From ba9c2f1e3a743bb9efdd1010605ff50c90acb7a7 Mon Sep 17 00:00:00 2001
From: Geoffrey White <40627776+geoffw0@users.noreply.github.com>
Date: Wed, 2 Oct 2024 15:31:14 +0100
Subject: [PATCH 01/15] Rust: Add extractor warnings query.

---
 rust/ql/lib/codeql/rust/Diagnostics.qll       |  5 +++++
 .../queries/diagnostics/ExtractionWarnings.ql | 19 +++++++++++++++++++
 2 files changed, 24 insertions(+)
 create mode 100644 rust/ql/src/queries/diagnostics/ExtractionWarnings.ql

diff --git a/rust/ql/lib/codeql/rust/Diagnostics.qll b/rust/ql/lib/codeql/rust/Diagnostics.qll
index 5902bb594141..8c207e708889 100644
--- a/rust/ql/lib/codeql/rust/Diagnostics.qll
+++ b/rust/ql/lib/codeql/rust/Diagnostics.qll
@@ -52,3 +52,8 @@ class Diagnostic extends @diagnostic {
 class ExtractionError extends Diagnostic {
   ExtractionError() { this.getTag() = "parse_error" }
 }
+
+/** A diagnostic that is warning severity. */
+class ExtractionWarning extends Diagnostic {
+  ExtractionWarning() { this.getSeverity() = 30 }
+}
diff --git a/rust/ql/src/queries/diagnostics/ExtractionWarnings.ql b/rust/ql/src/queries/diagnostics/ExtractionWarnings.ql
new file mode 100644
index 000000000000..99773cc6d53a
--- /dev/null
+++ b/rust/ql/src/queries/diagnostics/ExtractionWarnings.ql
@@ -0,0 +1,19 @@
+/**
+ * @name Extraction warnings
+ * @description List all extraction warnings for files in the source code directory.
+ * @kind diagnostic
+ * @id rust/diagnostics/extraction-warnings
+ */
+
+import codeql.rust.Diagnostics
+import codeql.files.FileSystem
+
+/** Gets the SARIF severity to associate with a warning. */
+int getSeverity() { result = 1 }
+
+from ExtractionWarning warning, File f
+where
+  f = warning.getLocation().getFile() and
+  exists(f.getRelativePath())
+select warning, "Extraction warning in " + f + " with message " + warning.getMessage(),
+  getSeverity()

From f30a642c8fcc9b8c34493ea170b41fb38c91e93b Mon Sep 17 00:00:00 2001
From: Geoffrey White <40627776+geoffw0@users.noreply.github.com>
Date: Wed, 2 Oct 2024 15:40:26 +0100
Subject: [PATCH 02/15] Rust: Add a test for the extractor warnings query.

---
 .../query-tests/diagnostics/ExtractionWarnings.expected     | 6 ++++++
 .../test/query-tests/diagnostics/ExtractionWarnings.qlref   | 1 +
 2 files changed, 7 insertions(+)
 create mode 100644 rust/ql/test/query-tests/diagnostics/ExtractionWarnings.expected
 create mode 100644 rust/ql/test/query-tests/diagnostics/ExtractionWarnings.qlref

diff --git a/rust/ql/test/query-tests/diagnostics/ExtractionWarnings.expected b/rust/ql/test/query-tests/diagnostics/ExtractionWarnings.expected
new file mode 100644
index 000000000000..0a68f2bce0ef
--- /dev/null
+++ b/rust/ql/test/query-tests/diagnostics/ExtractionWarnings.expected
@@ -0,0 +1,6 @@
+| does_not_compile.rs:2:6:2:5 | expected SEMICOLON | Extraction warning in does_not_compile.rs with message expected SEMICOLON | 1 |
+| does_not_compile.rs:2:9:2:8 | expected SEMICOLON | Extraction warning in does_not_compile.rs with message expected SEMICOLON | 1 |
+| does_not_compile.rs:2:13:2:12 | expected SEMICOLON | Extraction warning in does_not_compile.rs with message expected SEMICOLON | 1 |
+| does_not_compile.rs:2:21:2:20 | expected SEMICOLON | Extraction warning in does_not_compile.rs with message expected SEMICOLON | 1 |
+| does_not_compile.rs:2:26:2:25 | expected SEMICOLON | Extraction warning in does_not_compile.rs with message expected SEMICOLON | 1 |
+| does_not_compile.rs:2:32:2:31 | expected field name or number | Extraction warning in does_not_compile.rs with message expected field name or number | 1 |
diff --git a/rust/ql/test/query-tests/diagnostics/ExtractionWarnings.qlref b/rust/ql/test/query-tests/diagnostics/ExtractionWarnings.qlref
new file mode 100644
index 000000000000..ff6e566d20a7
--- /dev/null
+++ b/rust/ql/test/query-tests/diagnostics/ExtractionWarnings.qlref
@@ -0,0 +1 @@
+queries/diagnostics/ExtractionWarnings.ql

From ad7c96554fbf05eb7b0519672ad2bcb84f95ad83 Mon Sep 17 00:00:00 2001
From: Geoffrey White <40627776+geoffw0@users.noreply.github.com>
Date: Wed, 2 Oct 2024 18:29:47 +0100
Subject: [PATCH 03/15] Rust: Correct extraction errors query to output only
 errors.

