From 6f6feb57c205b01e8c03ddac485f298ffeff5e7d Mon Sep 17 00:00:00 2001 From: George Thomas Date: Tue, 6 Aug 2024 09:44:15 -0700 Subject: [PATCH 01/43] (PPS-710): use new branches of gen3datamodel and related repos --- poetry.lock | 861 ++++++++++++++++++++----------------------------- pyproject.toml | 12 +- 2 files changed, 356 insertions(+), 517 deletions(-) diff --git a/poetry.lock b/poetry.lock index a4f2681f..bdf1c47b 100644 --- a/poetry.lock +++ b/poetry.lock @@ -13,13 +13,13 @@ files = [ [[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 = 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--git a/pyproject.toml b/pyproject.toml index f1ceb9f2..d85e5b98 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -15,18 +15,18 @@ authlib = "*" # let authutils decide which version we're using authutils = ">=6.0.0" boto = ">=2.49.0" botocore = "*" -datamodelutils = ">=1.0.0" -dictionaryutils = ">=3.4.10" +datamodelutils = {git = "https://github.com/uc-cdis/datamodelutils", branch = "chore/update-gen3datamodel"} +dictionaryutils = {git = "https://github.com/uc-cdis/dictionaryutils", branch = "chore/update-jsonschema"} envelopes = ">=0.4" Flask = ">=2.2.5" Flask-SQLAlchemy-Session = ">=1.1" fuzzywuzzy = ">=0.6.1" gen3authz = ">=1.0.4" graphene = ">=2.0.1" -jsonschema = ">=3.2" +jsonschema = "*" lxml = ">=4.6.5" psycopg2 = ">=2.8.4" -PyYAML = ">=5.4.1" +PyYAML = "*" requests = ">=2.31.0,<3.0.0" simplejson = ">=3.8.1" sqlalchemy = ">=1.3.*" @@ -34,8 +34,8 @@ cdispyutils = ">=2.0.1" psqlgraph = ">=3.0.1" cdiserrors = ">=1.0.0" cdislogging = ">=1.0.0" -gen3dictionary = ">=2.0.3" -gen3datamodel = ">=3.1.0" +gen3dictionary = {git = "https://github.com/uc-cdis/datadictionary.git", branch = "chore/add-unit-tests"} +gen3datamodel = {git = "https://github.com/uc-cdis/gen3datamodel.git", branch = "chore/update-jsonschema"} indexclient = ">=2.1.1" urllib3 = "<2.0.0" From 1e8c563f4eb9716c20dd8d19d5119df0e9ca759c Mon Sep 17 00:00:00 2001 From: George Thomas Date: Tue, 6 Aug 2024 09:49:02 -0700 Subject: [PATCH 02/43] (PPS-710): replace 'gdcdatamodel' with 'gen3datamodel' --- sheepdog/api.py | 4 ++-- sheepdog/utils/transforms/__init__.py | 2 +- sheepdog/utils/transforms/bcr_xml_to_json.py | 2 +- sheepdog/utils/transforms/graph_to_doc.py | 4 ++-- 4 files changed, 6 insertions(+), 6 deletions(-) diff --git a/sheepdog/api.py b/sheepdog/api.py index 79352c74..b1457e2f 100644 --- a/sheepdog/api.py +++ b/sheepdog/api.py @@ -47,8 +47,8 @@ def app_register_blueprints(app): datadictionary = gdcdictionary.gdcdictionary dictionary.init(datadictionary) - from gdcdatamodel import models as md - from gdcdatamodel import validators as vd + from gen3datamodel import models as md + from gen3datamodel import validators as vd models.init(md) validators.init(vd) diff --git a/sheepdog/utils/transforms/__init__.py b/sheepdog/utils/transforms/__init__.py index 69a399ea..6e1bcd21 100644 --- a/sheepdog/utils/transforms/__init__.py +++ b/sheepdog/utils/transforms/__init__.py @@ -236,7 +236,7 @@ def get_converted_type_from_list(cls, prop_name, value): # Parse the item type from the dictionary schema. # NOTE: `cls.__pg_properties__.get(prop_name)` would be easier but the value is # only `list` and does not include the item type. - # https://github.com/uc-cdis/gdcdatamodel/blob/190f998/gdcdatamodel/models/__init__.py#L120 + # https://github.com/uc-cdis/gen3datamodel/blob/190f998/gdcdatamodel/models/__init__.py#L120 # Setting this ^ to `list[]` may work but it breaks other code. list_item_type = ( dictionary.schema.get(cls.label, {}) diff --git a/sheepdog/utils/transforms/bcr_xml_to_json.py b/sheepdog/utils/transforms/bcr_xml_to_json.py index 3950db00..093b11e0 100644 --- a/sheepdog/utils/transforms/bcr_xml_to_json.py +++ b/sheepdog/utils/transforms/bcr_xml_to_json.py @@ -575,7 +575,7 @@ class BcrClinicalXmlToJsonParser(object): def __init__(self, project_code, mapping=None): if mapping is None: mapping = pkg_resources.resource_string( - "gdcdatamodel", "xml_mappings/tcga_clinical.yaml" + "gen3datamodel", "xml_mappings/tcga_clinical.yaml" ) self.xpath_ref = yaml.safe_load(mapping) self.docs = [] diff --git a/sheepdog/utils/transforms/graph_to_doc.py b/sheepdog/utils/transforms/graph_to_doc.py index 0efb1a78..f76fa00a 100644 --- a/sheepdog/utils/transforms/graph_to_doc.py +++ b/sheepdog/utils/transforms/graph_to_doc.py @@ -792,7 +792,7 @@ def export_all(node_label, project_id, file_format, db, without_id): )) """ # Examples in coments throughout function will start from ``'case'`` as an - # example ``node_label`` (so ``gdcdatamodel.models.Case`` is the example + # example ``node_label`` (so ``gen3datamodel.models.Case`` is the example # class). titles_non_linked, titles_linked = get_all_titles(node_label, without_id) @@ -803,7 +803,7 @@ def export_all(node_label, project_id, file_format, db, without_id): # # Case._pg_links == { # 'experiments': { - # 'dst_type': gdcdatamodel.models.Experiment, + # 'dst_type': gen3datamodel.models.Experiment, # 'edge_out': '_CaseMemberOfExperiment_out', # } # } From 4d291f92e616955639d337cc72048b5be50ccb4c Mon Sep 17 00:00:00 2001 From: George Thomas Date: Tue, 6 Aug 2024 09:50:51 -0700 Subject: [PATCH 03/43] (PPS-710): replace 'gdcdatamodel' with 'gen3datamodel' --- bin/setup_psqlgraph.py | 2 +- bin/setup_transactionlogs.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/bin/setup_psqlgraph.py b/bin/setup_psqlgraph.py index 4c708d64..3a2d971a 100755 --- a/bin/setup_psqlgraph.py +++ b/bin/setup_psqlgraph.py @@ -3,7 +3,7 @@ import logging from sqlalchemy import create_engine -from gdcdatamodel.models import * +from gen3datamodel.models import * from psqlgraph import create_all, Node, Edge diff --git a/bin/setup_transactionlogs.py b/bin/setup_transactionlogs.py index d395c911..8a462005 100644 --- a/bin/setup_transactionlogs.py +++ b/bin/setup_transactionlogs.py @@ -5,7 +5,7 @@ import argparse from sqlalchemy import create_engine -from gdcdatamodel.models.submission import Base +from gen3datamodel.models.submission import Base def setup(host, port, user, password, database, use_ssl=False): From 5d36356ac8fb62c2627dfd3a8e6d6b928000d5cc Mon Sep 17 00:00:00 2001 From: George Thomas Date: Tue, 6 Aug 2024 09:58:15 -0700 Subject: [PATCH 04/43] (PPS-710): replace 'gdcdatamodel' with 'gen3datamodel' --- tests/integration/datadict/conftest.py | 4 ++-- tests/integration/datadictwithobjid/conftest.py | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/tests/integration/datadict/conftest.py b/tests/integration/datadict/conftest.py index eb298948..ad12efbd 100644 --- a/tests/integration/datadict/conftest.py +++ b/tests/integration/datadict/conftest.py @@ -181,8 +181,8 @@ def dictionary_setup(_app): get_mocked.return_value = resp datadictionary = DataDictionary(url=url) dictionary.init(datadictionary) - from gdcdatamodel import models as md - from gdcdatamodel import validators as vd + from gen3datamodel import models as md + from gen3datamodel import validators as vd models.init(md) validators.init(vd) diff --git a/tests/integration/datadictwithobjid/conftest.py b/tests/integration/datadictwithobjid/conftest.py index 7b1756ff..5badbd02 100644 --- a/tests/integration/datadictwithobjid/conftest.py +++ b/tests/integration/datadictwithobjid/conftest.py @@ -167,8 +167,8 @@ def dictionary_setup(_app): get_mocked.return_value = resp datadictionary = DataDictionary(url=url) dictionary.init(datadictionary) - from gdcdatamodel import models as md - from gdcdatamodel import validators as vd + from gen3datamodel import models as md + from gen3datamodel import validators as vd models.init(md) validators.init(vd) From 05048774a9368a409bbb35b6bdcb2874545fc868 Mon Sep 17 00:00:00 2001 From: George Thomas Date: Tue, 6 Aug 2024 10:42:32 -0700 Subject: [PATCH 05/43] (PPS-710): replace 'gdcdatamodel' with 'gen3datamodel' --- README.md | 2 +- docs/local_dev_environment.md | 2 +- run.py | 2 +- sample_usage.py | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index e9a7c3b2..3f38fe26 100644 --- a/README.md +++ b/README.md @@ -22,7 +22,7 @@ import sheepdog import datamodelutils from dictionaryutils import dictionary from gdcdictionary import gdcdictionary -from gdcdatamodel import models, validators +from gen3datamodel import models, validators dictionary.init(gdcdictionary) datamodelutils.validators.init(validators) diff --git a/docs/local_dev_environment.md b/docs/local_dev_environment.md index dc482e74..853615b0 100644 --- a/docs/local_dev_environment.md +++ b/docs/local_dev_environment.md @@ -195,7 +195,7 @@ For convenience, the minimal usage looks like the following: import datamodelutils from dictionaryutils import dictionary from gdcdictionary import gdcdictionary -from gdcdatamodel import models, validators +from gen3datamodel import models, validators from flask import Flask import sheepdog diff --git a/run.py b/run.py index 381b3690..f7e0e7f0 100755 --- a/run.py +++ b/run.py @@ -85,7 +85,7 @@ def set_user(*args, **kwargs): def run_with_fake_auth(): def get_project_ids(role="_member_", project_ids=None): - from gdcdatamodel import models as md + from gen3datamodel import models as md if project_ids is None: project_ids = [] diff --git a/sample_usage.py b/sample_usage.py index 0ed33874..86d1dd5d 100644 --- a/sample_usage.py +++ b/sample_usage.py @@ -1,7 +1,7 @@ import datamodelutils from dictionaryutils import dictionary from gdcdictionary import gdcdictionary -from gdcdatamodel import models, validators +from gen3datamodel import models, validators from flask import Flask import sheepdog From 643b42428c5ea61818a7203104d9e5ca016d8d3a Mon Sep 17 00:00:00 2001 From: EliseCastle23 <109446148+EliseCastle23@users.noreply.github.com> Date: Mon, 12 Aug 2024 10:55:27 -0600 Subject: [PATCH 06/43] adding nginx and gunicorn to sheepdog image --- Dockerfile | 128 ++++--- deployment/nginx/nginx.conf | 44 +++ deployment/uwsgi/uwsgi.ini | 32 -- deployment/wsgi/gunicorn.conf.py | 9 + deployment/wsgi/wsgi.py | 1 + dockerrun.bash | 4 + poetry.lock | 557 +++++++++++++++++-------------- pyproject.toml | 1 + 8 files changed, 438 insertions(+), 338 deletions(-) create mode 100644 deployment/nginx/nginx.conf delete mode 100644 deployment/uwsgi/uwsgi.ini create mode 100644 deployment/wsgi/gunicorn.conf.py create mode 100644 deployment/wsgi/wsgi.py create mode 100755 dockerrun.bash diff --git a/Dockerfile b/Dockerfile index 3841ed93..b5cf571e 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,65 +1,87 @@ -# To run: -# - Create and fill out `creds.json`: -# { -# "fence_host": "", -# "fence_username": "", -# "fence_password": "", -# "fence_database": "", -# "db_host": "", -# "db_username": "", -# "db_password": "", -# "db_database": "", -# "gdcapi_secret_key": "", -# "indexd_password": "", -# "hostname": "" -# } -# - Build the image: `docker build . -t sheepdog -f Dockerfile` -# - Run: `docker run -v /full/path/to/creds.json:/var/www/sheepdog/creds.json -p 81:80 sheepdog` -# To check running container: `docker exec -it sheepdog /bin/bash` - -FROM quay.io/cdis/python:python3.9-buster-2.0.0 +ARG AZLINUX_BASE_VERSION=master + +# 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=sheepdog +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 yum install -y gcc gcc-c++ make postgresql-devel + +RUN dnf install python3-devel -y + +USER gen3 + + +RUN python -m venv /venv + +COPY poetry.lock pyproject.toml /${appname}/ + +RUN pip install poetry && \ + poetry install -vv --only main --no-interaction + +COPY --chown=gen3:gen3 . /$appname + +# 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}\"" >> /$appname/version_data.py + +# Final stage +FROM base + +COPY --from=builder /venv /venv +COPY --from=builder /$appname /$appname + +# install nginx +RUN yum install nginx -y + +# allow nginx to bind to port 80 +RUN setcap 'cap_net_bind_service=+ep' /usr/sbin/nginx -RUN pip install --upgrade pip poetry -RUN apt-get update && apt-get install -y --no-install-recommends \ - build-essential libffi-dev musl-dev gcc libxml2-dev libxslt-dev \ - curl bash git vim +# chown nginx directories +RUN chown -R gen3:gen3 /var/log/nginx -RUN mkdir -p /var/www/$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/$appname +# pipe nginx logs to stdout and stderr +RUN ln -sf /dev/stdout /var/log/nginx/access.log && ln -sf /dev/stderr /var/log/nginx/error.log -EXPOSE 80 +# create /var/lib/nginx/tmp/client_body to allow nginx to write to fence +RUN mkdir -p /var/lib/nginx/tmp/client_body +RUN chown -R gen3:gen3 /var/lib/nginx/ -WORKDIR /$appname +# copy nginx config +COPY ./deployment/nginx/nginx.conf /etc/nginx/nginx.conf -# copy ONLY poetry artifact, install the dependencies but not indexd -# this will make sure than the dependencies is cached -COPY poetry.lock pyproject.toml /$appname/ -RUN poetry config virtualenvs.create false \ - && poetry install -vv --no-root --no-dev --no-interaction \ - && poetry show -v -# copy source code ONLY after installing dependencies -COPY . /$appname -COPY ./deployment/uwsgi/uwsgi.ini /etc/uwsgi/uwsgi.ini -COPY ./bin/settings.py /var/www/$appname/settings.py -COPY ./bin/confighelper.py /var/www/$appname/confighelper.py +# Switch to non-root user 'gen3' for the serving process +USER gen3 -# install sheepdog -RUN poetry config virtualenvs.create false \ - && poetry install -vv --no-dev --no-interaction \ - && poetry show -v +RUN source /venv/bin/activate -RUN COMMIT=`git rev-parse HEAD` && echo "COMMIT=\"${COMMIT}\"" >$appname/version_data.py \ - && VERSION=`git describe --always --tags` && echo "VERSION=\"${VERSION}\"" >>$appname/version_data.py +ENV PYTHONUNBUFFERED=1 \ + PYTHONIOENCODING=UTF-8 -WORKDIR /var/www/$appname +WORKDIR /var/www/${appname} -RUN ls -CMD /dockerrun.sh +CMD ["/sheepdog/dockerrun.bash"] +# CMD ["gunicorn", "-c", "/sheepdog/deployment/wsgi/gunicorn.conf.py"] \ No newline at end of file diff --git a/deployment/nginx/nginx.conf b/deployment/nginx/nginx.conf new file mode 100644 index 00000000..c81472fa --- /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; + } + } +} \ No newline at end of file diff --git a/deployment/uwsgi/uwsgi.ini b/deployment/uwsgi/uwsgi.ini deleted file mode 100644 index 2b88a5a9..00000000 --- a/deployment/uwsgi/uwsgi.ini +++ /dev/null @@ -1,32 +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 = 600 -socket-timeout = 600 -worker-reload-mercy = 45 -reload-mercy = 45 -mule-reload-mercy = 45 -disable-logging = true -wsgi-file=/var/www/sheepdog/settings.py -plugins = python3 -vacuum = true -pythonpath = /var/www/sheepdog/ -pythonpath = /sheepdog/ -# 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 diff --git a/deployment/wsgi/gunicorn.conf.py b/deployment/wsgi/gunicorn.conf.py new file mode 100644 index 00000000..1eaa94a1 --- /dev/null +++ b/deployment/wsgi/gunicorn.conf.py @@ -0,0 +1,9 @@ +wsgi_app = "deployment.wsgi.wsgi:application" +bind = "0.0.0.0:8000" +workers = 4 +preload_app = True +user = "gen3" +group = "gen3" +timeout = 300 +keepalive = 2 +keepalive_timeout = 5 diff --git a/deployment/wsgi/wsgi.py b/deployment/wsgi/wsgi.py new file mode 100644 index 00000000..a7a7578c --- /dev/null +++ b/deployment/wsgi/wsgi.py @@ -0,0 +1 @@ +from sheepdog.api import app as application diff --git a/dockerrun.bash b/dockerrun.bash new file mode 100755 index 00000000..3b444b09 --- /dev/null +++ b/dockerrun.bash @@ -0,0 +1,4 @@ +#!/bin/bash + +nginx +gunicorn -c "/sheepdog/deployment/wsgi/gunicorn.conf.py" \ No newline at end of file diff --git a/poetry.lock b/poetry.lock index bdf1c47b..a327dec7 100644 --- a/poetry.lock +++ b/poetry.lock @@ -68,13 +68,13 @@ trio = ["trio (>=0.23)"] [[package]] name = "attrs" -version = "24.1.0" +version = "24.2.0" description = "Classes Without Boilerplate" optional = false python-versions = ">=3.7" files = [ - {file = "attrs-24.1.0-py3-none-any.whl", hash = "sha256:377b47448cb61fea38533f671fba0d0f8a96fd58facd4dc518e3dac9dbea0905"}, - {file = "attrs-24.1.0.tar.gz", hash = "sha256:adbdec84af72d38be7628e353a09b6a6790d15cd71819f6e9d7b0faa8a125745"}, + {file = "attrs-24.2.0-py3-none-any.whl", hash = "sha256:81921eb96de3191c8258c199618104dd27ac608d9366f5e35d011eae1867ede2"}, + {file = "attrs-24.2.0.tar.gz", hash = "sha256:5cfb1b9148b5b086569baec03f20d7b6bf3bcacc9a42bebf87ffaaca362f6346"}, ] [package.extras] @@ -140,13 +140,13 @@ zstandard = ["zstandard"] [[package]] name = "babel" -version = "2.15.0" +version = "2.16.0" description = "Internationalization utilities" optional = false python-versions = ">=3.8" files = [ - {file = "Babel-2.15.0-py3-none-any.whl", hash = "sha256:08706bdad8d0a3413266ab61bd6c34d0c28d6e1e7badf40a2cebe67644e2e1fb"}, - {file = "babel-2.15.0.tar.gz", hash = "sha256:8daf0e265d05768bc6c7a314cf1321e9a123afc328cc635c18622a2f30a04413"}, + {file = "babel-2.16.0-py3-none-any.whl", hash = "sha256:368b5b98b37c06b7daf6696391c3240c938b37767d4584413e8438c5c435fa8b"}, + {file = "babel-2.16.0.tar.gz", hash = "sha256:d1f3554ca26605fe173f3de0c65f750f5a42f924499bf134de6423582298e316"}, ] [package.extras] @@ -187,17 +187,17 @@ files = [ [[package]] name = "boto3" -version = "1.34.154" +version = "1.34.158" description = "The AWS SDK for Python" optional = false python-versions = ">=3.8" files = [ - {file = "boto3-1.34.154-py3-none-any.whl", hash = "sha256:7ca22adef4c77ee128e1e1dc7d48bc9512a87cc6fe3d771b3f913d5ecd41c057"}, - {file = "boto3-1.34.154.tar.gz", hash = "sha256:864f06528c583dc7b02adf12db395ecfadbf9cb0da90e907e848ffb27128ce19"}, + {file = "boto3-1.34.158-py3-none-any.whl", 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bin/confighelper.py | 2 +- bin/settings.py | 45 ++++++++++++++++++++------------ deployment/wsgi/gunicorn.conf.py | 3 ++- 4 files changed, 34 insertions(+), 20 deletions(-) diff --git a/.secrets.baseline b/.secrets.baseline index 419f416c..2b80b030 100644 --- a/.secrets.baseline +++ b/.secrets.baseline @@ -136,7 +136,7 @@ "filename": "bin/settings.py", "hashed_secret": "347cd9c53ff77d41a7b22aa56c7b4efaf54658e3", "is_verified": false, - "line_number": 43 + "line_number": 54 } ], "docs/local_dev_environment.md": [ @@ -354,5 +354,5 @@ } ] }, - "generated_at": "2024-04-22T20:07:28Z" + "generated_at": "2024-08-12T21:26:18Z" } diff --git a/bin/confighelper.py b/bin/confighelper.py index a48419c7..ca2175a4 100644 --- a/bin/confighelper.py +++ b/bin/confighelper.py @@ -49,6 +49,6 @@ def load_json(file_name, app_name, search_folders=None): """ actual_files = find_paths(file_name, app_name, search_folders) if not actual_files: - return None + return {} with open(actual_files[0], "r") as reader: return json.load(reader) diff --git a/bin/settings.py b/bin/settings.py index edd18b7e..98243456 100644 --- a/bin/settings.py +++ b/bin/settings.py @@ -1,6 +1,6 @@ from sheepdog.api import app, app_init -from os import environ -import confighelper +import os +from . import confighelper APP_NAME = "sheepdog" @@ -22,39 +22,52 @@ def load_json(file_name): # Signpost: deprecated, replaced by index client. config["SIGNPOST"] = { - "host": environ.get("SIGNPOST_HOST") or "http://indexd-service", + "host": os.environ.get("SIGNPOST_HOST", "http://indexd-service"), "version": "v0", "auth": ("gdcapi", conf_data.get("indexd_password", "{{indexd_password}}")), } config["INDEX_CLIENT"] = { - "host": environ.get("INDEX_CLIENT_HOST") or "http://indexd-service", + "host": os.environ.get("INDEX_CLIENT_HOST") or "http://indexd-service", "version": "v0", "auth": ("gdcapi", conf_data.get("indexd_password", "{{indexd_password}}")), } config["FAKE_AUTH"] = False config["PSQLGRAPH"] = { - "host": conf_data["db_host"], - "user": conf_data["db_username"], - "password": conf_data["db_password"], - "database": conf_data["db_database"], + "host": conf_data.get("db_host", os.environ.get("PGHOST", "localhost")), + "user": conf_data.get("db_username", os.environ.get("PGUSER", "sheepdog")), + "password": conf_data.get("db_password", os.environ.get("PGPASSWORD", "sheepdog")), + "database": conf_data.get("db_database", os.environ.get("PGDATABASE", "sheepdog")), } config["FLASK_SECRET_KEY"] = conf_data.get("gdcapi_secret_key", "{{gdcapi_secret_key}}") -config["PSQL_USER_DB_CONNECTION"] = "postgresql://%s:%s@%s:5432/%s" % tuple( - [ - conf_data.get(key, key) - for key in ["fence_username", "fence_password", "fence_host", "fence_database"] - ] + +fence_username = conf_data.get( + "fence_username", os.environ.get("FENCE_DB_USERNAME", "fence") +) +fence_password = conf_data.get( + "fence_password", os.environ.get("FENCE_DB_PASSWORD", "fence") +) +fence_host = conf_data.get("fence_host", os.environ.get("FENCE_DB_HOST", "localhost")) +fence_database = conf_data.get( + "fence_database", os.environ.get("FENCE_DB_DATABASE", "fence") +) +config["PSQL_USER_DB_CONNECTION"] = "postgresql://%s:%s@%s:5432/%s" % ( + fence_username, + fence_password, + fence_host, + fence_database, ) -config["USER_API"] = "https://%s/user" % conf_data["hostname"] # for use by authutils +config["USER_API"] = "https://%s/user" % conf_data.get( + "hostname", os.environ.get("CONF_HOSTNAME", "localhost") +) # for use by authutils # use the USER_API URL instead of the public issuer URL to accquire JWT keys config["FORCE_ISSUER"] = True -config["DICTIONARY_URL"] = environ.get( +config["DICTIONARY_URL"] = os.environ.get( "DICTIONARY_URL", "https://s3.amazonaws.com/dictionary-artifacts/datadictionary/develop/schema.json", ) app_init(app) application = app -application.debug = environ.get("GEN3_DEBUG") == "True" +application.debug = os.environ.get("GEN3_DEBUG") == "True" diff --git a/deployment/wsgi/gunicorn.conf.py b/deployment/wsgi/gunicorn.conf.py index 1eaa94a1..2990bba6 100644 --- a/deployment/wsgi/gunicorn.conf.py +++ b/deployment/wsgi/gunicorn.conf.py @@ -1,4 +1,5 @@ -wsgi_app = "deployment.wsgi.wsgi:application" +# /sheepdoog/bin/settings.py +wsgi_app = "bin.settings:application" bind = "0.0.0.0:8000" workers = 4 preload_app = True From 33e328ff93b470ec394672e1b907c6ff637c0b02 Mon Sep 17 00:00:00 2001 From: Jawad Qureshi Date: Tue, 13 Aug 2024 12:21:15 +0200 Subject: [PATCH 08/43] adding nginx and gunicorn to sheepdog image --- Dockerfile | 2 +- bin/settings.py | 6 +++--- poetry.lock | 2 +- pyproject.toml | 2 +- 4 files changed, 6 insertions(+), 6 deletions(-) diff --git a/Dockerfile b/Dockerfile index b5cf571e..5986f7f8 100644 --- a/Dockerfile +++ b/Dockerfile @@ -54,7 +54,7 @@ COPY --from=builder /venv /venv COPY --from=builder /$appname /$appname # install nginx -RUN yum install nginx -y +RUN yum install nginx postgresql-devel -y # allow nginx to bind to port 80 RUN setcap 'cap_net_bind_service=+ep' /usr/sbin/nginx diff --git a/bin/settings.py b/bin/settings.py index 98243456..4fd4e60d 100644 --- a/bin/settings.py +++ b/bin/settings.py @@ -36,16 +36,16 @@ def load_json(file_name): "host": conf_data.get("db_host", os.environ.get("PGHOST", "localhost")), "user": conf_data.get("db_username", os.environ.get("PGUSER", "sheepdog")), "password": conf_data.get("db_password", os.environ.get("PGPASSWORD", "sheepdog")), - "database": conf_data.get("db_database", os.environ.get("PGDATABASE", "sheepdog")), + "database": conf_data.get("db_database", os.environ.get("PGDB", "sheepdog")), } config["FLASK_SECRET_KEY"] = conf_data.get("gdcapi_secret_key", "{{gdcapi_secret_key}}") fence_username = conf_data.get( - "fence_username", os.environ.get("FENCE_DB_USERNAME", "fence") + "fence_username", os.environ.get("FENCE_DB_USER", "fence") ) fence_password = conf_data.get( - "fence_password", os.environ.get("FENCE_DB_PASSWORD", "fence") + "fence_password", os.environ.get("FENCE_DB_PASS", "fence") ) fence_host = conf_data.get("fence_host", os.environ.get("FENCE_DB_HOST", "localhost")) fence_database = conf_data.get( diff --git a/poetry.lock b/poetry.lock index a327dec7..99840e7a 100644 --- a/poetry.lock +++ b/poetry.lock @@ -2414,4 +2414,4 @@ test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", [metadata] lock-version = "2.0" python-versions = ">=3.9,<3.10" -content-hash = "bb17ab71f88c34ca9f5a78c7a10ad956c7636a4234c88e1a91dac1fcef1502e6" +content-hash = "4376e3bc56aadfc9c8a208cdc4a03a4a125a93231a6988c44727315685741a79" diff --git a/pyproject.toml b/pyproject.toml index 8e46e07b..fbb4f8de 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -25,7 +25,7 @@ gen3authz = ">=1.0.4" graphene = ">=2.0.1" jsonschema = "*" lxml = ">=4.6.5" -psycopg2 = ">=2.8.4" +psycopg2-binary = ">=2.8.4" PyYAML = "*" requests = ">=2.31.0,<3.0.0" simplejson = ">=3.8.1" From 31ae1de800ec16d0a8d95fb6216be8410fed61a5 Mon Sep 17 00:00:00 2001 From: Jawad Qureshi Date: Tue, 27 Aug 2024 09:35:06 -0500 Subject: [PATCH 09/43] Update nginx.conf --- deployment/nginx/nginx.conf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/deployment/nginx/nginx.conf b/deployment/nginx/nginx.conf index c81472fa..bc2a8432 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 eb0c9d87745f42eaa1664ec718f82f782d81ee59 Mon Sep 17 00:00:00 2001 From: George Thomas Date: Wed, 28 Aug 2024 08:53:32 -0700 Subject: [PATCH 10/43] (PPS-710): re-lock to pick up changes in datamodelutils --- poetry.lock | 803 ++++++++++++++++++++++++++++------------------------ 1 file changed, 426 insertions(+), 377 deletions(-) diff --git a/poetry.lock b/poetry.lock index bdf1c47b..253a769b 100644 --- a/poetry.lock +++ b/poetry.lock @@ -68,13 +68,13 @@ trio = ["trio (>=0.23)"] [[package]] name = "attrs" -version = "24.1.0" +version = "24.2.0" description = "Classes Without Boilerplate" optional = false python-versions = ">=3.7" files = [ - {file = "attrs-24.1.0-py3-none-any.whl", hash = "sha256:377b47448cb61fea38533f671fba0d0f8a96fd58facd4dc518e3dac9dbea0905"}, - {file = "attrs-24.1.0.tar.gz", hash = "sha256:adbdec84af72d38be7628e353a09b6a6790d15cd71819f6e9d7b0faa8a125745"}, + {file = "attrs-24.2.0-py3-none-any.whl", hash = "sha256:81921eb96de3191c8258c199618104dd27ac608d9366f5e35d011eae1867ede2"}, + {file = "attrs-24.2.0.tar.gz", hash = "sha256:5cfb1b9148b5b086569baec03f20d7b6bf3bcacc9a42bebf87ffaaca362f6346"}, ] [package.extras] @@ -87,13 +87,13 @@ tests-mypy = ["mypy (>=1.11.1)", "pytest-mypy-plugins"] [[package]] name = "authlib" -version = "1.3.1" +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-1.3.1-py2.py3-none-any.whl", hash = "sha256:d35800b973099bbadc49b42b256ecb80041ad56b7fe1216a362c7943c088f377"}, - {file = "authlib-1.3.1.tar.gz", hash = "sha256:7ae843f03c06c5c0debd63c9db91f9fda64fa62a42a77419fa15fbb7e7a58917"}, + {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] @@ -140,13 +140,13 @@ zstandard = ["zstandard"] [[package]] name = "babel" -version = "2.15.0" +version = "2.16.0" description = "Internationalization utilities" optional = false python-versions = ">=3.8" files = [ - {file = "Babel-2.15.0-py3-none-any.whl", hash = "sha256:08706bdad8d0a3413266ab61bd6c34d0c28d6e1e7badf40a2cebe67644e2e1fb"}, - {file = "babel-2.15.0.tar.gz", hash = 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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 RUN yum install -y gcc gcc-c++ make postgresql-devel From 138e2b9872d293c9a9e19ae48da749f3a377f4ca Mon Sep 17 00:00:00 2001 From: George Thomas Date: Tue, 22 Oct 2024 15:31:32 -0700 Subject: [PATCH 15/43] re-lock --- poetry.lock | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/poetry.lock b/poetry.lock index ef270ae6..9769aad9 100644 --- a/poetry.lock +++ b/poetry.lock @@ -173,17 +173,17 @@ files = [ [[package]] name = "boto3" -version = "1.35.44" +version = "1.35.46" description = "The AWS SDK for Python" optional = false python-versions = ">=3.8" files = [ - {file = "boto3-1.35.44-py3-none-any.whl", hash = "sha256:18416d07b41e6094101a44f8b881047dcec6b846dad0b9f83b9bbf2f0cd93d07"}, - {file = "boto3-1.35.44.tar.gz", hash = "sha256:7f8e8a252458d584d8cf7877c372c4f74ec103356eedf43d2dd9e479f47f3639"}, + {file = "boto3-1.35.46-py3-none-any.whl", hash = "sha256:a839ce09a844d92e0039f95851e88da9df80c89ebb4c7818b3e78247fd97a8a7"}, + {file = "boto3-1.35.46.tar.gz", hash = "sha256:c9bab807b372d5b076d6aeb1d6513131fa0b74e32d8895128f8568b6521296ea"}, ] [package.dependencies] -botocore = ">=1.35.44,<1.36.0" +botocore = ">=1.35.46,<1.36.0" jmespath = ">=0.7.1,<2.0.0" s3transfer = ">=0.10.0,<0.11.0" @@ -192,13 +192,13 @@ crt = ["botocore[crt] (>=1.21.0,<2.0a0)"] [[package]] name = "botocore" -version = "1.35.44" +version = "1.35.46" description = "Low-level, data-driven core of boto 3." optional = false python-versions = ">=3.8" files = [ - {file = "botocore-1.35.44-py3-none-any.whl", hash = "sha256:55388e80624401d017a9a2b8109afd94814f7e666b53e28fce51375cfa8d9326"}, - {file = "botocore-1.35.44.tar.gz", hash = "sha256:1fcd97b966ad8a88de4106fe1bd3bbd6d8dadabe99bbd4a6aadcf11cb6c66b39"}, + {file = "botocore-1.35.46-py3-none-any.whl", hash = "sha256:8bbc9a55cae65a8db7f2e33ff087f4dbfc13fce868e8e3c5273ce9af367a555a"}, + {file = "botocore-1.35.46.tar.gz", hash = "sha256:8c0ff5fdd611a28f5752189d171c69690dbc484fa06d74376890bb0543ec3dc1"}, ] [package.dependencies] @@ -1338,13 +1338,13 @@ source = ["Cython (>=3.0.11)"] [[package]] name = "mako" -version = "1.3.5" +version = "1.3.6" description = "A super-fast templating language that borrows the best ideas from the existing templating languages." optional = false python-versions = ">=3.8" files = [ - {file = "Mako-1.3.5-py3-none-any.whl", hash = "sha256:260f1dbc3a519453a9c856dedfe4beb4e50bd5a26d96386cb6c80856556bb91a"}, - {file = "Mako-1.3.5.tar.gz", hash = "sha256:48dbc20568c1d276a2698b36d968fa76161bf127194907ea6fc594fa81f943bc"}, + {file = "Mako-1.3.6-py3-none-any.whl", hash = "sha256:a91198468092a2f1a0de86ca92690fb0cfc43ca90ee17e15d93662b4c04b241a"}, + {file = "mako-1.3.6.tar.gz", hash = "sha256:9ec3a1583713479fae654f83ed9fa8c9a4c16b7bb0daba0e6bbebff50c0d983d"}, ] [package.dependencies] From 0da46be21ad5951d304ebf5333ccd1c4bd2460f7 Mon Sep 17 00:00:00 2001 From: EliseCastle23 <109446148+EliseCastle23@users.noreply.github.com> Date: Fri, 1 Nov 2024 14:38:36 -0600 Subject: [PATCH 16/43] updating base image to python nginx --- Dockerfile | 59 +++-------------------- deployment/nginx/nginx.conf | 44 ------------------ deployment/wsgi/gunicorn.conf.py | 14 ++---- dockerrun.bash | 2 +- poetry.lock | 80 +++++++++++++++----------------- pyproject.toml | 2 +- 6 files changed, 50 insertions(+), 151 deletions(-) delete mode 100644 deployment/nginx/nginx.conf diff --git a/Dockerfile b/Dockerfile index 8b6a1075..a094af35 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,45 +1,27 @@ ARG AZLINUX_BASE_VERSION=master # Base stage with python-build-base -FROM quay.io/cdis/python-build-base:${AZLINUX_BASE_VERSION} AS base +FROM quay.io/cdis/python-nginx-al:${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:${AZLINUX_BASE_VERSION} as base +# FROM 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/python-build-base:${AZLINUX_BASE_VERSION} AS base ENV appname=sheepdog -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 /$appname # Builder stage FROM base AS builder - -RUN yum install -y gcc gcc-c++ make postgresql-devel - -RUN dnf install python3-devel -y - USER gen3 - -RUN python -m venv /venv - COPY poetry.lock pyproject.toml /${appname}/ -RUN pip install poetry && \ - 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 --without dev --no-interaction @@ -50,38 +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 /$appname -# install nginx -RUN yum install nginx postgresql-devel -y - -# allow nginx to bind to port 80 -RUN setcap 'cap_net_bind_service=+ep' /usr/sbin/nginx - -# chown nginx directories -RUN chown -R gen3:gen3 /var/log/nginx - -# pipe nginx logs to stdout and stderr -RUN ln -sf /dev/stdout /var/log/nginx/access.log && ln -sf /dev/stderr /var/log/nginx/error.log - -# create /var/lib/nginx/tmp/client_body to allow nginx to write to fence -RUN mkdir -p /var/lib/nginx/tmp/client_body -RUN chown -R gen3:gen3 /var/lib/nginx/ - -# copy nginx config -COPY ./deployment/nginx/nginx.conf /etc/nginx/nginx.conf - - # Switch to non-root user 'gen3' for the serving process USER gen3 -RUN source /venv/bin/activate - -ENV PYTHONUNBUFFERED=1 \ - PYTHONIOENCODING=UTF-8 - -WORKDIR /var/www/${appname} +WORKDIR /$appname -CMD ["/sheepdog/dockerrun.bash"] -# CMD ["gunicorn", "-c", "/sheepdog/deployment/wsgi/gunicorn.conf.py"] \ No newline at end of file +CMD ["/sheepdog/dockerrun.bash"] \ No newline at end of file diff --git a/deployment/nginx/nginx.conf b/deployment/nginx/nginx.conf deleted file mode 100644 index bc2a8432..00000000 --- a/deployment/nginx/nginx.conf +++ /dev/null @@ -1,44 +0,0 @@ -user gen3; -worker_processes auto; -error_log /var/log/nginx/error.log notice; -pid /var/lib/nginx/nginx.pid; - -# Load dynamic modules. See /usr/share/doc/nginx/README.dynamic. -include /usr/share/nginx/modules/*.conf; - -events { - worker_connections 1024; -} - -http { - log_format main '$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; - } - } -} \ No newline at end of file diff --git a/deployment/wsgi/gunicorn.conf.py b/deployment/wsgi/gunicorn.conf.py index f60317d5..64092ba3 100644 --- a/deployment/wsgi/gunicorn.conf.py +++ b/deployment/wsgi/gunicorn.conf.py @@ -1,17 +1,9 @@ -# /sheepdoog/bin/settings.py -wsgi_app = "bin.settings:application" +wsgi_app = "deployment.wsgi.wsgi:application" bind = "0.0.0.0:8000" -workers = 4 -preload_app = False +workers = 1 +preload_app = True user = "gen3" group = "gen3" timeout = 300 keepalive = 2 keepalive_timeout = 5 - -import random -import time - - -def pre_fork(server, worker): - time.sleep(random.uniform(0, 2)) diff --git a/dockerrun.bash b/dockerrun.bash index 192b5560..c3e6f8f8 100755 --- a/dockerrun.bash +++ b/dockerrun.bash @@ -1,5 +1,5 @@ #!/bin/bash -gunicorn -c "/sheepdog/deployment/wsgi/gunicorn.conf.py" & +poetry run gunicorn -c "/sheepdog/deployment/wsgi/gunicorn.conf.py" & sleep 30 nginx -g 'daemon off;' \ No newline at end of file diff --git a/poetry.lock b/poetry.lock index ef270ae6..238bfd1c 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. [[package]] name = "alabaster" @@ -173,17 +173,17 @@ files = [ [[package]] name = "boto3" -version = "1.35.44" +version = "1.35.53" description = "The AWS SDK for Python" optional = false python-versions = ">=3.8" files = [ - {file = "boto3-1.35.44-py3-none-any.whl", hash = "sha256:18416d07b41e6094101a44f8b881047dcec6b846dad0b9f83b9bbf2f0cd93d07"}, - {file = "boto3-1.35.44.tar.gz", hash = "sha256:7f8e8a252458d584d8cf7877c372c4f74ec103356eedf43d2dd9e479f47f3639"}, + {file = "boto3-1.35.53-py3-none-any.whl", hash = "sha256:a9c0955df0b52b43749d81bde159343a40ea2a3537a46049336fe8193871b18e"}, + {file = "boto3-1.35.53.tar.gz", hash = "sha256:f4124548bb831e13504e805f2fbbfcee06df42fffea0655862c6eb9b95d6d1be"}, ] [package.dependencies] -botocore = ">=1.35.44,<1.36.0" +botocore = ">=1.35.53,<1.36.0" jmespath = ">=0.7.1,<2.0.0" s3transfer = ">=0.10.0,<0.11.0" @@ -192,13 +192,13 @@ crt = ["botocore[crt] (>=1.21.0,<2.0a0)"] [[package]] name = "botocore" -version = "1.35.44" +version = "1.35.53" description = "Low-level, data-driven core of boto 3." optional = false python-versions = ">=3.8" files = [ - {file = "botocore-1.35.44-py3-none-any.whl", hash = "sha256:55388e80624401d017a9a2b8109afd94814f7e666b53e28fce51375cfa8d9326"}, - {file = "botocore-1.35.44.tar.gz", hash = "sha256:1fcd97b966ad8a88de4106fe1bd3bbd6d8dadabe99bbd4a6aadcf11cb6c66b39"}, + {file = "botocore-1.35.53-py3-none-any.whl", hash = "sha256:12869640f2f9fab3152ea312a6906d5bc6ae15522cc74b6367ee1c273269a28b"}, + {file = "botocore-1.35.53.tar.gz", hash = "sha256:e610ae076ad1eaed5680d3990493659bbabdffd67b15c61d8373a23e4bc41062"}, ] [package.dependencies] @@ -856,42 +856,38 @@ strict-rfc3339 = "0.7" [[package]] name = "gen3dictionary" -version = "2.0.5" +version = "2.0.4" description = "" optional = false -python-versions = "^3.9" -files = [] -develop = false +python-versions = "<4.0,>=3.9" +files = [ + {file = "gen3dictionary-2.0.4.tar.gz", hash = "sha256:6a798008f32c4a5c1833fbc03e841ebe12bb5b743812ec7c00211c0268f15c05"}, +] [package.dependencies] dictionaryutils = "*" jsonschema = "*" -PyYAML = ">= 6.0" - -[package.source] -type = "git" -url = "https://github.com/uc-cdis/datadictionary.git" -reference = "chore/add-unit-tests" -resolved_reference = "ec977442de6249e5131109dd6d503b41ab654fb6" +PyYAML = "*" [[package]] name = "graphene" -version = "3.4" +version = "3.4.1" description = "GraphQL Framework for Python" optional = false python-versions = "*" files = [ - {file = "graphene-3.4-py2.py3-none-any.whl", hash = "sha256:28bf359b802cdb808130a5521135d4c88a262564598cfdc91628d2c172b99dce"}, - {file = "graphene-3.4.tar.gz", hash = "sha256:65e5ec84c5b7fb4fc41518acfbafb62ebb393d3982fbba00cd5393e431a80b97"}, + {file = "graphene-3.4.1-py2.py3-none-any.whl", hash = "sha256:ca98f853201293871cdc7f55faf2523a9bc077181fe0f4947db5a243e5c67083"}, + {file = "graphene-3.4.1.tar.gz", hash = "sha256:828a8d7b1bce450566a72cc8733716c20f3acfc659960de73dd38f46dc302040"}, ] [package.dependencies] graphql-core = ">=3.1,<3.3" graphql-relay = ">=3.1,<3.3" +python-dateutil = ">=2.7.0,<3" typing-extensions = ">=4.7.1,<5" [package.extras] -dev = ["coveralls (>=3.3,<5)", "pytest (>=8,<9)", "pytest-asyncio (>=0.16,<2)", "pytest-benchmark (>=4,<5)", "pytest-cov (>=5,<6)", "pytest-mock (>=3,<4)", "ruff (==0.5.0)"] +dev = ["coveralls (>=3.3,<5)", "mypy (>=1.10,<2)", "pytest (>=8,<9)", "pytest-asyncio (>=0.16,<2)", "pytest-benchmark (>=4,<5)", "pytest-cov (>=5,<6)", "pytest-mock (>=3,<4)", "ruff (==0.5.0)", "types-python-dateutil (>=2.8.1,<3)"] test = ["coveralls (>=3.3,<5)", "pytest (>=8,<9)", "pytest-asyncio (>=0.16,<2)", "pytest-benchmark (>=4,<5)", "pytest-cov (>=5,<6)", "pytest-mock (>=3,<4)"] [[package]] @@ -1338,13 +1334,13 @@ source = ["Cython (>=3.0.11)"] [[package]] name = "mako" -version = "1.3.5" +version = "1.3.6" description = "A super-fast templating language that borrows the best ideas from the existing templating languages." optional = false python-versions = ">=3.8" files = [ - {file = "Mako-1.3.5-py3-none-any.whl", hash = "sha256:260f1dbc3a519453a9c856dedfe4beb4e50bd5a26d96386cb6c80856556bb91a"}, - {file = "Mako-1.3.5.tar.gz", hash = "sha256:48dbc20568c1d276a2698b36d968fa76161bf127194907ea6fc594fa81f943bc"}, + {file = "Mako-1.3.6-py3-none-any.whl", hash = "sha256:a91198468092a2f1a0de86ca92690fb0cfc43ca90ee17e15d93662b4c04b241a"}, + {file = "mako-1.3.6.tar.gz", hash = "sha256:9ec3a1583713479fae654f83ed9fa8c9a4c16b7bb0daba0e6bbebff50c0d983d"}, ] [package.dependencies] @@ -1695,17 +1691,17 @@ dev = ["argcomplete", "attrs (>=19.2)", "hypothesis (>=3.56)", "mock", "pygments [[package]] name = "pytest-cov" -version = "5.0.0" +version = "6.0.0" description = "Pytest plugin for measuring coverage." optional = false -python-versions = ">=3.8" +python-versions = ">=3.9" files = [ - {file = "pytest-cov-5.0.0.tar.gz", hash = "sha256:5837b58e9f6ebd335b0f8060eecce69b662415b16dc503883a02f45dfeb14857"}, - {file = "pytest_cov-5.0.0-py3-none-any.whl", hash = "sha256:4f0764a1219df53214206bf1feea4633c3b558a2925c8b59f144f682861ce652"}, + {file = "pytest-cov-6.0.0.tar.gz", hash = "sha256:fde0b595ca248bb8e2d76f020b465f3b107c9632e6a1d1705f17834c89dcadc0"}, + {file = "pytest_cov-6.0.0-py3-none-any.whl", hash = "sha256:eee6f1b9e61008bd34975a4d5bab25801eb31898b032dd55addc93e96fcaaa35"}, ] [package.dependencies] -coverage = {version = ">=5.2.1", extras = ["toml"]} +coverage = {version = ">=7.5", extras = ["toml"]} pytest = ">=4.6" [package.extras] @@ -1893,23 +1889,23 @@ crt = ["botocore[crt] (>=1.33.2,<2.0a.0)"] [[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 = "simplejson" @@ -2342,13 +2338,13 @@ socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"] [[package]] name = "werkzeug" -version = "3.0.4" +version = "3.1.1" 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-3.1.1-py3-none-any.whl", hash = "sha256:a71124d1ef06008baafa3d266c02f56e1836a5984afd6dd6c9230669d60d9fb5"}, + {file = "werkzeug-3.1.1.tar.gz", hash = "sha256:8cd39dfbdfc1e051965f156163e2974e52c210f130810e9ad36858f0fd3edad4"}, ] [package.dependencies] @@ -2400,4 +2396,4 @@ type = ["pytest-mypy"] [metadata] lock-version = "2.0" python-versions = ">=3.9,<3.10" -content-hash = "e7fe4673e205a54ba50d506ffca643229f85a8fc7e791032d4aa87de5c808961" +content-hash = "2050e04fc7fee0186fcd3815550ae819337bfc4ec2af173af279b9452baf7b20" diff --git a/pyproject.toml b/pyproject.toml index 625e324b..7f5ce061 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -34,7 +34,7 @@ cdispyutils = ">=2.0.1" psqlgraph = ">=3.0.1" cdiserrors = ">=1.0.0" cdislogging = ">=1.0.0" -gen3dictionary = {git = "https://github.com/uc-cdis/datadictionary.git", branch = "chore/add-unit-tests"} +gen3dictionary = ">=2.0.3" gen3datamodel = ">=3.2.1" gunicorn = ">=21.2.0" indexclient = ">=2.1.1" From a68808c2294c3f3810b6f2261addec92b400f4fa Mon Sep 17 00:00:00 2001 From: EliseCastle23 <109446148+EliseCastle23@users.noreply.github.com> Date: Fri, 1 Nov 2024 14:42:10 -0600 Subject: [PATCH 17/43] updating lock file --- poetry.lock | 17 +++++++---------- 1 file changed, 7 insertions(+), 10 deletions(-) diff --git a/poetry.lock b/poetry.lock index 323f20de..c57aaf03 100644 --- a/poetry.lock +++ b/poetry.lock @@ -173,17 +173,17 @@ files = [ [[package]] name = "boto3" -version = "1.35.53" +version = "1.35.54" description = "The AWS SDK for Python" optional = false python-versions = ">=3.8" files = [ - {file = "boto3-1.35.53-py3-none-any.whl", hash = "sha256:a9c0955df0b52b43749d81bde159343a40ea2a3537a46049336fe8193871b18e"}, - {file = "boto3-1.35.53.tar.gz", hash = "sha256:f4124548bb831e13504e805f2fbbfcee06df42fffea0655862c6eb9b95d6d1be"}, + {file = "boto3-1.35.54-py3-none-any.whl", hash = "sha256:2d5e160b614db55fbee7981001c54476cb827c441cef65b2fcb2c52a62019909"}, + {file = "boto3-1.35.54.tar.gz", hash = "sha256:7d9c359bbbc858a60b51c86328db813353c8bd1940212cdbd0a7da835291c2e1"}, ] [package.dependencies] -botocore = ">=1.35.53,<1.36.0" +botocore = ">=1.35.54,<1.36.0" jmespath = ">=0.7.1,<2.0.0" s3transfer = ">=0.10.0,<0.11.0" @@ -192,13 +192,13 @@ crt = ["botocore[crt] (>=1.21.0,<2.0a0)"] [[package]] name = "botocore" -version = "1.35.53" +version = "1.35.54" description = "Low-level, data-driven core of boto 3." optional = false python-versions = ">=3.8" files = [ - {file = "botocore-1.35.53-py3-none-any.whl", hash = "sha256:12869640f2f9fab3152ea312a6906d5bc6ae15522cc74b6367ee1c273269a28b"}, - {file = "botocore-1.35.53.tar.gz", hash = "sha256:e610ae076ad1eaed5680d3990493659bbabdffd67b15c61d8373a23e4bc41062"}, + {file = "botocore-1.35.54-py3-none-any.whl", hash = "sha256:9cca1811094b6cdc144c2c063a3ec2db6d7c88194b04d4277cd34fc8e3473aff"}, + {file = "botocore-1.35.54.tar.gz", hash = "sha256:131bb59ce59c8a939b31e8e647242d70cf11d32d4529fa4dca01feea1e891a76"}, ] [package.dependencies] @@ -1335,15 +1335,12 @@ source = ["Cython (>=3.0.11)"] [[package]] name = "mako" version = "1.3.6" -version = "1.3.6" description = "A super-fast templating language that borrows the best ideas from the existing templating languages." optional = false python-versions = ">=3.8" files = [ {file = "Mako-1.3.6-py3-none-any.whl", hash = "sha256:a91198468092a2f1a0de86ca92690fb0cfc43ca90ee17e15d93662b4c04b241a"}, {file = "mako-1.3.6.tar.gz", hash = "sha256:9ec3a1583713479fae654f83ed9fa8c9a4c16b7bb0daba0e6bbebff50c0d983d"}, - {file = "Mako-1.3.6-py3-none-any.whl", hash = "sha256:a91198468092a2f1a0de86ca92690fb0cfc43ca90ee17e15d93662b4c04b241a"}, - {file = "mako-1.3.6.tar.gz", hash = "sha256:9ec3a1583713479fae654f83ed9fa8c9a4c16b7bb0daba0e6bbebff50c0d983d"}, ] [package.dependencies] From 077de4d30ccdd584638d0fefc3288883ae7b7634 Mon Sep 17 00:00:00 2001 From: EliseCastle23 <109446148+EliseCastle23@users.noreply.github.com> Date: Thu, 7 Nov 2024 10:57:55 -0700 Subject: [PATCH 18/43] modifying settings.py --- .secrets.baseline | 4 ++-- bin/settings.py | 23 +++++++++-------------- 2 files changed, 11 insertions(+), 16 deletions(-) diff --git a/.secrets.baseline b/.secrets.baseline index 2b80b030..30e22d57 100644 --- a/.secrets.baseline +++ b/.secrets.baseline @@ -136,7 +136,7 @@ "filename": "bin/settings.py", "hashed_secret": "347cd9c53ff77d41a7b22aa56c7b4efaf54658e3", "is_verified": false, - "line_number": 54 + "line_number": 49 } ], "docs/local_dev_environment.md": [ @@ -354,5 +354,5 @@ } ] }, - "generated_at": "2024-08-12T21:26:18Z" + "generated_at": "2024-11-07T17:57:50Z" } diff --git a/bin/settings.py b/bin/settings.py index 4fd4e60d..c3970a43 100644 --- a/bin/settings.py +++ b/bin/settings.py @@ -12,26 +12,23 @@ def load_json(file_name): conf_data = load_json("creds.json") config = app.config -config["AUTH"] = "https://auth.service.consul:5000/v3/" -config["AUTH_ADMIN_CREDS"] = None -config["INTERNAL_AUTH"] = None - # ARBORIST deprecated, replaced by ARBORIST_URL # ARBORIST_URL is initialized in app_init() directly config["ARBORIST"] = "http://arborist-service/" -# Signpost: deprecated, replaced by index client. -config["SIGNPOST"] = { - "host": os.environ.get("SIGNPOST_HOST", "http://indexd-service"), - "version": "v0", - "auth": ("gdcapi", conf_data.get("indexd_password", "{{indexd_password}}")), -} config["INDEX_CLIENT"] = { "host": os.environ.get("INDEX_CLIENT_HOST") or "http://indexd-service", "version": "v0", - "auth": ("gdcapi", conf_data.get("indexd_password", "{{indexd_password}}")), + # The user should be "sheepdog", but for legacy reasons, we use "gdcapi" instead + "auth": ( + ( + environ.get("INDEXD_USER", "gdcapi"), + environ.get("INDEXD_PASS") + or conf_data.get("indexd_password", "{{indexd_password}}"), + ) + ), } -config["FAKE_AUTH"] = False + config["PSQLGRAPH"] = { "host": conf_data.get("db_host", os.environ.get("PGHOST", "localhost")), "user": conf_data.get("db_username", os.environ.get("PGUSER", "sheepdog")), @@ -39,8 +36,6 @@ def load_json(file_name): "database": conf_data.get("db_database", os.environ.get("PGDB", "sheepdog")), } -config["FLASK_SECRET_KEY"] = conf_data.get("gdcapi_secret_key", "{{gdcapi_secret_key}}") - fence_username = conf_data.get( "fence_username", os.environ.get("FENCE_DB_USER", "fence") ) From fb714166f38070b2eb8cbe7fdb063a86cce6d6cb Mon Sep 17 00:00:00 2001 From: EliseCastle23 <109446148+EliseCastle23@users.noreply.github.com> Date: Thu, 7 Nov 2024 11:01:00 -0700 Subject: [PATCH 19/43] updating lock file --- poetry.lock | 28 ++++++++++++++-------------- pyproject.toml | 2 +- 2 files changed, 15 insertions(+), 15 deletions(-) diff --git a/poetry.lock b/poetry.lock index c57aaf03..7c3be0c6 100644 --- a/poetry.lock +++ b/poetry.lock @@ -13,13 +13,13 @@ files = [ [[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] @@ -173,17 +173,17 @@ files = [ [[package]] name = "boto3" -version = "1.35.54" +version = "1.35.55" description = "The AWS SDK for Python" optional = false python-versions = ">=3.8" files = [ - {file = "boto3-1.35.54-py3-none-any.whl", hash = "sha256:2d5e160b614db55fbee7981001c54476cb827c441cef65b2fcb2c52a62019909"}, - {file = "boto3-1.35.54.tar.gz", hash = "sha256:7d9c359bbbc858a60b51c86328db813353c8bd1940212cdbd0a7da835291c2e1"}, + {file = "boto3-1.35.55-py3-none-any.whl", hash = "sha256:c7a0a0bc5ae3bed5d38e8bfe5a56b31621e79bdd7c1ea6e5ba4326d820cde3a5"}, + {file = "boto3-1.35.55.tar.gz", hash = "sha256:82fa8cdb00731aeffe7a5829821ae78d75c7ae959b638c15ff3b4681192ace90"}, ] [package.dependencies] -botocore = ">=1.35.54,<1.36.0" +botocore = ">=1.35.55,<1.36.0" jmespath = ">=0.7.1,<2.0.0" s3transfer = ">=0.10.0,<0.11.0" @@ -192,13 +192,13 @@ crt = ["botocore[crt] (>=1.21.0,<2.0a0)"] [[package]] name = "botocore" -version = "1.35.54" +version = "1.35.55" description = "Low-level, data-driven core of boto 3." optional = false python-versions = ">=3.8" files = [ - {file = "botocore-1.35.54-py3-none-any.whl", hash = "sha256:9cca1811094b6cdc144c2c063a3ec2db6d7c88194b04d4277cd34fc8e3473aff"}, - {file = "botocore-1.35.54.tar.gz", hash = "sha256:131bb59ce59c8a939b31e8e647242d70cf11d32d4529fa4dca01feea1e891a76"}, + {file = "botocore-1.35.55-py3-none-any.whl", hash = "sha256:3d54739e498534c9d7a6e9732ae2d17ed29c7d5e29fe36c956d8488b859538b0"}, + {file = "botocore-1.35.55.tar.gz", hash = "sha256:61ae18f688250372d7b6046e35c86f8fd09a7c0f0064b52688f3490b4d6c9d6b"}, ] [package.dependencies] @@ -2338,13 +2338,13 @@ socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"] [[package]] name = "werkzeug" -version = "3.1.1" +version = "3.1.2" description = "The comprehensive WSGI web application library." optional = false python-versions = ">=3.9" files = [ - {file = "werkzeug-3.1.1-py3-none-any.whl", hash = "sha256:a71124d1ef06008baafa3d266c02f56e1836a5984afd6dd6c9230669d60d9fb5"}, - {file = "werkzeug-3.1.1.tar.gz", hash = "sha256:8cd39dfbdfc1e051965f156163e2974e52c210f130810e9ad36858f0fd3edad4"}, + {file = "werkzeug-3.1.2-py3-none-any.whl", hash = "sha256:4f7d1a5de312c810a8a2c6f0b47e9f6a7cffb7c8322def35e4d4d9841ff85597"}, + {file = "werkzeug-3.1.2.tar.gz", hash = "sha256:f471a4cd167233077e9d2a8190c3471c5bc520c636a9e3c1e9300c33bced03bc"}, ] [package.dependencies] @@ -2396,4 +2396,4 @@ type = ["pytest-mypy"] [metadata] lock-version = "2.0" python-versions = ">=3.9,<3.10" -content-hash = "2050e04fc7fee0186fcd3815550ae819337bfc4ec2af173af279b9452baf7b20" +content-hash = "9c2c6b2d6e45b2be57ef3632472dd9961ecc174e97e276d40eafe13d73a2afe3" diff --git a/pyproject.toml b/pyproject.toml index 7f5ce061..cadb54f9 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -26,7 +26,7 @@ graphene = ">=2.0.1" jsonschema = "*" lxml = ">=4.6.5" psycopg2-binary = ">=2.8.4" -PyYAML = "*" +PyYAML = ">=5.4.1" requests = ">=2.31.0,<3.0.0" simplejson = ">=3.8.1" sqlalchemy = ">=1.3.*" From 769e392a368d1d2e667f6f5e1f3a8e642d5056f5 Mon Sep 17 00:00:00 2001 From: EliseCastle23 <109446148+EliseCastle23@users.noreply.github.com> Date: Thu, 7 Nov 2024 11:18:35 -0700 Subject: [PATCH 20/43] fixing build error --- poetry.lock | 2 +- pyproject.toml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/poetry.lock b/poetry.lock index 7c3be0c6..13404855 100644 --- a/poetry.lock +++ b/poetry.lock @@ -2396,4 +2396,4 @@ type = ["pytest-mypy"] [metadata] lock-version = "2.0" python-versions = ">=3.9,<3.10" -content-hash = "9c2c6b2d6e45b2be57ef3632472dd9961ecc174e97e276d40eafe13d73a2afe3" +content-hash = "2050e04fc7fee0186fcd3815550ae819337bfc4ec2af173af279b9452baf7b20" diff --git a/pyproject.toml b/pyproject.toml index cadb54f9..7f5ce061 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -26,7 +26,7 @@ graphene = ">=2.0.1" jsonschema = "*" lxml = ">=4.6.5" psycopg2-binary = ">=2.8.4" -PyYAML = ">=5.4.1" +PyYAML = "*" requests = ">=2.31.0,<3.0.0" simplejson = ">=3.8.1" sqlalchemy = ">=1.3.