Merge branch 'dev'

pom.xml

@@ -3,7 +3,7 @@
 
   <groupId>ca.gc.aafc</groupId>
   <artifactId>seqdb.api</artifactId>
-  <version>2.8.0</version>
+  <version>2.9.0</version>
   <packaging>jar</packaging>
 
   <name>seqdb-api</name>
@@ -21,21 +21,23 @@
     <!-- Override SpringBoot version (3.6) to avoid NoClassDefFoundError: org/apache/maven/doxia/siterenderer/DocumentContent -->
     <maven-site-plugin.version>3.7.1</maven-site-plugin.version>
 
-    <dependency.check.version>8.1.2</dependency.check.version>
+    <dependency.check.version>8.3.1</dependency.check.version>
     <jacoco-maven-plugin.version>0.8.8</jacoco-maven-plugin.version>
     <maven-checkstyle-plugin.version>3.1.2</maven-checkstyle-plugin.version>
     <checkstyle.version>9.3</checkstyle.version>
     <asciidoctor-maven-plugin.version>2.1.0</asciidoctor-maven-plugin.version>
-    <dina-base-api.version>0.104</dina-base-api.version>
+    <dina-base-api.version>0.110</dina-base-api.version>
     <postgresql.version>42.4.3</postgresql.version>
     <snakeyaml.version>1.33</snakeyaml.version>    
     <spring-boot-maven-plugin.fork>false</spring-boot-maven-plugin.fork>
+
+    <spring-security.version>5.7.10</spring-security.version>
   </properties>
 
   <parent>
     <groupId>org.springframework.boot</groupId>
     <artifactId>spring-boot-starter-parent</artifactId>
-    <version>2.7.11</version>
+    <version>2.7.13</version>
   </parent>
 
   <!--  temporary until we can migrate to a newer version of Crnk-->

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

@@ -3,7 +3,9 @@
 import java.time.OffsetDateTime;
 import java.util.UUID;
 
+import ca.gc.aafc.dina.dto.ExternalRelationDto;
 import ca.gc.aafc.dina.dto.RelatedEntity;
+import ca.gc.aafc.dina.repository.meta.JsonApiExternalRelation;
 import ca.gc.aafc.seqdb.api.entities.libraryprep.LibraryPrep;
 import io.crnk.core.resource.annotations.JsonApiId;
 import io.crnk.core.resource.annotations.JsonApiRelation;
@@ -34,14 +36,16 @@ public class LibraryPrepDto {
 
   @JsonApiRelation
   private LibraryPrepBatchDto libraryPrepBatch;
-
-  @JsonApiRelation
-  private MolecularSampleDto molecularSample;
 
   @JsonApiRelation
   private NgsIndexDto indexI5;
 
   @JsonApiRelation
   private NgsIndexDto indexI7;
 
+  @JsonApiExternalRelation(type = "material-sample")
+  @JsonApiRelation
+  private ExternalRelationDto materialSample;
+
+
 }

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

@@ -47,4 +47,6 @@ public class SeqReactionDto {
   private Integer wellColumn;
   private String wellRow;
 
+  private int cellNumber;
+
 }

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

@@ -12,6 +12,7 @@
 import javax.persistence.JoinColumn;
 import javax.persistence.ManyToOne;
 import javax.persistence.Table;
+import javax.persistence.Transient;
 import javax.validation.constraints.Max;
 import javax.validation.constraints.Min;
 import javax.validation.constraints.NotBlank;
@@ -82,4 +83,8 @@ public class SeqReaction implements DinaEntity {
   @Pattern(regexp = "[a-zA-Z]")
   @Column(name = "well_row")
   private String wellRow;
+
+  // calculated field
+  @Transient
+  private int cellNumber;
 }

src/main/java/ca/gc/aafc/seqdb/api/entities/libraryprep/LibraryPrep.java

@@ -21,7 +21,6 @@
 import org.hibernate.annotations.NaturalId;
 
 import ca.gc.aafc.dina.entity.DinaEntity;
-import ca.gc.aafc.seqdb.api.entities.MolecularSample;
 import lombok.AllArgsConstructor;
 import lombok.Builder;
 import lombok.Data;
@@ -67,9 +66,8 @@ public class LibraryPrep implements DinaEntity {
   private LibraryPrepBatch libraryPrepBatch;
 