---
 rust/ql/lib/codeql/rust/Diagnostics.qll                     | 4 ++--
 rust/ql/src/queries/diagnostics/ExtractionErrors.ql         | 2 +-
 .../test/query-tests/diagnostics/ExtractionErrors.expected  | 6 ------
 3 files changed, 3 insertions(+), 9 deletions(-)

diff --git a/rust/ql/lib/codeql/rust/Diagnostics.qll b/rust/ql/lib/codeql/rust/Diagnostics.qll
index 8c207e708889..8f77b64c5123 100644
--- a/rust/ql/lib/codeql/rust/Diagnostics.qll
+++ b/rust/ql/lib/codeql/rust/Diagnostics.qll
@@ -48,9 +48,9 @@ class Diagnostic extends @diagnostic {
   string toString() { result = this.getMessage() }
 }
 
-/** A diagnostic relating to a particular error in extracting a file. */
+/** A diagnostic that is error severity. */
 class ExtractionError extends Diagnostic {
-  ExtractionError() { this.getTag() = "parse_error" }
+  ExtractionError() { this.getSeverity() = 40 }
 }
 
 /** A diagnostic that is warning severity. */
diff --git a/rust/ql/src/queries/diagnostics/ExtractionErrors.ql b/rust/ql/src/queries/diagnostics/ExtractionErrors.ql
index a04c4e618c41..68be66f8ca9b 100644
--- a/rust/ql/src/queries/diagnostics/ExtractionErrors.ql
+++ b/rust/ql/src/queries/diagnostics/ExtractionErrors.ql
@@ -8,7 +8,7 @@
 import codeql.rust.Diagnostics
 import codeql.files.FileSystem
 
-/** Gets the SARIF severity to associate an error. */
+/** Gets the SARIF severity to associate with an error. */
 int getSeverity() { result = 2 }
 
 from ExtractionError error, File f
diff --git a/rust/ql/test/query-tests/diagnostics/ExtractionErrors.expected b/rust/ql/test/query-tests/diagnostics/ExtractionErrors.expected
index b6aaf7b6d373..e69de29bb2d1 100644
--- a/rust/ql/test/query-tests/diagnostics/ExtractionErrors.expected
+++ b/rust/ql/test/query-tests/diagnostics/ExtractionErrors.expected
@@ -1,6 +0,0 @@
-| does_not_compile.rs:2:6:2:5 | expected SEMICOLON | Extraction failed in does_not_compile.rs with error expected SEMICOLON | 2 |
-| does_not_compile.rs:2:9:2:8 | expected SEMICOLON | Extraction failed in does_not_compile.rs with error expected SEMICOLON | 2 |
-| does_not_compile.rs:2:13:2:12 | expected SEMICOLON | Extraction failed in does_not_compile.rs with error expected SEMICOLON | 2 |
-| does_not_compile.rs:2:21:2:20 | expected SEMICOLON | Extraction failed in does_not_compile.rs with error expected SEMICOLON | 2 |
-| does_not_compile.rs:2:26:2:25 | expected SEMICOLON | Extraction failed in does_not_compile.rs with error expected SEMICOLON | 2 |
-| does_not_compile.rs:2:32:2:31 | expected field name or number | Extraction failed in does_not_compile.rs with error expected field name or number | 2 |

From 12fbd18f3a9c8a08f548942ab732e565c8f3f7c2 Mon Sep 17 00:00:00 2001
From: Geoffrey White <40627776+geoffw0@users.noreply.github.com>
Date: Wed, 2 Oct 2024 18:32:25 +0100
Subject: [PATCH 04/15] Rust: Have ExtractionConsistency.ql report both.

---
 rust/ql/consistency-queries/ExtractionConsistency.ql | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/rust/ql/consistency-queries/ExtractionConsistency.ql b/rust/ql/consistency-queries/ExtractionConsistency.ql
index b839f2ad783c..20148f0cea2d 100644
--- a/rust/ql/consistency-queries/ExtractionConsistency.ql
+++ b/rust/ql/consistency-queries/ExtractionConsistency.ql
@@ -1,3 +1,5 @@
 import codeql.rust.Diagnostics
 
 query predicate extractionError(ExtractionError ee) { any() }
+
+query predicate extractionWarning(ExtractionWarning ew) { any() }

From a4c06b2bbcb4c1942505e123546225142191aa9f Mon Sep 17 00:00:00 2001
From: Geoffrey White <40627776+geoffw0@users.noreply.github.com>
Date: Wed, 2 Oct 2024 18:23:25 +0100
Subject: [PATCH 05/15] Rust: Define SuccessfullyExtractedFile and use it to
 simplify queries.

