fix: YubiKey CA signing, remove inline API copies, env-driven config

Critical: build_leaf_cert self-signed leaves with the leaf key instead of
the YubiKey-held Intermediate CA key. Now extracts TBS, signs via
pkcs11-tool (ECDSA-SHA384), reassembles, and verifies against the
intermediate CA public key before returning.

- setup-certauth.sh: ~1100 lines of stale inline api/ copies replaced with
  copy-from-repo (single source of truth); writes private
  /etc/certauth/certauth.env (0600); DB init loads env, no more
  swallowed errors; systemd unit gets EnvironmentFile=
- config.py: YubiKey serials no longer hard-coded (env, fail closed);
  aarch64-only PKCS#11 path replaced with arch-neutral default; all
  paths env-overridable (CERTAUTH_*)
- main.py: removed dead fastapi.security.CSRFProtection import (crashed
  startup); module-relative static/templates dirs; created_by resolved
  from the authenticated user instead of hard-coded 1; unclosed file
  handles fixed; domain_id 0 stored as NULL (FK bug)
- models.py: certificates.domain_id FK pointed at users(id), now domains(id)
- login: CSRF token now actually sent and validated
- tests: 23 tests (auth, API flows, DER helpers, signing pipeline)
- README, LICENSE, requirements.txt, pyproject.toml

.env.example

@@ -1,19 +1,50 @@
-# CertAuth Environment Variables
+# CertAuth API environment variables.
-# Copy this to .env and fill in your real values
+# Installed to /etc/certauth/certauth.env (mode 600, owned by the API user)
+# and loaded via EnvironmentFile= in certauth-api.service.
+#
+# The API fails closed on startup if any of the REQUIRED variables below
+# are missing.
 
-# Admin web login password
+# ---- REQUIRED -------------------------------------------------------------
-ADMIN_PASS=your-secure-admin-password
 
-# YubiKey 1 (Root CA) credentials
+# YubiKey hardware assignments (serials are printed by `ykman list`;
-YK_ROOT_PIN=your-yk1-pin
+# setup-certauth.sh auto-detects them at provision time)
-YK_ROOT_PUK=your-yk1-puk
+YK_ROOT_SERIAL=your-root-yubikey-serial
+YK_INT_SERIAL=your-intermediate-yubikey-serial
 
-# YubiKey 2 (Intermediate CA) credentials
+# YubiKey PINs (change from the defaults with:
-YK_INT_PIN=your-yk2-pin
+#   ykman piv access change-pin -P <old> --new-pin <new>)
-YK_INT_PUK=your-yk2-puk
+YK_ROOT_PIN=your-yk-root-pin
+YK_INT_PIN=your-yk-intermediate-pin
 
 # JWT signing secret (generate with: python3 -c "import secrets; print(secrets.token_hex(32))")
 JWT_SECRET=your-64-char-hex-secret
 
-# PFX download password
+# Admin web/API login password
+ADMIN_PASSWORD=your-secure-admin-password
+
+# ---- OPTIONAL (defaults shown) ---------------------------------------------
+
+# Admin username (default: certauth)
+ADMIN_USERNAME=certauth
+
+# Filesystem layout (defaults match setup-certauth.sh production layout)
+CERTAUTH_CA_BASE=/etc/ssl/ca
+CERTAUTH_ROOT_CA=/etc/ssl/ca/root/root-ca.crt
+CERTAUTH_INT_CA=/etc/ssl/ca/intermediate/intermediate-ca.crt
+CERTAUTH_CA_CHAIN=/etc/ssl/ca/ca-chain.crt
+CERTAUTH_ISSUED_DIR=/etc/ssl/ca/issued
+CERTAUTH_TMP_DIR=/var/lib/certauth/tmp
+CERTAUTH_DB_PATH=/var/lib/certauth/certauth.db
+
+# PKCS#11 (defaults work on aarch64 and x86_64 Ubuntu)
+PKCS11_MODULE=/usr/lib/opensc-pkcs11.so
+# pkcs11-tool --token-label; leave empty to match by key label only
+PKCS11_TOKEN_LABEL=
+
+# Leaf certificate subject (matches setup-certauth.sh defaults)
+CA_ORG=Home
+CA_COUNTRY=US
+
+# PFX download default password (overridable per download)
 PFX_PASS=certauth

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2025 Jarian Cottingham
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

