Contributing Dockerfile and script to run nondex in an automated fashion

auto-run-dockerized-nondex/Dockerfile

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+# Use a Maven image with a configurable Java version
+ARG JAVA_VERSION=17
+FROM maven:3.9.4-eclipse-temurin-${JAVA_VERSION}
+
+WORKDIR /app
+
+RUN apt-get update && apt-get install -y git && apt-get clean
+
+# Thanks - https://github.com/TestingResearchIllinois/idoft/pull/1491
+ENV MAVEN_OPTS="-XX:+TieredCompilation -XX:TieredStopAtLevel=1"
+
+COPY entrypoint.sh /entrypoint.sh
+
+RUN chmod +x /entrypoint.sh
+
+ENTRYPOINT ["/entrypoint.sh"]
+

auto-run-dockerized-nondex/README.md

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+# Dockerized Maven NonDex Runner
+
+This module provides a **generic and standardized Docker-based NonDex execution platform**, to detect flaky tests in Maven based Java projects.
+
+## Usage
+
+### Step 1: Build the Docker Image
+With the provided `Dockerfile` and `entrypoint.sh` files in your current directory, build the Docker image using:
+
+```bash
+docker build --build-arg JAVA_VERSION=17 -t nondex-runner .
+```
+### Step 2: Run the Docker Image
+Run the Docker container using the following command (sample below):
+
+```bash
+docker run \
+  -e REPO_URL=https://github.com/apache/myfaces-tobago.git \
+  -e RUN_NONDEX_WITH_FN=true \
+  -e MODULE="tobago-core" \
+  -e NONDEX_RUNS=50 \
+  -e TESTS="org.apache.myfaces.tobago.webapp.TobagoResponseWriterUnitTest" \
+  -v $(pwd)/nondex_logs:/app/nondex_logs \
+  nondex-runner
+
+```
+
+### Arguments
+
+| **Environment Variable**   | **Required** | **Description**                                                                                     |
+|-----------------------------|--------------|-----------------------------------------------------------------------------------------------------|
+| `REPO_URL`                 | **Yes**      | URL of the GitHub repository to clone and test.                                                    |
+| `RUN_NONDEX_WITH_FN`       | No           | Runs NonDex with the `--fail-never` flag if set to `true`. Default: `false`.                       |
+| `MODULE`                   | No           | The specific Maven module to target (passed with `-pl`).                                           |
+| `NONDEX_RUNS`              | No           | The number of NonDex runs (`-DnondexRuns=<value>`).                                                |
+| `TESTS`                    | No           | Specify a particular test or suite to run using Maven’s `-Dtest` option.                           |
+
+---
+
+## Script Workflow
+
+### 1. Clone the Repository
+The script clones the repository provided in the `REPO_URL` argument.
+
+### 2. Maven Clean Install
+The script runs:
+
+```bash
+mvn clean install -DskipTests
+```
+
+If the MODULE argument is provided, it uses:
+
+```bash
+mvn clean install -pl <module_name> -DskipTests
+```
+### 3. Execute Nondex
+The script executes
+
+```bash
+mvn edu.illinois:nondex-maven-plugin:2.1.7:nondex
+```
+
+With additional arguments if applicable:
+- `--fail-never` if `RUN_NONDEX_WITH_FN=true`.
+- `-pl <module_name>` if `MODULE` is provided.
+- `-DnondexRuns=<value>` if `NONDEX_RUNS` is set 
+- `-Dtest=<test_name>` if `TESTS` is specified.
+
+### Output
+
+- NonDex execution logs are written to the file `$(pwd)/nondex_logs/nondex-<datetime>.log`
+- The **final list of flaky tests** is extracted and saved in `$(pwd)/nondex_logs/nondex-flaky-tests-<datetime>.log`
+

