Add consistency checks

java/ql/src/utils/MinimalStubsFromSource.ql

@@ -18,6 +18,8 @@ class UsedInSource extends GeneratedDeclaration {
       this = any(Expr e | e.getEnclosingCallable().fromSource()).getType()
       or
       this = any(RefType t | t.fromSource())
+      or
+      this = any(TypeAccess ta | ta.fromSource())
     )
   }
 }
@@ -25,3 +27,21 @@ class UsedInSource extends GeneratedDeclaration {
 from GeneratedTopLevel t
 where not t.fromSource()
 select t.getQualifiedName(), t.stubFile()
+
+module Consistency {
+  query predicate noGeneratedStubs(string s) {
+    exists(GeneratedTopLevel t | s = t.getQualifiedName() |
+      not t.fromSource() and
+      not exists(t.stubFile())
+    )
+  }
+
+  query predicate multipleGeneratedStubs(string s) {
+    exists(GeneratedTopLevel t | s = t.getQualifiedName() |
+      not t.fromSource() and
+      strictcount(t.stubFile()) > 1
+    )
+  }
+}
+
+import Consistency

java/ql/src/utils/Stubs.qll

@@ -128,6 +128,10 @@ private class IndirectType extends GeneratedType {
       this = getAContainedType(t.getAGeneratedType()).(RefType).getSourceDeclaration()
     )
     or
+    this.getSourceDeclaration() instanceof GeneratedType
+    or
+    this = any(GeneratedType t).getSourceDeclaration()
+    or
     exists(GeneratedType t | this = t.(BoundedType).getATypeBound().getType())
     or
     exists(GeneratedDeclaration decl |

java/ql/src/utils/makeStubs.py

@@ -120,10 +120,21 @@ if run(['codeql', 'bqrs', 'decode', outputBqrsFile, '--format=json', '--output',
 with open(outputJsonFile) as f:
     results = json.load(f)
 
-if not '#select' in results or not 'tuples' in results['#select']:
+try:
+    results['#select']['tuples']
+    results['noGeneratedStubs']['tuples']
+    results['multipleGeneratedStubs']['tuples']
+except ValueError:
     print('Unexpected JSON output - no tuples found')
     exit(1)
 
+for (typ,) in results['noGeneratedStubs']['tuples']:
+    print(f"WARNING: No stubs generated for {typ}. This is probably a bug.")
+
+for (typ,) in results['multipleGeneratedStubs']['tuples']:
+    print(
+        f"WARNING: Multiple stubs generated for {typ}. This is probably a bug. One will be chosen arbitrarily.")
+
 for (typ, stub) in results['#select']['tuples']:
     stubFile = os.path.join(stubDir, typ.replace(".", "/") + ".java")
     os.makedirs(os.path.dirname(stubFile), exist_ok=True)