path: root/internal/pipeline/pipeline.go

// Copyright 2020 Nick White.
// Use of this source code is governed by the GPLv3
// license that can be found in the LICENSE file.

// pipeline is a package used by the bookpipeline command, which
// handles the core functionality, using channels heavily to
// coordinate jobs. Note that it is considered an "internal" package,
// not intended for external use, and no guarantee is made of the
// stability of any interfaces provided.
package pipeline

import (
	"bytes"
	"fmt"
	"io/ioutil"
	"log"
	"net/smtp"
	"os"
	"os/exec"
	"path/filepath"
	"regexp"
	"sort"
	"strings"
	"time"

	"rescribe.xyz/bookpipeline"
	"rescribe.xyz/preproc"
	"rescribe.xyz/utils/pkg/hocr"
)

const HeartbeatSeconds = 60

type Clouder interface {
	Init() error
	ListObjects(bucket string, prefix string) ([]string, error)
	Download(bucket string, key string, fn string) error
	Upload(bucket string, key string, path string) error
	CheckQueue(url string, timeout int64) (bookpipeline.Qmsg, error)
	AddToQueue(url string, msg string) error
	DelFromQueue(url string, handle string) error
	QueueHeartbeat(msg bookpipeline.Qmsg, qurl string, duration int64) (bookpipeline.Qmsg, error)
}

type Pipeliner interface {
	Clouder
	PreQueueId() string
	WipeQueueId() string
	OCRPageQueueId() string
	AnalyseQueueId() string
	WIPStorageId() string
	GetLogger() *log.Logger
	Log(v ...interface{})
}

type MinPipeliner interface {
	Pipeliner
	MinimalInit() error
}

type pageimg struct {
	hocr, img string
}

type mailSettings struct {
	server, port, user, pass, from, to string
}

func GetMailSettings() (mailSettings, error) {
	p := filepath.Join(os.Getenv("HOME"), ".config", "bookpipeline", "mailsettings")
	b, err := ioutil.ReadFile(p)
	if err != nil {
		return mailSettings{}, fmt.Errorf("Error reading mailsettings from %s: %v", p, err)
	}
	f := strings.Fields(string(b))
	if len(f) != 6 {
		return mailSettings{}, fmt.Errorf("Error parsing mailsettings, need %d fields, got %d", 6, len(f))
	}
	return mailSettings{f[0], f[1], f[2], f[3], f[4], f[5]}, nil
}

func download(dl chan string, process chan string, conn Pipeliner, dir string, errc chan error, logger *log.Logger) {
	for key := range dl {
		fn := filepath.Join(dir, filepath.Base(key))
		logger.Println("Downloading", key)
		err := conn.Download(conn.WIPStorageId(), key, fn)
		if err != nil {
			for range dl {
			} // consume the rest of the receiving channel so it isn't blocked
			close(process)
			errc <- err
			return
		}
		process <- fn
	}
	close(process)
}

func up(c chan string, done chan bool, conn Pipeliner, bookname string, errc chan error, logger *log.Logger) {
	for path := range c {
		name := filepath.Base(path)
		key := bookname + "/" + name
		logger.Println("Uploading", key)
		err := conn.Upload(conn.WIPStorageId(), key, path)
		if err != nil {
			for range c {
			} // consume the rest of the receiving channel so it isn't blocked
			errc <- err
			return
		}
		err = os.Remove(path)
		if err != nil {
			for range c {
			} // consume the rest of the receiving channel so it isn't blocked
			errc <- err
			return
		}
	}

	done <- true
}

func upAndQueue(c chan string, done chan bool, toQueue string, conn Pipeliner, bookname string, training string, errc chan error, logger *log.Logger) {
	for path := range c {
		name := filepath.Base(path)
		key := bookname + "/" + name
		logger.Println("Uploading", key)
		err := conn.Upload(conn.WIPStorageId(), key, path)
		if err != nil {
			for range c {
			} // consume the rest of the receiving channel so it isn't blocked
			errc <- err
			return
		}
		err = os.Remove(path)
		if err != nil {
			for range c {
			} // consume the rest of the receiving channel so it isn't blocked
			errc <- err
			return
		}
		logger.Println("Adding", key, training, "to queue", toQueue)
		err = conn.AddToQueue(toQueue, key+" "+training)
		if err != nil {
			for range c {
			} // consume the rest of the receiving channel so it isn't blocked
			errc <- err
			return
		}
	}

