/
db.go
959 lines (860 loc) · 21 KB
/
db.go
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package sopp
import (
"bufio"
"bytes"
"encoding/binary"
"errors"
"fmt"
"io"
"os"
"strings"
"github.com/RoaringBitmap/roaring"
"github.com/boltdb/bolt"
"github.com/boutros/sopp/rdf"
)
// Exported errors
var (
// ErrNotFound is an error signifying that the resource (Triple/Term)
// is not present in the database.
ErrNotFound = errors.New("not found")
// ErrDBFull is returned when the database cannot store more terms.
// Note: this will most likely be lower than MaxTerms, since the ID's of
// deleted terms are not reclaimed.
ErrDBFull = errors.New("database full: term limit reached")
)
const (
// MaxTerms is the maximum number of unique RDF terms that can be stored.
MaxTerms = 4294967295
)
// Buckets in the key-value store:
var (
// RDF Terms
bucketTerms = []byte("terms") // uint32 -> term
bucketIdxTerms = []byte("iterms") // term -> uint32
// Triple indices composite key bitmap
bucketSPO = []byte("spo") // Subect + Predicate -> Object
bucketOSP = []byte("osp") // Object + Subject -> Predicate
bucketPOS = []byte("pos") // Predicate + Object -> Subject
)
// DB is a RDF triple store backed by a key-value store.
type DB struct {
// kv is the key-value database (BoltDB) backing the triple store
kv *bolt.DB
// The majority of the URIs in a RDF graph are typically made up
// using the same base URI, so we optimize storage for those by
// making it the default case, and only storing the absolute part
// of an URI when it's not the default one.
//
// The base should include the scheme and hostname, ex: http://example.org/
//
// It must not be changed as long as the database is open, but may
// be set in the call to Open() when opening a database.
base string
// TODOs >>
// muPred protects the bimap of predicates
//muPred sync.RWMutex
// The number of predicates used in a RDF is usually quite low, so we
// maintain a cache of those in a bi-directional map
//pred bimap.URI2uint32
}
// Stats holds some statistics of the triple store.
type Stats struct {
NumTerms int
//NumTriples int
File string
SizeInBytes int
}
// Stats return statistics about the triple store.
func (db *DB) Stats() (Stats, error) {
st := Stats{}
if err := db.kv.View(func(tx *bolt.Tx) error {
bkt := tx.Bucket(bucketTerms)
st.NumTerms = bkt.Stats().KeyN
//st.NumTriples = int(atomic.LoadInt64(&db.numTr))
st.File = db.kv.Path()
s, err := os.Stat(st.File)
if err != nil {
return err
}
st.SizeInBytes = int(s.Size())
return nil
}); err != nil {
return st, err
}
return st, nil
}
// Open creates and opens a database at the given path.
// If the file does not exist it will be created.
// Only one process can have access to the file at a time.
func Open(path string, base string) (*DB, error) {
kv, err := bolt.Open(path, 0666, nil)
if err != nil {
return nil, err
}
db := &DB{
kv: kv,
base: base,
}
return db.setup()
}
// Close closes the database, relasing the lock on the database file.
func (db *DB) Close() error {
return db.kv.Close()
}
// setup makes sure the database has all the required buckets.
func (db *DB) setup() (*DB, error) {
err := db.kv.Update(func(tx *bolt.Tx) error {
// Make sure all the required buckets are present
for _, b := range [][]byte{bucketTerms, bucketIdxTerms, bucketSPO, bucketPOS, bucketOSP} {
_, err := tx.CreateBucketIfNotExists(b)
if err != nil {
return err
}
}
/*
// Count number of triples
bkt = tx.Bucket(bSPO)
cur = bkt.Cursor()
var n uint64
for k, v := cur.First(); k != nil; k, v = cur.Next() {
if v != nil {
bitmap := roaring.NewBitmap()
_, err := bitmap.ReadFrom(bytes.NewReader(v))
if err != nil {
return err
}
n += bitmap.GetCardinality()
} // else ?
