[issue-2375] [issue-2377] Re-enables PermissionTest and SecurityIT tests

pom.xml

@@ -436,6 +436,7 @@
         <version>2.22.2</version>
         <configuration>
           <skipTests>${skipUnitTests}</skipTests>
+          <trimStackTrace>false</trimStackTrace>
         </configuration>
       </plugin>
       <plugin>
@@ -465,12 +466,14 @@
         <version>2.22.2</version>
         <configuration>
           <skipITs>${skipITtests}</skipITs>
+          <trimStackTrace>false</trimStackTrace>
         </configuration>
         <executions>
           <execution>
             <phase>test</phase>
             <goals>
               <goal>integration-test</goal>
+              <goal>verify</goal>
             </goals>
             <configuration>
               <includes>
@@ -583,6 +586,13 @@
         <artifactId>redshift-jdbc42-no-awssdk</artifactId>
         <version>1.2.10.1009</version>
       </dependency>
+			<dependency>
+				<groupId>io.zonky.test.postgres</groupId>
+				<artifactId>embedded-postgres-binaries-bom</artifactId>
+				<version>17.6.0</version>
+				<type>pom</type>
+				<scope>import</scope>
+			</dependency>
     </dependencies>
   </dependencyManagement>
 
@@ -1218,12 +1228,13 @@
       <groupId>org.ehcache</groupId>
       <artifactId>ehcache</artifactId>
       <version>3.9.11</version>
-    </dependency>    <dependency>
-      <groupId>com.opentable.components</groupId>
-      <artifactId>otj-pg-embedded</artifactId>
-      <version>0.13.1</version>
-      <scope>test</scope>
     </dependency>
+		<dependency>
+			<groupId>io.zonky.test</groupId>
+			<artifactId>embedded-postgres</artifactId>
+			<version>2.1.1</version>
+			<scope>test</scope>
+		</dependency>
     <dependency>
       <groupId>org.springframework.boot</groupId>
       <artifactId>spring-boot-starter-test</artifactId>
@@ -2024,5 +2035,53 @@
         </plugins>
       </build>
     </profile>
+		<profile>
+			<id>windows-x86-zonky-postgres</id>
+			<activation>
+				<os>
+					<family>Windows</family>
+					<arch>amd64</arch>
+				</os>
+			</activation>
+			<dependencies>
+				<dependency>
+					<groupId>io.zonky.test.postgres</groupId>
+					<artifactId>embedded-postgres-binaries-windows-amd64</artifactId>
+					<scope>test</scope>
+				</dependency>
+			</dependencies>
+		</profile>
+		<profile>
+			<id>apple-silicon-zonky-postgres</id>
+			<activation>
+				<os>
+					<family>mac</family>
+					<arch>aarch64</arch>
+				</os>
+			</activation>
+			<dependencies>
+				<dependency>
+					<groupId>io.zonky.test.postgres</groupId>
+					<artifactId>embedded-postgres-binaries-darwin-arm64v8</artifactId>
+					<scope>test</scope>
+				</dependency>
+			</dependencies>
+		</profile>
+		<profile>
+			<id>linux-x86-zonky-postgres</id>
+			<activation>
+				<os>
+					<family>unix</family>
+					<arch>amd64</arch>
+				</os>
+			</activation>
+			<dependencies>
+				<dependency>
+					<groupId>io.zonky.test.postgres</groupId>
+					<artifactId>embedded-postgres-binaries-linux-amd64-alpine</artifactId>
+					<scope>test</scope>
+				</dependency>
+			</dependencies>
+		</profile>
   </profiles>
 </project>

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

@@ -31,9 +31,10 @@
 import java.io.IOException;
 import java.sql.Connection;
 import java.sql.SQLException;
+
+import io.zonky.test.db.postgres.embedded.EmbeddedPostgres;
 import org.junit.rules.ExternalResource;
 
-import com.opentable.db.postgres.embedded.EmbeddedPostgres;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 

src/test/java/org/ohdsi/webapi/pathway/PathwayAnalysisTest.java

@@ -42,14 +42,19 @@
 import org.ohdsi.sql.SqlTranslate;
 import org.ohdsi.webapi.AbstractDatabaseTest;
 import org.ohdsi.webapi.job.JobExecutionResource;
+import org.ohdsi.webapi.pathway.converter.PathwayAnalysisToPathwayVersionConverter;
+import org.ohdsi.webapi.pathway.converter.PathwayVersionToPathwayVersionFullDTOConverter;
 import org.ohdsi.webapi.pathway.converter.SerializedPathwayAnalysisToPathwayAnalysisConverter;
 import org.ohdsi.webapi.pathway.domain.PathwayAnalysisEntity;
 import org.ohdsi.webapi.pathway.domain.PathwayAnalysisGenerationEntity;
+import org.ohdsi.webapi.pathway.dto.PathwayAnalysisExportDTO;
 import org.ohdsi.webapi.source.Source;
 import org.ohdsi.webapi.source.SourceDaimon;
 import org.ohdsi.webapi.source.SourceRepository;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Value;
+import org.springframework.core.convert.ConversionService;
+import org.springframework.core.convert.support.DefaultConversionService;
 
