view pkg/imports/sr.go @ 1136:a5069da2f0b7

Independent imports in terms of affected tables/dependencies are now run concurrently.
author Sascha L. Teichmann <sascha.teichmann@intevation.de>
date Thu, 08 Nov 2018 15:50:28 +0100
parents 2e6b47cdb2ca
children 2fb6c0a6ec8a
line wrap: on
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// This is Free Software under GNU Affero General Public License v >= 3.0
// without warranty, see README.md and license for details.
//
// SPDX-License-Identifier: AGPL-3.0-or-later
// License-Filename: LICENSES/AGPL-3.0.txt
//
// Copyright (C) 2018 by via donau
//   – Österreichische Wasserstraßen-Gesellschaft mbH
// Software engineering by Intevation GmbH
//
// Author(s):
//  * Sascha L. Teichmann <sascha.teichmann@intevation.de>

package imports

import (
	"archive/zip"
	"bufio"
	"context"
	"crypto/sha1"
	"database/sql"
	"encoding/hex"
	"encoding/json"
	"errors"
	"fmt"
	"io"
	"log"
	"os"
	"path"
	"path/filepath"
	"strconv"
	"strings"
	"time"

	shp "github.com/jonas-p/go-shp"

	"gemma.intevation.de/gemma/pkg/octree"
)

type SoundingResult string

const SoundingResultDateFormat = "2006-01-02"

type (
	SoundingResultDate struct{ time.Time }

	SoundingResultMeta struct {
		Date           SoundingResultDate `json:"date"`
		Bottleneck     string             `json:"bottleneck"`
		EPSG           uint               `json:"epsg"`
		DepthReference string             `json:"depth-reference"`
	}
)

const wgs84 = 4326

const (
	contourStepWidth = 0.1
	contourTolerance = 0.1
)

const SRJobKind JobKind = "sr"

type srJobCreator struct{}

func (srJobCreator) Create(_ JobKind, data string) (Job, error) {
	return SoundingResult(data), nil
}

func (srJobCreator) Depends() []string {
	return []string{
		"waterway.sounding_results",
		"waterway.sounding_results_contour_lines",
		"waterway.bottlenecks",
	}
}

func init() {
	RegisterJobCreator(SRJobKind, srJobCreator{})
}

const (
	checkDepthReferenceSQL = `
SELECT true FROM depth_references WHERE depth_reference = $1`

	checkBottleneckSQL = `
SELECT true FROM waterway.bottlenecks WHERE objnam = $1`

	insertPointsSQL = `
INSERT INTO waterway.sounding_results (
  bottleneck_id,
  date_info,
  depth_reference,
  point_cloud,
  area
) VALUES (
  (SELECT bottleneck_id from waterway.bottlenecks where objnam = $1),
  $2::date,
  $3,
  ST_Transform(ST_GeomFromWKB($4, $6::integer), 4326)::geography,
  (SELECT CASE WHEN $5::bytea IS NULL THEN
    ST_Transform(
      ST_ConcaveHull(
          ST_Force2D(ST_GeomFromWKB($4, $6::integer)), 0.7), 4326)::geography
  ELSE
    ST_Transform(ST_GeomFromWKB($5, $6::integer), 4326)::geography
  END)
)
RETURNING
  id,
  CASE WHEN ST_Y(ST_Centroid(point_cloud::geometry)) > 0 THEN
    32600
  ELSE
    32700
  END + floor((ST_X(ST_Centroid(point_cloud::geometry))+180)/6)::int + 1`

	insertOctreeSQL = `
UPDATE waterway.sounding_results SET
  octree_checksum = $2, octree_index = $3
WHERE id = $1`

	insertContourSQL = `
INSERT INTO waterway.sounding_results_contour_lines (
  sounding_result_id,
  height,
  lines
)
SELECT
  $1,
  $2,
  ST_Transform(
    ST_Multi(
      ST_CollectionExtract(
        ST_Intersection(
          ST_Transform(sr.area::geometry, $3::integer),
          ST_SimplifyPreserveTopology(
            ST_GeomFromWKB($4, $3::integer),
            $5
          )
        ),
        2
      )
    ),
    4326
  )
FROM waterway.sounding_results sr
WHERE id = $1
`
)