@@ -0,0 +1,107 @@
+# CertAuth Key Vault
+
+Self-contained Certificate Authority with YubiKey-backed signing. Two
+YubiKey 5 Nano devices act as HSMs — one for the Root CA, one for the
+Intermediate CA. Every certificate sign requires physical touch + PIN, so
+compromising the server does not compromise the CA keys.
+
+```
+Root CA (YubiKey 1)  →  Intermediate CA (YubiKey 2)  →  Leaf certs
+   25-year validity        15-year validity              1-year validity
+```
+
+## Components
+
+| Path | Purpose |
+| --- | --- |
+| `api/` | FastAPI service: REST API + Jinja2 web UI |
+| `setup-certauth.sh` | Idempotent provisioner: fresh Ubuntu 24.04+ → full CA (aarch64/x86_64) |
+| `certauth-api.service` | systemd unit for the API |
+| `Caddyfile` | Caddy TLS-terminating reverse proxy in front of the API |
+| `nginx-example.com` | Reference nginx config for the wider homelab vhost layout |
+| `landing/` | Landing pages for the CA domain |
+| `SKILL.md` | Operator/agent runbook: API usage, endpoints, workflows |
+| `.env.example` | All environment variables documented |
+
+## Architecture
+
+- **Signing**: `pkcs11-tool` against the OpenSC PKCS#11 module; ECDSA-SHA384.
+  Private keys never leave the YubiKeys; only extracted public keys are
+  cached on disk.
+- **Auth**: JWT bearer tokens for the REST API, session cookie for the web
+  UI, per-request CSRF tokens on all state-changing web endpoints.
+- **Storage**: SQLite (WAL) for domains, certificate requests, audit log,
+  and CRL entries.
+- **CRL**: revoked serials tracked in the DB; `scripts`-style daily CRL
+  refresh is documented in `SKILL.md`.
+
+## Quick start (provision a node)
+
+```bash
+sudo bash setup-certauth.sh
+```
+
+Prerequisites: fresh Ubuntu 24.04+, two YubiKey 5 Nanos plugged in, root.
+The script configures everything (CA hierarchy, API, Caddy, systemd) and
+prints the generated PINs. Configuration is overridable via environment
+(`CA_ORG`, `YK1_SERIAL`, `NETWORK_CIDR`, ...).
+
+## Running the API standalone
+
+```bash
+pip install -r requirements.txt
+export YK_ROOT_SERIAL=... YK_INT_SERIAL=...
+export YK_ROOT_PIN=... YK_INT_PIN=...
+export JWT_SECRET=$(python3 -c "import secrets; print(secrets.token_hex(32))")
+export ADMIN_PASSWORD=...
+python3 -m uvicorn main:app --host 127.0.0.1 --port 8000   # from api/
+```
+
+All filesystem paths default to the production layout (`/etc/ssl/ca`,
+`/var/lib/certauth`) and are overridable via `CERTAUTH_*` environment
+variables — see `.env.example`.
+
+## API (summary)
+
+| Method | Path | Purpose |
+| --- | --- | --- |
+| POST | `/api/token` | Login → JWT |
+| GET | `/api/me` | Validate token |
+| GET/POST | `/api/domains` | List / register domain |
+| GET | `/api/certs` | List certificate requests |
+| POST | `/api/certs/request` | Create pending request (cn, sans) |
+| POST | `/api/certs/{id}/sign` | Sign via YubiKey (touch + PIN) |
+| GET | `/api/certs/{id}/pem` | Download leaf + chain |
+| GET | `/api/certs/{id}/pfx` | Download PKCS#12 (password-protected) |
+| GET | `/api/health` | Liveness |
+| GET | `/api/ca-chain` | Download CA chain |
+
+Web UI: `/` dashboard, `/login`, `/domains`, `/certs`, `/history`,
+`/setup` (provisioning helper pages).
+
+Full usage examples: see `SKILL.md`.
+
+## Tests
+
+```bash
+pip install pytest
+pytest tests/ -v
+```
+
+Unit tests cover auth (JWT round-trip, rejection of invalid tokens),
+login/token endpoints, domain + certificate-request flows, and password
+hashing. Signing paths that require a physical YubiKey are exercised at
+the integration level on the provisioned node.
+
+## Security notes
+
+- YubiKey serials, PINs, JWT secret, and admin password are environment
+  driven and **fail closed** at import time — the service will not start
+  with missing configuration.
+- Leaf keys are written `0600`, certs `0640`, under the issued directory.
+- CSRF tokens use constant-time comparison (`secrets.compare_digest`).
+- Error strings are HTML-escaped before rendering into pages.
+
+## License
+
+MIT — see [LICENSE](LICENSE).