   @NotNull
-  @ManyToOne(fetch = FetchType.LAZY)
-  @JoinColumn(name = "sampleid")
-  private MolecularSample molecularSample;
+  @Column(name = "material_sample")
+  private UUID materialSample;
 
   @ManyToOne(fetch = FetchType.LAZY)
   @JoinColumn(name = "Indexi5id")

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

@@ -1,10 +1,23 @@
 package ca.gc.aafc.seqdb.api.service;
 
+import ca.gc.aafc.dina.entity.StorageGridLayout;
 import ca.gc.aafc.dina.jpa.BaseDAO;
+import ca.gc.aafc.dina.jpa.PredicateSupplier;
 import ca.gc.aafc.dina.service.DefaultDinaService;
+import ca.gc.aafc.dina.translator.NumberLetterTranslator;
+import ca.gc.aafc.seqdb.api.entities.SeqBatch;
 import ca.gc.aafc.seqdb.api.entities.SeqReaction;
 import ca.gc.aafc.seqdb.api.validation.SeqReactionValidator;
+
+import java.util.List;
+import java.util.Set;
+import java.util.function.BiFunction;
+import javax.persistence.criteria.CriteriaBuilder;
+import javax.persistence.criteria.Order;
+import javax.persistence.criteria.Root;
 import lombok.NonNull;
+
+import org.apache.commons.lang3.StringUtils;
 import org.springframework.stereotype.Service;
 import org.springframework.validation.SmartValidator;
 
@@ -23,6 +36,35 @@ public SeqReactionService(
     this.validator = validator;
   }
 
+  @Override
+  public <T> List<T> findAll(@NonNull Class<T> entityClass, @NonNull PredicateSupplier<T> where,
+                             BiFunction<CriteriaBuilder, Root<T>, List<Order>> orderBy,
+                             int startIndex, int maxResult, @NonNull Set<String> includes,
+                             @NonNull Set<String> relationships)  {
+
+    List<T> itemsList = super.findAll(entityClass, where, orderBy, startIndex, maxResult, includes, relationships);
+    if(SeqReaction.class == entityClass) {
+      itemsList.forEach(t -> setCellNumber((SeqReaction) t));
+    }
+    return itemsList;
+  }
+
+  private void setCellNumber(SeqReaction item) {
+
+    SeqBatch batch = item.getSeqBatch();
+    if (batch == null || batch.getStorageRestriction() == null) {
+      return;
+    }
+
+    // We assume row and col are valid, so we only check for row presence
+    if (StringUtils.isBlank(item.getWellRow())) {
+      return;
+    }
+
+    StorageGridLayout restriction = batch.getStorageRestriction().getLayout();
+    item.setCellNumber(restriction.calculateCellNumber(NumberLetterTranslator.toNumber(item.getWellRow()), item.getWellColumn()));
+  }
+
   @Override
   protected void preCreate(SeqReaction entity) {
     entity.setUuid(UUID.randomUUID());

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

@@ -44,4 +44,5 @@
   <include file="db/changelog/migrations/37-Add_batchType_to_PCRBatch.xml"/>
   <include file="db/changelog/migrations/38-Add_sequencingType_to_SeqBatch.xml"/>
   <include file="db/changelog/migrations/39-Add_isCompleted_to_SeqBatch.xml"/>
+  <include file="db/changelog/migrations/40-Change_LibraryPrep_molecularSample_to_MaterialSample.xml"/>
 </databaseChangeLog>

src/main/resources/db/changelog/migrations/40-Change_LibraryPrep_molecularSample_to_MaterialSample.xml

@@ -0,0 +1,18 @@
+<?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="40-Change_LibraryPrep_molecularSample_to_MaterialSample" context="schema-change" author="cgendreau">
+
+        <dropColumn tableName="librarypreps">
+            <column name="sampleid"/>
+        </dropColumn>
+
+        <addColumn tableName="librarypreps">
+            <column name="material_sample" type="uuid"/>
+        </addColumn>
+    </changeSet>
+</databaseChangeLog>

