refactor file/module names

I had some early confusion around whether SLEEP refered to individual
files or the collection of files making a register (it seems to mean the
whole register).

Will probably need to refactor again.

1 files changed, 556 insertions, 0 deletions

diff --git a/src/sleep_register.rs b/src/sleep_register.rs
new file mode 100644
index 0000000..e798cad
--- /dev/null
+++ b/src/sleep_register.rs
@@ -0,0 +1,556 @@
+
+use std::io::prelude::*;
+use std::fs::File;
+use std::path::Path;
+use std::io::SeekFrom;
+use integer_encoding::FixedInt;
+use std::fs::OpenOptions;
+use crypto::blake2b::Blake2b;
+use crypto::digest::Digest;
+use crypto::ed25519;
+use rand::{Rng, OsRng};
+
+use errors::*;
+use sleep_file::*;
+
+/// Abstract access to Hypercore register
+pub trait HyperRegister {
+
+    /// Whether the register store contains the given (data) entry
+    fn has(&self, index: u64) -> Result<bool>;
+
+    /// Whether the register store contains *all* known (data) entries
+    fn has_all(&self) -> Result<bool>;
+
+    /// If the contiguous range of entries is in the store
+    fn has_range(&self, start: u64, end: u64) -> Result<bool>;
+
+    /// Reads a single data entry from the store.
+    fn get_data_entry(&mut self, index: u64) -> Result<Vec<u8>>;
+
+    /// Writes an entry to the store. Requires the private key to be present.
+    fn append(&mut self, data: &[u8]) -> Result<u64>;
+
+    /// Count of data entries for this register. This is the total count (highest entry index plus
+    /// one); this particular store might be sparse.
+    fn len(&self) -> Result<u64>;
+
+    /// Total size of this register in bytes.
+    fn len_bytes(&mut self) -> Result<u64>;
+
+    /// [UNIMPLEMENTED] Intended to do a deeper merkel-tree verification of all stored data
+    fn verify(&mut self) -> Result<()>;
+
+    /// Quick sanity checks on register store robust-ness
+    fn check(&mut self) -> Result<()>;
+
+    /// Can this register be appended to?
+    fn writable(&self) -> bool;
+
+    /// Returns a single tree entry (using tree indexing, not data indexing).
+    fn get_tree_entry(&mut self, index: u64) -> Result<Vec<u8>>;
+}
+
+impl HyperRegister {
+
+    fn hash_leaf(data: &[u8]) -> [u8; 40] {
+        let mut buf = [0; 40];
+        u64::to_be(data.len() as u64)
+            .encode_fixed(&mut buf[32..40]);
+        let mut hash = Blake2b::new(32);
+        hash.input(&[0; 1]);
+        hash.input(&buf[32..40]);
+        hash.input(&data);
+        hash.result(&mut buf[0..32]);
+        buf
+    }
+
+    fn hash_parent(lhash: &[u8], rhash: &[u8]) -> [u8; 40] {
+        let mut buf = [0; 40];
+        // TODO: check overflow
+        let sum_size = u64::from_be(FixedInt::decode_fixed(&lhash[32..40])) +
+                       u64::from_be(FixedInt::decode_fixed(&rhash[32..40]));
+        u64::to_be(sum_size as u64)
+            .encode_fixed(&mut buf[32..40]);
+
+        let mut hash = Blake2b::new(32);
+        hash.input(&[1; 1]);
+        hash.input(&buf[32..40]);
+        hash.input(&lhash[..]);
+        hash.input(&rhash[..]);
+        hash.result(&mut buf[0..32]);
+        buf
+    }
+
+    pub fn hash_roots(reg: &mut HyperRegister, index: u64) -> Result<Vec<u8>> {
+        let mut buf = [0; 40];
+        let mut hash = Blake2b::new(32);
+        let mut index_buf = [0; 8];
+        hash.input(&[2; 1]);
+        for ri in HyperRegister::tree_root_nodes(index) {
+            u64::to_be(ri).encode_fixed(&mut index_buf);
+            let node = reg.get_tree_entry(ri)?;
+            hash.input(&node[0..32]);
+            hash.input(&index_buf);
+            hash.input(&node[32..40]);
+        }
+        hash.result(&mut buf[0..32]);
+        Ok(buf.to_vec())
+
+    }
+
+    fn tree_root_nodes(data_count: u64) -> Vec<u64> {
+        // Calculates the root notes for a given length (of data entries, not tree entries)
+        // TODO: this should be an iterator
+        // NB: this is a relatively "hot" function, gets called (repeatedly?) on every mutation,
+        // and potentially in inner loops of lookups.
