update ver

.github/workflows/ci.yaml

@@ -18,6 +18,6 @@ jobs:
     name: Python Unit Test with Postgres
     uses: uc-cdis/.github/.github/workflows/python_unit_test.yaml@master
     with:
-       python-version: '3.9'
+       python-version: '3.13'
        test-script: 'tests/ci_commands_script.sh'
        run-coveralls: true

Dockerfile

@@ -1,7 +1,7 @@
-ARG AZLINUX_BASE_VERSION=master
+ARG AZLINUX_BASE_VERSION=3.13-pythonnginx
 
 # Base stage with python-build-base
-FROM quay.io/cdis/python-nginx-al:${AZLINUX_BASE_VERSION} AS base
+FROM quay.io/cdis/amazonlinux-base:${AZLINUX_BASE_VERSION} AS base
 
 ENV appname=indexd
 
@@ -14,27 +14,45 @@ FROM base AS builder
 
 USER gen3
 
-# copy ONLY poetry artifact, install the dependencies but not the app;
-# this will make sure that the dependencies are cached
+# Copy poetry manifests for dependency caching
 COPY poetry.lock pyproject.toml /${appname}/
+
+# Remove the old poetry pipx package from base image, currently set to <2.0
+RUN pipx uninstall poetry
+# Install poetry version >=2.0 for export compatibility
+RUN pip install --upgrade "poetry>=2.0.0,<3.0.0"
+
+# Install the plugin for requirements export
+RUN poetry self add poetry-plugin-export
+
+# Install dependencies, not app files
 RUN poetry install -vv --no-root --only main --no-interaction
 
 COPY --chown=gen3:gen3 . /${appname}
 COPY --chown=gen3:gen3 ./deployment/wsgi/wsgi.py /${appname}/wsgi.py
 
-# install the app
+# Install app
 RUN poetry install --without dev --no-interaction
 
+# Export requirements for pip in final image
+RUN poetry export -f requirements.txt --output requirements.txt --without-hashes
+
 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
 
+USER root
+
 COPY --from=builder /${appname} /${appname}
+COPY --chown=gen3:gen3 ./dockerrun.bash /${appname}/dockerrun.bash
 
 RUN dnf -y install vim
 
+# Install dependencies
+RUN pip install --no-cache-dir -r /${appname}/requirements.txt
+
 # Switch to non-root user 'gen3' for the serving process
 USER gen3
 

bin/indexd_settings.py

@@ -1,6 +1,6 @@
 from os import environ
 import json
-import config_helper
+import indexd.config_helper as config_helper
 from indexd.index.drivers.alchemy import SQLAlchemyIndexDriver
 from indexd.alias.drivers.alchemy import SQLAlchemyAliasDriver
 from indexd.auth.drivers.alchemy import SQLAlchemyAuthDriver

bin/migrate_to_single_table.py

@@ -4,7 +4,7 @@
 import argparse
 import backoff
 import json
-import bin.config_helper as config_helper
+import indexd.config_helper as config_helper
 from cdislogging import get_logger
 from sqlalchemy import create_engine
 from sqlalchemy.ext.declarative import declarative_base

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "indexd"
-version = "5.1.2"
+version = "6.0.0"
 description = "Gen3 Indexing Service"
 authors = ["CTDS UChicago <[email protected]>"]
 license = "Apache-2.0"
@@ -10,23 +10,25 @@ include = [
 ]
 
 [tool.poetry.dependencies]
-python = ">=3.9.2,<4.0"
+python = ">=3.13,<4.0"
 alembic = "^1.9.4"
 authutils = ">=6,<8"
 cdislogging = "^1.0.0"
-cdiserrors =  "^1.0.0"
 doiclient = {git = "https://github.com/uc-cdis/doiclient", rev = "1.0.0"}
 dosclient = {git = "https://github.com/uc-cdis/dosclient", rev = "1.1.0"}
-gen3authz = "^1.0.4"
+gen3authz = "^3.0.0"
 hsclient = {git = "https://github.com/uc-cdis/hsclient", rev = "1.0.0"}
 indexclient = "^2.1.0"
 jsonschema = "^3.2"
-psycopg2-binary = ">=2.7"
 gunicorn = ">=22.0.0"
 flask = "^2.3.3"
 sqlalchemy = "^1.4.0"
 sqlalchemy-utils = "^0.37.3"
 PyYAML = ">=5.3,<7"
+gitpython = "^3.1.45"
+requests = "^2.32.5"
+setuptools = "^80.9.0"
+psycopg2-binary = "^2.9.11"
 
 [tool.poetry.group.dev.dependencies]
 coveralls = "^3.0.1"
@@ -36,8 +38,9 @@ pytest-cov = "^2.12.0"
 pytest-flask = "^1.2.0"
 responses = "^0.13.0"
 swagger_spec_validator = "^2.6.0"
+deptry = "^0.23.1"
 
 
 [build-system]
-requires = ["poetry>=0.12"]
-build-backend = "poetry.masonry.api"
+requires = ["poetry-core>=2.0.0"]
+build-backend = "poetry.core.masonry.api"