Merge pull request #1110 from PhenoApps/validate_categorical_barcode_…

…data

validate_categorical_barcode_data

app/src/main/java/com/fieldbook/tracker/activities/CollectActivity.java

@@ -73,6 +73,7 @@
 import com.fieldbook.tracker.traits.PhotoTraitLayout;
 import com.fieldbook.tracker.traits.formats.TraitFormat;
 import com.fieldbook.tracker.traits.formats.coders.StringCoder;
+import com.fieldbook.tracker.traits.formats.Scannable;
 import com.fieldbook.tracker.traits.formats.presenters.ValuePresenter;
 import com.fieldbook.tracker.utilities.CameraXFacade;
 import com.fieldbook.tracker.utilities.BluetoothHelper;
@@ -672,31 +673,29 @@ public void refreshMain() {
      * @return boolean flag false when data is out of bounds, true otherwise
      */
     @Override
-    public boolean validateData() {
-        final String strValue = collectInputView.getText();
+    public boolean validateData(@Nullable String data) {
         final TraitObject currentTrait = traitBox.getCurrentTrait();
 
         if (currentTrait == null) return false;
 
-        if (strValue.equals("NA")) return true;
+        if (data == null) return true;
 
-        final String trait = currentTrait.getName();
+        if (data.equals("NA")) return true;
 
-        if (traitBox.existsNewTraits()
-                && traitBox.getCurrentTrait() != null
-                && strValue.length() > 0
-                && !traitBox.getCurrentTrait().isValidValue(strValue)) {
+        if (data.isEmpty()) return true;
 
-            //checks if the trait is numerical and within the bounds (otherwise returns false)
-            if (currentTrait.isOver(strValue)) {
-                Utils.makeToast(getApplicationContext(),getString(R.string.trait_error_maximum_value)
-                        + ": " + currentTrait.getMaximum());
-            } else if (currentTrait.isUnder(strValue)) {
-                Utils.makeToast(getApplicationContext(),getString(R.string.trait_error_minimum_value)
-                        + ": " + currentTrait.getMinimum());
-            }
+        BaseTraitLayout layout = traitLayouts.getTraitLayout(currentTrait.getFormat());
+        TraitFormat format = Formats.Companion.findTrait(currentTrait.getFormat());
+
+        String value = data;
+        if (format instanceof Scannable) {
+            value = ((Scannable) format).preprocess(data);
+        }
+
+        if (!layout.validate(value)) {
+
+            removeTrait(currentTrait);
 
-            removeTrait(trait);
             collectInputView.clear();
 
             soundHelper.playError();
@@ -770,7 +769,7 @@ private void initToolbars() {
             // if a brapi observation that has been synced, don't allow deleting
             String format = getTraitFormat();
             if (status && !Formats.Companion.isCameraTrait(format)) {
-                brapiDelete(getTraitName(), false);
+                brapiDelete(getCurrentTrait(), false);
             } else {
                 traitLayouts.deleteTraitListener(getTraitFormat());
             }
@@ -1301,9 +1300,8 @@ public String getLocationByPreferences() {
                 .getLocationByCollectMode(this, preferences, expId, obsUnit, geoNavHelper.getMInternalLocation(), geoNavHelper.getMExternalLocation(), database);
     }
 
-    private void brapiDelete(String parent, Boolean hint) {
+    private void brapiDelete(TraitObject trait, Boolean hint) {
         Utils.makeToast(this, getString(R.string.brapi_delete_message));
-        TraitObject trait = traitBox.getCurrentTrait();
         updateObservation(trait, getString(R.string.brapi_na), null);
         if (hint) {
             setNaTextBrapiEmptyField();
@@ -1313,19 +1311,20 @@ private void brapiDelete(String parent, Boolean hint) {
     }
 
     // Delete trait, including from database
-    public void removeTrait(String parent) {
+    public void removeTrait(TraitObject trait) {
+
         if (rangeBox.isEmpty()) {
             return;
         }
 