+        if data_count == 0 {
+            return vec![];
+        }
+
+        // Convert the count to a (descending) list of power-of-2 components
+        let mut x = 0;
+        let mut components = vec![];
+        while 2u64.pow(x) <= data_count {
+            if (data_count & 2u64.pow(x)) != 0 {
+                components.push(2u64.pow(x));
+            }
+            x += 1;
+        }
+        components.reverse();
+
+        // Add and accumulate
+        let mut accum = 0;
+        let mut roots = vec![];
+        for x in components {
+            roots.push(accum + (x - 1));
+            accum += 2*x;
+        }
+        roots
+    }
+
+    pub fn get_data_offset(reg: &mut HyperRegister, index: u64) -> Result<u64> {
+        // TODO: this is a naive (linear) implementation
+        // log(N) would go up previous parent nodes (eg, use root_nodes())
+        let mut sum: u64 = 0;
+        for i in 0..index {
+            let leaf = reg.get_tree_entry(i*2)?;
+            sum += u64::from_be(FixedInt::decode_fixed(&leaf[32..40]));
+        }
+        Ok(sum)
+    }
+
+    /// Every node has a parent, so this function won't fail unless index is over 2^62, in which
+    /// case it would overflow and panics instead.
+    fn tree_parent_index(index: u64) -> u64 {
+        for i in 0..62 {
+            // find lowest-significant zero bit
+            if (index & (1 << i)) == 0 {
+                // set that bit and clear next higher
+                return ((index | (1 << i))) & !(1 << (i+1));
+            }
+        }
+        panic!("Parent lookup overflowed, huge index!");
+    }
+
+    /// Calling this on a leaf node is an error, as is calling very high node numbers (> 2^62)
+    fn tree_child_indices(index: u64) -> Result<(u64,u64)> {
+        if index % 2 == 0 {
+            bail!("Leaf tree nodes have no children");
+        }
+        for i in 0..62 {
+            // find lowest-significant zero bit...
+            if (index & (1 << i)) == 0 {
+                // larger child has this bit high, next lower bit cleared
+                let right = ((index | (1 << i))) & !(1 << (i-1));
+                // smaller child has next lower bit cleared
+                let left = index & !(1 << (i-1));
+                return Ok((left, right));
+            }
+        }
+        bail!("Child lookup overflowed, huge index!");
+    }
+}
+
+#[test]
+fn test_tree_root_nodes() {
+    assert_eq!(HyperRegister::tree_root_nodes(0), vec![]);
+    assert_eq!(HyperRegister::tree_root_nodes(1), vec![0]);
+    assert_eq!(HyperRegister::tree_root_nodes(2), vec![1]);
+    assert_eq!(HyperRegister::tree_root_nodes(3), vec![1,4]);
+    assert_eq!(HyperRegister::tree_root_nodes(4), vec![3]);
+    assert_eq!(HyperRegister::tree_root_nodes(5), vec![3,8]);
+    assert_eq!(HyperRegister::tree_root_nodes(6), vec![3,9]);
+    assert_eq!(HyperRegister::tree_root_nodes(7), vec![3,9,12]);
+    assert_eq!(HyperRegister::tree_root_nodes(8), vec![7]);
+}
+
+#[test]
+fn test_tree_parent_index() {
+    assert_eq!(HyperRegister::tree_parent_index(0), 1);
+    assert_eq!(HyperRegister::tree_parent_index(1), 3);
+    assert_eq!(HyperRegister::tree_parent_index(2), 1);
+    assert_eq!(HyperRegister::tree_parent_index(3), 7);
+    assert_eq!(HyperRegister::tree_parent_index(4), 5);
+    assert_eq!(HyperRegister::tree_parent_index(5), 3);
+    assert_eq!(HyperRegister::tree_parent_index(6), 5);
+    assert_eq!(HyperRegister::tree_parent_index(7), 15);
+    assert_eq!(HyperRegister::tree_parent_index(8), 9);
+    assert_eq!(HyperRegister::tree_parent_index(9), 11);
+    assert_eq!(HyperRegister::tree_parent_index(21), 19);
+    assert_eq!(HyperRegister::tree_parent_index(22), 21);
+}
+
+#[test]
+fn test_tree_child_indices() {
+    assert!(HyperRegister::tree_child_indices(0).is_err());
+    assert!(HyperRegister::tree_child_indices(1024).is_err());
+    assert_eq!(HyperRegister::tree_child_indices(1).unwrap(),  (0, 2));
+
+    assert_eq!(HyperRegister::tree_child_indices(3).unwrap(),  (1, 5));
+    assert_eq!(HyperRegister::tree_child_indices(5).unwrap(),  (4, 6));