auto-run-dockerized-nondex/entrypoint.sh

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+#!/bin/bash
+set -e
+
+# Checking if the git repo url is set
+if [ -z "$REPO_URL" ]; then
+  echo "Error: REPO_URL is not set. It is a required argument."
+  exit 1
+fi
+
+echo "Cloning repository: $REPO_URL"
+git clone "$REPO_URL" repo
+
+cd repo
+
+echo "Printing java version for reference"
+java --version
+
+# Initialize the Maven install command
+MVN_INSTALL_CMD="mvn clean install"
+
+# Add the -pl option if MODULE is provided
+if [ -n "$MODULE" ]; then
+  MVN_INSTALL_CMD="$MVN_INSTALL_CMD -pl $MODULE"
+fi
+
+# Output and execute the command
+echo "Running 'mvn clean install' with command: $MVN_INSTALL_CMD"
+eval $MVN_INSTALL_CMD
+
+# Creating a directory for logs, volume mount to get onto your local
+NONDEX_LOG_DIR=/app/nondex_logs
+mkdir -p "$NONDEX_LOG_DIR"
+
+# Building nondex command using the various options configured - eg. mvn -pl <module_path> edu.illinois:nondex-maven-plugin:2.1.7:nondex -Dtest="<tests>" --fail-never
+NONDEX_CMD="mvn"
+
+if [ -n "$MODULE" ]; then
+  NONDEX_CMD="$NONDEX_CMD -pl $MODULE"
+fi
+
+NONDEX_CMD="$NONDEX_CMD edu.illinois:nondex-maven-plugin:2.1.7:nondex"
+
+if [ -n "$TESTS" ]; then
+  NONDEX_CMD="$NONDEX_CMD -Dtest=\"$TESTS\""
+fi
+
+if [ -n "$NONDEX_RUNS" ]; then
+  NONDEX_CMD="$NONDEX_CMD -DnondexRuns=$NONDEX_RUNS"
+fi
+
+if [ "$RUN_NONDEX_WITH_FN" == "true" ]; then
+  NONDEX_CMD="$NONDEX_CMD --fail-never"
+fi
+
+echo "Final NonDex command: $NONDEX_CMD"
+
+NONDEX_LOG_FILE="$NONDEX_LOG_DIR/nondex-logs-$(date +%Y%m%d-%H%M%S).log"
+NONDEX_FAILURE_FILE="$NONDEX_LOG_DIR/nondex-flaky-tests-$(date +%Y%m%d-%H%M%S).txt"
+
+echo "Running the NonDex plugin. Logs will be saved to $NONDEX_LOG_FILE"
+eval $NONDEX_CMD | tee "$NONDEX_LOG_FILE"
+
+if [ ! -f "$NONDEX_LOG_FILE" ]; then
+  echo "Error: NonDex log file not found at $NONDEX_LOG_FILE."
+  echo "Listing all files in $NONDEX_LOG_DIR:"
+  ls -R /app/nondex_logs
+  exit 1
+fi
+
+# Scraping the nondex file to get flaky tests
+echo "Processing NonDex log file: $NONDEX_LOG_FILE"
+
+if grep -q "\[INFO\] Across all seeds:" "$NONDEX_LOG_FILE"; then
+  # Extract failing tests
+  awk '
+  /\[INFO\] Across all seeds:/ { in_section=1; next }
+  /\[INFO\] Test results can be found at:/ { in_section=0 }
+  in_section && /^\[INFO\]/ { print substr($0, index($0, $5)) }
+  ' "$NONDEX_LOG_FILE" | sort -u > "$NONDEX_FAILURE_FILE"
+
+  if [ -s "$NONDEX_FAILURE_FILE" ]; then
+    echo "Failing tests have been written to: $NONDEX_FAILURE_FILE"
+  else
+    echo "No failing tests were found in the NonDex log file."
+    rm -f "$NONDEX_FAILURE_FILE"
+  fi
+else
+  echo "No 'Across all seeds:' section found in the NonDex log file."
+fi
+