WIP staging work

pom.xml

@@ -131,16 +131,27 @@
     </dependency>
     <!-- For JSR-303, javax.validation -->
     <dependency>
-      <groupId>org.hibernate.validator</groupId>
-      <artifactId>hibernate-validator</artifactId>
-      <version>7.0.1.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

@@ -21,12 +21,10 @@
 
 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;
 
 @SpringBootApplication
-@EnableMongoRepositories
 @EnableAsync
 @EnableScheduling
 public class CwlViewerApplication {

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

@@ -0,0 +1,34 @@
+package org.commonwl.view.util;
+
+import com.fasterxml.jackson.core.JsonProcessingException;
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+import javax.persistence.AttributeConverter;
+import javax.persistence.Converter;
+
+/**
+ * @see <a href="https://stackoverflow.com/questions/25738569/how-to-map-a-map-json-column-to-java-object-with-jpa">https://stackoverflow.com/questions/25738569/how-to-map-a-map-json-column-to-java-object-with-jpa</a>
+ */
+@Converter(autoApply = true)
+public class JpaConverterJson implements AttributeConverter<Object, String> {
+
+    private static final ObjectMapper objectMapper = new ObjectMapper();
+
+    @Override
+    public String convertToDatabaseColumn(Object meta) {
+        try {
+            return objectMapper.writeValueAsString(meta);
+        } catch (JsonProcessingException ex) {
+            return null;
+        }
+    }
+
+    @Override
+    public Object convertToEntityAttribute(String dbData) {
+        try {
+            return objectMapper.readValue(dbData, Object.class);
+        } catch (JsonProcessingException ex) {
+            return null;
+        }
+    }
+}

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

@@ -3,26 +3,39 @@
 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.JpaConverterJson;
+
+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.util.List;
 
 /**
  * A workflow pending completion of cwltool
  */
 @JsonIgnoreProperties(value = {"id", "tempRepresentation", "workflowList"})
 @JsonInclude(JsonInclude.Include.NON_EMPTY)
+@Entity
+@Table(name = "queued_workflow")
+@SuppressWarnings("JpaAttributeTypeInspection")
 public class QueuedWorkflow {
 
     // ID for database
     @Id
+    @GeneratedValue(strategy = GenerationType.IDENTITY)
     public String id;
 
     // Very barebones workflow to build loading thumbnail and overview
     private Workflow tempRepresentation;
 
     // List of packed workflows for packed workflows
     // TODO: Refactor so this is not necessary
+    @Column(columnDefinition = "jsonb")
+    @Convert(converter= JpaConverterJson.class)
     private List<WorkflowOverview> workflowList;
 
     // Cwltool details

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

@@ -1,7 +1,7 @@
 package org.commonwl.view.workflow;
 
 import org.commonwl.view.git.GitDetails;
-import org.springframework.data.mongodb.repository.Query;
+import org.springframework.data.jpa.repository.Query;
 import org.springframework.data.repository.PagingAndSortingRepository;
 
 import java.util.Date;
@@ -17,20 +17,22 @@ public interface QueuedWorkflowRepository extends PagingAndSortingRepository<Que
      * @param retrievedFrom Details of where the queued workflow is from
      * @return The queued workflow
      */
-    @Query("{\"tempRepresentation.retrievedFrom\": ?0}")
+    @Query(value = "select q.* from queued_workflow q where q.tempRepresentation->>retrieved_from = ?0", nativeQuery = true)
     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
      */
+    @Query(value = "delete from queued_workflow q where q.tempRepresentation->>retrieved_from = ?0", nativeQuery = true)
     void deleteByTempRepresentation_RetrievedFrom(GitDetails retrievedFrom);
 
     /**
      * 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 <= ?0", nativeQuery = true)
     Long deleteByTempRepresentation_RetrievedOnLessThanEqual(Date retrievedOn);
 
 
@@ -39,6 +41,7 @@ public interface QueuedWorkflowRepository extends PagingAndSortingRepository<Que
      * @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 <= ?0", nativeQuery = true)
     List<QueuedWorkflow> findByTempRepresentation_RetrievedOnLessThanEqual(Date retrievedOn);
 
 

