test: refactor so tests start quicker and there is a 'testFast' optio…

…n to skip slow tests (#2498)

* test: refactor so tests start quicker and there is a 'testFast' option to skip slow tests

* Update dev_quickstart.md

* fix code smells

* fix code smells

* fix dealing with 'v' to without

* typo

* remove changes to wrong branch

backend/build.gradle

@@ -95,12 +95,26 @@ subprojects {
         test.outputs.upToDateWhen { false }
     }
 
-    //enable environment variables to be set by test
-    tasks.test {
+    test {
         jvmArgs("--add-opens=java.base/java.util=ALL-UNNAMED")
+        useJUnitPlatform ()
+        failFast true
+        testLogging {
+            events "passed", "skipped", "failed" //, "standardOut", "standardError"
+
+            showExceptions true
+            exceptionFormat "full"
+            showCauses true
+            showStackTraces true
+
+            showStandardStreams = false
+        }
     }
-    test {
-        useJUnitPlatform()
+    tasks.register('testFast', Test)  {
+        jvmArgs("--add-opens=java.base/java.util=ALL-UNNAMED")
+        useJUnitPlatform {
+            excludeTags "slow"
+        }
         failFast true
         testLogging {
             events "passed", "skipped", "failed" //, "standardOut", "standardError"

backend/molgenis-emx2-datamodels/src/test/java/org/molgenis/emx2/datamodels/TestLoaders.java

@@ -7,13 +7,15 @@
 
 import org.junit.jupiter.api.BeforeAll;
 import org.junit.jupiter.api.MethodOrderer;
+import org.junit.jupiter.api.Tag;
 import org.junit.jupiter.api.Test;
 import org.junit.jupiter.api.TestMethodOrder;
 import org.molgenis.emx2.Database;
 import org.molgenis.emx2.Schema;
 import org.molgenis.emx2.sql.TestDatabaseFactory;
 
 @TestMethodOrder(MethodOrderer.MethodName.class)
+@Tag("slow")
 public class TestLoaders {
   public static final String COHORT_STAGING = "CohortStaging";
   public static final String NETWORK_STAGING = "NetworkStaging";

backend/molgenis-emx2-io/src/test/java/org/molgenis/emx2/io/TestColumnTypeIsFile.java

@@ -10,6 +10,7 @@
 import java.nio.file.Files;
 import java.nio.file.Path;
 import org.junit.jupiter.api.BeforeAll;
+import org.junit.jupiter.api.Tag;
 import org.junit.jupiter.api.Test;
 import org.molgenis.emx2.*;
 import org.molgenis.emx2.datamodels.PetStoreLoader;
@@ -18,6 +19,7 @@
 import org.molgenis.emx2.io.tablestore.TableStoreForXlsxFile;
 import org.molgenis.emx2.sql.TestDatabaseFactory;
 
+@Tag("slow")
 public class TestColumnTypeIsFile {
 
   private static final String SCHEMA_NAME = "TestColumnTypeIsFile";

backend/molgenis-emx2-io/src/test/java/org/molgenis/emx2/io/TestExcelStore.java

@@ -7,10 +7,12 @@
 import java.nio.file.Path;
 import java.util.ArrayList;
 import java.util.List;
+import org.junit.jupiter.api.Tag;
 import org.junit.jupiter.api.Test;
 import org.molgenis.emx2.Row;
 import org.molgenis.emx2.io.tablestore.TableStoreForXlsxFile;
 
+@Tag("slow")
 public class TestExcelStore {
 
   @Test

backend/molgenis-emx2-io/src/test/java/org/molgenis/emx2/io/TestImportExportAllExamples.java

@@ -3,6 +3,7 @@
 import java.io.IOException;
 import java.util.List;
 import org.junit.jupiter.api.BeforeAll;
+import org.junit.jupiter.api.Tag;
 import org.junit.jupiter.api.Test;
 import org.molgenis.emx2.*;
 import org.molgenis.emx2.datamodels.PetStoreLoader;
@@ -14,6 +15,7 @@
 import org.molgenis.emx2.io.emx2.Emx2;
 import org.molgenis.emx2.sql.TestDatabaseFactory;
 
+@Tag("slow")
 public class TestImportExportAllExamples {
 
   static Database db;

backend/molgenis-emx2-io/src/test/java/org/molgenis/emx2/io/TestImportExportEmx2MetadataIODataAndMetadata.java

