Merge pull request #40 from charvolant/master

Release 1.4.7

.travis.yml

@@ -5,12 +5,13 @@ jdk:
 branches:
   only:
   - master
+  - develop
 before_install:
 - mkdir -p ~/.m2; wget -q -O ~/.m2/settings.xml https://raw.githubusercontent.com/AtlasOfLivingAustralia/travis-build-configuration/master/travis_maven_settings.xml
-- sudo mkdir -p /data/lucene; sudo wget -O /data/lucene/namematching-20200214.tgz https://biocache.ala.org.au/archives/nameindexes/20200214/namematching-20200214.tgz
+- sudo mkdir -p /data/lucene; sudo wget -O /data/lucene/namematching-20210811-3.tgz https://archives.ala.org.au/archives/nameindexes/20210811-3/namematching-20210811-3.tgz
 - cd /data/lucene
-- sudo tar zxvf namematching-20200214.tgz
-- sudo ln -s namematching-20200214 namematching
+- sudo tar zxvf namematching-20210811-3.tgz
+- sudo ln -s namematching-20210811-3 namematching
 - ls -laF
 - cd $TRAVIS_BUILD_DIR
 

README.md

@@ -1,4 +1,4 @@
-# sds   [![Build Status](https://travis-ci.com/AtlasOfLivingAustralia/sds.svg?branch#master)](https://travis-ci.com/AtlasOfLivingAustralia/sds)
+# sds   [![Build Status](https://travis-ci.com/AtlasOfLivingAustralia/sds.svg?branch=master)](https://app.travis-ci.com/github/AtlasOfLivingAustralia/sds)
 
 
 The sensitive data service manages sensitivity concerns in the conservation and biosecurity areas.
@@ -65,7 +65,7 @@ value for the property is http://spatial.ala.org.au/layers-service/intersect/
 to sensitive species are correctly determined. This property is only used by the Tests and sds-webapp2.  When you construct
 your sensitive data service you will need to an ALASearcher to be used:
 au.org.ala.sds.SensitiveSpeciesFinderFactory#getSensitiveSpeciesFinder(String dataUrl, ALANameSearcher nameSearcher).  The
-default value for this is /data/lucene/namematching_v13 which should be overridden with the correct value.
+default value for this is /data/lucene/namematching which can either be used as a link or be overridden with the correct value.
 
  * list-url - the URL to the list tool that is used to generate the species xml file, by default https://lists.ala.org.au
 

README.txt

@@ -59,7 +59,7 @@ namematching-index - The location to the name matching index. The SDS uses the n
 to sensitive species are correctly determined. This property is only used by the Tests and sds-webapp2.  When you construct
 your sensitive data service you will need to an ALASearcher to be used:
 au.org.ala.sds.SensitiveSpeciesFinderFactory#getSensitiveSpeciesFinder(String dataUrl, ALANameSearcher nameSearcher).  The
-default value for this is /data/lucene/namematching_v13 which should be overridden with the correct value.
+default value for this is /data/lucene/namematching which can either be used as a link or be overridden with the correct value.
 
 list-url - the URL to the list tool that is used to generate the species xml file, by default https://lists.ala.org.au
 

pom.xml

@@ -9,7 +9,7 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>au.org.ala</groupId>
     <artifactId>sds</artifactId>
-    <version>1.4.6</version>
+    <version>1.4.7</version>
     <issueManagement>
         <system>GitHub</system>
         <url>https://github.com/AtlasOfLivingAustralia/sds/issues</url>
@@ -55,14 +55,8 @@
         </dependency>
         <dependency>
             <groupId>au.org.ala</groupId>
-            <artifactId>ala-name-matching</artifactId>
-            <version>3.5</version>
-            <exclusions>
-                <exclusion>
-                    <groupId>ch.qos.logback</groupId>
-                    <artifactId>logback-classic</artifactId>
-                </exclusion>
-            </exclusions>
+            <artifactId>ala-name-matching-search</artifactId>
+            <version>4.2</version>
             <scope>compile</scope>
         </dependency>
         <dependency>

src/main/java/au/org/ala/sds/validation/ConservationService.java

@@ -71,6 +71,9 @@ public ValidationOutcome validate(Map<String, String> occurrence) {
         GeneralisedLocation gl = GeneralisedLocationFactory.getGeneralisedLocation(latitude, longitude, instances, zones);
         ValidationOutcome outcome = new ValidationOutcome(report);
 
