Merge pull request #14 from ginkgobioworks/cleanup-august-2024

Fix a bunch of warnings
ginkgobioworks · Aug 13, 2024 · 59f66a8 · 59f66a8
2 parents 0e9fedd + 353cfbf
commit 59f66a8
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Showing 7 changed files with 38 additions and 49 deletions.
diff --git a/.gitignore b/.gitignore
@@ -1,5 +1,6 @@
 # our test dbs
 *.db-*
+*.db
 
 # Generated by Cargo
 # will have compiled files and executables

diff --git a/src/lib.rs b/src/lib.rs
@@ -39,12 +39,12 @@ pub struct Genotype {
 
 pub fn parse_genotype(gt: &str) -> Vec<Option<Genotype>> {
     let mut genotypes = vec![];
-    let mut phase = match gt.contains("/") {
+    let mut phase = match gt.contains('/') {
         true => Phasing::Unphased,
         false => Phasing::Phased,
     };
-    for (index, entry) in gt.split_inclusive(|c| c == '|' || c == '/').enumerate() {
-        let mut allele;
+    for entry in gt.split_inclusive(|c| c == '|' || c == '/') {
+        let allele;
         let mut phasing = Phasing::Unphased;
         if entry.ends_with(['/', '|']) {
             let (allele_str, phasing_str) = entry.split_at(entry.len() - 1);
@@ -99,7 +99,7 @@ mod tests {
 
     #[test]
     fn it_queries() {
-        let mut conn = get_connection();
+        let conn = get_connection();
         let sequence_count: i32 = conn
             .query_row(
                 "SELECT count(*) from sequence where hash = 'foo'",

diff --git a/src/models.rs b/src/models.rs
@@ -1,13 +1,10 @@
-use noodles::vcf::variant::record::info::field::value::array::Values;
-use petgraph::data::Build;
 use petgraph::graphmap::DiGraphMap;
 use petgraph::Direction;
 use rusqlite::types::Value;
 use rusqlite::{params_from_iter, Connection};
 use sha2::{Digest, Sha256};
 use std::collections::{HashMap, HashSet};
 use std::fmt::*;
-use std::hash::Hash;
 
 pub mod block;
 pub mod edge;
@@ -175,11 +172,10 @@ impl BlockGroup {
             let target_id: Option<i32> = edge.get(2).unwrap();
             let chrom_index = edge.get(3).unwrap();
             let phased = edge.get(4).unwrap();
-            let mut new_edge;
             if target_id.is_some() && source_id.is_some() {
                 let target_id = target_id.unwrap();
                 let source_id = source_id.unwrap();
-                new_edge = Edge::create(
+                Edge::create(
                     conn,
                     Some(*block_map.get(&source_id).unwrap_or(&source_id)),
                     Some(*block_map.get(&target_id).unwrap_or(&target_id)),
@@ -188,7 +184,7 @@ impl BlockGroup {
                 );
             } else if target_id.is_some() {
                 let target_id = target_id.unwrap();
-                new_edge = Edge::create(
+                Edge::create(
                     conn,
                     None,
                     Some(*block_map.get(&target_id).unwrap_or(&target_id)),
@@ -197,7 +193,7 @@ impl BlockGroup {
                 );
             } else if source_id.is_some() {
                 let source_id = source_id.unwrap();
-                new_edge = Edge::create(
+                Edge::create(
                     conn,
                     Some(*block_map.get(&source_id).unwrap_or(&source_id)),
                     None,
@@ -415,7 +411,7 @@ impl BlockGroup {
         let mut previous_block: Option<&Block> = None;
         for block_id in &path.blocks {
             let block = blocks.get(block_id).unwrap();
-            let block_length = (block.end - block.start);
+            let block_length = block.end - block.start;
             path_end += block_length;
 
