/
init.go
588 lines (514 loc) · 13.9 KB
/
init.go
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package extractor
import (
"context"
"database/sql"
"fmt"
"go.uber.org/zap"
"os"
"os/signal"
"strconv"
"sync"
"time"
)
type extractionResponse struct {
extractor Extractor
isSuccess bool
}
//Init sets up extractors and loaders
func Init(l *zap.SugaredLogger, conf *Configuration, isUpdate bool) {
ctx := context.Background()
ctx, cancel := context.WithCancel(ctx)
defer cancel()
waitForSignal(ctx, l)
if isUpdate {
updateFromLastUCI(ctx, l, conf)
updateRemovedSources(ctx, l, conf)
err := LoadSources(ctx, l, conf)
if err != nil {
m := fmt.Sprint("Error loading sources", err)
fmt.Println(m)
l.Fatal(m)
}
} else {
startExtraction(ctx, l, conf)
}
match := validateLoad(ctx, l, conf)
m := fmt.Sprint("Db count and index count match: ", match)
fmt.Println(m)
}
func validateLoad(ctx context.Context, l *zap.SugaredLogger, conf *Configuration) bool {
db, err := sql.Open("godror", conf.OracleConn)
if err != nil {
m := fmt.Sprint("Go oracle open ERROR ", err)
fmt.Println(m)
l.Panic(m)
panic(err)
}
defer func(db *sql.DB) {
err := db.Close()
if err != nil {
m := fmt.Sprint("Go oracle Closing DB ", err)
fmt.Println(m)
l.Error(m)
}
}(db)
var query = `SELECT count(distinct(ucpa.UCI))
FROM
UC_XREF xref,
UC_SOURCE so,
UC_STRUCTURE ucpa
WHERE xref.UCI = ucpa.UCI
AND xref.src_id = so.src_id
ORDER BY ucpa.UCI`
l.Debug(query)
rows, err := db.QueryContext(ctx, query)
if err != nil {
m := fmt.Sprint("Error running query ", err)
fmt.Println(m)
l.Panic(m)
panic(err)
}
defer rows.Close()
var dbCount int
for rows.Next() {
err := rows.Scan(
&dbCount)
if err != nil {
m := fmt.Sprint("Error scanning ", err)
fmt.Println(m)
l.Panic(m)
panic(err)
}
}
em, err := getElasticManager(ctx, l, conf)
if err != nil {
m := fmt.Sprint("Error creating elastic manager ", err)
fmt.Println(m)
l.Panic(m)
panic(err)
}
countResult, err := em.getCount()
if err != nil {
m := fmt.Sprint("Error getting the total count ", err)
fmt.Println(m)
l.Panic(m)
panic(err)
}
m := fmt.Sprintf("UCI total numbers - Database: %d Index: %d", dbCount, countResult)
fmt.Println(m)
if dbCount == int(countResult) {
return true
}
return false
}
func updateFromLastUCI(ctx context.Context, l *zap.SugaredLogger, conf *Configuration) {
conf.MaxConcurrent = 2
var queryRange = 10000000
m := "STARTING UPDATING PROCESS"
fmt.Println(m)
l.Info(m)
em, err := getElasticManager(ctx, l, conf)
if err != nil {
m := fmt.Sprint("Error creating elastic manager ", err)
fmt.Println(m)
l.Panic(m)
panic(err)
}
lastUCI, err := em.getLastIndexedUCI()
if err != nil {
l.Panic(err)
}
em.Close()
conf.QueryMax.Start = lastUCI - 1
conf.QueryMax.Finish = lastUCI + queryRange
startExtraction(ctx, l, conf)
}
func updateRemovedSources(ctx context.Context, l *zap.SugaredLogger, conf *Configuration) {
conf.MaxConcurrent = 1
m := "Updating Removed Sources"
fmt.Println(m)
l.Info(m)
em, err := getElasticManager(ctx, l, conf)
if err != nil {
m := fmt.Sprint("Error creating elastic manager ", err)
fmt.Println(m)
l.Panic(m)
panic(err)
}
lastUpdatedDate, err := em.getLastUpdated()
if err != nil {
m := fmt.Sprint("Error getting last updated ", err)
fmt.Println(m)
l.Panic(m)
}
em.Close()
var queryTemplate = `
