Adding implementation of tdwg/bdq#287 using @jhnwllr's catalog of cen…

…troids PCLI file converted to a shape file. This was passing all but one row in @Tasilee's test validation data, but have also added the proposed test for large coordinate uncertainty relative to country size proposed as a change to the specification.

src/main/java/org/filteredpush/qc/georeference/DwCGeoRefDQDefaults.java

@@ -16,6 +16,7 @@
 import org.datakurator.ffdq.api.DQResponse;
 import org.datakurator.ffdq.api.result.AmendmentValue;
 import org.datakurator.ffdq.api.result.ComplianceValue;
+import org.datakurator.ffdq.api.result.IssueValue;
 import org.filteredpush.qc.georeference.util.GettyLookup;
 
 /**
@@ -388,4 +389,29 @@ public static DQResponse<AmendmentValue> amendmentCountrycodeFromCoordinates(
     	) {
     	return DwCGeoRefDQ.amendmentCountrycodeFromCoordinates(decimalLatitude, decimalLongitude, countryCode, null);
     } 
+
+    /**
+     * Are the supplied geographic coordinates within a defined buffer of the center of the country?
+     * using the default source authority and spatial buffer.
+     *
+     * Provides: 287 ISSUE_COORDINATES_CENTEROFCOUNTRY
+     * Version: 2023-09-17
+     *
+     * @param decimalLatitude the provided dwc:decimalLatitude to evaluate as ActedUpon.
+     * @param decimalLongitude the provided dwc:decimalLongitude to evaluate as ActedUpon.
+     * @param countryCode the provided dwc:countryCode to evaluate as Consulted.
+     * @return DQResponse the response of type AmendmentValue to return
+     */
+    @Amendment(label="ISSUE_COORDINATES_CENTEROFCOUNTRY", description="Are the supplied geographic coordinates within a defined buffer of the center of the country?")
+    @Provides("256e51b3-1e08-4349-bb7e-5186631c3f8e")
+    @ProvidesVersion("https://rs.tdwg.org/bdqcore/terms/256e51b3-1e08-4349-bb7e-5186631c3f8e/2024-08-20")
+    @Specification("EXTERNAL_PREREQUISITES_NOT_MET if the bdq:sourceAuthority is not available; INTERNAL_PREREQUISITES_NOT_MET if any of dwc:countryCode, dwc:decimalLatitude, dwc:decimalLongitude are EMPTY; POTENTIAL_ISSUE if the geographic coordinates are within the distance given by bdq:spatialBufferInMeters from the center (or one of the centers), of the bdq:sourceAuthority provides more than one per country code of the supplied dwc:countryCode as represented in the bdq:sourceAuthority; otherwise NOT_ISSUE.")
+    public static DQResponse<IssueValue> issueCoordinatesCenterofcountry(
+        @ActedUpon("dwc:decimalLatitude") String decimalLatitude, 
+        @ActedUpon("dwc:decimalLongitude") String decimalLongitude, 
+        @Consulted("dwc:countryCode") String countryCode,
+        @Consulted("dwc:coordinateUncertaintyInMeters") String coordinateUncertaintyInMeters
+    ) {
+    	return DwCGeoRefDQ.issueCoordinatesCenterofcountry(decimalLatitude, decimalLongitude, countryCode, coordinateUncertaintyInMeters, null, null);
+    }
 }

src/main/java/org/filteredpush/qc/georeference/EnumGeoRefSourceAuthority.java

@@ -30,6 +30,7 @@ public enum EnumGeoRefSourceAuthority {
     NE_ADMIN_0,
     GADM_ADM1, 
     GETTY_TGN,
+    GBIF_CENTROIDS,
     DATAHUB,
     INVALID;
 

src/main/java/org/filteredpush/qc/georeference/GeoRefSourceAuthority.java

@@ -86,6 +86,12 @@ public GeoRefSourceAuthority(String authorityString) throws SourceAuthorityExcep
 	    	this.authority = EnumGeoRefSourceAuthority.GETTY_TGN;	
 	    } else if (authorityString.toUpperCase().equals("GETTY TGN")) {
 	    	this.authority = EnumGeoRefSourceAuthority.GETTY_TGN;	
+	    } else if (authorityString.toUpperCase().equals("GBIF CATALOGUE OF COUNTRY CENTROIDES")) {
+	    	this.authority = EnumGeoRefSourceAuthority.GBIF_CENTROIDS;	
+	    } else if (authorityString.toUpperCase().equals("GBIF CATALOGUE OF COUNTRY CENTROIDS")) {
+	    	this.authority = EnumGeoRefSourceAuthority.GBIF_CENTROIDS;	
+	    } else if (authorityString.toUpperCase().equals("CATALOGUE-OF-CENTROIDS")) {
+	    	this.authority = EnumGeoRefSourceAuthority.GBIF_CENTROIDS;	
 	    } else if (authorityString.toUpperCase().startsWith("HTTPS://INVALID/")) { 
 	    	this.authority = EnumGeoRefSourceAuthority.INVALID;	
 	    } else { 

