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Query cleanup #87

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merged 3 commits into from
Nov 8, 2024
Merged

Query cleanup #87

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35c6ae2
Clean up path query method
dkhofer Nov 7, 2024
a6e8e3f
Use rusqlite params for queries
dkhofer Nov 8, 2024
6c736ac
More query cleanup
dkhofer Nov 8, 2024
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7 changes: 4 additions & 3 deletions src/exports/fasta.rs
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Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
use noodles::fasta;
use rusqlite;
use rusqlite::{types::Value as SQLValue, Connection};
use std::fs::File;
use std::path::PathBuf;
Expand All @@ -17,16 +18,16 @@ pub fn export_fasta(
block_groups = BlockGroup::query(
conn,
"select * from block_groups where collection_name = ?1 AND sample_name = ?2;",
vec![
rusqlite::params!(
SQLValue::from(collection_name.to_string()),
SQLValue::from(sample_name.to_string()),
],
),
);
} else {
block_groups = BlockGroup::query(
conn,
"select * from block_groups where collection_name = ?1 AND sample_name IS NULL;",
vec![SQLValue::from(collection_name.to_string())],
rusqlite::params!(SQLValue::from(collection_name.to_string())),
);
}

Expand Down
8 changes: 4 additions & 4 deletions src/exports/gfa.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -34,10 +34,10 @@ pub fn export_gfa(
let block_groups = BlockGroup::query(
conn,
"select * from block_groups where collection_name = ?1 AND sample_name = ?2;",
vec![
rusqlite::params!(
SQLValue::from(collection_name.to_string()),
SQLValue::from(sample.clone()),
],
),
);
if block_groups.is_empty() {
panic!(
Expand Down Expand Up @@ -176,7 +176,7 @@ fn write_paths(
collection_name: &str,
blocks: &[GroupBlock],
) {
let paths = Path::get_paths_for_collection(conn, collection_name);
let paths = Path::query_for_collection(conn, collection_name);
let edges_by_path_id =
PathEdge::edges_for_paths(conn, paths.iter().map(|path| path.id).collect());

Expand Down Expand Up @@ -362,7 +362,7 @@ mod tests {

assert_eq!(all_sequences, all_sequences2);

let paths = Path::get_paths_for_collection(&conn, "test collection 2");
let paths = Path::query_for_collection(&conn, "test collection 2");
assert_eq!(paths.len(), 1);
assert_eq!(paths[0].sequence(&conn), "AAAATTTTGGGGCCCC");
}
Expand Down
4 changes: 2 additions & 2 deletions src/gfa_reader.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -702,7 +702,7 @@ impl<'a, T: SampleType, S: Opt, U: Opt> Pansn<'a, T, S, U> {

/// Get all path
#[allow(clippy::type_complexity)]
pub fn get_paths_direct(&self) -> Vec<(String, Vec<&Path<T, S, U>>)> {
pub fn query_direct(&self) -> Vec<(String, Vec<&Path<T, S, U>>)> {
let mut result = Vec::new();
for x in self.genomes.iter() {
for y in x.haplotypes.iter() {
Expand All @@ -720,6 +720,6 @@ impl<'a, T: SampleType, S: Opt, U: Opt> Pansn<'a, T, S, U> {
"Number of individual haplotypes: {}",
self.get_haplo_path().len()
);
println!("Total number of paths: {}", self.get_paths_direct().len());
println!("Total number of paths: {}", self.query_direct().len());
}
}
11 changes: 9 additions & 2 deletions src/imports/fasta.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,7 @@ use crate::models::{
};
use crate::{calculate_hash, operation_management};
use noodles::fasta;
use rusqlite;
use rusqlite::{session, Connection};

pub fn import_fasta(
Expand Down Expand Up @@ -205,14 +206,20 @@ mod tests {
conn,
op_conn,
);
assert_eq!(Node::query(conn, "select * from nodes;", vec![]).len(), 3);
assert_eq!(
Node::query(conn, "select * from nodes;", rusqlite::params!()).len(),
3
);
import_fasta(
&fasta_path.to_str().unwrap().to_string(),
&collection,
false,
conn,
op_conn,
);
assert_eq!(Node::query(conn, "select * from nodes;", vec![]).len(), 3);
assert_eq!(
Node::query(conn, "select * from nodes;", rusqlite::params!()).len(),
3
);
}
}
45 changes: 23 additions & 22 deletions src/imports/gfa.rs
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Original file line number Diff line number Diff line change
@@ -1,3 +1,4 @@
use rusqlite;
use rusqlite::Connection;
use std::collections::{HashMap, HashSet};
use std::path::Path as FilePath;
Expand Down Expand Up @@ -234,20 +235,20 @@ mod tests {
import_gfa(&gfa_path, &collection_name, conn);

let block_group_id = BlockGroup::get_id(conn, &collection_name, None, "");
let path = Path::get_paths(
let path = Path::query(
conn,
"select * from paths where block_group_id = ?1 AND name = ?2",
vec![
rusqlite::params!(
SQLValue::from(block_group_id),
SQLValue::from("m123".to_string()),
],
),
)[0]
.clone();

let result = path.sequence(conn);
assert_eq!(result, "ATCGATCGATCGATCGATCGGGAACACACAGAGA");

let node_count = Node::query(conn, "select * from nodes", vec![]).len() as i64;
let node_count = Node::query(conn, "select * from nodes", rusqlite::params!()).len() as i64;
assert_eq!(node_count, 6);
}