---
 rust/ql/lib/codeql/files/FileSystem.qll        | 18 ++++++++++++++++++
 .../NumberOfFilesExtractedWithErrors.ql        |  7 ++++---
 .../NumberOfSuccessfullyExtractedFiles.ql      |  7 ++-----
 3 files changed, 24 insertions(+), 8 deletions(-)

diff --git a/rust/ql/lib/codeql/files/FileSystem.qll b/rust/ql/lib/codeql/files/FileSystem.qll
index ee7a2235476e..fd7ad56c74a0 100644
--- a/rust/ql/lib/codeql/files/FileSystem.qll
+++ b/rust/ql/lib/codeql/files/FileSystem.qll
@@ -5,6 +5,7 @@ private import codeql.util.FileSystem
 private import codeql.rust.elements.SourceFile
 private import codeql.rust.elements.AstNode
 private import codeql.rust.elements.Comment
+private import codeql.rust.Diagnostics
 
 private module Input implements InputSig {
   abstract class ContainerBase extends @container {
@@ -56,3 +57,20 @@ class File extends Container, Impl::File {
       )
   }
 }
+
+/**
+ * A successfully extracted file, that is, a file that was extracted and
+ * contains no extraction errors or warnings.
+ */
+class SuccessfullyExtractedFile extends File {
+  SuccessfullyExtractedFile() {
+    not exists(Diagnostic d |
+      d.getLocation().getFile() = this and
+      (
+        d instanceof ExtractionError
+        or
+        d instanceof ExtractionWarning
+      )
+    )
+  }
+}
diff --git a/rust/ql/src/queries/summary/NumberOfFilesExtractedWithErrors.ql b/rust/ql/src/queries/summary/NumberOfFilesExtractedWithErrors.ql
index 1af3f0f88ec0..23db30f53e96 100644
--- a/rust/ql/src/queries/summary/NumberOfFilesExtractedWithErrors.ql
+++ b/rust/ql/src/queries/summary/NumberOfFilesExtractedWithErrors.ql
@@ -2,14 +2,15 @@
  * @id rust/summary/number-of-files-extracted-with-errors
  * @name Total number of Rust files that were extracted with errors
  * @description The total number of Rust files in the source code directory that
- *  were extracted, but where at least one extraction error occurred in the process.
+ *  were extracted, but where at least one extraction error (or warning) occurred
+ *  in the process.
  * @kind metric
  * @tags summary
  */
 
 import codeql.files.FileSystem
-import codeql.rust.Diagnostics
 
 select count(File f |
-    exists(ExtractionError e | e.getLocation().getFile() = f) and exists(f.getRelativePath())
+    exists(f.getRelativePath()) and
+    not f instanceof SuccessfullyExtractedFile
   )
diff --git a/rust/ql/src/queries/summary/NumberOfSuccessfullyExtractedFiles.ql b/rust/ql/src/queries/summary/NumberOfSuccessfullyExtractedFiles.ql
index eb86577b4b80..c960599ad18f 100644
--- a/rust/ql/src/queries/summary/NumberOfSuccessfullyExtractedFiles.ql
+++ b/rust/ql/src/queries/summary/NumberOfSuccessfullyExtractedFiles.ql
@@ -2,14 +2,11 @@
  * @id rust/summary/number-of-successfully-extracted-files
  * @name Total number of Rust files that were extracted without error
  * @description The total number of Rust files in the source code directory that
- *  were extracted without encountering any extraction errors.
+ *  were extracted without encountering any extraction errors (or warnings).
  * @kind metric
  * @tags summary
  */
 
-import codeql.rust.Diagnostics
 import codeql.files.FileSystem
 
-select count(File f |
-    not exists(ExtractionError e | e.getLocation().getFile() = f) and exists(f.getRelativePath())
-  )
+select count(SuccessfullyExtractedFile f | exists(f.getRelativePath()))

From 88abc8f72f8b96d139909bc97d4fb6137fb22334 Mon Sep 17 00:00:00 2001
From: Geoffrey White <40627776+geoffw0@users.noreply.github.com>
Date: Wed, 2 Oct 2024 17:29:32 +0100
Subject: [PATCH 06/15] Rust: Add to summary stats.