src/main/java/org/filteredpush/qc/georeference/util/GEOUtil.java

@@ -20,6 +20,7 @@
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
+import org.filteredpush.qc.georeference.SourceAuthorityException;
 import org.geotools.api.data.FileDataStore;
 import org.geotools.api.data.FileDataStoreFinder;
 import org.geotools.api.data.SimpleFeatureSource;
@@ -373,8 +374,9 @@ public static boolean isOnLand(double Xvalue, double Yvalue, boolean invertSense
      *         false if the x/y value is inside land and invertSense is true
      *         true if the x/y value is outside land and invertSense is true
      * @param bufferInMeters a double.
+     * @throws SourceAuthorityException 
      */
-    public static boolean isOnOrNearLand(double Xvalue, double Yvalue, boolean invertSense, double bufferInMeters) { 
+    public static boolean isOnOrNearLand(double Xvalue, double Yvalue, boolean invertSense, double bufferInMeters) throws SourceAuthorityException { 
     	boolean result = false;
 
     	double bufferKm = bufferInMeters/1000;

src/main/java/org/filteredpush/qc/georeference/util/GISDataLoader.java

@@ -9,11 +9,14 @@
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
+import org.filteredpush.qc.georeference.SourceAuthorityException;
 import org.geotools.api.data.FileDataStore;
 import org.geotools.api.data.FileDataStoreFinder;
 import org.geotools.api.data.SimpleFeatureSource;
+import org.geotools.api.feature.simple.SimpleFeature;
 import org.geotools.api.filter.Filter;
 import org.geotools.data.simple.SimpleFeatureCollection;
+import org.geotools.data.simple.SimpleFeatureIterator;
 import org.geotools.filter.text.cql2.CQLException;
 import org.geotools.filter.text.ecql.ECQL;
 
@@ -93,8 +96,9 @@ public boolean pointIsWithinLand(double longitude, double latitude, boolean inve
 	 * @param invertSense a boolean.
 	 * @return a boolean.
 	 * @param distanceKm a double.
+	 * @throws SourceAuthorityException 
 	 */
-	public boolean pointIsWithinOrNearLand(double longitude, double latitude, boolean invertSense, double distanceKm) {
+	public boolean pointIsWithinOrNearLand(double longitude, double latitude, boolean invertSense, double distanceKm) throws SourceAuthorityException {
 
 		boolean result = false;
 
@@ -115,8 +119,10 @@ public boolean pointIsWithinOrNearLand(double longitude, double latitude, boolea
 		    result = !collection.isEmpty();
 		} catch (IOException e) {
 			logger.error(e.getMessage(), e);
+			throw new SourceAuthorityException("Error reading spatial data file: " + e.getMessage());
 		} catch (CQLException e) {
 			logger.error(e.getMessage(), e);
+			throw new SourceAuthorityException("Error querying spatial data file: " + e.getMessage());
 		} finally { 
 			// close 
 			if (store!=null) { 
@@ -135,6 +141,110 @@ public boolean pointIsWithinOrNearLand(double longitude, double latitude, boolea
 		return result;
 	}
 
