### Install Vul4J and Initialize Data Directory

Source: https://github.com/tuhh-softsec/vul4j/blob/main/README.md

Install Vul4J using uv sync, activate the virtual environment, and initialize the default data directory. Ensure the data directory is empty before initialization.

```shell
uv sync
source .venv/bin/activate
vul4j init
```

--------------------------------

### Start Vul4J Docker Container

Source: https://github.com/tuhh-softsec/vul4j/blob/main/README.md

Starts a pre-built Vul4J Docker image, naming the container 'vul4j' for interactive use.

```shell
$ docker run -it --name vul4j tuhhsoftsec/vul4j
```

--------------------------------

### Check Vul4J Installation Status

Source: https://github.com/tuhh-softsec/vul4j/blob/main/README.md

Verify that Vul4J has been installed correctly and all dependencies are recognized by running the status command.

```shell
vul4j status
```

--------------------------------

### Install Spotbugs with Vul4J

Source: https://github.com/tuhh-softsec/vul4j/blob/main/README.md

Ensures Spotbugs is installed and configured correctly for Vul4J. If Spotbugs is not found, Vul4J can install it automatically.

```shell
vul4j get-spotbugs
```

--------------------------------

### Configure Vul4J with Java Home Paths

Source: https://github.com/tuhh-softsec/vul4j/blob/main/README.md

Configure the JAVA_HOME paths for different Java versions in the `~/vul4j_data/vul4j.ini` file. This is crucial for Vul4J to locate your Java installations.

```ini
JAVA7_HOME = <path-to-java-7-home-directory>
JAVA8_HOME = <path-to-java-8-home-directory>
JAVA11_HOME = <path-to-java-11-home-directory>
JAVA16_HOME = <path-to-java-16-home-directory>
```

--------------------------------

### Run Vul4J Docker Container

Source: https://github.com/tuhh-softsec/vul4j/blob/main/README.md

Start a standalone container from the locally built Vul4J Docker image. This provides an isolated environment with all necessary tools pre-installed.

```shell
./run_docker.sh
```

--------------------------------

### Vulnerability Test Results JSON

Source: https://github.com/tuhh-softsec/vul4j/blob/main/README.md

Example JSON output detailing the results of running a vulnerability's test suite, including metrics and specific test failures.

```json
{
  "vul_id": "VUL4J-10",
  "cve_id": "CVE-2013-2186",
  "repository": {
    "name": "apache_commons-fileupload",
    "url": "https://github.com/apache/commons-fileupload",
    "human_patch_url": "https://github.com/apache/commons-fileupload/commit/163a6061fbc077d4b6e4787d26857c2baba495d1"
  },
  "tests": {
    "overall_metrics": {
      "number_running": 69,
      "number_passing": 67,
      "number_error": 0,
      "number_failing": 2,
      "number_skipping": 0
    },
    "failures": [
      {
        "test_class": "org.apache.commons.fileupload.DiskFileItemSerializeTest",
        "test_method": "testInvalidRepositoryWithNullChar",
        "failure_name": "java.lang.AssertionError",
        "detail": "Expected exception: java.io.IOException",
        "is_error": false
      },
      {
        "test_class": "org.apache.commons.fileupload.DiskFileItemSerializeTest",
        "test_method": "testInvalidRepository",
        "failure_name": "java.lang.AssertionError",
        "detail": "Expected exception: java.io.IOException",
        "is_error": false
      }
    ],
    "passing_tests": [
      "org.apache.commons.fileupload.util.mime.QuotedPrintableDecoderTestCase#invalidQuotedPrintableEncoding",
      "org.apache.commons.fileupload.util.mime.QuotedPrintableDecoderTestCase#unsafeDecodeLowerCase",
      ...
      "org.apache.commons.fileupload.DefaultFileItemTest#testBelowThreshold"
    ],
    "skipping_tests": []
  }
}
```

