View patches

Cargo.toml

@@ -33,6 +33,7 @@ flate2 = "1.0.35"
 gb-io = "0.7.1"
 thiserror = "1.0.69"
 indicatif = "0.17.9"
+html-escape = "0.2.13"
 
 [dev-dependencies]
 cargo-llvm-cov = "0.6.14"

src/config.rs

@@ -14,10 +14,15 @@ pub static BASE_DIR: LazyLock<RwLock<PathBuf>> =
     LazyLock::new(|| RwLock::new(env::current_dir().unwrap()));
 }
 
-pub fn get_operation_connection() -> Connection {
-    let db_path = get_gen_db_path();
+pub fn get_operation_connection(db_path: impl Into<Option<PathBuf>>) -> Connection {
+    let db_path = db_path.into();
+    let path = if let Some(s) = db_path {
+        s
+    } else {
+        get_gen_db_path()
+    };
     let mut conn =
-        Connection::open(&db_path).unwrap_or_else(|_| panic!("Error connecting to {:?}", &db_path));
+        Connection::open(&path).unwrap_or_else(|_| panic!("Error connecting to {:?}", &path));
     run_operation_migrations(&mut conn);
     conn
 }

src/graph.rs

@@ -7,7 +7,7 @@ use petgraph::prelude::EdgeRef;
 use petgraph::visit::{GraphRef, IntoEdges, IntoNeighbors, IntoNeighborsDirected, NodeCount};
 use petgraph::Direction;
 use std::collections::{HashMap, HashSet, VecDeque};
-use std::fmt::Debug;
+use std::fmt::{self, Debug};
 use std::hash::Hash;
 use std::iter::from_fn;
 
@@ -19,6 +19,16 @@ pub struct GraphNode {
     pub sequence_end: i64,
 }
 
+impl fmt::Display for GraphNode {
+    fn fmt(&self, f: &mut fmt::Formatter<'_>) -> fmt::Result {
+        write!(
+            f,
+            "{}[{}-{}]",
+            self.node_id, self.sequence_start, self.sequence_end
+        )
+    }
+}
+
 impl GraphNode {
     pub fn length(&self) -> i64 {
         self.sequence_end - self.sequence_start

src/lib.rs

@@ -21,6 +21,7 @@ pub mod range;
 #[cfg(test)]
 pub mod test_helpers;
 pub mod updates;
+pub mod views;
 
 use crate::migrations::run_migrations;
 use noodles::vcf::variant::record::samples::series::value::genotype::Phasing;

src/main.rs

@@ -24,13 +24,15 @@ use gen::updates::gaf::{transform_csv_to_fasta, update_with_gaf};
 use gen::updates::genbank::update_with_genbank;
 use gen::updates::library::update_with_library;
 use gen::updates::vcf::{update_with_vcf, VcfError};
+use gen::views::patch::view_patches;
 use itertools::Itertools;
 use noodles::core::Region;
 use rusqlite::{types::Value, Connection};
 use std::fmt::Debug;
 use std::fs::File;
+use std::io::Write;
 use std::ops::Deref;
-use std::path::PathBuf;
+use std::path::{Path, PathBuf};
 use std::{io, str};
 
 #[derive(Parser)]
@@ -171,6 +173,16 @@ enum Commands {
         #[clap(index = 1)]
         patch: String,
     },
+    /// View a patch
+    #[command(name = "patch-view", arg_required_else_help(true))]
+    PatchView {
+        /// The prefix to save dot files under. Defaults to patch filename
+        #[arg(long, short)]
+        prefix: Option<String>,
+        /// The patch file
+        #[clap(index = 1)]
+        patch: String,
+    },
     /// Initialize a gen repository
     Init {},
     /// Manage and create branches
@@ -317,7 +329,7 @@ fn main() {
         return;
     }
 
-    let operation_conn = get_operation_connection();
+    let operation_conn = get_operation_connection(None);
     if let Some(Commands::Defaults {
         database,
         collection,
@@ -774,6 +786,32 @@ fn main() {
             let patches = patch::load_patches(&mut f);
             patch::apply_patches(&conn, &operation_conn, &patches);
         }
+        Some(Commands::PatchView { prefix, patch }) => {
+            let patch_path = Path::new(patch);
+            let mut f = File::open(patch_path).unwrap();
+            let patches = patch::load_patches(&mut f);
+            let diagrams = view_patches(&patches);
+            for (patch_hash, patch_diagrams) in diagrams.iter() {
+                for (bg_id, dot) in patch_diagrams.iter() {
+                    let path = if let Some(p) = prefix {
+                        format!("{p}_{patch_hash}_{bg_id}.dot")
+                    } else {
+                        format!(
+                            "{patch_base}_{patch_hash}_{bg_id}.dot",
+                            patch_base = patch_path
+                                .with_extension("")
+                                .file_name()
+                                .unwrap()
+                                .to_str()
+                                .unwrap()
+                        )
+                    };
+                    let mut f = File::create(path).unwrap();
+                    f.write_all(dot.as_bytes())
+                        .expect("Failed to write diagram");
+                }
+            }
+        }
         None => {}
         // these will never be handled by this method as we search for them earlier.
         Some(Commands::Init {}) => {

src/models/node.rs

@@ -13,6 +13,7 @@ pub const PATH_END_NODE_ID: i64 = 2;
 pub struct Node {
     pub id: i64,
     pub sequence_hash: String,
+    pub hash: Option<String>,
 }
 
 impl Query for Node {
@@ -21,6 +22,7 @@ impl Query for Node {
         Node {
             id: row.get(0).unwrap(),
             sequence_hash: row.get(1).unwrap(),
+            hash: row.get(2).unwrap(),
         }
     }
 }
@@ -128,6 +130,32 @@ impl Node {
     }
 
     pub fn is_terminal(node_id: i64) -> bool {
-        node_id == PATH_START_NODE_ID || node_id == PATH_END_NODE_ID
+        Node::is_start_node(node_id) || Node::is_end_node(node_id)
+    }
+
+    pub fn is_start_node(node_id: i64) -> bool {
+        node_id == PATH_START_NODE_ID
+    }
+
+    pub fn is_end_node(node_id: i64) -> bool {
+        node_id == PATH_END_NODE_ID
+    }
+
+    pub fn get_start_node() -> Node {
+        Node {
+            id: PATH_START_NODE_ID,
+            sequence_hash: "start-node-yyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyy"
+                .to_string(),
+            hash: None,
+        }
+    }
+
+    pub fn get_end_node() -> Node {
+        Node {
+            id: PATH_END_NODE_ID,
+            sequence_hash: "end-node-zzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzz"
+                .to_string(),
+            hash: None,
+        }
     }
 }