@@ -6,6 +6,7 @@
 import java.nio.file.Path;
 import java.util.Comparator;
 import org.junit.jupiter.api.BeforeAll;
+import org.junit.jupiter.api.Tag;
 import org.junit.jupiter.api.Test;
 import org.molgenis.emx2.Database;
 import org.molgenis.emx2.Schema;
@@ -14,6 +15,7 @@
 import org.molgenis.emx2.sql.TestDatabaseFactory;
 import org.molgenis.emx2.utils.StopWatch;
 
+@Tag("slow")
 public class TestImportExportEmx2MetadataIODataAndMetadata {
 
   static Database database;

backend/molgenis-emx2-io/src/test/java/org/molgenis/emx2/io/TestLegacyImport.java

@@ -6,6 +6,7 @@
 import java.io.File;
 import java.util.List;
 import org.junit.jupiter.api.BeforeAll;
+import org.junit.jupiter.api.Tag;
 import org.junit.jupiter.api.Test;
 import org.molgenis.emx2.Database;
 import org.molgenis.emx2.Row;
@@ -15,6 +16,7 @@
 import org.molgenis.emx2.io.tablestore.TableStoreForCsvInZipFile;
 import org.molgenis.emx2.sql.TestDatabaseFactory;
 
+@Tag("slow")
 public class TestLegacyImport {
   static Database db;
 

backend/molgenis-emx2-io/src/test/java/org/molgenis/emx2/io/TestReadWriteStores.java

@@ -14,13 +14,15 @@
 import java.util.UUID;
 import java.util.stream.Collectors;
 import java.util.stream.StreamSupport;
+import org.junit.jupiter.api.Tag;
 import org.junit.jupiter.api.Test;
 import org.molgenis.emx2.MolgenisException;
 import org.molgenis.emx2.Row;
 import org.molgenis.emx2.datamodels.util.CompareTools;
 import org.molgenis.emx2.io.tablestore.*;
 import org.molgenis.emx2.utils.StopWatch;
 
+@Tag("slow")
 public class TestReadWriteStores {
   @Test
   public void testCsvDirectoryStore() throws IOException {

backend/molgenis-emx2-semantics/src/test/java/org/molgenis/emx2/semantics/LinkedDataServiceTest.java

@@ -7,6 +7,7 @@
 import java.io.StringWriter;
 import java.nio.file.Path;
 import org.junit.jupiter.api.BeforeAll;
+import org.junit.jupiter.api.Tag;
 import org.junit.jupiter.api.Test;
 import org.molgenis.emx2.Database;
 import org.molgenis.emx2.Schema;
@@ -16,6 +17,7 @@
 import org.molgenis.emx2.sql.TestDatabaseFactory;
 import org.molgenis.emx2.utils.StopWatch;
 
+@Tag("slow")
 public class LinkedDataServiceTest {
 
   static Database database;

backend/molgenis-emx2-semantics/src/test/java/org/molgenis/emx2/semantics/beaconv2/Beaconv2_EntryTypesTest.java

@@ -5,11 +5,13 @@
 import static org.mockito.Mockito.mock;
 import static org.mockito.Mockito.when;
 
+import org.junit.jupiter.api.Tag;
 import org.junit.jupiter.api.Test;
 import org.molgenis.emx2.beaconv2.endpoints.EntryTypes;
 import org.molgenis.emx2.json.JsonUtil;
 import spark.Request;
 
+@Tag("slow")
 public class Beaconv2_EntryTypesTest {
 
   @Test

backend/molgenis-emx2-semantics/src/test/java/org/molgenis/emx2/semantics/beaconv2/Beaconv2_ModelEndpointsTest.java

@@ -7,6 +7,7 @@
 import com.fasterxml.jackson.core.JsonProcessingException;
 import java.util.List;
 import org.junit.jupiter.api.BeforeAll;
+import org.junit.jupiter.api.Tag;
 import org.junit.jupiter.api.Test;
 import org.molgenis.emx2.Database;
 import org.molgenis.emx2.Schema;
@@ -19,6 +20,7 @@
 import spark.Request;
 import spark.Response;
 
+@Tag("slow")
 public class Beaconv2_ModelEndpointsTest {
 
   static Database database;

backend/molgenis-emx2-semantics/src/test/java/org/molgenis/emx2/semantics/fairdatapoint/FAIRDataPointBadDistributionInDatasetTest.java