}
db.numTr = int64(n)
*/
return nil
})
return db, err
}
// Insert stores the given Triple.
func (db *DB) Insert(tr rdf.Triple) error {
err := db.kv.Update(func(tx *bolt.Tx) error {
sID, err := db.addTerm(tx, tr.Subj)
if err != nil {
return err
}
// TODO get pID from cache
pID, err := db.addTerm(tx, tr.Pred)
if err != nil {
return err
}
oID, err := db.addTerm(tx, tr.Obj)
if err != nil {
return err
}
return db.storeTriple(tx, sID, pID, oID)
})
return err
}
// Delete removes the given Triple from the indices. It also removes
// any Term unique to that Triple from the store.
// It return ErrNotFound if the Triple is not stored
func (db *DB) Delete(tr rdf.Triple) error {
err := db.kv.Update(func(tx *bolt.Tx) error {
sID, err := db.getID(tx, tr.Subj)
if err != nil {
return err
}
// TODO get pID from cache
pID, err := db.getID(tx, tr.Pred)
if err != nil {
return err
}
oID, err := db.getID(tx, tr.Obj)
if err != nil {
return err
}
return db.removeTriple(tx, sID, pID, oID)
})
return err
}
// Has checks if the given Triple is stored.
func (db *DB) Has(tr rdf.Triple) (exists bool, err error) {
err = db.kv.View(func(tx *bolt.Tx) error {
sID, err := db.getID(tx, tr.Subj)
if err == ErrNotFound {
return nil
} else if err != nil {
return err
}
// TODO get pID from cache, and move to top before sID
pID, err := db.getID(tx, tr.Pred)
if err == ErrNotFound {
return nil
} else if err != nil {
return err
}
oID, err := db.getID(tx, tr.Obj)
if err == ErrNotFound {
return nil
} else if err != nil {
return err
}
bkt := tx.Bucket(bucketSPO)
sp := make([]byte, 8)
copy(sp, u32tob(sID))
copy(sp[4:], u32tob(pID))
bitmap := roaring.NewBitmap()
bo := bkt.Get(sp)
if bo == nil {
return nil
}
_, err = bitmap.ReadFrom(bytes.NewReader(bo))
if err != nil {
return err
}
exists = bitmap.Contains(oID)
return nil
})
return exists, err
}
// Describe returns a graph with all the triples where the given node
// is subject. If asObject is true, it also includes the triples where
// the node is object.
func (db *DB) Describe(node rdf.URI, asObject bool) (*rdf.Graph, error) {
g := rdf.NewGraph()
err := db.kv.View(func(tx *bolt.Tx) error {
bkt := tx.Bucket(bucketIdxTerms)
bt := db.encode(node)
bs := bkt.Get(bt)
if bs == nil {
return nil
}
// seek in SPO index:
// WHERE { <node> ?p ?o }
sid := btou32(bs)
cur := tx.Bucket(bucketSPO).Cursor()
outerSPO:
for k, v := cur.Seek(u32tob(sid - 1)); k != nil; k, v = cur.Next() {
switch bytes.Compare(k[:4], bs) {
case 0:
bkt = tx.Bucket(bucketTerms)
b := bkt.Get(k[4:])
if b == nil {
return errors.New("bug: term ID in index, but not stored")
}
// TODO get pred from cache
pred, err := db.decode(b)
if err != nil {
return err
}
bitmap := roaring.NewBitmap()
_, err = bitmap.ReadFrom(bytes.NewReader(v))
if err != nil {
return err
}
it := bitmap.Iterator()
for it.HasNext() {
o := it.Next()
b = bkt.Get(u32tob(o))
if b == nil {
return errors.New("bug: term ID in index, but not stored")
}
obj, err := db.decode(b)
if err != nil {
return err
}
g.Insert(rdf.Triple{Subj: node, Pred: pred.(rdf.URI), Obj: obj})
}
case 1:
break outerSPO
}
}
if !asObject {
return nil
}
// seek in OSP index:
// WHERE { ?s ?p <node> }
cur = tx.Bucket(bucketOSP).Cursor()
outerOSP:
for k, v := cur.Seek(u32tob(sid - 1)); k != nil; k, v = cur.Next() {
switch bytes.Compare(k[:4], bs) {
case 0:
bkt = tx.Bucket(bucketTerms)
b := bkt.Get(k[4:])
if b == nil {
return errors.New("bug: term ID in index, but not stored")
}
subj, err := db.decode(b)
if err != nil {
return err
}
bitmap := roaring.NewBitmap()
_, err = bitmap.ReadFrom(bytes.NewReader(v))
if err != nil {
return err
}
it := bitmap.Iterator()
for it.HasNext() {
o := it.Next()
b = bkt.Get(u32tob(o))
if b == nil {
return errors.New("bug: term ID in index, but not stored")
}
// TODO get pred from cache
pred, err := db.decode(b)
if err != nil {
return err
}
g.Insert(rdf.Triple{Subj: subj.(rdf.URI), Pred: pred.(rdf.URI), Obj: node})
}
case 1:
break outerOSP
}
}
return nil
})
return g, err
}
// Import imports triples from an Turtle stream, in batches of given size.