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

@@ -27,11 +27,17 @@
 import org.commonwl.view.cwl.CWLElement;
 import org.commonwl.view.cwl.CWLStep;
 import org.commonwl.view.git.GitDetails;
-import org.springframework.data.annotation.Id;
-import org.springframework.data.mongodb.core.index.Indexed;
-import org.springframework.data.mongodb.core.mapping.Document;
+import org.commonwl.view.util.JpaConverterJson;
 import org.springframework.format.annotation.DateTimeFormat;
 
+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.Index;
+import javax.persistence.Table;
 import java.util.Date;
 import java.util.Map;
 
@@ -40,18 +46,24 @@
  */
 @JsonInclude(JsonInclude.Include.NON_NULL)
 @JsonIgnoreProperties(value = {"id", "roBundlePath", "roBundleLink"})
-@Document
+@Entity
+@Table(name = "workflow",
+        indexes = {
+                @Index(columnList = "retrievedFrom", unique = true),
+                @Index(columnList = "retrievedOn")
+        })
+@SuppressWarnings("JpaAttributeTypeInspection")
 public class Workflow {
 
     // ID for database
     @Id
+    @GeneratedValue(strategy = GenerationType.IDENTITY)
     public String id;
 
     // Metadata
-    @Indexed(unique = true)
     private GitDetails retrievedFrom;
+
     @DateTimeFormat(pattern="yyyy-MM-dd HH:mm:ss z")
-    @Indexed
     private Date retrievedOn;
 
     // The last commit from the branch at the time of fetching
@@ -65,8 +77,14 @@ public class Workflow {
     // Contents of the workflow
     private String label;
     private String doc;
+    @Column(columnDefinition = "jsonb")
+    @Convert(converter= JpaConverterJson.class)
     private Map<String, CWLElement> inputs;
+    @Column(columnDefinition = "jsonb")
+    @Convert(converter= JpaConverterJson.class)
     private Map<String, CWLElement> outputs;
+    @Column(columnDefinition = "jsonb")
+    @Convert(converter= JpaConverterJson.class)
     private Map<String, CWLStep> steps;
 
     // Currently only DockerRequirement is parsed for this

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

@@ -19,14 +19,14 @@
 
 package org.commonwl.view.workflow;
 
-import java.util.List;
-
 import org.commonwl.view.git.GitDetails;
 import org.springframework.data.domain.Page;
 import org.springframework.data.domain.Pageable;
-import org.springframework.data.mongodb.repository.Query;
+import org.springframework.data.jpa.repository.Query;
 import org.springframework.data.repository.PagingAndSortingRepository;
 
+import java.util.List;
+
 /**
  * Stores and retrieved workflow objects from the database
  *
@@ -48,7 +48,7 @@ public interface WorkflowRepository extends PagingAndSortingRepository<Workflow,
      * @param path The path to the workflow within the repository
      * @return The workflow model
      */
-    @Query("{\"lastCommit\": ?0, \"retrievedFrom.path\": ?1}")
+    @Query(value = "select * from workflow w where w.lastCommit = ?1 and w.retrievedFrom->>path = ?2", nativeQuery = true)
     List<Workflow> findByCommitAndPath(String commitId, String path);
 
     /**
@@ -58,7 +58,7 @@ public interface WorkflowRepository extends PagingAndSortingRepository<Workflow,
      *            The latest commit ID of the workflow
      * @return The workflow model
      */
-    @Query("{\"lastCommit\": ?0}")
+    @Query("select w from Workflow w where w.lastCommit = ?1")
     List<Workflow> findByCommit(String commitId);
 
     /**

src/main/resources/application.properties

@@ -42,21 +42,18 @@ gitAPI.cloneSubmodules = true
 #=======================
 # Postgres settings
 #=======================
-spring.jpa.hibernate.ddl-auto=none
+spring.datasource.url=jdbc:postgresql://localhost:5432/cwlviewer
+spring.datasource.username=sa
+spring.datasource.password=sa
 
 spring.sql.init.mode=always
 spring.sql.init.platform=postgres
-spring.datasource.url=jdbc:postgresql://localhost:5432/cwlviewer
-spring.datasource.username=postgres
-spring.datasource.password=s$cret
 
+spring.jpa.show-sql=false
+spring.jpa.database-platform=org.hibernate.dialect.PostgreSQLDialect
+spring.jpa.hibernate.ddl-auto=none
 spring.jpa.properties.hibernate.jdbc.lob.non_contextual_creation=true
 