SELECT ucpa.UCI,
ucpa.STANDARDINCHI,
ucpa.STANDARDINCHIKEY,
ucpa.PARENT_SMILES,
xref.SRC_COMPOUND_ID,
xref.ASSIGNMENT,
xref.CREATED,
xref.LASTUPDATED,
so.src_id,
so.NAME_LONG,
so.NAME_LABEL,
so.DESCRIPTION,
so.BASE_ID_URL,
so.NAME,
so.BASE_ID_URL_AVAILABLE,
so.AUX_FOR_URL,
so.PRIVATE
FROM UC_XREF xref,
UC_SOURCE so,
UC_STRUCTURE ucpa
WHERE xref.UCI in (
SELECT UCI
FROM UC_XREF
WHERE LASTUPDATED IS NOT NULL
AND LASTUPDATED >= %s
)
AND xref.UCI = ucpa.UCI
AND xref.src_id = so.src_id
ORDER BY ucpa.UCI`
sd := lastUpdatedDate.AddDate(0, 0, -15)
fd := fmt.Sprintf(`TO_DATE('%s', 'YYYYMMDD')`, sd.Format("20060102"))
query := fmt.Sprintf(queryTemplate, fd)
l.Debug(query)
extractOne(ctx, l, conf, query)
}
func extractOne(ctx context.Context, l *zap.SugaredLogger, conf *Configuration, query string) {
var extractors []*Extractor
l.Info("Starting One extractor")
ti := time.Now()
var extractorwg sync.WaitGroup
exResponse := make(chan extractionResponse)
extractorsAttempts := map[int]int{}
l.Infof("MaxConcurrent set: %d", conf.MaxConcurrent)
lock := make(chan int, conf.MaxConcurrent)
monitorExtraction(ctx, l, conf, lock, &extractorwg, exResponse, &extractorsAttempts, &extractors)
if conf.MaxAttempts <= 0 {
l.Panic("Maximum number of extractor attempts must be defined and greater than zero")
return
}
l.Info("MaxAttempts: ", conf.MaxAttempts)
ex := Extractor{
id: 1,
Oraconn: conf.OracleConn,
Query: query,
Logger: l,
LastIDAdded: 0,
}
extractorsAttempts[1] = 1
extractorwg.Add(1)
launchExtractor(ctx, l, conf, &ex, exResponse, lock, &extractorwg)
extractorwg.Wait()
l.Info("Wrapping it up")
elapsedTime(l, ti)
}
func monitorExtraction(ctx context.Context, l *zap.SugaredLogger, conf *Configuration, lock chan int, extractorwg *sync.WaitGroup, exResponse chan extractionResponse, exAt *map[int]int, extractors *[]*Extractor) {
ctx, cancel := context.WithCancel(ctx)
extractorsAttempts := *exAt
go func() {
for {
select {
case res := <-exResponse:
if !res.isSuccess {
m := fmt.Sprintf("FAILED extractor ID: %d - %d to %d ", res.extractor.id, res.extractor.QueryStart, res.extractor.QueryLimit)
fmt.Println(m)
l.Warnf(m)
if extractorsAttempts[res.extractor.id] >= conf.MaxAttempts {
m := fmt.Sprintf("CRITICAL Extractor ID: %d Maximum amount of attemps %d reached extractor", res.extractor.id, extractorsAttempts[res.extractor.id])
fmt.Println(m)
l.Error(m)
cancel()
break
}
query := fmt.Sprintf(conf.Query, res.extractor.QueryStart, res.extractor.QueryLimit)
ex := Extractor{
id: res.extractor.id,
Oraconn: conf.OracleConn,
Query: query,
QueryStart: res.extractor.QueryStart,
QueryLimit: res.extractor.QueryLimit,
Logger: l,
LastIDAdded: 0,
}
extractorwg.Add(1)
go launchExtractor(ctx, l, conf, &ex, exResponse, lock, extractorwg)
*extractors = append(*extractors, &ex)
extractorsAttempts[res.extractor.id] = extractorsAttempts[res.extractor.id] + 1
m = fmt.Sprintf("ATTEMPT %d Extractor ID: %d", extractorsAttempts[res.extractor.id], res.extractor.id)
println(m)
l.Warn(m)
} else {
m := fmt.Sprintf("DONE Extractor ID: %d - %d to %d finished", res.extractor.id, res.extractor.QueryStart, res.extractor.QueryLimit)
l.Info(m)
fmt.Println(m)
}
case <-ctx.Done():
m := "Canceled extractors response listener because of context done"