Expand All @@ -266,7 +267,7 @@ mod tests {
HashSet::from_iter(vec!["AAAATTTTGGGGCCCC".to_string()])
);

let node_count = Node::query(conn, "select * from nodes", vec![]).len() as i64;
let node_count = Node::query(conn, "select * from nodes", rusqlite::params!()).len() as i64;
assert_eq!(node_count, 6);
}

Expand All @@ -279,20 +280,20 @@ mod tests {
import_gfa(&gfa_path, &collection_name, conn);

let block_group_id = BlockGroup::get_id(conn, &collection_name, None, "");
let path = Path::get_paths(
let path = Path::query(
conn,
"select * from paths where block_group_id = ?1 AND name = ?2",
vec![
rusqlite::params!(
SQLValue::from(block_group_id),
SQLValue::from("291344".to_string()),
],
),
)[0]
.clone();

let result = path.sequence(conn);
assert_eq!(result, "ACCTACAAATTCAAAC");

let node_count = Node::query(conn, "select * from nodes", vec![]).len() as i64;
let node_count = Node::query(conn, "select * from nodes", rusqlite::params!()).len() as i64;
assert_eq!(node_count, 6);
}

Expand All @@ -305,20 +306,20 @@ mod tests {
import_gfa(&gfa_path, &collection_name, conn);

let block_group_id = BlockGroup::get_id(conn, &collection_name, None, "");
let path = Path::get_paths(
let path = Path::query(
conn,
"select * from paths where block_group_id = ?1 AND name = ?2",
vec![
rusqlite::params!(
SQLValue::from(block_group_id),
SQLValue::from("124".to_string()),
],
),
)[0]
.clone();

let result = path.sequence(conn);
assert_eq!(result, "TATGCCAGCTGCGAATA");

let node_count = Node::query(conn, "select * from nodes", vec![]).len() as i64;
let node_count = Node::query(conn, "select * from nodes", rusqlite::params!()).len() as i64;
assert_eq!(node_count, 6);
}

Expand All @@ -330,17 +331,17 @@ mod tests {
let conn = &get_connection(None);
import_gfa(&gfa_path, &collection_name, conn);

let paths = Path::get_paths_for_collection(conn, &collection_name);
let paths = Path::query_for_collection(conn, &collection_name);
assert_eq!(paths.len(), 20);

let block_group_id = BlockGroup::get_id(conn, &collection_name, None, "");
let path = Path::get_paths(
let path = Path::query(
conn,
"select * from paths where block_group_id = ?1 AND name = ?2",
vec![
rusqlite::params!(
SQLValue::from(block_group_id),
SQLValue::from("BBa_J23100".to_string()),
],
),
)[0]
.clone();

Expand Down Expand Up @@ -423,7 +424,7 @@ mod tests {
assert_eq!(all_sequences.len(), 1024);
assert_eq!(all_sequences, expected_sequences);

let node_count = Node::query(conn, "select * from nodes", vec![]).len() as i64;
let node_count = Node::query(conn, "select * from nodes", rusqlite::params!()).len() as i64;
assert_eq!(node_count, 28);
}

Expand All @@ -437,13 +438,13 @@ mod tests {
import_gfa(&gfa_path, &collection_name, conn);

let block_group_id = BlockGroup::get_id(conn, &collection_name, None, "");
let path = Path::get_paths(
let path = Path::query(
conn,
"select * from paths where block_group_id = ?1 AND name = ?2",
vec![
rusqlite::params!(
SQLValue::from(block_group_id),
SQLValue::from("124".to_string()),
],
),
)[0]
.clone();

Expand All @@ -453,7 +454,7 @@ mod tests {
let all_sequences = BlockGroup::get_all_sequences(conn, block_group_id, false);
assert_eq!(all_sequences, HashSet::from_iter(vec!["AA".to_string()]));

let node_count = Node::query(conn, "select * from nodes", vec![]).len() as i64;
let node_count = Node::query(conn, "select * from nodes", rusqlite::params!()).len() as i64;
assert_eq!(node_count, 4);
}
}
6 changes: 3 additions & 3 deletions src/models/accession.rs
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
use crate::models::edge::EdgeData;
use crate::models::strand::Strand;
use crate::models::traits::Query;
use crate::models::traits::*;
use rusqlite::types::Value;
use rusqlite::{params_from_iter, Connection, Result as SQLResult, Row};
use serde::{Deserialize, Serialize};
Expand Down Expand Up @@ -199,7 +199,7 @@ impl AccessionEdge {
let formatted_edge_rows = edge_rows.join(", ");

let select_statement = format!("SELECT * FROM accession_edges WHERE (source_node_id, source_coordinate, source_strand, target_node_id, target_coordinate, target_strand, chromosome_index) in ({0});", formatted_edge_rows);
let existing_edges = AccessionEdge::query(conn, &select_statement, vec![]);
let existing_edges = AccessionEdge::query(conn, &select_statement, rusqlite::params!());
for edge in existing_edges.iter() {
edge_map.insert(AccessionEdgeData::from(edge), edge.id);
}
Expand Down Expand Up @@ -333,7 +333,7 @@ mod tests {
Accession::query(
conn,
"select * from accessions where name = ?1",
vec![Value::from("test".to_string())]
rusqlite::params!(Value::from("test".to_string())),
),
vec![Accession {
id: accession.id,
Expand Down
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