	done <- true
}

func Preprocess(thresholds []float64) func(chan string, chan string, chan error, *log.Logger) {
	return func(pre chan string, up chan string, errc chan error, logger *log.Logger) {
		for path := range pre {
			logger.Println("Preprocessing", path)
			done, err := preproc.PreProcMulti(path, thresholds, "binary", 0, true, 5, 30, 120, 30)
			if err != nil {
				for range pre {
				} // consume the rest of the receiving channel so it isn't blocked
				errc <- err
				return
			}
			_ = os.Remove(path)
			for _, p := range done {
				up <- p
			}
		}
		close(up)
	}
}

func Wipe(towipe chan string, up chan string, errc chan error, logger *log.Logger) {
	for path := range towipe {
		logger.Println("Wiping", path)
		s := strings.Split(path, ".")
		base := strings.Join(s[:len(s)-1], "")
		outpath := base + "_bin0.0.png"
		err := preproc.WipeFile(path, outpath, 5, 0.03, 30, 120, 0.005, 30)
		if err != nil {
			for range towipe {
			} // consume the rest of the receiving channel so it isn't blocked
			errc <- err
			return
		}
		up <- outpath
	}
	close(up)
}

func Ocr(training string, tesscmd string) func(chan string, chan string, chan error, *log.Logger) {
	return func(toocr chan string, up chan string, errc chan error, logger *log.Logger) {
		if tesscmd == "" {
			tesscmd = "tesseract"
		}
		for path := range toocr {
			logger.Println("OCRing", path)
			name := strings.Replace(path, ".png", "", 1)
			cmd := exec.Command(tesscmd, "-l", training, path, name, "-c", "tessedit_create_hocr=1", "-c", "hocr_font_info=0")
			var stdout, stderr bytes.Buffer
			cmd.Stdout = &stdout
			cmd.Stderr = &stderr
			err := cmd.Run()
			if err != nil {
				for range toocr {
				} // consume the rest of the receiving channel so it isn't blocked
				errc <- fmt.Errorf("Error ocring %s with training %s: %s\nStdout: %s\nStderr: %s\n", path, training, err, stdout.String(), stderr.String())
				return
			}
			up <- name + ".hocr"
		}
		close(up)
	}
}

func Analyse(conn Pipeliner) func(chan string, chan string, chan error, *log.Logger) {
	return func(toanalyse chan string, up chan string, errc chan error, logger *log.Logger) {
		confs := make(map[string][]*bookpipeline.Conf)
		bestconfs := make(map[string]*bookpipeline.Conf)
		savedir := ""

		for path := range toanalyse {
			if savedir == "" {
				savedir = filepath.Dir(path)
			}
			logger.Println("Calculating confidence for", path)
			avg, err := hocr.GetAvgConf(path)
			if err != nil && err.Error() == "No words found" {
				continue
			}
			if err != nil {
				for range toanalyse {
				} // consume the rest of the receiving channel so it isn't blocked
				errc <- fmt.Errorf("Error retreiving confidence for %s: %s", path, err)
				return
			}
			base := filepath.Base(path)
			codestart := strings.Index(base, "_bin")
			name := base[0:codestart]
			var c bookpipeline.Conf
			c.Path = path
			c.Code = base[codestart:]
			c.Conf = avg
			confs[name] = append(confs[name], &c)
		}

		fn := filepath.Join(savedir, "conf")
		logger.Println("Saving confidences in file", fn)
		f, err := os.Create(fn)
		if err != nil {
			errc <- fmt.Errorf("Error creating file %s: %s", fn, err)
			return
		}
		defer f.Close()