-        String exp_id = Integer.toString(preferences.getInt(GeneralKeys.SELECTED_FIELD_ID, 0));
-        TraitObject trait = traitBox.getCurrentTrait();
-        if (database.isBrapiSynced(exp_id, getObservationUnit(), trait.getId(), getRep())) {
-            brapiDelete(parent, true);
+        String fieldId = Integer.toString(preferences.getInt(GeneralKeys.SELECTED_FIELD_ID, 0));
+
+        if (database.isBrapiSynced(fieldId, getObservationUnit(), trait.getId(), getRep())) {
+            brapiDelete(trait, true);
         } else {
             // Always remove existing trait before inserting again
             // Based on plot_id, prevent duplicate
-            traitBox.remove(parent, getObservationUnit(), getRep());
+            traitBox.remove(trait, getObservationUnit(), getRep());
         }
     }
 
@@ -2079,12 +2078,21 @@ protected void onActivityResult(int requestCode, int resultCode, Intent data) {
 
                     TraitObject currentTrait = traitBox.getCurrentTrait();
                     BaseTraitLayout currentTraitLayout = traitLayouts.getTraitLayout(currentTrait.getFormat());
-                    currentTraitLayout.loadLayout();
+                    TraitFormat traitFormat = Formats.Companion.findTrait(currentTrait.getFormat());
+
+                    String oldValue = "";
+                    ObservationModel currentObs = getCurrentObservation();
+                    if (currentObs != null) {
+                        oldValue = currentObs.getValue();
+                    }
 
+                    if (scannedBarcode != null && traitFormat instanceof Scannable && validateData(scannedBarcode)) {
+                        updateObservation(currentTrait, ((Scannable) traitFormat).preprocess(scannedBarcode), null);
+                    } else {
+                        updateObservation(currentTrait, oldValue, null);
+                    }
 
-                    updateObservation(currentTrait, scannedBarcode, null);
                     currentTraitLayout.loadLayout();
-                    validateData();
                 }
                 break;
             case PhotoTraitLayout.PICTURE_REQUEST_CODE:
@@ -2652,7 +2660,7 @@ public void showObservationMetadataDialog(){
         }
     }
 
-    private ObservationModel getCurrentObservation() {
+    public ObservationModel getCurrentObservation() {
         String rep = getCollectInputView().getRep();
         List<ObservationModel> models = Arrays.asList(getDatabase().getRepeatedValues(getStudyId(), getObservationUnit(), getTraitDbId()));
             for (ObservationModel m : models) {

app/src/main/java/com/fieldbook/tracker/interfaces/CollectController.kt

@@ -3,6 +3,7 @@ package com.fieldbook.tracker.interfaces
 import android.content.Context
 import android.location.Location
 import android.os.Handler
+import com.fieldbook.tracker.database.models.ObservationModel
 import com.fieldbook.tracker.devices.camera.UsbCameraApi
 import com.fieldbook.tracker.devices.camera.GoProApi
 import com.fieldbook.tracker.devices.camera.CanonApi
@@ -59,5 +60,6 @@ interface CollectController: FieldController {
     fun getFfmpegHelper(): FfmpegHelper
     fun getCanonApi(): CanonApi
     fun takePicture()
+    fun getCurrentObservation(): ObservationModel?
     fun getRotationRelativeToDevice(): SensorHelper.RotationModel?
 }

app/src/main/java/com/fieldbook/tracker/interfaces/CollectRangeController.kt

@@ -3,7 +3,7 @@ package com.fieldbook.tracker.interfaces
 import com.fieldbook.tracker.views.CollectInputView
 
 interface CollectRangeController: CollectController {
-    fun validateData(): Boolean
+    fun validateData(data: String?): Boolean
     fun initWidgets(rangeSuppress: Boolean)
     fun cancelAndFinish()
     fun callFinish()

