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2 Jun
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‎.github/scripts/run_test copy.sh.save‎

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#!/bin/bash
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set -e
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PYTHON_VERSION="$1"
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DESCRIPTION="$2"
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COVERAGE_XML="sonarcloud-coverage-$3.xml"
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# show cwd
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echo "Current working directory: $(pwd)"
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# list contents of venv
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ls -la .
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########### debug
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echo "Which Python:"
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which python$PYTHON_VERSION || echo "python$PYTHON_VERSION not found in PATH"
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echo "Available interpreters:"
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pyenv versions || true
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echo "Using Python Version $PYTHON_VERSION"
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poetry config virtualenvs.in-project true
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##############
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# Only create/use the env and install if .venv does not exist
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echo "Checking for Poetry virtual environment (.venv)"
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poetry env list
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if [ ! -d ".venv" ]; then
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echo "Creating virtual environment (.venv) with Poetry"
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poetry env use "$PYTHON_VERSION"
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########### debug
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echo "Poetry environment info:"
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poetry env info || true
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###########
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poetry install
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poetry env list
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else
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echo "Using cached virtual environment (.venv)"
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fi
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if poetry run coverage run -m unittest discover; then
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echo "$DESCRIPTION tests passed"
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else
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echo "$DESCRIPTION tests failed" >> ../failed_tests.txt
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fi
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poetry run coverage xml -o "../$COVERAGE_XML"

‎.github/scripts/run_test.sh‎

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@@ -11,16 +11,27 @@ echo "Current working directory: $(pwd)"
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ls -la .
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########### debug
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echo "Which Python:"
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which python$PYTHON_VERSION || echo "python$PYTHON_VERSION not found in PATH"
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echo "Using Python Version $PYTHON_VERSION"
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poetry config virtualenvs.in-project true
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##############
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# Only create/use the env and install if .venv does not exist
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echo "Checking for Poetry virtual environment (.venv)"
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poetry env list
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if [ ! -d ".venv" ]; then
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echo "Creating virtual environment (.venv) with Poetry"
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poetry env use "$PYTHON_VERSION"
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########### debug
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echo "Poetry environment info:"
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poetry env info || true
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###########
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poetry install
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poetry env list
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else