+    assert_eq!(HyperRegister::tree_child_indices(7).unwrap(),  (3, 11));
+    assert_eq!(HyperRegister::tree_child_indices(9).unwrap(),  (8, 10));
+    assert_eq!(HyperRegister::tree_child_indices(11).unwrap(), (9, 13));
+    assert_eq!(HyperRegister::tree_child_indices(13).unwrap(), (12, 14));
+    assert_eq!(HyperRegister::tree_child_indices(15).unwrap(), (7, 23));
+    assert_eq!(HyperRegister::tree_child_indices(19).unwrap(), (17, 21));
+}
+
+/// Implementation of HyperRegister using a local directory of SLEEP files
+#[derive(Debug)]
+pub struct SleepDirRegister {
+    tree_sleep: SleepFile,
+    sign_sleep: SleepFile,
+    bitfield_sleep: SleepFile,
+    data_file: Option<File>,
+    // Except, these should be Ed25519 keys, not bytes
+    pub_key: Vec<u8>,
+    secret_key: Option<Vec<u8>>,
+}
+
+fn read_key_file(path: &Path, is_secret: bool) -> Result<Vec<u8>> {
+
+    let expected = if is_secret { 64 } else { 32 };
+    let mut key = vec![];
+    let mut key_file = OpenOptions::new()
+        .read(true)
+        .write(false)
+        .open(path)?;
+    key_file.read_to_end(&mut key)?;
+    if key.len() != expected {
+        bail!("Bad key file (len {} != {}): {:?}", key.len(), expected, path);
+    }
+    Ok(key)
+}
+
+fn write_key_file(path: &Path, key: &[u8], is_secret: bool) -> Result<()> {
+
+    let expected = if is_secret { 64 } else { 32 };
+    if key.len() != expected {
+        bail!("Bad key file (len {} != {}): {:?}", key.len(), expected, path);
+    }
+    let mut key_file = OpenOptions::new()
+        .write(true)
+        .create_new(true)
+        .open(path)?;
+    key_file.write_all(&key)?;
+    Ok(())
+}
+
+impl SleepDirRegister {
+
+    pub fn open(directory: &Path, prefix: &str, writable: bool) -> Result<SleepDirRegister> {
+        // read public key from disk
+        let pub_key: Vec<u8> = read_key_file(
+            &directory.join(Path::new(&(prefix.to_owned() + ".key"))),
+            false)?;
+        let mut secret_key = None;
+        if writable {
+            secret_key = Some(read_key_file(
+                &directory.join(Path::new(&(prefix.to_owned() + ".secret_key"))),
+                true)?);
+        }
+        let data_path = &(prefix.to_owned() + ".data");
+        let data_path = Path::new(data_path);
+        let data_file = if data_path.is_file() {
+            Some(OpenOptions::new()
+                .read(true)
+                .write(writable)
+                .open(data_path)?)
+        } else {
+            None
+        };
+        let tree_sleep = SleepFile::open(
+            &directory.join(Path::new(&(prefix.to_owned() + ".tree"))), writable)?;
+        let sign_sleep = SleepFile::open(
+            &directory.join(Path::new(&(prefix.to_owned() + ".signatures"))), writable)?;
+        let bitfield_sleep = SleepFile::open(
+            &directory.join(Path::new(&(prefix.to_owned() + ".bitfield"))), writable)?;
+        let mut sf = SleepDirRegister {
+            tree_sleep,
+            sign_sleep,
+            bitfield_sleep,
+            data_file,
+            pub_key,
+            secret_key,
+        };
+        sf.check()?;
+        Ok(sf)
+    }
+
+    /// In addition to what one would expect, also creates an Ed25519 key-pair using OsRng
+    pub fn create(directory: &Path, prefix: &str) -> Result<SleepDirRegister> {
+        let mut rand_seed = vec![0; 32];
+        let mut rng = OsRng::new()?;
+        rng.fill_bytes(&mut rand_seed);
+        let (secret_key, pub_key) = ed25519::keypair(&rand_seed);
+        write_key_file(
+            &directory.join(Path::new(&(prefix.to_owned() + ".key"))),
+            &pub_key,
+            false)?;
+        write_key_file(
+            &directory.join(Path::new(&(prefix.to_owned() + ".secret_key"))),
+            &secret_key,
+            true)?;
+        let data_file = OpenOptions::new()
+            .read(true)
+            .write(true)
+            .create_new(true)
+            .open(directory.join(Path::new(&(prefix.to_owned() + ".data"))))?;
+        let tree_sleep = SleepFile::create(
+            &directory.join(Path::new(&(prefix.to_owned() + ".tree"))),
