Merge branch 'main' into santander-java-crypto-check

2025-12-16 16:53:25 +01:00 · 2025-10-18 17:56:43 -04:00
parent c01c060476 66f95bcbcd
commit 2b683c210f
415 changed files with 13870 additions and 1146 deletions
--- a/java/ql/integration-tests/java/buildless-dependency-different-repository/test.py
+++ b/java/ql/integration-tests/java/buildless-dependency-different-repository/test.py
@@ -1,12 +1,29 @@
 import subprocess
 import logging
+import time
+import socket
+
+
+def wait_for_port(port, process, timeout=100):
+    start = time.time()
+    while time.time() - start < timeout:
+        # Check if process died
+        if process.poll() is not None:
+            raise RuntimeError(f"Server process exited with code {process.returncode}")
+        try:
+            with socket.create_connection(("localhost", port), timeout=1):
+                return True
+        except (socket.timeout, ConnectionRefusedError, OSError):
+            time.sleep(0.2)
+    raise RuntimeError(f"Port {port} not ready within {timeout}s")


 def test(codeql, java):
-    # Each of these serves the "repo" and "repo2" directories on http://localhost:924[89]
-    repo_server_process = subprocess.Popen(["python3", "-m", "http.server", "9428", "-b", "localhost"], cwd="repo")
-    repo_server_process2 = subprocess.Popen(["python3", "-m", "http.server", "9429", "-b", "localhost"], cwd="repo2")
+    repo_server_process = subprocess.Popen(["python3", "-m", "http.server", "9428", "-b", "localhost"], cwd="repo", stderr=subprocess.PIPE, stdout=subprocess.PIPE)
+    repo_server_process2 = subprocess.Popen(["python3", "-m", "http.server", "9429", "-b", "localhost"], cwd="repo2", stderr=subprocess.PIPE, stdout=subprocess.PIPE)
    try:
+        wait_for_port(9428, repo_server_process)
+        wait_for_port(9429, repo_server_process2)
        codeql.database.create(
            extractor_option="buildless=true",
            _env={"CODEQL_EXTRACTOR_JAVA_OPTION_BUILDLESS_CLASSPATH_FROM_BUILD_FILES": "true"},
--- a/java/ql/integration-tests/java/query-suite/java-code-scanning.qls.expected
+++ b/java/ql/integration-tests/java/query-suite/java-code-scanning.qls.expected
@@ -21,6 +21,7 @@ ql/java/ql/src/Security/CWE/CWE-094/JexlInjection.ql
 ql/java/ql/src/Security/CWE/CWE-094/MvelInjection.ql
 ql/java/ql/src/Security/CWE/CWE-094/SpelInjection.ql
 ql/java/ql/src/Security/CWE/CWE-094/TemplateInjection.ql
+ql/java/ql/src/Security/CWE/CWE-1004/SensitiveCookieNotHttpOnly.ql
 ql/java/ql/src/Security/CWE/CWE-1104/MavenPomDependsOnBintray.ql
 ql/java/ql/src/Security/CWE/CWE-113/NettyResponseSplitting.ql
 ql/java/ql/src/Security/CWE/CWE-113/ResponseSplitting.ql
--- a/java/ql/integration-tests/java/query-suite/java-security-and-quality.qls.expected
+++ b/java/ql/integration-tests/java/query-suite/java-security-and-quality.qls.expected
@@ -127,6 +127,7 @@ ql/java/ql/src/Security/CWE/CWE-094/JexlInjection.ql
 ql/java/ql/src/Security/CWE/CWE-094/MvelInjection.ql
 ql/java/ql/src/Security/CWE/CWE-094/SpelInjection.ql
 ql/java/ql/src/Security/CWE/CWE-094/TemplateInjection.ql
+ql/java/ql/src/Security/CWE/CWE-1004/SensitiveCookieNotHttpOnly.ql
 ql/java/ql/src/Security/CWE/CWE-1104/MavenPomDependsOnBintray.ql
 ql/java/ql/src/Security/CWE/CWE-113/NettyResponseSplitting.ql
 ql/java/ql/src/Security/CWE/CWE-113/ResponseSplitting.ql
--- a/java/ql/integration-tests/java/query-suite/java-security-extended.qls.expected
+++ b/java/ql/integration-tests/java/query-suite/java-security-extended.qls.expected
@@ -30,6 +30,7 @@ ql/java/ql/src/Security/CWE/CWE-094/JexlInjection.ql
 ql/java/ql/src/Security/CWE/CWE-094/MvelInjection.ql
 ql/java/ql/src/Security/CWE/CWE-094/SpelInjection.ql
 ql/java/ql/src/Security/CWE/CWE-094/TemplateInjection.ql
+ql/java/ql/src/Security/CWE/CWE-1004/SensitiveCookieNotHttpOnly.ql
 ql/java/ql/src/Security/CWE/CWE-1104/MavenPomDependsOnBintray.ql
 ql/java/ql/src/Security/CWE/CWE-113/NettyResponseSplitting.ql
 ql/java/ql/src/Security/CWE/CWE-113/ResponseSplitting.ql
--- a/java/ql/integration-tests/java/query-suite/not_included_in_qls.expected
+++ b/java/ql/integration-tests/java/query-suite/not_included_in_qls.expected
@@ -190,7 +190,6 @@ ql/java/ql/src/experimental/Security/CWE/CWE-094/ScriptInjection.ql
 ql/java/ql/src/experimental/Security/CWE/CWE-094/SpringImplicitViewManipulation.ql
 ql/java/ql/src/experimental/Security/CWE/CWE-094/SpringViewManipulation.ql
 ql/java/ql/src/experimental/Security/CWE/CWE-1004/InsecureTomcatConfig.ql
-ql/java/ql/src/experimental/Security/CWE/CWE-1004/SensitiveCookieNotHttpOnly.ql
 ql/java/ql/src/experimental/Security/CWE/CWE-200/InsecureWebResourceResponse.ql
 ql/java/ql/src/experimental/Security/CWE/CWE-200/SensitiveAndroidFileLeak.ql
 ql/java/ql/src/experimental/Security/CWE/CWE-208/PossibleTimingAttackAgainstSignature.ql
--- a/java/ql/lib/CHANGELOG.md
+++ b/java/ql/lib/CHANGELOG.md
@@ -1,3 +1,9 @@
+## 7.7.2
+
+### Minor Analysis Improvements
+
+* Fields of certain objects are considered tainted if the object is tainted. This holds, for example, for objects that occur directly as sources in the active threat model (for instance, a remote flow source). This has now been amended to also include array types, such that if an array like `MyPojo[]` is a source, then fields of a tainted `MyPojo` are now also considered tainted.
+
 ## 7.7.1