api/config.py

@@ -1,29 +1,61 @@
-import os
+"""CertAuth configuration.
-import secrets
 
-YK_ROOT_SERIAL = "35450561"
+All hardware identifiers and filesystem paths are environment-driven so the
-YK_ROOT_PIN = os.environ.get("YK_ROOT_PIN")
+service can run on aarch64/x86_64 and in test environments. Secrets and
-if not YK_ROOT_PIN:
+YubiKey assignments fail closed at import time.
-    raise RuntimeError("YK_ROOT_PIN environment variable is required")
+"""
-YK_INT_SERIAL = "33930436"
+
-YK_INT_PIN = os.environ.get("YK_INT_PIN")
+import os
-if not YK_INT_PIN:
+
-    raise RuntimeError("YK_INT_PIN environment variable is required")
+
-ROOT_CA_PATH = "/etc/ssl/ca/root/root-ca.crt"
+def _required(name: str) -> str:
-INT_CA_PATH = "/etc/ssl/ca/intermediate/intermediate-ca.crt"
+    value = os.environ.get(name)
-CA_CHAIN_PATH = "/etc/ssl/ca/ca-chain.crt"
+    if not value:
-ISSUED_DIR = "/etc/ssl/ca/issued"
+        raise RuntimeError(f"{name} environment variable is required")
-DB_PATH = "/var/lib/certauth/certauth.db"
+    return value
-JWT_SECRET_ENV = os.environ.get("JWT_SECRET")
+
-if not JWT_SECRET_ENV:
+
-    JWT_SECRET_ENV = secrets.token_hex(32)
+# YubiKey hardware: serials must be supplied by the operator (auto-detected at
-SECRET_KEY = JWT_SECRET_ENV
+# setup time by setup-certauth.sh). Never hard-code device serials in source.
+YK_ROOT_SERIAL = _required("YK_ROOT_SERIAL")
+YK_INT_SERIAL = _required("YK_INT_SERIAL")
+YK_ROOT_PIN = _required("YK_ROOT_PIN")
+YK_INT_PIN = _required("YK_INT_PIN")
+
+# Filesystem layout (defaults match the production layout created by
+# setup-certauth.sh; override via environment for testing or custom installs).
+CA_BASE = os.environ.get("CERTAUTH_CA_BASE", "/etc/ssl/ca")
+ROOT_CA_PATH = os.environ.get("CERTAUTH_ROOT_CA", f"{CA_BASE}/root/root-ca.crt")
+INT_CA_PATH = os.environ.get("CERTAUTH_INT_CA", f"{CA_BASE}/intermediate/intermediate-ca.crt")
+CA_CHAIN_PATH = os.environ.get("CERTAUTH_CA_CHAIN", f"{CA_BASE}/ca-chain.crt")
+ISSUED_DIR = os.environ.get("CERTAUTH_ISSUED_DIR", f"{CA_BASE}/issued")
+TMP_DIR = os.environ.get("CERTAUTH_TMP_DIR", "/var/lib/certauth/tmp")
+DB_PATH = os.environ.get("CERTAUTH_DB_PATH", "/var/lib/certauth/certauth.db")
+
+# Extracted YubiKey public keys (written by setup-certauth.sh).
+YK_PUB_ROOT = os.environ.get("YK_PUB_ROOT", "/tmp/yk1-root-pub.pem")
+YK_PUB_INT = os.environ.get("YK_PUB_INT", "/tmp/yk2-int-pub.pem")
+
+# PKCS#11 module for pkcs11-tool. Default works on both aarch64 and x86_64
+# Ubuntu; override for nonstandard installs.
+PKCS11_MODULE = os.environ.get("PKCS11_MODULE", "/usr/lib/opensc-pkcs11.so")
+# Optional pkcs11-tool --token-label. Empty = match the setup-script
+# invocation (key label only), which works with both YubiKeys attached.
+PKCS11_TOKEN_LABEL = os.environ.get("PKCS11_TOKEN_LABEL", "")
+
+# Leaf certificate subject defaults (match setup-certauth.sh defaults)
+CA_ORG = os.environ.get("CA_ORG", "Home")
+CA_COUNTRY = os.environ.get("CA_COUNTRY", "US")
+
+# JWT / web session
+JWT_SECRET = _required("JWT_SECRET")
+SECRET_KEY = JWT_SECRET
 ALGORITHM = "HS256"
 ACCESS_TOKEN_EXPIRE_MINUTES = 60
+
+# Admin bootstrap account
 ADMIN_USERNAME = os.environ.get("ADMIN_USERNAME", "certauth")
-ADMIN_PASSWORD = os.environ.get("ADMIN_PASSWORD")
+ADMIN_PASSWORD = _required("ADMIN_PASSWORD")
-if not ADMIN_PASSWORD:
+
-    raise RuntimeError("ADMIN_PASSWORD environment variable is required")
+# PFX download default password (overridable per download)
-PKCS11_MODULE = "/usr/lib/aarch64-linux-gnu/opensc-pkcs11.so"
+PFX_DEFAULT_PASSWORD = os.environ.get("PFX_PASS", "certauth")
-YK_PUB_ROOT = "/tmp/yk1-root-pub.pem"
-YK_PUB_INT = "/tmp/yk2-int-pub.pem"

api/main.py

@@ -1,28 +1,37 @@
 import os
 import secrets
-import hashlib
-import subprocess
-import json
 import logging
 import html
 from datetime import datetime, timezone
 from fastapi import FastAPI, Request, Depends, HTTPException, Form
-from fastapi.responses import HTMLResponse, FileResponse, RedirectResponse, JSONResponse, PlainTextResponse
+from fastapi.responses import HTMLResponse, FileResponse, RedirectResponse, PlainTextResponse
 from fastapi.staticfiles import StaticFiles
-from fastapi.security import CSRFProtection
 from pydantic import BaseModel
 from jose import jwt
 from jinja2 import Environment, FileSystemLoader, select_autoescape
-from config import *
+from config import (
-from models import get_db, init_db, hash_password, verify_password
+    ALGORITHM,
+    CA_CHAIN_PATH,
+    INT_CA_PATH,
+    ISSUED_DIR,
+    PFX_DEFAULT_PASSWORD,
+    ROOT_CA_PATH,
+    SECRET_KEY,
+    TMP_DIR,
+)
+from models import get_db, init_db, verify_password
 from auth import create_access_token, get_current_user
 from signing import build_leaf_cert
 from cryptography.hazmat.primitives import serialization
 
 logger = logging.getLogger(__name__)
 
+BASE_DIR = os.path.dirname(os.path.abspath(__file__))
+STATIC_DIR = os.environ.get("CERTAUTH_STATIC_DIR", os.path.join(BASE_DIR, "static"))
+TEMPLATES_DIR = os.environ.get("CERTAUTH_TEMPLATES_DIR", os.path.join(BASE_DIR, "templates"))
+
 app = FastAPI(title="CertAuth Key Vault")
-app.mount("/static", StaticFiles(directory="/opt/certauth/api/static"), name="static")
+app.mount("/static", StaticFiles(directory=STATIC_DIR, check_dir=False), name="static")
 
 _csrf_secrets = {}
 
@@ -50,7 +59,7 @@ def get_user_from_cookie(request: Request):
         return None
 
 jinja_env = Environment(
-    loader=FileSystemLoader("/opt/certauth/api/templates"),
+    loader=FileSystemLoader(TEMPLATES_DIR),
     autoescape=select_autoescape(["html", "xml"]),
 )
 
@@ -67,6 +76,11 @@ def startup():
     except Exception as e:
         logger.warning("CA chain setup failed: %s", sanitize_error(str(e)))
 
+def get_user_id(conn, username: str) -> int:
+    row = conn.execute("SELECT id FROM users WHERE username = ?", (username,)).fetchone()
+    return row["id"] if row else 1
+
+
 def render(name, ctx):
     return HTMLResponse(jinja_env.get_template(name).render(**ctx))
 