-spring.data.mongodb.host = localhost
-spring.data.mongodb.port = 27017
-# For complete list of MongoDB properties, see
-# https://github.com/spring-projects/spring-boot/blob/v1.4.2.RELEASE/spring-boot-autoconfigure/src/main/java/org/springframework/boot/autoconfigure/mongo/MongoProperties.java
-
 #=======================
 # SPARQL endpoint
 #=======================

src/test/java/org/commonwl/view/workflow/PostgreSQLContextInitializer.java

@@ -0,0 +1,36 @@
+package org.commonwl.view.workflow;
+
+import org.springframework.boot.test.util.TestPropertyValues;
+import org.springframework.context.ApplicationContextInitializer;
+import org.springframework.context.ApplicationEvent;
+import org.springframework.context.ApplicationListener;
+import org.springframework.context.ConfigurableApplicationContext;
+import org.springframework.context.event.ContextClosedEvent;
+import org.testcontainers.containers.PostgreSQLContainer;
+
+/**
+ * A test application context initializer that creates the database Docker container used for functional tests.
+ */
+public class PostgreSQLContextInitializer implements ApplicationContextInitializer<ConfigurableApplicationContext> {
+
+    @Override
+    public void initialize(ConfigurableApplicationContext applicationContext) {
+        PostgreSQLContainer<?> postgreSQLContainer = new PostgreSQLContainer<>("postgres:9.6.12")
+                .withDatabaseName("cwlviewer")
+                .withUsername("sa")
+                .withPassword("sa");
+        postgreSQLContainer.start();
+        TestPropertyValues.of("spring.datasource.url=" + postgreSQLContainer.getJdbcUrl(),
+                "spring.datasource.username=" + postgreSQLContainer.getUsername(),
+                "spring.datasource.password=" + postgreSQLContainer.getPassword(),
+                "spring.jpa.hibernate.ddl-auto=create")
+                .applyTo(applicationContext.getEnvironment());
+        applicationContext.addApplicationListener(new ApplicationListener<ContextClosedEvent>() {
+            @Override
+            public void onApplicationEvent(ContextClosedEvent event) {
+                postgreSQLContainer.stop();
+            }
+        });
+    }
+
+}

src/test/java/org/commonwl/view/workflow/QueuedWorkflowRepositoryTest.java

@@ -6,31 +6,39 @@
 import org.junit.jupiter.api.Test;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.boot.test.context.SpringBootTest;
+import org.springframework.test.context.ContextConfiguration;
+import org.springframework.transaction.annotation.Transactional;
+import org.testcontainers.containers.PostgreSQLContainer;
+import org.testcontainers.junit.jupiter.Container;
+import org.testcontainers.junit.jupiter.Testcontainers;
 
 import static org.junit.jupiter.api.Assertions.assertNotNull;
 import static org.junit.jupiter.api.Assertions.assertNull;
 
-// N.B. "To use embedded mongo, the spring.mongodb.embedded.version property must now be set."
-// https://github.com/spring-projects/spring-boot/wiki/Spring-Boot-2.6-Release-Notes#embedded-mongo
+@Testcontainers
 @SpringBootTest(
-        properties={
-                "spring.mongodb.embedded.version=3.2.2",
-                "spring.data.mongodb.port=0"
-        },
         classes={WebConfig.class, CwlViewerApplication.class, QueuedWorkflowRepository.class}
 )
+@ContextConfiguration(initializers = PostgreSQLContextInitializer.class)
 public class QueuedWorkflowRepositoryTest {
 
+    @Container
+    public static PostgreSQLContainer<?> postgreSQLContainer = new PostgreSQLContainer<>("postgres:9.6.12")
+            .withDatabaseName("cwlviewer")
+            .withUsername("sa")
+            .withPassword("sa");
+
     @Autowired
     QueuedWorkflowRepository repository;
 
     @Test
+    @Transactional
     public void deleteQueuedWorkflowByRetrievedFromTest() {
 
         assertNotNull(repository);
 
         // create stub queued workflow
-        GitDetails gitDetails = new GitDetails("test_repo_url", "test_branch", "test_path");
+        GitDetails gitDetails = new GitDetails("https://github.com/common-workflow-language/cwlviewer/", "main", "/");
         gitDetails.setPackedId("test_packedId");
 
         Workflow workflow = new Workflow();