Annotate execute request source code with code location

Cargo.toml

@@ -25,9 +25,10 @@ license = "MIT"
 authors = ["Posit Software, PBC"]
 
 [workspace.dependencies]
+biome_line_index = { git = "https://github.com/lionel-/biome", rev = "41d799cfa4cedd25625fc3f6bd7898532873f051" }
+biome_rowan = { git = "https://github.com/lionel-/biome", rev = "41d799cfa4cedd25625fc3f6bd7898532873f051" }
 aether_lsp_utils = { git = "https://github.com/posit-dev/air", rev = "4cbd36d552e27d8930cff1602d56bfd9ce4c1ed1" }
 aether_parser = { git = "https://github.com/posit-dev/air", package = "air_r_parser", rev = "4cbd36d552e27d8930cff1602d56bfd9ce4c1ed1" }
 aether_syntax = { git = "https://github.com/posit-dev/air", package = "air_r_syntax", rev = "4cbd36d552e27d8930cff1602d56bfd9ce4c1ed1" }
-biome_line_index = { git = "https://github.com/lionel-/biome", rev = "41d799cfa4cedd25625fc3f6bd7898532873f051" }
 # For https://github.com/ebkalderon/tower-lsp/pull/428
 tower-lsp = { branch = "bugfix/patches", git = "https://github.com/lionel-/tower-lsp" }

crates/amalthea/Cargo.toml

@@ -34,6 +34,7 @@ serde_with = "3.0.0"
 serde_repr = "0.1.17"
 tracing = "0.1.40"
 assert_matches = "1.5.0"
+url = "2.5.7"
 
 [dev-dependencies]
 env_logger = "0.10.0"

crates/amalthea/src/fixtures/dummy_frontend.rs

@@ -16,6 +16,8 @@ use crate::socket::socket::Socket;
 use crate::wire::comm_msg::CommWireMsg;
 use crate::wire::execute_input::ExecuteInput;
 use crate::wire::execute_request::ExecuteRequest;
+use crate::wire::execute_request::ExecuteRequestPositron;
+use crate::wire::execute_request::JupyterPositronLocation;
 use crate::wire::handshake_reply::HandshakeReply;
 use crate::wire::input_reply::InputReply;
 use crate::wire::jupyter_message::JupyterMessage;
@@ -49,6 +51,7 @@ pub struct DummyFrontend {
 
 pub struct ExecuteRequestOptions {
     pub allow_stdin: bool,
+    pub positron: Option<ExecuteRequestPositron>,
 }
 
 impl DummyConnection {
@@ -234,6 +237,7 @@ impl DummyFrontend {
             user_expressions: serde_json::Value::Null,
             allow_stdin: options.allow_stdin,
             stop_on_error: false,
+            positron: options.positron,
         })
     }
 
@@ -265,7 +269,38 @@ impl DummyFrontend {
     where
         F: FnOnce(String),
     {
-        self.send_execute_request(code, ExecuteRequestOptions::default());
+        self.execute_request_with_options(code, result_check, Default::default())
+    }
+
+    #[track_caller]
+    pub fn execute_request_with_location<F>(
+        &self,
+        code: &str,
+        result_check: F,
+        code_location: JupyterPositronLocation,
+    ) -> u32
+    where
+        F: FnOnce(String),
+    {
+        self.execute_request_with_options(code, result_check, ExecuteRequestOptions {
+            positron: Some(ExecuteRequestPositron {
+                code_location: Some(code_location),
+            }),
+            ..Default::default()
+        })
+    }
+
+    #[track_caller]
+    pub fn execute_request_with_options<F>(
+        &self,
+        code: &str,
+        result_check: F,
+        options: ExecuteRequestOptions,
+    ) -> u32
+    where
+        F: FnOnce(String),
+    {
+        self.send_execute_request(code, options);
         self.recv_iopub_busy();
 
         let input = self.recv_iopub_execute_input();
@@ -703,6 +738,9 @@ impl DummyFrontend {
 
 impl Default for ExecuteRequestOptions {
     fn default() -> Self {
-        Self { allow_stdin: false }
+        Self {
+            allow_stdin: false,
+            positron: None,
+        }
     }
 }

crates/amalthea/src/wire/execute_request.rs

@@ -5,9 +5,11 @@
  *
  */
 
+use anyhow::Context;
 use serde::Deserialize;
 use serde::Serialize;
 use serde_json::Value;
+use url::Url;
 
 use crate::wire::jupyter_message::MessageType;
 
