# Create a group 'gen3' with GID 1000 and a user 'gen3' with UID 1000 +RUN groupadd -g 1000 gen3 && \ + useradd -m -s /bin/bash -u 1000 -g gen3 gen3 && \ + chown -R gen3:gen3 /$appname && \ + chown -R gen3:gen3 /venv + + +# Builder stage FROM base as builder -RUN source /venv/bin/activate +USER gen3 + + +RUN python -m venv /venv -WORKDIR /$appname +COPY poetry.lock pyproject.toml /${appname}/ -COPY poetry.lock pyproject.toml /$appname/ -RUN pip install --upgrade poetry \ - && poetry install --without dev --no-interaction +RUN pip install --upgrade poetry && \ + poetry install -vv --only main --no-interaction -COPY . /$appname -COPY ./deployment/wsgi/wsgi.py /$appname/wsgi.py +COPY --chown=gen3:gen3 . /$appname +COPY --chown=gen3:gen3 ./deployment/wsgi/wsgi.py /$appname/wsgi.py + +# Run poetry again so this app itself gets installed too RUN poetry install --without dev --no-interaction -RUN COMMIT=`git rev-parse HEAD` && echo "COMMIT=\"${COMMIT}\"" >$appname/index/version_data.py \ - && VERSION=`git describe --always --tags` && echo "VERSION=\"${VERSION}\"" >>$appname/index/version_data.py +RUN git config --global --add safe.directory /${appname} && COMMIT=`git rev-parse HEAD` && echo "COMMIT=\"${COMMIT}\"" > /$appname/version_data.py \ + && VERSION=`git describe --always --tags` && echo "VERSION=\"${VERSION}\"" >> /$appname/version_data.py +# Final stage FROM base -RUN source /venv/bin/activate - COPY --from=builder /venv /venv COPY --from=builder /$appname /$appname -WORKDIR /$appname + +# Switch to non-root user 'gen3' for the serving process +USER gen3 + +RUN source /venv/bin/activate ENV PYTHONUNBUFFERED=1 \ PYTHONIOENCODING=UTF-8 + CMD ["gunicorn", "-c", "deployment/wsgi/gunicorn.conf.py"] From 7fd7b7e68666b0df8d0fed2d6508c0f20733a604 Mon Sep 17 00:00:00 2001 From: EliseCastle23 <109446148+EliseCastle23@users.noreply.github.com> Date: Fri, 9 Aug 2024 16:00:13 -0600 Subject: [PATCH 24/54] adding nginx to indexd --- Dockerfile | 20 ++++++++++++++++- deployment/nginx/nginx.conf | 44 +++++++++++++++++++++++++++++++++++++ dockerrun.bash | 4 ++++ 3 files changed, 67 insertions(+), 1 deletion(-) create mode 100644 deployment/nginx/nginx.conf create mode 100755 dockerrun.bash diff --git a/Dockerfile b/Dockerfile index ed075f6a..a7454607 100644 --- a/Dockerfile +++ b/Dockerfile @@ -49,6 +49,24 @@ FROM base COPY --from=builder /venv /venv COPY --from=builder /$appname /$appname +# install nginx +RUN yum install nginx -y + +RUN setcap 'cap_net_bind_service=+ep' /usr/sbin/nginx + +# chown nginx directories +RUN chown -R gen3:gen3 /var/log/nginx + +# pipe nginx logs to stdout and stderr +RUN ln -sf /dev/stdout /var/log/nginx/access.log && ln -sf /dev/stderr /var/log/nginx/error.log + +# create /var/lib/nginx/tmp/client_body to allow nginx to write to indexd +RUN mkdir -p /var/lib/nginx/tmp/client_body +RUN chown -R gen3:gen3 /var/lib/nginx/ + +# copy nginx config +COPY ./deployment/nginx/nginx.conf /etc/nginx/nginx.conf + # Switch to non-root user 'gen3' for the serving process USER gen3 @@ -58,4 +76,4 @@ RUN source /venv/bin/activate ENV PYTHONUNBUFFERED=1 \ PYTHONIOENCODING=UTF-8 -CMD ["gunicorn", "-c", "deployment/wsgi/gunicorn.conf.py"] +CMD ["/indexd/dockerrun.bash"] diff --git a/deployment/nginx/nginx.conf b/deployment/nginx/nginx.conf new file mode 100644 index 00000000..f3a48b67 --- /dev/null +++ b/deployment/nginx/nginx.conf @@ -0,0 +1,44 @@ +user gen3; +worker_processes auto; +error_log /var/log/nginx/error.log notice; +pid /var/lib/nginx/nginx.pid; + +# Load dynamic modules. See /usr/share/doc/nginx/README.dynamic. +include /usr/share/nginx/modules/*.conf; + +events { + worker_connections 1024; +} + +http { + log_format main '$remote_addr - $remote_user [$time_local] "$request" ' + '$status $body_bytes_sent "$http_referer" ' + '"$http_user_agent" "$http_x_forwarded_for"'; + + access_log /var/log/nginx/access.log main; + + sendfile on; + tcp_nopush on; + keepalive_timeout 65; + types_hash_max_size 4096; + + include /etc/nginx/mime.types; + default_type application/octet-stream; + + # Load modular configuration files from the /etc/nginx/conf.d directory. + # See http://nginx.org/en/docs/ngx_core_module.html#include + # for more information. + include /etc/nginx/conf.d/*.conf; + + server { + + listen 80; + server_name localhost; + + location / { + proxy_pass http://localhost:8000; + proxy_set_header Host $host; + proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for; + } + } +} diff --git a/dockerrun.bash b/dockerrun.bash new file mode 100755 index 00000000..8b14b2bb --- /dev/null +++ b/dockerrun.bash @@ -0,0 +1,4 @@ +#!/bin/bash + +nginx +gunicorn -c "/indexd/deployment/wsgi/gunicorn.conf.py" From 64e536ec114f59fc8424251cfb4a12c56225bd88 Mon Sep 17 00:00:00 2001 From: EliseCastle23 <109446148+EliseCastle23@users.noreply.github.com> Date: Mon, 12 Aug 2024 11:04:47 -0600 Subject: [PATCH 25/54] dummy commit --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index a7454607..6f6ccf2b 100644 --- a/Dockerfile +++ b/Dockerfile @@ -49,7 +49,7 @@ FROM base COPY --from=builder /venv /venv COPY --from=builder /$appname /$appname -# install nginx +# Install nginx RUN yum install nginx -y RUN setcap 'cap_net_bind_service=+ep' /usr/sbin/nginx From 54ff527827acd0722d56f43455e5a218c84e1857 Mon Sep 17 00:00:00 2001 From: EliseCastle23 <109446148+EliseCastle23@users.noreply.github.com> Date: Mon, 12 Aug 2024 12:38:26 -0600 Subject: [PATCH 26/54] fixing case issue --- Dockerfile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index 6f6ccf2b..f977b382 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,7 +1,7 @@ ARG AZLINUX_BASE_VERSION=master # Base stage with python-build-base -FROM quay.io/cdis/python-build-base:${AZLINUX_BASE_VERSION} as base +FROM quay.io/cdis/python-build-base:${AZLINUX_BASE_VERSION} AS base # Comment this in, and comment out the line above, if quay is down # FROM 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/python-build-base:${AZLINUX_BASE_VERSION} as base @@ -22,7 +22,7 @@ RUN groupadd -g 1000 gen3 && \ # Builder stage -FROM base as builder +FROM base AS builder USER gen3 From db11bff8950e12b636e577d4bb5b5b75d0013b3f Mon Sep 17 00:00:00 2001 From: EliseCastle23 <109446148+EliseCastle23@users.noreply.github.com> Date: Wed, 4 Sep 2024 10:50:19 -0600 Subject: [PATCH 27/54] pushing up pyproject.toml changes --- pyproject.toml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 82da8ac4..638bfb92 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "indexd" -version = "5.0.0" +version = "5.0.4" description = "Gen3 Indexing Service" authors = ["CTDS UChicago "] license = "Apache-2.0" @@ -10,7 +10,7 @@ include = [ ] [tool.poetry.dependencies] -python = "3.9.