 No user-facing changes.
--- a/java/ql/lib/change-notes/2025-10-07-array-entrypointtype.md
+++ b/java/ql/lib/change-notes/2025-10-07-array-entrypointtype.md
@@ -1,4 +1,5 @@
---
-category: minorAnalysis
---
+## 7.7.2
+
+### Minor Analysis Improvements
+
 * Fields of certain objects are considered tainted if the object is tainted. This holds, for example, for objects that occur directly as sources in the active threat model (for instance, a remote flow source). This has now been amended to also include array types, such that if an array like `MyPojo[]` is a source, then fields of a tainted `MyPojo` are now also considered tainted.
--- a/java/ql/lib/codeql-pack.release.yml
+++ b/java/ql/lib/codeql-pack.release.yml
@@ -1,2 +1,2 @@
 ---
-lastReleaseVersion: 7.7.1
+lastReleaseVersion: 7.7.2
--- a/java/ql/lib/qlpack.yml
+++ b/java/ql/lib/qlpack.yml
@@ -1,5 +1,5 @@
 name: codeql/java-all
-version: 7.7.2-dev
+version: 7.7.3-dev
 groups: java
 dbscheme: config/semmlecode.dbscheme
 extractor: java
--- a/java/ql/src/CHANGELOG.md
+++ b/java/ql/src/CHANGELOG.md
@@ -1,3 +1,7 @@
+## 1.8.2
+
+No user-facing changes.
+
 ## 1.8.1

 No user-facing changes.
--- a/java/ql/src/experimental/Security/CWE/CWE-1004/SensitiveCookieNotHttpOnly.java
+++ b/java/ql/src/experimental/Security/CWE/CWE-1004/SensitiveCookieNotHttpOnly.java
--- a/java/ql/src/experimental/Security/CWE/CWE-1004/SensitiveCookieNotHttpOnly.qhelp
+++ b/java/ql/src/experimental/Security/CWE/CWE-1004/SensitiveCookieNotHttpOnly.qhelp
@@ -2,11 +2,13 @@
 <qhelp>

  <overview>
-    <p>Cross-Site Scripting (XSS) is categorized as one of the OWASP Top 10 Security Vulnerabilities. The <code>HttpOnly</code> flag directs compatible browsers to prevent client-side script from accessing cookies. Including the <code>HttpOnly</code> flag in the Set-Cookie HTTP response header for a sensitive cookie helps mitigate the risk associated with XSS where an attacker's script code attempts to read the contents of a cookie and exfiltrate information obtained.</p>
+    <p>Cookies without the <code>HttpOnly</code> flag set are accessible to client-side scripts (such as JavaScript) running in the same origin. 
+In case of a Cross-Site Scripting (XSS) vulnerability, the cookie can be stolen by a malicious script.
+If a sensitive cookie does not need to be accessed directly by client-side scripts, the <code>HttpOnly</code> flag should be set.</p>
  </overview>

  <recommendation>
-    <p>Use the <code>HttpOnly</code> flag when generating a cookie containing sensitive information to help mitigate the risk of client side script accessing the protected cookie.</p>
+    <p>Use the <code>HttpOnly</code> flag when generating a cookie containing sensitive information to help mitigate the risk of client-side scripts accessing the protected cookie.</p>
  </recommendation>