@@ -105,7 +119,7 @@ async def create_domain(
     cur = conn.cursor()
     cur.execute(
         "INSERT INTO domains (name, description, created_by) VALUES (?,?,?)",
-        (name, description, 1),
+        (name, description, get_user_id(conn, user)),
     )
     conn.commit()
     conn.close()
@@ -134,7 +148,7 @@ async def request_cert(
     cur = conn.cursor()
     cur.execute(
         "INSERT INTO certificates (domain_id, subject, san, status, created_by) VALUES (?,?,?,?,?)",
-        (domain_id, cn, sans, "pending", 1),
+        (domain_id or None, cn, sans, "pending", get_user_id(conn, user)),
     )
     conn.commit()
     cid = cur.lastrowid
@@ -158,10 +172,12 @@ async def sign_cert(cert_id: int, user: str = Depends(get_current_user)):
         raise HTTPException(500, "Signing failed")
     if err:
         raise HTTPException(500, "Signing failed")
-    cf = f"/etc/ssl/ca/issued/cert-{result['serial']}.crt"
+    cf = f"{ISSUED_DIR}/cert-{result['serial']}.crt"
-    kf = f"/etc/ssl/ca/issued/cert-{result['serial']}.key"
+    kf = f"{ISSUED_DIR}/cert-{result['serial']}.key"
-    open(cf, "w").write(result["cert_pem"])
+    with open(cf, "w") as f:
-    open(kf, "w").write(result["key_pem"])
+        f.write(result["cert_pem"])
+    with open(kf, "w") as f:
+        f.write(result["key_pem"])
     os.chmod(cf, 0o640)
     os.chmod(kf, 0o600)
     conn = get_db()
@@ -185,7 +201,7 @@ async def download_pem(cert_id: int, request: Request = None):
     conn.close()
     if not row or row["status"] != "issued":
         raise HTTPException(404)
-    pem_path = f"/var/lib/certauth/tmp/cert-{row['serial']}.pem"
+    pem_path = f"{TMP_DIR}/cert-{row['serial']}.pem"
     with open(row["cert_path"]) as f:
         cert_pem = f.read()
     with open(CA_CHAIN_PATH) as f:
@@ -197,7 +213,7 @@ async def download_pem(cert_id: int, request: Request = None):
 @app.get("/api/certs/{cert_id}/pfx")
 async def download_pfx(
     cert_id: int,
-    password: str = "certauth",
+    password: str = PFX_DEFAULT_PASSWORD,
     request: Request = None,
 ):
     user = get_user_from_cookie(request)
@@ -236,7 +252,7 @@ async def download_pfx(
         cas=chain_certs or None,
         encryption_algorithm=BestAvailableEncryption(password.encode()),
     )
-    pfx_path = f"/var/lib/certauth/tmp/cert-{row['serial']}.pfx"
+    pfx_path = f"{TMP_DIR}/cert-{row['serial']}.pfx"
     with open(pfx_path, "wb") as f:
         f.write(pfx_data)
     return FileResponse(pfx_path, media_type="application/x-pkcs12", filename=f"cert-{row['serial']}.pfx")
@@ -293,6 +309,11 @@ async def login_post(
     password: str = Form(...),
     csrf_token: str = Form(""),
 ):
+    if not verify_csrf_token("anon", csrf_token):
+        return render(
+            "login.html",
+            {"request": None, "error": "Invalid request", "csrf_token": get_csrf_token("anon")},
+        )
     conn = get_db()
     row = conn.execute(
         "SELECT * FROM users WHERE username = ?", (username,)
@@ -327,11 +348,13 @@ async def sign_cert_web(cert_id: int, request: Request = None):
     try:
         result, err = build_leaf_cert(row["subject"], row["san"], 365)
         if err:
-            return HTMLResponse(f"<span class='text-red-400'>Issue failed</span>")
+            return HTMLResponse("<span class='text-red-400'>Issue failed</span>")
-        cf = f"/etc/ssl/ca/issued/cert-{result['serial']}.crt"
+        cf = f"{ISSUED_DIR}/cert-{result['serial']}.crt"
-        kf = f"/etc/ssl/ca/issued/cert-{result['serial']}.key"
+        kf = f"{ISSUED_DIR}/cert-{result['serial']}.key"
-        open(cf, "w").write(result["cert_pem"])
+        with open(cf, "w") as f:
-        open(kf, "w").write(result["key_pem"])
+            f.write(result["cert_pem"])
+        with open(kf, "w") as f:
+            f.write(result["key_pem"])
         os.chmod(cf, 0o640)
         os.chmod(kf, 0o600)
         conn2 = get_db()
@@ -380,7 +403,7 @@ async def create_domain_web(
     cur = conn.cursor()
     cur.execute(
         "INSERT INTO domains (name, description, created_by) VALUES (?,?,?)",
-        (name, description, 1),
+        (name, description, get_user_id(conn, user.get("sub"))),
     )
     conn.commit()
     conn.close()
@@ -411,7 +434,7 @@ async def request_cert_web(
         domain_id = row[0] if row else None
     cur.execute(
         "INSERT INTO certificates (domain_id, subject, san, status, created_by) VALUES (?,?,?,?,?)",
-        (domain_id, cn, sans, "pending", 1),
+        (domain_id, cn, sans, "pending", get_user_id(conn, user.get("sub"))),
     )
     conn.commit()
     conn.close()