---
 rust/ql/src/queries/summary/SummaryStats.ql     | 17 +++++++++++++++--
 .../diagnostics/SummaryStats.expected           |  6 +++++-
 2 files changed, 20 insertions(+), 3 deletions(-)

diff --git a/rust/ql/src/queries/summary/SummaryStats.ql b/rust/ql/src/queries/summary/SummaryStats.ql
index 447325514cac..a3494ccb769c 100644
--- a/rust/ql/src/queries/summary/SummaryStats.ql
+++ b/rust/ql/src/queries/summary/SummaryStats.ql
@@ -7,16 +7,29 @@
  */
 
 import rust
+import codeql.rust.Diagnostics
 import Stats
 
 from string key, string value
 where
-  key = "Files extracted" and value = count(File f | exists(f.getRelativePath())).toString()
-  or
   key = "Elements extracted" and value = count(Element e | not e instanceof Unextracted).toString()
   or
   key = "Elements unextracted" and value = count(Unextracted e).toString()
   or
+  key = "Extraction errors" and value = count(ExtractionError e).toString()
+  or
+  key = "Extraction warnings" and value = count(ExtractionWarning w).toString()
+  or
+  key = "Files extracted - total" and value = count(File f | exists(f.getRelativePath())).toString()
+  or
+  key = "Files extracted - with errors" and
+  value =
+    count(File f | exists(f.getRelativePath()) and not f instanceof SuccessfullyExtractedFile)
+        .toString()
+  or
+  key = "Files extracted - without errors" and
+  value = count(SuccessfullyExtractedFile f | exists(f.getRelativePath())).toString()
+  or
   key = "Lines of code extracted" and value = getLinesOfCode().toString()
   or
   key = "Lines of user code extracted" and value = getLinesOfUserCode().toString()
diff --git a/rust/ql/test/query-tests/diagnostics/SummaryStats.expected b/rust/ql/test/query-tests/diagnostics/SummaryStats.expected
index ff07c0f589a6..cc467865b00f 100644
--- a/rust/ql/test/query-tests/diagnostics/SummaryStats.expected
+++ b/rust/ql/test/query-tests/diagnostics/SummaryStats.expected
@@ -1,5 +1,9 @@
 | Elements extracted | 210 |
 | Elements unextracted | 0 |
-| Files extracted | 6 |
+| Extraction errors | 6 |
+| Extraction warnings | 0 |
+| Files extracted - total | 6 |
+| Files extracted - with errors | 1 |
+| Files extracted - without errors | 5 |
 | Lines of code extracted | 48 |
 | Lines of user code extracted | 48 |

From da84889242e786e7b2bdbd844e7bfdf7cef6fab6 Mon Sep 17 00:00:00 2001
From: Geoffrey White <40627776+geoffw0@users.noreply.github.com>
Date: Thu, 3 Oct 2024 12:50:40 +0100
Subject: [PATCH 07/15] Rust: Use @diagnostic_error, @diagnostic_warning rather
 than constants.

---
 rust/ql/lib/codeql/rust/Diagnostics.qll | 8 ++------
 1 file changed, 2 insertions(+), 6 deletions(-)

diff --git a/rust/ql/lib/codeql/rust/Diagnostics.qll b/rust/ql/lib/codeql/rust/Diagnostics.qll
index 8f77b64c5123..58de14b8fcf5 100644
--- a/rust/ql/lib/codeql/rust/Diagnostics.qll
+++ b/rust/ql/lib/codeql/rust/Diagnostics.qll
@@ -49,11 +49,7 @@ class Diagnostic extends @diagnostic {
 }
 
 /** A diagnostic that is error severity. */
-class ExtractionError extends Diagnostic {
-  ExtractionError() { this.getSeverity() = 40 }
-}
+class ExtractionError extends Diagnostic, @diagnostic_error { }
 
 /** A diagnostic that is warning severity. */
-class ExtractionWarning extends Diagnostic {
-  ExtractionWarning() { this.getSeverity() = 30 }
-}
+class ExtractionWarning extends Diagnostic, @diagnostic_warning { }

From 32dbdb39133c80ab29386d78cb62e96b8e68d5db Mon Sep 17 00:00:00 2001
From: Geoffrey White <40627776+geoffw0@users.noreply.github.com>
Date: Thu, 3 Oct 2024 12:50:59 +0100
Subject: [PATCH 08/15] Rust: Update summary stats .expected file.

---
 rust/ql/test/query-tests/diagnostics/SummaryStats.expected | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/rust/ql/test/query-tests/diagnostics/SummaryStats.expected b/rust/ql/test/query-tests/diagnostics/SummaryStats.expected
index cc467865b00f..8fe7ee7fb47c 100644
--- a/rust/ql/test/query-tests/diagnostics/SummaryStats.expected
+++ b/rust/ql/test/query-tests/diagnostics/SummaryStats.expected
@@ -1,7 +1,7 @@
 | Elements extracted | 210 |
 | Elements unextracted | 0 |
-| Extraction errors | 6 |
-| Extraction warnings | 0 |
+| Extraction errors | 0 |
+| Extraction warnings | 6 |
 | Files extracted - total | 6 |
 | Files extracted - with errors | 1 |
 | Files extracted - without errors | 5 |

From 2e772a80c4bed04c04083e6f8eb2c20e4dc8effb Mon Sep 17 00:00:00 2001
From: Geoffrey White <40627776+geoffw0@users.noreply.github.com>
Date: Thu, 3 Oct 2024 15:15:32 +0100
Subject: [PATCH 09/15] Rust: Accept minor consistency .expected changes.

