TaxonomyService does not enforce 'subsp.', upgrade will include subtaxa

src/main/java/org/genesys2/server/listener/sample/TaxonomyUpgrade.java

@@ -68,13 +68,21 @@ public class TaxonomyUpgrade extends RunAsAdminListener {
 				continue;
 			}
 			String species = t1.getSpecies();
-
 			String spAuthor = null;
 			String subtaxa = null;
 			String subtAuthor = null;
 
+			String x = genus + ' ' + species;
+			if (t1.getTaxonName().startsWith(x)) {
+				String foo = t1.getTaxonName().substring(x.length()).trim();
+				if (StringUtils.isNotBlank(foo)) {
+					subtaxa = foo;
+				}
+			}
+
 			// Make new taxonomy
 			Taxonomy2 t2 = taxonomyService.ensureTaxonomy2(genus, species, spAuthor, subtaxa, subtAuthor);
+			counter.incrementAndGet();
 
 			// Update all accessions
 			count = taxonomyService.upgradeTaxonomy(t1, t2);

src/main/java/org/genesys2/server/service/impl/TaxonomyServiceImpl.java

@@ -125,10 +125,6 @@ public class TaxonomyServiceImpl implements TaxonomyService {
 			species = "sp.";
 		}
 
-		if (StringUtils.isNotBlank(species) && !StringUtils.equals(species, "sp.") && StringUtils.isBlank(subtaxa)) {
-			subtaxa = "subsp.";
-		}
-
 		Taxonomy2 existing = taxonomy2Repository.findByGenusAndSpeciesAndSpAuthorAndSubtaxaAndSubtAuthor(genus, species, spAuthor, subtaxa, subtAuthor);
 		if (existing == null) {
 			return internalEnsure(genus, species, spAuthor, subtaxa, subtAuthor);
@@ -139,11 +135,11 @@ public class TaxonomyServiceImpl implements TaxonomyService {
 	private synchronized Taxonomy2 internalEnsure(String genus, String species, String spAuthor, String subtaxa, String subtAuthor) {
 		Taxonomy2 genusTaxa = null;
 		Taxonomy2 speciesTaxa = null;
-		if (species != null && !StringUtils.equals(species, "sp.") && (subtaxa != null || spAuthor != null || subtAuthor != null)) {
+		if (!StringUtils.equals(species, "sp.") || (subtaxa != null || spAuthor != null || subtAuthor != null)) {
 			genusTaxa = internalEnsure(genus, "sp.", null, null, null);
 		}
-		if (species != null && !StringUtils.equals(species, "sp.") && !StringUtils.equals(subtaxa, "subsp.") && spAuthor != null && subtAuthor != null) {
-			speciesTaxa = internalEnsure(genus, species, null, "subsp.", null);
+		if (!StringUtils.equals(species, "sp.") && (subtaxa != null || spAuthor != null || subtAuthor != null)) {
+			speciesTaxa = internalEnsure(genus, species, null, null, null);
 		}
 
 		// Loop it a bit if required
@@ -202,8 +198,7 @@ public class TaxonomyServiceImpl implements TaxonomyService {
 
 	@Override
 	public long getTaxonomy2Id(String genus, String species) {
-		Taxonomy2 tax = taxonomy2Repository.findByGenusAndSpeciesAndSpAuthorAndSubtaxaAndSubtAuthor(genus, species, null, "subsp.", null);
-		System.err.println("tax2=" + tax);
+		Taxonomy2 tax = taxonomy2Repository.findByGenusAndSpeciesAndSpAuthorAndSubtaxaAndSubtAuthor(genus, species, null, null, null);
 		return tax.getId();
 	}
 