+            0x05025702,
+            40,
+            Some("BLAKE2b".to_string()))?;
+        let sign_sleep = SleepFile::create(
+            &directory.join(Path::new(&(prefix.to_owned() + ".signatures"))),
+            0x05025701,
+            64,
+            Some("Ed25519".to_string()))?;
+        let bitfield_sleep = SleepFile::create(
+            &directory.join(Path::new(&(prefix.to_owned() + ".bitfield"))),
+            0x05025700,
+            3328,
+            None)?;
+        let mut sf = SleepDirRegister {
+            tree_sleep,
+            sign_sleep,
+            bitfield_sleep,
+            data_file: Some(data_file),
+            pub_key: pub_key.to_vec(),
+            secret_key: Some(secret_key.to_vec()),
+        };
+        sf.check()?;
+        Ok(sf)
+    }
+}
+
+impl HyperRegister for SleepDirRegister {
+
+    /// TODO: this version only works for "dense" registers: it just checks if the index is in the
+    /// total length, instead of using the bitfield.
+    fn has(&self, index: u64) -> Result<bool> {
+        return Ok(index < self.len()?);
+    }
+
+    fn has_all(&self) -> Result<bool> {
+        self.has_range(0, self.len()?)
+    }
+
+    fn has_range(&self, start: u64, end: u64) -> Result<bool> {
+        // This function is un-motivated and could be removed
+        assert!(end > start);
+        for i in start..end {
+            if !self.has(i)? {
+                return Ok(false);
+            }
+        }
+        Ok(true)
+    }
+
+    fn get_data_entry(&mut self, index: u64) -> Result<Vec<u8>> {
+
+        // Get metadata about chunk (offset and length)
+        let offset = HyperRegister::get_data_offset(self, index)?;
+
+        // Do we even have this chunk?
+        if !self.has(index)? {
+            bail!("Don't have that chunk");
+        }
+
+        let data_file = if let Some(ref mut df) = self.data_file {
+            df
+        } else {
+            bail!("No data file in this register");
+        };
+        let leaf = self.tree_sleep.read(index*2)?;
+        let data_len = u64::from_be(FixedInt::decode_fixed(&leaf[32..40]));
+        // avoid foot-gun in development: cap at ~1 billion bytes
+        assert!(data_len < 2u64.pow(29));
+
+        // Read chunk
+        let mut data = vec![0; data_len as usize];
+        data_file.seek(SeekFrom::Start(offset))?;
+        data_file.read_exact(&mut data)?;
+
+        // TODO: check the hash? separate function?
+        Ok(data)
+    }
+
+    fn get_tree_entry(&mut self, index: u64) -> Result<Vec<u8>> {
+        self.tree_sleep.read(index)
+    }
+
+    fn append(&mut self, data: &[u8]) -> Result<u64> {
+
+        if !self.data_file.is_some() {
+            bail!("No data file in this register");
+        };
+
+        let index = self.len()?;
+        // 1. Hash data chunk
+        let leaf_hash = HyperRegister::hash_leaf(data);
+
+        // 2. Append data to data file
+        if let Some(ref mut df) = self.data_file {
+            df.seek(SeekFrom::End(0))?;
+            df.write_all(data)?;
+            df.sync_data()?;
+        }
+
+        // 3. Add hash to tree file, update merkel tree
+        self.tree_sleep.write(index*2, &leaf_hash)?;
+        let mut parent = HyperRegister::tree_parent_index(index*2);
+        while parent < index*2 {
+            let (left, right) = HyperRegister::tree_child_indices(parent)?;
+            let (left, right) = (self.tree_sleep.read(left)?,
+                                 self.tree_sleep.read(right)?);
+            let parent_hash = HyperRegister::hash_parent(&left[0..40], &right[0..40]);
+            self.tree_sleep.write(parent, &parent_hash[0..40])?;
+            parent = HyperRegister::tree_parent_index(parent);
+        }
+ 
+        // 4. Add signature to signature file
+        let root_hash = HyperRegister::hash_roots(self, index+1)?;
+        let root_sig = ed25519::signature(&root_hash, &self.secret_key.clone().unwrap());
+        self.sign_sleep.append(&root_sig)?;
+ 
+        // 5. Update bitfile
+        Ok(index)
+    }
+
+    fn len(&self) -> Result<u64> {
+        // Length in entry count.