             let (contains_start, contains_end, overlap) =
@@ -448,7 +444,7 @@ impl BlockGroup {
                 if end_split_point == next_block.start {
                     new_edges.push((Some(new_block_id), Some(next_block.id)));
                 } else {
-                    let (left_block, right_block) =
+                    let (left_block, _right_block) =
                         Block::split(conn, &next_block, end_split_point, chromosome_index, phased)
                             .unwrap();
                     Block::delete(conn, next_block.id);
@@ -465,7 +461,7 @@ impl BlockGroup {
                         new_edges.push((Some(pb.id), Some(new_block_id)));
                     }
                 } else {
-                    let (left_block, right_block) =
+                    let (left_block, _right_block) =
                         Block::split(conn, block, split_point, chromosome_index, phased).unwrap();
                     Block::delete(conn, block.id);
                     new_edges.push((Some(left_block.id), Some(new_block_id)));
@@ -479,7 +475,7 @@ impl BlockGroup {
                     // the previous change ends right before this block starts, so it's an insert
                     new_edges.push((Some(new_block_id), Some(block.id)));
                 } else {
-                    let (left_block, right_block) =
+                    let (_left_block, right_block) =
                         Block::split(conn, block, split_point, chromosome_index, phased).unwrap();
                     Block::delete(conn, block.id);
                     new_edges.push((Some(new_block_id), Some(right_block.id)));
@@ -586,9 +582,7 @@ impl ChangeLog {
 #[cfg(test)]
 mod tests {
     use super::*;
-    use crate::get_connection as get_db_connection;
     use crate::migrations::run_migrations;
-    use std::fs;
     use std::hash::Hash;
 
     fn get_connection() -> Connection {
@@ -603,17 +597,17 @@ mod tests {
         let t_seq_hash = Sequence::create(conn, "DNA", "TTTTTTTTTT", true);
         let c_seq_hash = Sequence::create(conn, "DNA", "CCCCCCCCCC", true);
         let g_seq_hash = Sequence::create(conn, "DNA", "GGGGGGGGGG", true);
-        let collection = Collection::create(conn, "test");
+        let _collection = Collection::create(conn, "test");
         let block_group = BlockGroup::create(conn, "test", None, "hg19");
         let a_block = Block::create(conn, &a_seq_hash, block_group.id, 0, 10, "+");
         let t_block = Block::create(conn, &t_seq_hash, block_group.id, 0, 10, "+");
         let c_block = Block::create(conn, &c_seq_hash, block_group.id, 0, 10, "+");
         let g_block = Block::create(conn, &g_seq_hash, block_group.id, 0, 10, "+");
-        let edge_0 = Edge::create(conn, None, Some(a_block.id), 0, 0);
-        let edge_1 = Edge::create(conn, Some(a_block.id), Some(t_block.id), 0, 0);
-        let edge_2 = Edge::create(conn, Some(t_block.id), Some(c_block.id), 0, 0);
-        let edge_3 = Edge::create(conn, Some(c_block.id), Some(g_block.id), 0, 0);
-        let edge_4 = Edge::create(conn, Some(g_block.id), None, 0, 0);
+        let _edge_0 = Edge::create(conn, None, Some(a_block.id), 0, 0);
+        let _edge_1 = Edge::create(conn, Some(a_block.id), Some(t_block.id), 0, 0);
+        let _edge_2 = Edge::create(conn, Some(t_block.id), Some(c_block.id), 0, 0);
+        let _edge_3 = Edge::create(conn, Some(c_block.id), Some(g_block.id), 0, 0);
+        let _edge_4 = Edge::create(conn, Some(g_block.id), None, 0, 0);
         let path = Path::create(
             conn,
             "chr1",

diff --git a/src/models/block.rs b/src/models/block.rs
@@ -1,4 +1,3 @@
-use crate::models::Path;
 use rusqlite::{params_from_iter, types::Value, Connection};
 
 use crate::models::edge::{Edge, UpdatedEdge};
@@ -232,7 +231,7 @@ impl Block {
 
     pub fn get_blocks(conn: &Connection, query: &str, placeholders: Vec<Value>) -> Vec<Block> {
         let mut stmt = conn.prepare(query).unwrap();
-        let mut rows = stmt
+        let rows = stmt
             .query_map(params_from_iter(placeholders), |row| {
                 Ok(Block {
                     id: row.get(0)?,
@@ -421,21 +420,21 @@ mod tests {
 
     #[test]
     fn get_sequence() {
-        let conn = get_connection();
+        let conn = &mut get_connection();
         let sequence = "AAATTTCCCGGG".to_string();
-        let seq = Sequence::create(&conn, "DNA", &sequence, true);
-        let coll = Collection::create(&conn, "test");
-        let bg = BlockGroup::create(&conn, "test", None, "test");
-        let block = Block::create(&conn, &seq, bg.id, 0, 12, "+");
+        let seq = Sequence::create(conn, "DNA", &sequence, true);
+        Collection::create(conn, "test collection");
+        let bg = BlockGroup::create(conn, "test collection", None, "test");
+        let block = Block::create(conn, &seq, bg.id, 0, 12, "+");
         assert_eq!(
-            Block::get_sequence(&conn, block.id),
-            (sequence, "1".to_string())
+            Block::get_sequence(conn, block.id),
+            (sequence, "+".to_string())
         );
 
