// Make sure that mail info in db and maildir are identical
// TODO Synchronize messages removed in maildir to db
func SynchronizeInfo(cdir CachedMaildir, db *bolt.DB) {
cdir.dir.Unseen()
keys, err := cdir.dir.Keys()
if err != nil {
log.Fatal(err)
}
tx, err := db.Begin(true)
if err != nil {
log.Fatal(err)
}
bucket := tx.Bucket([]byte(cdir.flagsBucket))
for _, key := range keys {
ret := bucket.Get([]byte(key))
if ret == nil {
// We don't know about this message
flags, err := cdir.dir.Flags(key)
if err != nil {
println(err)
}
bucket.Put([]byte(key), []byte(flags))
}
}
tx.Commit()
}
func (db *DB) Open(dbPath string) error {
var (
err error
boltDB *bolt.DB
)
boltDB, err = bolt.Open(dbPath, 0600, nil)
if err != nil {
return err
}
var tx *bolt.Tx
tx, err = boltDB.Begin(true)
if err != nil {
return err
}
bucketName := []byte(base64.StdEncoding.EncodeToString([]byte(dbPath)))
_, err = tx.CreateBucketIfNotExists(bucketName)
if err != nil {
tx.Rollback()
return err
}
if err = tx.Commit(); err != nil {
return err
}
db.boltDB = boltDB
db.dbPath = dbPath
db.bucketName = bucketName
return nil
}
func createIncident(incident *Incident, db *bolt.DB) error {
if incident.Time == 0 {
incident.Time = time.Now().UnixNano()
}
key, err := time.Unix(0, incident.Time).MarshalBinary()
if err != nil {
return err
}
val, err := json.Marshal(incident)
if err != nil {
return err
}
tx, err := db.Begin(true)
if err != nil {
return err
}
b := tx.Bucket([]byte(incidentsBucket))
err = b.Put(key, val)
if err != nil {
tx.Rollback()
return err
}
err = tx.Commit()
if err != nil {
return err
}
return nil
}
func persist(db *bolt.DB, args []string) error {
tx, err := db.Begin(true)
if err != nil {
return err
}
log.Debugln("start transaction.")
for _, v := range args {
log.Debugln(v)
bucket := tx.Bucket([]byte(BUCKET_NAME))
if bucket == nil {
bucket, err = tx.CreateBucket([]byte(BUCKET_NAME))
if err != nil {
return err
}
count := btoi(bucket.Get([]byte(v)))
count += 1
err = bucket.Put([]byte(v), itob(count))
if err != nil {
tx.Rollback()
return err
}
}
}
tx.Commit()
return nil
}
func getLastNTweets(DB *bolt.DB, TweetCnt int) ([]anaconda.Tweet, error) {
var Result []anaconda.Tweet
Tx, err := DB.Begin(false)
if err != nil {
return []anaconda.Tweet{}, err
}
Bucket := Tx.Bucket([]byte("tweets"))
Cursor := Bucket.Cursor()
k, v := Cursor.Last()
for i := 0; i < TweetCnt; i++ {
if k == nil {
break
}
var tweet anaconda.Tweet
if err := json.Unmarshal(v, &tweet); err != nil {
return []anaconda.Tweet{}, err
}
Result = append(Result, tweet)
k, v = Cursor.Prev()