		logger.Println("Finding best confidence for each page, and saving all confidences")
		for base, conf := range confs {
			var best float64
			for _, c := range conf {
				if c.Conf > best {
					best = c.Conf
					bestconfs[base] = c
				}
				_, err = fmt.Fprintf(f, "%s\t%02.f\n", c.Path, c.Conf)
				if err != nil {
					errc <- fmt.Errorf("Error writing confidences file: %s", err)
					return
				}
			}
		}
		up <- fn

		logger.Println("Creating best file listing the best file for each page")
		fn = filepath.Join(savedir, "best")
		f, err = os.Create(fn)
		if err != nil {
			errc <- fmt.Errorf("Error creating file %s: %s", fn, err)
			return
		}
		defer f.Close()
		for _, conf := range bestconfs {
			_, err = fmt.Fprintf(f, "%s\n", filepath.Base(conf.Path))
		}
		up <- fn

		var pgs []string
		for _, conf := range bestconfs {
			pgs = append(pgs, conf.Path)
		}
		sort.Strings(pgs)

		logger.Println("Downloading binarised and original images to create PDFs")
		bookname, err := filepath.Rel(os.TempDir(), savedir)
		if err != nil {
			errc <- fmt.Errorf("Failed to do filepath.Rel of %s to %s: %s", os.TempDir(), savedir, err)
			return
		}
		colourpdf := new(bookpipeline.Fpdf)
		err = colourpdf.Setup()
		if err != nil {
			errc <- fmt.Errorf("Failed to set up PDF: %s", err)
			return
		}
		binarisedpdf := new(bookpipeline.Fpdf)
		err = binarisedpdf.Setup()
		if err != nil {
			errc <- fmt.Errorf("Failed to set up PDF: %s", err)
			return
		}
		binhascontent, colourhascontent := false, false

		var colourimgs, binimgs []pageimg

		for _, pg := range pgs {
			base := filepath.Base(pg)
			nosuffix := strings.TrimSuffix(base, ".hocr")
			p := strings.SplitN(base, "_bin", 2)

			var fn string
			if len(p) > 1 {
				fn = p[0] + ".jpg"
			} else {
				fn = nosuffix + ".jpg"
			}

			binimgs = append(binimgs, pageimg{hocr: base, img: nosuffix + ".png"})
			colourimgs = append(colourimgs, pageimg{hocr: base, img: fn})
		}

		for _, pg := range binimgs {
			logger.Println("Downloading binarised page to add to PDF", pg.img)
			err := conn.Download(conn.WIPStorageId(), bookname+"/"+pg.img, filepath.Join(savedir, pg.img))
			if err != nil {
				logger.Println("Download failed; skipping page", pg.img)
			} else {
				err = binarisedpdf.AddPage(filepath.Join(savedir, pg.img), filepath.Join(savedir, pg.hocr), true)
				if err != nil {
					errc <- fmt.Errorf("Failed to add page %s to PDF: %s", pg.img, err)
					return
				}
				binhascontent = true
				err = os.Remove(filepath.Join(savedir, pg.img))
				if err != nil {
					errc <- err
					return
				}
			}
		}

		if binhascontent {
			fn = filepath.Join(savedir, bookname+".binarised.pdf")
			err = binarisedpdf.Save(fn)
			if err != nil {
				errc <- fmt.Errorf("Failed to save binarised pdf: %s", err)
				return
			}
			up <- fn
			key := bookname + "/" + bookname + ".binarised.pdf"
			conn.Log("Uploading", key)
			err := conn.Upload(conn.WIPStorageId(), key, fn)
			if err != nil {
			}
		}

