Fix unit tests, moving queries to an implementation class for JSONB d…

…e/serialization.

pom.xml

@@ -70,6 +70,11 @@
       <artifactId>spring-data-commons</artifactId>
       <version>2.6.1</version>
     </dependency>
+    <dependency>
+      <groupId>com.vladmihalcea</groupId>
+      <artifactId>hibernate-types-55</artifactId>
+      <version>2.14.0</version>
+    </dependency>
     <!-- Postgres -->
     <dependency>
       <groupId>org.postgresql</groupId>
@@ -131,16 +136,27 @@
     </dependency>
     <!-- For JSR-303, javax.validation -->
     <dependency>
-      <groupId>org.hibernate.validator</groupId>
-      <artifactId>hibernate-validator</artifactId>
-      <version>7.0.2.Final</version>
+      <groupId>org.springframework.boot</groupId>
+      <artifactId>spring-boot-starter-validation</artifactId>
     </dependency>
     <!-- Test dependencies -->
     <dependency>
       <groupId>org.springframework.boot</groupId>
       <artifactId>spring-boot-starter-test</artifactId>
       <scope>test</scope>
     </dependency>
+    <dependency>
+      <groupId>org.testcontainers</groupId>
+      <artifactId>junit-jupiter</artifactId>
+      <version>1.16.2</version>
+      <scope>test</scope>
+    </dependency>
+    <dependency>
+      <groupId>org.testcontainers</groupId>
+      <artifactId>postgresql</artifactId>
+      <version>1.16.2</version>
+      <scope>test</scope>
+    </dependency>
     <dependency>
       <groupId>org.mockito</groupId>
       <artifactId>mockito-all</artifactId>

src/main/java/org/commonwl/view/CwlViewerApplication.java

@@ -21,14 +21,14 @@
 
 import org.springframework.boot.SpringApplication;
 import org.springframework.boot.autoconfigure.SpringBootApplication;
-import org.springframework.data.mongodb.repository.config.EnableMongoRepositories;
 import org.springframework.scheduling.annotation.EnableAsync;
 import org.springframework.scheduling.annotation.EnableScheduling;
+import org.springframework.transaction.annotation.EnableTransactionManagement;
 
 @SpringBootApplication
-@EnableMongoRepositories
 @EnableAsync
 @EnableScheduling
+@EnableTransactionManagement
 public class CwlViewerApplication {
 
 	public static void main(String[] args) {

src/main/java/org/commonwl/view/git/GitDetails.java

@@ -24,11 +24,12 @@
 import java.io.Serializable;
 import java.net.URI;
 import java.net.URISyntaxException;
+import java.util.Objects;
 
 /**
  * Represents all the parameters necessary to access a file/directory with Git
  */
-@JsonIgnoreProperties(value = {"internalUrl"})
+@JsonIgnoreProperties(value = {"internalUrl"}, ignoreUnknown = true)
 public class GitDetails implements Serializable {
 
     private String repoUrl;
@@ -226,4 +227,19 @@ public static String normaliseUrl(String url) {
                   .replace("www.", "");
     }
 
+    @Override
+    public boolean equals(Object o) {
+        if (this == o) return true;
+        if (o == null || getClass() != o.getClass()) return false;
+        GitDetails that = (GitDetails) o;
+        return Objects.equals(repoUrl, that.repoUrl) &&
+                Objects.equals(branch, that.branch) &&
+                Objects.equals(path, that.path) &&
+                Objects.equals(packedId, that.packedId);
+    }
+
+    @Override
+    public int hashCode() {
+        return Objects.hash(repoUrl, branch, path, packedId);
+    }
 }

src/main/java/org/commonwl/view/util/BaseEntity.java

@@ -0,0 +1,14 @@
+package org.commonwl.view.util;
+
+import com.vladmihalcea.hibernate.type.json.JsonBinaryType;
+import org.hibernate.annotations.TypeDef;
+import org.hibernate.annotations.TypeDefs;
+
+import javax.persistence.MappedSuperclass;
+
+@TypeDefs({
+        @TypeDef(name = "json", typeClass = JsonBinaryType.class)
+})
+@MappedSuperclass
+public class BaseEntity {
+}

src/main/java/org/commonwl/view/workflow/QueuedWorkflow.java

@@ -3,31 +3,59 @@
 import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
 import com.fasterxml.jackson.annotation.JsonInclude;
 import org.commonwl.view.cwl.CWLToolStatus;
-import org.springframework.data.annotation.Id;
-
+import org.commonwl.view.util.BaseEntity;
+import org.hibernate.annotations.GenericGenerator;
+import org.hibernate.annotations.Type;
+
+import javax.persistence.Column;
+import javax.persistence.Convert;
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.Table;
+import java.io.Serializable;
 import java.util.List;
+import java.util.Objects;
 
