Updates for spatial queries

- ES query builder
- SPATIAL INDEX on accession_geo#georef

pom.xml

@@ -563,6 +563,12 @@
 				</exclusion>
 			</exclusions>
 		</dependency>
+		<dependency>
+			<groupId>com.github.lonnyj</groupId>
+			<artifactId>liquibase-spatial</artifactId>
+			<version>1.2.1</version>
+		</dependency>
+		
 		<dependency>
 			<groupId>org.genesys-pgr</groupId>
 			<artifactId>glis-client-resttemplate</artifactId>

src/main/java/org/genesys2/server/component/elastic/ElasticQueryBuilder.java

@@ -33,6 +33,7 @@ import com.querydsl.core.types.SubQueryExpression;
 import com.querydsl.core.types.TemplateExpression;
 import com.querydsl.core.types.Visitor;
 import com.querydsl.core.types.dsl.NumberPath;
+import com.querydsl.spatial.SpatialOps;
 
 public class ElasticQueryBuilder implements Visitor<Void, Void> {
 	private static Logger LOG = LoggerFactory.getLogger(ElasticQueryBuilder.class);
@@ -149,6 +150,15 @@ public class ElasticQueryBuilder implements Visitor<Void, Void> {
 			Path<?> path = (Path<?>) args.get(0);
 			PathMetadata pmd = path.getMetadata();
 			mustNotClauses.add(existsQuery(customizedPath(pmd.getParent().toString() + "." + pmd.getName())));
+		} else if (operator == SpatialOps.WITHIN) {
+			LOG.debug("WITHIN: {}", args);
+			for (Expression<?> expr : args) {
+				printExpression("WITHIN.. ", expr);
+			}
+			Path<?> a0 = (Path<?>) args.get(0);
+			Expression<?> a1 = args.get(1);
+
+			handleWithin(a0, a1);
 		} else {
 			LOG.error("Op {}: {}", operator, args);
 		}
@@ -207,6 +217,16 @@ public class ElasticQueryBuilder implements Visitor<Void, Void> {
 			mustClauses.add(termsQuery(customizedPath(getParentPath(pmd.getParent()) + "." + pmd.getName()), toValues(value)));
 		}
 	}
+	
+	private void handleWithin(Path<?> path, Expression<?> value) {
+		PathMetadata pmd = path.getMetadata();
+		if (pmd.getPathType() == PathType.COLLECTION_ANY) {
+			LOG.debug("Path ANY for {}={}", pmd.getParent(), value);
+			mustClauses.add(termsQuery(customizedPath(pmd.getParent().toString()), toValues(value)));
+		} else {
+			mustClauses.add(termsQuery(customizedPath(getParentPath(pmd.getParent()) + "." + pmd.getName()), toValues(value)));
+		}
+	}
 
 	private String getParentPath(Path<?> path) {
 		String pathValue = path.toString();

src/main/java/org/genesys2/server/model/genesys/AccessionGeo.java

@@ -29,10 +29,9 @@ import javax.persistence.PreUpdate;
 import javax.persistence.Table;
 import javax.persistence.Version;
 
+import com.vividsolutions.jts.geom.Coordinate;
+import com.vividsolutions.jts.geom.GeometryFactory;
 import com.vividsolutions.jts.geom.Point;
-import com.vividsolutions.jts.io.ParseException;
-import com.vividsolutions.jts.io.WKTReader;
-import org.apache.commons.lang3.StringUtils;
 import org.genesys.blocks.auditlog.annotations.Audited;
 import org.genesys.blocks.model.BasicModel;
 import org.genesys.blocks.model.JsonViews;
@@ -55,7 +54,8 @@ import com.fasterxml.jackson.annotation.JsonView;
 public class AccessionGeo extends BasicModel implements GeoReferencedEntity, AccessionRelated, SelfCleaning {
 
 	private static final long serialVersionUID = 8046638388176612388L;
-
+	private static final GeometryFactory GEOMETRY_FACTORY = new GeometryFactory();
+	
 	@Version
 	private long version = 0;
 
@@ -71,6 +71,7 @@ public class AccessionGeo extends BasicModel implements GeoReferencedEntity, Acc
 
 	@JsonIgnore
 	@Type(type = "org.hibernate.spatial.GeometryType")
+	@Column(name = "georef", nullable = false)
 	private Point location;
 
 	private Double uncertainty;
@@ -109,10 +110,11 @@ public class AccessionGeo extends BasicModel implements GeoReferencedEntity, Acc
 		}
 
 		if (this.longitude != null && this.latitude != null) {
-			String wkt = (new StringBuffer()).append("POINT (").append(this.longitude).append(" ").append(this.latitude).append(")").toString();
-			try {
-				this.location = (Point) new WKTReader().read(wkt);
-			} catch (ParseException ignored) {}
+			this.location =  GEOMETRY_FACTORY.createPoint(new Coordinate(this.longitude, this.latitude));
+		} else {
+			// this.location = null;
+			// FIXME mysql is dumb: All parts of a SPATIAL index must be NOT NULL.
+			this.location = GEOMETRY_FACTORY.createPoint(new Coordinate(-666, -666));
 		}
 
 		tileIndex = WorldClimUtil.getWorldclim25Tile(this.longitude, this.latitude);

src/main/java/org/genesys2/server/service/filter/AccessionGeoFilter.java

@@ -17,12 +17,9 @@ package org.genesys2.server.service.filter;
 
 import static org.genesys2.server.model.genesys.QAccessionGeo.accessionGeo;
 
-import java.util.Iterator;
 import java.util.List;
+import java.util.stream.Collectors;
 
