Feature/seqware 1905 workflow job hierarchy (#341)

* Fix attachment of batched provisioned-in jobs

* Properly separate out long tests into new profile

* More test moving to long profile

Author: denis-yuen

README.md

@@ -94,6 +94,8 @@ When this is complete:
 (This runs all unit tests and integration tests that only require postgres as a prerequisite)
     mvn clean install -DskipITs=false -P extITs,embeddedTomcat
 (runs all unit tests and all integration tests including those that require Oozie)
+    mvn clean install -DskipITs=false -P allITs,embeddedTomcat
+(runs all unit tests and all integration tests including those that require Oozie or take longer than can fix on Travis-CI)
 
 In the last case, the extended integration tests profile is used to trigger integration tests that run our command line utilities. 
 In order to point your command-line tools at the web service brought up by the integration tests, you will need to comment out your crontab and modify your SeqWare ~/.seqware/settings to include:
@@ -112,11 +114,11 @@ It is possible to disable our embedded tomcat instance and run against both a re
     EXTENDED_TEST_DB_USER=seqware
     EXTENDED_TEST_DB_PASSWORD=seqware
 
-Then set your SW_REST_URL to the web service that uses the above database and invoke the following command. Note that you will need to deploy the seqware-webservice war yourself. 
+Then set your SW\_REST\_URL to the web service that uses the above database and invoke the following command. Note that you will need to deploy the seqware-webservice war yourself. 
 
     mvn clean install -DskipITs=false -P 'extITs,!embeddedTomcat'
 
-Alternatively, if you wish to still use an embedded tomcat instance for testing, modify the properties at the beginning of your seqware-webservice/pom.xml to match the above databases and invoke the integration tests with your SW_REST_URL set to http://localhost:8889/seqware-webservice
+Alternatively, if you wish to still use an embedded tomcat instance for testing, modify the properties at the beginning of your seqware-webservice/pom.xml to match the above databases and invoke the integration tests with your SW\_REST\_URL set to http://localhost:8889/seqware-webservice
 
     mvn clean install -DskipITs=false -P extITs,embeddedTomcat
 

seqware-ext-testing/pom.xml

@@ -217,6 +217,8 @@
 
     <profiles>
         <profile>
+            <!-- run integration tests (IT) that require postgres and tomcat -->
+            <!-- run extended integration tests (ET) that require Oozie -->
             <id>extITs</id>
             <build>
                 <plugins>
@@ -237,6 +239,32 @@
                 </plugins>
             </build>
         </profile>
+        <profile>
+            <!-- run integration tests (IT) that require postgres and tomcat -->
+            <!-- run extended integration tests (ET) that require Oozie -->
+            <!-- run long integration tests (LT) that take more time than can be provided by Travis-CI -->
+            <id>allITs</id>
+            <build>
+                <plugins>
+                    <plugin>
+                        <groupId>org.apache.maven.plugins</groupId>
+                        <artifactId>maven-failsafe-plugin</artifactId>
+                        <version>${maven-failsafe-plugin.version}</version>
+
+                        <configuration>
+                            <includes>
+                                <include>**/IT*.java</include>
+                                <include>**/*IT.java</include>
+                                <include>**/ET*.java</include>
+                                <include>**/*ET.java</include>
+                                <include>**/LT*.java</include>
+                                <include>**/*LT.java</include>
+                            </includes>
+                        </configuration>
+                    </plugin>
+                </plugins>
+            </build>
+        </profile>
         <profile>
             <id>embeddedTomcat</id>
             <build>

seqware-ext-testing/src/test/java/io/seqware/pipeline/whitestar/WhiteStarTest.java renamed to seqware-ext-testing/src/test/java/io/seqware/pipeline/whitestar/WhiteStarLT.java

@@ -27,7 +27,6 @@
 import org.junit.AfterClass;
 import org.junit.Assert;
 import org.junit.BeforeClass;
-import org.junit.Ignore;
 import org.junit.Rule;
 import org.junit.Test;
 import org.junit.contrib.java.lang.system.ExpectedSystemExit;
@@ -45,7 +44,7 @@
  *
  * @author dyuen
  */
-public class WhiteStarTest {
+public class WhiteStarLT {
 
     @Rule
     public final ExpectedSystemExit exit = ExpectedSystemExit.none();
@@ -61,7 +60,6 @@ public static void teardownWhiteStarTest() {
     }
 