func (sr SoundingResult) Do(conn *sql.Conn, feedback Feedback) error {

	z, err := zip.OpenReader(filepath.Join(string(sr), "sr.zip"))
	if err != nil {
		return err
	}
	defer z.Close()

	feedback.Info("Looking for 'meta.json'\n")
	mf := find("meta.json", z.File)
	if mf == nil {
		return errors.New("Cannot find 'meta.json'")
	}

	m, err := loadMeta(mf)
	if err != nil {
		return err
	}

	if err := m.validate(conn); err != nil {
		return err
	}

	feedback.Info("Looking for '*.xyz'\n")
	xyzf := find(".xyz", z.File)
	if xyzf == nil {
		return errors.New("Cannot find any *.xyz file")
	}

	xyz, err := loadXYZ(xyzf, feedback)
	if err != nil {
		return err
	}

	if len(xyz) == 0 {
		return errors.New("XYZ does not contain any vertices.")
	}

	// Is there a boundary shapefile in the ZIP archive?
	polygon, err := loadBoundary(z)
	if err != nil {
		return err
	}

	ctx := context.Background()

	tx, err := conn.BeginTx(ctx, nil)
	if err != nil {
		return err
	}
	defer tx.Rollback()

	var id int64
	var epsg uint32
	start := time.Now()

	err = tx.QueryRow(insertPointsSQL,
		m.Bottleneck,
		m.Date.Time,
		m.DepthReference,
		xyz.AsWKB(),
		polygon.AsWBK(),
		m.EPSG,
	).Scan(&id, &epsg)
	xyz, polygon = nil, nil // not need from now on.
	feedback.Info("storing points took %s\n", time.Since(start))
	if err != nil {
		return err
	}

	feedback.Info("Best suited UTM EPSG: %d\n", epsg)

	feedback.Info("Triangulate...\n")
	start = time.Now()
	tin, err := octree.GenerateTinByID(conn, ctx, id, epsg)
	feedback.Info("triangulation took %s\n", time.Since(start))
	if err != nil {
		return err
	}

	if tin == nil {
		return errors.New("cannot load TIN from database")
	}

	feedback.Info("Building octree...\n")
	builder := octree.NewBuilder(tin)
	start = time.Now()
	builder.Build()
	octreeIndex, err := builder.Bytes()
	tin = nil // not needed from now on
	feedback.Info("building octree took %s\n", time.Since(start))
	if err != nil {
		return err
	}

	feedback.Info("Store octree...\n")
	start = time.Now()
	h := sha1.New()
	h.Write(octreeIndex)
	checksum := hex.EncodeToString(h.Sum(nil))
	_, err = tx.Exec(insertOctreeSQL, id, checksum, octreeIndex)
	feedback.Info("storing octree index took %s\n", time.Since(start))
	if err != nil {
		return err
	}

	tree := builder.Tree()
	builder = nil // not needed from now on

	feedback.Info("Generate contour lines...\n")
	start = time.Now()
	err = generateContours(tree, tx, id)
	feedback.Info("generating and storing contour lines took %s\n", time.Since(start))
	if err != nil {
		return err
	}

	feedback.Info("Storing sounding result was successful.\n")
	return tx.Commit()
}

func (srd *SoundingResultDate) UnmarshalJSON(data []byte) error {
	var s string
	if err := json.Unmarshal(data, &s); err != nil {
		return err
	}
	d, err := time.Parse(SoundingResultDateFormat, s)
	if err == nil {
		*srd = SoundingResultDate{d}
	}
	return err
}

func (sr SoundingResult) CleanUp() error {
	return os.RemoveAll(string(sr))
}

func find(needle string, haystack []*zip.File) *zip.File {
	needle = strings.ToLower(needle)
	for _, straw := range haystack {
		if strings.HasSuffix(strings.ToLower(straw.Name), needle) {
			return straw
		}
	}
	return nil
}

