some small fixes and tests for BioTree.

src/data/FileProcessor.java

@@ -32,7 +32,7 @@ public class FileProcessor {
 	/**
 	 * Sets a new path string
 	 */
-	public void setPath(String newPath) {
+	public static void setPath(String newPath) {
 		path = newPath;
 	}
 	

src/data/TestBioTree.java

-package data;
-
-import static org.junit.Assert.*;
-
-import java.io.IOException;
-
-import org.junit.Before;
-import org.junit.Test;
-
-import data.biotree.BioTree;
-
-public class TestBioTree {
-
-	@Before
-	public static void main(String[] args) throws IOException {
-		BioTree.init();
-		BioTree.processRecord(125125);
-		BioTree.processRecord(125125);
-		BioTree.processRecord(125125);
-		BioTree.processRecord(125125);
-		BioTree.processRecord(125125);
-		BioTree.processRecord(125125);
-		BioTree.processRecord(125123);
-		BioTree.processRecord(125122);
-		BioTree.processRecord(125392);
-		BioTree.processRecord(125391);
-		BioTree.processRecord(600000000);
-		//System.out.println(nodes.size());
-		//System.out.println(nodes.get(123207));
-		//Iterable<Integer> keys = nodes.keys();
-		//for (Integer i: keys) {
-		//	System.out.println(nodes.get(i));
-			//System.out.println(String.format("%-26s %s", nodes.get(i).getName(), nodes.get(i).getTaxonType()));
-		//}
-		BioTree.printTree();
-	}
-	
-
-}

src/data/biotree/BioTree.java

@@ -23,7 +23,7 @@ import search.RedBlackTree;
  */
 public class BioTree implements Serializable {
 	/**
-	 * 
+	 * Serializable version ID. Requires by Serializable interface.
 	 */
 	private static final long serialVersionUID = 4291273291916906661L;
 	/**
@@ -232,8 +232,14 @@ public class BioTree implements Serializable {
 	 * @throws ParseException 
 	 * @throws IOException 
 	 */
-	public static TaxonNode getTaxonRecord(String scientificName) throws IOException, ParseException {
-		return idNodes.get(nameToTaxonId(scientificName));
+	public static TaxonNode getTaxonRecord(String scientificName) {
+		try {
+			Integer taxonId = nameToTaxonId(scientificName);
+			if (taxonId == null) return null;
+			return idNodes.get(taxonId);
+		} catch (IOException | ParseException e0) {
+			return null;
+		}
 	}
 	
 	/**

src/data/biotree/TestBio.java

+package data.biotree;
+
+import static org.junit.Assert.*;
+
+import org.json.simple.parser.ParseException;
+import org.junit.Before;
+import org.junit.BeforeClass;
+import org.junit.Test;
+
+import data.FileProcessor;
+import search.trawl.BasicSearch;
+
+/**
+ * Testing was performed on a small dataset for which we know the correct numbers of data for each
+ * taxon. Takes a while to process the dataset since most of the species in the set are unique and
+ * thus require API calls.
+ * @author TrawlStars, Inc.
+ *
+ */
+public class TestBio {
+
+	/**
+	 * Loads the small dataset into memory using the FileProcessor.
+	 * @throws Exception Cannot find dataset given.
+	 */
+	@BeforeClass
+	public static void setUp() throws Exception {
+		//load small test dataset 
+		BioTree.init();
+		FileProcessor.setPath("smalldata.csv");
+		FileProcessor.initProcessing();
+	}
+
+	@Test
+	public void testAnuraExists() throws ParseException {
+		assert(BioTree.getTaxonRecord("Anura") != null);
+	}
+	
+	@Test
+	public void testGetTaxonNode() {
+		//test that Esox is in dataset
+		assert(BioTree.getTaxonRecord("Esox lucius") != null);
+	}
+	
+	@Test
+	public void testGetTaxonNodeFails() {
+		//test that Esox is in dataset
+		assert(BioTree.getTaxonRecord("Mythical Creature") == null);
+	}
+	
+	@Test
+	public void testGetCount() {
+		//test count is correct
+		assert(BioTree.getTaxonRecord("Esox lucius").getCount() == 4);
+	}
+	
+	@Test
+	public void testGetName() {
+		//test name correct
+		assert(BioTree.getTaxonRecord("Esox lucius").getName().equals("Esox lucius"));
+	}
+	
+	@Test
+	public void testGetParent() {
+		//test that the correct parent has been stored in the dataset
+		assert(BioTree.getTaxonRecord("Esox lucius").getParent().getTaxonId() == 154208);
+	}
+	
+	@Test
+	public void testGetChildren() {
+		//test that the correct parent has been stored in the dataset
+		for (TaxonNode tx: BioTree.getTaxonRecord("Esox").getChildren())
+			assert(tx.getName().equals("Esox lucius") || tx.getName().equals("Esox masquinongy"));
+	}
+
+}

src/data/biotree/TestBioTree.java

+package data.biotree;
+
+import static org.junit.Assert.*;
+
+import java.io.IOException;
+
+import org.json.simple.parser.ParseException;
+import org.junit.Before;
+import org.junit.Test;
+
+import data.FileProcessor;
+
+public class TestBioTree {
+
+	@Before
+	public static void main(String[] args) throws IOException {
+//		BioTree.init();
+//		BioTree.processRecord(125125);
+//		BioTree.processRecord(125125);
+//		BioTree.processRecord(125125);
+//		BioTree.processRecord(125125);
+//		BioTree.processRecord(125125);
+//		BioTree.processRecord(125125);
+//		BioTree.processRecord(125123);
+//		BioTree.processRecord(125122);
+//		BioTree.processRecord(125392);
+//		BioTree.processRecord(125391);
+//		BioTree.processRecord(600000000);
+//		//System.out.println(nodes.size());
+//		//System.out.println(nodes.get(123207));
+//		//Iterable<Integer> keys = nodes.keys();
+//		//for (Integer i: keys) {
+//		//	System.out.println(nodes.get(i));
+//			//System.out.println(String.format("%-26s %s", nodes.get(i).getName(), nodes.get(i).getTaxonType()));
+//		//}
+//		BioTree.printTree();
+	}
+	
+	@Test
+	public void testSmallDataset() throws NumberFormatException, ParseException, IOException {
+		BioTree.init();
+		//FileProcessor.setPath("smalldata.csv");
+		FileProcessor.initProcessing();
+		assert(BioTree.getTaxonRecord("Anura") != null);
+		assert(false);
+	}
+	
+
+}

src/model/TrawlExpert.java

@@ -15,7 +15,9 @@ import search.trawl.BasicSearchResult;
 
 /**
  * The model of the TrawlExpert codebase. Gives hooks to views such as the server
- * and the command-line interface.
+ * and the command-line interface. Attempts to load serialized data from the disc,
+ * but if that fails it will regenerate the BioTree and Record kd-tree from the
+ * original dataset, then save the serialized data when it's done.
  * @author Christopher W. Schankula
  *
  */
@@ -77,7 +79,7 @@ public class TrawlExpert {
 	public TaxonNode getTaxonRecord(String scientificName) {
 		try {
 			return BioTree.getTaxonRecord(scientificName);
-		} catch (IOException | ParseException e) {
+		} catch (ParseException e) {
 
 		}
 		return null;