@@ -33,6 +35,119 @@ pub struct ExecuteRequest {
     /// Whether the kernel should discard the execution queue if evaluating the
     /// code results in an error
     pub stop_on_error: bool,
+
+    /// Posit extension
+    pub positron: Option<ExecuteRequestPositron>,
+}
+
+#[serde_with::skip_serializing_none]
+#[derive(Debug, Serialize, Deserialize, Clone)]
+pub struct ExecuteRequestPositron {
+    pub code_location: Option<JupyterPositronLocation>,
+}
+
+#[derive(Debug, Serialize, Deserialize, Clone)]
+pub struct JupyterPositronLocation {
+    pub uri: String,
+    pub range: JupyterPositronRange,
+}
+
+#[derive(Debug, Serialize, Deserialize, Clone)]
+pub struct JupyterPositronRange {
+    pub start: JupyterPositronPosition,
+    pub end: JupyterPositronPosition,
+}
+
+#[derive(Debug, Serialize, Deserialize, Clone)]
+pub struct JupyterPositronPosition {
+    pub line: u32,
+    /// Column offset in UTF-8 bytes
+    pub character: u32,
+}
+
+/// Code location with `character` in UTF-8 offset
+#[derive(Debug, Clone)]
+pub struct CodeLocation {
+    pub uri: Url,
+    pub start: Position,
+    pub end: Position,
+}
+
+/// `character` in UTF-8 offset
+#[derive(Debug, Clone)]
+pub struct Position {
+    pub line: u32,
+    pub character: u32,
+}
+
+impl ExecuteRequest {
+    pub fn code_location(&self) -> anyhow::Result<Option<CodeLocation>> {
+        let Some(positron) = &self.positron else {
+            return Ok(None);
+        };
+        let Some(location) = &positron.code_location else {
+            return Ok(None);
+        };
+
+        let uri = Url::parse(&location.uri).context("Failed to parse URI from code location")?;
+        let range = &location.range;
+
+        // Validate that range is not inverted
+        if range.end.line < range.start.line ||
+            (range.end.line == range.start.line && range.end.character < range.start.character)
+        {
+            return Err(anyhow::anyhow!(
+                "Invalid range: end ({}, {}) is before start ({}, {})",
+                range.end.line,
+                range.end.character,
+                range.start.line,
+                range.start.character
+            ));
+        }
+
+        // Validate that the span dimensions match the code extents
+        let span_lines = (range.end.line - range.start.line) as usize;
+        let code_newlines = self.code.matches('\n').count();
+
+        if code_newlines != span_lines {
+            return Err(anyhow::anyhow!(
+                "Line count mismatch: location spans {span_lines} lines, but code has {code_newlines} newlines"
+            ));
+        }
+
+        // Validate last line byte length
+        let last_line = if self.code.ends_with('\n') {
+            ""
+        } else {
+            self.code.lines().last().unwrap_or("")
+        };
+        let last_line = last_line.strip_suffix('\r').unwrap_or(last_line);
+
+        let expected_bytes = if span_lines == 0 {
+            range.end.character - range.start.character
+        } else {
+            range.end.character
+        };
+
+        if last_line.len() as u32 != expected_bytes {
+            return Err(anyhow::anyhow!(
+                "Expected last line to have {expected_bytes} bytes, got {}",
+                last_line.len()
+            ));
+        }
+
+        Ok(Some(CodeLocation {
+            uri,
+            start: Position {
+                line: range.start.line,
+                character: range.start.character,
+            },
+            end: Position {
+                line: range.end.line,
+                character: range.end.character,
+            },
+        }))
+    }
 }
 
 impl MessageType for ExecuteRequest {

crates/ark/Cargo.toml

@@ -20,6 +20,7 @@ anyhow = "1.0.80"
 async-trait = "0.1.66"
 base64 = "0.21.0"
 biome_line_index.workspace = true
+biome_rowan.workspace = true
 bus = "2.3.0"
 cfg-if = "1.0.0"
 crossbeam = { version = "0.8.2", features = ["crossbeam-channel"] }