---
 .../utf8/CONSISTENCY/ExtractionConsistency.expected              | 1 +
 .../diagnostics/CONSISTENCY/ExtractionConsistency.expected       | 1 +
 2 files changed, 2 insertions(+)

diff --git a/rust/ql/test/extractor-tests/utf8/CONSISTENCY/ExtractionConsistency.expected b/rust/ql/test/extractor-tests/utf8/CONSISTENCY/ExtractionConsistency.expected
index 23b423a489a1..45026be3af2b 100644
--- a/rust/ql/test/extractor-tests/utf8/CONSISTENCY/ExtractionConsistency.expected
+++ b/rust/ql/test/extractor-tests/utf8/CONSISTENCY/ExtractionConsistency.expected
@@ -1,3 +1,4 @@
+extractionWarning
 | lib.rs:3:9:3:8 | expected `;` or `{` |
 | lib.rs:3:9:3:8 | expected an item |
 | lib.rs:3:21:3:20 | expected BANG |
diff --git a/rust/ql/test/query-tests/diagnostics/CONSISTENCY/ExtractionConsistency.expected b/rust/ql/test/query-tests/diagnostics/CONSISTENCY/ExtractionConsistency.expected
index 157aafc87852..0d5ffb095614 100644
--- a/rust/ql/test/query-tests/diagnostics/CONSISTENCY/ExtractionConsistency.expected
+++ b/rust/ql/test/query-tests/diagnostics/CONSISTENCY/ExtractionConsistency.expected
@@ -1,3 +1,4 @@
+extractionWarning
 | does_not_compile.rs:2:6:2:5 | expected SEMICOLON |
 | does_not_compile.rs:2:9:2:8 | expected SEMICOLON |
 | does_not_compile.rs:2:13:2:12 | expected SEMICOLON |

From 4c7ec59306a432242f510618611f4fddf3099cc3 Mon Sep 17 00:00:00 2001
From: Geoffrey White <40627776+geoffw0@users.noreply.github.com>
Date: Thu, 3 Oct 2024 14:16:12 +0100
Subject: [PATCH 10/15] Ruby: Sync identical files.

---
 ruby/ql/lib/codeql/ruby/Diagnostics.qll | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/ruby/ql/lib/codeql/ruby/Diagnostics.qll b/ruby/ql/lib/codeql/ruby/Diagnostics.qll
index 5902bb594141..58de14b8fcf5 100644
--- a/ruby/ql/lib/codeql/ruby/Diagnostics.qll
+++ b/ruby/ql/lib/codeql/ruby/Diagnostics.qll
@@ -48,7 +48,8 @@ class Diagnostic extends @diagnostic {
   string toString() { result = this.getMessage() }
 }
 
-/** A diagnostic relating to a particular error in extracting a file. */
-class ExtractionError extends Diagnostic {
-  ExtractionError() { this.getTag() = "parse_error" }
-}
+/** A diagnostic that is error severity. */
+class ExtractionError extends Diagnostic, @diagnostic_error { }
+
+/** A diagnostic that is warning severity. */
+class ExtractionWarning extends Diagnostic, @diagnostic_warning { }

From 1ea94faccf7113ae339190c1151926184fbbfe7d Mon Sep 17 00:00:00 2001
From: Geoffrey White <40627776+geoffw0@users.noreply.github.com>
Date: Thu, 3 Oct 2024 17:27:52 +0100
Subject: [PATCH 11/15] Ruby: Make similar changes to differentiate extraction
 errors and warnings, and mostly restore original behaviour.

---
 ruby/ql/consistency-queries/AstConsistency.ql  |  2 ++
 ruby/ql/lib/codeql/files/FileSystem.qll        | 18 ++++++++++++++++++
 .../NumberOfFilesExtractedWithErrors.ql        |  7 ++++---
 .../NumberOfSuccessfullyExtractedFiles.ql      |  8 +++-----
 .../CONSISTENCY/AstConsistency.expected        |  2 +-
 .../diagnostics/ExtractionErrors.expected      |  1 -
 6 files changed, 28 insertions(+), 10 deletions(-)

diff --git a/ruby/ql/consistency-queries/AstConsistency.ql b/ruby/ql/consistency-queries/AstConsistency.ql
index 2a9fea8fea90..d7792a8ae4d0 100644
--- a/ruby/ql/consistency-queries/AstConsistency.ql
+++ b/ruby/ql/consistency-queries/AstConsistency.ql
@@ -31,3 +31,5 @@ query predicate multipleToString(AstNode n, string s) {
 }
 