--------------------------------

### Vul4J Command-Line Interface Help

Source: https://github.com/tuhh-softsec/vul4j/blob/main/README.md

Displays the help message for the `vul4j` command-line tool, outlining available subcommands and options for managing and analyzing vulnerabilities.

```bash
$ vul4j --help

usage: vul4j [-h] [-l LOG] {init,status,checkout,compile,test,apply,sast,reproduce,verify,info,classpath,get-spotbugs,evaluate} ...

A Dataset of Java vulnerabilities.

positional arguments:
  {init,status,checkout,compile,test,apply,sast,reproduce,verify,info,classpath,get-spotbugs,evaluate}
    init                Create the Vul4J data directory and default config.
    status              Lists vul4j requirements and their availability.
    checkout            Checkout a vulnerability into the specified directory.
    compile             Compile the checked out vulnerability.
    test                Run testsuite for the checked out vulnerability.
    apply               Apply the specified file versions.
    sast                Run Spotbugs analysis.
    reproduce (verify)  Verify the reproducibility of vulnerabilities in the dataset.
    info                Print information about a vulnerability.
    classpath           Print the classpath of the checked out vulnerability.
    get-spotbugs        Download Spotbugs into the user directory.
    evaluate            Evaluate candidate patches from unified git diffs.

options:
  -h, --help            show this help message and exit
  -l, --log LOG         Specify displayed log level for this command.

```

--------------------------------

### Build Vul4J Local Docker Image

Source: https://github.com/tuhh-softsec/vul4j/blob/main/README.md

Build a local Docker image for Vul4J that includes Maven, SpotBugs, and JDK 7/8/11/16. This image can be used for consistent development and testing environments.

```shell
docker build --platform linux/amd64 -t vul4j:local .
```

--------------------------------

### Build Standalone Vul4J Docker Image

Source: https://github.com/tuhh-softsec/vul4j/blob/main/README.md

Builds the Vul4J Docker image, populating it with the repository, build tools, and dependencies. This process includes warming up dependency caches.

```shell
docker build --platform linux/amd64 --progress=plain \
  -t vul4j:local .
```

--------------------------------

### Run Vul4J Docker Container Interactively

Source: https://github.com/tuhh-softsec/vul4j/blob/main/README.md

Run the Vul4J Docker image interactively, allowing you to execute commands within the container. The container is removed upon exit.

```shell
docker run --platform linux/amd64 -it --rm \
  vul4j:local
```

--------------------------------

### Run Test Suite for Vulnerability

Source: https://github.com/tuhh-softsec/vul4j/blob/main/README.md

Executes the test suite for a given vulnerability project and stores results in a JSON file.

```shell
$ vul4j test -d /tmp/vul4j/VUL4J-10
```

--------------------------------

### Reproduce a Vulnerability with Vul4J

Source: https://github.com/tuhh-softsec/vul4j/blob/main/README.md

Command to reproduce a specific vulnerability by its ID. This process involves checking out the project, applying the vulnerable version, cleaning, compiling, and running tests. It then applies the human patch, cleans, compiles, and runs tests again to verify the fix.

```shell
$ vul4j reproduce --id VUL4J-10
```

```text
2024-06-13 20:35:31 | ===================== START REPRODUCE ======================
2024-06-13 20:35:31 | Reproducing 1 vulnerabilities...
2024-06-13 20:35:31 | --------------------------VUL4J-10--------------------------
2024-06-13 20:35:31 | Checking out project...
2024-06-13 20:35:31 | --> Applying version: vulnerable
2024-06-13 20:35:31 | Cleaning project...
2024-06-13 20:35:33 | Compiling...
2024-06-13 20:35:41 | Running PoV tests...
2024-06-13 20:35:46 | Number of running tests: 1
2024-06-13 20:35:46 | Failing tests: [
  "org.apache.commons.fileupload.DiskFileItemSerializeTesttestInvalidRepositoryWithNullChar"
]
2024-06-13 20:35:46 | No fixed warnings found in the dataset for VUL4J-10. Skipping Spotbugs...
2024-06-13 20:35:46 | --> Applying version: human_patch
2024-06-13 20:35:46 | Cleaning project...
2024-06-13 20:35:48 | Compiling...
2024-06-13 20:35:56 | Running PoV tests...
2024-06-13 20:36:01 | Number of running tests: 1
2024-06-13 20:36:01 | Number of passing tests: 1
2024-06-13 20:36:01 | No fixed warnings found in the dataset for VUL4J-10. Skipping Spotbugs...
2024-06-13 20:36:01 | Vulnerabilities: PASS, Spotbugs: SKIP!
2024-06-13 20:36:01 | ====================== END REPRODUCE =======================
```

