Merge pull request #207 from AAFC-BICoE/29608_Add_storage_unit_to_Seq…

…Batch

29608 add storage unit to seq batch

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

@@ -6,6 +6,7 @@
 import java.util.List;
 import java.util.UUID;
 
+import ca.gc.aafc.seqdb.api.entities.StorageRestriction;
 import org.javers.core.metamodel.annotation.Id;
 import org.javers.core.metamodel.annotation.PropertyName;
 import org.javers.core.metamodel.annotation.TypeName;
@@ -53,4 +54,14 @@ public class SeqBatchDto {
   @JsonApiRelation
   private ExternalRelationDto protocol;
 
+  @JsonApiExternalRelation(type = "storage-unit")
+  @JsonApiRelation
+  private ExternalRelationDto storageUnit;
+
+  @JsonApiExternalRelation(type = "storage-unit-type")
+  @JsonApiRelation
+  private ExternalRelationDto storageUnitType;
+
+  private StorageRestriction storageRestriction;
+
 }

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

@@ -15,6 +15,7 @@
 import javax.persistence.JoinColumn;
 import javax.persistence.ManyToOne;
 import javax.persistence.Table;
+import javax.validation.Valid;
 import javax.validation.constraints.NotBlank;
 import javax.validation.constraints.NotNull;
 import javax.validation.constraints.Size;
@@ -83,4 +84,18 @@ public class SeqBatch implements DinaEntity {
   private Region region;
 
   private UUID protocol;
+
+  @Column(name = "storage_unit")
+  private UUID storageUnit;
+
+  /**
+   * storage-unit-type should only be used when no specific storageUnit is used.
+   */
+  @Column(name = "storage_unit_type")
+  private UUID storageUnitType;
+
+  @Type(type = "jsonb")
+  @Column(name = "storage_restriction", columnDefinition = "jsonb")
+  @Valid
+  private StorageRestriction storageRestriction;
 }

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

@@ -2,6 +2,7 @@
 
 import java.util.UUID;
 
+import ca.gc.aafc.seqdb.api.validation.SeqBatchValidator;
 import org.springframework.stereotype.Service;
 import org.springframework.validation.SmartValidator;
 
@@ -12,16 +13,25 @@
 
 @Service
 public class SeqBatchService extends DefaultDinaService<SeqBatch> {
-
+
+  private final SeqBatchValidator validator;
+
   public SeqBatchService(
     @NonNull BaseDAO baseDAO,
-    @NonNull SmartValidator sv) {
+    @NonNull SmartValidator sv,
+    SeqBatchValidator validator) {
     super(baseDAO, sv);
+    this.validator = validator;
   }
 
   @Override
   protected void preCreate(SeqBatch entity) {
     entity.setUuid(UUID.randomUUID());
   }
 
+  @Override
+  public void validateBusinessRules(SeqBatch entity) {
+    applyBusinessRule(entity, validator);
+  }
+
 }

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

@@ -0,0 +1,44 @@
+package ca.gc.aafc.seqdb.api.validation;
+
+import ca.gc.aafc.seqdb.api.entities.SeqBatch;
+import org.springframework.context.MessageSource;
+import org.springframework.context.i18n.LocaleContextHolder;
+import org.springframework.stereotype.Component;
+import org.springframework.validation.Errors;
+import org.springframework.validation.Validator;
+
+@Component
+public class SeqBatchValidator implements Validator {
+
+  private static final String ERROR_MESSAGE_KEY = "validation.constraint.violation.storageUnitOrType";
+
+  private final MessageSource messageSource;
+
+  public SeqBatchValidator(MessageSource messageSource) {
+    this.messageSource = messageSource;
+  }
+
+  @Override
+  public boolean supports(Class<?> clazz) {
+    return SeqBatch.class.isAssignableFrom(clazz);
+  }
+
+  @Override
+  public void validate(Object target, Errors errors) {
+    if (!supports(target.getClass())) {
+      throw new IllegalArgumentException("SeqBatchValidator not supported for class " + target.getClass());
+    }
+    checkStorageOrTypeNotBoth(errors, (SeqBatch) target);
+  }
+
+  private void checkStorageOrTypeNotBoth(Errors errors, SeqBatch seqBatch) {
+    if (seqBatch.getStorageUnit() != null && seqBatch.getStorageUnitType() != null) {
+      String errorMessage = getMessage(ERROR_MESSAGE_KEY);
+      errors.rejectValue("storageUnit", ERROR_MESSAGE_KEY, errorMessage);
+    }
+  }
+
+  private String getMessage(String key) {
+    return messageSource.getMessage(key, null, LocaleContextHolder.getLocale());
+  }
+}