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

@@ -1,48 +1,40 @@
 package ca.gc.aafc.seqdb.api.repository;
 
-import static org.junit.jupiter.api.Assertions.assertEquals;
-import static org.junit.jupiter.api.Assertions.assertNotNull;
-import static org.junit.jupiter.api.Assertions.assertNull;
-import static org.junit.jupiter.api.Assertions.assertThrows;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.inject.Inject;
-import javax.validation.ValidationException;
-
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
 
 import ca.gc.aafc.seqdb.api.dto.LibraryPrepBatchDto;
 import ca.gc.aafc.seqdb.api.dto.LibraryPrepDto;
-import ca.gc.aafc.seqdb.api.dto.MolecularSampleDto;
 import ca.gc.aafc.seqdb.api.entities.ContainerType;
 import ca.gc.aafc.seqdb.api.entities.Product;
-import ca.gc.aafc.seqdb.api.entities.MolecularSample;
 import ca.gc.aafc.seqdb.api.entities.libraryprep.LibraryPrep;
 import ca.gc.aafc.seqdb.api.testsupport.factories.ContainerTypeFactory;
 import ca.gc.aafc.seqdb.api.testsupport.factories.LibraryPrepFactory;
 import ca.gc.aafc.seqdb.api.testsupport.factories.ProductFactory;
+import ca.gc.aafc.seqdb.api.testsupport.fixtures.LibraryPrepTestFixture;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertNotNull;
+import static org.junit.jupiter.api.Assertions.assertNull;
+import static org.junit.jupiter.api.Assertions.assertThrows;
+
 import io.crnk.core.queryspec.QuerySpec;
+import javax.inject.Inject;
+import javax.validation.ValidationException;
 
 public class LibraryPrepRepositoryIT extends BaseRepositoryTest {
 
   private static final String TEST_QUALITY = "test quality";
 
   private LibraryPrep testLibPrep;
   private LibraryPrepBatchDto testBatchDto;
-  private List<MolecularSample> testSamples;
 
   @Inject
   private LibraryPrepBatchRepository libraryPrepBatchRepository;
 
   @Inject
   private LibraryPrepRepository libraryPrepRepository;
 
-  @Inject
-  private MolecularSampleRepository molecularSampleRepository;
-
   private LibraryPrep createTestLibraryPrep() {
 
     ContainerType testContainerType = ContainerTypeFactory.newContainerType()
@@ -53,14 +45,8 @@ private LibraryPrep createTestLibraryPrep() {
     Product testProduct = ProductFactory.newProduct().build();
     persist(testProduct);
 
-    MolecularSample testMolecularSample = new MolecularSample();
-    testMolecularSample.setName("test sample");
-
-    persist(testMolecularSample);
-
     testLibPrep = LibraryPrepFactory.newLibraryPrep()
         .quality(TEST_QUALITY)
-        .molecularSample(testMolecularSample)
         .build();
     testLibPrep.getLibraryPrepBatch().setContainerType(testContainerType);
     persist(testLibPrep.getLibraryPrepBatch());
@@ -70,15 +56,7 @@ private LibraryPrep createTestLibraryPrep() {
     // field for the test. This doesn't matter in prod.
     entityManager.flush();
     entityManager.refresh(testLibPrep.getLibraryPrepBatch());
-
-    testSamples = new ArrayList<>();
-    for (int i = 1; i <= 22; i++) {
-      MolecularSample sample = new MolecularSample();
-      sample.setName("sample " + i);
-      testSamples.add(sample);
-      persist(sample);
-    }
-
+
     testBatchDto = libraryPrepBatchRepository.findOne(
         testLibPrep.getLibraryPrepBatch().getUuid(),
         new QuerySpec(LibraryPrepBatchDto.class)
@@ -105,23 +83,17 @@ public void findLibPrep_whenLibPrepExists_libPrepReturned() {
 