  <example>
@@ -23,5 +25,6 @@
      OWASP:
      <a href="https://owasp.org/www-community/HttpOnly">HttpOnly</a>
    </li>
+    <li>MDN: <a href="https://developer.mozilla.org/en-US/docs/Web/HTTP/Reference/Headers/Set-Cookie#httponly">Set-Cookie HttpOnly</a>.</li>
  </references>
 </qhelp>
--- a/java/ql/src/experimental/Security/CWE/CWE-1004/SensitiveCookieNotHttpOnly.ql
+++ b/java/ql/src/experimental/Security/CWE/CWE-1004/SensitiveCookieNotHttpOnly.ql
@@ -1,13 +1,13 @@
 /**
 * @name Sensitive cookies without the HttpOnly response header set
- * @description Sensitive cookies without the 'HttpOnly' flag set leaves session cookies vulnerable to
+ * @description A sensitive cookie without the 'HttpOnly' flag set may be vulnerable to
 *              an XSS attack.
 * @kind path-problem
 * @problem.severity warning
- * @precision medium
+ * @precision high
+ * @security-severity 5.0
 * @id java/sensitive-cookie-not-httponly
 * @tags security
- *       experimental
 *       external/cwe/cwe-1004
 */

@@ -15,16 +15,15 @@
 * Sketch of the structure of this query: we track cookie names that appear to be sensitive
 * (e.g. `session` or `token`) to a `ServletResponse.addHeader(...)` or `.addCookie(...)`
 * method that does not set the `httpOnly` flag. Subsidiary configurations
- * `MatchesHttpOnlyConfiguration` and `SetHttpOnlyInCookieConfiguration` are used to establish
+ * `MatchesHttpOnlyToRawHeaderConfig` and `SetHttpOnlyInCookieConfig` are used to establish
 * when the `httpOnly` flag is likely to have been set, before configuration
- * `MissingHttpOnlyConfiguration` establishes that a non-`httpOnly` cookie has a sensitive-seeming name.
+ * `MissingHttpOnlyConfig` establishes that a non-`httpOnly` cookie has a sensitive-seeming name.
 */

 import java
 import semmle.code.java.dataflow.FlowSteps
 import semmle.code.java.frameworks.Servlets
 import semmle.code.java.dataflow.TaintTracking
-import MissingHttpOnlyFlow::PathGraph

 /** Gets a regular expression for matching common names of sensitive cookies. */
 string getSensitiveCookieNameRegex() { result = "(?i).*(auth|session|token|key|credential).*" }
@@ -50,8 +49,8 @@ class SensitiveCookieNameExpr extends Expr {
 }

 /** A method call that sets a `Set-Cookie` header. */
-class SetCookieMethodCall extends MethodCall {
-  SetCookieMethodCall() {
+class SetCookieRawHeaderMethodCall extends MethodCall {
+  SetCookieRawHeaderMethodCall() {
    (
      this.getMethod() instanceof ResponseAddHeaderMethod or
      this.getMethod() instanceof ResponseSetHeaderMethod
@@ -62,19 +61,19 @@ class SetCookieMethodCall extends MethodCall {

 /**
 * A taint configuration tracking flow from the text `httponly` to argument 1 of
- * `SetCookieMethodCall`.
+ * `SetCookieRawHeaderMethodCall`.
 */
-module MatchesHttpOnlyConfig implements DataFlow::ConfigSig {
+module MatchesHttpOnlyToRawHeaderConfig implements DataFlow::ConfigSig {
  predicate isSource(DataFlow::Node source) {
    source.asExpr().(CompileTimeConstantExpr).getStringValue().toLowerCase().matches("%httponly%")
  }

  predicate isSink(DataFlow::Node sink) {
-    sink.asExpr() = any(SetCookieMethodCall ma).getArgument(1)
+    sink.asExpr() = any(SetCookieRawHeaderMethodCall ma).getArgument(1)
  }
 }

-module MatchesHttpOnlyFlow = TaintTracking::Global<MatchesHttpOnlyConfig>;
+module MatchesHttpOnlyToRawHeaderFlow = TaintTracking::Global<MatchesHttpOnlyToRawHeaderConfig>;

 /** A class descended from `javax.servlet.http.Cookie`. */
 class CookieClass extends RefType {
@@ -103,29 +102,11 @@ predicate removesCookie(MethodCall ma) {
 }