 query predicate extractionError(ExtractionError error) { any() }
+
+query predicate extractionWarning(ExtractionWarning error) { any() }
diff --git a/ruby/ql/lib/codeql/files/FileSystem.qll b/ruby/ql/lib/codeql/files/FileSystem.qll
index 528dde52fd91..8985cc333447 100644
--- a/ruby/ql/lib/codeql/files/FileSystem.qll
+++ b/ruby/ql/lib/codeql/files/FileSystem.qll
@@ -2,6 +2,7 @@
 
 private import codeql.Locations
 private import codeql.util.FileSystem
+private import codeql.ruby.Diagnostics
 
 private module Input implements InputSig {
   abstract class ContainerBase extends @container {
@@ -34,3 +35,20 @@ class File extends Container, Impl::File {
   /** Holds if this file was extracted from ordinary source code. */
   predicate fromSource() { any() }
 }
+
+/**
+ * A successfully extracted file, that is, a file that was extracted and
+ * contains no extraction errors or warnings.
+ */
+class SuccessfullyExtractedFile extends File {
+  SuccessfullyExtractedFile() {
+    not exists(Diagnostic d |
+      d.getLocation().getFile() = this and
+      (
+        d instanceof ExtractionError
+        or
+        d instanceof ExtractionWarning
+      )
+    )
+  }
+}
diff --git a/ruby/ql/src/queries/summary/NumberOfFilesExtractedWithErrors.ql b/ruby/ql/src/queries/summary/NumberOfFilesExtractedWithErrors.ql
index 8623ed911d5a..1cbc28b6cc6b 100644
--- a/ruby/ql/src/queries/summary/NumberOfFilesExtractedWithErrors.ql
+++ b/ruby/ql/src/queries/summary/NumberOfFilesExtractedWithErrors.ql
@@ -2,14 +2,15 @@
  * @id rb/summary/number-of-files-extracted-with-errors
  * @name Total number of Ruby files that were extracted with errors
  * @description The total number of Ruby code files that we extracted, but where
- *  at least one extraction error occurred in the process.
+ *  at least one extraction error (or warning) occurred in the process.
  * @kind metric
  * @tags summary
  */
 
 import codeql.ruby.AST
-import codeql.ruby.Diagnostics
+import codeql.files.FileSystem
 
 select count(File f |
-    exists(ExtractionError e | e.getLocation().getFile() = f) and exists(f.getRelativePath())
+    exists(f.getRelativePath()) and
+    not f instanceof SuccessfullyExtractedFile
   )
diff --git a/ruby/ql/src/queries/summary/NumberOfSuccessfullyExtractedFiles.ql b/ruby/ql/src/queries/summary/NumberOfSuccessfullyExtractedFiles.ql
index 236374ff2261..afd667cf58c5 100644
--- a/ruby/ql/src/queries/summary/NumberOfSuccessfullyExtractedFiles.ql
+++ b/ruby/ql/src/queries/summary/NumberOfSuccessfullyExtractedFiles.ql
@@ -2,14 +2,12 @@
  * @id rb/summary/number-of-successfully-extracted-files
  * @name Total number of Ruby files that were extracted without error
  * @description The total number of Ruby code files that we extracted without
- *   encountering any extraction errors
+ *   encountering any extraction errors (or warnings).
  * @kind metric
  * @tags summary
  */
 
 import codeql.ruby.AST
-import codeql.ruby.Diagnostics
+import codeql.files.FileSystem
 
-select count(File f |
-    not exists(ExtractionError e | e.getLocation().getFile() = f) and exists(f.getRelativePath())
-  )
+select count(SuccessfullyExtractedFile f | exists(f.getRelativePath()))
diff --git a/ruby/ql/test/query-tests/diagnostics/CONSISTENCY/AstConsistency.expected b/ruby/ql/test/query-tests/diagnostics/CONSISTENCY/AstConsistency.expected
index 5dc14116b917..93df75151a77 100644
--- a/ruby/ql/test/query-tests/diagnostics/CONSISTENCY/AstConsistency.expected
+++ b/ruby/ql/test/query-tests/diagnostics/CONSISTENCY/AstConsistency.expected
@@ -1,2 +1,2 @@
-extractionError
+extractionWarning
 | src/not_ruby.rb:5:25:5:26 | A parse error occurred. Check the syntax of the file. If the file is invalid, correct the error or exclude the file from analysis. |
diff --git a/ruby/ql/test/query-tests/diagnostics/ExtractionErrors.expected b/ruby/ql/test/query-tests/diagnostics/ExtractionErrors.expected
index dc37ca3642b3..e69de29bb2d1 100644
--- a/ruby/ql/test/query-tests/diagnostics/ExtractionErrors.expected
+++ b/ruby/ql/test/query-tests/diagnostics/ExtractionErrors.expected
@@ -1 +0,0 @@
-| src/not_ruby.rb:5:25:5:26 | A parse error occurred. Check the syntax of the file. If the file is invalid, correct the error or exclude the file from analysis. | Extraction failed in src/not_ruby.rb with error A parse error occurred. Check the syntax of the file. If the file is invalid, correct the error or exclude the file from analysis. | 2 |

From 86cc2dc5a1e117b8a9f3e58c639c41d1509593d3 Mon Sep 17 00:00:00 2001
From: Geoffrey White <40627776+geoffw0@users.noreply.github.com>
Date: Thu, 3 Oct 2024 17:29:25 +0100
Subject: [PATCH 12/15] Ruby: Add rb/diagnostics/extraction-warnings so that we
 don't miss anything we had before.

