Merge branch 'dev' into 35276_add_metagenomic_workflow_resource

src/main/java/ca/gc/aafc/seqdb/api/ResourceRepositoryConfig.java

@@ -1,6 +1,12 @@
 package ca.gc.aafc.seqdb.api;
 
+import io.crnk.core.engine.registry.ResourceRegistry;
+import javax.inject.Inject;
+
 import ca.gc.aafc.dina.DinaBaseApiAutoConfiguration;
+import ca.gc.aafc.seqdb.api.dto.SequenceManagedAttributeDto;
+import ca.gc.aafc.seqdb.api.util.ManagedAttributeIdMapper;
+
 import org.springframework.boot.autoconfigure.domain.EntityScan;
 import org.springframework.context.annotation.ComponentScan;
 import org.springframework.context.annotation.Configuration;
@@ -11,4 +17,14 @@
 @EntityScan("ca.gc.aafc.seqdb.api.entities")
 @ComponentScan(basePackageClasses = DinaBaseApiAutoConfiguration.class)
 public class ResourceRepositoryConfig {
+
+  @Inject
+  @SuppressWarnings({"deprecation", "unchecked"})
+  public void setupManagedAttributeLookup(ResourceRegistry resourceRegistry) {
+    var resourceInfo = resourceRegistry.getEntry(SequenceManagedAttributeDto.class)
+      .getResourceInformation();
+
+    resourceInfo.setIdStringMapper(
+      new ManagedAttributeIdMapper(resourceInfo.getIdStringMapper()));
+  }
 }

src/main/java/ca/gc/aafc/seqdb/api/dto/GenericMolecularAnalysisDto.java

@@ -1,9 +1,12 @@
 package ca.gc.aafc.seqdb.api.dto;
 
+import io.crnk.core.resource.annotations.JsonApiField;
 import io.crnk.core.resource.annotations.JsonApiId;
 import io.crnk.core.resource.annotations.JsonApiRelation;
 import io.crnk.core.resource.annotations.JsonApiResource;
+import io.crnk.core.resource.annotations.PatchStrategy;
 import java.time.OffsetDateTime;
+import java.util.Map;
 import java.util.UUID;
 import lombok.AllArgsConstructor;
 import lombok.Builder;
@@ -41,4 +44,11 @@ public class GenericMolecularAnalysisDto {
   @JsonApiRelation
   private ExternalRelationDto protocol;
 
+  /**
+   * Map of Managed attribute key to value object.
+   */
+  @JsonApiField(patchStrategy = PatchStrategy.SET)
+  @Builder.Default
+  private Map<String, String> managedAttributes = Map.of();
+
 }

src/main/java/ca/gc/aafc/seqdb/api/entities/GenericMolecularAnalysis.java

@@ -1,6 +1,7 @@
 package ca.gc.aafc.seqdb.api.entities;
 
 import java.time.OffsetDateTime;
+import java.util.Map;
 import java.util.UUID;
 import javax.persistence.Column;
 import javax.persistence.Entity;
@@ -20,6 +21,7 @@
 import org.hibernate.annotations.Generated;
 import org.hibernate.annotations.GenerationTime;
 import org.hibernate.annotations.NaturalId;
+import org.hibernate.annotations.Type;
 
 import ca.gc.aafc.dina.entity.DinaEntity;
 
@@ -61,4 +63,10 @@ public class GenericMolecularAnalysis implements DinaEntity {
   @Size(max = 50)
   private String analysisType;
 
+  @Type(type = "jsonb")
+  @NotNull
+  @Builder.Default
+  @Column(name = "managed_attributes")
+  private Map<String, String> managedAttributes = Map.of();
+
 }

src/main/java/ca/gc/aafc/seqdb/api/service/GenericMolecularAnalysisService.java

@@ -3,24 +3,51 @@
 import java.util.UUID;
 import lombok.NonNull;
 
+import org.apache.commons.collections.MapUtils;
 import org.springframework.stereotype.Service;
 import org.springframework.validation.SmartValidator;
 
 import ca.gc.aafc.dina.jpa.BaseDAO;
 import ca.gc.aafc.dina.service.DefaultDinaService;
 import ca.gc.aafc.seqdb.api.entities.GenericMolecularAnalysis;
+import ca.gc.aafc.seqdb.api.entities.SequenceManagedAttribute;
+import ca.gc.aafc.seqdb.api.validation.SequenceManagedAttributeValueValidator;
 
 @Service
 public class GenericMolecularAnalysisService extends DefaultDinaService<GenericMolecularAnalysis> {
 
