Fix: reinstate tests (#2368)

* fix: reinstate tests

* tmp: skip broken CohortCharacterizationServiceTest tests

This allows the other tests to be reinstated while these two
can then be fixed separately.

* tmp: skip broken PermissionTest tests

This allows the other tests to be reinstated while these two
can then be fixed separately.

* tmp: skip broken StudyInfoTest

...this one seems to only work depending on the order of execution...
it lacks the setup() method where a pre-filled db is guaranteed, like
for example in CohortCharacterizationServiceTest

* fix: mark abstract class as abstract

Author: pieterlukasse

.github/workflows/ci.yaml

@@ -43,8 +43,7 @@ jobs:
         run: mvn -B -DskipTests=true -DskipUnitTests=true -P${{ env.MAVEN_PROFILE }} package
 
       - name: Test
-        # Skipping unit and integration tests for now, because they keep failing.
-        run: mvn -B -DskipUnitTests=true -DskipITtests=true -P${{ env.MAVEN_PROFILE }} test
+        run: mvn -B -P${{ env.MAVEN_PROFILE }} test
 
   # Check that the docker image builds correctly
   # Push to ohdsi/atlas:master for commits on master.

src/test/java/org/ohdsi/webapi/cohortcharacterization/CohortCharacterizationServiceTest.java

@@ -8,6 +8,7 @@
 import net.lingala.zip4j.exception.ZipException;
 import org.apache.commons.lang3.builder.ToStringBuilder;
 import org.junit.Before;
+import org.junit.Ignore;
 import org.junit.Test;
 import org.ohdsi.analysis.Utils;
 import org.ohdsi.circe.helper.ResourceHelper;
@@ -100,11 +101,13 @@ public void setUp() throws Exception {
         prepareResultSchema();
     }
 
+    @Ignore
     @Test
     public void testExportGeneration() throws Exception {
         doTestExportGeneration(CC_JSON, PARAM_JSON);
     }
 
+    @Ignore
     @Test
     public void testExportGenerationWithStrata() throws Exception {
         doTestExportGeneration(CC_WITH_STRATA_JSON, PARAM_JSON_WITH_STRATA);

src/test/java/org/ohdsi/webapi/security/PermissionTest.java

@@ -25,6 +25,7 @@
 import static org.junit.Assert.assertFalse;
 import static org.junit.Assert.assertTrue;
 import org.junit.Before;
+import org.junit.Ignore;
 import org.junit.Test;
 import org.ohdsi.webapi.AbstractDatabaseTest;
 import org.ohdsi.webapi.shiro.PermissionManager;
@@ -64,6 +65,7 @@ public void setup() {
     ThreadContext.bind(subject);    
   }
 
+  @Ignore
   @Test
   public void permsTest() throws Exception {
     // need to clear authorization cache before each test
@@ -86,6 +88,7 @@ public void permsTest() throws Exception {
 
   }
 
+  @Ignore
   @Test
   public void wildcardTest() throws Exception {
     // need to clear authorization cache before each test

src/test/java/org/ohdsi/webapi/test/WebApiIT.java

@@ -41,7 +41,7 @@
 @ActiveProfiles("test")
 @DbUnitConfiguration(databaseConnection = {"primaryDataSource"})
 @TestExecutionListeners({DependencyInjectionTestExecutionListener.class, DbUnitTestExecutionListener.class, DirtiesContextTestExecutionListener.class})
-public class WebApiIT {
+public abstract class WebApiIT {
     protected final Logger log = LoggerFactory.getLogger(getClass());
 
     protected final String SOURCE_KEY = "Embedded_PG";

src/test/java/org/ohdsi/webapi/test/feasibility/StudyInfoTest.java

@@ -17,6 +17,8 @@
 
 import javax.persistence.EntityManager;
 import javax.persistence.PersistenceContext;
+
+import org.junit.Ignore;
 import org.junit.Test;
 import org.ohdsi.webapi.AbstractDatabaseTest;
 import org.ohdsi.webapi.feasibility.FeasibilityStudy;
@@ -48,6 +50,7 @@ public class StudyInfoTest extends AbstractDatabaseTest {
   @PersistenceContext
   protected EntityManager entityManager;
 
+  @Ignore
   @Test
   @Transactional(transactionManager="transactionManager")
   public void testStudyCRUD() {