- FIX: Fixed an issue with preloaded traits. Since multiple dataset w…

…ere introduced, this feature has been broken. With this commit, the functionality has been restored. You can now preload traits per dataset and they will be persistent even when switching between datasets.

app/build.gradle

@@ -17,8 +17,8 @@ android {
         applicationId "uk.ac.hutton.android.germinatescan"
         minSdkVersion 16
         targetSdkVersion 28
-        versionCode 35
-        versionName "1.19.02.05"
+        versionCode 37
+        versionName "1.19.04.02"
         multiDexEnabled true
         vectorDrawables.useSupportLibrary = true
     }
@@ -55,6 +55,7 @@ dependencies {
     implementation 'com.android.support:palette-v7:28.0.0'
     implementation 'com.android.support:design:28.0.0'
     implementation 'com.andkulikov:transitionseverywhere:1.7.0'
+    implementation 'com.google.code.gson:gson:2.8.5'
     // Supports Android 4.0.3 and later (API level 15)
     implementation 'com.journeyapps:zxing-android-embedded:3.2.0@aar'
     implementation 'com.google.zxing:core:3.2.0'

app/proguard-rules.pro

@@ -21,4 +21,27 @@
 -keep class **.R$*
 
 -keep class com.google.android.gms.** { *; }
--dontwarn com.google.android.gms.**
+-dontwarn com.google.android.gms.**
+
+##---------------Begin: proguard configuration for Gson  ----------
+# Gson uses generic type information stored in a class file when working with fields. Proguard
+# removes such information by default, so configure it to keep all of it.
+-keepattributes Signature
+
+# For using GSON @Expose annotation
+-keepattributes *Annotation*
+
+# Gson specific classes
+-dontwarn sun.misc.**
+#-keep class com.google.gson.stream.** { *; }
+
+# Application classes that will be serialized/deserialized over Gson
+-keep class com.google.gson.examples.android.model.** { *; }
+
+# Prevent proguard from stripping interface information from TypeAdapterFactory,
+# JsonSerializer, JsonDeserializer instances (so they can be used in @JsonAdapter)
+-keep class * implements com.google.gson.TypeAdapterFactory
+-keep class * implements com.google.gson.JsonSerializer
+-keep class * implements com.google.gson.JsonDeserializer
+
+##---------------End: proguard configuration for Gson  ----------

app/src/main/java/uk/ac/hutton/android/germinatescan/activity/BarcodeReader.java

@@ -444,15 +444,19 @@ public boolean onOptionsItemSelected(MenuItem item)
 								@Override
 								public void onClick(DialogInterface dialog, int which)
 								{
-									startActivityForResult(new Intent(getApplicationContext(), PhenotypeActivity.class), REQUEST_CODE_IMPORT_PHENOTYPES);
+									Intent intent = new Intent(BarcodeReader.this, PhenotypeActivity.class);
+									intent.putExtra(PhenotypeActivity.EXTRA_DATASET_ID, dataset.getId());
+									startActivityForResult(intent, REQUEST_CODE_IMPORT_PHENOTYPES);
 								}
 							})
 							.setNegativeButton(R.string.general_no, null)
 							.show();
 				}
 				else
 				{
-					startActivityForResult(new Intent(getApplicationContext(), PhenotypeActivity.class), REQUEST_CODE_IMPORT_PHENOTYPES);
+					Intent intent = new Intent(BarcodeReader.this, PhenotypeActivity.class);
+					intent.putExtra(PhenotypeActivity.EXTRA_DATASET_ID, dataset.getId());
+					startActivityForResult(intent, REQUEST_CODE_IMPORT_PHENOTYPES);
 				}
 				break;
 		}
@@ -722,8 +726,6 @@ public void onClick(DialogInterface dialog, int which)
 		}
 		else if (requestCode == REQUEST_DATA_SOURCE && resultCode == Activity.RESULT_OK)
 		{
-			prefs.remove(PreferenceUtils.PREFS_PRELOADED_PHENOTYPES);
-			prefs.remove(PreferenceUtils.PREFS_PRELOADED_PHENOTYPES_COUNTER);
 			override = true;
 		}
 		/* Return from preferences */
@@ -737,7 +739,9 @@ else if (requestCode == REQUEST_CODE_IMPORT_PHENOTYPES && resultCode == Activity
 		{
 			resetDatabase();
 
