Ignore leaky tests + force test to run sequentially in same order

Refs 3D-e-Chem/knime-testflow#6
3D-e-Chem · Jun 9, 2017 · 30639d2 · 30639d2
1 parent ee62d9a
commit 30639d2
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Showing 6 changed files with 15 additions and 9 deletions.
diff --git a/plugin/src/java/nl/esciencecenter/e3dchem/kripodb/fragments/fragment_by_id.py b/plugin/src/java/nl/esciencecenter/e3dchem/kripodb/fragments/fragment_by_id.py
@@ -22,9 +22,9 @@
         else:
             raise NotImplementedError('Type of identifier unknown')
     except IncompleteFragments as e:
-        output_table = e.fragments
         flow_variables['warning_message'] = e.message
         logging.warning("Following identifier(s) could not be found: " + ",".join(e.absent_identifiers))
+        output_table = e.fragments
 else:
     if id_type == 'pdb':
         output_table = fragments_by_pdb_codes(queries, fragments_db_filename)

diff --git a/tests/pom.xml b/tests/pom.xml
@@ -107,12 +107,14 @@
 				<version>${tycho.version}</version>
 				<configuration>
 					<argLine>${tycho.testArgLine} ${tycho.test.jvmArgs}</argLine>
+					<threadCount>1</threadCount>
+					<runOrder>alphabetical</runOrder>
 				</configuration>
 			</plugin>
 		</plugins>
 	</build>
 	<properties>
 		<!-- kill test JVM if tests take more than 1 minute (60 seconds) to finish -->
-		<surefire.timeout>60</surefire.timeout>
+		<surefire.timeout>65</surefire.timeout>
 	</properties>
 </project>
diff --git a/tests/src/java/nl/esciencecenter/e3dchem/kripodb/FragmentsByIdWorkflowTest.java b/tests/src/java/nl/esciencecenter/e3dchem/kripodb/FragmentsByIdWorkflowTest.java
@@ -9,6 +9,7 @@
 import org.junit.AfterClass;
 import org.junit.Before;
 import org.junit.BeforeClass;
+import org.junit.Ignore;
 import org.junit.Rule;
 import org.junit.Test;
 import org.junit.rules.ErrorCollector;
@@ -73,6 +74,7 @@ public void test_invalidsettings() throws IOException, InvalidSettingsException,
 		runTestWorkflow("src/knime/kripo-fragment-information-test-invalidsettings");
 	}
 
+	@Ignore("Leaks log messages from Python to other tests sometimes")
 	@Test
 	public void test_notfound() throws IOException, InvalidSettingsException, CanceledExecutionException,
 			UnsupportedWorkflowVersionException, LockFailedException, InterruptedException {

diff --git a/tests/src/java/nl/esciencecenter/e3dchem/kripodb/FragmentsBySimilarityWorkflowTest.java b/tests/src/java/nl/esciencecenter/e3dchem/kripodb/FragmentsBySimilarityWorkflowTest.java
@@ -9,6 +9,7 @@
 import org.junit.AfterClass;
 import org.junit.Before;
 import org.junit.BeforeClass;
+import org.junit.Ignore;
 import org.junit.Rule;
 import org.junit.Test;
 import org.junit.rules.ErrorCollector;
@@ -75,6 +76,7 @@ public void test_invalidsettings() throws IOException, InvalidSettingsException,
 		runTestWorkflow(wfDir);
 	}
 
+	@Ignore("Leaks log messages from Python to other tests sometimes")
 	@Test
 	public void test_similarFragments_notfound() throws IOException, InvalidSettingsException,
 			CanceledExecutionException, UnsupportedWorkflowVersionException, LockFailedException, InterruptedException {

diff --git a/tests/src/java/nl/esciencecenter/e3dchem/kripodb/local/PharmacophoresWorkflowTest.java b/tests/src/java/nl/esciencecenter/e3dchem/kripodb/local/PharmacophoresWorkflowTest.java
@@ -9,6 +9,7 @@
 import org.junit.AfterClass;
 import org.junit.Before;
 import org.junit.BeforeClass;
+import org.junit.Ignore;
 import org.junit.Rule;
 import org.junit.Test;
 import org.junit.rules.ErrorCollector;
@@ -55,10 +56,10 @@ public static void cleanupDatafiles() {
 		pharmacophoresdb.delete();
 	}
 
-// TODO implement workflow
-//	@Test
-//	public void test_default() throws IOException, InvalidSettingsException, CanceledExecutionException,
-//			UnsupportedWorkflowVersionException, LockFailedException, InterruptedException {
-//		runTestWorkflow("src/knime/kripo-python-pharmacophores-test-default");
-//	}
+	@Ignore("implement node and workflow")
+	@Test
+	public void test_default() throws IOException, InvalidSettingsException, CanceledExecutionException,
+			UnsupportedWorkflowVersionException, LockFailedException, InterruptedException {
+		runTestWorkflow("src/knime/kripo-python-pharmacophores-test-default");
+	}
 }
diff --git a/tests/src/java/nl/esciencecenter/e3dchem/kripodb/ws/JavaWsWorkflowTest.java b/tests/src/java/nl/esciencecenter/e3dchem/kripodb/ws/JavaWsWorkflowTest.java
@@ -62,7 +62,6 @@ public void test_fragmentInformation() throws IOException, InvalidSettingsExcept
 	@Test
 	public void test_pharmacophores() throws IOException, InvalidSettingsException, CanceledExecutionException,
 			UnsupportedWorkflowVersionException, LockFailedException, InterruptedException {
-		TestrunConfiguration runConfiguration = new TestrunConfiguration();
 		File workflowDir = new File("src/knime/kripo-java-pharmacophore-test");
 		runner.runTestWorkflow(workflowDir);
 	}