     @Test
-    @Ignore("see https://github.com/SeqWare/seqware/issues/324")
     public void testWhiteStarStandardWorkflow() throws Exception {
         Path createTempFile = createSettingsFile("whitestar", "inmemory");
         createAndRunWorkflow(createTempFile, false);
@@ -74,7 +72,7 @@ public void testWhiteStarParallelWorkflow() throws Exception {
         createAndRunWorkflow(createTempFile, false);
     }
 
-    protected static void createAndRunWorkflow(Path settingsFile, boolean metadata) throws Exception, IOException {
+    static void createAndRunWorkflow(Path settingsFile, boolean metadata) throws Exception {
         // create a helloworld
         Path tempDir = Files.createTempDirectory("tempTestingDirectory");
         PluginRunner it = new PluginRunner();
@@ -122,7 +120,7 @@ protected static void createAndRunWorkflow(Path settingsFile, boolean metadata)
 
     }
 
-    protected static Path createSettingsFile(String engine, String metadataMethod) throws IOException {
+    static Path createSettingsFile(String engine, String metadataMethod) throws IOException {
         // override seqware settings file
         List<String> whiteStarProperties = new ArrayList<>();
         whiteStarProperties.add("SW_METADATA_METHOD=" + metadataMethod);

seqware-ext-testing/src/test/java/io/seqware/pipeline/whitestar/WhiteStarMetadataET.java renamed to seqware-ext-testing/src/test/java/io/seqware/pipeline/whitestar/WhiteStarMetadataLT.java

@@ -16,19 +16,20 @@
  */
 package io.seqware.pipeline.whitestar;
 
-import java.nio.file.Path;
 import org.junit.AfterClass;
 import org.junit.BeforeClass;
 import org.junit.Rule;
 import org.junit.Test;
 import org.junit.contrib.java.lang.system.ExpectedSystemExit;
 
+import java.nio.file.Path;
+
 /**
  * Run a helloworld using whitestar.
  *
  * @author dyuen
  */
-public class WhiteStarMetadataET {
+public class WhiteStarMetadataLT {
 
     @Rule
     public final ExpectedSystemExit exit = ExpectedSystemExit.none();
@@ -45,20 +46,20 @@ public static void teardownWhiteStarTest() {
 
     @Test
     public void testWhiteStarSGEWorkflow() throws Exception {
-        Path createTempFile = WhiteStarTest.createSettingsFile("whitestar-sge", "webservice");
-        WhiteStarTest.createAndRunWorkflow(createTempFile, true);
+        Path createTempFile = WhiteStarLT.createSettingsFile("whitestar-sge", "webservice");
+        WhiteStarLT.createAndRunWorkflow(createTempFile, true);
     }
 
     @Test
     public void testWhiteStarParallelWorkflowWithMetadata() throws Exception {
-        Path createTempFile = WhiteStarTest.createSettingsFile("whitestar-parallel", "webservice");
-        WhiteStarTest.createAndRunWorkflow(createTempFile, true);
+        Path createTempFile = WhiteStarLT.createSettingsFile("whitestar-parallel", "webservice");
+        WhiteStarLT.createAndRunWorkflow(createTempFile, true);
     }
 
     @Test
     public void testWhiteStarWorkflowWithMetadata() throws Exception {
-        Path createTempFile = WhiteStarTest.createSettingsFile("whitestar-parallel", "webservice");
-        WhiteStarTest.createAndRunWorkflow(createTempFile, true);
+        Path createTempFile = WhiteStarLT.createSettingsFile("whitestar-parallel", "webservice");
+        WhiteStarLT.createAndRunWorkflow(createTempFile, true);
     }
 
 }

seqware-ext-testing/src/test/java/net/sourceforge/seqware/pipeline/cli_tutorial/CLIAdminTutorialSuiteET.java renamed to seqware-ext-testing/src/test/java/net/sourceforge/seqware/pipeline/cli_tutorial/CLIAdminTutorialSuiteLT.java

@@ -29,7 +29,7 @@
  */
 @RunWith(Suite.class)
 @Suite.SuiteClasses(value = { CLIAdminPhase1.class })
-public class CLIAdminTutorialSuiteET extends TutorialSuite {
+public class CLIAdminTutorialSuiteLT extends TutorialSuite {
     @BeforeClass
     public static void resetDatabase() {
         ExtendedTestDatabaseCreator.resetDatabaseWithUsers();

seqware-ext-testing/src/test/java/net/sourceforge/seqware/pipeline/cli_tutorial/CLIDeveloperTutorialSuiteET.java renamed to seqware-ext-testing/src/test/java/net/sourceforge/seqware/pipeline/cli_tutorial/CLIDeveloperTutorialSuiteLT.java

