From f21b6c73cf0e019d8429b29ed29f9bebe13679b4 Mon Sep 17 00:00:00 2001 From: Bob Van Hove <1587584+bobvh@users.noreply.github.com> Date: Fri, 29 May 2026 14:16:15 -0400 Subject: [PATCH] =?UTF-8?q?docs(cli):=20rename=20"block=20group"=20?= =?UTF-8?q?=E2=86=92=20"sequence=20graph"=20in=20user-visible=20strings?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-Authored-By: Claude Sonnet 4.6 --- src/commands/graph_operations/derive_chunks.rs | 2 +- src/commands/graph_operations/derive_subgraph.rs | 2 +- src/commands/mod.rs | 2 +- src/errors.rs | 6 ++++-- src/main.rs | 2 +- src/views/block_group.rs | 15 +++++++++------ 6 files changed, 17 insertions(+), 12 deletions(-) diff --git a/src/commands/graph_operations/derive_chunks.rs b/src/commands/graph_operations/derive_chunks.rs index d205f252..0a60c09f 100644 --- a/src/commands/graph_operations/derive_chunks.rs +++ b/src/commands/graph_operations/derive_chunks.rs @@ -132,7 +132,7 @@ pub fn derive_chunks_operation( } let summary_str = format!( - " {}: {} new derived block group(s)", + " {}: {} new derived sequence graph(s)", new_sample_name, chunk_range_length, ); diff --git a/src/commands/graph_operations/derive_subgraph.rs b/src/commands/graph_operations/derive_subgraph.rs index b9c555b5..c3250642 100644 --- a/src/commands/graph_operations/derive_subgraph.rs +++ b/src/commands/graph_operations/derive_subgraph.rs @@ -77,7 +77,7 @@ pub fn derive_subgraph_operation( return Err(err.into()); } - let summary_str = format!(" {}: new derived block group", new_sample_name,); + let summary_str = format!(" {}: new derived sequence graph", new_sample_name,); let _op = end_operation( db_context, diff --git a/src/commands/mod.rs b/src/commands/mod.rs index 66ed00fe..d5f6a938 100644 --- a/src/commands/mod.rs +++ b/src/commands/mod.rs @@ -281,7 +281,7 @@ pub enum Commands { #[arg(short, long)] sample: Option, }, - /// Search for an exact sequence across all block groups + /// Search for an exact sequence across all sequence graphs /// /// Each match is reported with a blocks column formatted as [hash:start-end, ...], /// where hash is a 12-character node hash prefix from the original node the block diff --git a/src/errors.rs b/src/errors.rs index 79fa5ad4..e62c2275 100644 --- a/src/errors.rs +++ b/src/errors.rs @@ -28,7 +28,7 @@ pub enum SequenceUpdateError { NodeError(#[from] NodeError), #[error("Path creation error: {0}")] PathError(#[from] PathError), - #[error("Block group creation error: {0}")] + #[error("Sequence graph creation error: {0}")] BlockGroupError(#[from] BlockGroupError), #[error("Sample creation error: {0}")] SampleError(#[from] SampleError), @@ -48,7 +48,9 @@ pub enum SequenceUpdateError { MissingCoordinates(String), #[error("Unsupported region type for sequence update: {0}")] UnsupportedRegionType(String), - #[error("Resolved path '{path_name}' was not found in target block group '{block_group_name}'")] + #[error( + "Resolved path '{path_name}' was not found in target sequence graph '{block_group_name}'" + )] MissingResolvedPath { path_name: String, block_group_name: String, diff --git a/src/main.rs b/src/main.rs index b251fb52..06dc44d1 100644 --- a/src/main.rs +++ b/src/main.rs @@ -211,7 +211,7 @@ fn call_cli() -> Result<(), Box> { } Err(_) => { eprintln!( - "No block group found with name {:?} and sample {:?} in collection {}", + "No sequence graph found with name {:?} and sample {:?} in collection {}", name, sample_name, collection_name ); } diff --git a/src/views/block_group.rs b/src/views/block_group.rs index 5409eec0..3d5ba19b 100644 --- a/src/views/block_group.rs +++ b/src/views/block_group.rs @@ -183,7 +183,7 @@ pub fn view_block_group( ) -> Result<(), Box> { let progress_bar = get_handler(); let bar = progress_bar.add(get_time_elapsed_bar()); - let _ = progress_bar.println("Loading block group"); + let _ = progress_bar.println("Loading sequence graph"); // Get the node object corresponding to the position given by the user let origin = if let Some(position_str) = position { @@ -218,7 +218,7 @@ pub fn view_block_group( if block_group.is_err() { panic!( - "No block group found with name {:?} and sample {:?} in collection {} ", + "No sequence graph found with name {:?} and sample {:?} in collection {} ", name, sample_name.clone(), collection_name @@ -250,7 +250,7 @@ pub fn view_block_group( Ok(bg) => bg, Err(err) => { // TODO: Handle these with messages instead of panic'ing - panic!("Failed to load block group {bg_id}: {err}"); + panic!("Failed to load sequence graph {bg_id}: {err}"); } }); @@ -404,7 +404,7 @@ pub fn view_block_group( Ok(highlighting_enabled) => { if highlighting_enabled { info!( - "Path highlighting enabled for block group {}", + "Path highlighting enabled for sequence graph {}", block_group_id ); } else { @@ -416,7 +416,7 @@ pub fn view_block_group( } } } else { - warn!("No block group selected for path highlighting"); + warn!("No sequence graph selected for path highlighting"); } } _ => { @@ -1118,7 +1118,10 @@ pub fn view_block_group( Ok(bg) => bg, Err(err) => { // TODO: Handle these with messages instead of panic'ing - panic!("Failed to load block group {}: {err}", new_block_group_id); + panic!( + "Failed to load sequence graph {}: {err}", + new_block_group_id + ); } };