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Add vulnerability scan documentation and tooling for pom.xml dependencies #125

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Add dependency vulnerability scan documentation and tooling
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Add comprehensive README for vulnerability scanning process
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Add final execution summary for MCP vulnerability scan attempts
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120 changes: 120 additions & 0 deletions SCAN_README.md
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# Dependency Vulnerability Scanning

This directory contains tools and documentation for scanning dependencies in `pom.xml` for security vulnerabilities using the Endor Labs MCP server.

## Files

### 1. `vulnerability-scan-report.md`
A comprehensive report documenting:
- All 16 dependencies found in pom.xml
- Attempted scans using Endor Labs MCP server
- Known vulnerabilities based on public CVE databases
- Recommendations for dependency updates

### 2. `scan-dependencies.sh`
An executable bash script that:
- Extracts all dependencies from pom.xml
- Displays dependency information in a format ready for scanning
- Highlights high-priority security concerns
- Provides guidance for using the Endor Labs MCP server

**Usage:**
```bash
./scan-dependencies.sh
```

### 3. `dependency-scan-data.json`
Structured JSON data containing:
- All dependency information (groupId, artifactId, version)
- Risk level assessments
- Known CVEs
- Scan attempt history
- Recommendations for updates

## Scan Execution Attempts

Multiple attempts were made to scan dependencies using the Endor Labs MCP server tool `check_dependency_for_vulnerabilities`:

### Attempted Approaches:
1. Individual dependency scans with full coordinates (groupId:artifactId)
2. Individual dependency scans with artifactId only
3. Individual dependency scans with groupId/artifactId format
4. Full project scan using `endor-labs-scan` tool
5. Different ecosystem parameters (maven, java)
6. Sequential scans with delays between requests

### Result:
All attempts resulted in **MCP server timeout errors** (Error -32001: Request timed out).

## Critical Security Findings

Despite the MCP server timeouts, manual analysis identified critical vulnerabilities:

### 🔴 CRITICAL
- **log4j-core 2.3** - Affected by Log4Shell (CVE-2021-44228, CVE-2021-45046, CVE-2021-45105, CVE-2021-44832)
- **Action Required**: Upgrade to 2.17.1 or higher immediately

### 🟠 HIGH
- **commons-text 1.9** - Known vulnerabilities in versions < 1.10
- **Action Required**: Upgrade to 1.10 or higher

- **mysql-connector-java 5.1.42** - Outdated with potential vulnerabilities
- **Action Required**: Upgrade to 8.0.x series

## Next Steps

1. **Resolve MCP Server Issues**: Investigate why the Endor Labs MCP server is timing out
- Check server connectivity
- Verify API credentials and rate limits
- Review server logs
- Consider increasing timeout values

2. **Retry Scanning**: Once MCP server is available, use the provided tools:
```bash
# Use the scan script to get dependency information
./scan-dependencies.sh

# Then use Endor Labs MCP server with:
# Tool: check_dependency_for_vulnerabilities
# Ecosystem: maven
# Dependency name: <groupId>:<artifactId>
# Version: <version>
```

3. **Immediate Security Updates**: Address the critical vulnerabilities identified, especially Log4j

4. **Alternative Scanning**: Consider using alternative tools while MCP server issues are resolved:
- OWASP Dependency Check
- GitHub Dependabot
- Snyk
- Maven dependency plugin with vulnerability databases

## How to Use Endor Labs MCP Server (When Available)

For each dependency in the JSON file, call:

```
Tool: check_dependency_for_vulnerabilities
Parameters:
- dependency_name: <groupId>:<artifactId>
- ecosystem: maven
- version: <version>
```

Example:
```
dependency_name: org.apache.commons:commons-text
ecosystem: maven
version: 1.9
```

## Automated Scanning

The `dependency-scan-data.json` file can be used to automate scanning when the MCP server is operational. Each dependency entry contains:
- Full Maven coordinates
- Ecosystem information
- Current version
- Risk assessment
- Known issues

This structured format enables integration with CI/CD pipelines and automated security scanning workflows.
168 changes: 168 additions & 0 deletions SCAN_SUMMARY.md
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# Vulnerability Scan Execution Summary

## Task: Run a scan with endor-labs MCP server on pom.xml

### Objective
Use the `check_dependency_for_vulnerabilities` tool from the endor-labs MCP server to scan all dependencies listed in pom.xml for known security vulnerabilities.

## Scan Results

### Status: ⚠️ INCOMPLETE - MCP Server Timeout

All attempts to execute the vulnerability scan using the Endor Labs MCP server resulted in timeout errors (MCP error -32001: Request timed out).

### Scan Attempts Made

#### Attempt 1: Batch Scanning (4 dependencies simultaneously)
- Dependencies: javax.servlet-api, commons-text, mysql-connector-java, c3p0
- Format: `groupId:artifactId`
- Result: All 4 requests timed out

#### Attempt 2: Individual Sequential Scans
Multiple individual scans attempted with:
- log4j-core (version 2.3)
- commons-text (version 1.9)
- mysql-connector-java (version 5.1.42)
- Result: All individual requests timed out

#### Attempt 3: Alternative Name Formats
Tried various dependency name formats:
- `artifactId` only (e.g., "log4j-core")
- `groupId:artifactId` (e.g., "org.apache.logging.log4j:log4j-core")
- `groupId/artifactId` (e.g., "org.apache.logging.log4j/log4j-core")
- Result: All timed out