 /**
- * Holds if the MethodCall `ma` is a test method call indicated by:
- *    a) in a test directory such as `src/test/java`
- *    b) in a test package whose name has the word `test`
- *    c) in a test class whose name has the word `test`
- *    d) in a test class implementing a test framework such as JUnit or TestNG
+ * A taint configuration tracking the flow of a cookie that has had the
+ * `HttpOnly` flag set, or has been removed, to a `ServletResponse.addCookie`
+ * call.
 */
-predicate isTestMethod(MethodCall ma) {
-  exists(Method m |
-    m = ma.getEnclosingCallable() and
-    (
-      m.getDeclaringType().getName().toLowerCase().matches("%test%") or // Simple check to exclude test classes to reduce FPs
-      m.getDeclaringType().getPackage().getName().toLowerCase().matches("%test%") or // Simple check to exclude classes in test packages to reduce FPs
-      exists(m.getLocation().getFile().getAbsolutePath().indexOf("/src/test/java")) or //  Match test directory structure of build tools like maven
-      m instanceof TestMethod // Test method of a test case implementing a test framework such as JUnit or TestNG
-    )
-  )
-}
-
-/**
- * A taint configuration tracking flow of a method that sets the `HttpOnly` flag,
- * or one that removes a cookie, to a `ServletResponse.addCookie` call.
- */
-module SetHttpOnlyOrRemovesCookieConfig implements DataFlow::ConfigSig {
+module SetHttpOnlyOrRemovesCookieToAddCookieConfig implements DataFlow::ConfigSig {
  predicate isSource(DataFlow::Node source) {
    source.asExpr() =
      any(MethodCall ma | setsCookieHttpOnly(ma) or removesCookie(ma)).getQualifier()
@@ -137,25 +118,25 @@ module SetHttpOnlyOrRemovesCookieConfig implements DataFlow::ConfigSig {
  }
 }

-module SetHttpOnlyOrRemovesCookieFlow = TaintTracking::Global<SetHttpOnlyOrRemovesCookieConfig>;
+module SetHttpOnlyOrRemovesCookieToAddCookieFlow =
+  TaintTracking::Global<SetHttpOnlyOrRemovesCookieToAddCookieConfig>;

 /**
- * A cookie that is added to an HTTP response and which doesn't have `httpOnly` set, used as a sink
- * in `MissingHttpOnlyConfiguration`.
+ * A cookie that is added to an HTTP response and which doesn't have `HttpOnly` set, used as a sink
+ * in `MissingHttpOnlyConfig`.
 */
-class CookieResponseSink extends DataFlow::ExprNode {
-  CookieResponseSink() {
+class CookieResponseWithoutHttpOnlySink extends DataFlow::ExprNode {
+  CookieResponseWithoutHttpOnlySink() {
    exists(MethodCall ma |
      (
        ma.getMethod() instanceof ResponseAddCookieMethod and
        this.getExpr() = ma.getArgument(0) and
-        not SetHttpOnlyOrRemovesCookieFlow::flowTo(this)
+        not SetHttpOnlyOrRemovesCookieToAddCookieFlow::flowTo(this)
        or
-        ma instanceof SetCookieMethodCall and
+        ma instanceof SetCookieRawHeaderMethodCall and
        this.getExpr() = ma.getArgument(1) and
-        not MatchesHttpOnlyFlow::flowTo(this) // response.addHeader("Set-Cookie", "token=" +authId + ";HttpOnly;Secure")
-      ) and
-      not isTestMethod(ma) // Test class or method
+        not MatchesHttpOnlyToRawHeaderFlow::flowTo(this) // response.addHeader("Set-Cookie", "token=" +authId + ";HttpOnly;Secure")
+      )
    )
  }
 }
@@ -178,15 +159,21 @@ predicate setsHttpOnlyInNewCookie(ClassInstanceExpr cie) {

 /**
 * A taint configuration tracking flow from a sensitive cookie without the `HttpOnly` flag
- * set to its HTTP response.
+ * set to an HTTP response.
+ *
+ * Tracks string literals containing sensitive names (`SensitiveCookieNameExpr`), to an `addCookie` call (as a `Cookie` object)
+ * or an `addHeader` call (as a string) (`CookieResponseWithoutHttpOnlySink`).
+ *
+ * Passes through `Cookie` constructors and `toString` calls.
 */
 module MissingHttpOnlyConfig implements DataFlow::ConfigSig {
  predicate isSource(DataFlow::Node source) { source.asExpr() instanceof SensitiveCookieNameExpr }

-  predicate isSink(DataFlow::Node sink) { sink instanceof CookieResponseSink }
+  predicate isSink(DataFlow::Node sink) { sink instanceof CookieResponseWithoutHttpOnlySink }

  predicate isBarrier(DataFlow::Node node) {
    // JAX-RS's `new NewCookie("session-access-key", accessKey, "/", null, null, 0, true, true)` and similar
+    // Cookie constructors that set the `HttpOnly` flag are considered barriers to the flow of sensitive names.
    setsHttpOnlyInNewCookie(node.asExpr())
  }

@@ -212,13 +199,8 @@ module MissingHttpOnlyConfig implements DataFlow::ConfigSig {

 module MissingHttpOnlyFlow = TaintTracking::Global<MissingHttpOnlyConfig>;