}
if err := Tx.Rollback(); err != nil {
return []anaconda.Tweet{}, err
}
return Result, nil
}
func getTwitterData(DB *bolt.DB) {
anaconda.SetConsumerKey("KmxA5PMS1WaVdSnJrYtq5XANb")
anaconda.SetConsumerSecret("yt7ydv2qFt7BpyHrMK3UzIj7HXGGv7ezcVTnELxhgh2WMGj9IA")
api := anaconda.NewTwitterApi(
"268263175-deYL6a9YyDMy8YRDQI0p9NDBoKuZScRKG24Dpqkj",
"PrFnSYOzsZjPYc5zhN9qeviyyHH0x1sKkiOYSSyPdWrnS")
tweets, err := api.GetHomeTimeline(url.Values{
"count": {"10"},
})
if err != nil {
// TODO -- Handle timeouts here
panic(err)
}
Tx, err := DB.Begin(true)
if err != nil {
// TODO -- Handle this gracely
panic(err)
}
Bucket := Tx.Bucket([]byte("tweets"))
for _, t := range tweets {
tweetText := t.Text
if t.RetweetedStatus != nil {
tweetText = t.RetweetedStatus.Text
}
tweetText = replaceURLS(tweetText, func(s string) string {
fmt.Println("Replacing ", s)
for retries := 0; retries < 3; retries++ {
newS, err := getRedirectedURL(s)
if err != nil {
time.Sleep(time.Duration(1+retries) * time.Second)
continue
}
return newS
}
return s
})
if t.RetweetedStatus != nil {
t.RetweetedStatus.Text = tweetText
} else {
t.Text = tweetText
}
data, err := json.Marshal(t)
if err != nil {
Tx.Rollback()
DB.Sync()
panic(err)
}
key := []byte(strconv.FormatInt(t.Id, 16))
if err = Bucket.Put(key, data); err != nil {
Tx.Rollback()
DB.Sync()
panic(err)
}
}
Tx.Commit()
}
func (self *Progress) tx(db *bolt.DB) *bolt.Tx {
tx, err := db.Begin(true)
if err != nil {
log.Println(err)
return nil
}
return tx
}
func upgrade2To3(db *bolt.DB) error {
fmt.Println("Upgrading v2 to v3...")
tx, err := db.Begin(true)
if err != nil {
return err
}
defer tx.Rollback()
fmt.Println("Upgrading bucket", string(logBucket))
lb := tx.Bucket(logBucket)
c := lb.Cursor()
for k, v := c.First(); k != nil; k, v = c.Next() {
var delta proto.LogDelta
err := delta.Unmarshal(v)
if err != nil {
return err
}
delta.Quad.Upgrade()
data, err := delta.Marshal()
if err != nil {
return err
}
lb.Put(k, data)
}
if err := tx.Commit(); err != nil {
return err
}
tx, err = db.Begin(true)
if err != nil {
return err
}
defer tx.Rollback()
fmt.Println("Upgrading bucket", string(nodeBucket))
nb := tx.Bucket(nodeBucket)
c = nb.Cursor()
for k, v := c.First(); k != nil; k, v = c.Next() {
var vd proto.NodeData
err := vd.Unmarshal(v)
if err != nil {
return err
}
vd.Upgrade()
data, err := vd.Marshal()
if err != nil {
return err
}
nb.Put(k, data)
}
if err := tx.Commit(); err != nil {
return err
}
return nil
}
func prometheusLoad(db *bolt.DB) error {
log.Printf("loading prometheus metrics...")