l.Warn(m)
println(m)
return
}
}
}()
}
func startExtraction(ctx context.Context, l *zap.SugaredLogger, conf *Configuration) {
ti := time.Now()
var extractors []*Extractor
interval := conf.Interval
start := conf.QueryMax.Start
finish := conf.QueryMax.Finish
var extractorwg sync.WaitGroup
exResponse := make(chan extractionResponse)
extractorsAttempts := map[int]int{}
l.Infof("MaxConcurrent set: %d", conf.MaxConcurrent)
lock := make(chan int, conf.MaxConcurrent)
monitorExtraction(ctx, l, conf, lock, &extractorwg, exResponse, &extractorsAttempts, &extractors)
if conf.MaxAttempts <= 0 {
l.Panic("Maximum number of extractor attempts must be defined and greater than zero")
}
l.Info("MaxAttempts: ", conf.MaxAttempts)
iterations := ((finish - start) / interval) + 1
l.Info("Iterations: ", iterations)
for i := 0; i < iterations; i++ {
init := start + (i * interval)
end := init + interval
m := fmt.Sprintf("Dispatching Extractor ID: %d from %d to %d ", i, init, end)
l.Infof(m)
println(m)
query := fmt.Sprintf(conf.Query, init, end)
ex := Extractor{
id: i,
Oraconn: conf.OracleConn,
Query: query,
QueryStart: init,
QueryLimit: end,
Logger: l,
LastIDAdded: 0,
}
extractorsAttempts[i] = 1
extractorwg.Add(1)
go launchExtractor(ctx, l, conf, &ex, exResponse, lock, &extractorwg)
extractors = append(extractors, &ex)
// Giving the first extractor a head start
if i == 0 {
time.Sleep(300 * time.Millisecond)
}
}
extractorwg.Wait()
l.Info("Wrapping it up")
printStatus(l, extractors)
elapsedTime(l, ti)
}
func launchExtractor(ctx context.Context, l *zap.SugaredLogger, cn *Configuration, ex *Extractor, exResponse chan extractionResponse, lock chan int, wg *sync.WaitGroup) {
lock <- 0
m := fmt.Sprintf("STARTED Extractor ID: %d from %d to %d", ex.id, ex.QueryStart, ex.QueryLimit)
l.Infof(m)
println(m)
defer deLock(lock, l, ex.QueryStart, ex.id)
defer wg.Done()
ctx, cancel := context.WithCancel(ctx)
defer cancel()
logger := l
var err error
select {
case <-ctx.Done():
m := fmt.Sprintf("CANCELED Extractor ID:%d", ex.id)
logger.Warn(m)
cancel()
return
default:
}
em, err := getElasticManager(ctx, l, cn)
if err != nil {
logger.Panic("Error creating elastic manager ", err)
panic(err)
}
defer em.Close()
ex.ElasticManager = em
exError := make(chan error)
inFinish := make(chan int)
ex.inFinish = inFinish
ex.exerror = exError
isExtractorDone := false
go func() {
err := ex.Start(ctx)
if err != nil {
m := fmt.Sprint("Error starting extractor ", err)
fmt.Println(m)
logger.Error(m)
}
}()
d:
for {
select {
case <-inFinish:
m := fmt.Sprintf("Finishing database extraction %d last extracted: %d", ex.id, ex.PreviousCompound.UCI)
l.Info(m)
isExtractorDone = true
if ex.PreviousCompound.UCI == 0 {
break d
}
if isExtractorDone && em.totalDoneJobs >= em.totalSentJobs {
break d
}
case err := <-exError:
m := fmt.Sprintf("Extractor ID: %d error", ex.id)
logger.Error(m)
fmt.Println(err.Error())
exResponse <- extractionResponse{
extractor: *ex,
isSuccess: false,
}
return
case <-ctx.Done():
m := fmt.Sprintf("Context canceled Extractor ID:%d", ex.id)
logger.Warn(m)
cancel()
return
case esResponse := <-em.Respchan:
l.Debugf("Got response, Extractor status: %t TOTAL DONE JOBS: %d TOTAL SENT JOBS: %d", isExtractorDone, em.totalDoneJobs, em.totalSentJobs)
