From 00a10c9169b8b00e17dacada65d1acc9178d7d21 Mon Sep 17 00:00:00 2001
From: David Mehren <dmehren1@gmail.com>
Date: Fri, 1 Jun 2018 09:13:08 +0200
Subject: [PATCH] [BPTree] Add serialization/deserialization
---
Cargo.toml | 5 +++-
src/lib.rs | 3 ++
src/trees/bp_tree.rs | 47 +++++++++++++++++++++++++++++--
testdata/bptree_invalid.testdata | Bin 0 -> 115 bytes
4 files changed, 52 insertions(+), 3 deletions(-)
create mode 100644 testdata/bptree_invalid.testdata
diff --git a/Cargo.toml b/Cargo.toml
index 4d0a043..a327b5d 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -7,4 +7,7 @@ authors = ["David Mehren <dmehren1@gmail.com>"]
bv = "0.7"
bio = "0.19.0"
id_tree = "1.3.0"
-failure = "0.1.1"
\ No newline at end of file
+failure = "0.1.1"
+serde = "1.0.64"
+serde_derive = "1.0.64"
+bincode = "1.0.0"
\ No newline at end of file
diff --git a/src/lib.rs b/src/lib.rs
index 2b18f66..e21698b 100644
--- a/src/lib.rs
+++ b/src/lib.rs
@@ -3,6 +3,9 @@ extern crate bv;
extern crate id_tree;
#[macro_use]
extern crate failure;
+#[macro_use]
+extern crate serde_derive;
+extern crate bincode;
pub mod common;
pub mod trees;
diff --git a/src/trees/bp_tree.rs b/src/trees/bp_tree.rs
index eb4ffcc..693bce5 100644
--- a/src/trees/bp_tree.rs
+++ b/src/trees/bp_tree.rs
@@ -1,18 +1,29 @@
+use bincode::{deserialize, serialize};
use bio::data_structures::rank_select::RankSelect;
use bv::{BitVec, BitsMut};
use common::succinct_tree::SuccinctTree;
-use failure::Error;
+use failure::{Error, ResultExt};
use id_tree::Tree;
use std::fmt;
use std::fmt::Debug;
use std::fmt::Formatter;
+use std::fs;
+use std::fs::File;
+use std::io::Write;
+#[derive(Serialize, Deserialize)]
pub struct BPTree {
bits: BitVec<u8>,
rankselect: RankSelect,
rminmax: String,
}
+impl PartialEq for BPTree {
+ fn eq(&self, other: &BPTree) -> bool {
+ self.bits == other.bits
+ }
+}
+
impl SuccinctTree<BPTree> for BPTree {
fn is_leaf(&self, index: u64) -> bool {
unimplemented!()
@@ -64,6 +75,19 @@ impl BPTree {
rminmax: "foo".to_string(),
})
}
+
+ pub fn from_file(path: String) -> Result<BPTree, Error> {
+ let file = fs::read(path).context("Could not read saved tree.")?;
+ let tree: BPTree = deserialize(&file).context("Error while deserializing tree.")?;
+ Ok(tree)
+ }
+
+ pub fn save_to(&self, path: String) -> Result<(), Error> {
+ let encoded = serialize(&self).context("Error while serializing tree.")?;
+ let mut file = File::create(path).context("Could not save tree.")?;
+ file.write_all(&encoded)?;
+ Ok(())
+ }
}
#[cfg(test)]
@@ -84,7 +108,26 @@ mod tests {
#[test]
#[should_panic(expected = "ErrorMessage { msg: \"Bit vector not valid.\" }")]
fn new_from_bitvec_invalid() {
- let mut bitvec = BitVec::new_fill(false, 2);
+ let bitvec = BitVec::new_fill(false, 2);
BPTree::from_bitvec(bitvec.clone()).unwrap();
}
+
+ #[test]
+ fn save_load() {
+ let tree = BPTree::stub_create();
+ tree.save_to("testdata/bptree.testdata".to_string())
+ .unwrap();
+ let result = BPTree::from_file("testdata/bptree.testdata".to_string()).unwrap();
+ assert_eq!(
+ tree, result,
+ "The loaded tree is not equal to the original one."
+ );
+ }
+
+ #[test]
+ #[should_panic(expected = "Error while deserializing tree.")]
+ fn load_invaild() {
+ BPTree::from_file("testdata/bptree_invalid.testdata".to_string()).unwrap();
+ }
+
}
diff --git a/testdata/bptree_invalid.testdata b/testdata/bptree_invalid.testdata
new file mode 100644
index 0000000000000000000000000000000000000000..4318da13396d0f974a32b7f727f5bf23ac866417
GIT binary patch
literal 115
zcmZQ#fB`Nj!vRWjKxqXA1_nk31_qcoLI*?~#7`_vDNam*YG9COU|<000`WmQK{PXn
LU|?WK%g+Y@uek)W
literal 0
HcmV?d00001
--
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