api/models.py

@@ -33,7 +33,7 @@ def init_db():
     );
     CREATE TABLE IF NOT EXISTS certificates (
         id INTEGER PRIMARY KEY AUTOINCREMENT,
-        domain_id INTEGER REFERENCES users(id),
+        domain_id INTEGER REFERENCES domains(id),
         subject TEXT NOT NULL,
         san TEXT,
         serial TEXT UNIQUE,

api/signing.py

@@ -1,48 +1,107 @@
-import subprocess
+"""Certificate signing via the YubiKey-held Intermediate CA key.
-import os
+
+The private key never leaves the YubiKey. Signing works in three steps:
+
+1. Build the TBS (to-be-signed) certificate bytes.
+2. Hand the TBS to ``pkcs11-tool`` (OpenSC PKCS#11) which signs it on the
+   YubiKey with ECDSA-SHA384.
+3. Reassemble the certificate DER from TBS + signature algorithm + YubiKey
+   signature, then verify it against the Intermediate CA public key before
+   trusting the result.
+"""
+
 import logging
+import os
+import subprocess
 import tempfile
 from datetime import datetime, timedelta, timezone
+
 from cryptography import x509
 from cryptography.hazmat.primitives import hashes, serialization
 from cryptography.hazmat.primitives.asymmetric import ec
-from cryptography.hazmat.primitives.serialization import Encoding, NoEncryption, BestAvailableEncryption
+from cryptography.hazmat.primitives.serialization import Encoding, NoEncryption
-from cryptography.x509.oid import NameOID, ExtensionOID
+from cryptography.x509.oid import NameOID
-from config import *
+
+from config import (
+    CA_COUNTRY,
+    CA_ORG,
+    INT_CA_PATH,
+    PKCS11_MODULE,
+    PKCS11_TOKEN_LABEL,
+    YK_INT_PIN,
+)
+from models import get_db
 
 logger = logging.getLogger(__name__)
 
-TMP_DIR = tempfile.mkdtemp(prefix="certauth_")
+# Scratch dir for pkcs11-tool input/output files (per-process, unlinked after).
-os.makedirs(TMP_DIR, exist_ok=True)
+PKCS11_TMP = tempfile.mkdtemp(prefix="certauth_")
 
-def get_root_pub_key():
-    with open(YK_PUB_ROOT, "rb") as f:
-        return serialization.load_pem_public_key(f.read())
 
-def get_int_pub_key():
+def _der_read_len(data: bytes, i: int) -> tuple:
-    with open(YK_PUB_INT, "rb") as f:
+    """Read a DER length field at offset i -> (length, offset_after_field)."""
-        return serialization.load_pem_public_key(f.read())
+    b0 = data[i]
+    if b0 < 0x80:
+        return b0, i + 1
+    n = b0 & 0x7F
+    return int.from_bytes(data[i + 1:i + 1 + n], "big"), i + 1 + n
 
-def get_root_ca_cert():
+
-    with open(ROOT_CA_PATH, "rb") as f:
+def _der_seq(body: bytes) -> bytes:
+    if len(body) < 0x80:
+        return b"\x30" + bytes([len(body)]) + body
+    lb = len(body).to_bytes((len(body).bit_length() + 7) // 8, "big")
+    return b"\x30" + bytes([0x80 | len(lb)]) + lb + body
+
+
+def _split_cert_der(der: bytes):
+    """Split a certificate DER into (tbs, signature_algorithm, signature)."""
+    if der[0] != 0x30:
+        raise ValueError("not a DER certificate")
+    _, body_start = _der_read_len(der, 1)
+    # tbsCertificate SEQUENCE
+    if der[body_start] != 0x30:
+        raise ValueError("bad tbsCertificate tag")
+    tbs_len, tbs_len_end = _der_read_len(der, body_start + 1)
+    tbs_end = tbs_len_end + tbs_len
+    tbs = der[body_start:tbs_end]
+    # signatureAlgorithm SEQUENCE
+    if der[tbs_end] != 0x30:
+        raise ValueError("bad signatureAlgorithm tag")
+    alg_len, alg_len_end = _der_read_len(der, tbs_end + 1)
+    alg_end = alg_len_end + alg_len
+    alg = der[tbs_end:alg_end]
+    return tbs, alg, der[alg_end:]
+
+
+def get_int_ca_cert():
+    with open(INT_CA_PATH, "rb") as f:
         return x509.load_pem_x509_certificate(f.read())
 
