Merge pull request #61 from IntegratedBreedingPlatform/BMS-2006-SetUp…

…3.0.8Env

BMS-2025 Set temporary GID to 0 to prevent possible override from existing germplasm

src/main/java/org/generationcp/breeding/manager/listimport/actions/ProcessImportedGermplasmAction.java

@@ -253,19 +253,9 @@ protected void performThirdPedigreeAction() {
 		        	germplasm = new Germplasm();
 		        }
 
-		        if(searchByNameOrNewGermplasmIsNeeded) {
-		        	// gid at creation is temporary, will be set properly below
-		        	germplasm = createGermplasmObject(i, 0, 0, 0, ibdbUserId, dateIntValue);
-
-		        	if(germplasmMatchesCount==1 && germplasmDetailsComponent.automaticallyAcceptSingleMatchesCheckbox()){
-		                //If a single match is found, multiple matches will be 
-		                //   handled by SelectGemrplasmWindow and 
-		                //   then receiveGermplasmFromWindowAndUpdateGermplasmData()
-		                List<Germplasm> foundGermplasm = this.germplasmDataManager.getGermplasmByName(importedGermplasm.getDesig(), 0, 1, Operation.EQUAL);
-		                germplasm.setGid(foundGermplasm.get(0).getGid());
-		                doNotCreateGermplasmsWithId.add(foundGermplasm.get(0).getGid());
-		            }
-		        }
+		        germplasm = updateGidForSingleMatch(ibdbUserId, dateIntValue,
+						importedGermplasm, germplasmMatchesCount, germplasm,
+						searchByNameOrNewGermplasmIsNeeded);
 
 		        Name name = createNameObject(ibdbUserId, dateIntValue, importedGermplasm.getDesig());
 
@@ -288,6 +278,39 @@ protected void performThirdPedigreeAction() {
 	}
 
 
+	/**
+	 * Update GID to the existing germplasm's id. Otherwise, gid is set to 0
+	 * 
+	 * @param ibdbUserId
+	 * @param dateIntValue
+	 * @param importedGermplasm
+	 * @param germplasmMatchesCount
+	 * @param germplasm
+	 * @param searchByNameOrNewGermplasmIsNeeded
+	 * @return
+	 */
+	Germplasm updateGidForSingleMatch(Integer ibdbUserId,
+			Integer dateIntValue, ImportedGermplasm importedGermplasm,
+			int germplasmMatchesCount, Germplasm germplasm,
+			boolean searchByNameOrNewGermplasmIsNeeded)
+			throws MiddlewareQueryException {
+		if(searchByNameOrNewGermplasmIsNeeded) {
+			// gid at creation is temporary, will be set properly below
+			germplasm = createGermplasmObject(0, 0, 0, 0, ibdbUserId, dateIntValue);
+
+			if(germplasmMatchesCount==1 && germplasmDetailsComponent.automaticallyAcceptSingleMatchesCheckbox()){
+		        //If a single match is found, multiple matches will be 
+		        //   handled by SelectGemrplasmWindow and 
+		        //   then receiveGermplasmFromWindowAndUpdateGermplasmData()
+		        List<Germplasm> foundGermplasm = this.germplasmDataManager.getGermplasmByName(importedGermplasm.getDesig(), 0, 1, Operation.EQUAL);
+		        germplasm.setGid(foundGermplasm.get(0).getGid());
+		        doNotCreateGermplasmsWithId.add(foundGermplasm.get(0).getGid());
+		    }
+		}
+		return germplasm;
+	}
+
+
 	protected boolean isNeedToDisplayGermplasmSelectionWindow(int germplasmMatchesCount) {
 		return (germplasmMatchesCount>1) 
 				|| (germplasmMatchesCount > 0 && !germplasmDetailsComponent.automaticallyAcceptSingleMatchesCheckbox());
@@ -609,6 +632,13 @@ public void addNameToGermplasm(Name name, Integer gid){
 		doNotCreateGermplasmsWithId.add(gid);
 		newDesignationsForExistingGermplasm.add(name);
 	}
+
+
+	public void setGermplasmDataManager(
+			GermplasmDataManager germplasmDataManager) {
+		this.germplasmDataManager = germplasmDataManager;
+
+	}
 
 
 

src/test/java/org/generationcp/breeding/manager/data/initializer/ImportedGermplasmListDataInitializer.java

