Fix MongoDB test

Had to add a new dependency for the embedded MongoDB server used for tests.

The version of MongoDB used for tests (embedded) also needs to be defined now. And
MongoDB/SpringData integration appears to be more strict. A query like
{ obj.property: ?0 } failed, and took me a long time to recognize that it was missing
quotes, so { 'obj.property': ?0 } fixed it.

Finally, there was also an issue with serialization. For some reason now the Mongo
repository was failing to serialize a response for Workflow. The object contained a
final String that was used for the base URL of permanent links, and Mongo/Spring/etc
wanted a way to set that value in the constructor. Tried the @PersistenceConstructor
annotation but that didn't work. In the end it was easy to fix it by making the
final String now a constant

Author: kinow

pom.xml

@@ -130,6 +130,11 @@
 			<version>1.10.19</version>
 			<scope>test</scope>
 		</dependency>
+		<dependency>
+			<groupId>de.flapdoodle.embed</groupId>
+			<artifactId>de.flapdoodle.embed.mongo</artifactId>
+			<scope>test</scope>
+		</dependency>
 	</dependencies>
 
 	<build>

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

@@ -17,7 +17,7 @@ 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("{\"tempRepresentation.retrievedFrom\": ?0}")
     QueuedWorkflow findByRetrievedFrom(GitDetails retrievedFrom);
 
     /**

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

@@ -19,9 +19,9 @@
 
 package org.commonwl.view.workflow;
 
-import java.util.Date;
-import java.util.Map;
-
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
+import com.fasterxml.jackson.annotation.JsonInclude;
+import com.fasterxml.jackson.annotation.JsonProperty;
 import org.commonwl.view.WebConfig;
 import org.commonwl.view.WebConfig.Format;
 import org.commonwl.view.cwl.CWLElement;
@@ -32,9 +32,8 @@
 import org.springframework.data.mongodb.core.mapping.Document;
 import org.springframework.format.annotation.DateTimeFormat;
 
-import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
-import com.fasterxml.jackson.annotation.JsonInclude;
-import com.fasterxml.jackson.annotation.JsonProperty;
+import java.util.Date;
+import java.util.Map;
 
 /**
  * Representation of a workflow
@@ -78,7 +77,7 @@ public class Workflow {
     // DOT graph of the contents
     private String visualisationDot;
 
-    private final String permaLinkBase = "https://w3id.org/cwl/view";
+    private static final String PERMANENT_LINK_BASE_URL = "https://w3id.org/cwl/view";
 
 	private String licenseLink;
 
@@ -244,7 +243,7 @@ public String getPermalink() {
      * Permalink for a particular representation of this workflow. Note that
      * resolving the permalink will use the official deployment of the CWL Viewer.
      *
-     * @see {@link https://w3id.org/cwl/view}
+     * @see <a href="https://w3id.org/cwl/view">https://w3id.org/cwl/view</a>
      * @param format
      *            Format of representation, or <code>null</code> for format-neutral
      *            permalink that supports content negotiation.
@@ -263,7 +262,7 @@ public String getPermalink(WebConfig.Format format) {
         if (format != null) {
             formatPart = formatPartSep + "format=" + format.name();
         }
-        return permaLinkBase + "/git/" + lastCommit +
+        return PERMANENT_LINK_BASE_URL + "/git/" + lastCommit +
                 "/" + retrievedFrom.getPath() + packedPart + formatPart;
     }
 
@@ -275,7 +274,7 @@ public String getPermalink(WebConfig.Format format) {
     @JsonProperty(value = "@id", index = 0)
     public String getIdentifier() {
         String packedPart = (retrievedFrom.getPackedId() != null) ? "#" + retrievedFrom.getPackedId() : "";
-        return permaLinkBase + "/git/" + lastCommit + "/" + retrievedFrom.getPath() + packedPart;
+        return PERMANENT_LINK_BASE_URL + "/git/" + lastCommit + "/" + retrievedFrom.getPath() + packedPart;
 
     }
 

src/main/resources/application.properties

@@ -26,6 +26,11 @@ singleFileSizeLimit = 5242880
 # File size limit for the contents of the research object bundle (not counting external links)
 totalFileSizeLimit = 1073741824
 
+# Newer versions of Spring disallow pattern matching like '/workflows/**/*.git/{branch}/**', due
+# to the "No more pattern data allowed after {*...} or ** pattern element" error. This reverts to
+# the old behaviour.
+spring.mvc.pathmatch.matching-strategy=ant_path_matcher
+
 #=======================
 # Git API settings
 #=======================

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

@@ -1,17 +1,25 @@
 package org.commonwl.view.workflow;
 
+import org.commonwl.view.CwlViewerApplication;
 import org.commonwl.view.MongoConfig;
+import org.commonwl.view.WebConfig;
 import org.commonwl.view.git.GitDetails;
 import org.junit.jupiter.api.Test;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.boot.test.autoconfigure.data.mongo.DataMongoTest;
+import org.springframework.boot.test.context.SpringBootTest;
+import org.springframework.test.context.ActiveProfiles;
 import org.springframework.test.context.ContextConfiguration;
 
 import static org.junit.jupiter.api.Assertions.assertNotNull;
 import static org.junit.jupiter.api.Assertions.assertNull;
 
-@DataMongoTest
-@ContextConfiguration(classes={MongoConfig.class})
+// 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
+@SpringBootTest(
+        properties={"spring.mongodb.embedded.version=3.2.2"},
+        classes={MongoConfig.class, WebConfig.class, CwlViewerApplication.class, QueuedWorkflowRepository.class}
+)
 public class QueuedWorkflowRepositoryTest {
 
     @Autowired
@@ -51,4 +59,22 @@ public void deleteQueuedWorkflowByRetrievedFromTest() {
 
     }
 
+    @Test
+    public void deleteQueuedWorkflowByRetrievedFromTest2() {
+        // create stub queued workflow
+        GitDetails gitDetails = new GitDetails("test_repo_url", "test_branch", "test_path");
+        gitDetails.setPackedId("test_packedId");
+
+        Workflow workflow = new Workflow();
+        workflow.setRetrievedFrom(gitDetails);
+
+        QueuedWorkflow queuedWorkflow = new QueuedWorkflow();
+        queuedWorkflow.setTempRepresentation(workflow);
+
+        // save queued workflow
+        repository.save(queuedWorkflow);
+
+        assertNotNull(workflow);
+    }
+
 }