-			preloadedPhenotypes = data.getStringArrayListExtra(PhenotypeActivity.EXTRA_LIST);
+			DatasetManager datasetManager = new DatasetManager(this, dataset.getId());
+			dataset = datasetManager.getById(dataset.getId());
+			preloadedPhenotypes = dataset.getPreloadedPhenotypes();
 
 			updateHandler();
 		}
@@ -954,9 +958,6 @@ private void resetDatabase()
 
 		updateWelcomeMessageVisibility();
 
-		prefs.remove(PreferenceUtils.PREFS_PRELOADED_PHENOTYPES);
-		prefs.remove(PreferenceUtils.PREFS_PRELOADED_PHENOTYPES_COUNTER);
-
 		updateHandler();
 	}
 
@@ -965,7 +966,7 @@ private void updateHandler()
 		boolean restored = false;
 		if (preloadedPhenotypes == null)
 		{
-			preloadedPhenotypes = prefs.getListObject(PreferenceUtils.PREFS_PRELOADED_PHENOTYPES, String.class);
+			preloadedPhenotypes = dataset.getPreloadedPhenotypes();
 			restored = true;
 		}
 
@@ -976,7 +977,7 @@ private void updateHandler()
 
 			if (restored)
 			{
-				counter = prefs.getInt(PreferenceUtils.PREFS_PRELOADED_PHENOTYPES_COUNTER, 0);
+				counter = dataset.getCurrentPhenotype();
 				if (adapter.getItemCount() > 0)
 					currentPlant = adapter.getItemsInRow(adapter.getItem(adapter.getItemCount() - 1)).get(0).getBarcode();
 			}
@@ -989,7 +990,7 @@ else if (adapter.getItemCount() < 1)
 						.show();
 			}
 
-			handler = new PhenotypeBarcodeHandler(this, preloadedPhenotypes, currentPlant, counter)
+			handler = new PhenotypeBarcodeHandler(this, dataset, preloadedPhenotypes, currentPlant, counter)
 			{
 				@Override
 				protected Barcode getCurrentPlant()

app/src/main/java/uk/ac/hutton/android/germinatescan/activity/PhenotypeActivity.java

@@ -33,14 +33,16 @@
 import butterknife.*;
 import uk.ac.hutton.android.germinatescan.R;
 import uk.ac.hutton.android.germinatescan.adapter.*;
+import uk.ac.hutton.android.germinatescan.database.*;
+import uk.ac.hutton.android.germinatescan.database.manager.*;
 import uk.ac.hutton.android.germinatescan.util.*;
 
 /**
  * @author Sebastian Raubach
  */
 public class PhenotypeActivity extends ThemedActivity
 {
-	public static final String EXTRA_LIST = "PHENOTYPE_LIST";
+	public static final String EXTRA_DATASET_ID = "DATASET_ID";
 
 	@BindView(R.id.phenotype_text)
 	EditText     phenotypeInput;
@@ -51,6 +53,8 @@ public class PhenotypeActivity extends ThemedActivity
 
 	private ItemTouchHelper            helper;
 	private StringReorderDeleteAdapter adapter;
+	private DatasetManager             datasetManager;
+	private Dataset                    dataset;
 
 	@Override
 	protected Integer getLayoutId()
@@ -71,6 +75,19 @@ protected void onCreate(Bundle savedInstanceState)
 
 		ButterKnife.bind(this);
 
+		Bundle extras = getIntent().getExtras();
+
+		if (extras != null)
+		{
+			long datasetId = extras.getLong(EXTRA_DATASET_ID, -1l);
+
+			if (datasetId != -1)
+			{
+				datasetManager = new DatasetManager(getApplicationContext(), datasetId);
+				dataset = datasetManager.getById(datasetId);
+			}
+		}
+
 		adapter = new StringReorderDeleteAdapter(this, new ArrayList<String>(), new StringReorderDeleteAdapter.OnStartDragListener()
 		{
 			@Override
@@ -174,7 +191,14 @@ private void finishImport()
 		List<String> items = adapter.getItems();
 
 		if (!CollectionUtils.isEmpty(items))
-			data.putStringArrayListExtra(EXTRA_LIST, new ArrayList<>(items));
+		{
+			dataset.setPreloadedPhenotypes(items);
+		}
+		else
+		{
+			dataset.setPreloadedPhenotypes(null);
+		}
+		datasetManager.update(dataset);
 
 		if (getParent() == null)
 		{

app/src/main/java/uk/ac/hutton/android/germinatescan/database/DatabaseHandler.java

