Merge pull request #206 from AAFC-BICoE/29599_Add_coordinates_to_seq_…

…reaction

29599 Add coordinates to seq reaction

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

@@ -44,4 +44,7 @@ public class SeqReactionDto {
   @JsonApiRelation
   private PcrPrimerDto seqPrimer;
 
+  private Integer wellColumn;
+  private String wellRow;
+
 }

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

@@ -12,8 +12,11 @@
 import javax.persistence.JoinColumn;
 import javax.persistence.ManyToOne;
 import javax.persistence.Table;
+import javax.validation.constraints.Max;
+import javax.validation.constraints.Min;
 import javax.validation.constraints.NotBlank;
 import javax.validation.constraints.NotNull;
+import javax.validation.constraints.Pattern;
 
 import ca.gc.aafc.seqdb.api.entities.pcr.PcrBatchItem;
 import org.hibernate.annotations.Generated;
@@ -70,5 +73,13 @@ public class SeqReaction implements DinaEntity {
   @ManyToOne(fetch = FetchType.LAZY)
   @JoinColumn(name = "seq_primer_id")
   private PcrPrimer seqPrimer;
-
+
+  @Min(value = 1)
+  @Max(value = 255)
+  @Column(name = "well_column")
+  private Integer wellColumn;
+
+  @Pattern(regexp = "[a-zA-Z]")
+  @Column(name = "well_row")
+  private String wellRow;
 }

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

@@ -3,6 +3,7 @@
 import ca.gc.aafc.dina.jpa.BaseDAO;
 import ca.gc.aafc.dina.service.DefaultDinaService;
 import ca.gc.aafc.seqdb.api.entities.SeqReaction;
+import ca.gc.aafc.seqdb.api.validation.SeqReactionValidator;
 import lombok.NonNull;
 import org.springframework.stereotype.Service;
 import org.springframework.validation.SmartValidator;
@@ -12,15 +13,24 @@
 @Service
 public class SeqReactionService extends DefaultDinaService<SeqReaction> {
 
+  private final SeqReactionValidator validator;
+
   public SeqReactionService(
     @NonNull BaseDAO baseDAO,
+    SeqReactionValidator validator,
     @NonNull SmartValidator sv) {
     super(baseDAO, sv);
+    this.validator = validator;
   }
 
   @Override
   protected void preCreate(SeqReaction entity) {
     entity.setUuid(UUID.randomUUID());
   }
 
+  @Override
+  public void validateBusinessRules(SeqReaction entity) {
+    applyBusinessRule(entity, validator);
+  }
+
 }

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

@@ -0,0 +1,34 @@
+package ca.gc.aafc.seqdb.api.validation;
+
+import ca.gc.aafc.seqdb.api.entities.SeqReaction;
+import org.apache.commons.lang3.StringUtils;
+import org.springframework.context.MessageSource;
+import org.springframework.stereotype.Component;
+import org.springframework.validation.Errors;
+
+@Component
+public class SeqReactionValidator extends AbstractLocationValidator {
+
+  public SeqReactionValidator(MessageSource messageSource) {
+    super(messageSource);
+  }
+
+  @Override
+  public boolean supports(Class<?> clazz) {
+    return SeqReaction.class.isAssignableFrom(clazz);
+  }
+
+  @Override
+  public void validate(Object target, Errors errors) {
+    if (!supports(target.getClass())) {
+      throw new IllegalArgumentException("SeqReactionValidator not supported for class " + target.getClass());
+    }
+    SeqReaction seqReaction = (SeqReaction) target;
+    // make sure we have a location to validate
+    if (StringUtils.isBlank(seqReaction.getWellRow()) && seqReaction.getWellColumn() == null) {
+      return;
+    }
+    checkRowAndColumn(seqReaction.getWellRow(), seqReaction.getWellColumn(), errors);
+  }
+
+}

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

@@ -37,4 +37,5 @@
   <include file="db/changelog/migrations/30-Allow_storage_unit_type_on_pcrbatch.xml"/>
   <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"/>
 </databaseChangeLog>

src/main/resources/db/changelog/migrations/33-Add_well_coordinates_SeqReaction.xml

@@ -0,0 +1,16 @@
+<?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="33-Add_well_coordinates_SeqReaction" context="schema-change" author="cgendreau">
+        <addColumn tableName="seq_reaction">
+            <column name="well_column" type="INTEGER"/>
+            <column name="well_row" type="VARCHAR(2)"/>
+        </addColumn>
+        <sql>
+            ALTER TABLE seq_reaction ADD CONSTRAINT well_column_seqreaction_check CHECK (well_column &gt;=1 AND well_column &lt;= 255)
+        </sql>
+    </changeSet>
+</databaseChangeLog>

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

@@ -11,6 +11,8 @@ public static SeqReactionDto newSeqReaction() {
     SeqReactionDto seqReactionDto = new SeqReactionDto();
     seqReactionDto.setGroup(GROUP);
     seqReactionDto.setCreatedBy(CREATED_BY);
+    seqReactionDto.setWellRow("B");
+    seqReactionDto.setWellColumn(8);
     return seqReactionDto;
   }