Merge pull request #458 from ncats/cv_and_mixtures

Preventing leading and trailing blanks in text CV terms and in mixture component type

Author: ChemMitch

gsrs-module-substance-example/src/test/java/example/substance/validation/MixtureValidationTest.java

@@ -18,10 +18,10 @@
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.security.test.context.support.WithMockUser;
 
+import java.util.UUID;
 import java.util.stream.Stream;
 
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.*;
 
 /**
  * Created by katzelda on 7/20/18.
@@ -199,4 +199,36 @@ public void mixtureMustAtLeast2OneOfComponents() throws Exception{
 
 
     }
+
+    @Test
+    public void mixtureComponentsTypeMustHaveNoTrailingBlanks() throws Exception{
+
+        String inputComponentType = "MAY_BE_PRESENT_ONE_OF ";
+        String componentTypeTrimmed =inputComponentType.trim();
+        String inputComponentType2 = " MUST_BE_PRESENT";
+        String componentType2Trimmed = inputComponentType2.trim();
+        JsonNode toSubmit = new MixtureSubstanceBuilder()
+                .addName("foo " + UUID.randomUUID())
+                .addComponents(inputComponentType, s1)
+                .addComponents(inputComponentType2, s2)
+                .addComponents(componentTypeTrimmed, s3)
+                .buildJson();
+
+        GsrsEntityService.CreationResult<Substance> result = substanceEntityService.createEntity(toSubmit);
+
+        ValidationResponse response = result.getValidationResponse();
+        assertTrue(response.isValid());
+        //this is split up and stored as a variable for java 8 type inference to work...
+        Stream<ValidationMessage>s1 = response.getValidationMessages().stream();
+
+        assertEquals(2, s1
+                .filter(m->m.getMessageType() == ValidationMessage.MESSAGE_TYPE.WARNING)
+                .map(ValidationMessage::getMessage)
+                .filter(m-> m.contains(MixtureValidator.NO_LEAD_TRAIL_SPACES_IN_TYPE))
+                .count());
+        MixtureSubstance completed = (MixtureSubstance) result.getCreatedEntity();
+        assertEquals(2, completed.mixture.components.stream().map(component -> component.type).filter(t->t.equals(componentTypeTrimmed)).count());
+        assertEquals(1, completed.mixture.components.stream().map(component -> component.type).filter(t->t.equals(componentType2Trimmed)).count());
+    }
+
 }

gsrs-module-substances-core/src/main/java/ix/ginas/utils/validation/validators/CVValidator.java

@@ -3,9 +3,11 @@
 import ix.core.validator.GinasProcessingMessage;
 import ix.core.validator.ValidatorCallback;
 import ix.ginas.models.v1.ControlledVocabulary;
+import ix.ginas.models.v1.VocabularyTerm;
 import ix.ginas.utils.validation.AbstractValidatorPlugin;
 import lombok.extern.slf4j.Slf4j;
 
+import java.util.ArrayList;
 import java.util.List;
 import java.util.Map;
 import java.util.stream.Collectors;
@@ -50,5 +52,33 @@ public void validate(ControlledVocabulary objnew, ControlledVocabulary objold, V
             callback.setInvalid();
             log.info("found duplicate vocabulary displays: {}", String.join(", ", duplicateDisplays));
         }
+        List<String> displaysWithBlanks = new ArrayList<>();
+        List<String> valuesWithBlanks = new ArrayList<>();
+        for(VocabularyTerm term : objnew.terms) {
+            if (term.display != null && term.display.length() != term.display.trim().length()) {
+                log.trace("found display with space: {}", term.display);
+                displaysWithBlanks.add(term.display);
+                term.display = term.display.trim();
+            }
+            if (term.value != null && term.value.length() != term.value.trim().length()) {
+                log.trace("found value with space: {}", term.value);
+                valuesWithBlanks.add(term.value);
+                term.value = term.value.trim();
+            }
+        }
+        if( !displaysWithBlanks.isEmpty()) {
+            GinasProcessingMessage displaysMessage =
+                    GinasProcessingMessage.WARNING_MESSAGE("One or more vocabulary term displays have leading or trailing spaces. These spaces were removed")
+                    .appliableChange(true);
+            callback.addMessage(displaysMessage);
+            log.trace("added warning about display value(s) with blanks");
+        }
+        if( !valuesWithBlanks.isEmpty()){
+            GinasProcessingMessage valuesMessage =
+                    GinasProcessingMessage.WARNING_MESSAGE("One or more vocabulary term values have leading or trailing spaces. These spaces were removed")
+                    .appliableChange(true);
+            callback.addMessage(valuesMessage);
+            log.trace("added warning about value(s) with blanks");
+        }
     }
 }

gsrs-module-substances-core/src/main/java/ix/ginas/utils/validation/validators/MixtureValidator.java

@@ -27,6 +27,7 @@ public class MixtureValidator extends AbstractValidatorPlugin<Substance> {
     @Autowired
     private ReferenceRepository referenceRepository;
 
+    public final static String NO_LEAD_TRAIL_SPACES_IN_TYPE = "Mixture component type must not start or end with a space";
     @Override
     @Transactional(readOnly = true)
     public void validate(Substance objnew, Substance objold, ValidatorCallback callback) {
@@ -47,10 +48,14 @@ public void validate(Substance objnew, Substance objold, ValidatorCallback callb
                 if (c.substance == null) {
                     callback.addMessage(GinasProcessingMessage
                             .ERROR_MESSAGE("Mixture components must reference a substance record, found:\"null\""));
-                }else if(c.type == null || c.type.length()<=0){
+                }else if(c.type == null || c.type.length()<=0) {
                     callback.addMessage(GinasProcessingMessage.ERROR_MESSAGE("Mixture components must specify a type"));
+                } else if(c.type.length() != c.type.trim().length()) {
+                    c.type = c.type.trim();
+                    GinasProcessingMessage message = GinasProcessingMessage.WARNING_MESSAGE(NO_LEAD_TRAIL_SPACES_IN_TYPE);
+                    message.appliableChange(true);
+                    callback.addMessage(message);
                 }else {
-//                    Substance comp = SubstanceFactory.getFullSubstance(c.substance);
                     if (!substanceRepository.exists(c.substance)) {
                         callback.addMessage(GinasProcessingMessage
                                 .WARNING_MESSAGE("Mixture substance references \"%s\" which is not yet registered",