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

@@ -38,4 +38,5 @@
   <include file="db/changelog/migrations/31-Add_reaction_date_to_seqbatch.xml"/>
   <include file="db/changelog/migrations/32-Add_sequencing_facility.xml"/>
   <include file="db/changelog/migrations/33-Add_well_coordinates_SeqReaction.xml"/>
+  <include file="db/changelog/migrations/34-Add_storage_SeqBatch.xml"/>
 </databaseChangeLog>

src/main/resources/db/changelog/migrations/34-Add_storage_SeqBatch.xml

@@ -0,0 +1,15 @@
+<?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="34-Add_storage_SeqBatch" context="schema-change" author="cgendreau">
+        <addColumn tableName="seq_batch">
+            <column name="storage_unit" type="uuid"/>
+            <column name="storage_unit_type" type="uuid"/>
+            <column name="storage_restriction" type="jsonb"/>
+        </addColumn>
+    </changeSet>
+</databaseChangeLog>

src/test/java/ca/gc/aafc/seqdb/api/openapi/SeqBatchOpenApiIT.java

@@ -53,15 +53,18 @@ void seqBatch_SpecValid() {
     SeqBatchDto seqBatch = SeqBatchTestFixture.newSeqBatch();
     // clear external relationships
     seqBatch.setExperimenters(null);
+    seqBatch.setStorageUnit(null);
+    seqBatch.setStorageUnitType(null);
 
     OpenAPI3Assertions.assertRemoteSchema(OpenAPIConstants.SEQDB_API_SPECS_URL, "SeqBatch",
             sendPost(SeqBatchDto.TYPENAME, JsonAPITestHelper.toJsonAPIMap(SeqBatchDto.TYPENAME, JsonAPITestHelper.toAttributeMap(seqBatch),
                     JsonAPITestHelper.toRelationshipMap(
                             List.of(JsonAPIRelationship.of("region", RegionDto.TYPENAME, regionUuid),
                                     JsonAPIRelationship.of("thermocyclerProfile", ThermocyclerProfileDto.TYPENAME, thermocyclerProfileUuid),
-                                    JsonAPIRelationship.of("protocol", "protocol", UUID.randomUUID().toString()))),
+                                    JsonAPIRelationship.of("protocol", "protocol", UUID.randomUUID().toString()),
+                                    JsonAPIRelationship.of("storageUnit", "storage-unit", UUID.randomUUID().toString()))),
                     null)
             ).extract().asString(),
-            ValidationRestrictionOptions.builder().allowableMissingFields(Set.of("experimenters")).build());
+            ValidationRestrictionOptions.builder().allowableMissingFields(Set.of("experimenters", "storageUnitType")).build());
   }
 }

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

@@ -7,6 +7,7 @@
 import java.util.UUID;
 
 import javax.inject.Inject;
+import javax.validation.ValidationException;
 
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
@@ -85,6 +86,16 @@ public void createSeqBatch_onSuccess_SeqBatchCreated() {
     assertEquals(TEST_PROTOCOL_UUID.toString(), created.getProtocol().getId());
   }
 
+  @Test
+  public void createSeqBatch_proveBothStorage_Exception() {
+    SeqBatchDto newDto = SeqBatchTestFixture.newSeqBatch();
+    newDto.setRegion(regionTest);
+    newDto.setThermocyclerProfile(thermocyclerProfileTest);
+    newDto.setStorageUnit(ExternalRelationDto.builder().id(UUID.randomUUID().toString()).type("storage-unit").build());
+    newDto.setStorageUnitType(ExternalRelationDto.builder().id(UUID.randomUUID().toString()).type("storage-unit-type").build());
+    assertThrows(ValidationException.class, () -> seqBatchRepository.create(newDto));
+  }
+
   @Test
   public void updateSeqBatch_onSuccess_PcrBatchUpdated() {
     SeqBatchDto newDto = SeqBatchTestFixture.newSeqBatch();

src/test/java/ca/gc/aafc/seqdb/api/testsupport/fixtures/SeqBatchTestFixture.java

@@ -1,6 +1,7 @@
 package ca.gc.aafc.seqdb.api.testsupport.fixtures;
 
 import ca.gc.aafc.seqdb.api.dto.SeqBatchDto;
+import ca.gc.aafc.seqdb.api.testsupport.factories.StorageRestrictionFactory;
 import ca.gc.aafc.seqdb.api.testsupport.factories.TestableEntityFactory;
 
 import java.time.LocalDate;
@@ -16,6 +17,8 @@ public static SeqBatchDto newSeqBatch() {
     seqBatchDto.setCreatedBy(CREATED_BY);
     seqBatchDto.setReactionDate(LocalDate.of(2020,3,2));
     seqBatchDto.setName(TestableEntityFactory.generateRandomName(10));
+
+    seqBatchDto.setStorageRestriction(StorageRestrictionFactory.newStorageRestriction().build());
     return seqBatchDto;
   }