app/src/main/java/com/fieldbook/tracker/interfaces/CollectTraitController.kt

@@ -5,7 +5,7 @@ import com.fieldbook.tracker.traits.LayoutCollections
 import com.fieldbook.tracker.views.CollectInputView
 
 interface CollectTraitController: CollectController {
-    fun validateData(): Boolean
+    fun validateData(data: String?): Boolean
     fun getTraitLayouts(): LayoutCollections
     fun isCyclingTraitsAdvances(): Boolean
     fun refreshLock()

app/src/main/java/com/fieldbook/tracker/objects/TraitObject.java

@@ -1,9 +1,15 @@
 package com.fieldbook.tracker.objects;
 
+import android.graphics.Color;
 import android.util.Log;
 
 import androidx.annotation.NonNull;
 
+import com.fieldbook.tracker.utilities.CategoryJsonUtil;
+
+import org.brapi.v2.model.pheno.BrAPIScaleValidValuesCategories;
+
+import java.util.ArrayList;
 import java.util.List;
 import java.util.Objects;
 
@@ -144,47 +150,38 @@ public void setObservationLevelNames(List<String> observationLevelNames) {
         this.observationLevelNames = observationLevelNames;
     }
 
-    public boolean isValidValue(final String s) {
-        // this code is not perfect.
-        // I think that it is necessary to check
-        // the minimum and the maximum values
-        return !isUnder(s) && !isOver(s);
-    }
 
-    public boolean isUnder(final String s) {
-        if (!(format.equals("numeric")))
-            return false;
 
-        Log.d("FB",s);
-        if (minimum.length() > 0) {     // minimum exists
-            try {
-                final double v = Double.parseDouble(s);
-                final double lowerValue = Double.parseDouble(minimum);
-                return v < lowerValue;
-            } catch (NumberFormatException e) {
-                return true;
-            }
-        } else {
-            return false;
-        }
-    }
+    public boolean isValidCategoricalValue(final String inputCategory) {
+
+        //check if its the new json
+        try {
 
-    public boolean isOver(final String s) {
-        if (!(format.equals("numeric")))
-            return false;
+            ArrayList<BrAPIScaleValidValuesCategories> c = CategoryJsonUtil.Companion.decode(inputCategory);
 
-        Log.d("FB",s);
-        if (maximum.length() > 0) {     // maximum exists
-            try {
-                final double v = Double.parseDouble(s);
-                final double upperValue = Double.parseDouble(maximum);
-                return v > upperValue;
-            } catch (NumberFormatException e) {
-                return true;
+            if (!c.isEmpty()) {
+
+                //get the value from the single-sized array
+                BrAPIScaleValidValuesCategories labelVal = c.get(0);
+
+                //check that this pair is a valid label/val pair in the category,
+                //if it is then set the text based on the preference
+                return CategoryJsonUtil.Companion.contains(c, labelVal);
             }
-        } else {
-            return false;
+
+        } catch (Exception e) {
+
+            e.printStackTrace(); //if it fails to decode, assume its an old string
+
+//            if (CategoryJsonUtil.Companion.contains(cats, value)) {
+//
+//                getCollectInputView().setText(value);
+//
+//                getCollectInputView().setTextColor(Color.parseColor(getDisplayColor()));
+//            }
         }
+
+        return false;
     }
 
     @Override

app/src/main/java/com/fieldbook/tracker/traits/AudioTraitLayout.java

@@ -136,7 +136,7 @@ private void refreshButtonState() {
     @Override
     public void deleteTraitListener() {
         deleteRecording();
-        removeTrait(getCurrentTrait().getName());
+        removeTrait(getCurrentTrait());
         super.deleteTraitListener();
         recordingLocation = null;
         mediaPlayer = null;
@@ -263,7 +263,7 @@ private void stopPlayback() {
 
         private void startRecording() {
             try {
-                removeTrait(getCurrentTrait().getName());
+                removeTrait(getCurrentTrait());
                 audioRecordingText.setText("");
                 fieldAudioHelper.startRecording(false);
             } catch (Exception e) {

app/src/main/java/com/fieldbook/tracker/traits/BaseTraitLayout.java

@@ -10,6 +10,7 @@
 import android.widget.EditText;
 import android.widget.LinearLayout;
 
