Add integration test for autobuild truststore merging (github/codeql-team#4482)

java/ql/integration-tests/java/buildless-inherit-trust-store/test.autobuild.expected

@@ -0,0 +1,4 @@
+diagnostics
+| file://:0:0:0:0 | Appending source destination directory target/generated-sources/annotations to sourcepath |
+#select
+| DepClass |

java/ql/integration-tests/java/buildless-inherit-trust-store/test.py

@@ -1,21 +1,45 @@
+"""
+Integration tests for truststore inheritance and merging.
+
+Tests that CodeQL can connect to HTTPS servers with custom CA certificates:
+1. test_buildless: Buildless mode inherits truststore from MAVEN_OPTS
+2. test_autobuild_merge_trust_store: Autobuild merges system truststore with
+   CODEQL_PROXY_CA_CERTIFICATE (fixes github/codeql-team#4482)
+"""
 import subprocess
 import os
+import pytest
 import runs_on
+from contextlib import contextmanager
 
 
-def test(codeql, java, cwd):
-    # This serves the "repo" directory on https://locahost:4443
+@contextmanager
+def _https_server(cwd):
+    """Start an HTTPS server serving the repo/ directory on https://localhost:4443."""
     command = ["python3", "../server.py"]
     if runs_on.github_actions and runs_on.posix:
         # On GitHub Actions, we saw the server timing out while running in parallel with other tests
         # we work around that by running it with higher permissions
         command = ["sudo"] + command
     repo_server_process = subprocess.Popen(command, cwd="repo")
-    certspath = cwd / "jdk8_shipped_cacerts_plus_cert_pem"
-    # If we override MAVEN_OPTS, we'll break cross-test maven isolation, so we need to append to it instead
-    maven_opts = os.environ["MAVEN_OPTS"] + f" -Djavax.net.ssl.trustStore={certspath}"
-
     try:
+        yield
+    finally:
+        repo_server_process.kill()
+
+
+@pytest.mark.ql_test(expected=".buildless.expected")
+def test_buildless(codeql, java, cwd, check_diagnostics, check_buildless_fetches):
+    """Test that buildless mode inherits truststore from MAVEN_OPTS."""
+    # Use buildless-specific expected file suffixes
+    check_diagnostics.expected_suffix = ".buildless.expected"
+    check_buildless_fetches.expected_suffix = ".buildless.expected"
+
+    with _https_server(cwd):
+        certspath = cwd / "jdk8_shipped_cacerts_plus_cert_pem"
+        # If we override MAVEN_OPTS, we'll break cross-test maven isolation, so we need to append to it instead
+        maven_opts = os.environ["MAVEN_OPTS"] + f" -Djavax.net.ssl.trustStore={certspath}"
+
         codeql.database.create(
             extractor_option="buildless=true",
             _env={
@@ -23,5 +47,39 @@ def test(codeql, java, cwd):
                 "CODEQL_JAVA_EXTRACTOR_TRUST_STORE_PATH": str(certspath),
             },
         )
-    finally:
-        repo_server_process.kill()
+
+
+@pytest.mark.ql_test(expected=".autobuild.expected")
+def test_autobuild_merge_trust_store(codeql, java, cwd, check_diagnostics):
+    """
+    Test that autobuild merges system truststore with CODEQL_PROXY_CA_CERTIFICATE.
+
+    This tests the fix for github/codeql-team#4482 where autobuild was overriding
+    JAVA_TOOL_OPTIONS truststore with a new one containing only the proxy CA,
+    causing PKIX failures when connecting to internal HTTPS servers.
+    """
+    # Use autobuild-specific expected file suffix
+    check_diagnostics.expected_suffix = ".autobuild.expected"
+
+    with _https_server(cwd):
+        certspath = cwd / "jdk8_shipped_cacerts_plus_cert_pem"
+
+        # Read the certificate to use as CODEQL_PROXY_CA_CERTIFICATE
+        with open(cwd / "cert.pem", "r") as f:
+            proxy_ca_cert = f.read()
+
+        # Set JAVA_TOOL_OPTIONS to use our custom truststore
+        # This is the key setting that was being overridden before the fix
+        java_tool_options = f"-Djavax.net.ssl.trustStore={certspath}"
+
+        # Run autobuild with the truststore configured
+        # Before the fix: autobuild would create a new truststore with ONLY the proxy CA,
+        #                 losing the custom CA from JAVA_TOOL_OPTIONS, causing PKIX failures
+        # After the fix:  autobuild merges the system truststore + proxy CA
+        codeql.database.create(
+            build_mode="autobuild",
+            _env={
+                "JAVA_TOOL_OPTIONS": java_tool_options,
+                "CODEQL_PROXY_CA_CERTIFICATE": proxy_ca_cert,
+            },
+        )