@@ -7,6 +7,7 @@
 import java.util.HashMap;
 import java.util.Map;
 import org.junit.jupiter.api.BeforeAll;
+import org.junit.jupiter.api.Tag;
 import org.junit.jupiter.api.Test;
 import org.molgenis.emx2.*;
 import org.molgenis.emx2.datamodels.FAIRDataHubLoader;
@@ -22,6 +23,7 @@
  * invalidate the overarching FDP Catalog, which must have 1+ datasets. But since this is a 'dataset
  * problem', we leave it at that level.
  */
+@Tag("slow")
 public class FAIRDataPointBadDistributionInDatasetTest {
 
   static Database database;

backend/molgenis-emx2-semantics/src/test/java/org/molgenis/emx2/semantics/fairdatapoint/FAIRDataPointDistributionNotInDatasetTest.java

@@ -6,6 +6,7 @@
 import static org.mockito.Mockito.when;
 
 import org.junit.jupiter.api.BeforeAll;
+import org.junit.jupiter.api.Tag;
 import org.junit.jupiter.api.Test;
 import org.molgenis.emx2.Database;
 import org.molgenis.emx2.Schema;
@@ -18,6 +19,7 @@
  * FDP Distribution must be referenced as a table name by at least 1 FDP Dataset. If not, this
  * Distribution should not be presented.
  */
+@Tag("slow")
 public class FAIRDataPointDistributionNotInDatasetTest {
 
   static Database database;

backend/molgenis-emx2-semantics/src/test/java/org/molgenis/emx2/semantics/fairdatapoint/FAIRDataPointTest.java

@@ -6,6 +6,7 @@
 import static org.molgenis.emx2.fairdatapoint.FormatMimeTypes.formatToMediaType;
 
 import org.junit.jupiter.api.BeforeAll;
+import org.junit.jupiter.api.Tag;
 import org.junit.jupiter.api.Test;
 import org.molgenis.emx2.Database;
 import org.molgenis.emx2.Schema;
@@ -17,6 +18,7 @@
 import org.molgenis.emx2.sql.TestDatabaseFactory;
 import spark.Request;
 
+@Tag("slow")
 public class FAIRDataPointTest {
 
   static Database database;

backend/molgenis-emx2-semantics/src/test/java/org/molgenis/emx2/semantics/graphgenome/GraphGenomeTest.java

@@ -9,6 +9,7 @@
 import java.io.OutputStream;
 import java.util.List;
 import org.junit.jupiter.api.BeforeAll;
+import org.junit.jupiter.api.Tag;
 import org.junit.jupiter.api.Test;
 import org.molgenis.emx2.Database;
 import org.molgenis.emx2.Schema;
@@ -18,6 +19,7 @@
 import spark.Request;
 import spark.Response;
 
+@Tag("slow")
 public class GraphGenomeTest {
 
   static Database database;

backend/molgenis-emx2-sql/src/test/java/org/molgenis/emx2/sql/ChangeLogUtilsTest.java → backend/molgenis-emx2-sql-it/src/test/java/org/molgenis/emx2/sql/ChangeLogUtilsTest.java

@@ -4,9 +4,9 @@
 
 import org.junit.jupiter.api.Test;
 
-public class ChangeLogUtilsTest {
+class ChangeLogUtilsTest {
   @Test
-  public void testBuildProcessAuditFunction() {
+  void testBuildProcessAuditFunction() {
     String expectedFunction =
         """
                         CREATE OR REPLACE FUNCTION "pet store"."process_Pet_audit"() RETURNS TRIGGER AS $Pet_audit$
@@ -31,7 +31,7 @@ public void testBuildProcessAuditFunction() {
   }
 
   @Test
-  public void testBuildAuditTrigger() {
+  void testBuildAuditTrigger() {
     String expectedTrigger =
         """
                         CREATE TRIGGER Pet_audit
@@ -43,7 +43,7 @@ public void testBuildAuditTrigger() {
   }
 
   @Test
-  public void testBuildAuditTriggerWithSpaceInTableName() {
+  void testBuildAuditTriggerWithSpaceInTableName() {
     String expectedTrigger =
         """
                         CREATE TRIGGER My_pets_audit
@@ -55,14 +55,14 @@ public void testBuildAuditTriggerWithSpaceInTableName() {
   }
 
   @Test
-  public void testRemoveProcessAuditFunction() {
+  void testRemoveProcessAuditFunction() {
     assertEquals(
         "DROP FUNCTION IF EXISTS \"my schema\".\"process_my_table_audit\"() CASCADE",
         ChangeLogUtils.buildProcessAuditFunctionRemove("my schema", "my table").strip());
   }
 