 /**
  *
@@ -87,6 +92,9 @@ public class PathwayAnalysisTest extends AbstractDatabaseTest {
   @Autowired
   private PathwayService pathwayService;
 
+	@Autowired
+	private ConversionService conversionService;
+
   @Value("${datasource.ohdsi.schema}")
   private String ohdsiSchema;
 
@@ -110,7 +118,8 @@ public void setUp() throws Exception {
     resetSequence(String.format("%s.%s", ohdsiSchema, "pathway_analysis_sequence"));
     truncateTable(String.format("%s.%s", ohdsiSchema, "generation_cache"));
     prepareCdmSchema();
-    prepareResultSchema();    
+    prepareResultSchema();
+		SerializedPathwayAnalysisToPathwayAnalysisConverter.setConversionService(conversionService);
   }
 
   @After

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

@@ -25,7 +25,6 @@
 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;
@@ -65,7 +64,6 @@ public void setup() {
     ThreadContext.bind(subject);    
   }
 
-//  @Ignore
   @Test
   public void permsTest() throws Exception {
     // need to clear authorization cache before each test
@@ -88,7 +86,6 @@ 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/ITStarter.java

@@ -1,6 +1,6 @@
 package org.ohdsi.webapi.test;
 
-import com.opentable.db.postgres.embedded.EmbeddedPostgres;
+import io.zonky.test.db.postgres.embedded.EmbeddedPostgres;
 import org.apache.shiro.subject.SimplePrincipalCollection;
 import org.apache.shiro.subject.Subject;
 import org.junit.AfterClass;

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

@@ -1,9 +1,12 @@
 package org.ohdsi.webapi.test;
 
 
+import com.github.springtestdbunit.DbUnitTestExecutionListener;
 import com.github.springtestdbunit.annotation.DatabaseOperation;
 import com.github.springtestdbunit.annotation.DatabaseTearDown;
+import com.github.springtestdbunit.annotation.DbUnitConfiguration;
 import com.google.common.collect.ImmutableMap;
+import org.apache.catalina.webresources.TomcatURLStreamHandlerFactory;
 import org.glassfish.jersey.server.model.Parameter;
 import org.glassfish.jersey.server.model.Resource;
 import org.glassfish.jersey.server.model.ResourceMethod;
@@ -12,23 +15,38 @@
 import org.junit.Rule;
 import org.junit.Test;
 import org.junit.rules.ErrorCollector;
+import org.junit.runner.RunWith;
 import org.ohdsi.webapi.JerseyConfig;
+import org.ohdsi.webapi.WebApi;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Value;
+import org.springframework.boot.test.context.SpringBootTest;
 import org.springframework.boot.test.web.client.TestRestTemplate;
 import org.springframework.http.*;
-import org.springframework.test.annotation.DirtiesContext;
+import org.springframework.test.context.ActiveProfiles;
+import org.springframework.test.context.TestExecutionListeners;
+import org.springframework.test.context.TestPropertySource;
+import org.springframework.test.context.junit4.SpringRunner;
 import org.springframework.web.util.UriComponentsBuilder;
 
 import javax.ws.rs.core.MediaType;
+import java.io.IOException;
 import java.net.URI;
 import java.util.*;
 
 import static org.assertj.core.api.Java6Assertions.assertThat;
+import static org.springframework.test.context.TestExecutionListeners.MergeMode.MERGE_WITH_DEFAULTS;
 
+@RunWith(SpringRunner.class)
+@SpringBootTest(classes = {WebApi.class, WebApiIT.DbUnitConfiguration.class}, webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT)
+@ActiveProfiles("test")
+@DbUnitConfiguration(databaseConnection = "dbUnitDatabaseConnection")
+@TestExecutionListeners(value = {DbUnitTestExecutionListener.class}, mergeMode = MERGE_WITH_DEFAULTS)
 @DatabaseTearDown(value = "/database/empty.xml", type = DatabaseOperation.DELETE_ALL)
-public class SecurityIT extends WebApiIT {
+@TestPropertySource(properties = {"security.provider=AtlasRegularSecurity"})
+public class SecurityIT {
 
     private final Map<String, HttpStatus> EXPECTED_RESPONSE_CODES = ImmutableMap.<String, HttpStatus>builder()
             .put("/info/", HttpStatus.OK)
@@ -47,25 +65,26 @@ public class SecurityIT extends WebApiIT {
     @Autowired
     private JerseyConfig jerseyConfig;
 