tx, err := db.Begin(false)
if err != nil {
return err
}
defer tx.Rollback()
b := tx.Bucket([]byte(prometheusBucket))
b.ForEach(func(k, v []byte) error {
PrometheusQueryMap[string(k)] = string(v)
log.Printf(" loaded prometheus metric %s=%s", string(k), string(v))
return nil
})
return nil
}
func prometheusAdd(db *bolt.DB, name, query string) error {
log.Printf("add prometheus metrics %s=%s", name, query)
tx, err := db.Begin(true)
if err != nil {
return err
}
b := tx.Bucket([]byte(prometheusBucket))
b.Put([]byte(name), []byte(query))
err = tx.Commit()
if err != nil {
PrometheusQueryMap[name] = query
}
return err
}
func NewCachedMailDir(mdirPath string, db *bolt.DB) (dir CachedMaildir) {
mdir := maildir.Dir(mdirPath)
bucketName := path.Base(mdirPath)
tx, err := db.Begin(true)
if err != nil {
log.Fatal(err)
}
_, err = tx.CreateBucketIfNotExists([]byte(bucketName + "_flags"))
if err != nil {
log.Fatal(err)
}
tx.Commit()
dir = CachedMaildir{dir: &mdir, flagsBucket: bucketName + "_flags"}
SynchronizeInfo(dir, db)
return
}
func boltSender(db *bolt.DB, tourl string) {
pr, pw := io.Pipe()
go func() {
tx, err := db.Begin(false)
if err != nil {
panic(err)
}
_, err = tx.WriteTo(pw)
if err != nil {
panic(err)
}
pw.Close()
}()
fmt.Println("before post")
_, err := http.Post(tourl, "plain/text", pr)
fmt.Println("after post")
if err != nil {
panic(err)
}
}
func getIncidentsByDay(day int64, db *bolt.DB) ([]string, error) {
since := time.Unix(0, 0).Add(time.Duration(day) * 24 * time.Hour)
until := since.Add(24 * time.Hour)
sinceb, err := since.MarshalBinary()
if err != nil {
return nil, err
}
untilb, err := until.MarshalBinary()
if err != nil {
return nil, err
}
tx, err := db.Begin(false)
if err != nil {
return nil, err
}
defer tx.Rollback()
eventslice := []string{}
c := tx.Bucket([]byte(incidentsBucket)).Cursor()
fk, _ := c.First()
if fk == nil {
return nil, fmt.Errorf("no available incidents")
}
if bytes.Compare(sinceb, fk) < 0 {
ft := &time.Time{}
err := ft.UnmarshalBinary(fk)
if err != nil {
return nil, err
}
return nil, fmt.Errorf("no available incidents before %d", int(ft.Sub(time.Unix(0, 0)).Hours())/24)
}
for k, v := c.Seek(sinceb); k != nil && bytes.Compare(k, untilb) <= 0; k, v = c.Next() {
eventslice = append(eventslice, string(v))
}
return eventslice, nil
}
func defragdb(odb, tmpdb *bolt.DB, limit int) error {
// open a tx on tmpdb for writes
tmptx, err := tmpdb.Begin(true)
if err != nil {
return err
}
// open a tx on old db for read
tx, err := odb.Begin(false)
if err != nil {
return err
}
defer tx.Rollback()
c := tx.Cursor()
count := 0
for next, _ := c.First(); next != nil; next, _ = c.Next() {
b := tx.Bucket(next)
if b == nil {
return fmt.Errorf("backend: cannot defrag bucket %s", string(next))
}
tmpb, berr := tmptx.CreateBucketIfNotExists(next)
if berr != nil {
return berr
}
b.ForEach(func(k, v []byte) error {
count++
if count > limit {
err = tmptx.Commit()
if err != nil {
return err
}
tmptx, err = tmpdb.Begin(true)
if err != nil {
return err
}
tmpb = tmptx.Bucket(next)
count = 0
}
err = tmpb.Put(k, v)
if err != nil {
return err
}
return nil
})
}
return tmptx.Commit()
}
// Ensure that opening a transaction while the DB is closed returns an error.
func TestDB_BeginRW_Closed(t *testing.T) {
var db bolt.DB
tx, err := db.Begin(true)
equals(t, err, bolt.ErrDatabaseNotOpen)
assert(t, tx == nil, "")
}
// Ensure that a database cannot open a transaction when it's not open.
func TestDB_Begin_DatabaseNotOpen(t *testing.T) {
var db bolt.DB
tx, err := db.Begin(false)
assert(t, tx == nil, "")
equals(t, err, bolt.ErrDatabaseNotOpen)
}
// Ensure that opening a transaction while the DB is closed returns an error.
func TestDB_BeginRW_Closed(t *testing.T) {
var db bolt.DB
if _, err := db.Begin(true); err != bolt.ErrDatabaseNotOpen {
t.Fatalf("unexpected error: %s", err)
}
}
func upgrade1To2(db *bolt.DB) error {
fmt.Println("Upgrading v1 to v2...")
