BI-2053-fix - fix scaleName and units bug

src/main/java/org/breedinginsight/brapps/importer/services/processors/ExperimentProcessor.java

@@ -765,6 +765,16 @@ private void validateObservations(ValidationErrors validationErrors,
             // had been saved prior to import
             } else if (existingObsByObsHash.containsKey(importHash) && !isObservationMatched(importHash, importObsValue, phenoCol, rowNum)) {
 
+                // different data means validations still need to happen
+                // TODO consider moving these two calls into a separate method since called twice together
+                validateObservationValue(colVarMap.get(phenoCol.name()), phenoCol.getString(rowNum), phenoCol.name(), validationErrors, rowNum);
+
+                //Timestamp validation
+                if(timeStampColByPheno.containsKey(phenoCol.name())) {
+                    Column<?> timeStampCol = timeStampColByPheno.get(phenoCol.name());
+                    validateTimeStampValue(timeStampCol.getString(rowNum), timeStampCol.name(), validationErrors, rowNum);
+                }
+
                 // add a change log entry when updating the value of an observation
                 if (commit) {
                     BrAPIObservation pendingObservation = observationByHash.get(importHash).getBrAPIObject();

src/main/java/org/breedinginsight/services/TraitService.java

@@ -43,6 +43,7 @@
 import javax.inject.Singleton;
 import java.util.*;
 import java.util.stream.Collectors;
+import org.breedinginsight.utilities.Utilities;
 
 @Slf4j
 @Singleton
@@ -255,21 +256,26 @@ public void assignTraitsProgramObservationLevel(List<Trait> traits, UUID program
     }
 
     public void preprocessTraits(List<Trait> traits) {
-
-        // Set data type to numerical when method class is computation and include name and full name as synonyms
         for (Trait trait: traits) {
             List<String> brApiSynonyms = trait.getSynonyms() == null ? new ArrayList<>() : trait.getSynonyms();
+            // Include name and full name as synonyms.
             if (trait.getObservationVariableName() != null && !brApiSynonyms.contains(trait.getObservationVariableName())) {
                 brApiSynonyms.add(trait.getObservationVariableName());
             }
             if (trait.getFullName() != null && !brApiSynonyms.contains(trait.getFullName())) {
                 brApiSynonyms.add(trait.getFullName());
             }
-            if (trait.getMethod() != null && trait.getMethod().getMethodClass() != null &&
+
+            if (trait.getScale() != null) {
+                // Set data type to numerical when method class is computation.
+                if (trait.getMethod() != null && trait.getMethod().getMethodClass() != null &&
                 trait.getMethod().getMethodClass().equalsIgnoreCase(Method.COMPUTATION_TYPE)) {
-                if (trait.getScale() != null) {
                     trait.getScale().setDataType(DataType.NUMERICAL);
                 }
+                // Set scaleName to units, fallback to scale class if units is null.
+                String units = trait.getScale().getUnits();
+                String dataType = trait.getScale().getDataType() == null ? null : Utilities.capitalize(trait.getScale().getDataType().getLiteral());
+                trait.getScale().setScaleName(units == null ? dataType : units);
             }
         }
 

src/main/java/org/breedinginsight/services/validators/TraitValidatorService.java

@@ -63,12 +63,12 @@ public ValidationErrors checkRequiredTraitFields(List<Trait> traits, TraitValida
                 ValidationError error = traitValidatorErrors.getMissingScaleMsg();
                 errors.addError(traitValidatorErrors.getRowNumber(i), error);
             } else {
-                if (scale.getDataType() != null & scale.getDataType() == DataType.NUMERICAL &&
+                if (scale.getDataType() != null && scale.getDataType() == DataType.NUMERICAL &&
                         (isBlank(scale.getUnits()))) {
                     ValidationError error = traitValidatorErrors.getMissingScaleUnitMsg();
                     errors.addError(traitValidatorErrors.getRowNumber(i), error);
                 }
-                if (scale.getDataType() == null || scale.getDataType() == null) {
+                if (scale.getDataType() == null) {
                     ValidationError error = traitValidatorErrors.getMissingScaleDataTypeMsg();
                     errors.addError(traitValidatorErrors.getRowNumber(i), error);
                 }

src/main/java/org/breedinginsight/utilities/Utilities.java

@@ -247,6 +247,14 @@ public static List<Program> getAllProgramsFlyway(Context context, String default
         return programs;
     }
 
