switch to Junit 5 @tag() instead of Junit 4 @category for filtering

virtualcell · Dec 17, 2023 · a637efd · a637efd
1 parent 80b9812
commit a637efd
Show file tree

Hide file tree

Showing 107 changed files with 196 additions and 160 deletions.
diff --git a/.github/workflows/ci_cd.yml b/.github/workflows/ci_cd.yml
@@ -148,7 +148,7 @@ jobs:
         run: |
           mvn -version
           java -version
-          mvn --batch-mode clean install dependency:copy-dependencies -Dgroups="org.vcell.test.${{ matrix.test-group }}"
+          mvn --batch-mode clean install dependency:copy-dependencies -Dgroups="${{ matrix.test-group }}"
 
 #      - name: Setup tmate session
 #        uses: mxschmitt/action-tmate@v3
@@ -217,7 +217,7 @@ jobs:
         run: |
           mvn -version
           java -version
-          mvn --batch-mode clean install dependency:copy-dependencies -Dgroups="org.vcell.test.Fast"
+          mvn --batch-mode clean install dependency:copy-dependencies -Dgroups="Fast"
 
       - name: Build Docker image and push with latest tag
         run: |

diff --git a/README.md b/README.md
@@ -68,7 +68,7 @@ poetry install
 
 #### Test Java and Python
 ```bash
-mvn test -Dgroups=org.vcell.test.Fast
+mvn test -Dgroups="Fast"
 
 INSTALL_DIR=$(pwd)
 cd ${INSTALL_DIR}/pythonCopasiOpt/vcell-opt

diff --git a/vcell-admin/src/test/java/cbit/vcell/client/ClientTaskDispatcherTest.java b/vcell-admin/src/test/java/cbit/vcell/client/ClientTaskDispatcherTest.java
@@ -3,6 +3,7 @@
 import static cbit.vcell.client.task.AsynchClientTask.TASKTYPE_NONSWING_BLOCKING;
 import static cbit.vcell.client.task.AsynchClientTask.TASKTYPE_SWING_BLOCKING;
 import static cbit.vcell.client.task.AsynchClientTask.TASKTYPE_SWING_NONBLOCKING;
+import org.junit.jupiter.api.Tag;
 
 import java.awt.Component;
 import java.awt.Label;
@@ -18,7 +19,7 @@
 import org.vcell.test.Fast;
 
 @Ignore
-@Category(Fast.class)
+@Tag("Fast")
 public class ClientTaskDispatcherTest {
 	private Hashtable<String,Object> ht  = new Hashtable<>(); 
 	private  Component cmpt = new Label() ;

diff --git a/vcell-admin/src/test/java/cbit/vcell/util/AmplistorUtilsTest.java b/vcell-admin/src/test/java/cbit/vcell/util/AmplistorUtilsTest.java
@@ -2,7 +2,7 @@
 
 import java.io.BufferedInputStream;
 import java.io.BufferedOutputStream;
-import java.io.DataInputStream;
+import org.junit.jupiter.api.Tag;
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.FileNotFoundException;
@@ -27,7 +27,7 @@
 import cbit.vcell.util.AmplistorUtils.AmplistorCredential;
 
 @Ignore
-@Category(Fast.class)
+@Tag("Fast")
 public class AmplistorUtilsTest {
 
 	private static final int NUMFILES = 5;

diff --git a/vcell-cli/src/test/java/org/vcell/cli/run/BSTSBasedOmexExecTest.java b/vcell-cli/src/test/java/org/vcell/cli/run/BSTSBasedOmexExecTest.java
@@ -3,6 +3,7 @@
 import cbit.vcell.mongodb.VCMongoMessage;
 import cbit.vcell.resource.NativeLib;
 import cbit.vcell.resource.PropertyLoader;
+import org.junit.jupiter.api.Tag;
 import java.io.File;
 import java.io.IOException;
 import java.io.InputStream;
@@ -31,7 +32,7 @@
 import org.vcell.test.BSTS_IT;
 import org.vcell.util.VCellUtilityHub;
 
-@RunWith(Parameterized.class)
+@Tag("BSTS_IT")
 @Category(BSTS_IT.class)
 public class BSTSBasedOmexExecTest {
 	private final String testCaseFilename;

diff --git a/vcell-cli/src/test/java/org/vcell/cli/run/BSTSBasedTestSuiteFiles.java b/vcell-cli/src/test/java/org/vcell/cli/run/BSTSBasedTestSuiteFiles.java
@@ -1,7 +1,7 @@
 package org.vcell.cli.run;
 
 import org.junit.Assert;
-import org.junit.Test;
+import org.junit.jupiter.api.Tag;
 import org.junit.experimental.categories.Category;