		for _, pg := range colourimgs {
			logger.Println("Downloading colour page to add to PDF", pg.img)
			colourfn := pg.img
			err = conn.Download(conn.WIPStorageId(), bookname+"/"+colourfn, filepath.Join(savedir, colourfn))
			if err != nil {
				colourfn = strings.Replace(pg.img, ".jpg", ".png", 1)
				logger.Println("Download failed; trying", colourfn)
				err = conn.Download(conn.WIPStorageId(), bookname+"/"+colourfn, filepath.Join(savedir, colourfn))
				if err != nil {
					logger.Println("Download failed; skipping page", pg.img)
				}
			}
			if err == nil {
				err = colourpdf.AddPage(filepath.Join(savedir, colourfn), filepath.Join(savedir, pg.hocr), true)
				if err != nil {
					errc <- fmt.Errorf("Failed to add page %s to PDF: %s", pg.img, err)
					return
				}
				colourhascontent = true
				err = os.Remove(filepath.Join(savedir, colourfn))
				if err != nil {
					errc <- err
					return
				}
			}
		}
		if colourhascontent {
			fn = filepath.Join(savedir, bookname+".colour.pdf")
			err = colourpdf.Save(fn)
			if err != nil {
				errc <- fmt.Errorf("Failed to save colour pdf: %s", err)
				return
			}
			up <- fn
		}

		logger.Println("Creating graph")
		fn = filepath.Join(savedir, "graph.png")
		f, err = os.Create(fn)
		if err != nil {
			errc <- fmt.Errorf("Error creating file %s: %s", fn, err)
			return
		}
		defer f.Close()
		err = bookpipeline.Graph(bestconfs, filepath.Base(savedir), f)
		if err != nil && err.Error() != "Not enough valid confidences" {
			errc <- fmt.Errorf("Error rendering graph: %s", err)
			return
		}
		up <- fn

		close(up)
	}
}

func heartbeat(conn Pipeliner, t *time.Ticker, msg bookpipeline.Qmsg, queue string, msgc chan bookpipeline.Qmsg, errc chan error) {
	currentmsg := msg
	for range t.C {
		m, err := conn.QueueHeartbeat(currentmsg, queue, HeartbeatSeconds*2)
		if err != nil {
			// This is for better debugging of the heartbeat issue
			conn.Log("Error with heartbeat", err)
			os.Exit(1)
			// TODO: would be better to ensure this error stops any running
			//       processes, as they will ultimately fail in the case of
			//       it. could do this by setting a global variable that
			//       processes check each time they loop.
			errc <- err
			t.Stop()
			return
		}
		if m.Id != "" {
			conn.Log("Replaced message handle as visibilitytimeout limit was reached")
			currentmsg = m
			// TODO: maybe handle communicating new msg more gracefully than this
			for range msgc {
			} // throw away any old msgc
			msgc <- m
		}
	}
}

// allOCRed checks whether all pages of a book have been OCRed.
// This is determined by whether every _bin0.?.png file has a
// corresponding .hocr file.
func allOCRed(bookname string, conn Pipeliner) bool {
	objs, err := conn.ListObjects(conn.WIPStorageId(), bookname)
	if err != nil {
		return false
	}

	preprocessedPattern := regexp.MustCompile(`_bin[0-9].[0-9].png$`)

	atleastone := false
	for _, png := range objs {
		if preprocessedPattern.MatchString(png) {
			atleastone = true
			found := false
			b := strings.TrimSuffix(filepath.Base(png), ".png")
			hocrname := bookname + "/" + b + ".hocr"
			for _, hocr := range objs {
				if hocr == hocrname {
					found = true
					break
				}
			}
			if found == false {
				return false
			}
		}
	}
	if atleastone == false {
		return false
	}
	return true
}

// OcrPage OCRs a page based on a message. It may make sense to
// roll this back into processBook (on which it is based) once
// working well.
func OcrPage(msg bookpipeline.Qmsg, conn Pipeliner, process func(chan string, chan string, chan error, *log.Logger), fromQueue string, toQueue string) error {
	dl := make(chan string)
	msgc := make(chan bookpipeline.Qmsg)
	processc := make(chan string)
	upc := make(chan string)
	done := make(chan bool)
	errc := make(chan error)

	msgparts := strings.Split(msg.Body, " ")
	bookname := filepath.Dir(msgparts[0])
	if len(msgparts) > 1 && msgparts[1] != "" {
		process = Ocr(msgparts[1], "")
	}

	d := filepath.Join(os.TempDir(), bookname)
	err := os.MkdirAll(d, 0755)
	if err != nil {
		return fmt.Errorf("Failed to create directory %s: %s", d, err)
	}

	t := time.NewTicker(HeartbeatSeconds * time.Second)
	go heartbeat(conn, t, msg, fromQueue, msgc, errc)

