Get rarray for queries working

src/models/path.rs

@@ -4,6 +4,7 @@ use std::collections::{HashMap, HashSet};
 use intervaltree::IntervalTree;
 use itertools::Itertools;
 use rusqlite::types::Value;
+use rusqlite::Params;
 use rusqlite::{params_from_iter, Connection};
 use serde::{Deserialize, Serialize};
 
@@ -146,6 +147,25 @@ impl Path {
         rows.next().unwrap().unwrap()
     }
 
+    pub fn full_query(conn: &Connection, query: &str, params: impl Params) -> Vec<Path> {
+        let mut stmt = conn.prepare(query).unwrap();
+        let rows = stmt
+            .query_map(params, |row| {
+                let path_id = row.get(0).unwrap();
+                Ok(Path {
+                    id: path_id,
+                    block_group_id: row.get(1)?,
+                    name: row.get(2)?,
+                })
+            })
+            .unwrap();
+        let mut paths = vec![];
+        for row in rows {
+            paths.push(row.unwrap());
+        }
+        paths
+    }
+
     pub fn get_paths(conn: &Connection, query: &str, placeholders: Vec<Value>) -> Vec<Path> {
         let mut stmt = conn.prepare(query).unwrap();
         let rows = stmt

src/updates/fasta.rs

@@ -1,6 +1,7 @@
 use noodles::fasta;
+use rusqlite;
 use rusqlite::{types::Value as SQLValue, Connection};
-use std::{io, str};
+use std::{io, rc::Rc, str};
 
 use crate::models::{
     block_group::{BlockGroup, PathChange},
@@ -46,17 +47,15 @@ pub fn update_with_fasta(
 
     let path_ids = operation_paths
         .iter()
-        .map(|operation_path| operation_path.path_id.to_string())
-        .collect::<Vec<String>>();
-    let query = format!(
-        "select * from path where block_group_id = {block_group_id} and id in ({path_ids});",
-        path_ids = path_ids.join(", ")
-    );
-    let paths = Path::query(conn, &query, vec![]);
+        .map(|operation_path| SQLValue::from(operation_path.path_id))
+        .collect::<Vec<SQLValue>>();
+    let query = "select * from path where block_group_id = ?1 and id in rarray(?2);";
+    let params = rusqlite::params!(SQLValue::from(block_group_id), Rc::new(path_ids));
+    let paths = Path::full_query(conn, query, params);
 
     if paths.len() != 1 {
         panic!(
-            "Expected one path for block group {} (contig name: {}",
+            "Expected one path for block group {} (contig name: {})",
             block_group_id, contig_name
         );
     }