*" +python = ">=3.9,<4.0" alembic = "^1.9.4" authutils = "^6.0.0" cdislogging = "^1.0.0" @@ -21,12 +21,12 @@ gen3authz = "^1.0.4" hsclient = {git = "https://github.com/uc-cdis/hsclient", rev = "1.0.0"} indexclient = "^2.1.0" jsonschema = "^3.2" -flask = "^2.0.1" psycopg2-binary = "^2.7" +gunicorn = "^21.2.0" +flask = "^2.3.3" sqlalchemy = "~1.3.3" sqlalchemy-utils = "^0.37.3" -PyYAML = "^5.4" -gunicorn = "^21.2.0" +PyYAML = ">=5.3,<7" [tool.poetry.dev-dependencies] cdisutilstest = {git = "https://github.com/uc-cdis/cdisutils-test", rev = "1.0.0"} From 8bb67cf07ef9320dae717aee7a06f41178ca104a Mon Sep 17 00:00:00 2001 From: EliseCastle23 <109446148+EliseCastle23@users.noreply.github.com> Date: Wed, 4 Sep 2024 11:51:30 -0600 Subject: [PATCH 28/54] pushing up poetry lock change --- poetry.lock | 610 ++++++++++++++++++++++++++++++---------------------- 1 file changed, 356 insertions(+), 254 deletions(-) diff --git a/poetry.lock b/poetry.lock index 4ad452c8..a8699a6e 100644 --- a/poetry.lock +++ b/poetry.lock @@ -2,13 +2,13 @@ [[package]] name = "alembic" -version = "1.13.1" +version = "1.13.2" description = "A database migration tool for SQLAlchemy." optional = false python-versions = ">=3.8" files = [ - {file = "alembic-1.13.1-py3-none-any.whl", hash = "sha256:2edcc97bed0bd3272611ce3a98d98279e9c209e7186e43e75bbb1b2bdfdbcc43"}, - {file = "alembic-1.13.1.tar.gz", hash = "sha256:4932c8558bf68f2ee92b9bbcb8218671c627064d5b08939437af6d77dc05e595"}, + {file = "alembic-1.13.2-py3-none-any.whl", hash = "sha256:6b8733129a6224a9a711e17c99b08462dbf7cc9670ba8f2e2ae9af860ceb1953"}, + {file = "alembic-1.13.2.tar.gz", hash = "sha256:1ff0ae32975f4fd96028c39ed9bb3c867fe3af956bd7bb37343b54c9fe7445ef"}, ] [package.dependencies] @@ -21,13 +21,13 @@ tz = ["backports.zoneinfo"] [[package]] name = "anyio" -version = "4.3.0" +version = "4.4.0" description = "High level compatibility layer for multiple asynchronous event loop implementations" optional = false python-versions = ">=3.8" files = [ - {file = "anyio-4.3.0-py3-none-any.whl", hash = "sha256:048e05d0f6caeed70d731f3db756d35dcc1f35747c8c403364a8332c630441b8"}, - {file = "anyio-4.3.0.tar.gz", hash = "sha256:f75253795a87df48568485fd18cdd2a3fa5c4f7c5be8e5e36637733fce06fed6"}, + {file = "anyio-4.4.0-py3-none-any.whl", hash = "sha256:c1b2d8f46a8a812513012e1107cb0e68c17159a7a594208005a57dc776e1bdc7"}, + {file = "anyio-4.4.0.tar.gz", hash = "sha256:5aadc6a1bbb7cdb0bede386cac5e2940f5e2ff3aa20277e991cf028e0585ce94"}, ] [package.dependencies] @@ -53,32 +53,32 @@ files = [ [[package]] name = "attrs" -version = "23.2.0" +version = "24.2.0" description = "Classes Without Boilerplate" optional = false python-versions = ">=3.7" files = [ - {file = "attrs-23.2.0-py3-none-any.whl", hash = "sha256:99b87a485a5820b23b879f04c2305b44b951b502fd64be915879d77a7e8fc6f1"}, - {file = "attrs-23.2.0.tar.gz", hash = "sha256:935dc3b529c262f6cf76e50877d35a4bd3c1de194fd41f47a2b7ae8f19971f30"}, + {file = "attrs-24.2.0-py3-none-any.whl", hash = "sha256:81921eb96de3191c8258c199618104dd27ac608d9366f5e35d011eae1867ede2"}, + {file = "attrs-24.2.0.tar.gz", hash = "sha256:5cfb1b9148b5b086569baec03f20d7b6bf3bcacc9a42bebf87ffaaca362f6346"}, ] [package.extras] -cov = ["attrs[tests]", "coverage[toml] (>=5.3)"] -dev = ["attrs[tests]", "pre-commit"] -docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope-interface"] -tests = ["attrs[tests-no-zope]", "zope-interface"] -tests-mypy = ["mypy (>=1.6)", "pytest-mypy-plugins"] -tests-no-zope = ["attrs[tests-mypy]", "cloudpickle", "hypothesis", "pympler", "pytest (>=4.3.0)", "pytest-xdist[psutil]"] +benchmark = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-codspeed", "pytest-mypy-plugins", "pytest-xdist[psutil]"] +cov = ["cloudpickle", "coverage[toml] (>=5.3)", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"] +dev = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pre-commit", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"] +docs = ["cogapp", "furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier (<24.7)"] +tests = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"] +tests-mypy = ["mypy (>=1.11.1)", "pytest-mypy-plugins"] [[package]] name = "authlib" -version = "1.3.0" +version = "1.3.2" description = "The ultimate Python library in building OAuth and OpenID Connect servers and clients." optional = false python-versions = ">=3.8" files = [ - {file = "Authlib-1.3.0-py2.py3-none-any.whl", hash = "sha256:9637e4de1fb498310a56900b3e2043a206b03cb11c05422014b0302cbc814be3"}, - {file = "Authlib-1.3.0.tar.gz", hash = "sha256:959ea62a5b7b5123c5059758296122b57cd2585ae2ed1c0622c21b371ffdae06"}, + {file = "Authlib-1.3.2-py2.py3-none-any.whl", hash = "sha256:ede026a95e9f5cdc2d4364a52103f5405e75aa156357e831ef2bfd0bc5094dfc"}, + {file = "authlib-1.3.2.tar.gz", hash = "sha256:4b16130117f9eb82aa6eec97f6dd4673c3f960ac0283ccdae2897ee4bc030ba2"}, ] [package.dependencies] @@ -86,19 +86,20 @@ cryptography = "*" [[package]] name = "authutils" -version = "6.2.3" +version = "6.2.5" description = "Gen3 auth utility functions" optional = false -python-versions = ">=3.9,<4.0" +python-versions = "<4.0,>=3.9" files = [ - {file = "authutils-6.2.3-py3-none-any.whl", hash = "sha256:8c4e7e24183cbc1055ab91eaf9d2966f0da5b739be0fabfe380749674ba3057e"}, - {file = "authutils-6.2.3.tar.gz", hash = "sha256:c44e1f309b2b5b6db1276f69e1e18ec5c6be1ae33bfe52608a30049b8669ff7b"}, + {file = "authutils-6.2.5-py3-none-any.whl", hash = "sha256:ef91c9c7c750123c28b7376be9ca00b4e89b2d52fa183dec9bfe681d8eac6227"}, + {file = "authutils-6.2.5.tar.gz", hash = "sha256:0d496721e9f0d8c69b34aff8f6fccdc7768ca4f104504d68e70fd647d4c23b19"}, ] [package.dependencies] authlib = ">=1.1.0" cached-property = ">=1.4,<2.0" cdiserrors = "<2.0.0" +cryptography = ">=41.0.6" httpx = ">=0.23.0,<1.0.0" pyjwt = {version = ">=2.4.0,<3.0", extras = ["crypto"]} xmltodict = ">=0.9,<1.0" @@ -120,13 +121,13 @@ files = [ [[package]] name = "blinker" -version = "1.7.0" +version = "1.8.2" description = "Fast, simple object-to-object and broadcast signaling" optional = false python-versions = ">=3.8" files = [ - {file = "blinker-1.7.0-py3-none-any.whl", hash = "sha256:c3f865d4d54db7abc53758a01601cf343fe55b84c1de4e3fa910e420b438d5b9"}, - {file = "blinker-1.7.0.tar.gz", hash = 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a/Dockerfile b/Dockerfile index f977b382..2724f556 100644 --- a/Dockerfile +++ b/Dockerfile @@ -52,6 +52,7 @@ COPY --from=builder /$appname /$appname # Install nginx RUN yum install nginx -y +# allows nginx to run on port 80 without being root user RUN setcap 'cap_net_bind_service=+ep' /usr/sbin/nginx # chown nginx directories diff --git a/deployment/nginx/nginx.conf b/deployment/nginx/nginx.conf index f3a48b67..c64485a9 100644 --- a/deployment/nginx/nginx.conf +++ b/deployment/nginx/nginx.conf @@ -36,7 +36,7 @@ http { server_name localhost; location / { - proxy_pass http://localhost:8000; + proxy_pass http://127.0.0.1:8000; proxy_set_header Host $host; proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for; } From 4db16ed394fa39d3da65d43bbcb23f1b19317838 Mon Sep 17 00:00:00 2001 From: EliseCastle23 <109446148+EliseCastle23@users.noreply.github.com> Date: Thu, 5 Sep 2024 08:11:48 -0600 Subject: [PATCH 30/54] setting to only amd --- .github/workflows/image_build_push.