*" From fcb68f994a208da30cc1aad9d332f0f66a6f0c11 Mon Sep 17 00:00:00 2001 From: EliseCastle23 <109446148+EliseCastle23@users.noreply.github.com> Date: Thu, 7 Nov 2024 12:19:44 -0700 Subject: [PATCH 21/43] updating poetry lock --- poetry.lock | 28 ++++++++++++++-------------- 1 file changed, 14 insertions(+), 14 deletions(-) diff --git a/poetry.lock b/poetry.lock index 13404855..b50a9eb5 100644 --- a/poetry.lock +++ b/poetry.lock @@ -13,13 +13,13 @@ files = [ [[package]] name = "alembic" -version = "1.14.0" +version = "1.13.3" description = "A database migration tool for SQLAlchemy." optional = false python-versions = ">=3.8" files = [ - {file = "alembic-1.14.0-py3-none-any.whl", hash = "sha256:99bd884ca390466db5e27ffccff1d179ec5c05c965cfefc0607e69f9e411cb25"}, - {file = "alembic-1.14.0.tar.gz", hash = "sha256:b00892b53b3642d0b8dbedba234dbf1924b69be83a9a769d5a624b01094e304b"}, + {file = "alembic-1.13.3-py3-none-any.whl", hash = "sha256:908e905976d15235fae59c9ac42c4c5b75cfcefe3d27c0fbf7ae15a37715d80e"}, + {file = "alembic-1.13.3.tar.gz", hash = "sha256:203503117415561e203aa14541740643a611f641517f0209fcae63e9fa09f1a2"}, ] [package.dependencies] @@ -173,17 +173,17 @@ files = [ [[package]] name = "boto3" -version = "1.35.55" +version = "1.35.54" description = "The AWS SDK for Python" optional = false python-versions = ">=3.8" files = [ - {file = "boto3-1.35.55-py3-none-any.whl", hash = "sha256:c7a0a0bc5ae3bed5d38e8bfe5a56b31621e79bdd7c1ea6e5ba4326d820cde3a5"}, - {file = "boto3-1.35.55.tar.gz", hash = "sha256:82fa8cdb00731aeffe7a5829821ae78d75c7ae959b638c15ff3b4681192ace90"}, + {file = "boto3-1.35.54-py3-none-any.whl", hash = "sha256:2d5e160b614db55fbee7981001c54476cb827c441cef65b2fcb2c52a62019909"}, + {file = "boto3-1.35.54.tar.gz", hash = "sha256:7d9c359bbbc858a60b51c86328db813353c8bd1940212cdbd0a7da835291c2e1"}, ] [package.dependencies] -botocore = ">=1.35.55,<1.36.0" +botocore = ">=1.35.54,<1.36.0" jmespath = ">=0.7.1,<2.0.0" s3transfer = ">=0.10.0,<0.11.0" @@ -192,13 +192,13 @@ crt = ["botocore[crt] (>=1.21.0,<2.0a0)"] [[package]] name = "botocore" -version = "1.35.55" +version = "1.35.54" description = "Low-level, data-driven core of boto 3." optional = false python-versions = ">=3.8" files = [ - {file = "botocore-1.35.55-py3-none-any.whl", hash = "sha256:3d54739e498534c9d7a6e9732ae2d17ed29c7d5e29fe36c956d8488b859538b0"}, - {file = "botocore-1.35.55.tar.gz", hash = "sha256:61ae18f688250372d7b6046e35c86f8fd09a7c0f0064b52688f3490b4d6c9d6b"}, + {file = "botocore-1.35.54-py3-none-any.whl", hash = "sha256:9cca1811094b6cdc144c2c063a3ec2db6d7c88194b04d4277cd34fc8e3473aff"}, + {file = "botocore-1.35.54.tar.gz", hash = "sha256:131bb59ce59c8a939b31e8e647242d70cf11d32d4529fa4dca01feea1e891a76"}, ] [package.dependencies] @@ -2338,13 +2338,13 @@ socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"] [[package]] name = "werkzeug" -version = "3.1.2" +version = "3.1.1" description = "The comprehensive WSGI web application library." optional = false python-versions = ">=3.9" files = [ - {file = "werkzeug-3.1.2-py3-none-any.whl", hash = "sha256:4f7d1a5de312c810a8a2c6f0b47e9f6a7cffb7c8322def35e4d4d9841ff85597"}, - {file = "werkzeug-3.1.2.tar.gz", hash = "sha256:f471a4cd167233077e9d2a8190c3471c5bc520c636a9e3c1e9300c33bced03bc"}, + {file = "werkzeug-3.1.1-py3-none-any.whl", hash = "sha256:a71124d1ef06008baafa3d266c02f56e1836a5984afd6dd6c9230669d60d9fb5"}, + {file = "werkzeug-3.1.1.tar.gz", hash = "sha256:8cd39dfbdfc1e051965f156163e2974e52c210f130810e9ad36858f0fd3edad4"}, ] [package.dependencies] @@ -2396,4 +2396,4 @@ type = ["pytest-mypy"] [metadata] lock-version = "2.0" python-versions = ">=3.9,<3.10" -content-hash = "2050e04fc7fee0186fcd3815550ae819337bfc4ec2af173af279b9452baf7b20" +content-hash = "2050e04fc7fee0186fcd3815550ae819337bfc4ec2af173af279b9452baf7b20" \ No newline at end of file From da2df89d0601cf458389b3c4b041b83089a9b742 Mon Sep 17 00:00:00 2001 From: EliseCastle23 <109446148+EliseCastle23@users.noreply.github.com> Date: Fri, 8 Nov 2024 10:37:31 -0700 Subject: [PATCH 22/43] testing installing packages to fix build error --- Dockerfile | 2 ++ 1 file changed, 2 insertions(+) diff --git a/Dockerfile b/Dockerfile index a094af35..e11d9fcd 100644 --- a/Dockerfile +++ b/Dockerfile @@ -34,6 +34,8 @@ FROM base COPY --from=builder /$appname /$appname +RUN dnf install -y python3-devel postgresql-devel + # Switch to non-root user 'gen3' for the serving process USER gen3 From 62055f0896a28ac3673c46c317b7f1a1c136a1c7 Mon Sep 17 00:00:00 2001 From: EliseCastle23 <109446148+EliseCastle23@users.noreply.github.com> Date: Fri, 8 Nov 2024 11:05:07 -0700 Subject: [PATCH 23/43] moving command --- Dockerfile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index e11d9fcd..e345115d 100644 --- a/Dockerfile +++ b/Dockerfile @@ -18,6 +18,8 @@ USER gen3 COPY poetry.lock pyproject.toml /${appname}/ +RUN dnf install -y python3-devel postgresql-devel + RUN poetry install -vv --without dev --no-interaction COPY --chown=gen3:gen3 . /$appname @@ -34,8 +36,6 @@ FROM base COPY --from=builder /$appname /$appname -RUN dnf install -y python3-devel postgresql-devel - # Switch to non-root user 'gen3' for the serving process USER gen3 From fef6157a5da134a0a147a889cf964ee936afa9fb Mon Sep 17 00:00:00 2001 From: EliseCastle23 <109446148+EliseCastle23@users.noreply.github.com> Date: Fri, 8 Nov 2024 11:08:21 -0700 Subject: [PATCH 24/43] moving command again --- Dockerfile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index e345115d..12acd11a 100644 --- a/Dockerfile +++ b/Dockerfile @@ -14,12 +14,12 @@ RUN chown -R gen3:gen3 /$appname # Builder stage FROM base AS builder +RUN dnf install -y python3-devel postgresql-devel + USER gen3 COPY poetry.lock pyproject.toml /${appname}/ -RUN dnf install -y python3-devel postgresql-devel - RUN poetry install -vv --without dev --no-interaction COPY --chown=gen3:gen3 . /$appname From bea25df53fdce160c8cb89ba4637d217c14f8eb4 Mon Sep 17 00:00:00 2001 From: EliseCastle23 <109446148+EliseCastle23@users.noreply.github.com> Date: Fri, 8 Nov 2024 11:16:32 -0700 Subject: [PATCH 25/43] test --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 12acd11a..e16e87b0 100644 --- a/Dockerfile +++ b/Dockerfile @@ -14,7 +14,7 @@ RUN chown -R gen3:gen3 /$appname # Builder stage FROM base AS builder -RUN dnf install -y python3-devel postgresql-devel +RUN dnf install -y python3-devel postgresql-devel gcc USER gen3 From 43a1e6b9d40119af81989bf4ddb0392fdb2a38b4 Mon Sep 17 00:00:00 2001 From: EliseCastle23 <109446148+EliseCastle23@users.noreply.github.com> Date: Fri, 8 Nov 2024 11:48:11 -0700 Subject: [PATCH 26/43] test adding gcc only --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index e16e87b0..3c369b1d 100644 --- a/Dockerfile +++ b/Dockerfile @@ -14,7 +14,7 @@ RUN chown -R gen3:gen3 /$appname # Builder stage FROM base AS builder -RUN dnf install -y python3-devel postgresql-devel gcc +RUN dnf install -y gcc USER gen3 From fc144e4158ddba88a8bd7e780338374f7bf625d8 Mon Sep 17 00:00:00 2001 From: EliseCastle23 <109446148+EliseCastle23@users.noreply.github.com> Date: Fri, 8 Nov 2024 11:56:04 -0700 Subject: [PATCH 27/43] testing --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 3c369b1d..3f282f03 100644 --- a/Dockerfile +++ b/Dockerfile @@ -14,7 +14,7 @@ RUN chown -R gen3:gen3 /$appname # Builder stage FROM base AS builder -RUN dnf install -y gcc +RUN dnf install -y postgresql-devel gcc USER gen3 From cbd124ab48a754c49fd6db153900cb0f5b22ea37 Mon Sep 17 00:00:00 2001 From: EliseCastle23 <109446148+EliseCastle23@users.noreply.github.com> Date: Fri, 8 Nov 2024 12:04:28 -0700 Subject: [PATCH 28/43] testing python devel and gcc --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 3f282f03..2f2499b4 100644 --- a/Dockerfile +++ b/Dockerfile @@ -14,7 +14,7 @@ RUN chown -R gen3:gen3 /$appname # Builder stage FROM base AS builder -RUN dnf install -y postgresql-devel gcc +RUN dnf install -y python3-devel gcc USER gen3 From a6184571ae5fbb940220df46db298c1c8f9d662d Mon Sep 17 00:00:00 2001 From: EliseCastle23 <109446148+EliseCastle23@users.noreply.github.com> Date: Fri, 8 Nov 2024 12:12:55 -0700 Subject: [PATCH 29/43] python3-devel postgresql-devel gcc --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 2f2499b4..e16e87b0 100644 --- a/Dockerfile +++ b/Dockerfile @@ -14,7 +14,7 @@ RUN chown -R gen3:gen3 /$appname # Builder stage FROM base AS builder -RUN dnf install -y python3-devel gcc +RUN dnf install -y python3-devel postgresql-devel gcc USER gen3 From 4e534bde5f83f5c9a9cce784f7f1e9228be6ea54 Mon Sep 17 00:00:00 2001 From: EliseCastle23 <109446148+EliseCastle23@users.noreply.github.com> Date: Fri, 8 Nov 2024 15:52:34 -0700 Subject: [PATCH 30/43] sheepdog app init updates --- Dockerfile | 1 - bin/pyproject.toml | 63 ++++++++++++++++++++++++++++++++ bin/settings.py | 2 +- deployment/wsgi/gunicorn.conf.py | 2 +- deployment/wsgi/wsgi.py | 1 - sheepdog/api.py | 4 -- 6 files changed, 65 insertions(+), 8 deletions(-) create mode 100644 bin/pyproject.toml delete mode 100644 deployment/wsgi/wsgi.py diff --git a/Dockerfile b/Dockerfile index e16e87b0..2477e5cb 100644 --- a/Dockerfile +++ b/Dockerfile @@ -23,7 +23,6 @@ COPY poetry.lock pyproject.toml /${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 # Run poetry again so this app itself gets installed too RUN poetry install --without dev --no-interaction diff --git a/bin/pyproject.toml b/bin/pyproject.toml new file mode 100644 index 00000000..7f5ce061 --- /dev/null +++ b/bin/pyproject.toml @@ -0,0 +1,63 @@ +[tool.poetry] +name = "sheepdog" +version = "5.1.5" +description = "Gen3 Submission Service" +authors = ["CTDS UChicago "] +license = "Apache-2.0" +repository = "https://github.com/uc-cdis/sheepdog" +include = [ + "NOTICE", +] + +[tool.poetry.dependencies] +python = ">=3.9,<3.10" +authlib = "*" # let authutils decide which version we're using +authutils = ">=6.0.0" +boto = ">=2.49.0" +botocore = "*" +datamodelutils = ">=1.1.0" +dictionaryutils = ">=3.4.11" +envelopes = ">=0.4" +Flask = ">=2.2.5" +Flask-SQLAlchemy-Session = ">=1.1" +fuzzywuzzy = ">=0.6.1" +gen3authz = ">=1.0.4" +graphene = ">=2.0.1" +jsonschema = "*" +lxml = ">=4.6.5" +psycopg2-binary = ">=2.8.4" +PyYAML = "*" +requests = ">=2.31.0,<3.0.0" +simplejson = ">=3.8.1" +sqlalchemy = ">=1.3.