Fixes for issue AtlasOfLivingAustralia#12 Based on maniplulating the …

…instance list. This will be replaced in the main branch with something that reports per-query instances and per-species instances separately.

ala-sensitive-data-client/src/test/java/au/org/ala/sds/ws/ALASensitiveDataServiceApplicationIT.java

@@ -11,6 +11,7 @@
 
 import java.io.*;
 import java.net.URL;
+import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 
@@ -118,10 +119,10 @@ public void testGetSpecies1() throws Exception {
         URL req = new URL("http://localhost:9189/ws/species");
         List result = readList(req);
         assertNotNull(result);
-        assertEquals(1, result.size());
+        assertEquals(2, result.size());
         assertTrue(result.get(0) instanceof Map);
         Map instance = (Map) result.get(0);
-        assertEquals("Pterostylis oreophila", instance.get("scientificName"));
+        assertEquals("Pandion haliaetus", instance.get("scientificName"));
         assertEquals("species", instance.get("taxonRank"));
     }
 
@@ -186,4 +187,49 @@ public void testGetReport3() throws Exception {
         assertFalse(report.isSensitive());
     }
 
+    @Test
+    public void testGetReport4() throws Exception {
+        List<Generalisation> generalisations = this.client.getGeneralisations();
+        SensitivityReport report = this.client.report("Pandion haliaetus", null, null, "South Australia", "Australia", null);
+        assertNotNull(report);
+        assertTrue(report.isSensitive());
+        Map<String, String> supplied = new HashMap<>();
+        Map<String, Object> original = new HashMap<>();
+        Map<String, Object> updated = new HashMap<>();
+        supplied.put("stateProvince", "South Australia");
+        supplied.put("country", "Australia");
+        supplied.put("decimalLatitude", "-35.49386");
+        supplied.put("decimalLongitude", "138.54762");
+        supplied.put("eventDate", "2022-10-30");
+        for (Generalisation g: generalisations) {
+            g.process(supplied, original, updated, report);
+        }
+        assertEquals("Record is South Australia in SA Category 2 Conservation Sensitive. Generalised to 10km by SA DEWNR.", updated.get("dataGeneralizations"));
+        assertEquals("138.6", updated.get("decimalLongitude"));
+        assertEquals("-35.5", updated.get("decimalLatitude"));
+        assertNull(updated.get("eventDate"));
+    }
+    @Test
+    public void testGetReport5() throws Exception {
+        List<Generalisation> generalisations = this.client.getGeneralisations();
+        SensitivityReport report = this.client.report("Pandion haliaetus", null, null, "Western Australia", "Australia", null);
+        assertNotNull(report);
+        assertTrue(report.isSensitive());
+        Map<String, String> supplied = new HashMap<>();
+        Map<String, Object> original = new HashMap<>();
+        Map<String, Object> updated = new HashMap<>();
+        supplied.put("stateProvince", "West Australia");
+        supplied.put("country", "Australia");
+        supplied.put("decimalLatitude", "-32.70613");
+        supplied.put("decimalLongitude", "124.97978");
+        supplied.put("eventDate", "2022-09-21");
+        for (Generalisation g: generalisations) {
+            g.process(supplied, original, updated, report);
+        }
+        assertEquals("Record is Western Australia in Sensitive. Generalised to 10km by WA DEC.", updated.get("dataGeneralizations"));
+        assertEquals("125.0", updated.get("decimalLongitude"));
+        assertEquals("-32.7", updated.get("decimalLatitude"));
+        assertNull(updated.get("eventDate"));
+    }
+
 }

ala-sensitive-data-client/src/test/resources/sensitive-species-data-it-1.xml

@@ -5,4 +5,10 @@
       <conservationInstance category="High" authority="ACT Government" dataResourceId="dr2627" generalisation="1km" zone="ACT" />
     </instances>
   </sensitiveSpecies>
+  <sensitiveSpecies name="Pandion haliaetus" family="Accipitridae" guid="https://biodiversity.org.au/afd/taxa/23a8017a-3a2b-4a52-8ca6-d168bf52659c" rank="SPECIES" commonName="osprey">
+    <instances>
+      <conservationInstance category="" authority="WA DEC" dataResourceId="dr467" generalisation="10km" zone="WA" />
+      <conservationInstance category="C2" authority="SA DEWNR" dataResourceId="dr884" generalisation="10km" zone="SA" />
+    </instances>
+  </sensitiveSpecies>
 </sensitiveSpeciesList>

ala-sensitive-data-server/docker/Dockerfile

@@ -1,4 +1,4 @@
-FROM java:openjdk-8-jre-alpine
+FROM amazoncorretto:11.0.18-alpine3.17
 