+	/**
+	 * Determine if a point is near the centroid of a country. 
+	 *
+	 * @param longitude a double representation of the longigude.
+	 * @param latitude a double representation of the latitude.
+	 * @param countryCode to check for centroids of.
+	 * @param distanceKm the buffer distance in km.
+	 * @return true if latitude and longitude are within buffer distance of a centroid for the country code.
+	 * @throws SourceAuthorityException 
+	 */
+	public static boolean isPointNearCentroid(double longitude, double latitude, String countryCode, double distanceKm) throws SourceAuthorityException {
+
+		boolean result = false;
+
+        URL centroidShapeFile = GEOUtil.class.getResource("/org.filteredpush.kuration.services/gbif_pcli_country_centroids.shp");
+        FileDataStore store = null;
+		try {
+			store = FileDataStoreFinder.getDataStore(centroidShapeFile);
+            SimpleFeatureSource featureSource = store.getFeatureSource();
+            logger.debug(featureSource.getInfo().toString());
+            logger.debug(featureSource.getName().toString());
+            double distanceD = distanceKm / 111d; // GeoTools ignores units, uses units of underlying projection (degrees in this case), fudge by dividing km by number of km in one degree of latitude (this will describe a wide ellipse far north or south).
+		    StringBuffer filterString = new StringBuffer();
+		    filterString.append("DWITHIN(the_geom, POINT(" + Double.toString(longitude) + " " + Double.toString(latitude) + "), "+ distanceD +", kilometers)");
+		    filterString.append(" AND ");
+            filterString.append("iso2 ILIKE '"+ countryCode +"' ");
+		    logger.debug(filterString);
+		    Filter filter = ECQL.toFilter(filterString.toString());
+		    SimpleFeatureCollection collection=featureSource.getFeatures(filter);
+		    result = !collection.isEmpty();
+		} catch (IOException e) {
+			logger.error(e.getMessage(), e);
+			throw new SourceAuthorityException("Error reading country centroids: " + e.getMessage());
+		} catch (CQLException e) {
+			logger.error(e.getMessage(), e);
+			throw new SourceAuthorityException("Error reading country centroids: " + e.getMessage());
+		} finally { 
+			// close 
+			if (store!=null) { 
+				try { 
+					store.dispose();
+				} catch (Exception e) { 
+					logger.error(e.getMessage());
+				}
+			}
+		}
+
+		return result;
+	}
 
+	/**
+	 * Obtain a value for the area of a country. 
+	 *
+	 * @param countryCode to check for area.
+	 * @return area of country in square km, or null if not found
+	 */
+	public static Double getAreaOfCountry(String countryCode) {
+
+		Double result = null;
+
+        URL centroidShapeFile = GEOUtil.class.getResource("/org.filteredpush.kuration.services/gbif_pcli_country_centroids.shp");
+        FileDataStore store = null;
+		try {
+			store = FileDataStoreFinder.getDataStore(centroidShapeFile);
+            SimpleFeatureSource featureSource = store.getFeatureSource();
+            logger.debug(featureSource.getInfo().toString());
+            logger.debug(featureSource.getName().toString());
+		    StringBuffer filterString = new StringBuffer();
+            filterString.append("iso2 ILIKE '"+ countryCode +"' ");
+		    logger.debug(filterString);
+		    Filter filter = ECQL.toFilter(filterString.toString());
+		    SimpleFeatureCollection collection=featureSource.getFeatures(filter);
+		    if (!collection.isEmpty()) { 
+		    	SimpleFeatureIterator i = collection.features();
+		    	boolean found = false;
+		    	while (i.hasNext() && !found) { 
+		    		SimpleFeature feature = i.next();
+		    		Object areaObject = feature.getAttribute("area_sqkm");
+		    		logger.debug(areaObject);
+		    		try { 
+		    			result = (Double)areaObject;
+		    			found = true;
+		    		} catch (ClassCastException e) { 
+		    			logger.debug(e.getMessage());
+		    		}
+		    	}
+		    	i.close();
+		    }
+		} catch (IOException e) {
+			logger.error(e.getMessage(), e);
+		} catch (CQLException e) {
+			logger.error(e.getMessage(), e);
+		} finally { 
+			// close 
+			if (store!=null) { 
+				try { 
+					store.dispose();
+				} catch (Exception e) { 
+					logger.error(e.getMessage());
+				}
+			}
+		}
+
+		return result;
+	}
 
 }

src/main/resources/org.filteredpush.kuration.services/gbif_pcli_country_centroids.cpg

@@ -0,0 +1 @@
+UTF-8

src/main/resources/org.filteredpush.kuration.services/gbif_pcli_country_centroids.prj

@@ -0,0 +1 @@
+GEOGCS["GCS_WGS_1984",DATUM["D_WGS_1984",SPHEROID["WGS_1984",6378137.0,298.257223563]],PRIMEM["Greenwich",0.0],UNIT["Degree",0.0174532925199433]]

src/main/resources/org.filteredpush.kuration.services/gbif_pcli_country_centroids.qmd