src/test/java/org/genesys2/server/test/TaxonomyEnsureTest.java

+package org.genesys2.server.test;
+
+import static org.junit.Assert.fail;
+import static org.junit.Assert.assertTrue;
+
+import org.apache.commons.lang.StringUtils;
+import org.genesys2.server.model.genesys.Taxonomy2;
+import org.genesys2.server.service.TaxonomyService;
+import org.genesys2.server.service.impl.TaxonomyServiceImpl;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Import;
+import org.springframework.test.context.ContextConfiguration;
+import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
+
+@RunWith(SpringJUnit4ClassRunner.class)
+@ContextConfiguration(classes = TaxonomyEnsureTest.Config.class, initializers = PropertyPlacholderInitializer.class)
+public class TaxonomyEnsureTest {
+
+	@Import(JpaDataConfig.class)
+	public static class Config {
+
+		@Bean
+		public TaxonomyService taxonomyService() {
+			return new TaxonomyServiceImpl();
+		}
+
+	}
+
+	// use it without @Scheduled
+	@Autowired
+	private TaxonomyService taxonomyService;
+	
+	@Test
+	public void testSubstr() {
+		String genus="Aaaa";
+		String species="bbbb";
+		String taxonName = "Aaaa bbbb fb.";
+		String x = genus + ' ' + species;
+
+		assertTrue(taxonName.startsWith(x));
+
+		if (taxonName.startsWith(x)) {
+			String subtaxa = taxonName.substring(x.length()).trim();
+			assertTrue(StringUtils.isNotBlank(subtaxa));
+			assertTrue("fb.".equals(subtaxa));
+		}
+	}
+
+	@Test
+	public void testEnsure1() {
+		try {
+			Taxonomy2 tax = taxonomyService.ensureTaxonomy2("Aaaaa", "bbbb", null, "alfalfa", null);
+			assertTrue("id missing", tax.getId() != null);
+			assertTrue("taxGenus should not be null", tax.getTaxGenus() != null);
+			assertTrue("taxSpecies should not be null", tax.getTaxSpecies() != null);
+			assertTrue("taxGenus should not be this", !tax.getTaxGenus().equals(tax.getId()));
+			assertTrue("taxSpecies should not be this", !tax.getTaxSpecies().equals(tax.getId()));
+			assertTrue("taxSpecies should not match taxGenus", !tax.getTaxSpecies().equals(tax.getTaxGenus()));
+
+			Taxonomy2 taxGenus = taxonomyService.get(tax.getTaxGenus());
+			assertTrue("taxGenus should have species=sp. and not " + taxGenus.getSpecies(), taxGenus.getSpecies().equals("sp."));
+
+			Taxonomy2 taxSpecies = taxonomyService.get(tax.getTaxSpecies());
+			assertTrue("taxSpecies should have species=bbbb and not " + taxSpecies.getSpecies(), taxSpecies.getSpecies().equals(tax.getSpecies()));
+
+		} catch (Exception e) {
+			fail("This should not have any exceptions!");
+		}
+	}
+
+	@Test
+	public void testNullSpecies() {
+		try {
+			Taxonomy2 tax = taxonomyService.ensureTaxonomy2("Aaaaa", null, null, null, null);
+			assertTrue("id missing", tax.getId() != null);
+			assertTrue("taxGenus should not be null", tax.getTaxGenus() != null);
+			assertTrue("taxSpecies should not be null", tax.getTaxSpecies() != null);
+			assertTrue("taxGenus must be this", tax.getTaxGenus().equals(tax.getId()));
+			assertTrue("taxSpecies must be this", tax.getTaxSpecies().equals(tax.getId()));
+			assertTrue("taxSpecies should match taxGenus", tax.getTaxSpecies().equals(tax.getTaxGenus()));
+		} catch (Exception e) {
+			fail("This should not have any exceptions!");
+		}
+	}
+	
+
+	@Test
+	public void testSpSpecies() {
+		try {
+			Taxonomy2 tax = taxonomyService.ensureTaxonomy2("Aaaaa", "sp", null, null, null);
+			assertTrue("id missing", tax.getId() != null);
+			assertTrue("species must be sp.", tax.getSpecies().equals("sp."));
+			assertTrue("taxGenus should not be null", tax.getTaxGenus() != null);
+			assertTrue("taxSpecies should not be null", tax.getTaxSpecies() != null);
+			assertTrue("taxGenus must be this", tax.getTaxGenus().equals(tax.getId()));
+			assertTrue("taxSpecies must be this", tax.getTaxSpecies().equals(tax.getId()));
+			assertTrue("taxSpecies should match taxGenus", tax.getTaxSpecies().equals(tax.getTaxGenus()));
+		} catch (Exception e) {
+			fail("This should not have any exceptions!");
+		}
+	}
+}