tx, err := db.Begin(true)
if err != nil {
return err
}
defer tx.Rollback()
fmt.Println("Upgrading bucket", string(logBucket))
lb := tx.Bucket(logBucket)
c := lb.Cursor()
for k, v := c.First(); k != nil; k, v = c.Next() {
var delta graph.Delta
err := json.Unmarshal(v, &delta)
if err != nil {
return err
}
newd := deltaToProto(delta)
data, err := newd.Marshal()
if err != nil {
return err
}
lb.Put(k, data)
}
if err := tx.Commit(); err != nil {
return err
}
tx, err = db.Begin(true)
if err != nil {
return err
}
defer tx.Rollback()
fmt.Println("Upgrading bucket", string(nodeBucket))
nb := tx.Bucket(nodeBucket)
c = nb.Cursor()
for k, v := c.First(); k != nil; k, v = c.Next() {
var vd proto.NodeData
err := json.Unmarshal(v, &vd)
if err != nil {
return err
}
data, err := vd.Marshal()
if err != nil {
return err
}
nb.Put(k, data)
}
if err := tx.Commit(); err != nil {
return err
}
for _, bucket := range [4][]byte{spoBucket, ospBucket, posBucket, cpsBucket} {
tx, err = db.Begin(true)
if err != nil {
return err
}
defer tx.Rollback()
fmt.Println("Upgrading bucket", string(bucket))
b := tx.Bucket(bucket)
cur := b.Cursor()
for k, v := cur.First(); k != nil; k, v = cur.Next() {
var h proto.HistoryEntry
err := json.Unmarshal(v, &h)
if err != nil {
return err
}
data, err := h.Marshal()
if err != nil {
return err
}
b.Put(k, data)
}
if err := tx.Commit(); err != nil {
return err
}
}
return nil
}
func (cmd *CompactCommand) compact(dst, src *bolt.DB) error {
// commit regularly, or we'll run out of memory for large datasets if using one transaction.
var size int64
tx, err := dst.Begin(true)
if err != nil {
return err
}
defer tx.Rollback()
if err := cmd.walk(src, func(keys [][]byte, k, v []byte, seq uint64) error {
// On each key/value, check if we have exceeded tx size.
sz := int64(len(k) + len(v))
if size+sz > cmd.TxMaxSize && cmd.TxMaxSize != 0 {
// Commit previous transaction.
if err := tx.Commit(); err != nil {
return err
}
// Start new transaction.
tx, err = dst.Begin(true)
if err != nil {
return err
}
size = 0
}
size += sz
// Create bucket on the root transaction if this is the first level.
nk := len(keys)
if nk == 0 {
bkt, err := tx.CreateBucket(k)
if err != nil {
return err
}
if err := bkt.SetSequence(seq); err != nil {
return err
}
return nil
}
// Create buckets on subsequent levels, if necessary.
b := tx.Bucket(keys[0])
if nk > 1 {
for _, k := range keys[1:] {
b = b.Bucket(k)
}
}
// If there is no value then this is a bucket call.
if v == nil {
bkt, err := b.CreateBucket(k)
if err != nil {
return err
}
if err := bkt.SetSequence(seq); err != nil {
return err
}
return nil
}
// Otherwise treat it as a key/value pair.
return b.Put(k, v)
}); err != nil {
return err
}
return tx.Commit()
}
func loadQualifier(db *bolt.DB) {
tx, err := db.Begin(true)
if err != nil {
log.Fatal(err)
}
// Use the transaction...