 /**
  * A workflow pending completion of cwltool
  */
 @JsonIgnoreProperties(value = {"id", "tempRepresentation", "workflowList"})
 @JsonInclude(JsonInclude.Include.NON_EMPTY)
-public class QueuedWorkflow {
+@Entity
+@Table(name = "queued_workflow")
+@SuppressWarnings("JpaAttributeTypeInspection")
+public class QueuedWorkflow extends BaseEntity implements Serializable {
 
     // ID for database
     @Id
+    @GenericGenerator(name = "uuid2", strategy = "uuid2")
+    @GeneratedValue(strategy = GenerationType.IDENTITY, generator = "uuid2")
+    @Column(length = 36, nullable = false, updatable = false)
     public String id;
 
     // Very barebones workflow to build loading thumbnail and overview
+    @Column(columnDefinition = "jsonb", length = 10000)
+    @Type(type = "json")
+    @Convert(disableConversion = true)
     private Workflow tempRepresentation;
 
     // List of packed workflows for packed workflows
     // TODO: Refactor so this is not necessary
+    @Column(columnDefinition = "jsonb", length = 10000)
+    @Type(type = "json")
+    @Convert(disableConversion = true)
     private List<WorkflowOverview> workflowList;
 
     // Cwltool details
+    @Column(columnDefinition = "jsonb", length = 10000)
+    @Type(type = "json")
+    @Convert(disableConversion = true)
     private CWLToolStatus cwltoolStatus = CWLToolStatus.RUNNING;
+    @Column(length = 1000)
     private String cwltoolVersion = "";
+    @Column(length = 1000)
     private String message;
 
     public String getId() {
@@ -73,4 +101,22 @@ public List<WorkflowOverview> getWorkflowList() {
     public void setWorkflowList(List<WorkflowOverview> workflowList) {
         this.workflowList = workflowList;
     }
+
+    @Override
+    public boolean equals(Object o) {
+        if (this == o) return true;
+        if (o == null || getClass() != o.getClass()) return false;
+        QueuedWorkflow that = (QueuedWorkflow) o;
+        return Objects.equals(id, that.id) &&
+                Objects.equals(tempRepresentation, that.tempRepresentation) &&
+                Objects.equals(workflowList, that.workflowList) &&
+                cwltoolStatus == that.cwltoolStatus &&
+                Objects.equals(cwltoolVersion, that.cwltoolVersion) &&
+                Objects.equals(message, that.message);
+    }
+
+    @Override
+    public int hashCode() {
+        return Objects.hash(id, tempRepresentation, workflowList, cwltoolStatus, cwltoolVersion, message);
+    }
 }

src/main/java/org/commonwl/view/workflow/QueuedWorkflowRepository.java

@@ -1,45 +1,32 @@
 package org.commonwl.view.workflow;
 
-import org.commonwl.view.git.GitDetails;
-import org.springframework.data.mongodb.repository.Query;
-import org.springframework.data.repository.PagingAndSortingRepository;
+import org.springframework.data.jpa.repository.JpaRepository;
+import org.springframework.data.jpa.repository.Query;
 
 import java.util.Date;
 import java.util.List;
 
 /**
  * Stores workflows in the queue waiting for cwltool
  */
-public interface QueuedWorkflowRepository extends PagingAndSortingRepository<QueuedWorkflow, String> {
-
-    /**
-     * Finds a queued workflow based on where it was retrieved from
-     * @param retrievedFrom Details of where the queued workflow is from
-     * @return The queued workflow
-     */
-    @Query("{\"tempRepresentation.retrievedFrom\": ?0}")
-    QueuedWorkflow findByRetrievedFrom(GitDetails retrievedFrom);
-
-    /**
-     * Deletes a queued workflow based on where it was retrieved from
-     * @param retrievedFrom Details of where the queued workflow is from
-     */
-    void deleteByTempRepresentation_RetrievedFrom(GitDetails retrievedFrom);
+public interface QueuedWorkflowRepository extends JpaRepository<QueuedWorkflow, String>, QueuedWorkflowRepositoryCustom {
 