+  private static final SequenceManagedAttributeValueValidator.SequenceManagedAttributeValidationContext
+    GENERIC_MOLECULAR_ANALYSIS_VALIDATION_CONTEXT =
+    SequenceManagedAttributeValueValidator.SequenceManagedAttributeValidationContext
+      .from(SequenceManagedAttribute.ManagedAttributeComponent.GENERIC_MOLECULAR_ANALYSIS);
+
+  private final SequenceManagedAttributeValueValidator sequenceManagedAttributeValueValidator;
+
   public GenericMolecularAnalysisService(
-    @NonNull BaseDAO baseDAO, @NonNull SmartValidator sv) {
+    @NonNull BaseDAO baseDAO,
+    @NonNull SequenceManagedAttributeValueValidator sequenceManagedAttributeValueValidator,
+    @NonNull SmartValidator sv) {
     super(baseDAO, sv);
+
+    this.sequenceManagedAttributeValueValidator = sequenceManagedAttributeValueValidator;
   }
 
   @Override
   protected void preCreate(GenericMolecularAnalysis entity) {
     entity.setUuid(UUID.randomUUID());
   }
 
+  @Override
+  public void validateBusinessRules(GenericMolecularAnalysis entity) {
+    validateManagedAttribute(entity);
+  }
+
+  private void validateManagedAttribute(GenericMolecularAnalysis genericMolecularAnalysis) {
+    if (MapUtils.isNotEmpty(genericMolecularAnalysis.getManagedAttributes())) {
+      sequenceManagedAttributeValueValidator.validate(genericMolecularAnalysis,
+        genericMolecularAnalysis.getManagedAttributes(),
+        GENERIC_MOLECULAR_ANALYSIS_VALIDATION_CONTEXT);
+    }
+  }
+
 }

src/main/java/ca/gc/aafc/seqdb/api/util/ManagedAttributeIdMapper.java

@@ -0,0 +1,31 @@
+package ca.gc.aafc.seqdb.api.util;
+
+import io.crnk.core.engine.parser.StringMapper;
+import java.util.UUID;
+import lombok.RequiredArgsConstructor;
+
+/**
+ * Lets you use either the UUID or the component type + key as the ID.
+ * e.g. /managed-attribute/generic_molecular_analysis.attribute_name.
+ */
+@RequiredArgsConstructor
+public class ManagedAttributeIdMapper implements StringMapper<Object> {
+  private final StringMapper<Object> stringMapper;
+
+  @Override
+  public Object parse(String input) {
+    // If the input's not in UUID format then use the raw string as the ID:
+    try {
+      UUID.fromString(input);
+    } catch (IllegalArgumentException e) {
+      return input;
+    }
+    return stringMapper.parse(input);
+  }
+
+  @Override
+  public String toString(Object input) {
+    return stringMapper.toString(input);
+  }
+
+}

src/main/java/ca/gc/aafc/seqdb/api/validation/SequenceManagedAttributeValueValidator.java