-deprecated query predicate problems(
-  DataFlow::Node sinkNode, MissingHttpOnlyFlow::PathNode source, MissingHttpOnlyFlow::PathNode sink,
-  string message1, DataFlow::Node sourceNode, string message2
-) {
-  MissingHttpOnlyFlow::flowPath(source, sink) and
-  sinkNode = sink.getNode() and
-  message1 = "$@ doesn't have the HttpOnly flag set." and
-  sourceNode = source.getNode() and
-  message2 = "This sensitive cookie"
-}
+import MissingHttpOnlyFlow::PathGraph
+
+from MissingHttpOnlyFlow::PathNode source, MissingHttpOnlyFlow::PathNode sink
+where MissingHttpOnlyFlow::flowPath(source, sink)
+select sink, source, sink, "$@ doesn't have the HttpOnly flag set.", source, "This sensitive cookie"
--- a/java/ql/src/Security/CWE/CWE-327/BrokenCryptoAlgorithm.qhelp
+++ b/java/ql/src/Security/CWE/CWE-327/BrokenCryptoAlgorithm.qhelp
@@ -3,11 +3,15 @@
  "qhelp.dtd">
 <qhelp>
 <overview>
-<p>Using broken or weak cryptographic algorithms can leave data vulnerable to being decrypted.</p>
+<p>Using broken or weak cryptographic algorithms may compromise security guarantees such as confidentiality, integrity, and authenticity.</p>

-<p>Many cryptographic algorithms provided by cryptography libraries are known to be weak, or 
-flawed. Using such an algorithm means that an attacker may be able to easily decrypt the encrypted
-data.</p>
+<p>Many cryptographic algorithms are known to be weak or flawed. The security guarantees of a system often rely on the underlying cryptography, so using a weak algorithm can have severe consequences. For example:
+</p>
+<ul>
+  <li>If a weak encryption algorithm is used, an attacker may be able to decrypt sensitive data.</li>
+  <li>If a weak hashing algorithm is used to protect data integrity, an attacker may be able to craft a malicious input that has the same hash as a benign one.</li>
+  <li>If a weak algorithm is used for digital signatures, an attacker may be able to forge signatures and impersonate legitimate users.</li>
+</ul>

