Merge pull request #711 from abatac/bms_integration_fix

Bms integration fix
PhenoApps · Aug 23, 2023 · 9b95171 · 9b95171
2 parents d4d6a9c + ca106cb
commit 9b95171
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diff --git a/app/src/main/java/com/fieldbook/tracker/brapi/BrapiLoadDialog.java b/app/src/main/java/com/fieldbook/tracker/brapi/BrapiLoadDialog.java
@@ -203,6 +203,12 @@ public Void apply(final BrapiStudyDetails study) {
                     @Override
                     public void run() {
                         BrapiStudyDetails.merge(studyDetails, study);
+
+                        // This is BMS specific. Remove the traits that are not part of the selected Observation Level.
+                        // To ensure that only relevant traits are included in the imported study/field.
+                        studyDetails.getTraits().removeIf(t -> t.getObservationLevelNames() != null &&
+                                t.getObservationLevelNames().stream().noneMatch(s -> s.equalsIgnoreCase(selectedObservationLevel.getObservationLevelName())));
+
                         loadStudy();
                         // Check if user should save yet
                         traitLoadStatus = true;

diff --git a/app/src/main/java/com/fieldbook/tracker/brapi/service/BrAPIServiceV2.java b/app/src/main/java/com/fieldbook/tracker/brapi/service/BrAPIServiceV2.java
@@ -23,6 +23,9 @@
 import com.fieldbook.tracker.utilities.CategoryJsonUtil;
 import com.fieldbook.tracker.utilities.FailureFunction;
 import com.fieldbook.tracker.utilities.SuccessFunction;
+import com.google.gson.Gson;
+import com.google.gson.JsonArray;
+import com.google.gson.reflect.TypeToken;
 
 import org.brapi.client.v2.BrAPIClient;
 import org.brapi.client.v2.model.exceptions.ApiException;
@@ -68,6 +71,7 @@
 import org.json.JSONException;
 import org.json.JSONObject;
 
+import java.lang.reflect.Type;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
@@ -79,6 +83,8 @@
 
 public class BrAPIServiceV2 extends AbstractBrAPIService implements BrAPIService {
 
+    private static final String ADDITIONAL_INFO_OBSERVATION_LEVEL_NAMES = "observationLevelNames";
+
     //used to identify field book db id in external references
     private final String fieldBookReferenceSource = "Field Book Upload";
 
@@ -1017,6 +1023,16 @@ private Pair<List<TraitObject>, Integer> mapTraits(List<BrAPIObservationVariable
 
             }
 
+            // The BMS implementation of BrAPI 2.x Variables includes an Observation Variable with observationLevelNames metadata in the additionalInfo field.
+            // This metadata helps identify the level(s) at which a variable is utilized within a study/field. The information will be utilized to filter the variables
+            // based on the selected Observation Level during BrAPI Field Import, ensuring that only relevant variables will be processed.
+            if (var.getAdditionalInfo() != null && var.getAdditionalInfo().has(ADDITIONAL_INFO_OBSERVATION_LEVEL_NAMES)) {
+                JsonArray observationVariableNames = var.getAdditionalInfo().getAsJsonArray(ADDITIONAL_INFO_OBSERVATION_LEVEL_NAMES);
+                // Convert the JsonArray to a List<String>
+                Type listType = new TypeToken<List<String>>() {}.getType();
+                trait.setObservationLevelNames(new Gson().fromJson(observationVariableNames, listType));
+            }
+
             // Set some config variables in fieldbook
             trait.setVisible(true);
             trait.setRealPosition(0);

diff --git a/app/src/main/java/com/fieldbook/tracker/objects/TraitObject.java b/app/src/main/java/com/fieldbook/tracker/objects/TraitObject.java
@@ -4,6 +4,8 @@
 
 import androidx.annotation.NonNull;
 
+import java.util.List;
+
 /**
  * Simple wrapper class for trait data
  */
@@ -22,6 +24,12 @@ public class TraitObject {
     private String traitDataSource;
     private String additionalInfo;
 
+    /**
+     * This is a BMS specific field. This will be populated when traits are imported from
+     * the BMS implementation of Brapi 2.0 GET /variables.
+     */
+    private List<String> observationLevelNames;
+
     public String getTrait() {
         return trait;
     }
@@ -126,6 +134,14 @@ public void setAdditionalInfo(String additionalInfo) {
         this.additionalInfo = additionalInfo;
     }
 
+    public List<String> getObservationLevelNames() {
+        return observationLevelNames;
+    }
+
+    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