---
 .../queries/diagnostics/ExtractionWarnings.ql | 19 +++++++++++++++++++
 .../diagnostics/ExtractionWarnings.expected   |  1 +
 .../diagnostics/ExtractionWarnings.qlref      |  1 +
 3 files changed, 21 insertions(+)
 create mode 100644 ruby/ql/src/queries/diagnostics/ExtractionWarnings.ql
 create mode 100644 ruby/ql/test/query-tests/diagnostics/ExtractionWarnings.expected
 create mode 100644 ruby/ql/test/query-tests/diagnostics/ExtractionWarnings.qlref

diff --git a/ruby/ql/src/queries/diagnostics/ExtractionWarnings.ql b/ruby/ql/src/queries/diagnostics/ExtractionWarnings.ql
new file mode 100644
index 000000000000..74f007390567
--- /dev/null
+++ b/ruby/ql/src/queries/diagnostics/ExtractionWarnings.ql
@@ -0,0 +1,19 @@
+/**
+ * @name Extraction warnings
+ * @description List all extraction warnings for files in the source code directory.
+ * @kind diagnostic
+ * @id rb/diagnostics/extraction-warnings
+ */
+
+import codeql.ruby.AST
+import codeql.ruby.Diagnostics
+
+/** Gets the SARIF severity to associate with a warning. */
+int getSeverity() { result = 1 }
+
+from ExtractionWarning warning, File f
+where
+  f = warning.getLocation().getFile() and
+  exists(f.getRelativePath())
+select warning, "Extraction warning in " + f + " with message " + warning.getMessage(),
+  getSeverity()
diff --git a/ruby/ql/test/query-tests/diagnostics/ExtractionWarnings.expected b/ruby/ql/test/query-tests/diagnostics/ExtractionWarnings.expected
new file mode 100644
index 000000000000..c47ec9c5d365
--- /dev/null
+++ b/ruby/ql/test/query-tests/diagnostics/ExtractionWarnings.expected
@@ -0,0 +1 @@
+| src/not_ruby.rb:5:25:5:26 | A parse error occurred. Check the syntax of the file. If the file is invalid, correct the error or exclude the file from analysis. | Extraction warning in src/not_ruby.rb with message A parse error occurred. Check the syntax of the file. If the file is invalid, correct the error or exclude the file from analysis. | 1 |
diff --git a/ruby/ql/test/query-tests/diagnostics/ExtractionWarnings.qlref b/ruby/ql/test/query-tests/diagnostics/ExtractionWarnings.qlref
new file mode 100644
index 000000000000..ff6e566d20a7
--- /dev/null
+++ b/ruby/ql/test/query-tests/diagnostics/ExtractionWarnings.qlref
@@ -0,0 +1 @@
+queries/diagnostics/ExtractionWarnings.ql

From d4414dabff35e74aace2743596d31108ad4cdb5e Mon Sep 17 00:00:00 2001
From: Geoffrey White <40627776+geoffw0@users.noreply.github.com>
Date: Thu, 3 Oct 2024 17:38:28 +0100
Subject: [PATCH 13/15] Ruby: Add change notes.

---
 ruby/ql/lib/change-notes/2024-10-03-extraction-warnings.md | 4 ++++
 ruby/ql/src/change-notes/2024-10-03-extraction-warnings.md | 4 ++++
 2 files changed, 8 insertions(+)
 create mode 100644 ruby/ql/lib/change-notes/2024-10-03-extraction-warnings.md
 create mode 100644 ruby/ql/src/change-notes/2024-10-03-extraction-warnings.md

diff --git a/ruby/ql/lib/change-notes/2024-10-03-extraction-warnings.md b/ruby/ql/lib/change-notes/2024-10-03-extraction-warnings.md
new file mode 100644
index 000000000000..5d6128354c3b
--- /dev/null
+++ b/ruby/ql/lib/change-notes/2024-10-03-extraction-warnings.md
@@ -0,0 +1,4 @@
+---
+category: minorAnalysis
+---
+* The `ExtractionError` class has been split into `ExtractionError` and `ExtractionWarning`, reporting extraction errors and warnings respectively.
diff --git a/ruby/ql/src/change-notes/2024-10-03-extraction-warnings.md b/ruby/ql/src/change-notes/2024-10-03-extraction-warnings.md
new file mode 100644
index 000000000000..ac97cd1e7ba2
--- /dev/null
+++ b/ruby/ql/src/change-notes/2024-10-03-extraction-warnings.md
@@ -0,0 +1,4 @@
+---
+category: minorAnalysis
+---
+* The `rb/diagnostics/extraction-errors` diagnostic query has been split into `rb/diagnostics/extraction-errors` and `rb/diagnostics/extraction-warnings`, counting extraction errors and warnings respectively.