@@ -17,10 +17,10 @@
 
 package net.sourceforge.seqware.pipeline.cli_tutorial;
 
-import net.sourceforge.seqware.pipeline.tutorial.*;
 import net.sourceforge.seqware.pipeline.plugins.ExtendedTestDatabaseCreator;
+import net.sourceforge.seqware.pipeline.tutorial.DeveloperPhase1;
+import net.sourceforge.seqware.pipeline.tutorial.TutorialSuite;
 import org.junit.BeforeClass;
-import org.junit.Ignore;
 import org.junit.runner.RunWith;
 import org.junit.runners.Suite;
 
@@ -34,10 +34,9 @@
  * @author dyuen
  */
 
-@Ignore("see https://github.com/SeqWare/seqware/issues/324")
 @RunWith(Suite.class)
 @Suite.SuiteClasses(value = { DeveloperPhase1.class, CLIDeveloperPhase2.class })
-public class CLIDeveloperTutorialSuiteET extends TutorialSuite {
+public class CLIDeveloperTutorialSuiteLT extends TutorialSuite {
     @BeforeClass
     public static void resetDatabase() {
         ExtendedTestDatabaseCreator.resetDatabaseWithUsers();

seqware-ext-testing/src/test/java/net/sourceforge/seqware/pipeline/cli_tutorial/CLIUserTutorialSuiteET.java renamed to seqware-ext-testing/src/test/java/net/sourceforge/seqware/pipeline/cli_tutorial/CLIUserTutorialSuiteLT.java

@@ -30,7 +30,7 @@
 @RunWith(Suite.class)
 @Suite.SuiteClasses(value = { CLIUserPhase1.class, CLIUserPhase2.class, CLIUserPhase3.class, CLIUserPhase4.class, CLIUserPhase5.class,
         CLIUserPhase6.class })
-public class CLIUserTutorialSuiteET extends TutorialSuite {
+public class CLIUserTutorialSuiteLT extends TutorialSuite {
     @BeforeClass
     public static void resetDatabase() {
         ExtendedTestDatabaseCreator.resetDatabaseWithUsers();

seqware-ext-testing/src/test/java/net/sourceforge/seqware/pipeline/debugging_tutorial/DebugWorkflowTutorialET.java renamed to seqware-ext-testing/src/test/java/net/sourceforge/seqware/pipeline/debugging_tutorial/DebugWorkflowTutorialLT.java

@@ -23,7 +23,6 @@
 import net.sourceforge.seqware.pipeline.plugins.ExtendedTestDatabaseCreator;
 import net.sourceforge.seqware.pipeline.plugins.ITUtility;
 import org.junit.Assert;
-import org.junit.Ignore;
 import org.junit.Test;
 
 import java.io.File;
@@ -36,10 +35,9 @@
  *
  * @author dyuen
  */
-public class DebugWorkflowTutorialET {
+public class DebugWorkflowTutorialLT {
 
     @Test
-    @Ignore("see https://github.com/SeqWare/seqware/issues/324")
     public void runThroughFirstFailAtLaunchTutorial() throws IOException {
         // here we test that the first error is properly propagated into the database and reported
         ExtendedTestDatabaseCreator.resetDatabaseWithUsers(false);
@@ -60,7 +58,7 @@ public void runThroughFirstFailAtLaunchTutorial() throws IOException {
         Log.info(genOutput);
 
         // Replace contents of WorkflowClient from both workflows with code from tutorial
-        String tarTemplatePath = DebugWorkflowTutorialET.class.getResource("FailLaunch.template").getPath();
+        String tarTemplatePath = DebugWorkflowTutorialLT.class.getResource("FailLaunch.template").getPath();
         // determine existing file paths
         File tarTarget = new File(tempDir, "BuggyWorkflow/src/main/java/com/github/seqware/BuggyWorkflowWorkflow.java");
 
@@ -82,7 +80,6 @@ public void runThroughFirstFailAtLaunchTutorial() throws IOException {
     }
 
     @Test
-    @Ignore("see https://github.com/SeqWare/seqware/issues/324")
     public void runThroughFirstFailAtRuntimeTutorial() throws IOException {
         // here we test that the first error is properly propagated into the database and reported
         ExtendedTestDatabaseCreator.resetDatabaseWithUsers(false);
@@ -103,7 +100,7 @@ public void runThroughFirstFailAtRuntimeTutorial() throws IOException {
         Log.info(genOutput);
 