@@ -0,0 +1,45 @@
+<!DOCTYPE qgis PUBLIC 'http://mrcc.com/qgis.dtd' 'SYSTEM'>
+<qgis version="3.22.16-Białowieża">
+  <identifier>https://github.com/jhnwllr/catalogue-of-centroids/</identifier>
+  <parentidentifier></parentidentifier>
+  <language></language>
+  <type></type>
+  <title>GBIF Catalog of Country Centroids</title>
+  <abstract>From John Waller https://github.com/jhnwllr/catalogue-of-centroids/ source file https://raw.githubusercontent.com/jhnwllr/catalogue-of-centroids/0959e14d0e7a90de28ae2bc23cf570b791e112ef/PCLI.tsv</abstract>
+  <contact>
+    <name></name>
+    <organization></organization>
+    <position></position>
+    <voice></voice>
+    <fax></fax>
+    <email></email>
+    <role></role>
+  </contact>
+  <links/>
+  <fees></fees>
+  <rights>John Waller</rights>
+  <rights>GBIF</rights>
+  <encoding></encoding>
+  <crs>
+    <spatialrefsys>
+      <wkt></wkt>
+      <proj4></proj4>
+      <srsid>0</srsid>
+      <srid>0</srid>
+      <authid></authid>
+      <description></description>
+      <projectionacronym></projectionacronym>
+      <ellipsoidacronym></ellipsoidacronym>
+      <geographicflag>false</geographicflag>
+    </spatialrefsys>
+  </crs>
+  <extent>
+    <spatial maxx="0" maxz="0" crs="" minx="0" miny="0" dimensions="2" minz="0" maxy="0"/>
+    <temporal>
+      <period>
+        <start></start>
+        <end></end>
+      </period>
+    </temporal>
+  </extent>
+</qgis>

src/main/resources/org.filteredpush.kuration.services/readme.txt

@@ -11,3 +11,5 @@ Flanders Marine Institute (2019). Maritime Boundaries Geodatabase: Maritime Boun
 Creative Commons Attribution 4.0 International License.
 
 The files land_and_eez.shp and merged_countries_and_eez.shp are made from mergers of the above data sources.  
+
+Country Centroids: This (gbif_pcli_country_centroids.shp) is a shape file created from the Centroids for Country Codes PCLI.tsv file compiled by John Waller for GBIF see: https://github.com/jhnwllr/catalogue-of-centroids.  The shapefile was created by importing the PCLI.tsv file into QGIS, then exporting as a shapefile. 

src/test/java/org/filteredpush/qc/geo/test/GeoTesterTest.java

@@ -3,7 +3,10 @@
  */
 package org.filteredpush.qc.geo.test;
 
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
 import org.filteredpush.qc.georeference.GeoTester;
+import org.filteredpush.qc.georeference.SourceAuthorityException;
 import org.filteredpush.qc.georeference.util.GEOUtil;
 import org.filteredpush.qc.georeference.util.GISDataLoader;
 import org.junit.Before;
@@ -21,6 +24,8 @@
  */
 public class GeoTesterTest {
     private GeoTester geoTester;
+
+    private static final Log logger = LogFactory.getLog(GEOUtil.class);
 
     @Before
     public void init() throws IOException {
@@ -162,7 +167,39 @@ public void testparseVerbatimLatLongToDecimalDegree() {
 	@Test
 	public void testisPrimaryAloneKnown() {
 		assertTrue(GEOUtil.isPrimaryAloneKnown("Rio Negro"));
-
+		assertTrue(GEOUtil.isPrimaryAloneKnown("Nevada"));
+		assertFalse(GEOUtil.isPrimaryAloneKnown("Not the name of a state"));
+	}
+
+	@Test
+	public void testisPointNearCentroid() { 
+		String countryCode="JM";
+		double decimalLongitude = -77.250d;
+		double decimalLatitude = 18.1667d;
+		double bufferKm = 3d;
+		try {
+			assertTrue(GISDataLoader.isPointNearCentroid(decimalLongitude, decimalLatitude, countryCode, bufferKm));
+		} catch (SourceAuthorityException e) {
+			fail("Unexpected exception: " + e.getMessage());
+		}
+
+		countryCode="JM";
+		decimalLongitude = 77.250d;
+		decimalLatitude = 18.1667d;
+		bufferKm = 3d;
+		try {
+			assertFalse(GISDataLoader.isPointNearCentroid(decimalLongitude, decimalLatitude, countryCode, bufferKm));
+		} catch (SourceAuthorityException e) {
+			fail("Unexpected exception: " + e.getMessage());
+		}
+
+	}
+
+	@Test
+	public void testgetAreaOfCountry() { 
+		String countryCode="JM";
+		logger.debug(GISDataLoader.getAreaOfCountry(countryCode));
+		assertEquals(11032d, GISDataLoader.getAreaOfCountry(countryCode), 1d);
 	}
 }