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/image_build_push.yaml b/.github/workflows/image_build_push.yaml index 2221aee4..779aad0e 100644 --- a/.github/workflows/image_build_push.yaml +++ b/.github/workflows/image_build_push.yaml @@ -6,6 +6,8 @@ jobs: ci: name: Build Image and Push to Quay uses: uc-cdis/.github/.github/workflows/image_build_push.yaml@master + with: + BUILD_PLATFORMS: "linux/amd64" secrets: ECR_AWS_ACCESS_KEY_ID: ${{ secrets.ECR_AWS_ACCESS_KEY_ID }} ECR_AWS_SECRET_ACCESS_KEY: ${{ secrets.ECR_AWS_SECRET_ACCESS_KEY }} From 3dd7ba4bc67c303f347bfc90a4ad6a08a4776b3c Mon Sep 17 00:00:00 2001 From: EliseCastle23 <109446148+EliseCastle23@users.noreply.github.com> Date: Fri, 6 Sep 2024 09:48:36 -0600 Subject: [PATCH 31/54] changing the startup command --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 2724f556..8c717f88 100644 --- a/Dockerfile +++ b/Dockerfile @@ -77,4 +77,4 @@ RUN source 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2ebde680bd5adaf60a1a0ce8fa06cfad2ea1f18e Mon Sep 17 00:00:00 2001 From: EliseCastle23 <109446148+EliseCastle23@users.noreply.github.com> Date: Tue, 22 Oct 2024 09:49:37 -0600 Subject: [PATCH 34/54] adding docker compose file for unit testing. --- docker-compose.yaml | 36 ++++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 docker-compose.yaml diff --git a/docker-compose.yaml b/docker-compose.yaml new file mode 100644 index 00000000..06abe766 --- /dev/null +++ b/docker-compose.yaml @@ -0,0 +1,36 @@ +version: '3.8' + +services: + postgres: + image: postgres:13 + environment: + POSTGRES_USER: postgres + POSTGRES_PASSWORD: postgres + POSTGRES_DB: postgres + POSTGRES_HOST_AUTH_METHOD: trust + ports: + - "5432:5432" + + python: + # image: python:3.9 + image: indexd-oct22:latest + volumes: + - .:/app + working_dir: /app + depends_on: + - postgres + network_mode: "service:postgres" + environment: + POSTGRES_USER: postgres + POSTGRES_PASSWORD: postgres + POSTGRES_DB: postgres + POSTGRES_HOST: postgres + POSTGRES_PORT: 5432 + PGHOST: postgres + command: > + bash -c " + source /venv/bin/activate && + poetry install && + bash tests/ci_commands_script.sh + # poetry run pytest -vv --cov=indexd --cov=migrations/versions --cov-append --cov-report xml tests + " From 9f6243f3ab45b95be6ae411c5280d55744e785ae Mon Sep 17 00:00:00 2001 From: EliseCastle23 <109446148+EliseCastle23@users.noreply.github.com> Date: Tue, 22 Oct 2024 10:09:58 -0600 Subject: [PATCH 35/54] adding fix for docker compose file --- docker-compose.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docker-compose.yaml b/docker-compose.yaml index 06abe766..c0157eef 100644 --- a/docker-compose.yaml +++ b/docker-compose.yaml @@ -12,8 +12,8 @@ services: - "5432:5432" python: - # image: python:3.9 - image: indexd-oct22:latest + image: quay.io/cdis/indexd:feat_GPE-788 + platform: linux/amd64 volumes: - .:/app working_dir: /app From 4e792a5340538c7cabf0ea0afd71cbdbc481b4a4 Mon Sep 17 00:00:00 2001 From: EliseCastle23 <109446148+EliseCastle23@users.noreply.github.com> Date: Tue, 22 Oct 2024 10:57:40 -0600 Subject: [PATCH 36/54] updating pyproject --- poetry.lock | 384 +++++++++++++++++++++++++++++++------------------ pyproject.toml | 2 +- 2 files changed, 247 insertions(+), 139 deletions(-) diff --git a/poetry.lock b/poetry.lock index d545b23c..c3a8347b 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.4 and should not be changed by hand. 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["mysql-connector-python", "mysql-connector-python"] +oracle = ["cx_oracle (>=7)", "cx_oracle (>=7,<8)"] +postgresql = ["psycopg2 (>=2.7)"] +postgresql-asyncpg = ["asyncpg", "asyncpg", "greenlet (!=0.4.17)", "greenlet (!=0.4.17)"] +postgresql-pg8000 = ["pg8000 (>=1.16.6,!=1.29.0)", "pg8000 (>=1.16.6,!=1.29.0)"] postgresql-psycopg2binary = ["psycopg2-binary"] postgresql-psycopg2cffi = ["psycopg2cffi"] pymysql = ["pymysql", "pymysql (<1)"] +sqlcipher = ["sqlcipher3_binary"] [[package]] name = "sqlalchemy-utils" @@ -1518,4 +1626,4 @@ type = ["pytest-mypy"] [metadata] lock-version = "2.0" python-versions = ">=3.9,<4.0" -content-hash = "051bfcd90ba310b8859f1b6a0197106bbba65746aaf101e892cda8efa55b831a" +content-hash = "8681bdae6413fe559de688ef3e29e669db286e5c882f2d4ee14f937ea2ef2675" diff --git a/pyproject.toml b/pyproject.toml index fa9ce647..b1355933 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -24,7 +24,7 @@ jsonschema = "^3.2" psycopg2-binary = "^2.7" gunicorn = "^22.0.0" flask = "^2.3.3" -sqlalchemy = "~1.3.3" +sqlalchemy = "^1.4.0" sqlalchemy-utils = "^0.37.3" PyYAML = ">=5.3,<7" From 1090ed5a46123e4ef76ccee8c2cf17539603619b Mon Sep 17 00:00:00 2001 From: EliseCastle23 <109446148+EliseCastle23@users.noreply.github.com> Date: Thu, 24 Oct 2024 11:30:12 -0600 Subject: [PATCH 37/54] updating dockerfile to consolidate --- Dockerfile | 50 +++++-------------------------------- deployment/nginx/nginx.conf | 44 -------------------------------- dockerrun.bash | 2 +- 3 files changed, 7 insertions(+), 89 deletions(-) delete mode 100644 deployment/nginx/nginx.conf diff --git a/Dockerfile b/Dockerfile index 8c717f88..46274345 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,38 +1,24 @@ ARG AZLINUX_BASE_VERSION=master -# Base stage with python-build-base -FROM quay.io/cdis/python-build-base:${AZLINUX_BASE_VERSION} AS base +## For local development +# FROM quay.io/cdis/python-nginx-al2:feat_python-nginx AS base -# Comment this in, and comment out the line above, if quay is down -# FROM 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/python-build-base:${AZLINUX_BASE_VERSION} as base +FROM 