 </overview>
 <recommendation>
--- a/java/ql/src/change-notes/2025-10-02-http-only-cookie-promote.md
+++ b/java/ql/src/change-notes/2025-10-02-http-only-cookie-promote.md
@@ -0,0 +1,4 @@
+---
+category: newQuery
+---
+* The `java/sensitive-cookie-not-httponly` query has been promoted from experimental to the main query pack.
--- a/java/ql/src/change-notes/released/1.8.2.md
+++ b/java/ql/src/change-notes/released/1.8.2.md
@@ -0,0 +1,3 @@
+## 1.8.2
+
+No user-facing changes.
--- a/java/ql/src/codeql-pack.release.yml
+++ b/java/ql/src/codeql-pack.release.yml
@@ -1,2 +1,2 @@
 ---
-lastReleaseVersion: 1.8.1
+lastReleaseVersion: 1.8.2
--- a/java/ql/src/qlpack.yml
+++ b/java/ql/src/qlpack.yml
@@ -1,5 +1,5 @@
 name: codeql/java-queries
-version: 1.8.2-dev
+version: 1.8.3-dev
 groups:
  - java
  - queries
--- a/java/ql/test/experimental/query-tests/security/CWE-1004/SensitiveCookieNotHttpOnly.qlref
+++ b/java/ql/test/experimental/query-tests/security/CWE-1004/SensitiveCookieNotHttpOnly.qlref
@@ -1,2 +0,0 @@
-query: experimental/Security/CWE/CWE-1004/SensitiveCookieNotHttpOnly.ql
-postprocess: utils/test/PrettyPrintModels.ql
--- a/java/ql/test/experimental/query-tests/security/CWE-1004/options
+++ b/java/ql/test/experimental/query-tests/security/CWE-1004/options
@@ -1 +0,0 @@
-// semmle-extractor-options: --javac-args -cp ${testdir}/../../../../stubs/servlet-api-2.4:${testdir}/../../../../stubs/jsr311-api-1.1.1:${testdir}/../../../../stubs/springframework-5.8.x
--- a/java/ql/test/experimental/query-tests/security/CWE-1004/SensitiveCookieNotHttpOnly.expected
+++ b/java/ql/test/experimental/query-tests/security/CWE-1004/SensitiveCookieNotHttpOnly.expected
@@ -1,3 +1,14 @@
+#select
+| SensitiveCookieNotHttpOnly.java:31:28:31:36 | jwtCookie | SensitiveCookieNotHttpOnly.java:24:33:24:43 | "jwt_token" : String | SensitiveCookieNotHttpOnly.java:31:28:31:36 | jwtCookie | $@ doesn't have the HttpOnly flag set. | SensitiveCookieNotHttpOnly.java:24:33:24:43 | "jwt_token" : String | This sensitive cookie |
+| SensitiveCookieNotHttpOnly.java:42:42:42:69 | ... + ... | SensitiveCookieNotHttpOnly.java:42:42:42:49 | "token=" : String | SensitiveCookieNotHttpOnly.java:42:42:42:69 | ... + ... | $@ doesn't have the HttpOnly flag set. | SensitiveCookieNotHttpOnly.java:42:42:42:49 | "token=" : String | This sensitive cookie |
+| SensitiveCookieNotHttpOnly.java:42:42:42:69 | ... + ... | SensitiveCookieNotHttpOnly.java:42:42:42:57 | ... + ... : String | SensitiveCookieNotHttpOnly.java:42:42:42:69 | ... + ... | $@ doesn't have the HttpOnly flag set. | SensitiveCookieNotHttpOnly.java:42:42:42:57 | ... + ... : String | This sensitive cookie |
+| SensitiveCookieNotHttpOnly.java:42:42:42:69 | ... + ... | SensitiveCookieNotHttpOnly.java:42:42:42:69 | ... + ... | SensitiveCookieNotHttpOnly.java:42:42:42:69 | ... + ... | $@ doesn't have the HttpOnly flag set. | SensitiveCookieNotHttpOnly.java:42:42:42:69 | ... + ... | This sensitive cookie |
+| SensitiveCookieNotHttpOnly.java:52:42:52:124 | toString(...) | SensitiveCookieNotHttpOnly.java:52:56:52:75 | "session-access-key" : String | SensitiveCookieNotHttpOnly.java:52:42:52:124 | toString(...) | $@ doesn't have the HttpOnly flag set. | SensitiveCookieNotHttpOnly.java:52:56:52:75 | "session-access-key" : String | This sensitive cookie |
+| SensitiveCookieNotHttpOnly.java:65:42:65:47 | keyStr | SensitiveCookieNotHttpOnly.java:63:51:63:70 | "session-access-key" : String | SensitiveCookieNotHttpOnly.java:65:42:65:47 | keyStr | $@ doesn't have the HttpOnly flag set. | SensitiveCookieNotHttpOnly.java:63:51:63:70 | "session-access-key" : String | This sensitive cookie |
+| SensitiveCookieNotHttpOnly.java:71:42:71:50 | secString | SensitiveCookieNotHttpOnly.java:70:28:70:35 | "token=" : String | SensitiveCookieNotHttpOnly.java:71:42:71:50 | secString | $@ doesn't have the HttpOnly flag set. | SensitiveCookieNotHttpOnly.java:70:28:70:35 | "token=" : String | This sensitive cookie |
+| SensitiveCookieNotHttpOnly.java:71:42:71:50 | secString | SensitiveCookieNotHttpOnly.java:70:28:70:43 | ... + ... : String | SensitiveCookieNotHttpOnly.java:71:42:71:50 | secString | $@ doesn't have the HttpOnly flag set. | SensitiveCookieNotHttpOnly.java:70:28:70:43 | ... + ... : String | This sensitive cookie |
+| SensitiveCookieNotHttpOnly.java:71:42:71:50 | secString | SensitiveCookieNotHttpOnly.java:70:28:70:55 | ... + ... : String | SensitiveCookieNotHttpOnly.java:71:42:71:50 | secString | $@ doesn't have the HttpOnly flag set. | SensitiveCookieNotHttpOnly.java:70:28:70:55 | ... + ... : String | This sensitive cookie |
+| SensitiveCookieNotHttpOnly.java:111:28:111:33 | cookie | SensitiveCookieNotHttpOnly.java:88:35:88:51 | "Presto-UI-Token" : String | SensitiveCookieNotHttpOnly.java:111:28:111:33 | cookie | $@ doesn't have the HttpOnly flag set. | SensitiveCookieNotHttpOnly.java:88:35:88:51 | "Presto-UI-Token" : String | This sensitive cookie |
 edges
 | SensitiveCookieNotHttpOnly.java:24:33:24:43 | "jwt_token" : String | SensitiveCookieNotHttpOnly.java:25:39:25:52 | tokenCookieStr : String | provenance |  |
 | SensitiveCookieNotHttpOnly.java:25:28:25:64 | new Cookie(...) : Cookie | SensitiveCookieNotHttpOnly.java:31:28:31:36 | jwtCookie | provenance | Sink:MaD:1 |
@@ -53,15 +64,4 @@ nodes
 | SensitiveCookieNotHttpOnly.java:91:16:91:21 | cookie : Cookie | semmle.label | cookie : Cookie |
 | SensitiveCookieNotHttpOnly.java:110:25:110:64 | createAuthenticationCookie(...) : Cookie | semmle.label | createAuthenticationCookie(...) : Cookie |
 | SensitiveCookieNotHttpOnly.java:111:28:111:33 | cookie | semmle.label | cookie |
-problems
-| SensitiveCookieNotHttpOnly.java:31:28:31:36 | jwtCookie | SensitiveCookieNotHttpOnly.java:24:33:24:43 | "jwt_token" : String | SensitiveCookieNotHttpOnly.java:31:28:31:36 | jwtCookie | $@ doesn't have the HttpOnly flag set. | SensitiveCookieNotHttpOnly.java:24:33:24:43 | "jwt_token" | This sensitive cookie |
-| SensitiveCookieNotHttpOnly.java:42:42:42:69 | ... + ... | SensitiveCookieNotHttpOnly.java:42:42:42:49 | "token=" : String | SensitiveCookieNotHttpOnly.java:42:42:42:69 | ... + ... | $@ doesn't have the HttpOnly flag set. | SensitiveCookieNotHttpOnly.java:42:42:42:49 | "token=" | This sensitive cookie |
-| SensitiveCookieNotHttpOnly.java:42:42:42:69 | ... + ... | SensitiveCookieNotHttpOnly.java:42:42:42:57 | ... + ... : String | SensitiveCookieNotHttpOnly.java:42:42:42:69 | ... + ... | $@ doesn't have the HttpOnly flag set. | SensitiveCookieNotHttpOnly.java:42:42:42:57 | ... + ... | This sensitive cookie |
-| SensitiveCookieNotHttpOnly.java:42:42:42:69 | ... + ... | SensitiveCookieNotHttpOnly.java:42:42:42:69 | ... + ... | SensitiveCookieNotHttpOnly.java:42:42:42:69 | ... + ... | $@ doesn't have the HttpOnly flag set. | SensitiveCookieNotHttpOnly.java:42:42:42:69 | ... + ... | This sensitive cookie |
-| SensitiveCookieNotHttpOnly.java:52:42:52:124 | toString(...) | SensitiveCookieNotHttpOnly.java:52:56:52:75 | "session-access-key" : String | SensitiveCookieNotHttpOnly.java:52:42:52:124 | toString(...) | $@ doesn't have the HttpOnly flag set. | SensitiveCookieNotHttpOnly.java:52:56:52:75 | "session-access-key" | This sensitive cookie |
-| SensitiveCookieNotHttpOnly.java:65:42:65:47 | keyStr | SensitiveCookieNotHttpOnly.java:63:51:63:70 | "session-access-key" : String | SensitiveCookieNotHttpOnly.java:65:42:65:47 | keyStr | $@ doesn't have the HttpOnly flag set. | SensitiveCookieNotHttpOnly.java:63:51:63:70 | "session-access-key" | This sensitive cookie |
-| SensitiveCookieNotHttpOnly.java:71:42:71:50 | secString | SensitiveCookieNotHttpOnly.java:70:28:70:35 | "token=" : String | SensitiveCookieNotHttpOnly.java:71:42:71:50 | secString | $@ doesn't have the HttpOnly flag set. | SensitiveCookieNotHttpOnly.java:70:28:70:35 | "token=" | This sensitive cookie |
-| SensitiveCookieNotHttpOnly.java:71:42:71:50 | secString | SensitiveCookieNotHttpOnly.java:70:28:70:43 | ... + ... : String | SensitiveCookieNotHttpOnly.java:71:42:71:50 | secString | $@ doesn't have the HttpOnly flag set. | SensitiveCookieNotHttpOnly.java:70:28:70:43 | ... + ... | This sensitive cookie |
-| SensitiveCookieNotHttpOnly.java:71:42:71:50 | secString | SensitiveCookieNotHttpOnly.java:70:28:70:55 | ... + ... : String | SensitiveCookieNotHttpOnly.java:71:42:71:50 | secString | $@ doesn't have the HttpOnly flag set. | SensitiveCookieNotHttpOnly.java:70:28:70:55 | ... + ... | This sensitive cookie |
-| SensitiveCookieNotHttpOnly.java:111:28:111:33 | cookie | SensitiveCookieNotHttpOnly.java:88:35:88:51 | "Presto-UI-Token" : String | SensitiveCookieNotHttpOnly.java:111:28:111:33 | cookie | $@ doesn't have the HttpOnly flag set. | SensitiveCookieNotHttpOnly.java:88:35:88:51 | "Presto-UI-Token" | This sensitive cookie |
 subpaths
--- a/java/ql/test/experimental/query-tests/security/CWE-1004/SensitiveCookieNotHttpOnly.java
+++ b/java/ql/test/experimental/query-tests/security/CWE-1004/SensitiveCookieNotHttpOnly.java
@@ -21,14 +21,14 @@ class SensitiveCookieNotHttpOnly {