if esResponse.BulkResponse.Errors {
logger.Error("Bulk response reported errors")
} else {
succeeded := esResponse.BulkResponse.Succeeded()
lastSucceded := succeeded[len(succeeded)-1]
logger.Infow(
"WORKER_RESPONSE",
"extractorID",
ex.id,
"extractorStarted",
ex.QueryStart,
"lastSucceeded",
lastSucceded.Id,
"Took",
esResponse.BulkResponse.Took,
)
li, err := strconv.Atoi(lastSucceded.Id)
if err != nil {
logger.Panic("Error turning ID into int ", err)
}
if ex.LastIDAdded < li {
ex.LastIDAdded = li
}
em.totalDoneJobs++
}
if esResponse.Failed > 0 {
m := fmt.Sprintf("Failed records on bulk. Extractor ID: %d", ex.id)
logger.Error(m)
ids := ""
reasons := ""
failed := esResponse.BulkResponse.Failed()
lastFailed := failed[len(failed)-1]
fr := esResponse.BulkResponse.Failed()
logger.Error(fr[0].Error.Reason)
logger.Errorw(
"WORKER_ERROR",
"extractorID",
ex.id,
"extractorStarted",
ex.QueryStart,
"Took",
esResponse.BulkResponse.Took,
"succeeded",
esResponse.Succeeded,
"indexed",
esResponse.Indexed,
"failed",
esResponse.Failed,
"startedOn",
failed[0].Id,
"lastFailed",
lastFailed.Id,
)
for _, it := range esResponse.BulkResponse.Failed() {
ids = ids + "," + it.Id
reasons = reasons + " " + it.Error.Reason
}
logger.Debug("IDs with error ", ids)
logger.Debug("Reasons: ", reasons)
exResponse <- extractionResponse{
extractor: *ex,
isSuccess: false,
}
cancel()
return
}
if isExtractorDone && em.totalDoneJobs >= em.totalSentJobs {
break d
}
case err = <-em.Errchan:
m := fmt.Sprintf("For worker started on %d Got error from bulk", ex.QueryStart)
println(m)
logger.Error(m)
println(err.Error())
exResponse <- extractionResponse{
extractor: *ex,
isSuccess: false,
}
return
}
}
logger.Infof("Waiting for elastic manager to finish. Extractor ID: %d", ex.id)
em.WaitGroup.Wait()
exResponse <- extractionResponse{
extractor: *ex,
isSuccess: true,
}
}
func deLock(lock chan int, l *zap.SugaredLogger, queryInit int, exID int) {
l.Warnf("DeLocking %d Extractor ID: %d", queryInit, exID)
<-lock
}
func getElasticManager(ctx context.Context, l *zap.SugaredLogger, cn *Configuration) (*ElasticManager, error) {
logger := l
if cn.BulkLimit <= 0 {
logger.Panic("BulkLimit must be a number higher than 0")
}
if cn.MaxBulkCalls <= 0 {
logger.Panic("MaxBulkCalls must be a number higher than 0")
}
es := ElasticManager{
Context: ctx,
IndexName: "unichem",
TypeName: "compound",
Bulklimit: cn.BulkLimit,
MaxBulkCalls: cn.MaxBulkCalls,
}
err := es.Init(ctx, cn, logger)
if err != nil {
logger.Error("Error init ElasticManager ", err)
return nil, err
}
return &es, nil
}
func waitForSignal(ctx context.Context, l *zap.SugaredLogger) {
c := make(chan os.Signal, 1)
ctx, cancel := context.WithCancel(ctx)
signal.Notify(c, os.Interrupt)
signal.Notify(c, os.Kill)
go func(cancel context.CancelFunc) {
ossig := <-c
l.Warnf("Received OS Signal: %+v", ossig)
cancel()
// os.Exit(1)
}(cancel)
}
func elapsedTime(l *zap.SugaredLogger, t time.Time) {
logger := l
e := time.Since(t)
m := fmt.Sprintf("Elapsed %s", e)
println(m)
logger.Infof(m)
}
func printStatus(l *zap.SugaredLogger, extractors []*Extractor) {
for _, ex := range extractors {
m := fmt.Sprintf("For worker started on %d Last compound UCI: %d", ex.QueryStart, ex.LastIDAdded)
println(m)
l.Warn(m)
}
}