         // Replace contents of WorkflowClient from both workflows with code from tutorial
-        String tarTemplatePath = DebugWorkflowTutorialET.class.getResource("FailRun.template").getPath();
+        String tarTemplatePath = DebugWorkflowTutorialLT.class.getResource("FailRun.template").getPath();
         // determine existing file paths
         File tarTarget = new File(tempDir, "BuggyWorkflow/src/main/java/com/github/seqware/BuggyWorkflowWorkflow.java");
 

seqware-ext-testing/src/test/java/net/sourceforge/seqware/pipeline/decider_tutorial/BasicDeciderTutorialET.java renamed to seqware-ext-testing/src/test/java/net/sourceforge/seqware/pipeline/decider_tutorial/BasicDeciderTutorialLT.java

@@ -18,33 +18,32 @@
 
 import com.google.common.io.Files;
 import io.seqware.cli.Main;
-import java.io.File;
-import java.io.IOException;
 import net.sourceforge.seqware.common.module.ReturnValue;
 import net.sourceforge.seqware.common.util.Log;
 import net.sourceforge.seqware.pipeline.plugins.ExtendedTestDatabaseCreator;
 import net.sourceforge.seqware.pipeline.plugins.ITUtility;
 import org.junit.Assert;
 import org.junit.BeforeClass;
-import org.junit.Ignore;
 import org.junit.Test;
 
+import java.io.File;
+import java.io.IOException;
+
 /**
  * These tests support the tutorial for BasicDeciders
  *
  * Causes issues with Travis-CI?
  * 
  * @author dyuen
  */
-public class BasicDeciderTutorialET {
+public class BasicDeciderTutorialLT {
 
     @BeforeClass
     public static void resetDatabase() {
         ExtendedTestDatabaseCreator.resetDatabaseWithUsers(false);
     }
 
     @Test
-    @Ignore("see https://github.com/SeqWare/seqware/issues/324")
     public void runThroughTutorial() throws IOException {
         // create some top level metadata
         Main main = new Main();
@@ -111,9 +110,9 @@ public void runThroughTutorial() throws IOException {
         Log.info(genOutput);
 
         // Replace contents of WorkflowClient from both workflows with code from tutorial
-        String tarTemplatePath = BasicDeciderTutorialET.class.getResource("TarWorkflow.template").getPath();
-        String gzTemplatePath = BasicDeciderTutorialET.class.getResource("GZWorkflow.template").getPath();
-        String workflowIniTemplatePath = BasicDeciderTutorialET.class.getResource("workflowini.template").getPath();
+        String tarTemplatePath = BasicDeciderTutorialLT.class.getResource("TarWorkflow.template").getPath();
+        String gzTemplatePath = BasicDeciderTutorialLT.class.getResource("GZWorkflow.template").getPath();
+        String workflowIniTemplatePath = BasicDeciderTutorialLT.class.getResource("workflowini.template").getPath();
         // determine existing file paths
         File tarTarget = new File(tempDir, "Tar/src/main/java/com/github/seqware/TarWorkflow.java");
         File gzTarget = new File(tempDir, "GZ/src/main/java/com/github/seqware/GZWorkflow.java");

seqware-ext-testing/src/test/java/net/sourceforge/seqware/pipeline/regression_testing/OutofOrderWorkflowET.java renamed to seqware-ext-testing/src/test/java/net/sourceforge/seqware/pipeline/regression_testing/OutofOrderWorkflowLT.java

@@ -23,7 +23,6 @@
 import net.sourceforge.seqware.pipeline.plugins.ExtendedTestDatabaseCreator;
 import net.sourceforge.seqware.pipeline.plugins.ITUtility;
 import org.junit.Assert;
-import org.junit.Ignore;
 import org.junit.Test;
 
 import java.io.File;
@@ -34,10 +33,9 @@
  * 
  * @author dyuen
  */
-public class OutofOrderWorkflowET {
+public class OutofOrderWorkflowLT {
 
     @Test
-    @Ignore("see https://github.com/SeqWare/seqware/issues/324")
     public void runSEQWARE1890() throws IOException {
         // here we test that the first error is properly propagated into the database and reported
         ExtendedTestDatabaseCreator.resetDatabaseWithUsers(false);
@@ -58,7 +56,7 @@ public void runSEQWARE1890() throws IOException {
         Log.info(genOutput);
 