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/python-nginx-al2:feat_python-nginx as base ENV appname=indexd -ENV POETRY_NO_INTERACTION=1 \ - POETRY_VIRTUALENVS_IN_PROJECT=1 \ - POETRY_VIRTUALENVS_CREATE=1 WORKDIR /${appname} -# create gen3 user -# Create a group 'gen3' with GID 1000 and a user 'gen3' with UID 1000 -RUN groupadd -g 1000 gen3 && \ - useradd -m -s /bin/bash -u 1000 -g gen3 gen3 && \ - chown -R gen3:gen3 /$appname && \ - chown -R gen3:gen3 /venv - +RUN chown -R gen3:gen3 /$appname # Builder stage FROM base AS builder USER gen3 - -RUN python -m venv /venv - COPY poetry.lock pyproject.toml /${appname}/ -RUN pip install --upgrade poetry && \ - poetry install -vv --only main --no-interaction +RUN poetry install -vv --only main --no-interaction COPY --chown=gen3:gen3 . /$appname COPY --chown=gen3:gen3 ./deployment/wsgi/wsgi.py /$appname/wsgi.py @@ -46,35 +32,11 @@ RUN git config --global --add safe.directory /${appname} && COMMIT=`git rev-pars # Final stage FROM base -COPY --from=builder /venv /venv COPY --from=builder /$appname /$appname -# Install nginx -RUN yum install nginx -y - -# allows nginx to run on port 80 without being root user -RUN setcap 'cap_net_bind_service=+ep' /usr/sbin/nginx - -# chown nginx directories -RUN chown -R gen3:gen3 /var/log/nginx - -# pipe nginx logs to stdout and stderr -RUN ln -sf /dev/stdout /var/log/nginx/access.log && ln -sf /dev/stderr /var/log/nginx/error.log - -# create /var/lib/nginx/tmp/client_body to allow nginx to write to indexd -RUN mkdir -p /var/lib/nginx/tmp/client_body -RUN chown -R gen3:gen3 /var/lib/nginx/ - -# copy nginx config -COPY ./deployment/nginx/nginx.conf /etc/nginx/nginx.conf - - # Switch to non-root user 'gen3' for the serving process USER gen3 -RUN source /venv/bin/activate - -ENV PYTHONUNBUFFERED=1 \ - PYTHONIOENCODING=UTF-8 +WORKDIR /$appname CMD ["/bin/bash", "-c", "/indexd/dockerrun.bash"] diff --git a/deployment/nginx/nginx.conf b/deployment/nginx/nginx.conf deleted file mode 100644 index c64485a9..00000000 --- a/deployment/nginx/nginx.conf +++ /dev/null @@ -1,44 +0,0 @@ -user gen3; -worker_processes auto; -error_log /var/log/nginx/error.log notice; -pid /var/lib/nginx/nginx.pid; - -# Load dynamic modules. See /usr/share/doc/nginx/README.dynamic. -include /usr/share/nginx/modules/*.conf; - -events { - worker_connections 1024; -} - -http { - log_format main '$remote_addr - $remote_user [$time_local] "$request" ' - '$status $body_bytes_sent "$http_referer" ' - '"$http_user_agent" "$http_x_forwarded_for"'; - - access_log /var/log/nginx/access.log main; - - sendfile on; - tcp_nopush on; - keepalive_timeout 65; - types_hash_max_size 4096; - - include /etc/nginx/mime.types; - default_type application/octet-stream; - - # Load modular configuration files from the /etc/nginx/conf.d directory. - # See http://nginx.org/en/docs/ngx_core_module.html#include - # for more information. - include /etc/nginx/conf.d/*.conf; - - server { - - listen 80; - server_name localhost; - - location / { - proxy_pass http://127.0.0.1:8000; - proxy_set_header Host $host; - proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for; - } - } -} diff --git a/dockerrun.bash b/dockerrun.bash index 8b14b2bb..ea022df9 100755 --- a/dockerrun.bash +++ b/dockerrun.bash @@ -1,4 +1,4 @@ #!/bin/bash - +source .venv/bin/activate nginx gunicorn -c "/indexd/deployment/wsgi/gunicorn.conf.py" From 82ee91ed34d9cf8ee710a91d9914d4ecada648f6 Mon Sep 17 00:00:00 2001 From: EliseCastle23 <109446148+EliseCastle23@users.noreply.github.com> Date: Thu, 24 Oct 2024 11:50:28 -0600 Subject: [PATCH 38/54] adding suggested updates --- Dockerfile | 2 +- docker-compose.yaml | 36 ------------------------------------ poetry.lock | 10 +++++----- pyproject.toml | 4 ++-- 4 files changed, 8 insertions(+), 44 deletions(-) delete mode 100644 docker-compose.yaml diff --git a/Dockerfile b/Dockerfile index 46274345..d95c2387 100644 --- a/Dockerfile +++ b/Dockerfile @@ -3,7 +3,7 @@ ARG AZLINUX_BASE_VERSION=master ## For local development # FROM quay.io/cdis/python-nginx-al2:feat_python-nginx AS base -FROM 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/python-nginx-al2:feat_python-nginx as base +FROM 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/python-nginx-al2:feat_python-nginx AS base ENV appname=indexd diff --git a/docker-compose.yaml b/docker-compose.yaml deleted file mode 100644 index c0157eef..00000000 --- a/docker-compose.yaml +++ /dev/null @@ -1,36 +0,0 @@ -version: '3.8' - -services: - postgres: - image: postgres:13 - environment: - POSTGRES_USER: postgres - POSTGRES_PASSWORD: postgres - POSTGRES_DB: postgres - POSTGRES_HOST_AUTH_METHOD: trust - ports: - - "5432:5432" - - python: - image: quay.io/cdis/indexd:feat_GPE-788 - platform: linux/amd64 - volumes: - - .:/app - working_dir: /app - depends_on: - - postgres - network_mode: "service:postgres" - environment: - POSTGRES_USER: postgres - POSTGRES_PASSWORD: postgres - POSTGRES_DB: postgres - POSTGRES_HOST: postgres - POSTGRES_PORT: 5432 - PGHOST: postgres - command: > - bash -c " - source /venv/bin/activate && - poetry install && - bash tests/ci_commands_script.sh - # poetry run pytest -vv --cov=indexd --cov=migrations/versions --cov-append --cov-report xml tests - " diff --git a/poetry.lock b/poetry.lock index c3a8347b..bca486ff 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.8.4 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. [[package]] name = "alembic" @@ -715,13 +715,13 @@ test = ["objgraph", "psutil"] [[package]] name = "gunicorn" -version = "22.0.0" +version = "23.0.0" description = "WSGI HTTP Server for UNIX" optional = false python-versions = ">=3.7" files = [ - {file = "gunicorn-22.0.0-py3-none-any.whl", hash = "sha256:350679f91b24062c86e386e198a15438d53a7a8207235a78ba1b53df4c4378d9"}, - {file = "gunicorn-22.0.0.tar.gz", hash = "sha256:4a0b436239ff76fb33f11c07a16482c521a7e09c1ce3cc293c2330afe01bec63"}, + {file = "gunicorn-23.0.0-py3-none-any.whl", hash = "sha256:ec400d38950de4dfd418cff8328b2c8faed0edb0d517d3394e457c317908ca4d"}, + {file = "gunicorn-23.0.0.tar.gz", hash = "sha256:f014447a0101dc57e294f6c18ca6b40227a4c90e9bdb586042628030cba004ec"}, ] [package.dependencies] @@ -1626,4 +1626,4 @@ type = ["pytest-mypy"] [metadata] lock-version = "2.0" python-versions = ">=3.9,<4.0" -content-hash = "8681bdae6413fe559de688ef3e29e669db286e5c882f2d4ee14f937ea2ef2675" +content-hash = "4b5a302fbaf7b402a29db5e2fe71958b13e3dc8e55f22c2cd3da10f1e4cb23c1" diff --git a/pyproject.toml b/pyproject.toml index b1355933..67da51f7 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -21,8 +21,8 @@ gen3authz = "^1.0.4" hsclient = {git = "https://github.com/uc-cdis/hsclient", rev = "1.0.0"} indexclient = "^2.1.0" jsonschema = "^3.2" -psycopg2-binary = "^2.7" -gunicorn = "^22.0.0" +psycopg2-binary = ">=2.7" +gunicorn = ">=22.0.0" flask = "^2.3.3" sqlalchemy = "^1.4.0" sqlalchemy-utils = "^0.37.3" From f0146e68040325e18243e4f39a33eebb91e3afd2 Mon Sep 17 00:00:00 2001 From: EliseCastle23 <109446148+EliseCastle23@users.noreply.github.com> Date: Thu, 24 Oct 2024 12:04:54 -0600 Subject: [PATCH 39/54] making suggested updates --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index d95c2387..7a318925 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,6 +1,6 @@ ARG AZLINUX_BASE_VERSION=master -## For local development +# For local development # FROM quay.io/cdis/python-nginx-al2:feat_python-nginx AS base FROM 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/python-nginx-al2:feat_python-nginx AS base From 49e07fdef6e9140d405177e8682f85b8b2c2e4f7 Mon Sep 17 00:00:00 2001 From: EliseCastle23 <109446148+EliseCastle23@users.noreply.github.com> Date: Thu, 24 Oct 2024 13:11:54 -0600 Subject: [PATCH 40/54] adding update to number of workers --- deployment/wsgi/gunicorn.conf.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/deployment/wsgi/gunicorn.conf.py b/deployment/wsgi/gunicorn.conf.py index 1eaa94a1..64092ba3 100644 --- a/deployment/wsgi/gunicorn.conf.py +++ b/deployment/wsgi/gunicorn.conf.py @@ -1,6 +1,6 @@ wsgi_app = "deployment.wsgi.wsgi:application" bind = "0.0.0.0:8000" -workers = 4 +workers = 1 preload_app = True user = "gen3" group = "gen3" From f223caa2f08e2fcb6bea6a75c26971c799cf30fa Mon Sep 17 00:00:00 2001 From: EliseCastle23 <109446148+EliseCastle23@users.noreply.github.com> Date: Thu, 24 Oct 2024 14:57:09 -0600 Subject: [PATCH 41/54] fixing base image ref --- Dockerfile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index 7a318925..7fe154ef 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,9 +1,9 @@ ARG AZLINUX_BASE_VERSION=master # For local development -# FROM quay.io/cdis/python-nginx-al2:feat_python-nginx AS base +FROM quay.io/cdis/python-nginx-al:feat_python-nginx AS base -FROM 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/python-nginx-al2:feat_python-nginx AS base +# FROM 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/python-nginx-al2:feat_python-nginx AS base ENV appname=indexd From d7b9b86a4ed09c10e6a4e6e30723d9b3d6a1dfed Mon Sep 17 00:00:00 2001 From: EliseCastle23 <109446148+EliseCastle23@users.noreply.github.com> Date: Thu, 31 Oct 2024 14:00:24 -0600 Subject: [PATCH 42/54] testing change to pyproject --- poetry.lock | 30 +++++++++++++++--------------- pyproject.toml | 4 ++-- 2 files changed, 17 insertions(+), 17 deletions(-) diff --git a/poetry.lock b/poetry.lock index bca486ff..fad35d1d 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.4 and should not be changed by hand. [[package]] name = "alembic" @@ -715,13 +715,13 @@ test = ["objgraph", "psutil"] [[package]] name = "gunicorn" -version = "23.0.0" +version = "22.0.0" description = "WSGI HTTP Server for UNIX" optional = false python-versions = ">=3.7" files = [ - {file = "gunicorn-23.0.0-py3-none-any.whl", hash = "sha256:ec400d38950de4dfd418cff8328b2c8faed0edb0d517d3394e457c317908ca4d"}, - {file = "gunicorn-23.0.0.tar.gz", hash = "sha256:f014447a0101dc57e294f6c18ca6b40227a4c90e9bdb586042628030cba004ec"}, + {file = "gunicorn-22.0.0-py3-none-any.whl", hash = "sha256:350679f91b24062c86e386e198a15438d53a7a8207235a78ba1b53df4c4378d9"}, + {file = "gunicorn-22.0.0.tar.gz", hash = "sha256:4a0b436239ff76fb33f11c07a16482c521a7e09c1ce3cc293c2330afe01bec63"}, ] [package.dependencies] @@ -1375,23 +1375,23 @@ tests = ["coverage (>=3.7.1,<6.0.0)", "flake8", "mypy", "pytest (>=4.6)", "pytes [[package]] name = "setuptools" -version = "75.2.0" +version = "75.3.0" description = "Easily download, build, install, upgrade, and uninstall Python packages" optional = false python-versions = ">=3.8" files = [ - {file = "setuptools-75.2.0-py3-none-any.whl", hash = "sha256:a7fcb66f68b4d9e8e66b42f9876150a3371558f98fa32222ffaa5bced76406f8"}, - {file = "setuptools-75.2.0.tar.gz", hash = "sha256:753bb6ebf1f465a1912e19ed1d41f403a79173a9acf66a42e7e6aec45c3c16ec"}, + {file = "setuptools-75.3.0-py3-none-any.whl", hash = "sha256:f2504966861356aa38616760c0f66568e535562374995367b4e69c7143cf6bcd"}, + {file = "setuptools-75.3.0.tar.gz", hash = "sha256:fba5dd4d766e97be1b1681d98712680ae8f2f26d7881245f2ce9e40714f1a686"}, ] [package.extras] check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)", "ruff (>=0.5.2)"] -core = ["importlib-metadata (>=6)", "importlib-resources (>=5.10.2)", "jaraco.collections", "jaraco.functools", "jaraco.text (>=3.7)", "more-itertools", "more-itertools (>=8.8)", "packaging", "packaging (>=24)", "platformdirs (>=2.6.2)", "tomli (>=2.0.1)", "wheel (>=0.43.0)"] +core = ["importlib-metadata (>=6)", "importlib-resources (>=5.10.2)", "jaraco.collections", "jaraco.functools", "jaraco.text (>=3.7)", "more-itertools", "more-itertools (>=8.8)", "packaging", "packaging (>=24)", "platformdirs (>=4.2.2)", "tomli (>=2.0.1)", "wheel (>=0.43.0)"] cover = ["pytest-cov"] doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "pyproject-hooks (!=1.1)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (>=1,<2)", "sphinx-reredirects", "sphinxcontrib-towncrier", "towncrier (<24.7)"] enabler = ["pytest-enabler (>=2.2)"] -test = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "ini2toml[lite] (>=0.14)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "jaraco.test", "packaging (>=23.2)", "pip (>=19.1)", "pyproject-hooks (!=1.1)", "pytest (>=6,!=8.1.*)", "pytest-home (>=0.5)", "pytest-perf", "pytest-subprocess", "pytest-timeout", "pytest-xdist (>=3)", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel (>=0.44.0)"] -type = ["importlib-metadata (>=7.0.2)", "jaraco.develop (>=7.21)", "mypy (==1.11.*)", "pytest-mypy"] +test = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "ini2toml[lite] (>=0.14)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "jaraco.test (>=5.5)", "packaging (>=23.2)", "pip (>=19.1)", "pyproject-hooks (!=1.1)", "pytest (>=6,!=8.1.*)", "pytest-home (>=0.5)", "pytest-perf", "pytest-subprocess", "pytest-timeout", "pytest-xdist (>=3)", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel (>=0.44.0)"] +type = ["importlib-metadata (>=7.0.2)", "jaraco.develop (>=7.21)", "mypy (==1.12.