-def sign_tbs_with_yk(tbs_bytes, yk_pin, token_label="certauth Intermediate CA"):
+
-    with tempfile.NamedTemporaryFile(suffix=".der", delete=False, dir=TMP_DIR) as tbs_file:
+def sign_tbs_with_yk(tbs_bytes, yk_pin, token_label=None):
+    """Sign DER bytes with the YubiKey SIGN key via pkcs11-tool.
+
+    Returns (signature_BIT_STRING, None) on success or (None, error).
+    """
+    with tempfile.NamedTemporaryFile(suffix=".der", delete=False, dir=PKCS11_TMP) as tbs_file:
         tbs_file.write(tbs_bytes)
         tbs_path = tbs_file.name
-    sig_path = os.path.join(TMP_DIR, f"sig_{os.path.basename(tbs_path)}")
+    sig_path = os.path.join(PKCS11_TMP, f"sig_{os.path.basename(tbs_path)}")
+    cmd = [
+        "sudo", "pkcs11-tool", "--module", PKCS11_MODULE,
+        "--login", "--pin-source", "stdin",
+        "--sign", "--mechanism", "ECDSA-SHA384",
+        "--label", "SIGN key",
+        "--input-file", tbs_path,
+        "--output-file", sig_path,
+    ]
+    label = token_label if token_label is not None else PKCS11_TOKEN_LABEL
+    if label:
+        cmd[3:3] = ["--token-label", label]
     try:
         r = subprocess.run(
-            [
+            cmd,
-                "sudo", "pkcs11-tool", "--module", PKCS11_MODULE,
-                "--login", "--pin-source", "stdin",
-                "--sign", "--mechanism", "ECDSA-SHA384",
-                "--token-label", token_label,
-                "--label", "SIGN key",
-                "--input-file", tbs_path,
-                "--output-file", sig_path,
-            ],
             input=yk_pin.encode(),
             capture_output=True,
             text=True,
@@ -53,6 +112,8 @@ def sign_tbs_with_yk(tbs_bytes, yk_pin, token_label="certauth Intermediate CA"):
             return None, "Signing failed"
         with open(sig_path, "rb") as f:
             raw = f.read()
+        # pkcs11-tool returns raw r||s (48 bytes each for P-384); wrap in a
+        # BIT STRING carrying the DER ECDSA-Sig-Value.
         rb = raw[:48].lstrip(b"\x00") or b"\x00"
         sb = raw[48:].lstrip(b"\x00") or b"\x00"
         if rb[0] & 0x80:
@@ -71,25 +132,25 @@ def sign_tbs_with_yk(tbs_bytes, yk_pin, token_label="certauth Intermediate CA"):
             except OSError:
                 pass
 
+
 def build_leaf_cert(cn, sans, days=365):
-    root_cert = get_root_ca_cert()
+    """Issue a leaf certificate for cn, signed by the Intermediate CA.
-    int_pub = get_int_pub_key()
+
-    root_pub = get_root_pub_key()
+    Returns ({serial, cert_pem, key_pem, expires_at}, None) or (None, error).
+    The private key stays on the server (leaf keys are not hardware-backed);
+    only the CA signing key requires the YubiKey.
+    """
+    int_cert = get_int_ca_cert()
     leaf_key = ec.generate_private_key(ec.SECP384R1())
     subject = x509.Name([
-        x509.NameAttribute(NameOID.COUNTRY_NAME, "US"),
+        x509.NameAttribute(NameOID.COUNTRY_NAME, CA_COUNTRY),
-        x509.NameAttribute(NameOID.ORGANIZATION_NAME, "Home"),
+        x509.NameAttribute(NameOID.ORGANIZATION_NAME, CA_ORG),
         x509.NameAttribute(NameOID.COMMON_NAME, cn),
     ])
-    issuer = x509.Name([
-        x509.NameAttribute(NameOID.COUNTRY_NAME, "US"),
-        x509.NameAttribute(NameOID.ORGANIZATION_NAME, "Home"),
-        x509.NameAttribute(NameOID.COMMON_NAME, "certauth Intermediate CA"),
-    ])
     builder = (
         x509.CertificateBuilder()
         .subject_name(subject)
-        .issuer_name(issuer)
+        .issuer_name(int_cert.subject)
         .public_key(leaf_key.public_key())
         .serial_number(x509.random_serial_number())
         .not_valid_before(datetime.now(timezone.utc))
@@ -124,9 +185,21 @@ def build_leaf_cert(cn, sans, days=365):
                 x509.SubjectAlternativeName(san_names),
                 critical=False,
             )
-    tbs_bytes = builder.signature_algorithm_oid
+
-    cert_bytes = builder.sign(leaf_key, hashes.SHA384())
+    # 1) TBS bytes: sign with a throwaway key of identical parameters —
-    serial = x509.load_der_x509_certificate(cert_bytes).serial_number
+    #    the TBS block is independent of the signing key.
+    dummy_key = ec.generate_private_key(ec.SECP384R1())
+    tbs, sig_alg, _ = _split_cert_der(builder.sign(dummy_key, hashes.SHA384()))
+
+    # 2) Real signature from the YubiKey.
+    yk_sig, err = sign_tbs_with_yk(tbs, YK_INT_PIN)
+    if err:
+        return None, err
+
+    # 3) Reassemble and verify before trusting.
+    cert = x509.load_der_x509_certificate(_der_seq(tbs + sig_alg + yk_sig))
+    cert.verify(int_cert.public_key())
+
     key_pem = leaf_key.private_bytes(
         encoding=Encoding.PEM,
         format=serialization.PrivateFormat.PKCS8,
@@ -134,14 +207,15 @@ def build_leaf_cert(cn, sans, days=365):
     ).decode()
     return (
         {
-            "serial": hex(serial),
+            "serial": hex(cert.serial_number),
-            "cert_pem": cert_bytes.public_bytes(Encoding.PEM).decode(),
+            "cert_pem": cert.public_bytes(Encoding.PEM).decode(),
             "key_pem": key_pem,
-            "expires_at": (datetime.now(timezone.utc) + timedelta(days=days)).isoformat(),
+            "expires_at": cert.not_valid_after_utc.isoformat(),
         },
         None,
     )
 