@@ -0,0 +1,109 @@
+
+package org.generationcp.breeding.manager.data.initializer;
+
+import java.util.ArrayList;
+import java.util.Date;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import org.generationcp.breeding.manager.crossingmanager.pojos.GermplasmName;
+import org.generationcp.breeding.manager.pojos.ImportedGermplasm;
+import org.generationcp.breeding.manager.pojos.ImportedGermplasmList;
+import org.generationcp.middleware.data.initializer.GermplasmTestDataInitializer;
+import org.generationcp.middleware.domain.inventory.ListEntryLotDetails;
+
+public class ImportedGermplasmListDataInitializer {
+
+	public static ImportedGermplasmList createImportedGermplasmList(final int noOfEntries) {
+		final String filename = "SourceList.xls";
+		final String name = "Import List 001";
+		final String title = "Import List 001 description";
+		final String type = "LST";
+		final Date date = new Date();
+
+		final ImportedGermplasmList importedGermplasmList = new ImportedGermplasmList(filename, name, title, type, date);
+		importedGermplasmList.setImportedGermplasms(createListOfImportedGermplasm(noOfEntries));
+		return importedGermplasmList;
+	}
+
+	public static List<ImportedGermplasm> createListOfImportedGermplasm(final int noOfEntries) {
+		final List<ImportedGermplasm> importedGermplasmList = new ArrayList<ImportedGermplasm>();
+
+		for (int i = 1; i <= noOfEntries; i++) {
+
+			importedGermplasmList.add(createImportedGermplasm(i));
+		}
+
+		return importedGermplasmList;
+	}
+
+	public static ImportedGermplasm createImportedGermplasm(final int id) {
+		final ImportedGermplasm importedGermplasm = new ImportedGermplasm();
+
+		importedGermplasm.setAttributeVariates(createAttributeVariates(id));
+
+		return importedGermplasm;
+	}
+
+	private static Map<String, String> createAttributeVariates(final int id) {
+		final Map<String, String> attributeVariates = new HashMap<String, String>();
+		attributeVariates.put("NOTE", "note value" + id);
+		return attributeVariates;
+	}
+
+	public static List<GermplasmName> createGermplasmNameObjects(final int noOfEntries) {
+		final List<GermplasmName> germplasmNameList = new ArrayList<GermplasmName>();
+
+		for (int i = 1; i <= noOfEntries; i++) {
+
+			final GermplasmName gName =
+					new GermplasmName(GermplasmTestDataInitializer.createGermplasm(i), GermplasmTestDataInitializer.createGermplasmName(i));
+
+			germplasmNameList.add(gName);
+		}
+
+		return germplasmNameList;
+	}
+
+	public static List<Integer> createListOfGemplasmIds(final int noOfIds) {
+		final List<Integer> ids = new ArrayList<Integer>();
+
+		for (int i = 1; i <= noOfIds; i++) {
+			ids.add(i);
+		}
+
+		return ids;
+	}
+
+	public static Map<ListEntryLotDetails, Double> createReservations(final int noOfEntries) {
+		final Map<ListEntryLotDetails, Double> reservations = new HashMap<ListEntryLotDetails,Double>();
+		for (Integer i = 0; i < noOfEntries; i++) {
+			reservations.put(ListInventoryDataInitializer.createLotDetail(i, 1), i.doubleValue());
+		}
+		return reservations;
+	}
+
+	public static List<Map<Integer, String>> createFactorsRowValuesListParserData() {
+		final List<Map<Integer, String>> testData = new ArrayList<Map<Integer,String>>();
+
+		final String[][] rawData =
+				{ {"ENTRY_NO", "Germplasm entry - enumerated (number)", "GERMPLASM ENTRY", "NUMBER", "ENUMERATED"},
+						{"GID", "Germplasm identifier - assigned (DBID)", "GERMPLASM ID", "GERMPLASM ID", "ASSIGNED"},
+						{"ENTRY_CODE", "Germplasm ID - Assigned (Code)", "GERMPLASM ENTRY", "CODE OF ENTRY_CODE", "ASSIGNED"},
+						{"DESIGNATION", "Germplasm identifier - assigned (DBCV)", "GERMPLASM ID", "GERMPLASM NAME", "ASSIGNED"},
+						{"CROSS", "The pedigree string of the germplasm", "CROSS HISTORY", "TEXT", "ASSIGNED"},
+						{"SEED_SOURCE", "Seed source - Selected (Code)", "SEED SOURCE", "CODE OF SEED_SOURCE", "SELECTED"}};
+
+		for (final String[] rowValue : rawData) {
+			final Map<Integer, String> map = new HashMap<Integer,String>();
+			for (int i = 0; i < rowValue.length; i++) {
+				map.put(i, rowValue[i]);
+			}
+
+			testData.add(map);
+		}
+
+		return testData;
+	}
+}

src/test/java/org/generationcp/breeding/manager/data/initializer/ListInventoryDataInitializer.java