-        let block = Block::create(&conn, &seq, bg.id, 0, 9, "+");
+        let block = Block::create(conn, &seq, bg.id, 0, 9, "+");
         assert_eq!(
-            Block::get_sequence(&conn, block.id),
-            ("AAATTTCCC".to_string(), "1".to_string())
+            Block::get_sequence(conn, block.id),
+            ("AAATTTCCC".to_string(), "+".to_string())
         );
     }
 }
diff --git a/src/models/edge.rs b/src/models/edge.rs
@@ -1,6 +1,3 @@
-use std::collections::HashMap;
-
-use crate::models::Path;
 use rusqlite::types::Value;
 use rusqlite::{params_from_iter, Connection};
 
@@ -21,8 +18,8 @@ impl Edge {
         chromosome_index: i32,
         phased: i32,
     ) -> Edge {
-        let mut query;
-        let mut id_query;
+        let query;
+        let id_query;
         let mut placeholders: Vec<Value> = vec![];
         if target_id.is_some() && source_id.is_some() {
             query = "INSERT INTO edges (source_id, target_id, chromosome_index, phased) VALUES (?1, ?2, ?3, ?4) RETURNING *";
@@ -175,7 +172,7 @@ impl Edge {
 
     pub fn get_edges(conn: &Connection, query: &str, placeholders: Vec<Value>) -> Vec<Edge> {
         let mut stmt = conn.prepare_cached(query).unwrap();
-        let mut rows = stmt
+        let rows = stmt
             .query_map(params_from_iter(placeholders), |row| {
                 Ok(Edge {
                     id: row.get(0)?,

diff --git a/src/models/path.rs b/src/models/path.rs
@@ -5,7 +5,6 @@ use petgraph::prelude::Dfs;
 use petgraph::Direction;
 use rusqlite::types::Value;
 use rusqlite::{params_from_iter, Connection};
-use std::hash::Hash;
 
 #[derive(Debug)]
 pub struct Path {
@@ -94,7 +93,7 @@ impl Path {
 
     pub fn get_paths(conn: &Connection, query: &str, placeholders: Vec<Value>) -> Vec<Path> {
         let mut stmt = conn.prepare(query).unwrap();
-        let mut rows = stmt
+        let rows = stmt
             .query_map(params_from_iter(placeholders), |row| {
                 let path_id = row.get(0).unwrap();
                 Ok(Path {
@@ -160,7 +159,7 @@ impl PathBlock {
             Err(rusqlite::Error::SqliteFailure(err, details)) => {
                 if err.code == rusqlite::ErrorCode::ConstraintViolation {
                     println!("{err:?} {details:?}");
-                    let mut query;
+                    let query;
                     let mut placeholders = vec![path_id];
                     if let Some(s) = source_block_id {
                         if let Some(t) = target_block_id {
@@ -198,7 +197,7 @@ impl PathBlock {
 
     pub fn query(conn: &Connection, query: &str, placeholders: Vec<Value>) -> Vec<PathBlock> {
         let mut stmt = conn.prepare(query).unwrap();
-        let mut rows = stmt
+        let rows = stmt
             .query_map(params_from_iter(placeholders), |row| {
                 Ok(PathBlock {
                     id: row.get(0)?,
@@ -241,10 +240,10 @@ impl PathBlock {
         blocks
     }
 
-    pub fn blocks_to_graph(conn: &Connection, path_id: i32) -> DiGraphMap<(u32), ()> {
+    pub fn blocks_to_graph(conn: &Connection, path_id: i32) -> DiGraphMap<u32, ()> {
         let query = "SELECT source_block_id, target_block_id from path_blocks where path_id = ?1;";
         let mut stmt = conn.prepare_cached(query).unwrap();
-        let mut rows = stmt
+        let rows = stmt
             .query_map((path_id,), |row| {
                 let source_id: Option<u32> = row.get(0).unwrap();
                 let target_id: Option<u32> = row.get(1).unwrap();
@@ -272,7 +271,6 @@ impl PathBlock {
 
 mod tests {
     use rusqlite::Connection;
-    use std::collections::HashSet;
     // Note this useful idiom: importing names from outer (for mod tests) scope.
     use super::*;
 

diff --git a/src/models/sequence.rs b/src/models/sequence.rs
@@ -51,7 +51,7 @@ impl Sequence {
         placeholders: Vec<Value>,
     ) -> Vec<Sequence> {
         let mut stmt = conn.prepare_cached(query).unwrap();
-        let mut rows = stmt
+        let rows = stmt
             .query_map(params_from_iter(placeholders), |row| {
                 Ok(Sequence {
                     hash: row.get(0).unwrap(),