+
 def revoke_certificate(serial_hex: str, reason: str = "key_compromise"):
     conn = get_db()
     conn.execute(

api/templates/login.html

@@ -14,6 +14,7 @@
         <div class="bg-red-900/50 border border-red-700 rounded p-3 mb-4 text-red-300 text-sm">{{ error }}</div>
         {% endif %}
         <form method="post" action="/login">
+            <input type="hidden" name="csrf_token" value="{{ csrf_token }}">
             <div class="mb-4">
                 <label class="block text-sm text-gray-400 mb-1">Username</label>
                 <input type="text" name="username" required

certauth-api.service

@@ -8,6 +8,7 @@ User=certauth
 Group=certauth
 WorkingDirectory=/opt/certauth/api
 Environment=PYTHONUNBUFFERED=1
+EnvironmentFile=/etc/certauth/certauth.env
 ExecStart=/usr/bin/python3 -m uvicorn main:app --host 127.0.0.1 --port 8000
 Restart=on-failure
 RestartSec=5

pyproject.toml

@@ -0,0 +1,42 @@
+[project]
+name = "certauth"
+version = "1.0.0"
+description = "YubiKey-backed self-contained Certificate Authority: FastAPI + web UI, PKCS#11 signing, SQLite store"
+readme = "README.md"
+requires-python = ">=3.9"
+license = { text = "MIT" }
+authors = [{ name = "Jarian Cottingham", email = "jarianc@proton.me" }]
+keywords = ["security", "certificate-authority", "yubikey", "pkcs11", "fastapi"]
+classifiers = [
+    "License :: OSI Approved :: MIT License",
+    "Programming Language :: Python :: 3",
+]
+dependencies = [
+    "fastapi>=0.110",
+    "uvicorn[standard]>=0.29",
+    "jinja2>=3.1",
+    "python-multipart>=0.0.9",
+    "bcrypt>=4.1",
+    "python-jose[cryptography]>=3.3",
+    "ecdsa>=0.18",
+    "cryptography>=42.0",
+]
+
+[project.optional-dependencies]
+dev = ["pytest>=7.0", "ruff>=0.1.0"]
+
+[build-system]
+requires = ["setuptools>=61.0"]
+build-backend = "setuptools.build_meta"
+
+[tool.ruff]
+line-length = 120
+target-version = "py39"
+exclude = [".git", "venv"]
+
+[tool.ruff.lint]
+select = ["E", "F", "W"]
+ignore = ["E501", "E741"]
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]

requirements.txt

@@ -0,0 +1,8 @@
+fastapi>=0.110
+uvicorn[standard]>=0.29
+jinja2>=3.1
+python-multipart>=0.0.9
+bcrypt>=4.1
+python-jose[cryptography]>=3.3
+ecdsa>=0.18
+cryptography>=42.0

tests/conftest.py

@@ -0,0 +1,31 @@
+"""Test setup: configure the environment before importing the app.
+
+The API fails closed on missing configuration (by design), so tests
+provide a complete, isolated environment pointing at a temp directory.
+"""
+
+import os
+import sys
+import tempfile
+from pathlib import Path
+
+API_DIR = Path(__file__).resolve().parent.parent / "api"
+sys.path.insert(0, str(API_DIR))
+
+_TMP = tempfile.mkdtemp(prefix="certauth-test-")
+
+os.environ["YK_ROOT_SERIAL"] = "10000001"
+os.environ["YK_INT_SERIAL"] = "10000002"
+os.environ["YK_ROOT_PIN"] = "123456"
+os.environ["YK_INT_PIN"] = "234567"
+os.environ["JWT_SECRET"] = "test-secret-0123456789abcdef0123456789abcdef"
+os.environ["ADMIN_USERNAME"] = "certauth"
+os.environ["ADMIN_PASSWORD"] = "test-admin-pass-123"
+os.environ["CERTAUTH_DB_PATH"] = os.path.join(_TMP, "test.db")
+os.environ["CERTAUTH_TMP_DIR"] = os.path.join(_TMP, "tmp")
+os.environ["CERTAUTH_CA_BASE"] = os.path.join(_TMP, "ca")
+os.environ["CERTAUTH_ISSUED_DIR"] = os.path.join(_TMP, "ca", "issued")
+os.environ["PKCS11_MODULE"] = "/usr/lib/opensc-pkcs11.so"
+
+os.makedirs(os.environ["CERTAUTH_ISSUED_DIR"], exist_ok=True)
+os.makedirs(os.environ["CERTAUTH_TMP_DIR"], exist_ok=True)

tests/test_api.py

@@ -0,0 +1,115 @@
+"""API endpoint tests (no YubiKey required)."""
+
+import pytest
+from fastapi.testclient import TestClient
+
+from main import app
+
+ADMIN = {"username": "certauth", "password": "test-admin-pass-123"}
+
+
+@pytest.fixture(scope="module")
+def client():
+    with TestClient(app) as c:
+        yield c
+
+
+@pytest.fixture(scope="module")
+def auth(client):
+    r = client.post("/api/token", json=ADMIN)
+    assert r.status_code == 200
+    return {"Authorization": f"Bearer {r.json()['access_token']}"}
+
+
+def test_health(client):
+    r = client.get("/api/health")
+    assert r.status_code == 200
+    assert r.json() == {"status": "ok"}
+
+
+def test_token_wrong_password(client):
+    r = client.post("/api/token", json={"username": "certauth", "password": "wrong"})
+    assert r.status_code == 401
+
+
+def test_token_unknown_user(client):
+    r = client.post("/api/token", json={"username": "nobody", "password": "x"})
+    assert r.status_code == 401
+
+
+def test_me(client, auth):
+    r = client.get("/api/me", headers=auth)
+    assert r.status_code == 200
+    assert r.json() == {"username": "certauth"}
+
+
+def test_me_without_token(client):
+    assert client.get("/api/me").status_code == 401
+
+
+def test_login_page_renders_with_csrf(client):
+    r = client.get("/login")
+    assert r.status_code == 200
+    assert "csrf_token" in r.text
+
+
+def test_dashboard_redirects_when_unauthenticated(client):
+    r = client.get("/", follow_redirects=False)
+    assert r.status_code == 302
+    assert r.headers["location"] == "/login"
+
+
+def test_login_requires_valid_csrf(client):
+    r = client.post(
+        "/login",
+        data={"username": "certauth", "password": "test-admin-pass-123", "csrf_token": "bogus"},
+        follow_redirects=False,
+    )
+    assert r.status_code == 200
+    assert "Invalid request" in r.text
+
+
+def test_domain_create_and_list(client, auth):
+    r = client.post(
+        "/api/domains",
+        data={"name": "test.example.ms", "description": "unit test domain"},
+        headers=auth,
+    )
+    assert r.status_code == 200
+    r = client.get("/api/domains", headers=auth)
+    assert r.status_code == 200
+    names = [d["name"] for d in r.json()]
+    assert "test.example.ms" in names
+
+
+def test_domain_requires_auth(client):
+    r = client.post("/api/domains", data={"name": "x.ms"})
+    assert r.status_code == 401
+
+
+def test_cert_request_lifecycle(client, auth):
+    client.post(
+        "/api/domains",
+        data={"name": "certtest.example.ms"},
+        headers=auth,
+    )
+    r = client.post(
+        "/api/certs/request",
+        data={"cn": "certtest.example.ms", "sans": "alt.example.ms"},
+        headers=auth,
+    )
+    assert r.status_code == 200
+    cert_id = r.json()["id"]
+
+    r = client.get("/api/certs", headers=auth)
+    row = next(c for c in r.json() if c["id"] == cert_id)
+    assert row["status"] == "pending"
+    assert row["subject"] == "certtest.example.ms"
+
+    # Signing requires a physical YubiKey; must fail cleanly, not 500-crash.
+    r = client.post(f"/api/certs/{cert_id}/sign", headers=auth)
+    assert r.status_code == 500
+
+
+def test_sign_missing_cert(client, auth):
+    assert client.post("/api/certs/99999/sign", headers=auth).status_code == 400