--------------------------------

### Run Vul4J Patch Evaluation

Source: https://github.com/tuhh-softsec/vul4j/blob/main/README.md

Executes the patch evaluation process using a JSON file containing patch candidates and outputs the results to a specified file and directory.

```shell
vul4j evaluate patches.json -o evaluation_results.json --output-dir evaluation_artifacts
```

--------------------------------

### Run SAST Analysis

Source: https://github.com/tuhh-softsec/vul4j/blob/main/README.md

Performs Static Application Security Testing (SAST) analysis using Spotbugs on the compiled project.

```shell
$ vul4j sast -d /tmp/vul4j/VUL4J-10
```

--------------------------------

### Clone Vul4J Repository

Source: https://github.com/tuhh-softsec/vul4j/blob/main/README.md

Clone the Vul4J repository to your local machine using Git.

```shell
git clone https://github.com/tuhh-softsec/vul4j
```

--------------------------------

### Verify Docker Image Reproducibility

Source: https://github.com/tuhh-softsec/vul4j/blob/main/README.md

Verifies the integrity of the built Vul4J Docker image by checking for failed reproductions. The first command ensures no vulnerabilities failed to reproduce, and the second checks for specific error messages in the reproduction log.

```shell
docker run --rm vul4j:local sh -lc 'test ! -s /root/vul4j_data/failed_vulnerabilities.txt'
```

```shell
docker run --rm vul4j:local sh -lc 'grep -E "Vulnerabilities: ERROR|Spotbugs: ERROR|did not reproduce successfully|Failed vulnerabilities" /root/vul4j_data/reproduction.txt || true'
```

--------------------------------

### Checkout Vulnerability

Source: https://github.com/tuhh-softsec/vul4j/blob/main/README.md

Checks out a specific vulnerability (e.g., VUL4J-10) into a designated directory.

```shell
$ vul4j checkout --id VUL4J-10 -d /tmp/vul4j/VUL4J-10
```

--------------------------------

### Compile Vulnerability Project

Source: https://github.com/tuhh-softsec/vul4j/blob/main/README.md

Compiles the project associated with a checked-out vulnerability.

```shell
$ vul4j compile -d /tmp/vul4j/VUL4J-10
```

--------------------------------

### Apply Candidate Patches Only

Source: https://github.com/tuhh-softsec/vul4j/blob/main/README.md

Applies candidate patch diffs without compiling or testing, exporting the applied patches to a specified directory.

```shell
vul4j evaluate patches.json --apply-only --output-dir applied_patches
```

--------------------------------

### Vul4J Evaluate Input JSON

Source: https://github.com/tuhh-softsec/vul4j/blob/main/README.md

This JSON structure defines the input for the `vul4j evaluate` command, specifying vulnerability IDs and candidate patches.

```json
[
  {
    "vul_id": "VUL4J-10",
    "candidates": [
      {
        "name": "candidate1",
        "diff": "diff --git a/src/main/java/Example.java b/src/main/java/Example.java\n--- a/src/main/java/Example.java\n+++ b/src/main/java/Example.java\n@@ -1 +1 @@\n-old\n+new\n"
      }
    ]
  }
]
```

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