Some cleanup

ginkgobioworks · Aug 21, 2024 · 3d1b48c · 3d1b48c
1 parent a67c60f
commit 3d1b48c
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Showing 2 changed files with 9 additions and 15 deletions.
diff --git a/src/models.rs b/src/models.rs
@@ -16,7 +16,7 @@ pub mod sequence;
 use crate::graph::all_simple_paths;
 use crate::models::block::Block;
 use crate::models::edge::Edge;
-use crate::models::new_edge::NewEdge;
+use crate::models::new_edge::{EdgeData, NewEdge};
 use crate::models::path::{NewBlock, Path, PathBlock};
 use crate::models::sequence::Sequence;
 use crate::{get_overlap, models};
@@ -513,7 +513,7 @@ impl BlockGroup {
         new_block: &NewBlock,
         chromosome_index: i32,
         phased: i32,
-    ) -> Vec<NewEdge> {
+    ) {
         // todo:
         // cases to check:
         //  change that is the size of a block
@@ -536,8 +536,7 @@ impl BlockGroup {
 
         if new_block.sequence_start == new_block.sequence_end {
             // Deletion
-            let new_edge = NewEdge {
-                id: 0,
+            let new_edge = EdgeData {
                 source_hash: start_block.sequence.hash.clone(),
                 source_coordinate: start - start_block.path_start + start_block.sequence_start,
                 target_hash: end_block.sequence.hash.clone(),
@@ -548,17 +547,15 @@ impl BlockGroup {
             new_edges.push(new_edge);
         } else {
             // Insertion/replacement
-            let new_start_edge = NewEdge {
-                id: 0,
+            let new_start_edge = EdgeData {
                 source_hash: start_block.sequence.hash.clone(),
                 source_coordinate: start - start_block.path_start + start_block.sequence_start,
                 target_hash: new_block.sequence.hash.clone(),
                 target_coordinate: new_block.sequence_start,
                 chromosome_index,
                 phased,
             };
-            let new_end_edge = NewEdge {
-                id: 0,
+            let new_end_edge = EdgeData {
                 source_hash: new_block.sequence.hash.clone(),
                 source_coordinate: new_block.sequence_end,
                 target_hash: end_block.sequence.hash.clone(),
@@ -574,8 +571,7 @@ impl BlockGroup {
         // retrieve it as one node of the overall graph
         if start < start_block.path_end {
             let split_coordinate = start - start_block.path_start + start_block.sequence_start;
-            let new_split_start_edge = NewEdge {
-                id: 0,
+            let new_split_start_edge = EdgeData {
                 source_hash: start_block.sequence.hash.clone(),
                 source_coordinate: split_coordinate,
                 target_hash: start_block.sequence.hash.clone(),
@@ -588,8 +584,7 @@ impl BlockGroup {
 
         if end > end_block.path_start {
             let split_coordinate = end - end_block.path_start + end_block.sequence_start;
-            let new_split_end_edge = NewEdge {
-                id: 0,
+            let new_split_end_edge = EdgeData {
                 source_hash: new_block.sequence.hash.clone(),
                 source_coordinate: split_coordinate,
                 target_hash: end_block.sequence.hash.clone(),
@@ -601,8 +596,7 @@ impl BlockGroup {
             new_edges.push(new_split_end_edge);
         }
 
-        // TODO: bulk create-or-get of new edges
-        new_edges
+        NewEdge::bulk_create(conn, new_edges);
     }
 }
 

diff --git a/src/models/new_edge.rs b/src/models/new_edge.rs
@@ -172,7 +172,7 @@ impl NewEdge {
         }
         let formatted_edge_rows_to_insert = edge_rows_to_insert.join(", ");
 
-        let insert_statement = format!("INSERT OR IGNORE INTO new_edges (source_hash, source_coordinate, target_hash, target_coordinate, chromosome_index, phased) VALUES {0} RETURNING (id);", formatted_edge_rows_to_insert);
+        let insert_statement = format!("INSERT INTO new_edges (source_hash, source_coordinate, target_hash, target_coordinate, chromosome_index, phased) VALUES {0} RETURNING (id);", formatted_edge_rows_to_insert);
         let mut stmt = conn.prepare(&insert_statement).unwrap();
         let rows = stmt.query_map([], |row| row.get(0)).unwrap();
         let mut edge_ids: Vec<i32> = vec![];