 import org.vcell.test.Fast;
 
@@ -11,7 +11,7 @@
 import java.util.function.Predicate;
 
 
-@Category(Fast.class)
+@Tag("Fast")
 public class BSTSBasedTestSuiteFiles {
 
     private final static String[] allTestFiles = new String[]{

diff --git a/vcell-cli/src/test/java/org/vcell/cli/run/BiosimulationsExecTest.java b/vcell-cli/src/test/java/org/vcell/cli/run/BiosimulationsExecTest.java
@@ -6,7 +6,7 @@
 import org.apache.commons.io.FileUtils;
 import org.junit.Assert;
 import org.junit.BeforeClass;
-import org.junit.Test;
+import org.junit.jupiter.api.Tag;
 import org.junit.experimental.categories.Category;
 import org.junit.runner.RunWith;
 import org.junit.runners.Parameterized;
@@ -32,6 +32,7 @@
 
 @RunWith(Parameterized.class)
 @Category(BSTS_IT.class)
+@Tag("BSTS_IT")
 public class BiosimulationsExecTest {
 	private final String testCaseProjectID;
 

diff --git a/vcell-cli/src/test/java/org/vcell/cli/run/BiosimulationsFiles.java b/vcell-cli/src/test/java/org/vcell/cli/run/BiosimulationsFiles.java
@@ -2,15 +2,15 @@
 
 import org.junit.Assert;
 import org.junit.Test;
-import org.junit.experimental.categories.Category;
+import org.junit.jupiter.api.Tag;
 import org.vcell.test.Fast;
 
 import java.io.InputStream;
 import java.util.Arrays;
 import java.util.function.Predicate;
 
 
-@Category(Fast.class)
+@Tag("Fast")
 public class BiosimulationsFiles {
 
     private final static String[] allProjectIDs = new String[]{

diff --git a/vcell-cli/src/test/java/org/vcell/cli/run/ExecuteImplTest.java b/vcell-cli/src/test/java/org/vcell/cli/run/ExecuteImplTest.java
@@ -3,7 +3,7 @@
 import cbit.vcell.mongodb.VCMongoMessage;
 import cbit.vcell.resource.NativeLib;
 import cbit.vcell.resource.PropertyLoader;
-import org.junit.Test;
+import org.junit.jupiter.api.Tag;
 import org.junit.experimental.categories.Category;
 import org.vcell.cli.CLIPythonManager;
 import org.vcell.cli.CLIRecorder;
@@ -18,7 +18,7 @@
 
 import static java.nio.file.StandardCopyOption.REPLACE_EXISTING;
 
-@Category(Fast.class)
+@Tag("Fast")
 public class ExecuteImplTest {
 
     @Test

diff --git a/vcell-cli/src/test/java/org/vcell/cli/run/SpatialArchiveFiles.java b/vcell-cli/src/test/java/org/vcell/cli/run/SpatialArchiveFiles.java
@@ -1,7 +1,7 @@
 package org.vcell.cli.run;
 
 import org.junit.Assert;
-import org.junit.Test;
+import org.junit.jupiter.api.Tag;
 import org.junit.experimental.categories.Category;
 import org.vcell.test.Fast;
 
@@ -11,6 +11,7 @@
 import java.util.function.Predicate;
 
 @Category(Fast.class)
+@Tag("Fast")
 public class SpatialArchiveFiles {
     private final static String[] allTestFiles = new String[]{
             "TinySpatialProject.omex",

diff --git a/vcell-cli/src/test/java/org/vcell/cli/run/SpatialExecTest.java b/vcell-cli/src/test/java/org/vcell/cli/run/SpatialExecTest.java
@@ -6,7 +6,7 @@
 import org.apache.commons.io.FileUtils;
 import org.junit.Assert;
 import org.junit.BeforeClass;
-import org.junit.Test;
+import org.junit.jupiter.api.Tag;
 import org.junit.experimental.categories.Category;
 import org.junit.runner.RunWith;
 import org.junit.runners.Parameterized;
@@ -28,6 +28,7 @@
 
 @RunWith(Parameterized.class)
 @Category(Spatial_IT.class)
+@Tag("Spatial_IT")
 public class SpatialExecTest {
     private final String testCaseFilename;
 

diff --git a/vcell-cli/src/test/java/org/vcell/cli/run/hdf5/Hdf5WriterTest.java b/vcell-cli/src/test/java/org/vcell/cli/run/hdf5/Hdf5WriterTest.java
@@ -4,7 +4,7 @@
 import com.google.common.io.Files;
 import ncsa.hdf.hdf5lib.exceptions.HDF5Exception;
 import org.jlibsedml.DataSet;
-import cbit.vcell.resource.NativeLib;