func loadMeta(f *zip.File) (*SoundingResultMeta, error) {
	r, err := f.Open()
	if err != nil {
		return nil, err
	}
	defer r.Close()
	var m SoundingResultMeta
	err = json.NewDecoder(r).Decode(&m)
	if err == nil {
		if m.EPSG == 0 {
			m.EPSG = wgs84
		}
	}
	return &m, err
}

func (m *SoundingResultMeta) validate(conn *sql.Conn) error {

	var b bool
	err := conn.QueryRowContext(context.Background(),
		checkDepthReferenceSQL,
		m.DepthReference).Scan(&b)
	switch {
	case err == sql.ErrNoRows:
		return fmt.Errorf("Unknown depth reference '%s'\n", m.DepthReference)
	case err != nil:
		return err
	case !b:
		return errors.New("Unexpected depth reference")
	}

	err = conn.QueryRowContext(context.Background(),
		checkBottleneckSQL,
		m.Bottleneck).Scan(&b)
	switch {
	case err == sql.ErrNoRows:
		return fmt.Errorf("Unknown bottleneck '%s'\n", m.Bottleneck)
	case err != nil:
		return err
	case !b:
		return errors.New("Unexpected bottleneck")
	}

	return nil
}

func loadXYZReader(r io.Reader, feedback Feedback) (octree.MultiPointZ, error) {
	mpz := make(octree.MultiPointZ, 0, 250000)
	s := bufio.NewScanner(r)

	for line := 1; s.Scan(); line++ {
		text := s.Text()
		var p octree.Vertex
		// fmt.Sscanf(text, "%f,%f,%f") is 4 times slower.
		idx := strings.IndexByte(text, ',')
		if idx == -1 {
			log.Printf("format error in line %d\n", line)
			continue
		}
		var err error
		if p.X, err = strconv.ParseFloat(text[:idx], 64); err != nil {
			feedback.Warn("format error in line %d: %v\n", line, err)
			continue
		}
		text = text[idx+1:]
		if idx = strings.IndexByte(text, ','); idx == -1 {
			feedback.Warn("format error in line %d\n", line)
			continue
		}
		if p.Y, err = strconv.ParseFloat(text[:idx], 64); err != nil {
			feedback.Warn("format error in line %d: %v\n", line, err)
			continue
		}
		text = text[idx+1:]
		if p.Z, err = strconv.ParseFloat(text, 64); err != nil {
			feedback.Warn("format error in line %d: %v\n", line, err)
			continue
		}
		mpz = append(mpz, p)
	}

	if err := s.Err(); err != nil {
		return nil, err
	}

	return mpz, nil
}

func loadXYZ(f *zip.File, feedback Feedback) (octree.MultiPointZ, error) {
	r, err := f.Open()
	if err != nil {
		return nil, err
	}
	defer r.Close()
	return loadXYZReader(r, feedback)
}

func loadBoundary(z *zip.ReadCloser) (Polygon, error) {
	shpF := find(".shp", z.File)
	if shpF == nil {
		return nil, nil
	}
	prefix := strings.TrimSuffix(shpF.Name, path.Ext(shpF.Name))
	dbfF := find(prefix+".dbf", z.File)
	if dbfF == nil {
		return nil, fmt.Errorf("No DBF file found for %s", shpF.Name)
	}

	shpR, err := shpF.Open()
	if err != nil {
		return nil, err
	}

	dbfR, err := dbfF.Open()
	if err != nil {
		shpR.Close()
		return nil, err
	}
	sr := shp.SequentialReaderFromExt(shpR, dbfR)
	defer sr.Close()

	if !sr.Next() {
		return nil, sr.Err()
	}

	_, s := sr.Shape()
	if s == nil {
		return nil, sr.Err()
	}

	return shapeToPolygon(s)
}

func generateContours(tree *octree.Tree, tx *sql.Tx, id int64) error {
	stmt, err := tx.Prepare(insertContourSQL)
	if err != nil {
		return err
	}
	defer stmt.Close()

	octree.DoContours(tree, contourStepWidth, func(res *octree.ContourResult) {
		if err == nil {
			_, err = stmt.Exec(
				id, res.Height, tree.EPSG,
				res.Lines.AsWKB2D(),
				contourTolerance)
		}
	})

	return err
}