 ARG ENV
 
@@ -15,7 +15,7 @@ COPY ./docker/sds-config.properties /data/sds/config/sds-config.properties
 
 RUN if [ "$ENV" = "gbif-backbone" ]; then \
     curl -sf  -o /data/lucene/namematching.tgz -L https://datos.gbif.es/others/namematching-gbif-backbone-2020-06-18.tgz; else \
-    curl -sf  -o /data/lucene/namematching.tgz -L https://archives.ala.org.au/archives/nameindexes/latest/namematching-20210811-3.tgz; fi
+    curl -sf  -o /data/lucene/namematching.tgz -L https://archives.ala.org.au/archives/nameindexes/20210811-3/namematching-20210811-3.tgz; fi
 #COPY namematching.tgz /data/lucene/namematching.tgz
 
 RUN tar zxf /data/lucene/namematching.tgz -C /data/lucene

ala-sensitive-data-server/docker/config.yml

@@ -20,7 +20,7 @@ server:
     - type: http
       port: 9190
 conservation:
-  index: /data/lucene/namematching-20210811-3
+  index: /data/lucene/namematching
   speciesUrl: file:///data/sds/sensitive-species-data.xml
   zonesUrl: file:///data/sds/sensitivity-zones.xml
   categoriesUrl: file:///data/sds/sensitivity-categories.xml

ala-sensitive-data-server/src/main/java/au/org/ala/sds/ws/resources/ApiTranslator.java

@@ -8,6 +8,7 @@
 import au.org.ala.sds.validation.ValidationOutcome;
 
 import java.util.HashMap;
+import java.util.List;
 import java.util.Map;
 import java.util.stream.Collectors;
 
@@ -34,17 +35,21 @@ public ApiTranslator(boolean useLibrary) {
     /**
      * Generate a sensitivity report from the SDS outcome.
      */
-    public SensitivityReport buildSensitivityReport(ValidationOutcome outcome) {
+    public SensitivityReport buildSensitivityReport(ValidationOutcome outcome, boolean allInstances) {
         if (outcome == null)
             return null;
         Map<String, Object> original = this.useLibrary && outcome.getResult() != null ? (Map<String, Object>) outcome.getResult().remove(ORIGINAL_VALUES) : new HashMap<>();
         Map<String, Object> result = this.useLibrary ? outcome.getResult() : new HashMap<>();
+        List<au.org.ala.sds.model.SensitivityInstance> instances = outcome.getInstances();
+        if (allInstances && outcome.getReport() instanceof SdsValidationReport) {
+            instances = ((SdsValidationReport) outcome.getReport()).getSpecies().getInstances();
+        }
         return SensitivityReport.builder()
             .valid(outcome.isValid())
             .sensitive(outcome.isSensitive())
             .loadable(outcome.isLoadable())
             .accessControl(outcome.isControlledAccess())
-            .report(this.buildValidationReport(outcome.getReport()))
+            .report(this.buildValidationReport(outcome.getReport(), instances))
             .original(original)
             .updated(result)
             .build();
@@ -53,15 +58,15 @@ public SensitivityReport buildSensitivityReport(ValidationOutcome outcome) {
     /**
      * Generate a validation report from an SDS validation report.
      */
-    public ValidationReport buildValidationReport(au.org.ala.sds.validation.ValidationReport report) {
+    public ValidationReport buildValidationReport(au.org.ala.sds.validation.ValidationReport report, List<au.org.ala.sds.model.SensitivityInstance> instances) {
         if (report == null)
             return null;
         ValidationReport.ValidationReportBuilder builder = ValidationReport.builder()
             .messages(report.getMessages().stream().map(m -> this.buildMessage(m)).collect(Collectors.toList()))
             .category(report.getCategory())
             .assertion(report.getAssertion());
         if (report instanceof SdsValidationReport)
-            builder.taxon(this.buildSensitiveTaxon(((SdsValidationReport) report).getSpecies()));
+            builder.taxon(this.buildSensitiveTaxon(((SdsValidationReport) report).getSpecies(), instances));
         return builder.build();
     }
 