+    /**
+     * Returns the input string with the first character capitalized, the rest lower cased.
+     * Note: does not account for whitespace, does not capitalize multiple words.
+     */
+    public static String capitalize(String input) {
+        return input.substring(0, 1).toUpperCase() + input.substring(1).toLowerCase();
+    }
+
     private static boolean isSafeChar(char c) {
         // Check if c is in the portable filename character set.
         // See https://pubs.opengroup.org/onlinepubs/9699919799/basedefs/V1_chap03.html#tag_03_282

src/test/java/org/breedinginsight/api/v1/controller/TraitControllerIntegrationTest.java

@@ -62,6 +62,7 @@
 import org.breedinginsight.daos.cache.ProgramCacheProvider;
 import org.breedinginsight.model.*;
 import org.breedinginsight.services.SpeciesService;
+import org.breedinginsight.utilities.Utilities;
 import org.jooq.DSLContext;
 import org.junit.jupiter.api.*;
 import org.mockito.stubbing.Answer;
@@ -455,7 +456,8 @@ public void checkBrapiValues() {
         String methodName = String.format("%s %s", trait1.getMethod().getDescription(), trait1.getMethod().getMethodClass());
         assertEquals(String.format("%s [%s]", methodName, validProgramKey),
                 variable.getMethod().getMethodName(), "Unexpected method name");
-        assertEquals(String.format("%s [%s]", trait1.getScale().getScaleName(), validProgramKey),
+        String expectedScaleName = trait1.getScale().getUnits() == null ? Utilities.capitalize(trait1.getScale().getDataType().getLiteral()) : trait1.getScale().getUnits();
+        assertEquals(String.format("%s [%s]", expectedScaleName, validProgramKey),
                 variable.getScale().getScaleName(), "Unexpected scale name");
         String traitName = String.format("%s %s", trait1.getEntity(), trait1.getAttribute());
         assertEquals(String.format("%s [%s]", traitName, validProgramKey),
@@ -484,7 +486,8 @@ public void checkBrapiValues() {
         methodName = String.format("%s %s", trait1.getMethod().getDescription(), trait1.getMethod().getMethodClass());
         assertEquals(String.format("%s [%s]", methodName, validProgramKey),
                 variable.getMethod().getMethodName(), "Unexpected method name");
-        assertEquals(String.format("%s [%s]", trait1.getScale().getScaleName(), validProgramKey),
+        expectedScaleName = trait1.getScale().getUnits() == null ? Utilities.capitalize(trait1.getScale().getDataType().getLiteral()) : trait1.getScale().getUnits();
+        assertEquals(String.format("%s [%s]", expectedScaleName, validProgramKey),
                 variable.getScale().getScaleName(), "Unexpected scale name");
         traitName = String.format("%s %s", trait1.getEntity(), trait1.getAttribute());
         assertEquals(String.format("%s [%s]", traitName, validProgramKey),
@@ -1060,7 +1063,8 @@ public void checkTraitResponse(JsonObject traitJson, Trait trait) {
         }
 
         JsonObject scale = traitJson.getAsJsonObject("scale");
-        assertEquals(trait.getScale().getScaleName(), scale.get("scaleName").getAsString(), "Scale names don't match");
+        String expectedScaleName = trait.getScale().getUnits() == null ? Utilities.capitalize(trait.getScale().getDataType().getLiteral()) : trait.getScale().getUnits();
+        assertEquals(expectedScaleName, scale.get("scaleName").getAsString(), "Scale names don't match");
         assertEquals(trait.getScale().getDataType().toString(), scale.get("dataType").getAsString(), "Scale data types don't match");
 
         JsonObject programOntology = traitJson.getAsJsonObject("programOntology");
@@ -1433,7 +1437,8 @@ public void putTraitComputation() {
         assertEquals(updateTrait.getObservationVariableName(), trait.get("observationVariableName").getAsString(), "wrong trait name");
         assertEquals(updateTrait.getProgramObservationLevel().getName(),
                 trait.get("programObservationLevel").getAsJsonObject().get("name").getAsString(), "wrong observation level");
-        assertEquals(updateTrait.getScale().getScaleName(),
+        String expectedScaleName = updateTrait.getScale().getUnits() == null ? Utilities.capitalize(updateTrait.getScale().getDataType().getLiteral()) : updateTrait.getScale().getUnits();
+        assertEquals(expectedScaleName,
                 trait.get("scale").getAsJsonObject().get("scaleName").getAsString(), "wrong scale name");
         assertEquals(updateTrait.getScale().getDataType().toString(),
                 trait.get("scale").getAsJsonObject().get("dataType").getAsString(), "wrong scale data type");
@@ -1590,8 +1595,4 @@ public void archiveTraitIdNotExist() {
 
     }
 
-
-
-
-
 }