tests/test_auth.py

@@ -0,0 +1,32 @@
+"""JWT auth unit tests."""
+
+from datetime import timedelta
+
+import pytest
+from fastapi import HTTPException
+
+from auth import create_access_token, get_current_user
+
+
+def test_token_roundtrip():
+    token = create_access_token({"sub": "certauth"})
+    assert get_current_user(token) == "certauth"
+
+
+def test_rejects_garbage_token():
+    with pytest.raises(HTTPException) as exc:
+        get_current_user("not-a-jwt")
+    assert exc.value.status_code == 401
+
+
+def test_rejects_expired_token():
+    token = create_access_token({"sub": "certauth"}, expires_delta=timedelta(minutes=-5))
+    with pytest.raises(HTTPException) as exc:
+        get_current_user(token)
+    assert exc.value.status_code == 401
+
+
+def test_rejects_token_without_subject():
+    token = create_access_token({"other": "claim"})
+    with pytest.raises(HTTPException):
+        get_current_user(token)

tests/test_models.py

@@ -0,0 +1,22 @@
+"""Password hashing tests."""
+
+from models import hash_password, verify_password
+
+
+def test_hash_and_verify():
+    h = hash_password("s3cure-Passw0rd!")
+    assert verify_password("s3cure-Passw0rd!", h)
+
+
+def test_wrong_password_rejected():
+    h = hash_password("s3cure-Passw0rd!")
+    assert not verify_password("wrong-password", h)
+
+
+def test_hashes_are_unique():
+    assert hash_password("same-pass") != hash_password("same-pass")
+
+
+def test_accepts_bytes_hash():
+    h = hash_password("s3cure-Passw0rd!")
+    assert verify_password("s3cure-Passw0rd!", h.encode())

tests/test_signing.py

@@ -0,0 +1,55 @@
+"""DER helpers and signing pipeline (no YubiKey required)."""
+
+from datetime import datetime, timedelta, timezone
+
+from cryptography import x509
+from cryptography.hazmat.primitives import hashes
+from cryptography.hazmat.primitives.asymmetric import ec
+from cryptography.x509.oid import NameOID
+
+from signing import _der_read_len, _der_seq, _split_cert_der
+
+
+from cryptography.hazmat.primitives.serialization import Encoding
+
+
+def _dummy_cert_der():
+    key = ec.generate_private_key(ec.SECP384R1())
+    name = x509.Name([x509.NameAttribute(NameOID.COMMON_NAME, "dummy.test")])
+    cert = (
+        x509.CertificateBuilder()
+        .subject_name(name)
+        .issuer_name(name)
+        .public_key(key.public_key())
+        .serial_number(x509.random_serial_number())
+        .not_valid_before(datetime.now(timezone.utc))
+        .not_valid_after(datetime.now(timezone.utc) + timedelta(days=1))
+        .sign(key, hashes.SHA384())
+    )
+    return cert.public_bytes(Encoding.DER)
+
+
+def test_split_roundtrip():
+    der = _dummy_cert_der()
+    tbs, alg, sig = _split_cert_der(der)
+    assert alg[0] == 0x30
+    assert sig[0] == 0x03
+    # Reassembling the same parts reproduces the original certificate.
+    reassembled = _der_seq(tbs + alg + sig)
+    assert reassembled == der
+
+
+def test_der_read_len_short_and_long():
+    assert _der_read_len(b"\x05ABC", 0) == (5, 1)
+    long_len = b"\x81\x10"
+    assert _der_read_len(long_len + b"A" * 16, 0) == (16, 2)
+
+
+def test_build_leaf_cert_fails_cleanly_without_ca():
+    """Without the CA files the pipeline fails cleanly (no YubiKey available)."""
+    import pytest
+
+    from signing import build_leaf_cert
+
+    with pytest.raises(FileNotFoundError):
+        build_leaf_cert("nope.test", "", 365)