_, err = tx.CreateBucket([]byte(BUCKET_QUALIFIER))
if err != nil {
log.Fatal(err)
}
// Commit the transaction and check for error.
if err := tx.Commit(); err != nil {
log.Fatal(err)
}
log.Println("\tLoading Qualifier MeSH XML from file: ", *qualifierXmlFile)
qualChannel, file, err := gomesh2016.QualifierChannelFromFile(*qualifierXmlFile)
if err != nil {
log.Fatal(err)
}
commitCounter := 0
counter := 0
tx, err = db.Begin(true)
if err != nil {
log.Fatal("error:", err)
}
b := tx.Bucket([]byte(BUCKET_QUALIFIER))
for qualifier := range qualChannel {
counter = counter + 1
if commitCounter == commitSize {
if err := tx.Commit(); err != nil {
log.Fatal(err)
}
tx, err = db.Begin(true)
if err != nil {
log.Fatal("error:", err)
}
b = tx.Bucket([]byte(BUCKET_PHARMACOLOGICAL))
commitCounter = 0
} else {
commitCounter = commitCounter + 1
}
key := qualifier.QualifierUI
value, err := json.Marshal(qualifier)
if err != nil {
log.Fatal("error:", err)
}
if commitCounter == commitSize {
log.Println(key)
log.Println(len(value))
// var b bytes.Buffer
// w := gzip.NewWriter(&b)
// w.Write(value)
// w.Close()
// log.Println(b.Len())
}
//log.Println(string(value))
err = b.Put([]byte(key), value)
if err != nil {
log.Fatal(err)
}
}
file.Close()
if err := tx.Commit(); err != nil {
log.Fatal(err)
}
log.Println("Loaded", counter, "quality")
}
func loadPharmacological(db *bolt.DB) {
tx, err := db.Begin(true)
if err != nil {
log.Fatal(err)
}
// Use the transaction...
_, err = tx.CreateBucket([]byte(BUCKET_PHARMACOLOGICAL))
if err != nil {
log.Fatal(err)
}
// Commit the transaction and check for error.
if err := tx.Commit(); err != nil {
log.Fatal(err)
}
log.Println("\tLoading Pharmacological MeSH XML from file: ", *pharmacologicalXmlFile)
pharmaChannel, file, err := gomesh2016.PharmacologicalChannelFromFile(*pharmacologicalXmlFile)
if err != nil {
log.Fatal(err)
}
commitCounter := 0
counter := 0
tx, err = db.Begin(true)
if err != nil {
log.Fatal("error:", err)
}
b := tx.Bucket([]byte(BUCKET_PHARMACOLOGICAL))
for pharma := range pharmaChannel {
counter = counter + 1
if commitCounter == commitSize {
if err := tx.Commit(); err != nil {
log.Fatal(err)
}
tx, err = db.Begin(true)
if err != nil {
log.Fatal("error:", err)
}
b = tx.Bucket([]byte(BUCKET_PHARMACOLOGICAL))
commitCounter = 0
} else {
commitCounter = commitCounter + 1
}
key := pharma.DescriptorReferredTo.DescriptorUI
value, err := json.Marshal(pharma)
if err != nil {
log.Fatal("error:", err)
}
if commitCounter == commitSize {
log.Println(key)
log.Println(len(value))
// var b bytes.Buffer
// w := gzip.NewWriter(&b)
// w.Write(value)
// w.Close()
// log.Println(b.Len())
}
//log.Println(string(value))
err = b.Put([]byte(key), value)
if err != nil {
log.Fatal(err)
}
}
file.Close()
if err := tx.Commit(); err != nil {
log.Fatal(err)
}
log.Println("Loaded", counter, "pharma")
}
func loadSupplemental(db *bolt.DB) {
tx, err := db.Begin(true)
if err != nil {
log.Fatal(err)
}
// Use the transaction...