@@ -77,7 +82,7 @@ public ValidationReport.Message buildMessage(Message message) {
     /**
      * Generate a sensitive taxon description from the SDS
      */
-    public SensitiveTaxon buildSensitiveTaxon(au.org.ala.sds.model.SensitiveTaxon taxon) {
+    public SensitiveTaxon buildSensitiveTaxon(au.org.ala.sds.model.SensitiveTaxon taxon, List<au.org.ala.sds.model.SensitivityInstance> instances) {
         if (taxon == null)
             return null;
         return SensitiveTaxon.builder()
@@ -87,7 +92,10 @@ public SensitiveTaxon buildSensitiveTaxon(au.org.ala.sds.model.SensitiveTaxon ta
             .acceptedName(taxon.getAcceptedName())
             .commonName(taxon.getCommonName())
             .taxonRank(taxon.getRank() == null ? null : taxon.getRank().getRank())
-            .instances(taxon.getInstances().stream().map(i -> this.buildSensitivityInstance(i)).collect(Collectors.toList()))
+            .instances(instances.stream()
+                    .map(i -> this.buildSensitivityInstance(i))
+                    .collect(Collectors.toList())
+            )
             .build();
     }
 

ala-sensitive-data-server/src/main/java/au/org/ala/sds/ws/resources/ConservationResource.java

@@ -274,7 +274,8 @@ public SensitivityReport report(
         @ApiParam(value = "The source data resource identifier", example = "dr1654") @QueryParam("dataResourceUid")String dataResourceUid,
         @ApiParam(value = "The state or province zone identifier", example = "NSW") @QueryParam("stateProvince") String stateProvince,
         @ApiParam(value = "The country zone identifier", example = "AUS") @QueryParam("country") String country,
-        @ApiParam(value = "The zone identifiers ", allowMultiple = true, example = "FFEZ") @QueryParam("zone") List<String> zones) {
+        @ApiParam(value = "The zone identifiers ", allowMultiple = true, example = "FFEZ") @QueryParam("zone") List<String> zones
+    ) {
         Map<String, String> properties = new HashMap<>();
         properties.put("samplesProvided", "yes");
         if (dataResourceUid != null && !dataResourceUid.isEmpty())
@@ -291,7 +292,7 @@ public SensitivityReport report(
             scientificName,
             taxonId
         );
-        SensitivityReport report = this.translator.buildSensitivityReport(outcome);
+        SensitivityReport report = this.translator.buildSensitivityReport(outcome, false);
         return report;
     }
 
@@ -324,7 +325,7 @@ public SensitivityReport process(ProcessQuery query) {
             query.getTaxonId()
         );
         this.amendOutcome(query, outcome);
-        SensitivityReport report = this.translator.buildSensitivityReport(outcome);
+        SensitivityReport report = this.translator.buildSensitivityReport(outcome, false);
         for (Generalisation generalisation: this.generalisations) {
             generalisation.process(query, report);
         }

ala-sensitive-data-server/src/main/java/au/org/ala/sds/ws/resources/ModelResource.java

@@ -64,7 +64,7 @@ public ModelResource(SDSConfiguration configuration){
                 .collect(Collectors.toList());
             sis = new URL(sdsConfig.getSpeciesUrl()).openStream();
             this.sensitive = new SensitiveSpeciesXmlDao(sis).getAll().stream()
-                .map(taxon -> translator.buildSensitiveTaxon(taxon))
+                .map(taxon -> translator.buildSensitiveTaxon(taxon, taxon.getInstances()))
                 .collect(Collectors.toList());
             this.layers = sdsConfig.getGeospatialLayers();
         } catch (Exception e){

ala-sensitive-data-server/src/test/java/au/org/ala/sds/ws/resources/ConservationResourceTest.java