         // Replace contents of WorkflowClient from both workflows with code from tutorial
-        String workflowJavaPath = OutofOrderWorkflowET.class.getResource("seqware1890.template").getPath();
+        String workflowJavaPath = OutofOrderWorkflowLT.class.getResource("seqware1890.template").getPath();
         // determine existing file paths
         File targetJavaPath = new File(tempDir, "HelloOutofOrder/src/main/java/com/github/seqware/HelloOutofOrderWorkflow.java");
 

seqware-ext-testing/src/test/java/net/sourceforge/seqware/pipeline/regression_testing/SkippingFilesWorkflowET.java renamed to seqware-ext-testing/src/test/java/net/sourceforge/seqware/pipeline/regression_testing/SkippingFilesWorkflowLT.java

@@ -24,7 +24,6 @@
 import net.sourceforge.seqware.pipeline.plugins.ITUtility;
 import org.apache.commons.dbutils.handlers.ArrayHandler;
 import org.junit.Assert;
-import org.junit.Ignore;
 import org.junit.Test;
 
 import java.io.File;
@@ -35,10 +34,9 @@
  * 
  * @author dyuen
  */
-public class SkippingFilesWorkflowET {
+public class SkippingFilesWorkflowLT {
 
     @Test
-    @Ignore("see https://github.com/SeqWare/seqware/issues/324")
     public void runSEQWARE2039() throws IOException {
         // here we test that the first error is properly propagated into the database and reported
         final ExtendedTestDatabaseCreator dbCreator = new ExtendedTestDatabaseCreator();
@@ -60,7 +58,7 @@ public void runSEQWARE2039() throws IOException {
         Log.info(genOutput);
 
         // Replace contents of WorkflowClient from both workflows with code from tutorial
-        String workflowJavaPath = SkippingFilesWorkflowET.class.getResource("seqware2039.template").getPath();
+        String workflowJavaPath = SkippingFilesWorkflowLT.class.getResource("seqware2039.template").getPath();
         // determine existing file paths
         File targetJavaPath = new File(tempDir, "Skipping/src/main/java/io/seqware/SkippingWorkflow.java");
 

seqware-ext-testing/src/test/java/net/sourceforge/seqware/pipeline/tutorial/OldAdminTutorialSuiteET.java renamed to seqware-ext-testing/src/test/java/net/sourceforge/seqware/pipeline/tutorial/OldAdminTutorialSuiteLT.java

@@ -18,7 +18,6 @@
 
 import net.sourceforge.seqware.pipeline.plugins.ExtendedTestDatabaseCreator;
 import org.junit.BeforeClass;
-import org.junit.Ignore;
 import org.junit.runner.RunWith;
 import org.junit.runners.Suite;
 
@@ -27,10 +26,9 @@
  * 
  * @author dyuen
  */
-@Ignore("see https://github.com/SeqWare/seqware/issues/324")
 @RunWith(Suite.class)
 @Suite.SuiteClasses(value = { AdminPhase1.class })
-public class OldAdminTutorialSuiteET extends TutorialSuite {
+public class OldAdminTutorialSuiteLT extends TutorialSuite {
     @BeforeClass
     public static void resetDatabase() {
         ExtendedTestDatabaseCreator.resetDatabaseWithUsers();

seqware-ext-testing/src/test/java/net/sourceforge/seqware/pipeline/tutorial/OldDeveloperTutorialSuiteET.java renamed to seqware-ext-testing/src/test/java/net/sourceforge/seqware/pipeline/tutorial/OldDeveloperTutorialSuiteLT.java

@@ -18,7 +18,6 @@
 
 import net.sourceforge.seqware.pipeline.plugins.ExtendedTestDatabaseCreator;
 import org.junit.BeforeClass;
-import org.junit.Ignore;
 import org.junit.runner.RunWith;
 import org.junit.runners.Suite;
 
@@ -28,10 +27,9 @@
  * 
  * @author dyuen
  */
-@Ignore("see https://github.com/SeqWare/seqware/issues/324")
 @RunWith(Suite.class)
 @Suite.SuiteClasses(value = { DeveloperPhase1.class, DeveloperPhase2.class })
-public class OldDeveloperTutorialSuiteET extends TutorialSuite {
+public class OldDeveloperTutorialSuiteLT extends TutorialSuite {
     @BeforeClass
     public static void resetDatabase() {
         ExtendedTestDatabaseCreator.resetDatabaseWithUsers();