@@ -0,0 +1,93 @@
+
+package org.generationcp.breeding.manager.data.initializer;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.generationcp.middleware.domain.inventory.ListDataInventory;
+import org.generationcp.middleware.domain.inventory.ListEntryLotDetails;
+import org.generationcp.middleware.domain.oms.Term;
+import org.generationcp.middleware.pojos.GermplasmListData;
+import org.generationcp.middleware.pojos.Location;
+
+public class ListInventoryDataInitializer {
+
+	public static final int NO_OF_LISTDATA = 5;
+
+	public static final int NO_OF_LOTS_PER_LISTDATA = 5;
+
+	public static List<GermplasmListData> createGermplasmListDataWithInventoryDetails() {
+		List<GermplasmListData> inventoryDetails = new ArrayList<GermplasmListData>();
+
+		for (int i = 0; i < NO_OF_LISTDATA; i++) {
+			GermplasmListData listData = new GermplasmListData();
+			int id = i + 1;
+			listData.setId(id);
+			listData.setEntryId(id);
+			listData.setDesignation("Germplasm" + id);
+			listData.setGid(id);
+			listData.setInventoryInfo(createInventoryInfo(id));
+			listData.setStatus(0);
+			inventoryDetails.add(listData);
+		}
+
+		return inventoryDetails;
+	}
+
+	public static ListDataInventory createInventoryInfo(int listDataId) {
+		ListDataInventory inventoryInfo = new ListDataInventory(listDataId, listDataId);
+		List<ListEntryLotDetails> lotDetails = new ArrayList<ListEntryLotDetails>();
+		for (int i = 0; i < NO_OF_LOTS_PER_LISTDATA; i++) {
+			lotDetails.add(createLotDetail(i, listDataId));
+		}
+		inventoryInfo.setLotRows(lotDetails);
+		inventoryInfo.setActualInventoryLotCount(1);
+		inventoryInfo.setReservedLotCount(2);
+		return inventoryInfo;
+	}
+
+	public static ListEntryLotDetails createLotDetail(int i, int listDataId) {
+		ListEntryLotDetails lotDetail = new ListEntryLotDetails();
+		int id = (i + 1) * listDataId;
+		lotDetail.setId(id);
+		lotDetail.setLotId(id);
+		lotDetail.setLocationOfLot(createLocation(id));
+		lotDetail.setLocId(i);
+		lotDetail.setScaleOfLot(createScale(id));
+		lotDetail.setScaleId(i);
+		lotDetail.setAvailableLotBalance(100D);
+		lotDetail.setActualLotBalance(100D);
+		lotDetail.setReservedTotalForEntry(100D);
+		lotDetail.setCommentOfLot("Lot Comment" + id);
+		return lotDetail;
+	}
+
+	public static Term createScale(int id) {
+		Term scale = new Term();
+		scale.setId(id);
+		scale.setName("Scale" + id);
+		return scale;
+	}
+
+	public static Location createLocation(int id) {
+		Location location = new Location();
+		location.setLocid(id);
+		location.setLname("Location" + id);
+		return location;
+	}
+
+	public static Term createTerm(String name) {
+		Term term = new Term();
+		term.setName(name);
+		term.setId(0);
+		return term;
+	}
+
+	public static Integer getNumberOfEntriesInInventoryView() {
+		return NO_OF_LISTDATA * NO_OF_LOTS_PER_LISTDATA;
+	}
+
+	public static Integer getNumberOfEntriesInListView() {
+		return NO_OF_LISTDATA;
+	}
+}

src/test/java/org/generationcp/breeding/manager/listimport/actions/ProcessImportedGermplasmActionTest.java