@@ -0,0 +1,110 @@
+package ca.gc.aafc.seqdb.api.validation;
+
+import org.apache.commons.lang3.tuple.Pair;
+import org.springframework.context.MessageSource;
+import org.springframework.context.i18n.LocaleContextHolder;
+import org.springframework.stereotype.Component;
+import org.springframework.validation.Errors;
+
+import ca.gc.aafc.dina.entity.DinaEntity;
+import ca.gc.aafc.dina.service.ManagedAttributeService;
+import ca.gc.aafc.dina.validation.ManagedAttributeValueValidator;
+import ca.gc.aafc.dina.validation.ValidationContext;
+import ca.gc.aafc.seqdb.api.entities.SequenceManagedAttribute;
+
+import java.util.EnumMap;
+import java.util.Map;
+import java.util.Objects;
+import java.util.Set;
+import javax.inject.Named;
+import lombok.NonNull;
+
+@Component
+public class SequenceManagedAttributeValueValidator extends ManagedAttributeValueValidator<SequenceManagedAttribute> {
+
+  private static final String INVALID_VALIDATION_CONTEXT_KEY = "managedAttribute.validation.context.invalid";
+  private static final String COMPONENT_FIELD_NAME = "managedAttributeComponent";
+
+  private final ManagedAttributeService<SequenceManagedAttribute> dinaService;
+  private final MessageSource messageSource;
+
+  public SequenceManagedAttributeValueValidator(
+    @Named("validationMessageSource") MessageSource baseMessageSource, // from dina-base
+    @NonNull MessageSource messageSource,
+    @NonNull ManagedAttributeService<SequenceManagedAttribute> dinaService) {
+    super(baseMessageSource, dinaService);
+    this.dinaService = dinaService;
+    this.messageSource = messageSource;
+  }
+
+  public <D extends DinaEntity> void validate(D entity, Map<String, String> managedAttributes, SequenceManagedAttributeValidationContext context) {
+    super.validate(entity, managedAttributes, context);
+  }
+
+  /**
+   * override base class version to also add a restriction on the component since the uniqueness
+   * for CollectionManagedAttribute is key + component.
+   * @param keys
+   * @param validationContext
+   * @return
+   */
+  @Override
+  protected Map<String, SequenceManagedAttribute> findAttributesForValidation(Set<String> keys, ValidationContext validationContext) {
+    return dinaService.findAttributesForKeys(keys, Pair.of(COMPONENT_FIELD_NAME, validationContext.getValue()));
+  }
+
+  @Override
+  protected boolean preValidateValue(SequenceManagedAttribute managedAttributeDefinition,
+                                     String value, Errors errors, ValidationContext validationContext) {
+
+    // expected context based on the component
+    SequenceManagedAttributeValidationContext expectedContext =
+      SequenceManagedAttributeValidationContext.from(managedAttributeDefinition.getManagedAttributeComponent());
+
+    if (!expectedContext.equals(validationContext)) {
+      errors.reject(INVALID_VALIDATION_CONTEXT_KEY, getMessageForKey(INVALID_VALIDATION_CONTEXT_KEY,
+        Objects.toString(validationContext), expectedContext.toString()));
+      return false;
+    }
+    return true;
+  }
+
+  /**
+   * Wrapper class to expose {@link ca.gc.aafc.seqdb.api.entities.SequenceManagedAttribute.ManagedAttributeComponent} as
+   * {@link ValidationContext}.
+   */
+  public static final class SequenceManagedAttributeValidationContext implements ValidationContext {
+    // make sure to only keep 1 instance per enum value
+    private static final EnumMap<SequenceManagedAttribute.ManagedAttributeComponent, SequenceManagedAttributeValidationContext>
+      INSTANCES = new EnumMap<>(SequenceManagedAttribute.ManagedAttributeComponent.class);
+
+    private final SequenceManagedAttribute.ManagedAttributeComponent managedAttributeComponent;
+
+    /**
+     * Use {@link #from(SequenceManagedAttribute.ManagedAttributeComponent)} method
+     * @param managedAttributeComponent
+     */
+    private SequenceManagedAttributeValidationContext(SequenceManagedAttribute.ManagedAttributeComponent managedAttributeComponent) {
+      this.managedAttributeComponent = managedAttributeComponent;
+    }
+
+    public static SequenceManagedAttributeValidationContext from(SequenceManagedAttribute.ManagedAttributeComponent managedAttributeComponent) {
+      return INSTANCES.computeIfAbsent(managedAttributeComponent, SequenceManagedAttributeValidationContext::new);
+    }
+
+    @Override
+    public String toString() {
+      return managedAttributeComponent.toString();
+    }
+
+    @Override
+    public Object getValue() {
+      return managedAttributeComponent;
+    }
+  }
+
+  // to be replaced by dina-base whne 0.132 will be released
+  private String getMessageForKey(String key, Object... objects) {
+    return messageSource.getMessage(key, objects, LocaleContextHolder.getLocale());
+  }
+}

src/main/resources/db/changelog/db.changelog-master.xml

@@ -60,4 +60,5 @@
   <include file="db/changelog/migrations/53-Add_attachments_to_MolecularAnalysisRun.xml"/>
   <include file="db/changelog/migrations/54-Add_metagenomics_tables.xml"/>
   <include file="db/changelog/migrations/55-Add_managed_attribute.xml"/>
+  <include file="db/changelog/migrations/56-Add_managed_attribute_to_molecular_analysis.xml"/>
 </databaseChangeLog>

src/main/resources/db/changelog/migrations/56-Add_managed_attribute_to_molecular_analysis.xml

@@ -0,0 +1,13 @@
+<?xml version="1.1" encoding="UTF-8" standalone="no"?>
+<databaseChangeLog
+        xmlns="http://www.liquibase.org/xml/ns/dbchangelog"
+        xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+        xsi:schemaLocation="http://www.liquibase.org/xml/ns/dbchangelog https://local.xsd/dbchangelog-4.4.xsd"
+        objectQuotingStrategy="QUOTE_ONLY_RESERVED_WORDS">
+
+    <changeSet id="56-Add_managed_attribute_to_molecular_analysis" context="schema-change" author="cgendreau">
+        <addColumn tableName="generic_molecular_analysis">
+            <column name="managed_attributes" type="jsonb" defaultValue="{}" />
+        </addColumn>
+    </changeSet>
+</databaseChangeLog>

src/main/resources/vocabulary/pcrBatchType.yml

@@ -14,10 +14,11 @@ vocabulary:
           title: Illumina (NGS)
         - lang: fr
           title: Illumina (NGS)
-    - key: round_2
-      name: Round 2
+    - key: illumina_metagenomics
+      name: Illumina Metagenomics
       multilingualTitle.titles:
         - lang: en
-          title: Round 2
+          title: Illumina Metagenomics
         - lang: fr
-          title: Round 2
+          title: Illumina Metagenomics
+

src/test/java/ca/gc/aafc/seqdb/api/repository/SequenceManagedAttributeRepositoryIT.java