	// these functions will do their jobs when their channels have data
	go download(dl, processc, conn, d, errc, conn.GetLogger())
	go process(processc, upc, errc, conn.GetLogger())
	go up(upc, done, conn, bookname, errc, conn.GetLogger())

	dl <- msgparts[0]
	close(dl)

	// wait for either the done or errc channel to be sent to
	select {
	case err = <-errc:
		t.Stop()
		_ = os.RemoveAll(d)
		return err
	case <-done:
	}

	if allOCRed(bookname, conn) && toQueue != "" {
		conn.Log("Sending", bookname, "to queue", toQueue)
		err = conn.AddToQueue(toQueue, bookname)
		if err != nil {
			t.Stop()
			_ = os.RemoveAll(d)
			return fmt.Errorf("Error adding to queue %s: %s", bookname, err)
		}
	}

	t.Stop()

	// check whether we're using a newer msg handle
	select {
	case m, ok := <-msgc:
		if ok {
			msg = m
			conn.Log("Using new message handle to delete message from queue")
		}
	default:
		conn.Log("Using original message handle to delete message from queue")
	}

	conn.Log("Deleting original message from queue", fromQueue)
	err = conn.DelFromQueue(fromQueue, msg.Handle)
	if err != nil {
		_ = os.RemoveAll(d)
		return fmt.Errorf("Error deleting message from queue: %s", err)
	}

	err = os.RemoveAll(d)
	if err != nil {
		return fmt.Errorf("Failed to remove directory %s: %s", d, err)
	}

	return nil
}

func ProcessBook(msg bookpipeline.Qmsg, conn Pipeliner, process func(chan string, chan string, chan error, *log.Logger), match *regexp.Regexp, fromQueue string, toQueue string) error {
	dl := make(chan string)
	msgc := make(chan bookpipeline.Qmsg)
	processc := make(chan string)
	upc := make(chan string)
	done := make(chan bool)
	errc := make(chan error)

	msgparts := strings.Split(msg.Body, " ")
	bookname := msgparts[0]

	var training string
	if len(msgparts) > 1 {
		training = msgparts[1]
	}

	d := filepath.Join(os.TempDir(), bookname)
	err := os.MkdirAll(d, 0755)
	if err != nil {
		return fmt.Errorf("Failed to create directory %s: %s", d, err)
	}

	t := time.NewTicker(HeartbeatSeconds * time.Second)
	go heartbeat(conn, t, msg, fromQueue, msgc, errc)

	// these functions will do their jobs when their channels have data
	go download(dl, processc, conn, d, errc, conn.GetLogger())
	go process(processc, upc, errc, conn.GetLogger())
	if toQueue == conn.OCRPageQueueId() {
		go upAndQueue(upc, done, toQueue, conn, bookname, training, errc, conn.GetLogger())
	} else {
		go up(upc, done, conn, bookname, errc, conn.GetLogger())
	}

	conn.Log("Getting list of objects to download")
	objs, err := conn.ListObjects(conn.WIPStorageId(), bookname)
	if err != nil {
		t.Stop()
		_ = os.RemoveAll(d)
		return fmt.Errorf("Failed to get list of files for book %s: %s", bookname, err)
	}
	var todl []string
	for _, n := range objs {
		if !match.MatchString(n) {
			conn.Log("Skipping item that doesn't match target", n)
			continue
		}
		todl = append(todl, n)
	}
	for _, a := range todl {
		dl <- a
	}
	close(dl)