@@ -187,6 +187,64 @@ public void testReport4() throws Exception {
     }
 
 
+    // Test taxon with multiple instances
+    @Test
+    public void testReport5() throws Exception {
+        SensitivityReport report = resource.report("Pandion haliaetus", null, "dr8359", "Western Australia", "Australia", null);
+        assertNotNull(report);
+        assertTrue(report.isValid());
+        assertTrue(report.isSensitive());
+        assertTrue(report.isLoadable());
+        assertFalse(report.isAccessControl());
+        ValidationReport vr = report.getReport();
+        assertNotNull(vr);
+        SensitiveTaxon taxon = vr.getTaxon();
+        assertNotNull(taxon);
+        assertEquals("Pandion haliaetus", taxon.getScientificName());
+        assertEquals("https://biodiversity.org.au/afd/taxa/23a8017a-3a2b-4a52-8ca6-d168bf52659c", taxon.getTaxonId());
+        assertNotNull(taxon.getInstances());
+        assertEquals(1, taxon.getInstances().size());
+        SensitivityInstance instance = taxon.getInstances().get(0);
+        assertEquals("WA DEC", instance.getAuthority());
+        assertEquals(SensitivityInstance.SensitivityType.CONSERVATION, instance.getType());
+        assertEquals("10km", instance.getGeneralisation().getGeneralisation());
+        assertNotNull(instance.getCategory());
+        assertEquals("Sensitive", instance.getCategory().getId());
+        assertEquals("dr467", instance.getDataResourceId());
+        assertNotNull(instance.getZone());
+        assertEquals("WA", instance.getZone().getId());
+    }
+
+
+    // Test taxon with multiple instances - only one requested
+    @Test
+    public void testReport6() throws Exception {
+        SensitivityReport report = resource.report("Pandion haliaetus", null, "dr8359", "South Australia", "Australia", null);
+        assertNotNull(report);
+        assertTrue(report.isValid());
+        assertTrue(report.isSensitive());
+        assertTrue(report.isLoadable());
+        assertFalse(report.isAccessControl());
+        ValidationReport vr = report.getReport();
+        assertNotNull(vr);
+        SensitiveTaxon taxon = vr.getTaxon();
+        assertNotNull(taxon);
+        assertEquals("Pandion haliaetus", taxon.getScientificName());
+        assertEquals("https://biodiversity.org.au/afd/taxa/23a8017a-3a2b-4a52-8ca6-d168bf52659c", taxon.getTaxonId());
+        assertNotNull(taxon.getInstances());
+        assertEquals(1, taxon.getInstances().size());
+        SensitivityInstance instance = taxon.getInstances().get(0);
+        assertEquals("SA DEWNR", instance.getAuthority());
+        assertEquals(SensitivityInstance.SensitivityType.CONSERVATION, instance.getType());
+        assertEquals("10km", instance.getGeneralisation().getGeneralisation());
+        assertNotNull(instance.getCategory());
+        assertEquals("C2", instance.getCategory().getId());
+        assertEquals("dr884", instance.getDataResourceId());
+        assertNotNull(instance.getZone());
+        assertEquals("SA", instance.getZone().getId());
+    }
+
+
     @Test
     public void testProcess1() throws Exception {
         Map<String, String> properties = new HashMap<>();
@@ -285,16 +343,7 @@ public void testProcess3() throws Exception {
         assertEquals("https://biodiversity.org.au/afd/taxa/2edc1a0c-b74a-49da-b053-b7e1328a54a7", taxon.getTaxonId());
         assertEquals("little waterfall frog", taxon.getCommonName());
         assertNotNull(taxon.getInstances());
-        assertEquals(1, taxon.getInstances().size());
-        SensitivityInstance instance = taxon.getInstances().get(0);
-        assertEquals("Qld DEHP", instance.getAuthority());
-        assertEquals(SensitivityInstance.SensitivityType.CONSERVATION, instance.getType());
-        assertEquals("10km", instance.getGeneralisation().getGeneralisation());
-        assertNotNull(instance.getCategory());
-        assertEquals("Sensitive", instance.getCategory().getId());
-        assertEquals("dr493", instance.getDataResourceId());
-        assertNotNull(instance.getZone());
-        assertEquals("QLD", instance.getZone().getId());
+        assertEquals(0, taxon.getInstances().size());
         Map<String, Object> result = report.getUpdated();
         assertNotNull(result);
         assertNull(result.get("decimalLongitude"));