+    @Value("${baseUri}")
+    private String baseUri;
+
     @Rule
     public ErrorCollector collector = new ErrorCollector();
 
     private final Logger LOG = LoggerFactory.getLogger(SecurityIT.class);
 
     @BeforeClass
-    public static void prepare() {
-
-        System.setProperty("security.provider", "AtlasRegularSecurity");
+    public static void before() throws IOException {
+        TomcatURLStreamHandlerFactory.disable();
+        ITStarter.before();
     }
 
     @AfterClass
-    public static void disableSecurity() {
-
-        System.setProperty("security.provider", "DisabledSecurity");
+    public static void after() {
+        ITStarter.tearDownSubject();
     }
 
     @Test
-    @DirtiesContext(methodMode = DirtiesContext.MethodMode.AFTER_METHOD)
     public void testServiceSecurity() {
 
         Map<String, List<ServiceInfo>> serviceMap = getServiceMap();
@@ -76,7 +95,7 @@ public void testServiceSecurity() {
                     serviceInfo.pathPrefix = "/" + serviceInfo.pathPrefix;
                 }
                 serviceInfo.pathPrefix = serviceInfo.pathPrefix.replaceAll("//", "/");
-                String rawUrl = getBaseUri() + serviceInfo.pathPrefix;
+                String rawUrl = baseUri + serviceInfo.pathPrefix;
                 URI uri = null;
                 try {
                     Map<String, String> parametersMap = prepareParameters(serviceInfo.parameters);
@@ -195,4 +214,4 @@ public String getMessage() {
             return serviceName + ": " + super.getMessage();
         }
     }
-}
+}

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

@@ -1,6 +1,7 @@
 package org.ohdsi.webapi.test;
 
 import static org.junit.Assert.assertEquals;
+import static org.springframework.test.context.TestExecutionListeners.MergeMode.MERGE_WITH_DEFAULTS;
 
 import com.github.springtestdbunit.DbUnitTestExecutionListener;
 import com.github.springtestdbunit.annotation.DbUnitConfiguration;
@@ -9,6 +10,7 @@
 import java.util.Arrays;
 import java.util.Collection;
 
+import com.github.springtestdbunit.bean.DatabaseDataSourceConnectionFactoryBean;
 import com.odysseusinc.arachne.commons.types.DBMSType;
 import com.odysseusinc.arachne.execution_engine_common.api.v1.dto.KerberosAuthMechanism;
 import org.apache.catalina.webresources.TomcatURLStreamHandlerFactory;
@@ -26,21 +28,23 @@
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.boot.test.context.SpringBootTest;
+import org.springframework.boot.test.context.TestConfiguration;
+import org.springframework.context.annotation.Bean;
 import org.springframework.jdbc.core.JdbcTemplate;
 import org.springframework.test.context.TestExecutionListeners;
 import org.springframework.test.context.junit4.SpringRunner;
 import org.springframework.http.HttpStatus;
 import org.springframework.http.ResponseEntity;
 import org.springframework.test.context.ActiveProfiles;
 import org.springframework.boot.test.web.client.TestRestTemplate;
-import org.springframework.test.context.support.DependencyInjectionTestExecutionListener;
-import org.springframework.test.context.support.DirtiesContextTestExecutionListener;
+
+import javax.sql.DataSource;
 
 @RunWith(SpringRunner.class)
-@SpringBootTest(classes = WebApi.class, webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT)
+@SpringBootTest(classes = {WebApi.class, WebApiIT.DbUnitConfiguration.class}, webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT)
 @ActiveProfiles("test")
-@DbUnitConfiguration(databaseConnection = {"primaryDataSource"})
-@TestExecutionListeners({DependencyInjectionTestExecutionListener.class, DbUnitTestExecutionListener.class, DirtiesContextTestExecutionListener.class})
+@DbUnitConfiguration(databaseConnection = "dbUnitDatabaseConnection")
+@TestExecutionListeners(value = {DbUnitTestExecutionListener.class}, mergeMode = MERGE_WITH_DEFAULTS)
 public abstract class WebApiIT {
     protected final Logger log = LoggerFactory.getLogger(getClass());
 
@@ -68,6 +72,15 @@ public abstract class WebApiIT {
             "/ddl/results/achilles_result_concept_count.sql"
     );
 
+		@TestConfiguration
+		public static class DbUnitConfiguration {
+			@Bean
+			DatabaseDataSourceConnectionFactoryBean dbUnitDatabaseConnection(DataSource primaryDataSource) {
+				DatabaseDataSourceConnectionFactoryBean dbUnitDatabaseConnection = new DatabaseDataSourceConnectionFactoryBean(primaryDataSource);
+				dbUnitDatabaseConnection.setSchema("public");
+				return dbUnitDatabaseConnection;
+			}
+		}
 
     @Value("${baseUri}")
     private String baseUri;