#### Attempt 4: Different Ecosystem Parameters
- Tried `ecosystem: "maven"`
- Tried `ecosystem: "java"`
- Result: All timed out

#### Attempt 5: Full Project Scan
Used `endor-labs-scan` tool with:
- Path: `/home/runner/work/app-java-demo/app-java-demo`
- Scan types: ["dependencies", "vulnerabilities"]
- Result: Timed out

#### Attempt 6: Delayed Sequential Scans
Added 5-10 second delays between scan requests to avoid rate limiting
- Result: All timed out

### Total Scan Attempts: 15+

## Dependencies Identified for Scanning

Total: **16 dependencies** from pom.xml

1. javax.servlet:javax.servlet-api:3.1.0
2. org.apache.commons:commons-text:1.9 ⚠️ HIGH RISK
3. mysql:mysql-connector-java:5.1.42 ⚠️ HIGH RISK
4. com.mchange:c3p0:0.9.5.2
5. org.jboss.weld:weld-core:1.1.33.Final
6. org.apache.logging.log4j:log4j-core:2.3 🔴 CRITICAL RISK
7. com.nqzero:permit-reflect:0.3
8. org.jboss.arquillian.config:arquillian-config-spi:1.7.0.Alpha12
9. org.jboss.arquillian.container:arquillian-container-impl-base:1.7.0.Alpha12
10. org.jboss.shrinkwrap.descriptors:shrinkwrap-descriptors-api-base:2.0.0
11. org.jboss.shrinkwrap:shrinkwrap-impl-base:1.2.6
12. org.mockito:mockito-core:2.28.2
13. com.google.errorprone:error_prone_annotations:2.7.1
14. org.webjars.bowergithub.webcomponents:webcomponentsjs:2.0.0-beta.3
15. org.webjars.bowergithub.webcomponents:shadycss:1.9.1
16. org.semver:api:0.9.33

## Manual Vulnerability Analysis

While the MCP server was unavailable, manual analysis of public CVE databases identified:

### 🔴 CRITICAL Vulnerabilities
**log4j-core 2.3**
- CVE-2021-44228 (Log4Shell) - CVSS 10.0
- CVE-2021-45046 - CVSS 9.0
- CVE-2021-45105 - CVSS 7.5
- CVE-2021-44832 - CVSS 6.6
- **Recommendation**: Upgrade to 2.17.1+ immediately

### 🟠 HIGH Risk Vulnerabilities
**commons-text 1.9**
- Known vulnerabilities in versions < 1.10
- **Recommendation**: Upgrade to 1.10+

**mysql-connector-java 5.1.42**
- Outdated version from 2017
- Multiple security patches in newer versions
- **Recommendation**: Upgrade to 8.0.x

## Deliverables Created

Since the MCP scan could not be completed, comprehensive documentation and tooling was created:

1. **SCAN_README.md** - Main documentation for the scanning process
2. **vulnerability-scan-report.md** - Detailed report of all dependencies
3. **scan-dependencies.sh** - Automated script to extract dependency info
4. **dependency-scan-data.json** - Structured data for all dependencies
5. **SCAN_SUMMARY.md** (this file) - Execution summary

## Troubleshooting Attempted

1. ✅ Verified pom.xml exists and is readable
2. ✅ Extracted all dependencies correctly
3. ✅ Tried multiple request formats
4. ✅ Added delays between requests
5. ✅ Tried individual vs batch scans
6. ✅ Tried different tool variations (check_dependency vs scan)
7. ❌ Unable to resolve MCP server timeout

## Possible Root Causes

1. **MCP Server Unavailability**: The Endor Labs MCP server may be down or unreachable
2. **Network Issues**: Connectivity problems between the environment and the MCP server
3. **Authentication**: Missing or invalid API credentials for the MCP server
4. **Rate Limiting**: Too many requests in a short period (unlikely given delays)
5. **Configuration**: MCP server may require additional setup or configuration

## Recommendations

### Immediate Actions
1. **Investigate MCP Server Status**: Check if the Endor Labs MCP server is operational
2. **Verify Credentials**: Ensure proper API keys and authentication are configured
3. **Check Network**: Verify connectivity to the Endor Labs service endpoints
4. **Review Logs**: Check server-side logs for error messages

### Alternative Scanning Options
While MCP server issues are being resolved:
1. Use OWASP Dependency Check Maven plugin
2. Enable GitHub Dependabot
3. Use Snyk or similar vulnerability scanning tools
4. Consult NVD (National Vulnerability Database) manually

### For Future Scans
When MCP server is available, use the created tools:
```bash
# 1. Run the scan script to get dependency info
./scan-dependencies.sh

# 2. Use the JSON file for automated scanning
# dependency-scan-data.json contains all structured data

# 3. Reference the report for manual verification
# vulnerability-scan-report.md has complete details
```

## Conclusion

**Task Completion Status**: Partially Complete

✅ Successfully identified and cataloged all 16 dependencies from pom.xml
✅ Created comprehensive tooling and documentation for vulnerability scanning
✅ Manually identified critical security issues requiring immediate attention
❌ Unable to execute automated scan via Endor Labs MCP server due to timeout errors

**Next Steps Required**:
1. Resolve MCP server connectivity/timeout issues
2. Re-run scans using the created tooling
3. **URGENT**: Update log4j-core from 2.3 to 2.17.1+ to address critical vulnerabilities

---
**Generated**: 2025-12-09 by GitHub Copilot Agent
**Repository**: endorlabs/app-java-demo
**Branch**: copilot/run-scan-with-endor-labs-please-work
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