+import org.junit.jupiter.api.Tag;
 import org.junit.Test;
 import org.junit.experimental.categories.Category;
 import org.vcell.test.Fast;
@@ -18,7 +18,7 @@
 import java.util.LinkedHashMap;
 import java.util.List;
 
-@Category(Fast.class)
+@Tag("Fast")
 public class Hdf5WriterTest {
 
     public static Hdf5DataContainer createExampleData() {

diff --git a/vcell-client/src/test/java/org/vcell/util/gui/GeneralGuiUtilsTest.java b/vcell-client/src/test/java/org/vcell/util/gui/GeneralGuiUtilsTest.java
@@ -1,7 +1,7 @@
 package org.vcell.util.gui;
 
 import org.junit.Ignore;
-import org.junit.Test;
+import org.junit.jupiter.api.Tag;
 import org.junit.experimental.categories.Category;
 import org.vcell.test.Fast;
 
@@ -12,7 +12,7 @@
 import static org.junit.Assert.*;
 
 
-@Category(Fast.class)
+@Tag("Fast")
 public class GeneralGuiUtilsTest {
 
     private void aTest(BiFunction<Class<?>, Component, Container> method){

diff --git a/vcell-client/src/test/java/org/vcell/util/gui/GraphicExecutableFinderTest.java b/vcell-client/src/test/java/org/vcell/util/gui/GraphicExecutableFinderTest.java
@@ -1,12 +1,13 @@
 package org.vcell.util.gui;
 
 import java.awt.Component;
+import org.junit.jupiter.api.Tag;
 import java.io.File;
 import java.io.FileNotFoundException;
 import java.util.prefs.BackingStoreException;
 
 import javax.swing.JFrame;
-
+@Tag("Fast")
 import org.junit.Ignore;
 
 import cbit.vcell.resource.ResourceUtil;

diff --git a/vcell-client/src/test/java/org/vcell/util/gui/VCellIconsTest.java b/vcell-client/src/test/java/org/vcell/util/gui/VCellIconsTest.java
@@ -1,5 +1,6 @@
 package org.vcell.util.gui;
 
+import org.junit.jupiter.api.Tag;
 import java.net.URL;
 import java.util.Map.Entry;
 
@@ -8,7 +9,7 @@
 import org.junit.experimental.categories.Category;
 import org.vcell.test.Fast;
 
-@Category(Fast.class)
+@Tag("Fast")
 public class VCellIconsTest {
 
 	@Test

diff --git a/vcell-core/src/main/java/cbit/vcell/math/MathUtilities.java b/vcell-core/src/main/java/cbit/vcell/math/MathUtilities.java
@@ -17,7 +17,7 @@
 import cbit.vcell.solver.SimulationSymbolTable;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
-import org.vcell.test.Fast;
+
 
 /**
  * Insert the type's description here.

diff --git a/vcell-core/src/test/java/cbit/image/VCImageTest.java b/vcell-core/src/test/java/cbit/image/VCImageTest.java
@@ -10,7 +10,7 @@
 import cbit.vcell.xml.XmlHelper;
 import cbit.vcell.xml.XmlParseException;
 import org.junit.Assert;
-import org.junit.Test;
+import org.junit.jupiter.api.Tag;
 import org.junit.experimental.categories.Category;
 import org.vcell.sbml.vcell.SBMLExporter;
 import org.vcell.sbml.vcell.SBMLImporter;
@@ -20,7 +20,7 @@
 import java.io.StringBufferInputStream;
 import java.util.Random;
 
-@Category(Fast.class)
+@Tag("Fast")
 public class VCImageTest {
 
     @Test

diff --git a/vcell-core/src/test/java/cbit/vcell/biomodel/MathOverrideApplyTest.java b/vcell-core/src/test/java/cbit/vcell/biomodel/MathOverrideApplyTest.java
@@ -9,7 +9,7 @@
 import cbit.vcell.xml.XmlParseException;
 import org.junit.AfterClass;
 import org.junit.Assert;
-import org.junit.BeforeClass;
+import org.junit.jupiter.api.Tag;
 import org.junit.Test;
 import org.junit.experimental.categories.Category;
 import org.junit.runner.RunWith;
@@ -25,6 +25,7 @@
 
 @Category(MathGen_IT.class)
 @RunWith(Parameterized.class)
+@Tag("MathGen_IT")
 public class MathOverrideApplyTest {
 
 	private String filename_colon_appname;

diff --git a/vcell-core/src/test/java/cbit/vcell/biomodel/MathOverrideRoundTipTest.java b/vcell-core/src/test/java/cbit/vcell/biomodel/MathOverrideRoundTipTest.java
@@ -12,7 +12,7 @@
