security: protect /openJupyter endpoint with API key and process control (fixes #361)

[GaneshPatil7517]

Hello @pradeeban Sir
This PR resolves Issue #361, a critical security vulnerability where the /openJupyter endpoint allowed unauthenticated spawning of Jupyter Lab processes.

Previously:
No authentication
No rate limiting
Unlimited process spawning
No process tracking
Full remote code execution exposure

Changes Made
Added API key authentication (X-API-KEY header)
Introduced environment variable CONCORE_API_KEY
Prevented multiple concurrent Jupyter launches
Added process tracking
Suppressed stdout/stderr exposure
Added optional /stopJupyter endpoint for cleanup

Security Impact
Eliminates unauthenticated RCE vector
Prevents resource exhaustion
Restricts access to authorized clients only
Improves process lifecycle control

Scope
Single file modification (fri/server/main.py)
New test file: tests/test_openjupyter_security.py (9 tests)
No changes to concore-lite
No Verilog changes
Minimal architectural impact

Configuration Required
Server must define:
CONCORE_API_KEY=<secure_random_string>
Clients must provide:
X-API-KEY header

Testing

Test Case	Expected	Result
Unauthorized request (no header)	403	PASSED
Wrong API key	403	PASSED
Server without key configured	500	PASSED
Authorized request starts Jupyter	200	PASSED
Duplicate launch while running	409	PASSED
Popen failure	500	PASSED
Stop without auth	403	PASSED
Stop with no running process	404	PASSED
Stop running process	200	PASSED

[Copilot]

Pull request overview

This PR addresses a critical security vulnerability (Issue #361) in the /openJupyter endpoint, which previously allowed unauthenticated remote code execution. The PR introduces API key authentication, process tracking, and additional security improvements across the codebase.

Changes:

• Added API key authentication to /openJupyter and new /stopJupyter endpoints
• Replaced print() statements with proper logging across tools/* files
• Removed obsolete concore2 module references throughout the codebase
• Added new CLI infrastructure and comprehensive test suite
• Improved input validation and error handling in server endpoints

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
fri/server/main.py	Added API key authentication, process tracking for Jupyter, input validation functions, and improved error handling
tests/test_openjupyter_security.py	Comprehensive test suite (9 tests) covering authentication, process control, and error scenarios
tools/*.py	Replaced print() with logging.info/debug/error for better production logging
tools/pwrap.py, cwrap.py	Changed http:// to https:// for controlcore.org API calls and improved file handling with context managers
Various 0mq/*.py files	Removed concore2 module dependencies, consolidated to single concore module
New CLI files	Added concore_cli package with commands for init, run, validate, status, stop
New test files	Added test infrastructure with conftest.py, test_concore.py, test_graph.py, etc.
Dockerfiles	Updated base images and improved security (added checksum validation, cleaned apt cache)
contribute.py	Removed hardcoded token, now uses environment variable

Comments suppressed due to low confidence (2)

fri/server/main.py:10

• Missing import for secrets module which would be needed if implementing constant-time comparison for API key validation. Add import secrets at the top of the file.

import re

fri/server/main.py:422

• The Windows branch uses subprocess.run with check=True (line 415), but the non-Windows branch uses check_output which also raises on non-zero exit but then tries to decode at line 422. This creates inconsistent error handling between platforms. Consider using subprocess.run with consistent error handling for both platforms.

        if(platform.uname()[0]=='Windows'):
            # Use cmd.exe /c to invoke contribute.bat on Windows
            proc = subprocess.run(["cmd.exe", "/c", "contribute.bat", STUDY_NAME, STUDY_NAME_PATH, AUTHOR_NAME, BRANCH_NAME, PR_TITLE, PR_BODY], cwd=concore_path, check=True, capture_output=True, text=True)
            output_string = proc.stdout
        else:
            if len(BRANCH_NAME)==0:
                proc = check_output([r"./contribute",STUDY_NAME,STUDY_NAME_PATH,AUTHOR_NAME],cwd=concore_path)
            else:
                proc = check_output([r"./contribute",STUDY_NAME,STUDY_NAME_PATH,AUTHOR_NAME,BRANCH_NAME,PR_TITLE,PR_BODY],cwd=concore_path)
            output_string = proc.decode()

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