*)", "pytest-mypy"] [[package]] name = "six" @@ -1578,13 +1578,13 @@ zstd = ["zstandard (>=0.18.0)"] [[package]] name = "werkzeug" -version = "3.0.4" +version = "3.1.0" description = "The comprehensive WSGI web application library." optional = false -python-versions = ">=3.8" +python-versions = ">=3.9" files = [ - {file = "werkzeug-3.0.4-py3-none-any.whl", hash = "sha256:02c9eb92b7d6c06f31a782811505d2157837cea66aaede3e217c7c27c039476c"}, - {file = "werkzeug-3.0.4.tar.gz", hash = "sha256:34f2371506b250df4d4f84bfe7b0921e4762525762bbd936614909fe25cd7306"}, + {file = "werkzeug-3.1.0-py3-none-any.whl", hash = "sha256:208a2e31a4a54c8b3d2244f2079ca1d3851629a7a7d546646059c64fb746023a"}, + {file = "werkzeug-3.1.0.tar.gz", hash = "sha256:6f2a0d38f25ba5a75c36c45b4ae350c7a23b57e3b974e9eb2d6851f2c648c00d"}, ] [package.dependencies] @@ -1626,4 +1626,4 @@ type = ["pytest-mypy"] [metadata] lock-version = "2.0" python-versions = ">=3.9,<4.0" -content-hash = "4b5a302fbaf7b402a29db5e2fe71958b13e3dc8e55f22c2cd3da10f1e4cb23c1" +content-hash = "8681bdae6413fe559de688ef3e29e669db286e5c882f2d4ee14f937ea2ef2675" diff --git a/pyproject.toml b/pyproject.toml index 67da51f7..b1355933 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -21,8 +21,8 @@ gen3authz = "^1.0.4" hsclient = {git = "https://github.com/uc-cdis/hsclient", rev = "1.0.0"} indexclient = "^2.1.0" jsonschema = "^3.2" -psycopg2-binary = ">=2.7" -gunicorn = ">=22.0.0" +psycopg2-binary = "^2.7" +gunicorn = "^22.0.0" flask = "^2.3.3" sqlalchemy = "^1.4.0" sqlalchemy-utils = "^0.37.3" From 11ad9b32ad6bbde7bedcf795b8d6c8b8e336d689 Mon Sep 17 00:00:00 2001 From: EliseCastle23 <109446148+EliseCastle23@users.noreply.github.com> Date: Fri, 1 Nov 2024 09:42:53 -0600 Subject: [PATCH 43/54] removing comment --- Dockerfile | 1 - 1 file changed, 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 7fe154ef..65b13102 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,6 +1,5 @@ ARG AZLINUX_BASE_VERSION=master -# For local development FROM quay.io/cdis/python-nginx-al:feat_python-nginx AS base # FROM 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/python-nginx-al2:feat_python-nginx AS base From b255010e8bb19141af2c0907aa2b34b9bb3e2528 Mon Sep 17 00:00:00 2001 From: EliseCastle23 <109446148+EliseCastle23@users.noreply.github.com> Date: Fri, 1 Nov 2024 10:30:10 -0600 Subject: [PATCH 44/54] adding "poetry run" to "gunicorn" command --- dockerrun.bash | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dockerrun.bash b/dockerrun.bash index ea022df9..b560f5ae 100755 --- a/dockerrun.bash +++ b/dockerrun.bash @@ -1,4 +1,4 @@ #!/bin/bash source .venv/bin/activate nginx -gunicorn -c "/indexd/deployment/wsgi/gunicorn.conf.py" +poetry run gunicorn -c "/indexd/deployment/wsgi/gunicorn.conf.py" From d12ad68337fba9a4317fa61156e16dc256541460 Mon Sep 17 00:00:00 2001 From: EliseCastle23 <109446148+EliseCastle23@users.noreply.github.com> Date: Fri, 1 Nov 2024 10:31:17 -0600 Subject: [PATCH 45/54] updating pyproject dependencies --- poetry.lock | 8 ++++---- pyproject.toml | 4 ++-- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/poetry.lock b/poetry.lock index fad35d1d..d780cbf5 100644 --- a/poetry.lock +++ b/poetry.lock @@ -715,13 +715,13 @@ test = ["objgraph", "psutil"] [[package]] name = "gunicorn" -version = "22.0.0" +version = "23.0.0" description = "WSGI HTTP Server for UNIX" optional = false python-versions = ">=3.7" files = [ - {file = "gunicorn-22.0.0-py3-none-any.whl", hash = "sha256:350679f91b24062c86e386e198a15438d53a7a8207235a78ba1b53df4c4378d9"}, - {file = "gunicorn-22.0.0.tar.gz", hash = "sha256:4a0b436239ff76fb33f11c07a16482c521a7e09c1ce3cc293c2330afe01bec63"}, + {file = "gunicorn-23.0.0-py3-none-any.whl", hash = "sha256:ec400d38950de4dfd418cff8328b2c8faed0edb0d517d3394e457c317908ca4d"}, + {file = "gunicorn-23.0.0.tar.gz", hash = "sha256:f014447a0101dc57e294f6c18ca6b40227a4c90e9bdb586042628030cba004ec"}, ] [package.dependencies] @@ -1626,4 +1626,4 @@ type = ["pytest-mypy"] [metadata] lock-version = "2.0" python-versions = ">=3.9,<4.0" -content-hash = "8681bdae6413fe559de688ef3e29e669db286e5c882f2d4ee14f937ea2ef2675" +content-hash = "4b5a302fbaf7b402a29db5e2fe71958b13e3dc8e55f22c2cd3da10f1e4cb23c1" diff --git a/pyproject.toml b/pyproject.toml index b1355933..67da51f7 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -21,8 +21,8 @@ gen3authz = "^1.0.4" hsclient = {git = "https://github.com/uc-cdis/hsclient", rev = "1.0.0"} indexclient = "^2.1.0" jsonschema = "^3.2" -psycopg2-binary = "^2.7" -gunicorn = "^22.0.0" +psycopg2-binary = ">=2.7" +gunicorn = ">=22.0.0" flask = "^2.3.3" sqlalchemy = "^1.4.0" sqlalchemy-utils = "^0.37.3" From 7a86165e477140ae6a0ee2c47d4df1d3b351ed03 Mon Sep 17 00:00:00 2001 From: EliseCastle23 <109446148+EliseCastle23@users.noreply.github.com> Date: Fri, 1 Nov 2024 10:46:59 -0600 Subject: [PATCH 46/54] updating poetry install command --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 65b13102..aa998bf1 100644 --- a/Dockerfile +++ b/Dockerfile @@ -23,7 +23,7 @@ COPY --chown=gen3:gen3 . /$appname COPY --chown=gen3:gen3 ./deployment/wsgi/wsgi.py /$appname/wsgi.py # Run poetry again so this app itself gets installed too -RUN poetry install --without dev --no-interaction +RUN poetry install --only main --no-interaction RUN git config --global --add safe.directory /${appname} && COMMIT=`git rev-parse HEAD` && echo "COMMIT=\"${COMMIT}\"" > /$appname/version_data.py \ && VERSION=`git describe --always --tags` && echo "VERSION=\"${VERSION}\"" >> /$appname/version_data.py From 6f93e8da1f160ec2837c8cdd1b21501059d7e8d7 Mon Sep 17 00:00:00 2001 From: Maribelle Hannah Gomez Date: Fri, 1 Nov 2024 11:56:50 -0500 Subject: [PATCH 47/54] update poetry install cmd --- Dockerfile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index aa998bf1..c7ee59f7 100644 --- a/Dockerfile +++ b/Dockerfile @@ -17,13 +17,13 @@ USER gen3 COPY poetry.lock pyproject.toml /${appname}/ -RUN poetry install -vv --only main --no-interaction +RUN poetry install -vv --without dev --no-interaction COPY --chown=gen3:gen3 . /$appname COPY --chown=gen3:gen3 ./deployment/wsgi/wsgi.py /$appname/wsgi.py # Run poetry again so this app itself gets installed too -RUN poetry install --only main --no-interaction +RUN poetry install --without dev --no-interaction RUN git config --global --add safe.directory /${appname} && COMMIT=`git rev-parse HEAD` && echo "COMMIT=\"${COMMIT}\"" > /$appname/version_data.py \ && VERSION=`git describe --always --tags` && echo "VERSION=\"${VERSION}\"" >> /$appname/version_data.py From aa0502d86198a03cfc1bdfc9144c79df13571cbc Mon Sep 17 00:00:00 2001 From: EliseCastle23 <109446148+EliseCastle23@users.noreply.github.com> Date: Fri, 1 Nov 2024 11:49:44 -0600 Subject: [PATCH 48/54] removing source command --- dockerrun.bash | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dockerrun.bash b/dockerrun.bash index b560f5ae..aee1b22d 100755 --- a/dockerrun.bash +++ b/dockerrun.bash @@ -1,4 +1,4 @@ #!