‎.github/workflows/sonarcloud.yml‎

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@@ -16,9 +16,8 @@ jobs:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: ['3.10', '3.11']
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python-version: ['3.11', '3.10']
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steps:
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- uses: actions/checkout@v4
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with:
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- uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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python-version: |
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3.10
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3.11
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cache: 'poetry'
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- name: Set up AWS credentials
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env:
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AWS_ACCESS_KEY_ID: "FOOBARKEY"
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AWS_SECRET_ACCESS_KEY: "FOOBARSECRET"
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run: |
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aws configure set aws_access_key_id $AWS_ACCESS_KEY_ID
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aws configure set aws_secret_access_key $AWS_SECRET_ACCESS_KEY
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- name: Chmod .github directory
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run: |
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chmod +x $SCRIPT_FOLDER/*.sh
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- name: Cache global Poetry virtualenvs
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- name: Set Poetry to use in-project venvs
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run: poetry config virtualenvs.in-project true
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# uses: actions/cache@v4
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# with:
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# path: ~/.cache/pypoetry/virtualenvs
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# key: ${{ runner.os }}-poetry-global-venv-py${{ matrix.python-version || 'all' }}-${{ hashFiles('**/poetry.lock') }}
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# restore-keys: |
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# ${{ runner.os }}-poetry-global-venv-py${{ matrix.python-version || 'all' }}-
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- name: Cache Poetry virtualenv (filenameprocessor)
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if: matrix.python-version == '3.10'
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uses: actions/cache@v4
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with:
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path: ./filenameprocessor/.venv
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key: ${{ runner.os }}-venv-fp-py3.10-${{ hashFiles('filenameprocessor/poetry.lock') }}
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path: ~/.cache/pypoetry/virtualenvs
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key: ${{ runner.os }}-poetry-venv-${{ matrix.python-version }}-${{ hashFiles('<project>/poetry.lock') }}
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restore-keys: |
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${{ runner.os }}-venv-fp-py3.10-
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${{ runner.os }}-poetry-venv-${{ matrix.python-version }}-
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- name: Cache Poetry virtualenv (recordprocessor)
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if: matrix.python-version == '3.10'
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uses: actions/cache@v4
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with:
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path: ./recordprocessor/.venv
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key: ${{ runner.os }}-venv-rp-py3.10-${{ hashFiles('recordprocessor/poetry.lock') }}
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restore-keys: |
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${{ runner.os }}-venv-rp-py3.10-
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- name: Cache Poetry virtualenv (recordforwarder)
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if: matrix.python-version == '3.11'
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uses: actions/cache@v4
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with:
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path: ./backend/.venv
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key: ${{ runner.os }}-venv-be-py3.11-${{ hashFiles('backend/poetry.lock') }}
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restore-keys: |
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${{ runner.os }}-venv-be-py3.11-
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- name: Cache Poetry virtualenv (ack_backend)
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if: matrix.python-version == '3.10'
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uses: actions/cache@v4
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with:
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path: ./ack_backend/.venv
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key: ${{ runner.os }}-venv-ack-py3.10-${{ hashFiles('ack_backend/poetry.lock') }}
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restore-keys: |
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${{ runner.os }}-venv-ack-py3.10-
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- name: Cache Poetry virtualenv (delta_backend)
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if: matrix.python-version == '3.11'
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uses: actions/cache@v4
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with:
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path: ./delta_backend/.venv
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key: ${{ runner.os }}-venv-delta-py3.11-${{ hashFiles('delta_backend/poetry.lock') }}
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restore-keys: |
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${{ runner.os }}-venv-delta-py3.11-
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- name: Run unittest with filenameprocessor-coverage (S)
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if: matrix.python-version == '3.10'
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working-directory: filenameprocessor
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id: filenameprocessor
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continue-on-error: true
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run: $RUN_TEST 3.10 filenameprocessor filenameprocessor-coverage.xml
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- name: Run unittest with recordprocessor-coverage (s)
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if: matrix.python-version == '3.10'
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working-directory: recordprocessor
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id: recordprocessor
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continue-on-error: true
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run: $RUN_TEST 3.10 recordprocessor recordprocessor-coverage.xml
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- name: Run unittest with recordforwarder-coverage
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if: matrix.python-version == '3.11'
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working-directory: backend
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id: recordforwarder
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continue-on-error: true
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- name: Set up AWS credentials
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env:
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AWS_ACCESS_KEY_ID: "FOOBARKEY"
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AWS_SECRET_ACCESS_KEY: "FOOBARSECRET"
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run: |
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poetry config virtualenvs.in-project true
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$RUN_TEST 3.11 recordforwarder recordforwarder-coverage.xml
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aws configure set aws_access_key_id $AWS_ACCESS_KEY_ID
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aws configure set aws_secret_access_key $AWS_SECRET_ACCESS_KEY
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# - name: Run unittest with filenameprocessor-coverage
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# working-directory: filenameprocessor
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# id: filenameprocessor
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# continue-on-error: true
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# run: |
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# poetry env use 3.10
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# poetry install
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# poetry run coverage run -m unittest discover || echo "filenameprocessor tests failed" >> ../failed_tests.txt
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# poetry run coverage xml -o ../sonarcloud-coverage-filenameprocessor-coverage.xml
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# - name: Run unittest with recordprocessor-coverage
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# working-directory: recordprocessor
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# id: recordprocessor
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# continue-on-error: true
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# run: |
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# poetry env use 3.10
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# poetry install
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# poetry run coverage run -m unittest discover || echo "recordprocessor tests failed" >> ../failed_tests.txt
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# poetry run coverage xml -o ../sonarcloud-coverage-recordprocessor-coverage.xml
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# # This step is redundant - all of these tests will be run in the backend step below
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# - name: Run unittest with recordforwarder-coverage
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# working-directory: backend
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# id: recordforwarder
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# continue-on-error: true
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# run: |
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# poetry env use 3.11
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# poetry install
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# poetry run coverage run -m unittest discover -s "./tests" -p "*batch*.py" || echo "recordforwarder tests failed" >> ../failed_tests.txt
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# poetry run coverage xml -o ../sonarcloud-coverage-recordforwarder-coverage.xml
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- name: Run unittest with coverage-ack-lambda
11994
if: matrix.python-version == '3.10'
12095
working-directory: ack_backend
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id: acklambda
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continue-on-error: true
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run: $RUN_TEST 3.10 ack-lambda ack-lambda.xml
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run: |
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$RUN_TEST 3.10 "ack-lambda" "ack-lambda.xml"
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- name: Run unittest with coverage-delta
126102
if: matrix.python-version == '3.11'
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129105
env:
130106
PYTHONPATH: delta_backend/src:delta_backend/tests
131107
continue-on-error: true
132-
run: $RUN_TEST 3.11 delta_backend delta.xml
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run: |
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$RUN_TEST 3.11 delta_backend delta.xml
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# - name: Run unittest with coverage-fhir-api
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# working-directory: backend
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# id: fhirapi
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# continue-on-error: true
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# run: |
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# poetry env use 3.11
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# poetry install
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# poetry run coverage run -m unittest discover || echo "fhir-api tests failed" >> ../failed_tests.txt
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# poetry run coverage xml -o ../sonarcloud-coverage.xml
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# - name: Run unittest with coverage-mesh-processor
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# working-directory: mesh_processor
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# id: meshprocessor
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# continue-on-error: true
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# run: |
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# poetry env use 3.10
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# poetry install
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# poetry run coverage run -m unittest discover || echo "mesh_processor tests failed" >> ../failed_tests.txt
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# poetry run coverage xml -o ../sonarcloud-mesh_processor-coverage.xml
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134131
- name: Run Test Failure Summary
135132
id: check_failure
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151148
uses: SonarSource/sonarqube-scan-action@master
152149
env:
153150
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # Needed to get PR information, if any
154-
SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
151+
SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}