+import androidx.annotation.NonNull;
 import androidx.annotation.Nullable;
 import androidx.preference.PreferenceManager;
 
@@ -69,6 +70,15 @@ public boolean isTraitType(String trait) {
 
     public abstract void init(Activity act);
 
+    /**
+     * validate is used in collect activity to check if the collected data is within the
+     * specification of the trait, such as min/max.
+     */
+    @NonNull
+    public Boolean validate(String data) {
+        return true;
+    }
+
     /**
      * Override to block multi-measure navigation with specific condition
      */
@@ -303,8 +313,8 @@ public void updateObservation(TraitObject trait, String value) {
         ((CollectActivity) getContext()).updateObservation(trait, value, null);
     }
 
-    public void removeTrait(String parent) {
-        ((CollectActivity) getContext()).removeTrait(parent);
+    public void removeTrait(TraitObject trait) {
+        ((CollectActivity) getContext()).removeTrait(trait);
     }
 
     public void triggerTts(String text) {

app/src/main/java/com/fieldbook/tracker/traits/BooleanTraitLayout.java

@@ -7,11 +7,14 @@
 import android.widget.ImageView;
 import android.widget.SeekBar;
 
+import androidx.annotation.NonNull;
 import androidx.annotation.Nullable;
 
 import com.fieldbook.tracker.R;
 import com.fieldbook.tracker.activities.CollectActivity;
 
+import java.util.Locale;
+
 public class BooleanTraitLayout extends BaseTraitLayout implements SeekBar.OnSeekBarChangeListener {
 
     private SeekBar threeStateSeekBar;
@@ -93,6 +96,16 @@ public void deleteTraitListener() {
         //resetToDefault();
     }
 
+    @NonNull
+    @Override
+    public Boolean validate(String data) {
+        try {
+            return data.toLowerCase(Locale.ROOT).equals("true") || data.toLowerCase(Locale.ROOT).equals("false");
+        } catch (Exception e) {
+            return false;
+        }
+    }
+
     private void resetToDefault() {
 
         String value = getCurrentTrait().getDefaultValue().trim();

app/src/main/java/com/fieldbook/tracker/traits/CategoricalTraitLayout.java

@@ -8,13 +8,15 @@
 import android.widget.Button;
 import android.widget.LinearLayout;
 
+import androidx.annotation.NonNull;
 import androidx.annotation.Nullable;
 import androidx.recyclerview.widget.RecyclerView;
 
 import com.fieldbook.tracker.R;
 import com.fieldbook.tracker.activities.CollectActivity;
 import com.fieldbook.tracker.preferences.GeneralKeys;
 import com.fieldbook.tracker.utilities.CategoryJsonUtil;
+import com.fieldbook.tracker.utilities.Utils;
 import com.google.android.flexbox.AlignItems;
 import com.google.android.flexbox.FlexDirection;
 import com.google.android.flexbox.FlexWrap;
@@ -317,4 +319,21 @@ public String decodeValue(String value) {
             } else return scale.get(0).getLabel();
         } else return "";
     }
+
+    @NonNull
+    @Override
+    public Boolean validate(String data) {
+
+        try {
+            ArrayList<BrAPIScaleValidValuesCategories> userChosenCats = CategoryJsonUtil.Companion.decode(data);
+            if (userChosenCats.isEmpty()) {
+                return true;
+            } else {
+                ArrayList<BrAPIScaleValidValuesCategories> cats = getCategories();
+                return CategoryJsonUtil.Companion.contains(cats, userChosenCats.get(0));
+            }
+        } catch (Exception e) {
+            return false;
+        }
+    }
 }