   @Test
   public void createLibPrep_onSuccess_libPrepCreated() {
-    MolecularSampleDto newSample = new MolecularSampleDto();
-    newSample.setName("new sample");
-    MolecularSampleDto newSampleCreated = molecularSampleRepository.create(newSample);
-
-    LibraryPrepDto newDto = new LibraryPrepDto();
-    newDto.setSize("test size");
-    newDto.setMolecularSample(newSampleCreated);
+
+    LibraryPrepDto newDto = LibraryPrepTestFixture.newLibraryPrep();
     newDto.setLibraryPrepBatch(testBatchDto);
-    newDto.setGroup("dina");
-
+
     LibraryPrepDto created = libraryPrepRepository.create(newDto);
 
     assertNotNull(created.getUuid());
     assertEquals("test size", created.getSize());
     assertEquals(
-        newSampleCreated.getUuid(),
-        created.getMolecularSample().getUuid()
+      LibraryPrepTestFixture.MATERIAL_SAMPLE_UUID.toString(),
+        created.getMaterialSample().getId()
     );
     assertEquals(
         testLibPrep.getLibraryPrepBatch().getUuid(),
@@ -131,29 +103,17 @@ public void createLibPrep_onSuccess_libPrepCreated() {
 
   @Test
   public void createLibPrep_whenCellsOverLap_setExistingCellCoordinatesToNull() {
-    LibraryPrepDto prep1 = new LibraryPrepDto();
+    LibraryPrepDto prep1 = LibraryPrepTestFixture.newLibraryPrep();
     prep1.setWellRow("B");
     prep1.setWellColumn(5);
-    prep1.setGroup("dina");
-    prep1.setMolecularSample(
-        molecularSampleRepository.findOne(
-            testSamples.get(0).getUuid(),
-            new QuerySpec(MolecularSampleDto.class)
-        )
-    );
+    prep1.setMaterialSample(LibraryPrepTestFixture.newMaterialSampleExternalRelationship());
     prep1.setLibraryPrepBatch(testBatchDto);
     LibraryPrepDto createdPrep1 = libraryPrepRepository.create(prep1);
 
-    LibraryPrepDto prep2 = new LibraryPrepDto();
+    LibraryPrepDto prep2 = LibraryPrepTestFixture.newLibraryPrep();
     prep2.setWellRow("B");
     prep2.setWellColumn(5);
-    prep2.setGroup("dina");
-    prep2.setMolecularSample(
-        molecularSampleRepository.findOne(
-            testSamples.get(1).getUuid(),
-            new QuerySpec(MolecularSampleDto.class)
-        )
-    );
+    prep2.setMaterialSample(LibraryPrepTestFixture.newMaterialSampleExternalRelationship());
     prep2.setLibraryPrepBatch(testBatchDto);
 
     LibraryPrepDto createdPrep2 = libraryPrepRepository.create(prep2);
@@ -177,7 +137,7 @@ public void updateLibPrep_whenWellRowLetterInvalid_throwValidationException() {
     );
     dto.setWellRow("!");
     dto.setWellColumn(1);
-    ValidationException exception = assertThrows(
+    assertThrows(
         ValidationException.class,
         () -> libraryPrepRepository.save(dto)
     );
@@ -209,7 +169,7 @@ public void updateLibPrep_whenColumnIs0_throwValidationException() {
     );
     dto.setWellRow("A");
     dto.setWellColumn(0);
-    ValidationException exception = assertThrows(
+    assertThrows(
         ValidationException.class,
         () -> libraryPrepRepository.save(dto)
     );

src/test/java/ca/gc/aafc/seqdb/api/testsupport/factories/LibraryPrepFactory.java

@@ -1,6 +1,7 @@
 package ca.gc.aafc.seqdb.api.testsupport.factories;
 
 import java.util.List;
+import java.util.UUID;
 import java.util.function.BiFunction;
 
 import ca.gc.aafc.seqdb.api.entities.libraryprep.LibraryPrep;
@@ -17,7 +18,7 @@ public static LibraryPrep.LibraryPrepBuilder newLibraryPrep() {
     return LibraryPrep.builder()
         .group("dina")
         .libraryPrepBatch(LibraryPrepBatchFactory.newLibraryPrepBatch().build())
-        .molecularSample(MolecularSampleFactory.newMolecularSample().build());
+        .materialSample(UUID.randomUUID());
   }
 
   public static List<LibraryPrep> newListOf(int qty) {