From 8a895740bafc0639ce607753853a8af77534fc1b Mon Sep 17 00:00:00 2001
From: Geoffrey White <40627776+geoffw0@users.noreply.github.com>
Date: Thu, 10 Oct 2024 14:05:39 +0100
Subject: [PATCH 14/15] Ruby: Move language specific code out of FileSystem.qll
 (at least for now).

---
 ruby/ql/lib/codeql/files/FileSystem.qll | 18 ------------------
 ruby/ql/lib/codeql/ruby/AST.qll         | 18 ++++++++++++++++++
 2 files changed, 18 insertions(+), 18 deletions(-)

diff --git a/ruby/ql/lib/codeql/files/FileSystem.qll b/ruby/ql/lib/codeql/files/FileSystem.qll
index 8985cc333447..528dde52fd91 100644
--- a/ruby/ql/lib/codeql/files/FileSystem.qll
+++ b/ruby/ql/lib/codeql/files/FileSystem.qll
@@ -2,7 +2,6 @@
 
 private import codeql.Locations
 private import codeql.util.FileSystem
-private import codeql.ruby.Diagnostics
 
 private module Input implements InputSig {
   abstract class ContainerBase extends @container {
@@ -35,20 +34,3 @@ class File extends Container, Impl::File {
   /** Holds if this file was extracted from ordinary source code. */
   predicate fromSource() { any() }
 }
-
-/**
- * A successfully extracted file, that is, a file that was extracted and
- * contains no extraction errors or warnings.
- */
-class SuccessfullyExtractedFile extends File {
-  SuccessfullyExtractedFile() {
-    not exists(Diagnostic d |
-      d.getLocation().getFile() = this and
-      (
-        d instanceof ExtractionError
-        or
-        d instanceof ExtractionWarning
-      )
-    )
-  }
-}
diff --git a/ruby/ql/lib/codeql/ruby/AST.qll b/ruby/ql/lib/codeql/ruby/AST.qll
index e8dc28692c07..e98749af4273 100644
--- a/ruby/ql/lib/codeql/ruby/AST.qll
+++ b/ruby/ql/lib/codeql/ruby/AST.qll
@@ -18,6 +18,7 @@ private import ast.internal.Scope
 private import ast.internal.Synthesis
 private import ast.internal.TreeSitter
 private import Customizations
+private import Diagnostics
 
 cached
 private module Cached {
@@ -166,3 +167,20 @@ class RubyFile extends File {
   /** Gets the number of lines of comments in this file. */
   int getNumberOfLinesOfComments() { result = count(int line | this.line(line, true)) }
 }
+
+/**
+ * A successfully extracted file, that is, a file that was extracted and
+ * contains no extraction errors or warnings.
+ */
+class SuccessfullyExtractedFile extends RubyFile {
+  SuccessfullyExtractedFile() {
+    not exists(Diagnostic d |
+      d.getLocation().getFile() = this and
+      (
+        d instanceof ExtractionError
+        or
+        d instanceof ExtractionWarning
+      )
+    )
+  }
+}

From 7420d07935d166daaf4f7387bac21339315035cb Mon Sep 17 00:00:00 2001
From: Geoffrey White <40627776+geoffw0@users.noreply.github.com>
Date: Thu, 10 Oct 2024 15:54:14 +0100
Subject: [PATCH 15/15] Update ruby/ql/lib/codeql/ruby/AST.qll

Co-authored-by: Arthur Baars <aibaars@github.com>
---
 ruby/ql/lib/codeql/ruby/AST.qll | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ruby/ql/lib/codeql/ruby/AST.qll b/ruby/ql/lib/codeql/ruby/AST.qll
index e98749af4273..bd42696a8dbe 100644
--- a/ruby/ql/lib/codeql/ruby/AST.qll
+++ b/ruby/ql/lib/codeql/ruby/AST.qll
@@ -172,7 +172,7 @@ class RubyFile extends File {
  * A successfully extracted file, that is, a file that was extracted and
  * contains no extraction errors or warnings.
  */
-class SuccessfullyExtractedFile extends RubyFile {
+class SuccessfullyExtractedFile extends File {
   SuccessfullyExtractedFile() {
     not exists(Diagnostic d |
       d.getLocation().getFile() = this and