*" +cdispyutils = ">=2.0.1" +psqlgraph = ">=3.0.1" +cdiserrors = ">=1.0.0" +cdislogging = ">=1.0.0" +gen3dictionary = ">=2.0.3" +gen3datamodel = ">=3.2.1" +gunicorn = ">=21.2.0" +indexclient = ">=2.1.1" +urllib3 = "<2.0.0" + +[tool.poetry.dev-dependencies] +pytest = ">=4.6.5" +pytest-cov = ">=2.5.1" +requests_mock = ">=1.4.0" +coverage = ">=5.3.0" +mock = ">=1.0.1" +pytest-flask = ">=1.2.0" +moto = "^4.2.9" +sphinxcontrib-httpdomain = ">=1.3.0" +codacy-coverage = ">=1.3.11" +Sphinx = ">=1.6.5" +sphinx_rtd_theme = "*" +flasgger = ">=0.9.1" +indexd = {git = "https://github.com/uc-cdis/indexd", rev = "5.0.3"} + +[build-system] +requires = ["poetry>=0.12"] +build-backend = "poetry.masonry.api" + +[tool.pytest.ini_options] +markers = ["ssl"] diff --git a/bin/settings.py b/bin/settings.py index c3970a43..eca150d4 100644 --- a/bin/settings.py +++ b/bin/settings.py @@ -1,6 +1,6 @@ from sheepdog.api import app, app_init import os -from . import confighelper +import bin.confighelper as confighelper APP_NAME = "sheepdog" diff --git a/deployment/wsgi/gunicorn.conf.py b/deployment/wsgi/gunicorn.conf.py index 64092ba3..4a4afaed 100644 --- a/deployment/wsgi/gunicorn.conf.py +++ b/deployment/wsgi/gunicorn.conf.py @@ -1,4 +1,4 @@ -wsgi_app = "deployment.wsgi.wsgi:application" +wsgi_app = "bin.settings:application" bind = "0.0.0.0:8000" workers = 1 preload_app = True diff --git a/deployment/wsgi/wsgi.py b/deployment/wsgi/wsgi.py deleted file mode 100644 index a7a7578c..00000000 --- a/deployment/wsgi/wsgi.py +++ /dev/null @@ -1 +0,0 @@ -from sheepdog.api import app as application diff --git a/sheepdog/api.py b/sheepdog/api.py index b1457e2f..ac214255 100644 --- a/sheepdog/api.py +++ b/sheepdog/api.py @@ -152,10 +152,6 @@ def app_init(app): db_init(app) # exclude es init as it's not used yet # es_init(app) - try: - app.secret_key = app.config["FLASK_SECRET_KEY"] - except KeyError: - app.logger.error("Secret key not set in config! Authentication will not work") # ARBORIST deprecated, replaced by ARBORIST_URL arborist_url = os.environ.get("ARBORIST_URL", os.environ.get("ARBORIST")) From 3e779c025063b8e0076cf33dd4e992e26569437e Mon Sep 17 00:00:00 2001 From: EliseCastle23 <109446148+EliseCastle23@users.noreply.github.com> Date: Fri, 8 Nov 2024 16:09:06 -0700 Subject: [PATCH 31/43] updating settings --- bin/settings.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/settings.py b/bin/settings.py index eca150d4..f95fbaff 100644 --- a/bin/settings.py +++ b/bin/settings.py @@ -1,5 +1,5 @@ from sheepdog.api import app, app_init -import os +from os import environ import bin.confighelper as confighelper APP_NAME = "sheepdog" From d6c320390e4cff6015bfdfb476f6a79b5e5827d5 Mon Sep 17 00:00:00 2001 From: EliseCastle23 <109446148+EliseCastle23@users.noreply.github.com> Date: Fri, 8 Nov 2024 16:15:09 -0700 Subject: [PATCH 32/43] adding extra import --- .secrets.baseline | 4 ++-- bin/settings.py | 1 + 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/.secrets.baseline b/.secrets.baseline index 30e22d57..12d6e3c8 100644 --- a/.secrets.baseline +++ b/.secrets.baseline @@ -136,7 +136,7 @@ "filename": "bin/settings.py", "hashed_secret": "347cd9c53ff77d41a7b22aa56c7b4efaf54658e3", "is_verified": false, - "line_number": 49 + "line_number": 50 } ], "docs/local_dev_environment.md": [ @@ -354,5 +354,5 @@ } ] }, - "generated_at": "2024-11-07T17:57:50Z" + "generated_at": "2024-11-08T23:15:04Z" } diff --git a/bin/settings.py b/bin/settings.py index f95fbaff..7832c528 100644 --- a/bin/settings.py +++ b/bin/settings.py @@ -1,5 +1,6 @@ from sheepdog.api import app, app_init from os import environ +import os import bin.confighelper as confighelper APP_NAME = "sheepdog" From dda286006c137e3dc8fa6cdbe551d749ac76d3ee Mon Sep 17 00:00:00 2001 From: EliseCastle23 <109446148+EliseCastle23@users.noreply.github.com> Date: Tue, 12 Nov 2024 08:52:57 -0700 Subject: [PATCH 33/43] pinning versions and updating variable syntax --- Dockerfile | 12 ++++---- poetry.lock | 78 +++++++++++++++++++++++++------------------------- pyproject.toml | 4 +-- 3 files changed, 47 insertions(+), 47 deletions(-) diff --git a/Dockerfile b/Dockerfile index 2477e5cb..966ba892 100644 --- a/Dockerfile +++ b/Dockerfile @@ -9,7 +9,7 @@ ENV appname=sheepdog WORKDIR /${appname} -RUN chown -R gen3:gen3 /$appname +RUN chown -R gen3:gen3 /${appname} # Builder stage FROM base AS builder @@ -22,22 +22,22 @@ COPY poetry.lock pyproject.toml /${appname}/ RUN poetry install -vv --without dev --no-interaction -COPY --chown=gen3:gen3 . /$appname +COPY --chown=gen3:gen3 . /${appname} # 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 ["/sheepdog/dockerrun.bash"] \ No newline at end of file diff --git a/poetry.lock b/poetry.lock index b50a9eb5..4a2603de 100644 --- a/poetry.lock +++ b/poetry.lock @@ -13,13 +13,13 @@ files = [ [[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] @@ -151,13 +151,13 @@ 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]] @@ -173,17 +173,17 @@ files = [ [[package]] name = "boto3" -version = "1.35.54" +version = "1.35.58" description = "The AWS SDK for Python" optional = false python-versions = ">=3.8" files = [ - {file = "boto3-1.35.54-py3-none-any.whl", hash = "sha256:2d5e160b614db55fbee7981001c54476cb827c441cef65b2fcb2c52a62019909"}, - {file = "boto3-1.35.54.tar.gz", hash = "sha256:7d9c359bbbc858a60b51c86328db813353c8bd1940212cdbd0a7da835291c2e1"}, + {file = "boto3-1.35.58-py3-none-any.whl", hash = "sha256:856896fd5fc5871758eb04b27bad5bbbf0fdb6143a923f9e8d10125351efdf98"}, + {file = "boto3-1.35.58.tar.gz", hash = "sha256:1ee139e63f1545ee0192914cfe422b68360b8c344a94e4612ac657dd7ece93de"}, ] [package.dependencies] -botocore = ">=1.35.54,<1.36.0" +botocore = ">=1.35.58,<1.36.0" jmespath = ">=0.7.1,<2.0.0" s3transfer = ">=0.10.0,<0.11.0" @@ -192,13 +192,13 @@ crt = ["botocore[crt] (>=1.21.0,<2.0a0)"] [[package]] name = "botocore" -version = "1.35.54" +version = "1.35.58" description = "Low-level, data-driven core of boto 3." optional = false python-versions = ">=3.8" files = [ - {file = "botocore-1.35.54-py3-none-any.whl", hash = "sha256:9cca1811094b6cdc144c2c063a3ec2db6d7c88194b04d4277cd34fc8e3473aff"}, - {file = "botocore-1.35.54.tar.gz", hash = "sha256:131bb59ce59c8a939b31e8e647242d70cf11d32d4529fa4dca01feea1e891a76"}, + {file = "botocore-1.35.58-py3-none-any.whl", hash = "sha256:647b8706ae6484ee4c2208235f38976d9f0e52f80143e81d7941075215e96111"}, + {file = "botocore-1.35.58.tar.gz", hash = "sha256:8303309c7b59ddf04b11d79813530809d6b10b411ac9f93916d2032c283d6881"}, ] [package.dependencies] @@ -871,13 +871,13 @@ PyYAML = "*" [[package]] name = "graphene" -version = "3.4.1" +version = "3.4.3" description = "GraphQL Framework for Python" optional = false python-versions = "*" files = [ - {file = "graphene-3.4.1-py2.py3-none-any.whl", hash = "sha256:ca98f853201293871cdc7f55faf2523a9bc077181fe0f4947db5a243e5c67083"}, - {file = "graphene-3.4.1.tar.gz", hash = "sha256:828a8d7b1bce450566a72cc8733716c20f3acfc659960de73dd38f46dc302040"}, + {file = "graphene-3.4.3-py2.py3-none-any.whl", hash = "sha256:820db6289754c181007a150db1f7fff544b94142b556d12e3ebc777a7bf36c71"}, + {file = "graphene-3.4.3.tar.gz", hash = "sha256:2a3786948ce75fe7e078443d37f609cbe5bb36ad8d6b828740ad3b95ed1a0aaa"}, ] [package.dependencies] @@ -1494,13 +1494,13 @@ xray = ["aws-xray-sdk (>=0.93,!=0.96)", "setuptools"] [[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]] @@ -1889,23 +1889,23 @@ crt = ["botocore[crt] (>=1.33.2,<2.0a.0)"] [[package]] name = "setuptools" -version = "75.3.0" +version = "75.4.0" 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-75.4.0-py3-none-any.whl", hash = "sha256:b3c5d862f98500b06ffdf7cc4499b48c46c317d8d56cb30b5c8bce4d88f5c216"}, + {file = "setuptools-75.4.0.tar.gz", hash = "sha256:1dc484f5cf56fd3fe7216d7b8df820802e7246cfb534a1db2aa64f14fcb9cdcb"}, ] [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 = "simplejson" @@ -2300,13 +2300,13 @@ files = [ [[package]] name = "tomli" -version = "2.0.2" +version = "2.1.0" description = "A lil' TOML parser" optional = false python-versions = ">=3.8" files = [ - {file = "tomli-2.0.2-py3-none-any.whl", hash = "sha256:2ebe24485c53d303f690b0ec092806a085f07af5a5aa1464f3931eec36caaa38"}, - {file = "tomli-2.0.2.tar.gz", hash = "sha256:d46d457a85337051c36524bc5349dd91b1877838e2979ac5ced3e710ed8a60ed"}, + {file = "tomli-2.1.0-py3-none-any.whl", hash = "sha256:a5c57c3d1c56f5ccdf89f6523458f60ef716e210fc47c4cfb188c5ba473e0391"}, + {file = "tomli-2.1.0.tar.gz", hash = "sha256:3f646cae2aec94e17d04973e4249548320197cfabdf130015d023de4b74d8ab8"}, ] [[package]] @@ -2338,13 +2338,13 @@ socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"] [[package]] name = "werkzeug" -version = "3.1.1" +version = "3.1.3" description = "The comprehensive WSGI web application library." optional = false python-versions = ">=3.9" files = [ - {file = "werkzeug-3.1.1-py3-none-any.whl", hash = "sha256:a71124d1ef06008baafa3d266c02f56e1836a5984afd6dd6c9230669d60d9fb5"}, - {file = "werkzeug-3.1.1.tar.gz", hash = "sha256:8cd39dfbdfc1e051965f156163e2974e52c210f130810e9ad36858f0fd3edad4"}, + {file = "werkzeug-3.1.3-py3-none-any.whl", hash = "sha256:54b78bf3716d19a65be4fceccc0d1d7b89e608834989dfae50ea87564639213e"}, + {file = "werkzeug-3.1.3.tar.gz", hash = "sha256:60723ce945c19328679790e3282cc758aa4a6040e4bb330f53d30fa546d44746"}, ] [package.dependencies] @@ -2376,13 +2376,13 @@ 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] @@ -2396,4 +2396,4 @@ type = ["pytest-mypy"] [metadata] lock-version = "2.0" python-versions = ">=3.9,<3.10" -content-hash = "2050e04fc7fee0186fcd3815550ae819337bfc4ec2af173af279b9452baf7b20" \ No newline at end of file +content-hash = "308f7a413c9fd1a9f5157c4990fe6169354357831e85ebe891fcd1c87d862757" diff --git a/pyproject.toml b/pyproject.toml index 7f5ce061..a7d5647c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -23,10 +23,10 @@ Flask-SQLAlchemy-Session = ">=1.1" fuzzywuzzy = ">=0.6.1" gen3authz = ">=1.0.4" graphene = ">=2.0.1" -jsonschema = "*" +jsonschema = ">=3.2" lxml = ">=4.6.5" psycopg2-binary = ">=2.8.4" -PyYAML = "*" +PyYAML = ">=5.4.1" requests = ">=2.31.0,<3.0.0" simplejson = ">=3.8.1" sqlalchemy = ">=1.3.