_, err = tx.CreateBucket([]byte(BUCKET_SUPPLEMENTAL))
if err != nil {
log.Fatal(err)
}
// Commit the transaction and check for error.
if err := tx.Commit(); err != nil {
log.Fatal(err)
}
log.Println("\tLoading Supplemental MeSH XML from file: ", *supplementalXmlFile)
suppChannel, file, err := gomesh2016.SupplementalChannelFromFile(*supplementalXmlFile)
if err != nil {
log.Fatal(err)
}
commitCounter := 0
counter := 0
tx, err = db.Begin(true)
if err != nil {
log.Fatal("error:", err)
}
b := tx.Bucket([]byte(BUCKET_SUPPLEMENTAL))
for s := range suppChannel {
counter = counter + 1
if commitCounter == commitSize {
if err := tx.Commit(); err != nil {
log.Fatal(err)
}
tx, err = db.Begin(true)
if err != nil {
log.Fatal("error:", err)
}
b = tx.Bucket([]byte(BUCKET_SUPPLEMENTAL))
commitCounter = 0
} else {
commitCounter = commitCounter + 1
}
key := s.SupplementalRecordUI
value, err := json.Marshal(s)
if err != nil {
log.Fatal("error:", err)
}
if commitCounter == commitSize {
log.Println(key)
log.Println(len(value))
// var b bytes.Buffer
// w := gzip.NewWriter(&b)
// w.Write(value)
// w.Close()
// log.Println(b.Len())
}
//log.Println(string(value))
err = b.Put([]byte(key), value)
if err != nil {
log.Fatal(err)
}
}
file.Close()
if err := tx.Commit(); err != nil {
log.Fatal(err)
}
log.Println("Loaded", counter, "supplemental")
}
func loadDescriptor(db *bolt.DB) {
tx, err := db.Begin(true)
if err != nil {
log.Fatal(err)
}
// Use the transaction...
_, err = tx.CreateBucket([]byte(BUCKET_DESCRIPTOR))
if err != nil {
log.Fatal(err)
}
// Commit the transaction and check for error.
if err := tx.Commit(); err != nil {
log.Fatal(err)
}
log.Println("\tLoading Description MeSH XML from file: ", *descriptorXmlFile)
descChannel, file, err := gomesh2016.DescriptorChannelFromFile(*descriptorXmlFile)
if err != nil {
log.Fatal(err)
}
commitCounter := 0
counter := 0
tx, err = db.Begin(true)
if err != nil {
log.Fatal("error:", err)
}
b := tx.Bucket([]byte(BUCKET_DESCRIPTOR))
size := 0
// This is the root of the tree
root := InitializeNode()
for desc := range descChannel {
if desc.TreeNumberList != nil{
for _, treeNumber := range desc.TreeNumberList.TreeNumber {
root.AddNode(treeNumber, desc.DescriptorUI, desc.DescriptorName)
//log.Println("---------")
//log.Println(tree)
m := strings.Split(treeNumber, ".")
if len(m) > size {
size = len(m)
}
}
}
counter = counter + 1
if commitCounter == commitSize {
if err := tx.Commit(); err != nil {
log.Fatal(err)
}
tx, err = db.Begin(true)
if err != nil {
log.Fatal("error:", err)
}
b = tx.Bucket([]byte(BUCKET_DESCRIPTOR))
commitCounter = 0
} else {
commitCounter = commitCounter + 1
}
key := desc.DescriptorUI
value, err := json.Marshal(desc)
if err != nil {
log.Fatal("error:", err)
}
if commitCounter == commitSize {
log.Println(key)
log.Println(len(value))
// var b bytes.Buffer
// w := gzip.NewWriter(&b)
// w.Write(value)
// w.Close()
// log.Println(b.Len())
}
//log.Println(string(value))
err = b.Put([]byte(key), value)
if err != nil {
log.Fatal(err)
}
}
file.Close()
if err := tx.Commit(); err != nil {
log.Fatal(err)
}
log.Println("Loaded", counter, "description")
log.Println("Size=", size)
// TREE
tx, err = db.Begin(true)
if err != nil {
log.Fatal(err)
}
treeBucket := tx.Bucket([]byte(BUCKET_TREE))
root.DepthTraverse(0, Visitor, treeBucket)
}