// It will ignore triples with blank nodes and errors.
// It returns the total number of triples imported.
func (db *DB) Import(r io.Reader, batchSize int) (int, error) {
dec := rdf.NewDecoder(r)
g := rdf.NewGraph()
c := 0 // totalt count
i := 0 // current batch count
for tr, err := dec.Decode(); err != io.EOF; tr, err = dec.Decode() {
if err != nil {
// log.Println(err.Error())
continue
}
g.Insert(tr)
i++
if i == batchSize {
err = db.ImportGraph(g)
if err != nil {
return c, err
}
c += i
i = 0
g = rdf.NewGraph()
}
}
if len(g.Nodes()) > 0 {
err := db.ImportGraph(g)
if err != nil {
return c, err
}
c += i
}
return c, nil
}
func (db *DB) ImportGraph(g *rdf.Graph) error {
return db.kv.Update(func(tx *bolt.Tx) error {
for subj, props := range g.Nodes() {
sID, err := db.addTerm(tx, subj)
if err != nil {
return err
}
for pred, terms := range props {
pID, err := db.addTerm(tx, pred)
if err != nil {
return err
}
for _, obj := range terms {
// TODO batch bitmap operations for all obj in terms
oID, err := db.addTerm(tx, obj)
if err != nil {
return err
}
err = db.storeTriple(tx, sID, pID, oID)
if err != nil {
return err
}
}
}
}
return nil
})
}
// Dump writes the entire database as a Turtle serialization to the given writer.
func (db *DB) Dump(to io.Writer) error {
// TODO getTerm without expanding base URI?
// base is prefixed added, but then stripped again here
w := bufio.NewWriter(to)
w.WriteString("@base <")
w.WriteString(db.base)
w.WriteString(">")
return db.kv.View(func(tx *bolt.Tx) error {
defer w.Flush()
var curSubj uint32
var subj, pred, obj rdf.Term
bkt := tx.Bucket(bucketSPO)
if err := bkt.ForEach(func(k, v []byte) error {
if len(k) != 8 {
panic("len(SPO key) != 8")
}
var err error
sID := btou32(k[:4])
if sID != curSubj {
// end previous statement
w.WriteString(" .\n")
curSubj = sID
if subj, err = db.getTerm(tx, sID); err != nil {
return err
}
w.WriteRune('<')
w.WriteString(strings.TrimPrefix(subj.String(), db.base))
w.WriteString("> ")
} else {
// continue with same subject
w.WriteString(" ;\n\t")
}
pID := btou32(k[4:])
if pred, err = db.getTerm(tx, pID); err != nil {
return err
}
if pred == rdf.RDFtype {
w.WriteString("a ")
} else {
w.WriteRune('<')
w.WriteString(strings.TrimPrefix(pred.String(), db.base))
w.WriteString("> ")
}
bitmap := roaring.NewBitmap()
if _, err := bitmap.ReadFrom(bytes.NewReader(v)); err != nil {
return err
}
i := bitmap.Iterator()
c := 0
for i.HasNext() {
if obj, err = db.getTerm(tx, i.Next()); err != nil {
return err
}
if c > 0 {
w.WriteString(", ")
}
switch t := obj.(type) {
case rdf.URI:
w.WriteRune('<')
w.WriteString(strings.TrimPrefix(obj.String(), db.base))
w.WriteRune('>')
case rdf.Literal:
// TODO bench & optimize
switch t.DataType() {
case rdf.RDFlangString:
fmt.Fprintf(w, "%q@%s", t.String(), t.Lang())
case rdf.XSDstring:
fmt.Fprintf(w, "%q", t.String())
default:
fmt.Fprintf(w, "%q^^<%s>", t.String(), strings.TrimPrefix(t.DataType().String(), db.base))
}
}
c++
}
return nil
}); err != nil {