	// wait for either the done or errc channel to be sent to
	select {
	case err = <-errc:
		t.Stop()
		_ = os.RemoveAll(d)
		// if the error is in preprocessing / wipeonly, chances are that it will never
		// complete, and will fill the ocrpage queue with parts which succeeded
		// on each run, so in that case it's better to delete the message from
		// the queue and notify us.
		if fromQueue == conn.PreQueueId() || fromQueue == conn.WipeQueueId() {
			conn.Log("Deleting message from queue due to a bad error", fromQueue)
			err2 := conn.DelFromQueue(fromQueue, msg.Handle)
			if err2 != nil {
				conn.Log("Error deleting message from queue", err2)
			}
			ms, err2 := GetMailSettings()
			if err2 != nil {
				conn.Log("Failed to mail settings ", err2)
			}
			if err2 == nil && ms.server != "" {
				logs, err2 := getLogs()
				if err2 != nil {
					conn.Log("Failed to get logs ", err2)
					logs = ""
				}
				msg := fmt.Sprintf("To: %s\r\nFrom: %s\r\n" +
					"Subject: [bookpipeline] Error in wipeonly / preprocessing queue with %s\r\n\r\n" +
					" Fail message: %s\r\nFull log:\r\n%s\r\n",
					ms.to, ms.from, bookname, err, logs)
				host := fmt.Sprintf("%s:%s", ms.server, ms.port)
				auth := smtp.PlainAuth("", ms.user, ms.pass, ms.server)
				err2 = smtp.SendMail(host, auth, ms.from, []string{ms.to}, []byte(msg))
				if err2 != nil {
					conn.Log("Error sending email ", err2)
				}
			}
		}
		return err
	case <-done:
	}

	if toQueue != "" && toQueue != conn.OCRPageQueueId() {
		conn.Log("Sending", bookname, "to queue", toQueue)
		err = conn.AddToQueue(toQueue, bookname)
		if err != nil {
			t.Stop()
			_ = os.RemoveAll(d)
			return fmt.Errorf("Error adding to queue %s: %s", bookname, err)
		}
	}

	t.Stop()

	// check whether we're using a newer msg handle
	select {
	case m, ok := <-msgc:
		if ok {
			msg = m
			conn.Log("Using new message handle to delete message from queue")
		}
	default:
		conn.Log("Using original message handle to delete message from queue")
	}

	conn.Log("Deleting original message from queue", fromQueue)
	err = conn.DelFromQueue(fromQueue, msg.Handle)
	if err != nil {
		_ = os.RemoveAll(d)
		return fmt.Errorf("Error deleting message from queue: %s", err)
	}

	err = os.RemoveAll(d)
	if err != nil {
		return fmt.Errorf("Failed to remove directory %s: %s", d, err)
	}

	return nil
}

// TODO: rather than relying on journald, would be nicer to save the logs
//       ourselves maybe, so that we weren't relying on a particular systemd
//       setup. this can be done by having the conn.Log also append line
//       to a file (though that would mean everything would have to go through
//       conn.Log, which we're not consistently doing yet). the correct thing
//       to do then would be to implement a new interface that covers the part
//       of log.Logger we use (e.g. Print and Printf), and then have an exported
//       conn struct that implements those, so that we could pass a log.Logger
//       or the new conn struct everywhere (we wouldn't be passing a log.Logger,
//       it's just good to be able to keep the compatibility)
func getLogs() (string, error) {
	cmd := exec.Command("journalctl", "-u", "bookpipeline", "-n", "all")
	var stdout, stderr bytes.Buffer
	cmd.Stdout = &stdout
	cmd.Stderr = &stderr
	err := cmd.Run()
	return stdout.String(), err
}

func SaveLogs(conn Pipeliner, starttime int64, hostname string) error {
	logs, err := getLogs()
	if err != nil {
		return fmt.Errorf("Error getting logs, error: %v", err)
	}
	key := fmt.Sprintf("bookpipeline.log.%d.%s", starttime, hostname)
	path := filepath.Join(os.TempDir(), key)
	f, err := os.Create(path)
	if err != nil {
		return fmt.Errorf("Error creating log file", err)
	}
	defer f.Close()
	_, err = f.WriteString(logs)
	if err != nil {
		return fmt.Errorf("Error saving log file", err)
	}
	_ = f.Close()
	err = conn.Upload(conn.WIPStorageId(), key, path)
	if err != nil {
		return fmt.Errorf("Error uploading log", err)
	}
	conn.Log("Log saved to", key)
	return nil
}