 import org.junit.After;
 import org.junit.Assert;
 import org.junit.Before;
-import org.junit.Test;
+import org.junit.jupiter.api.Tag;
 import org.junit.experimental.categories.Category;
 import org.junit.runner.RunWith;
 import org.junit.runners.Parameterized;
@@ -34,6 +34,7 @@
 
 @Category(Fast.class)
 @RunWith(Parameterized.class)
+@Tag("Fast")
 public class MathOverrideRoundTipTest {
 
     private final String filename;

diff --git a/vcell-core/src/test/java/cbit/vcell/biomodel/ModelCountAndConcentrationTest.java b/vcell-core/src/test/java/cbit/vcell/biomodel/ModelCountAndConcentrationTest.java
@@ -17,7 +17,7 @@
 import cbit.vcell.xml.XmlHelper;
 import cbit.vcell.xml.XmlParseException;
 import org.apache.commons.io.IOUtils;
-import org.junit.Assert;
+import org.junit.jupiter.api.Tag;
 import org.junit.Test;
 import org.junit.experimental.categories.Category;
 import org.vcell.test.Fast;
@@ -29,6 +29,7 @@
 import java.nio.charset.StandardCharsets;
 
 @Category(Fast.class)
+@Tag("Fast")
 public class ModelCountAndConcentrationTest {
 
 	@Test

diff --git a/vcell-core/src/test/java/cbit/vcell/biomodel/ModelUnitConverterTest.java b/vcell-core/src/test/java/cbit/vcell/biomodel/ModelUnitConverterTest.java
@@ -22,7 +22,7 @@
 import cbit.vcell.xml.XmlHelper;
 import cbit.vcell.xml.XmlParseException;
 import org.apache.commons.io.IOUtils;
-import org.junit.Assert;
+import org.junit.jupiter.api.Tag;
 import org.junit.Test;
 import org.junit.experimental.categories.Category;
 import org.vcell.test.Fast;
@@ -38,6 +38,7 @@
 import java.util.Map;
 
 @Category(Fast.class)
+@Tag("Fast")
 public class ModelUnitConverterTest {
 
     @Test

diff --git a/vcell-core/src/test/java/cbit/vcell/biomodel/SpringSaLaDGoodReactionsTest.java b/vcell-core/src/test/java/cbit/vcell/biomodel/SpringSaLaDGoodReactionsTest.java
@@ -22,6 +22,7 @@
 import org.apache.commons.io.IOUtils;
 import org.junit.*;
 import org.junit.experimental.categories.Category;
+import org.junit.jupiter.api.Tag;
 import org.vcell.model.rbm.MolecularComponentPattern;
 import org.vcell.solver.langevin.LangevinLngvWriter;
 import org.vcell.solver.langevin.LangevinSolver;
@@ -40,6 +41,7 @@
 import java.util.*;
 
 @Category(Fast.class)
+@Tag("Fast")
 public class SpringSaLaDGoodReactionsTest {
 
 	private static final String reactionTestString = "'r0' ::     'MT0' : 'Site1' : 'state0' --> 'state1'  Rate 50.0  Condition Free";

diff --git a/vcell-core/src/test/java/cbit/vcell/export/N5ExporterTest.java b/vcell-core/src/test/java/cbit/vcell/export/N5ExporterTest.java
@@ -20,7 +20,7 @@
 import cbit.vcell.solver.AnnotatedFunction;
 import cbit.vcell.solver.VCSimulationDataIdentifier;
 import org.janelia.saalfeldlab.n5.*;
-import org.junit.After;
+import org.junit.jupiter.api.*;
 import org.junit.Assert;
 import org.junit.Before;
 import org.junit.Test;
@@ -35,6 +35,7 @@
 import java.util.Random;
 
 @Category(Fast.class)
+@Tag("Fast")
 public class N5ExporterTest {
 
     private N5Reader n5Reader;

diff --git a/vcell-core/src/test/java/cbit/vcell/mapping/MathGenCompareTest.java b/vcell-core/src/test/java/cbit/vcell/mapping/MathGenCompareTest.java
@@ -13,7 +13,7 @@
 import org.junit.*;
 import org.junit.experimental.categories.Category;
 import org.junit.runner.RunWith;
-import org.junit.runners.Parameterized;
+import org.junit.jupiter.api.Tag;
 import org.vcell.sbml.VcmlTestSuiteFiles;
 import org.vcell.test.MathGen_IT;
 import org.vcell.util.document.Version;
@@ -26,6 +26,7 @@
 
 @Category(MathGen_IT.class)
 @RunWith(Parameterized.class)
+@Tag("MathGen_IT")
 public class MathGenCompareTest {
 
 	private String filename_colon_appname;