return err
}
w.WriteString(" .\n")
return nil
})
}
func (db *DB) forEach(fn func(rdf.Triple) error) error {
return db.kv.View(func(tx *bolt.Tx) error {
bkt := tx.Bucket(bucketSPO)
// iterate over each each triple in SPO index
if err := bkt.ForEach(func(k, v []byte) error {
if len(k) != 8 {
panic("len(SPO key) != 8")
}
sID := btou32(k[:4])
pID := btou32(k[4:])
var tr rdf.Triple
var err error
var term rdf.Term
if term, err = db.getTerm(tx, sID); err != nil {
return err
}
tr.Subj = term.(rdf.URI)
if term, err = db.getTerm(tx, pID); err != nil {
return err
}
tr.Pred = term.(rdf.URI)
bitmap := roaring.NewBitmap()
if _, err := bitmap.ReadFrom(bytes.NewReader(v)); err != nil {
return err
}
// Iterate over each term in object bitmap
i := bitmap.Iterator()
for i.HasNext() {
if tr.Obj, err = db.getTerm(tx, i.Next()); err != nil {
return err
}
if err := fn(tr); err != nil {
return err
}
}
return nil
}); err != nil {
return err
}
return nil
})
}
func (db *DB) addTerm(tx *bolt.Tx, term rdf.Term) (id uint32, err error) {
bt := db.encode(term)
if id, err = db.getIDb(tx, bt); err == nil {
// Term is allready in database
return id, nil
} else if err != ErrNotFound {
// Some other IO error occured
return 0, err
}
// get a new ID
bkt := tx.Bucket(bucketTerms)
n, err := bkt.NextSequence()
if err != nil {
return 0, err
}
if n > MaxTerms {
return 0, ErrDBFull
}
id = uint32(n)
idb := u32tob(uint32(n))
// store term and index it
err = bkt.Put(idb, bt)
if err != nil {
return 0, err
}
bkt = tx.Bucket(bucketIdxTerms)
err = bkt.Put(bt, idb)
return id, err
}
func (db *DB) storeTriple(tx *bolt.Tx, s, p, o uint32) error {
indices := []struct {
k1 uint32
k2 uint32
v uint32
bk []byte
}{
{s, p, o, bucketSPO},
{o, s, p, bucketOSP},
{p, o, s, bucketPOS},
}
key := make([]byte, 8)
for _, i := range indices {
bkt := tx.Bucket(i.bk)
copy(key, u32tob(i.k1))
copy(key[4:], u32tob(i.k2))
bitmap := roaring.NewBitmap()
bo := bkt.Get(key)
if bo != nil {
_, err := bitmap.ReadFrom(bytes.NewReader(bo))
if err != nil {
return err
}
}
newTriple := bitmap.CheckedAdd(i.v)
if !newTriple {
// Triple is allready stored
return nil
}
var b bytes.Buffer
_, err := bitmap.WriteTo(&b)
if err != nil {
return err
}
err = bkt.Put(key, b.Bytes())
if err != nil {
return err
}
}
//atomic.AddInt64(&db.numTr, 1)
return nil
}
// removeTriple removes a triple from the indices. If the triple
// contains any terms unique to that triple, they will also be removed.
func (db *DB) removeTriple(tx *bolt.Tx, s, p, o uint32) error {
// TODO think about what to do if present in one index but
// not in another: maybe panic? Cause It's a bug that should be fixed.
indices := []struct {
k1 uint32
k2 uint32
v uint32
bk []byte
}{
{s, p, o, bucketSPO},
{o, s, p, bucketOSP},
{p, o, s, bucketPOS},
}
key := make([]byte, 8)
for _, i := range indices {
bkt := tx.Bucket(i.bk)
copy(key, u32tob(i.k1))
copy(key[4:], u32tob(i.k2))
bo := bkt.Get(key)
if bo == nil {
// TODO should never happen, return bug error?