/bin/bash -source .venv/bin/activate + nginx poetry run gunicorn -c "/indexd/deployment/wsgi/gunicorn.conf.py" From 78634f63266599c04df6559ebc563b508dc8217b Mon Sep 17 00:00:00 2001 From: EliseCastle23 <109446148+EliseCastle23@users.noreply.github.com> Date: Fri, 1 Nov 2024 12:15:09 -0600 Subject: [PATCH 49/54] updating base image --- Dockerfile | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index c7ee59f7..fc3242d9 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,8 +1,9 @@ ARG AZLINUX_BASE_VERSION=master -FROM quay.io/cdis/python-nginx-al:feat_python-nginx AS base +# Base stage with python-build-base +FROM quay.io/cdis/python-nginx-al:${AZLINUX_BASE_VERSION} AS base -# FROM 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/python-nginx-al2:feat_python-nginx AS base +# FROM 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/python-build-base:${AZLINUX_BASE_VERSION} as base ENV appname=indexd From 69e82d7a2293efc39d95d8958e833bccb45f7fd4 Mon Sep 17 00:00:00 2001 From: EliseCastle23 <109446148+EliseCastle23@users.noreply.github.com> Date: Fri, 1 Nov 2024 12:15:58 -0600 Subject: [PATCH 50/54] updating "AS" --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index fc3242d9..f6156dfd 100644 --- a/Dockerfile +++ b/Dockerfile @@ -3,7 +3,7 @@ ARG AZLINUX_BASE_VERSION=master # Base stage with python-build-base FROM quay.io/cdis/python-nginx-al:${AZLINUX_BASE_VERSION} AS base -# FROM 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/python-build-base:${AZLINUX_BASE_VERSION} as base +# FROM 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/python-build-base:${AZLINUX_BASE_VERSION} AS base ENV appname=indexd From c537faada555689edfedd50d91a764aa939ebbd4 Mon Sep 17 00:00:00 2001 From: EliseCastle23 <109446148+EliseCastle23@users.noreply.github.com> Date: Fri, 1 Nov 2024 13:21:13 -0600 Subject: [PATCH 51/54] Update Dockerfile --- Dockerfile | 2 -- 1 file changed, 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index f6156dfd..3bdd59c1 100644 --- a/Dockerfile +++ b/Dockerfile @@ -3,8 +3,6 @@ ARG AZLINUX_BASE_VERSION=master # Base stage with python-build-base FROM quay.io/cdis/python-nginx-al:${AZLINUX_BASE_VERSION} AS base -# FROM 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/python-build-base:${AZLINUX_BASE_VERSION} AS base - ENV appname=indexd WORKDIR /${appname} From 2be1a745b6ec8463a893f4abd735901b6dd51f19 Mon Sep 17 00:00:00 2001 From: EliseCastle23 <109446148+EliseCastle23@users.noreply.github.com> Date: Tue, 12 Nov 2024 08:34:50 -0700 Subject: [PATCH 52/54] fixing variable syntax --- Dockerfile | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/Dockerfile b/Dockerfile index 3bdd59c1..784a7193 100644 --- a/Dockerfile +++ b/Dockerfile @@ -7,7 +7,7 @@ ENV appname=indexd WORKDIR /${appname} -RUN chown -R gen3:gen3 /$appname +RUN chown -R gen3:gen3 /${appname} # Builder stage FROM base AS builder @@ -18,23 +18,23 @@ COPY poetry.lock pyproject.toml /${appname}/ RUN poetry install -vv --without dev --no-interaction -COPY --chown=gen3:gen3 . /$appname -COPY --chown=gen3:gen3 ./deployment/wsgi/wsgi.py /$appname/wsgi.py +COPY --chown=gen3:gen3 . /${appname} +COPY --chown=gen3:gen3 ./deployment/wsgi/wsgi.py /${appname}/wsgi.py # Run poetry again so this app itself gets installed too RUN poetry install --without dev --no-interaction -RUN git config --global --add safe.directory /${appname} && COMMIT=`git rev-parse HEAD` && echo "COMMIT=\"${COMMIT}\"" > /$appname/version_data.py \ - && VERSION=`git describe --always --tags` && echo "VERSION=\"${VERSION}\"" >> /$appname/version_data.py +RUN git config --global --add safe.directory /${appname} && COMMIT=`git rev-parse HEAD` && echo "COMMIT=\"${COMMIT}\"" > /${appname}/version_data.py \ + && VERSION=`git describe --always --tags` && echo "VERSION=\"${VERSION}\"" >> /${appname}/version_data.py # Final stage FROM base -COPY --from=builder /$appname /$appname +COPY --from=builder /${appname} /${appname} # Switch to non-root user 'gen3' for the serving process USER gen3 -WORKDIR /$appname +WORKDIR /${appname} CMD ["/bin/bash", "-c", "/indexd/dockerrun.bash"] From d5e45788f15ee33c1dd9a02534bbc2730b3f42bb Mon Sep 17 00:00:00 2001 From: EliseCastle23 <109446148+EliseCastle23@users.noreply.github.com> Date: Wed, 13 Nov 2024 08:59:05 -0700 Subject: [PATCH 53/54] updating workflow to include arm images --- .github/workflows/image_build_push.yaml | 2 - poetry.lock | 50 ++++++++++++------------- 2 files changed, 25 insertions(+), 27 deletions(-) diff --git a/.github/workflows/image_build_push.yaml b/.github/workflows/image_build_push.yaml index 779aad0e..2221aee4 100644 --- a/.github/workflows/image_build_push.yaml +++ b/.github/workflows/image_build_push.yaml @@ -6,8 +6,6 @@ jobs: ci: name: Build Image and Push to Quay uses: uc-cdis/.github/.github/workflows/image_build_push.yaml@master - with: - BUILD_PLATFORMS: "linux/amd64" secrets: ECR_AWS_ACCESS_KEY_ID: ${{ secrets.ECR_AWS_ACCESS_KEY_ID }} ECR_AWS_SECRET_ACCESS_KEY: ${{ secrets.ECR_AWS_SECRET_ACCESS_KEY }} diff --git a/poetry.lock b/poetry.lock index d780cbf5..122a37eb 100644 --- a/poetry.lock +++ b/poetry.lock @@ -2,13 +2,13 @@ [[package]] name = "alembic" -version = "1.13.3" +version = "1.14.0" description = "A database migration tool for SQLAlchemy." optional = false python-versions = ">=3.8" files = [ - {file = "alembic-1.13.3-py3-none-any.whl", hash = "sha256:908e905976d15235fae59c9ac42c4c5b75cfcefe3d27c0fbf7ae15a37715d80e"}, - {file = "alembic-1.13.3.tar.gz", hash = "sha256:203503117415561e203aa14541740643a611f641517f0209fcae63e9fa09f1a2"}, + {file = "alembic-1.14.0-py3-none-any.whl", hash = "sha256:99bd884ca390466db5e27ffccff1d179ec5c05c965cfefc0607e69f9e411cb25"}, + {file = "alembic-1.14.0.tar.gz", hash = "sha256:b00892b53b3642d0b8dbedba234dbf1924b69be83a9a769d5a624b01094e304b"}, ] [package.dependencies] @@ -121,13 +121,13 @@ files = [ [[package]] name = "blinker" -version = "1.8.2" +version = "1.9.0" description = "Fast, simple object-to-object and broadcast signaling" optional = false -python-versions = ">=3.8" +python-versions = ">=3.9" files = [ - {file = "blinker-1.8.2-py3-none-any.whl", hash = "sha256:1779309f71bf239144b9399d06ae925637cf6634cf6bd131104184531bf67c01"}, - {file = "blinker-1.8.2.tar.gz", hash = "sha256:8f77b09d3bf7c795e969e9486f39c2c5e9c39d4ee07424be2bc594ece9642d83"}, + {file = "blinker-1.9.0-py3-none-any.whl", hash = "sha256:ba0efaa9080b619ff2f3459d1d500c57bddea4a6b424b60a91141db6fd2f08bc"}, + {file = "blinker-1.9.0.tar.gz", hash = "sha256:b4ce2265a7abece45e7cc896e98dbebe6cead56bcf805a3d23136d145f5445bf"}, ] [[package]] @@ -1026,13 +1026,13 @@ test = ["pytest (<5.4)", "pytest-cov"] [[package]] name = "packaging" -version = "24.1" +version = "24.2" description = "Core utilities for Python packages" optional = false python-versions = ">=3.8" files = [ - {file = "packaging-24.1-py3-none-any.whl", hash = "sha256:5b8f2217dbdbd2f7f384c41c628544e6d52f2d0f53c6d0c3ea61aa5d1d7ff124"}, - {file = "packaging-24.1.tar.gz", hash = "sha256:026ed72c8ed3fcce5bf8950572258698927fd1dbda10a5e981cdf0ac37f4f002"}, + {file = "packaging-24.2-py3-none-any.whl", hash = "sha256:09abb1bccd265c01f4a3aa3f7a7db064b36514d2cba19a2f694fe6150451a759"}, + {file = "packaging-24.2.tar.gz", hash = "sha256:c228a6dc5e932d346bc5739379109d49e8853dd8223571c7c5b55260edc0b97f"}, ] [[package]] @@ -1375,23 +1375,23 @@ tests = ["coverage (>=3.7.1,<6.0.0)", "flake8", "mypy", "pytest (>=4.6)", "pytes [[package]] name = "setuptools" -version = "75.3.0" +version = "75.5.0" description = "Easily download, build, install, upgrade, and uninstall Python packages" optional = false -python-versions = ">=3.8" +python-versions = ">=3.9" files = [ - {file = "setuptools-75.3.0-py3-none-any.whl", hash = "sha256:f2504966861356aa38616760c0f66568e535562374995367b4e69c7143cf6bcd"}, - {file = "setuptools-75.3.0.tar.gz", hash = "sha256:fba5dd4d766e97be1b1681d98712680ae8f2f26d7881245f2ce9e40714f1a686"}, + {file = "setuptools-75.5.0-py3-none-any.whl", hash = "sha256:87cb777c3b96d638ca02031192d40390e0ad97737e27b6b4fa831bea86f2f829"}, + {file = "setuptools-75.5.0.tar.gz", hash = "sha256:5c4ccb41111392671f02bb5f8436dfc5a9a7185e80500531b133f5775c4163ef"}, ] [package.extras] -check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)", "ruff (>=0.5.2)"] -core = ["importlib-metadata (>=6)", "importlib-resources (>=5.10.2)", "jaraco.collections", "jaraco.functools", "jaraco.text (>=3.7)", "more-itertools", "more-itertools (>=8.8)", "packaging", "packaging (>=24)", "platformdirs (>=4.2.2)", "tomli (>=2.0.1)", "wheel (>=0.43.0)"] +check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)", "ruff (>=0.7.0)"] +core = ["importlib-metadata (>=6)", "jaraco.collections", "jaraco.functools (>=4)", "jaraco.text (>=3.7)", "more-itertools", "more-itertools (>=8.8)", "packaging", "packaging (>=24.2)", "platformdirs (>=4.2.2)", "tomli (>=2.0.1)", "wheel (>=0.43.0)"] cover = ["pytest-cov"] doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "pyproject-hooks (!=1.1)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (>=1,<2)", "sphinx-reredirects", "sphinxcontrib-towncrier", "towncrier (<24.7)"] enabler = ["pytest-enabler (>=2.2)"] -test = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "ini2toml[lite] (>=0.14)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "jaraco.test (>=5.5)", "packaging (>=23.2)", "pip (>=19.1)", "pyproject-hooks (!=1.1)", "pytest (>=6,!=8.1.*)", "pytest-home (>=0.5)", "pytest-perf", "pytest-subprocess", "pytest-timeout", "pytest-xdist (>=3)", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel (>=0.44.0)"] -type = ["importlib-metadata (>=7.0.2)", "jaraco.develop (>=7.21)", "mypy (==1.12.*)", "pytest-mypy"] +test = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "ini2toml[lite] (>=0.14)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "jaraco.test (>=5.5)", "packaging (>=24.2)", "pip (>=19.1)", "pyproject-hooks (!=1.1)", "pytest (>=6,!=8.1.*)", "pytest-home (>=0.5)", "pytest-perf", "pytest-subprocess", "pytest-timeout", "pytest-xdist (>=3)", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel (>=0.44.0)"] +type = ["importlib-metadata (>=7.0.2)", "jaraco.develop (>=7.21)", "mypy (>=1.12,<1.14)", "pytest-mypy"] [[package]] name = "six" @@ -1578,13 +1578,13 @@ zstd = ["zstandard (>=0.18.0)"] [[package]] name = "werkzeug" -version = "3.1.0" +version = "3.1.3" description = "The comprehensive WSGI web application library." optional = false python-versions = ">=3.9" files = [ - {file = "werkzeug-3.1.0-py3-none-any.whl", hash = "sha256:208a2e31a4a54c8b3d2244f2079ca1d3851629a7a7d546646059c64fb746023a"}, - {file = "werkzeug-3.1.0.tar.gz", hash = "sha256:6f2a0d38f25ba5a75c36c45b4ae350c7a23b57e3b974e9eb2d6851f2c648c00d"}, + {file = "werkzeug-3.1.3-py3-none-any.whl", hash = "sha256:54b78bf3716d19a65be4fceccc0d1d7b89e608834989dfae50ea87564639213e"}, + {file = "werkzeug-3.1.3.tar.gz", hash = "sha256:60723ce945c19328679790e3282cc758aa4a6040e4bb330f53d30fa546d44746"}, ] [package.dependencies] @@ -1606,13 +1606,13 @@ files = [ [[package]] name = "zipp" -version = "3.20.2" +version = "3.21.0" description = "Backport of pathlib-compatible object wrapper for zip files" optional = false -python-versions = ">=3.8" +python-versions = ">=3.9" files = [ - {file = "zipp-3.20.2-py3-none-any.whl", hash = "sha256:a817ac80d6cf4b23bf7f2828b7cabf326f15a001bea8b1f9b49631780ba28350"}, - {file = "zipp-3.20.2.tar.gz", hash = "sha256:bc9eb26f4506fda01b81bcde0ca78103b6e62f991b381fec825435c836edbc29"}, + {file = "zipp-3.21.0-py3-none-any.whl", hash = "sha256:ac1bbe05fd2991f160ebce24ffbac5f6d11d83dc90891255885223d42b3cd931"}, + {file = "zipp-3.21.0.tar.gz", hash = "sha256:2c9958f6430a2040341a52eb608ed6dd93ef4392e02ffe219417c1b28b5dd1f4"}, ] [package.extras] From 783b95a4fc4fab1945240ac130688a737170eb7f Mon Sep 17 00:00:00 2001 From: EliseCastle23 <109446148+EliseCastle23@users.noreply.github.com> Date: Fri, 15 Nov 2024 10:03:18 -0700 Subject: [PATCH 54/54] removing unneeded file --- deployment/scripts/indexd/indexd_setup.sh | 14 -------------- 1 file changed, 14 deletions(-) delete mode 100644 deployment/scripts/indexd/indexd_setup.sh diff --git a/deployment/scripts/indexd/indexd_setup.sh b/deployment/scripts/indexd/indexd_setup.sh deleted file mode 100644 index 8a189938..00000000 --- a/deployment/scripts/indexd/indexd_setup.sh +++ /dev/null @@ -1,14 +0,0 @@ -#!/bin/bash -# entrypoint bash script for indexd - -## try to install python util, or else fallback to environment variables. - -# activate virtual env -pushd /indexd -# TODO: check if poetry can install globally -python -m venv py-venv && . py-venv/bin/activate && source $HOME/.poetry/env -poetry install -vv --no-dev --no-interaction && poetry show -v -python3 -m pip install cdispyutils -popd - -/dockerrun.bash