@@ -51,4 +51,20 @@ void create_recordCreated() {
       SequenceManagedAttribute.ManagedAttributeComponent.GENERIC_MOLECULAR_ANALYSIS,
       result.getManagedAttributeComponent());
   }
+
+  @Test
+  @WithMockKeycloakUser(groupRole = SequenceManagedAttributeTestFixture.GROUP + ":SUPER_USER")
+  void findOneByKey_whenKeyProvided_managedAttributeFetched() {
+    SequenceManagedAttributeDto newAttribute = SequenceManagedAttributeTestFixture.newManagedAttribute();
+    newAttribute.setName("Attribute 1");
+    newAttribute.setVocabularyElementType(TypedVocabularyElement.VocabularyElementType.INTEGER);
+    newAttribute.setManagedAttributeComponent(SequenceManagedAttribute.ManagedAttributeComponent.GENERIC_MOLECULAR_ANALYSIS);
+
+    UUID newAttributeUuid = repo.create(newAttribute).getUuid();
+
+    QuerySpec querySpec = new QuerySpec(SequenceManagedAttributeDto.class);
+    SequenceManagedAttributeDto fetchedAttribute = repo.findOne("generic_molecular_analysis.attribute_1", querySpec);
+
+    assertEquals(newAttributeUuid, fetchedAttribute.getUuid());
+  }
 }

src/test/java/ca/gc/aafc/seqdb/api/service/GenericMolecularAnalysisServiceIT.java

@@ -0,0 +1,61 @@
+package ca.gc.aafc.seqdb.api.service;
+
+import org.junit.jupiter.api.Test;
+
+import ca.gc.aafc.dina.vocabulary.TypedVocabularyElement;
+import ca.gc.aafc.seqdb.api.SequenceModuleBaseIT;
+import ca.gc.aafc.seqdb.api.entities.GenericMolecularAnalysis;
+import ca.gc.aafc.seqdb.api.entities.SequenceManagedAttribute;
+import ca.gc.aafc.seqdb.api.testsupport.factories.GenericMolecularAnalysisFactory;
+import ca.gc.aafc.seqdb.api.testsupport.factories.SequenceManagedAttributeFactory;
+
+import static org.junit.jupiter.api.Assertions.assertDoesNotThrow;
+import static org.junit.jupiter.api.Assertions.assertThrows;
+
+import java.util.Map;
+import javax.validation.ValidationException;
+
+public class GenericMolecularAnalysisServiceIT extends SequenceModuleBaseIT {
+
+  private static final String GROUP = "grp";
+
+  @Test
+  void assignedValueContainedInAcceptedValues_validationPasses() {
+    SequenceManagedAttribute testManagedAttribute = SequenceManagedAttributeFactory.newManagedAttribute()
+      .acceptedValues(new String[]{"val1", "val2"})
+      .managedAttributeComponent(SequenceManagedAttribute.ManagedAttributeComponent.GENERIC_MOLECULAR_ANALYSIS)
+      .build();
+
+    managedAttributeService.create(testManagedAttribute);
+
+    GenericMolecularAnalysis genericMolecularAnalysis = GenericMolecularAnalysisFactory
+      .newGenericMolecularAnalysis()
+      .managedAttributes(Map.of(testManagedAttribute.getKey(), testManagedAttribute.getAcceptedValues()[0]))
+      .build();
+
+    assertDoesNotThrow(() -> genericMolecularAnalysisService.create(genericMolecularAnalysis));
+  }
+
+  @Test
+  void validate_WhenInvalidIntegerType_ExceptionThrown() {
+    SequenceManagedAttribute testManagedAttribute =
+      SequenceManagedAttributeFactory.newManagedAttribute()
+        .createdBy("GenericMolecularAnalysisServiceIT")
+        .managedAttributeComponent(
+          SequenceManagedAttribute.ManagedAttributeComponent.GENERIC_MOLECULAR_ANALYSIS)
+        .group(GROUP)
+        .vocabularyElementType(TypedVocabularyElement.VocabularyElementType.INTEGER)
+        .acceptedValues(null)
+        .build();
+
+    managedAttributeService.create(testManagedAttribute);
+
+    GenericMolecularAnalysis genericMolecularAnalysis = GenericMolecularAnalysisFactory
+      .newGenericMolecularAnalysis()
+      .managedAttributes(Map.of(testManagedAttribute.getKey(), "1.2"))
+      .build();
+
+    assertThrows(ValidationException.class,
+      () -> genericMolecularAnalysisService.create(genericMolecularAnalysis));
+  }
+}