crates/ark/src/console_annotate.rs

@@ -0,0 +1,142 @@
+//
+// console_annotate.rs
+//
+// Copyright (C) 2025 Posit Software, PBC. All rights reserved.
+//
+
+use amalthea::wire::execute_request::CodeLocation;
+use biome_rowan::AstNode;
+
+pub(crate) fn annotate_input(code: &str, location: CodeLocation) -> String {
+    let node = aether_parser::parse(code, Default::default()).tree();
+    let Some(first_token) = node.syntax().first_token() else {
+        return code.into();
+    };
+
+    let line_directive = format!(
+        "#line {line} \"{uri}\"",
+        line = location.start.line + 1,
+        uri = location.uri
+    );
+
+    // Leading whitespace to ensure that R starts parsing expressions from
+    // the expected `character` offset.
+    let leading_padding = " ".repeat(location.start.character as usize);
+
+    // Collect existing leading trivia as (kind, text) tuples
+    let existing_trivia: Vec<_> = first_token
+        .leading_trivia()
+        .pieces()
+        .map(|piece| (piece.kind(), piece.text().to_string()))
+        .collect();
+
+    // Create new trivia with line directive prepended
+    let new_trivia: Vec<_> = vec![
+        (
+            biome_rowan::TriviaPieceKind::SingleLineComment,
+            line_directive.to_string(),
+        ),
+        (biome_rowan::TriviaPieceKind::Newline, "\n".to_string()),
+        (
+            biome_rowan::TriviaPieceKind::Whitespace,
+            leading_padding.to_string(),
+        ),
+    ]
+    .into_iter()
+    .chain(existing_trivia.into_iter())
+    .collect();
+
+    let new_first_token =
+        first_token.with_leading_trivia(new_trivia.iter().map(|(k, t)| (*k, t.as_str())));
+
+    let Some(new_node) = node
+        .syntax()
+        .clone()
+        .replace_child(first_token.into(), new_first_token.into())
+    else {
+        return code.into();
+    };
+
+    new_node.to_string()
+}
+
+#[cfg(test)]
+mod tests {
+    use amalthea::wire::execute_request::CodeLocation;
+    use amalthea::wire::execute_request::Position;
+    use url::Url;
+
+    use super::*;
+
+    fn make_location(line: u32, character: u32) -> CodeLocation {
+        CodeLocation {
+            uri: Url::parse("file:///test.R").unwrap(),
+            start: Position { line, character },
+            end: Position { line, character },
+        }
+    }
+
+    #[test]
+    fn test_annotate_input_basic() {
+        let code = "x <- 1\ny <- 2";
+        let location = make_location(0, 0);
+        let result = annotate_input(code, location);
+        insta::assert_snapshot!(result);
+    }
+
+    #[test]
+    fn test_annotate_input_shifted_line() {
+        let code = "x <- 1\ny <- 2";
+        let location = make_location(10, 0);
+        let result = annotate_input(code, location);
+        insta::assert_snapshot!(result);
+    }
+
+    #[test]
+    fn test_annotate_input_shifted_character() {
+        let code = "x <- 1\ny <- 2";
+        let location = make_location(0, 5);
+        let result = annotate_input(code, location);
+        insta::assert_snapshot!(result);
+    }
+
+    #[test]
+    fn test_annotate_input_shifted_line_and_character() {
+        let code = "x <- 1\ny <- 2";
+        let location = make_location(10, 5);
+        let result = annotate_input(code, location);
+        insta::assert_snapshot!(result);
+    }
+
+    #[test]
+    fn test_annotate_input_with_existing_whitespace() {
+        let code = "  x <- 1\n  y <- 2";
+        let location = make_location(0, 0);
+        let result = annotate_input(code, location);
+        insta::assert_snapshot!(result);
+    }
+
+    #[test]
+    fn test_annotate_input_with_existing_whitespace_shifted() {
+        let code = "  x <- 1\n  y <- 2";
+        let location = make_location(0, 2);
+        let result = annotate_input(code, location);
+        insta::assert_snapshot!(result);
+    }
+
+    #[test]
+    fn test_annotate_input_with_existing_comment() {
+        let code = "# comment\nx <- 1";
+        let location = make_location(0, 0);
+        let result = annotate_input(code, location);
+        insta::assert_snapshot!(result);
+    }
+
+    #[test]
+    fn test_annotate_input_empty_code() {
+        let code = "";
+        let location = make_location(0, 0);
+        let result = annotate_input(code, location);
+        insta::assert_snapshot!(result);
+    }
+}

crates/ark/src/repl_debug.rs → crates/ark/src/console_debug.rs

@@ -1,7 +1,7 @@
 //
-// repl_debug.rs
+// console_debug.rs
 //
-// Copyright (C) 2025 Posit Software, PBC. All rights reserved.
+// Copyright (C) 2026 Posit Software, PBC. All rights reserved.
 //
 
 use anyhow::anyhow;

crates/ark/src/dap/dap.rs

@@ -18,8 +18,8 @@ use harp::object::RObject;
 use stdext::result::ResultExt;
 use stdext::spawn;
 
+use crate::console_debug::FrameInfo;
 use crate::dap::dap_server;
-use crate::repl_debug::FrameInfo;
 use crate::request::RRequest;
 use crate::thread::RThreadSafe;