   @Test
-  public void testRemoveAuditTrigger() {
+  void testRemoveAuditTrigger() {
     assertEquals(
         "DROP TRIGGER IF EXISTS my_table_audit ON \"my schema\".\"my table\" CASCADE",
         ChangeLogUtils.buildAuditTriggerRemove("my schema", "my table").strip());

backend/molgenis-emx2-sql/src/test/java/org/molgenis/emx2/sql/SqlSchemaTest.java → backend/molgenis-emx2-sql-it/src/test/java/org/molgenis/emx2/sql/SqlSchemaTest.java

@@ -4,10 +4,13 @@
 import static org.mockito.Mockito.mock;
 import static org.mockito.Mockito.when;
 
+import org.junit.jupiter.api.Tag;
 import org.junit.jupiter.api.Test;
 import org.mockito.Mock;
 import org.molgenis.emx2.MolgenisException;
 
+@Tag("slow")
+// todo move to sql
 class SqlSchemaTest {
   @Mock SqlDatabase db;
   @Mock SqlSchemaMetadata metadata;

backend/molgenis-emx2-sql-it/src/test/java/org/molgenis/emx2/sql/TestBatchRequestsForSpeed.java

@@ -10,10 +10,12 @@
 import java.util.ArrayList;
 import java.util.List;
 import org.junit.jupiter.api.BeforeAll;
+import org.junit.jupiter.api.Tag;
 import org.junit.jupiter.api.Test;
 import org.molgenis.emx2.*;
 import org.molgenis.emx2.utils.StopWatch;
 
+@Tag("slow")
 public class TestBatchRequestsForSpeed {
   private static Database db;
 

backend/molgenis-emx2-sql-it/src/test/java/org/molgenis/emx2/sql/TestComputedValue.java

@@ -5,12 +5,14 @@
 import static org.molgenis.emx2.TableMetadata.table;
 
 import org.junit.jupiter.api.BeforeAll;
+import org.junit.jupiter.api.Tag;
 import org.junit.jupiter.api.Test;
 import org.molgenis.emx2.Database;
 import org.molgenis.emx2.Row;
 import org.molgenis.emx2.Schema;
 import org.molgenis.emx2.Table;
 
+@Tag("slow")
 public class TestComputedValue {
   static Database db;
   static Schema schema;

backend/molgenis-emx2-sql/src/test/java/org/molgenis/emx2/sql/InitTestDatabaseAndRunNonParallelTests.java

@@ -12,25 +12,27 @@
 import java.util.Collections;
 import java.util.List;
 import org.jooq.DSLContext;
-import org.junit.jupiter.api.BeforeAll;
+import org.junit.jupiter.api.Tag;
 import org.junit.jupiter.api.Test;
 import org.molgenis.emx2.Database;
 import org.molgenis.emx2.Schema;
 
-public class InitTestDatabaseAndRunNonParallelTests {
+class InitTestDatabaseAndRunNonParallelTests {
 
-  @BeforeAll
-  public static void createDatabase() {
+  @Test
+  void createDatabase() {
     // we want this run only once and NOT parallel for total test suite
     // AND we want run all other tests in parallel
     // so tests are in molgenis-emx2-sql-it ('integration test')
     // and 'init' only happens once, here
+    System.out.println("INITIALIZING DATABASE");
     Database db = new SqlDatabase(true);
     assertTrue(db.getDatabaseVersion() > 0);
   }
 
   @Test
-  public void testMigration2() {
+  @Tag("slow")
+  void testMigration2() {
     SqlDatabase database = (SqlDatabase) TestDatabaseFactory.getTestDatabase();
     database.dropCreateSchema("TestMigrations");
 

backend/molgenis-emx2-tasks/src/test/java/org/molgenis/emx2/tasks/TestScriptTask.java

@@ -5,8 +5,10 @@
 import static org.molgenis.emx2.tasks.TaskStatus.COMPLETED;
 import static org.molgenis.emx2.tasks.TaskStatus.ERROR;
 
+import org.junit.jupiter.api.Tag;
 import org.junit.jupiter.api.Test;
 
+@Tag("slow")
 public class TestScriptTask {
 
   @Test

backend/molgenis-emx2-tasks/src/test/java/org/molgenis/emx2/tasks/TestTask.java

@@ -2,8 +2,10 @@
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
 
+import org.junit.jupiter.api.Tag;
 import org.junit.jupiter.api.Test;
 
+@Tag("slow")
 public class TestTask {
 
   @Test