@@ -0,0 +1,108 @@
+
+package org.generationcp.breeding.manager.listimport.actions;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import junit.framework.Assert;
+
+import org.generationcp.breeding.manager.data.initializer.ImportedGermplasmListDataInitializer;
+import org.generationcp.breeding.manager.listimport.GermplasmFieldsComponent;
+import org.generationcp.breeding.manager.listimport.SpecifyGermplasmDetailsComponent;
+import org.generationcp.breeding.manager.pojos.ImportedGermplasm;
+import org.generationcp.middleware.data.initializer.GermplasmTestDataInitializer;
+import org.generationcp.middleware.exceptions.MiddlewareQueryException;
+import org.generationcp.middleware.manager.Operation;
+import org.generationcp.middleware.manager.api.GermplasmDataManager;
+import org.generationcp.middleware.pojos.Germplasm;
+import org.junit.Before;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.mockito.InjectMocks;
+import org.mockito.Mock;
+import org.mockito.Mockito;
+import org.mockito.runners.MockitoJUnitRunner;
+
+import com.vaadin.ui.ComboBox;
+
+@RunWith(MockitoJUnitRunner.class)
+public class ProcessImportedGermplasmActionTest {
+
+	@Mock
+	private SpecifyGermplasmDetailsComponent germplasmDetailsComponent;
+
+	@Mock
+	private GermplasmFieldsComponent germplasmFieldsComponent;
+
+	@Mock
+	private GermplasmDataManager germplasmDataManager;
+
+	@InjectMocks
+	private ProcessImportedGermplasmAction processImportedGermplasmAction;
+
+	final static Integer IBDB_USER_ID = 1;
+	final static Integer DATE_INT_VALUE = 20151105;
+
+	@Before
+	public void setUp() {
+		Mockito.doReturn(this.germplasmFieldsComponent).when(this.germplasmDetailsComponent).getGermplasmFieldsComponent();
+		final ComboBox locationComboBox = new ComboBox();
+		locationComboBox.addItem("1");
+		Mockito.doReturn(locationComboBox).when(this.germplasmFieldsComponent).getLocationComboBox();
+
+		final ComboBox methodComboBox = new ComboBox();
+		methodComboBox.addItem("1");
+		Mockito.doReturn(methodComboBox).when(this.germplasmFieldsComponent).getBreedingMethodComboBox();
+
+		this.processImportedGermplasmAction.setGermplasmDataManager(this.germplasmDataManager);
+	}
+
+	@Test
+	public void testUpdateGidWhenGermplasmIdIsExisting() throws MiddlewareQueryException {
+		final int gid = 100;
+		final ImportedGermplasm importedGermplasm = ImportedGermplasmListDataInitializer.createImportedGermplasm(gid);
+		importedGermplasm.setDesig("Name" + gid);
+
+		final int germplasmMatchesCount = 1;
+		final boolean searchByNameOrNewGermplasmIsNeeded = true;
+		Germplasm germplasm = GermplasmTestDataInitializer.createGermplasm(0);
+
+		Mockito.doReturn(true).when(this.germplasmDetailsComponent).automaticallyAcceptSingleMatchesCheckbox();
+
+		final List<Germplasm> germplasms = new ArrayList<Germplasm>();
+		germplasms.add(GermplasmTestDataInitializer.createGermplasm(gid));
+
+		Mockito.doReturn(germplasms).when(this.germplasmDataManager)
+				.getGermplasmByName(importedGermplasm.getDesig(), 0, 1, Operation.EQUAL);
+
+		germplasm =
+				this.processImportedGermplasmAction.updateGidForSingleMatch(IBDB_USER_ID, this.DATE_INT_VALUE, importedGermplasm,
+						germplasmMatchesCount, germplasm, searchByNameOrNewGermplasmIsNeeded);
+
+		Assert.assertEquals("Expecting that the gid set is from the existing germplasm.", gid, germplasm.getGid().intValue());
+	}
+
+	@Test
+	public void testUpdateGidWhenNoGermplasmIdIsExisting() throws MiddlewareQueryException {
+		final int gid = 0;
+		final ImportedGermplasm importedGermplasm = ImportedGermplasmListDataInitializer.createImportedGermplasm(gid);
+		importedGermplasm.setDesig("Name" + gid);
+
+		final int germplasmMatchesCount = 0;
+		final boolean searchByNameOrNewGermplasmIsNeeded = true;
+		Germplasm germplasm = GermplasmTestDataInitializer.createGermplasm(0);
+
+
+		try {
+			germplasm =
+					this.processImportedGermplasmAction.updateGidForSingleMatch(IBDB_USER_ID, this.DATE_INT_VALUE, importedGermplasm,
+							germplasmMatchesCount, germplasm, searchByNameOrNewGermplasmIsNeeded);
+
+			Mockito.verify(this.germplasmDetailsComponent, Mockito.times(0)).automaticallyAcceptSingleMatchesCheckbox();
+			Mockito.verify(this.germplasmDataManager, Mockito.times(0)).getGermplasmByName(importedGermplasm.getDesig(), 0, 1, Operation.EQUAL);
+		} catch (Exception e) {
+			Assert.fail();
+		}
+		Assert.assertEquals("Expecting that the gid is set to 0 when there is no existing germplasm.", 0, germplasm.getGid().intValue());
+	}
+}