    // BAD - Tests adding a sensitive cookie without the `HttpOnly` flag set.
    public void addCookie2(String jwt_token, String userId, HttpServletRequest request, HttpServletResponse response) {
-        String tokenCookieStr = "jwt_token";
+        String tokenCookieStr = "jwt_token"; // $Source
        Cookie jwtCookie = new Cookie(tokenCookieStr, jwt_token);
        Cookie userIdCookie = new Cookie("user_id", userId);
        jwtCookie.setPath("/");
        userIdCookie.setPath("/");
        jwtCookie.setMaxAge(3600*24*7);
        userIdCookie.setMaxAge(3600*24*7);
-        response.addCookie(jwtCookie);
+        response.addCookie(jwtCookie); // $Alert
        response.addCookie(userIdCookie);
    }

@@ -39,7 +39,7 @@ class SensitiveCookieNotHttpOnly {

    // BAD - Tests set a sensitive cookie header without the `HttpOnly` flag set.
    public void addCookie4(String authId, HttpServletRequest request, HttpServletResponse response) {
-        response.addHeader("Set-Cookie", "token=" +authId + ";Secure");
+        response.addHeader("Set-Cookie", "token=" +authId + ";Secure"); // $Alert
    }
    
    // GOOD - Tests set a sensitive cookie header using the class `javax.ws.rs.core.Cookie` with the `HttpOnly` flag set through string concatenation.
@@ -49,7 +49,7 @@ class SensitiveCookieNotHttpOnly {