return ErrNotFound
}
bitmap := roaring.NewBitmap()
_, err := bitmap.ReadFrom(bytes.NewReader(bo))
if err != nil {
return err
}
hasTriple := bitmap.CheckedRemove(i.v)
if !hasTriple {
// TODO should never happen, return bug error?
return ErrNotFound
}
// Remove from index if bitmap is empty
if bitmap.GetCardinality() == 0 {
err = bkt.Delete(key)
if err != nil {
return err
}
} else {
var b bytes.Buffer
_, err = bitmap.WriteTo(&b)
if err != nil {
return err
}
err = bkt.Put(key, b.Bytes())
if err != nil {
return err
}
}
}
//atomic.AddInt64(&db.numTr, -1)
return db.removeOrphanedTerms(tx, s, p, o)
}
func (db *DB) removeTerm(tx *bolt.Tx, termID uint32) error {
bkt := tx.Bucket(bucketTerms)
term := bkt.Get(u32tob(termID))
if term == nil {
// removeTerm should never be called on a allready deleted Term
return errors.New("bug: removeTerm: Term does not exist")
}
err := bkt.Delete(u32tob(termID))
if err != nil {
return err
}
bkt = tx.Bucket(bucketIdxTerms)
err = bkt.Delete(term)
if err != nil {
return err
}
return nil
}
// removeOrphanedTerms removes any of the given Terms if they are no longer
// part of any triple.
func (db *DB) removeOrphanedTerms(tx *bolt.Tx, s, p, o uint32) error {
// TODO by now we don't know whether object is a Literal or and URI.
// If we knew it to be a Literal, checking the OSP index would suffice.
for _, id := range unique(s, p, o) {
if notInIndex(tx, id, bucketSPO) && notInIndex(tx, id, bucketOSP) && notInIndex(tx, id, bucketPOS) {
err := db.removeTerm(tx, id)
if err != nil {
if err == ErrNotFound {
return errors.New("bug: removeOrphanedTerms removing Term allready gone")
}
return err
}
}
}
return nil
}
// unique removes any duplicates of the s,p,o IDs.
func unique(s, p, o uint32) []uint32 {
// TODO revise this function and its usage
res := make([]uint32, 0, 3)
res = append(res, s)
if p != s {
res = append(res, p)
}
if o != s && o != p {
res = append(res, o)
}
return res
}
func notInIndex(tx *bolt.Tx, id uint32, idx []byte) bool {
cur := tx.Bucket(idx).Cursor()
for k, _ := cur.Seek(u32tob(id - 1)); k != nil; k, _ = cur.Next() {
switch bytes.Compare(k[:4], u32tob(id)) {
case 0:
return false
case 1:
return true
}
}
return true
}
func (db *DB) getID(tx *bolt.Tx, term rdf.Term) (id uint32, err error) {
bkt := tx.Bucket(bucketIdxTerms)
bt := db.encode(term)
b := bkt.Get(bt)
if b == nil {
err = ErrNotFound
} else {
id = btou32(b)
}
return id, err
}
func (db *DB) getIDb(tx *bolt.Tx, term []byte) (id uint32, err error) {
bkt := tx.Bucket(bucketIdxTerms)
b := bkt.Get(term)
if b == nil {
err = ErrNotFound
} else {
id = btou32(b)
}
return id, err
}
// getTerm returns the term for a given ID.