+        // Specify instances
+        outcome.setInstances(instances);
+
         // Assemble result map
         Map<String, Object> results = new HashMap<String, Object>();
         Map<String, String> originalSensitiveValues = new HashMap<String, String>();

src/main/java/au/org/ala/sds/validation/ValidationOutcome.java

@@ -3,6 +3,9 @@
  */
 package au.org.ala.sds.validation;
 
+import au.org.ala.sds.model.SensitivityInstance;
+
+import java.util.List;
 import java.util.Map;
 
 /**
@@ -15,6 +18,7 @@ public class ValidationOutcome {
     private boolean sensitive = false;
     private boolean loadable = false;
     private boolean controlledAccess = false;
+    private List<SensitivityInstance> instances;
     private ValidationReport report;
     private Map<String, Object> result;
 
@@ -68,6 +72,14 @@ public void setControlledAccess(boolean controlledAccess){
         this.controlledAccess = controlledAccess;
     }
 
+    public List<SensitivityInstance> getInstances() {
+        return this.instances;
+    }
+
+    public void setInstances(List<SensitivityInstance> instances) {
+        this.instances = instances;
+    }
+
     public boolean isControlledAccess(){
         return this.controlledAccess;
     }
@@ -86,6 +98,7 @@ public String toString() {
                 "valid=" + valid +
                 ", sensitive=" + sensitive +
                 ", loadable=" + loadable +
+                ", instances=" + instances +
                 ", report=" + report +
                 ", result=" + result +
                 '}';

src/test/java/au/org/ala/sds/FileInputTest.java

@@ -1,26 +1,12 @@
 package au.org.ala.sds;
 
-import java.util.Map;
-
 import au.org.ala.names.search.ALANameSearcher;
-import org.apache.commons.lang.StringUtils;
-import org.junit.BeforeClass;
-import org.junit.Test;
-
-import au.org.ala.names.search.ALANameIndexer;
-import au.org.ala.sds.dao.DataRowHandler;
-import au.org.ala.sds.dao.DataStreamDao;
-import au.org.ala.sds.dao.DataStreamDaoFactory;
-import au.org.ala.sds.dto.DataColumnMapper;
-import au.org.ala.sds.dto.DataStreamProperties;
 import au.org.ala.sds.model.Message;
 import au.org.ala.sds.model.SensitiveTaxon;
-import au.org.ala.sds.util.Configuration;
-import au.org.ala.sds.validation.FactCollection;
-import au.org.ala.sds.validation.ServiceFactory;
-import au.org.ala.sds.validation.ValidationOutcome;
-import au.org.ala.sds.validation.ValidationReport;
-import au.org.ala.sds.validation.ValidationService;
+import au.org.ala.sds.validation.*;
+import org.apache.commons.lang.StringUtils;
+
+import java.util.Map;
 
 public class FileInputTest {
 

src/test/java/au/org/ala/sds/GeneraliseTest.java

@@ -189,6 +189,10 @@ public void notBirdsAustraliaInNsw() {
 
         assertTrue(outcome.isValid());
         assertTrue(outcome.isSensitive());
+        // Has two instances but only one valid for location
+        assertNotNull(outcome.getInstances());
+        assertEquals(1, outcome.getInstances().size());
+        assertEquals("New South Wales", outcome.getInstances().get(0).getZone().getName());
     }
 
     /**
@@ -322,7 +326,7 @@ public void vicSpeciesInVic() {
      */
     @Test
     public void findSpeciesByLsid() {
-        SensitiveTaxon ss = finder.findSensitiveSpeciesByLsid("urn:lsid:biodiversity.org.au:afd.taxon:0217f06f-664c-4c64-bc59-1b54650fa23d");
+        SensitiveTaxon ss = finder.findSensitiveSpeciesByLsid("https://biodiversity.org.au/afd/taxa/5815e99d-01cd-4a92-99ba-36f480c4834d");
         assertNotNull(ss);
         String latitude = "-33.630629";    // NSW
         String longitude = "150.441284";

src/test/java/au/org/ala/sds/PlantPestEradicatedTest.java

@@ -83,7 +83,7 @@ public void papayaFruitFlyInPQADuringEradication() {
         //assertNotNull(outcome.getAnnotation());
         assertNotNull(outcome.getReport().getAssertion());
         // Current version of SDS does not include plant pest status and name index does not contain name
-        assertEquals(MessageFactory.getMessageText(MessageFactory.PLANT_PEST_MSG_CAT2_A1, "Bactrocera papayae"),outcome.getReport().getAssertion());
+        assertEquals(MessageFactory.getMessageText(MessageFactory.PLANT_PEST_MSG_CAT2_A1, "Bactrocera (Bactrocera) dorsalis"),outcome.getReport().getAssertion());
     }
 