    // BAD - Tests set a sensitive cookie header using the class `javax.ws.rs.core.Cookie` without the `HttpOnly` flag set.
    public void addCookie6(String accessKey, HttpServletRequest request, HttpServletResponse response) {
-        response.setHeader("Set-Cookie", new NewCookie("session-access-key", accessKey, "/", null, null, 0, true).toString());
+        response.setHeader("Set-Cookie", new NewCookie("session-access-key", accessKey, "/", null, null, 0, true).toString()); // $Alert
    }

    // GOOD - Tests set a sensitive cookie header using the class `javax.ws.rs.core.Cookie` with the `HttpOnly` flag set through the constructor.
@@ -60,15 +60,15 @@ class SensitiveCookieNotHttpOnly {

    // BAD - Tests set a sensitive cookie header using the class `javax.ws.rs.core.Cookie` without the `HttpOnly` flag set.
    public void addCookie8(String accessKey, HttpServletRequest request, HttpServletResponse response) {
-        NewCookie accessKeyCookie = new NewCookie("session-access-key", accessKey, "/", null, 0, null, 86400, true);
+        NewCookie accessKeyCookie = new NewCookie("session-access-key", accessKey, "/", null, 0, null, 86400, true);  // $Source
        String keyStr = accessKeyCookie.toString();
-        response.setHeader("Set-Cookie", keyStr);
+        response.setHeader("Set-Cookie", keyStr); // $Alert
    }

    // BAD - Tests set a sensitive cookie header using a variable without the `HttpOnly` flag set.
    public void addCookie9(String authId, HttpServletRequest request, HttpServletResponse response) {
-        String secString = "token=" +authId + ";Secure";
-        response.addHeader("Set-Cookie", secString);
+        String secString = "token=" +authId + ";Secure";  // $Source
+        response.addHeader("Set-Cookie", secString); // $Alert
    }

    // GOOD - Tests set a sensitive cookie header with the `HttpOnly` flag set using `String.format(...)`.
@@ -85,7 +85,7 @@ class SensitiveCookieNotHttpOnly {
    }

    public Cookie createAuthenticationCookie(HttpServletRequest request, String jwt) {
-        String PRESTO_UI_COOKIE = "Presto-UI-Token";
+        String PRESTO_UI_COOKIE = "Presto-UI-Token"; // $Source
        Cookie cookie = new Cookie(PRESTO_UI_COOKIE, jwt);
        cookie.setPath("/ui");
        return cookie;
@@ -108,7 +108,7 @@ class SensitiveCookieNotHttpOnly {
    // BAD - Tests set a sensitive cookie header without the `HttpOnly` flag set using a wrapper method.
    public void addCookie12(HttpServletRequest request, HttpServletResponse response, String jwt) {
        Cookie cookie = createAuthenticationCookie(request, jwt);
-        response.addCookie(cookie);
+        response.addCookie(cookie); // $Alert
    }

    // GOOD - Tests remove a sensitive cookie header without the `HttpOnly` flag set using a wrapper method.
@@ -141,7 +141,7 @@ class SensitiveCookieNotHttpOnly {
    // This example is missed because the `cookie.setHttpOnly` call in `createCookie` is thought to maybe set the HTTP-only flag, and the `cookie`
    // object flows to this `addCookie` call.
    public void addCookie15(HttpServletRequest request, HttpServletResponse response, String refreshToken) {
-        response.addCookie(createCookie("refresh_token", refreshToken, false));
+        response.addCookie(createCookie("refresh_token", refreshToken, false)); // $MISSING:Alert
    }

    // GOOD - CSRF token doesn't need to have the `HttpOnly` flag set.
--- a/java/ql/test/query-tests/security/CWE-1004/SensitiveCookieNotHttpOnly.qlref
+++ b/java/ql/test/query-tests/security/CWE-1004/SensitiveCookieNotHttpOnly.qlref
@@ -0,0 +1,4 @@
+query: Security/CWE/CWE-1004/SensitiveCookieNotHttpOnly.ql
+postprocess: 
+- utils/test/InlineExpectationsTestQuery.ql
+- utils/test/PrettyPrintModels.ql
--- a/java/ql/test/query-tests/security/CWE-1004/options
+++ b/java/ql/test/query-tests/security/CWE-1004/options
@@ -0,0 +1 @@
+// semmle-extractor-options: --javac-args -cp ${testdir}/../../../stubs/servlet-api-2.4:${testdir}/../../../stubs/jsr311-api-1.1.1:${testdir}/../../../stubs/springframework-5.8.x
				`@@ -1 +0,0 @@`
				`// semmle-extractor-options: --javac-args -cp ${testdir}/../../../../stubs/servlet-api-2.4:${testdir}/../../../../stubs/jsr311-api-1.1.1:${testdir}/../../../../stubs/springframework-5.8.x`
				`@@ -0,0 +1 @@`
				`// semmle-extractor-options: --javac-args -cp ${testdir}/../../../stubs/servlet-api-2.4:${testdir}/../../../stubs/jsr311-api-1.1.1:${testdir}/../../../stubs/springframework-5.8.x`