@@ -52,7 +52,6 @@ public class DatabaseHandler extends SQLiteOpenHelper
 			+ KEY_MAIN_LNG + " REAL, " + KEY_MAIN_ALT + " REAL, " + KEY_MAIN_BARCODE + " TEXT, " + KEY_MAIN_ROW + " INTEGER, " + KEY_MAIN_COL + " INTEGER)";
 	private static final String CREATE_IMAGE_TABLE = "CREATE TABLE IF NOT EXISTS " + TABLE_IMAGES + " (" + KEY_IMAGES_ID + " INTEGER PRIMARY KEY AUTOINCREMENT, " + KEY_IMAGES_PATH + " TEXT, " + KEY_IMAGES_MAIN_ID
 			+ " INTEGER, FOREIGN KEY (" + KEY_IMAGES_MAIN_ID + ") REFERENCES " + TABLE_MAIN + " (" + KEY_MAIN_ID + "));" + ")";
-	public static DatabaseHandler INSTANCE;
 	private Context context;
 
 

app/src/main/java/uk/ac/hutton/android/germinatescan/database/Dataset.java

@@ -17,19 +17,28 @@
 
 package uk.ac.hutton.android.germinatescan.database;
 
+import com.google.gson.*;
+import com.google.gson.reflect.*;
+
 import java.util.*;
 
+import uk.ac.hutton.android.germinatescan.util.*;
+
 /**
  * @author Sebastian Raubach
  */
 
 public class Dataset extends DatabaseObject
 {
-	public static final String FIELD_NAME = "name";
-	public static final String FIELD_BARCODES_PER_ROW = "barcodes_per_row";
+	public static final String FIELD_NAME                 = "name";
+	public static final String FIELD_BARCODES_PER_ROW     = "barcodes_per_row";
+	public static final String FIELD_PRELOADED_PHENOTYPES = "preloaded_phenotypes";
+	public static final String FIELD_CURRENT_PHENOTYPE    = "current_phenotype";
 
-	private String name;
-	private int barcodesPerRow;
+	private String       name;
+	private int          barcodesPerRow;
+	private List<String> preloadedPhenotypes;
+	private Integer      currentPhenotype;
 
 	public Dataset(String name)
 	{
@@ -73,4 +82,53 @@ public Dataset setBarcodesPerRow(int barcodesPerRow)
 		this.barcodesPerRow = barcodesPerRow;
 		return this;
 	}
+
+	public List<String> getPreloadedPhenotypes()
+	{
+		return preloadedPhenotypes;
+	}
+
+	public Dataset setPreloadedPhenotypes(List<String> preloadedPhenotypes)
+	{
+		this.preloadedPhenotypes = preloadedPhenotypes;
+		return this;
+	}
+
+	public String getPreloadedPhenotypesAsString()
+	{
+		if (!CollectionUtils.isEmpty(preloadedPhenotypes))
+			return new Gson().toJson(preloadedPhenotypes);
+		else
+			return null;
+	}
+
+	public Dataset setPreloadedPhenotypesAsString(String preloadedPhenotypesAsString)
+	{
+		if (!StringUtils.isEmpty(preloadedPhenotypesAsString))
+		{
+			try
+			{
+				preloadedPhenotypes = new Gson().fromJson(preloadedPhenotypesAsString, new TypeToken<List<String>>()
+				{
+				}.getType());
+			}
+			catch (JsonParseException e)
+			{
+				preloadedPhenotypes = null;
+			}
+		}
+
+		return this;
+	}
+
+	public Integer getCurrentPhenotype()
+	{
+		return currentPhenotype;
+	}
+
+	public Dataset setCurrentPhenotype(Integer currentPhenotype)
+	{
+		this.currentPhenotype = currentPhenotype;
+		return this;
+	}
 }