     @Test
@@ -109,8 +109,14 @@ public void citrusCankerInPQABeforeEradication() {
         assertTrue(outcome.isLoadable());
         assertTrue(outcome.isControlledAccess());
         //test for the correct messages
-        assertEquals(MessageFactory.getMessageText(MessageFactory.PLANT_PEST_MSG_CAT2_B1, "Xanthomonas axonopodis citri","Emerald"),outcome.getReport().getAssertion());
-        assertTrue(outcome.getReport().getMessages().get(0).getMessageText().contains("Xanthomonas axonopodis citri,2004-01-29 and Emerald has been forwarded to a secure view with the Atlas of Living Australia"));
+        assertEquals(MessageFactory.getMessageText(MessageFactory.PLANT_PEST_MSG_CAT2_B1, "Xanthomonas citri (ex Hasse 1915) Gabriel et al. subsp. citri 2007","Emerald"),outcome.getReport().getAssertion());
+        assertEquals("Your record Xanthomonas citri (ex Hasse 1915) Gabriel et al. subsp. citri 2007,2004-01-29 and Emerald has been forwarded to a secure view with the Atlas of Living Australia.\n" +
+                "This record has been determined to have plant biosecurity sensitivity because the record is an earlier collection of a pest believed eradicated from Emerald and therefore Australia.\n" +
+                "Please note the following:\n" +
+                "1) Diagnostic keys and guidance on other tools for identifying many exotic plant pests, particularly those considered Emergency Plant Pests under the EPPRD, are becoming readily available through the Plant Biosecurity Toolbox and Biosecurity Bank developed by the CRC for Plant Biosecurity.\n" +
+                "2)  The Emergency Plant Pest Response Deed (Section 4) (http://www.planthealthaustralia.com.au/go/phau/epprd/epprd-information) imposes reporting obligations where an Emergency Plant Pest is suspected. Most States also have requirements for reporting the presence of many other potentially harmful exotic plant pests not included in the EPPRD.\n" +
+                "3) When the presence of an exotic plant pest is suspected, phone the Exotic Plant Pest Hotline 1800 084 881. (PPC2-B2)",
+                outcome.getReport().getMessages().get(0).getMessageText());
     }
 
     @Test
@@ -193,6 +199,6 @@ public void citrusCankerNoDate(){
         assertTrue(outcome.isControlledAccess());
         // Current version of SDS does not include plant pest status and name index does not contain name
         assertTrue(outcome.getReport().getMessages().get(0).getMessageText().contains("and Emerald has been forwarded to a secure view with the Atlas of Living Australia"));
-        assertEquals(MessageFactory.getMessageText(MessageFactory.PLANT_PEST_MSG_CAT2_A1, "Xanthomonas axonopodis citri"),outcome.getReport().getAssertion());
+        assertEquals(MessageFactory.getMessageText(MessageFactory.PLANT_PEST_MSG_CAT2_A1, "Xanthomonas citri (ex Hasse 1915) Gabriel et al. subsp. citri 2007"),outcome.getReport().getAssertion());
     }
 }

src/test/java/au/org/ala/sds/SearchTest.java

@@ -54,7 +54,7 @@ public void lookupCrex() {
 
     @Test
     public void lookupMitchellsByLsid() {
-        SensitiveTaxon ss = finder.findSensitiveSpeciesByLsid("urn:lsid:biodiversity.org.au:afd.taxon:0217f06f-664c-4c64-bc59-1b54650fa23d");
+        SensitiveTaxon ss = finder.findSensitiveSpeciesByLsid("https://biodiversity.org.au/afd/taxa/5815e99d-01cd-4a92-99ba-36f480c4834d");
         assertNotNull(ss);
         assertEquals("Lophochroa leadbeateri", ss.getTaxonName());
     }

src/test/resources/sds-test.properties

@@ -1,2 +1,2 @@
 # Overriden properties for tests
-name.index.dir=/data/lucene/namematching-20200214
+name.index.dir=/data/lucene/namematching-20210811-3