*" From 3d2bf6abdba9bd355ba13eac90afb889e44a16e7 Mon Sep 17 00:00:00 2001 From: EliseCastle23 <109446148+EliseCastle23@users.noreply.github.com> Date: Wed, 13 Nov 2024 15:46:56 -0700 Subject: [PATCH 34/43] adding "postgresql-libs" to ensure the "libpq.so.5" library is added --- Dockerfile | 2 ++ 1 file changed, 2 insertions(+) diff --git a/Dockerfile b/Dockerfile index 966ba892..8abe016f 100644 --- a/Dockerfile +++ b/Dockerfile @@ -33,6 +33,8 @@ RUN git config --global --add safe.directory /${appname} && COMMIT=`git rev-pars # Final stage FROM base +RUN yum install -y postgresql-libs + COPY --from=builder /${appname} /${appname} # Switch to non-root user 'gen3' for the serving process From e8bb8de27e416d29d9280dce2a153a4e4b9cced1 Mon Sep 17 00:00:00 2001 From: EliseCastle23 <109446148+EliseCastle23@users.noreply.github.com> Date: Fri, 15 Nov 2024 10:07:31 -0700 Subject: [PATCH 35/43] making suggested updates --- bin/pyproject.toml | 63 ---------------------------------------------- dockerrun.bash | 5 ++-- 2 files changed, 2 insertions(+), 66 deletions(-) delete mode 100644 bin/pyproject.toml diff --git a/bin/pyproject.toml b/bin/pyproject.toml deleted file mode 100644 index 7f5ce061..00000000 --- a/bin/pyproject.toml +++ /dev/null @@ -1,63 +0,0 @@ -[tool.poetry] -name = "sheepdog" -version = "5.1.5" -description = "Gen3 Submission Service" -authors = ["CTDS UChicago "] -license = "Apache-2.0" -repository = "https://github.com/uc-cdis/sheepdog" -include = [ - "NOTICE", -] - -[tool.poetry.dependencies] -python = ">=3.9,<3.10" -authlib = "*" # let authutils decide which version we're using -authutils = ">=6.0.0" -boto = ">=2.49.0" -botocore = "*" -datamodelutils = ">=1.1.0" -dictionaryutils = ">=3.4.11" -envelopes = ">=0.4" -Flask = ">=2.2.5" -Flask-SQLAlchemy-Session = ">=1.1" -fuzzywuzzy = ">=0.6.1" -gen3authz = ">=1.0.4" -graphene = ">=2.0.1" -jsonschema = "*" -lxml = ">=4.6.5" -psycopg2-binary = ">=2.8.4" -PyYAML = "*" -requests = ">=2.31.0,<3.0.0" -simplejson = ">=3.8.1" -sqlalchemy = ">=1.3.*" -cdispyutils = ">=2.0.1" -psqlgraph = ">=3.0.1" -cdiserrors = ">=1.0.0" -cdislogging = ">=1.0.0" -gen3dictionary = ">=2.0.3" -gen3datamodel = ">=3.2.1" -gunicorn = ">=21.2.0" -indexclient = ">=2.1.1" -urllib3 = "<2.0.0" - -[tool.poetry.dev-dependencies] -pytest = ">=4.6.5" -pytest-cov = ">=2.5.1" -requests_mock = ">=1.4.0" -coverage = ">=5.3.0" -mock = ">=1.0.1" -pytest-flask = ">=1.2.0" -moto = "^4.2.9" -sphinxcontrib-httpdomain = ">=1.3.0" -codacy-coverage = ">=1.3.11" -Sphinx = ">=1.6.5" -sphinx_rtd_theme = "*" -flasgger = ">=0.9.1" -indexd = {git = "https://github.com/uc-cdis/indexd", rev = "5.0.3"} - -[build-system] -requires = ["poetry>=0.12"] -build-backend = "poetry.masonry.api" - -[tool.pytest.ini_options] -markers = ["ssl"] diff --git a/dockerrun.bash b/dockerrun.bash index c3e6f8f8..c39a93b2 100755 --- a/dockerrun.bash +++ b/dockerrun.bash @@ -1,5 +1,4 @@ #!/bin/bash -poetry run gunicorn -c "/sheepdog/deployment/wsgi/gunicorn.conf.py" & -sleep 30 -nginx -g 'daemon off;' \ No newline at end of file +poetry run gunicorn -c "/sheepdog/deployment/wsgi/gunicorn.conf.py" +nginx \ No newline at end of file From b8085df85e6f9127b15f56b98cd7a544621fe975 Mon Sep 17 00:00:00 2001 From: EliseCastle23 <109446148+EliseCastle23@users.noreply.github.com> Date: Fri, 15 Nov 2024 11:42:15 -0700 Subject: [PATCH 36/43] removing commented command --- Dockerfile | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/Dockerfile b/Dockerfile index 8abe016f..884b16de 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:${AZLINUX_BASE_VERSION} AS base - ENV appname=sheepdog WORKDIR /${appname} @@ -42,4 +40,4 @@ USER gen3 WORKDIR /${appname} -CMD ["/sheepdog/dockerrun.bash"] \ No newline at end of file +CMD ["/sheepdog/dockerrun.bash"] From 5fc125f9c1c2be33875d74b73b003c1c8ccb00e2 Mon Sep 17 00:00:00 2001 From: EliseCastle23 <109446148+EliseCastle23@users.noreply.github.com> Date: Fri, 15 Nov 2024 14:42:34 -0700 Subject: [PATCH 37/43] editing nginx command --- dockerrun.bash | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dockerrun.bash b/dockerrun.bash index c39a93b2..b068da22 100755 --- a/dockerrun.bash +++ b/dockerrun.bash @@ -1,4 +1,4 @@ #!/bin/bash poetry run gunicorn -c "/sheepdog/deployment/wsgi/gunicorn.conf.py" -nginx \ No newline at end of file +nginx -g 'daemon off;' \ No newline at end of file From 375eee954465c20c8601e995cc9a230da8fb1f5b Mon Sep 17 00:00:00 2001 From: EliseCastle23 <109446148+EliseCastle23@users.noreply.github.com> Date: Fri, 15 Nov 2024 14:48:03 -0700 Subject: [PATCH 38/43] adding back sleep --- dockerrun.bash | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/dockerrun.bash b/dockerrun.bash index b068da22..ded845cf 100755 --- a/dockerrun.bash +++ b/dockerrun.bash @@ -1,4 +1,4 @@ -#!/bin/bash +poetry run gunicorn -c "/sheepdog/deployment/wsgi/gunicorn.conf.py" & +sleep 30 -poetry run gunicorn -c "/sheepdog/deployment/wsgi/gunicorn.conf.py" nginx -g 'daemon off;' \ No newline at end of file From 2e562ba93ad72e41abe6c0a0fbbc0c15c7663cfd Mon Sep 17 00:00:00 2001 From: EliseCastle23 <109446148+EliseCastle23@users.noreply.github.com> Date: Fri, 15 Nov 2024 14:54:00 -0700 Subject: [PATCH 39/43] fixing syntax error --- dockerrun.bash | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/dockerrun.bash b/dockerrun.bash index ded845cf..c3e6f8f8 100755 --- a/dockerrun.bash +++ b/dockerrun.bash @@ -1,4 +1,5 @@ +#!/bin/bash + poetry run gunicorn -c "/sheepdog/deployment/wsgi/gunicorn.conf.py" & sleep 30 - nginx -g 'daemon off;' \ No newline at end of file From b52a6d9c95070ed12520d2d7385f24c492679fa5 Mon Sep 17 00:00:00 2001 From: EliseCastle23 <109446148+EliseCastle23@users.noreply.github.com> Date: Fri, 15 Nov 2024 16:11:08 -0700 Subject: [PATCH 40/43] adding comment --- dockerrun.bash | 1 + 1 file changed, 1 insertion(+) diff --git a/dockerrun.bash b/dockerrun.bash index c3e6f8f8..712f7529 100755 --- a/dockerrun.bash +++ b/dockerrun.bash @@ -1,5 +1,6 @@ #!/bin/bash poetry run gunicorn -c "/sheepdog/deployment/wsgi/gunicorn.conf.py" & +# sleep to prevent nginx warning logs so nginx doesn't start before the app sleep 30 nginx -g 'daemon off;' \ No newline at end of file From 7308e9ecb601e67f8105281e5077dfd52a4bb34a Mon Sep 17 00:00:00 2001 From: EliseCastle23 <109446148+EliseCastle23@users.noreply.github.com> Date: Mon, 18 Nov 2024 15:33:54 -0700 Subject: [PATCH 41/43] Update dockerrun.bash --- dockerrun.bash | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/dockerrun.bash b/dockerrun.bash index 712f7529..13d75019 100755 --- a/dockerrun.bash +++ b/dockerrun.bash @@ -1,6 +1,4 @@ #!/bin/bash -poetry run gunicorn -c "/sheepdog/deployment/wsgi/gunicorn.conf.py" & -# sleep to prevent nginx warning logs so nginx doesn't start before the app -sleep 30 -nginx -g 'daemon off;' \ No newline at end of file +nginx +poetry run gunicorn -c "/sheepdog/deployment/wsgi/gunicorn.conf.py" From ed548c49dfc9c53a37e65748cd0db3b6fae533c5 Mon Sep 17 00:00:00 2001 From: Piotr Senkow Date: Fri, 20 Dec 2024 11:46:23 -0600 Subject: [PATCH 42/43] Necessary for flask apps internally. Kept per Alex VanTol's recommendation in code review --- sheepdog/api.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/sheepdog/api.py b/sheepdog/api.py index ac214255..b1457e2f 100644 --- a/sheepdog/api.py +++ b/sheepdog/api.py @@ -152,6 +152,10 @@ def app_init(app): db_init(app) # exclude es init as it's not used yet # es_init(app) + try: + app.secret_key = app.config["FLASK_SECRET_KEY"] + except KeyError: + app.logger.error("Secret key not set in config! Authentication will not work") # ARBORIST deprecated, replaced by ARBORIST_URL arborist_url = os.environ.get("ARBORIST_URL", os.environ.get("ARBORIST")) From cfa0e33cab02bef2e9ef9ad5acb63be496aa2477 Mon Sep 17 00:00:00 2001 From: Piotr Senkow Date: Fri, 20 Dec 2024 14:09:41 -0600 Subject: [PATCH 43/43] adding newly generate poetry.lock file after modifying pyproject.toml per Alex VanTol's code review --- poetry.lock | 300 ++++++++++++++++++++++++++++++---------------------- 1 file changed, 172 insertions(+), 128 deletions(-) diff --git a/poetry.lock b/poetry.lock index 4a2603de..604f3a24 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 1.8.5 and should not be changed by hand. [[package]] name = "alabaster" @@ -32,54 +32,54 @@ tz = ["backports.zoneinfo"] [[package]] name = "anyio" -version = "4.6.2.post1" +version = "4.7.0" description = "High level compatibility layer for multiple asynchronous event loop implementations" optional = false python-versions = ">=3.9" files = [ - {file = "anyio-4.6.2.post1-py3-none-any.whl", hash = "sha256:6d170c36fba3bdd840c73d3868c1e777e33676a69c3a72cf0a0d5d6d8009b61d"}, - {file = "anyio-4.6.2.post1.tar.gz", hash = "sha256:4c8bc31ccdb51c7f7bd251f51c609e038d63e34219b44aa86e47576389880b4c"}, + {file = "anyio-4.7.0-py3-none-any.whl", hash = "sha256:ea60c3723ab42ba6fff7e8ccb0488c898ec538ff4df1f1d5e642c3601d07e352"}, + {file = "anyio-4.7.0.tar.gz", hash = "sha256:2f834749c602966b7d456a7567cafcb309f96482b5081d14ac93ccd457f9dd48"}, ] [package.dependencies] exceptiongroup = {version = ">=1.0.2", markers = "python_version < \"3.11\""} idna = ">=2.8" sniffio = ">=1.1" -typing-extensions = {version = ">=4.1", markers = "python_version < 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