func (db *DB) getTerm(tx *bolt.Tx, id uint32) (rdf.Term, error) {
bkt := tx.Bucket(bucketTerms)
b := bkt.Get(u32tob(id))
if b == nil {
return nil, ErrNotFound
}
return db.decode(b)
}
func (db *DB) encode(t rdf.Term) []byte {
switch term := t.(type) {
case rdf.URI:
if strings.HasPrefix(string(term), db.base) {
l := len(db.base)
b := make([]byte, len(term)-l+1)
copy(b[1:], string(term)[l:])
return b
}
b := make([]byte, len(term)+1)
b[0] = 0x01
copy(b[1:], string(term))
return b
case rdf.Literal:
var dt byte
switch term.DataType() {
case rdf.XSDstring:
dt = 0x02
case rdf.RDFlangString:
ll := len(term.Lang())
b := make([]byte, len(term.String())+ll+2)
b[0] = 0x03
b[1] = uint8(ll)
copy(b[2:], []byte(term.Lang()))
copy(b[2+ll:], []byte(term.String()))
return b
case rdf.XSDboolean:
dt = 0x04
case rdf.XSDbyte:
dt = 0x05
case rdf.XSDint:
dt = 0x06
case rdf.XSDshort:
dt = 0x07
case rdf.XSDlong:
dt = 0x08
case rdf.XSDinteger:
dt = 0x09
case rdf.XSDunsignedShort:
dt = 0x0A
case rdf.XSDunsignedInt:
dt = 0x0B
case rdf.XSDunsignedLong:
dt = 0x0C
case rdf.XSDunsignedByte:
dt = 0x0D
case rdf.XSDfloat:
dt = 0x0E
case rdf.XSDdouble:
dt = 0x0F
case rdf.XSDdateTimeStamp:
dt = 0x10
default:
ll := len(term.DataType())
b := make([]byte, len(term.String())+ll+2)
b[0] = 0xFF
b[1] = uint8(ll)
copy(b[2:], []byte(term.DataType()))
copy(b[2+ll:], []byte(term.String()))
return b
}
b := make([]byte, len(term.String())+1)
b[0] = dt
copy(b[1:], string(term.String()))
return b
}
panic("unreachable")
}
func (db *DB) decode(b []byte) (rdf.Term, error) {
// We control the encoding, so the only way for this method to fail to decode
// into a RDF term is if the underlying stoarge has been corrupted on the file system level.
if len(b) == 0 {
return nil, errors.New("cannot decode empty byte slice into RDF term")
}
var dt rdf.URI
switch b[0] {
case 0x00:
return rdf.URI(db.base + string(b[1:])), nil
case 0x01:
return rdf.URI(string(b[1:])), nil
case 0x02:
return rdf.NewTypedLiteral(string(b[1:]), rdf.XSDstring), nil
case 0x03:
if len(b) < 2 {
return nil, fmt.Errorf("cannot decode as rdf:langString: %v", b)
}
ll := int(b[1])
if len(b) < ll+2 {
return nil, fmt.Errorf("cannot decode as rdf:langString: %v", b)
}
return rdf.NewLangLiteral(string(b[ll+2:]), string(b[2:2+ll])), nil
case 0x04:
dt = rdf.XSDboolean
case 0x05:
dt = rdf.XSDbyte
case 0x06:
dt = rdf.XSDint
case 0x07:
dt = rdf.XSDshort
case 0x08:
dt = rdf.XSDlong
case 0x09:
dt = rdf.XSDinteger
case 0x0A:
dt = rdf.XSDunsignedShort
case 0x0B:
dt = rdf.XSDunsignedInt
case 0x0C:
dt = rdf.XSDunsignedLong
case 0x0D:
dt = rdf.XSDunsignedByte
case 0x0E:
dt = rdf.XSDfloat
case 0x0F:
dt = rdf.XSDdouble
case 0x10:
dt = rdf.XSDdateTimeStamp
case 0xFF:
if len(b) < 2 {
return nil, fmt.Errorf("cannot decode as literal: %v", b)
}
ll := int(b[1])
if len(b) < ll {
return nil, fmt.Errorf("cannot decode as literal: %v", b)
}
return rdf.NewTypedLiteral(string(b[ll+2:]), rdf.NewURI(string(b[2:2+ll]))), nil
default:
return nil, fmt.Errorf("cannot decode RDF term: %v", b)
}
return rdf.NewTypedLiteral(string(b[1:]), dt), nil
}
// u32tob converts a uint32 into a 4-byte slice.
func u32tob(v uint32) []byte {
b := make([]byte, 4)
binary.BigEndian.PutUint32(b, v)
return b
}
// btou32 converts a 4-byte slice into an uint32.
func btou32(b []byte) uint32 {
return binary.BigEndian.Uint32(b)
}