-import com.vividsolutions.jts.geom.Polygon;
-import com.vividsolutions.jts.io.ParseException;
-import com.vividsolutions.jts.io.WKTReader;
 import org.genesys.blocks.model.filters.BasicModelFilter;
 import org.genesys.blocks.model.filters.NumberFilter;
 import org.genesys2.server.model.genesys.AccessionGeo;
@@ -30,11 +27,15 @@ import org.genesys2.server.model.genesys.QAccessionGeo;
 
 import com.querydsl.core.BooleanBuilder;
 import com.querydsl.core.types.Predicate;
+import com.vividsolutions.jts.geom.Coordinate;
+import com.vividsolutions.jts.geom.GeometryFactory;
+import com.vividsolutions.jts.geom.Polygon;
 
 /**
  * The Class CountryFilter.
  */
 public class AccessionGeoFilter extends BasicModelFilter<AccessionGeoFilter, AccessionGeo> {
+	private static final GeometryFactory GEOMETRY_FACTORY = new GeometryFactory();
 
 	/** The longitude. */
 	public NumberFilter<Double> longitude;
@@ -51,7 +52,7 @@ public class AccessionGeoFilter extends BasicModelFilter<AccessionGeoFilter, Acc
 	public ClimateFilter climate;
 
 	/** The polygon. */
-	public List<Number[]> polygon;
+	public List<Double[]> polygon;
 
 	/**
 	 * Builds the query.
@@ -93,35 +94,19 @@ public class AccessionGeoFilter extends BasicModelFilter<AccessionGeoFilter, Acc
 		if (climate != null) {
 			and.and(climate.buildQuery(accessiongeo.climate));
 		}
-		if (polygon != null && !polygon.isEmpty()) {
-			Polygon polygonObject = buildPolygon(polygon);
-			if (polygonObject != null) {
-				and.and(accessiongeo.location.within(polygonObject));
-			}
+		if (polygon != null && polygon.size() > 2) {
+			and.and(accessiongeo.location.within(toPolygon(polygon)));
 		}
 		
 		return and;
 	}
 
-	private Polygon buildPolygon(final List<Number[]> points) {
-		StringBuilder builder = new StringBuilder();
-		builder.append("POLYGON ((");
-
-		Iterator<Number[]> iterator = points.iterator();
-		while (iterator.hasNext()) {
-			Number[] point = iterator.next();
-			builder.append(point[0]).append(" ").append(point[1]);
-			if (iterator.hasNext()) {
-				builder.append(", ");
-			}
+	private static Polygon toPolygon(List<Double[]> polygon) {
+		List<Coordinate> arr = polygon.stream().map(p -> new Coordinate(p[0], p[1])).collect(Collectors.toList());
+		// close loop if not closed
+		if (! arr.get(arr.size() - 1).equals2D(arr.get(0))) {
+			arr.add(arr.get(0));
 		}
-		builder.append("))");
-
-		Polygon polygon = null;
-		try {
-			polygon = (Polygon) new WKTReader().read(builder.toString());
-		} catch (ParseException ignored) {}
-		return polygon;
+		return GEOMETRY_FACTORY.createPolygon(arr.toArray(new Coordinate[] {}));
 	}
-
 }

src/main/resources/liquibase/liquibase-changeLog.yml

@@ -5541,22 +5541,6 @@ databaseChangeLog:
         indexName: UK_tllx8suofq27njhc60y6h1ii9
         tableName: tile_climate
 
-- changeSet:
-    id:                    1550231443014-1
-    author:                mborodenko
-    changes:
-    - addColumn:
-        columns:
-        - column:
-            constraints:
-                nullable:  true
-            name:          point
-            type:          geometry
-        tableName:         accession_geo
-    - sql:
-        sql: >-
-          update accession_geo set point = GeomFromText(CONCAT('POINT (', longitude, ' ', latitude, ')')) where longitude is not null and latitude is not null
-
 - changeSet:
     id:          1550049944680-1
     author:      mborodenko
@@ -5594,3 +5578,33 @@ databaseChangeLog:
             name:  createdDate
         indexName: IX_accession_createdDate
         tableName: accession
+
+- changeSet:
+    id:                    1550231443014-5
+    author:                mborodenko & mobreza
+    changes:
+    - addColumn:
+        columns:
+        - column:
+            constraints:
+                nullable:  true
+            name:          georef
+            type:          point
+        tableName:         accession_geo
+    - sql:
+        sql: >-
+          update accession_geo set georef = POINT(latitude, longitude) where latitude is not null and longitude is not null
+    - sql:
+        sql: >-
+          update accession_geo set georef = POINT(-666, -666) where latitude is null or longitude is null
+    - addNotNullConstraint:
+        columnName:        georef
+        columnDataType:    point
+        tableName:         accession_geo
+    - createSpatialIndex:
+        geometryType:      Point
+        columns:
+        - column:
+            name:          georef
+        indexName:         IX_accessiongeo_georef
+        tableName:         accession_geo

src/test/java/org/genesys/test/server/api/v1/AccessionControllerTest.java

@@ -320,7 +320,7 @@ public class AccessionControllerTest extends AbstractApiTest {
 	@Test
 	public void testFindAccessionInsidePolygon() throws Exception {
 		// specify points of polygon
-		List<Number[]> pointsList = new ArrayList<>();
+		List<Double[]> pointsList = new ArrayList<>();
 		pointsList.add(new Double[]{ 80D, 70D });
 		pointsList.add(new Double[]{ 80D, 90D });
 		pointsList.add(new Double[]{ 60D, 90D });