‎.github/workflows/sonarcloud.yml.test‎

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name: SonarCloud
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on:
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push:
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branches:
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- master
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pull_request:
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types: [labeled, opened, synchronize, reopened, unlabeled]
9+
env:
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SCRIPT_FOLDER: ./.github/scripts
11+
RUN_TEST: source ../.github/scripts/run_test.sh
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13+
jobs:
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sonarcloud:
15+
name: SonarCloud
16+
runs-on: ubuntu-latest
17+
strategy:
18+
matrix:
19+
python-version: ['3.11']
20+
21+
steps:
22+
- uses: actions/checkout@v4
23+
with:
24+
fetch-depth: 0
25+
26+
- name: Install poetry
27+
run: pip install poetry==1.8.4
28+
29+
- uses: actions/setup-python@v5
30+
with:
31+
python-version: ${{ matrix.python-version }}
32+
cache: 'poetry'
33+
34+
- name: Set up AWS credentials
35+
env:
36+
AWS_ACCESS_KEY_ID: "FOOBARKEY"
37+
AWS_SECRET_ACCESS_KEY: "FOOBARSECRET"
38+
run: |
39+
aws configure set aws_access_key_id $AWS_ACCESS_KEY_ID
40+
aws configure set aws_secret_access_key $AWS_SECRET_ACCESS_KEY
41+
42+
- name: Chmod .github directory
43+
run: |
44+
chmod +x $SCRIPT_FOLDER/*.sh
45+
46+
- name: Cache global Poetry virtualenvs
47+
uses: actions/cache@v4
48+
with:
49+
path: ~/.cache/pypoetry/virtualenvs
50+
key: ${{ runner.os }}-poetry-global-venv-py${{ matrix.python-version }}-${{ hashFiles('**/poetry.lock') }}
51+
restore-keys: |
52+
${{ runner.os }}-poetry-global-venv-py${{ matrix.python-version }}-
53+
54+
- name: Run unittest with coverage-delta
55+
if: matrix.python-version == '3.11'
56+
working-directory: delta_backend
57+
id: delta
58+
env:
59+
PYTHONPATH: delta_backend/src:delta_backend/tests
60+
continue-on-error: true
61+
run: |
62+
$RUN_TEST 3.11 delta_backend delta.xml
63+
64+
- name: Run Test Failure Summary
65+
id: check_failure
66+
run: |
67+
if [ -s failed_tests.txt ]; then
68+
echo "The following tests failed:"
69+
cat failed_tests.txt
70+
71+
while IFS= read -r line; do
72+
echo "##[error]Test Failures: $line"
73+
done < failed_tests.txt
74+
75+
exit 1
76+
else
77+
echo "All tests passed."
78+
fi

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