+        let tree_len = self.tree_sleep.len()?;
+        if tree_len == 0 {
+            Ok(0)
+        } else if tree_len % 2 != 1 {
+            bail!("Even number of tree file SLEEP entries");
+        } else {
+            Ok((self.tree_sleep.len()? / 2) + 1)
+        }
+    }
+
+    fn len_bytes(&mut self) -> Result<u64> {
+        // TODO: this is a naive (linear) implementation
+        // log(N) would go up previous parent nodes (eg, use tree_root_nodes())
+        let mut sum: u64 = 0;
+        for i in 0..self.len()? {
+            let leaf = self.get_tree_entry(i*2)?;
+            sum += u64::from_be(FixedInt::decode_fixed(&leaf[32..40]));
+        }
+        Ok(sum)
+    }
+
+    fn verify(&mut self) -> Result<()> {
+        unimplemented!()
+    }
+
+    fn check(&mut self) -> Result<()> {
+        let sign_len = self.sign_sleep.len()?;
+        let tree_len = self.tree_sleep.len()?;
+        if (tree_len == 0) && (sign_len == 0) {
+            return Ok(())
+        }
+        if tree_len != (sign_len * 2) - 1 {
+            bail!("Inconsistent SLEEP signature/tree file sizes");
+        }
+        let computed = self.len_bytes()?;
+        if let Some(ref df) = self.data_file {
+            let file_size = df.metadata()?.len();
+            if file_size != computed {
+                bail!("Computed vs. data file size mismatch");
+            }
+        }
+        Ok(())
+    }
+
+    /// Checks if we have the secret key (such that we can append to this register)
+    fn writable(&self) -> bool {
+        return self.secret_key.is_some()
+    }
+}
+
+#[test]
+fn test_sdr_open() {
+
+    let mut sdr = SleepDirRegister::open(
+       Path::new("test-data/dat/simple/.dat/"), "metadata", false).unwrap();
+
+    // Values from 'dat log'
+    assert_eq!(sdr.len().unwrap(), 3);
+    assert_eq!(sdr.len_bytes().unwrap(), 145);
+
+    let mut sdr = SleepDirRegister::open(
+       Path::new("test-data/dat/simple/.dat/"), "content", false).unwrap();
+
+    // Values from 'dat log'
+    assert_eq!(sdr.len().unwrap(), 2);
+    assert_eq!(sdr.len_bytes().unwrap(), 204);
+}
+
+#[test]
+fn test_sdr_create() {
+
+    use tempdir::TempDir;
+    let tmp_dir = TempDir::new("geniza-test").unwrap();
+    let mut sdr = SleepDirRegister::create(tmp_dir.path(), "dummy").unwrap();
+
+    assert_eq!(sdr.len().unwrap(), 0);
+    assert_eq!(sdr.len_bytes().unwrap(), 0);
+}
+
+#[test]
+fn test_sdr_append() {
+
+    use tempdir::TempDir;
+    let tmp_dir = TempDir::new("geniza-test").unwrap();
+    let mut sdr = SleepDirRegister::create(tmp_dir.path(), "dummy").unwrap();
+
+    sdr.append("hello world!".as_bytes()).unwrap();
+    sdr.check().unwrap();
+    assert_eq!(sdr.len().unwrap(), 1);
+    assert_eq!(sdr.len_bytes().unwrap(), 12);
+    let count = 100;  // TODO: make this >1000 when things are faster
+    for _ in 0..count {
+        sdr.append(&[1,2,3,4,5]).unwrap();
+    }
+    sdr.check().unwrap();
+    assert_eq!(sdr.len().unwrap(), 1+count);
+    assert_eq!(sdr.len_bytes().unwrap(), 12 + (count*5));
+}
+
+#[test]
+fn test_sdr_has() {
+
+    use tempdir::TempDir;
+    let tmp_dir = TempDir::new("geniza-test").unwrap();
+    let mut sdr = SleepDirRegister::create(tmp_dir.path(), "dummy").unwrap();
+
+    sdr.append("hello world!".as_bytes()).unwrap();
+    sdr.check().unwrap();
+    assert_eq!(sdr.has_all().unwrap(), true);
+    assert_eq!(sdr.has(0).unwrap(), true);
+    assert_eq!(sdr.has(40).unwrap(), false);
+}