     /**
      * Deletes all queued workflows with date retrieved on older or equal to the Date argument passed.
+     *
      * @param retrievedOn Date of when the queued workflow was retrieved
      * @return The number of queued workflows deleted
      */
+    @Query(value = "delete from queued_workflow q where q.tempRepresentation->>retrieved_on <= ?1", nativeQuery = true)
     Long deleteByTempRepresentation_RetrievedOnLessThanEqual(Date retrievedOn);
 
-
     /**
      * Finds and returns all queued workflows with date retrieved on older or equal to the Date argument passed.
+     *
      * @param retrievedOn Details of where the queued workflow is from
      * @return A list of queued workflows
      */
+    @Query(value = "select q.* from queued_workflow q where q.tempRepresentation->>retrieved_on <= ?1", nativeQuery = true)
     List<QueuedWorkflow> findByTempRepresentation_RetrievedOnLessThanEqual(Date retrievedOn);
 
-
 }

src/main/java/org/commonwl/view/workflow/QueuedWorkflowRepositoryCustom.java

@@ -0,0 +1,21 @@
+package org.commonwl.view.workflow;
+
+import org.commonwl.view.git.GitDetails;
+import org.springframework.data.repository.query.Param;
+
+public interface QueuedWorkflowRepositoryCustom {
+    /**
+     * Finds a queued workflow based on where it was retrieved from.
+     *
+     * @param retrievedFrom Details of where the queued workflow is from
+     * @return The queued workflow
+     */
+    QueuedWorkflow findByRetrievedFrom(@Param("retrievedFrom") GitDetails retrievedFrom);
+
+    /**
+     * Deletes a queued workflow based on where it was retrieved from.
+     *
+     * @param retrievedFrom Details of where the queued workflow is from
+     */
+    void deleteByTempRepresentation_RetrievedFrom(GitDetails retrievedFrom);
+}

src/main/java/org/commonwl/view/workflow/QueuedWorkflowRepositoryImpl.java

@@ -0,0 +1,43 @@
+package org.commonwl.view.workflow;
+
+import com.vladmihalcea.hibernate.type.json.JsonBinaryType;
+import org.commonwl.view.git.GitDetails;
+import org.hibernate.query.Query;
+
+import javax.persistence.EntityManager;
+import javax.persistence.PersistenceContext;
+
+public class QueuedWorkflowRepositoryImpl implements QueuedWorkflowRepositoryCustom {
+
+    // Tested this query directly, and it works! Problem is elsewhere!
+    private static final String QUERY_FIND_BY_RETRIEVED_FROM = "SELECT q.* FROM queued_workflow q WHERE q.temp_representation -> 'retrievedFrom' = :retrievedFrom";
+
+    private static final String QUERY_DELETE_BY_RETRIEVED_FROM = "DELETE FROM queued_workflow q WHERE q.temp_representation -> 'retrievedFrom' = :retrievedFrom";
+
+    @PersistenceContext
+    EntityManager entityManager;
+
+    @Override
+    public QueuedWorkflow findByRetrievedFrom(GitDetails retrievedFrom) {
+        return (QueuedWorkflow) entityManager
+                .createNativeQuery(QUERY_FIND_BY_RETRIEVED_FROM, QueuedWorkflow.class)
+                .unwrap(Query.class)
+                .setParameter("retrievedFrom", retrievedFrom, JsonBinaryType.INSTANCE)
+                .getResultList()
+                .stream()
+                .findFirst()
+                .orElse(null)
+                ;
+    }
+
+    @Override
+    public void deleteByTempRepresentation_RetrievedFrom(GitDetails retrievedFrom) {
+        entityManager
+                .createNativeQuery(QUERY_DELETE_BY_RETRIEVED_FROM, QueuedWorkflow.class)
+                .unwrap(Query.class)
+                .setParameter("retrievedFrom", retrievedFrom, JsonBinaryType.INSTANCE)
+                .executeUpdate()
+        ;
+    }
+
+}