refactor Java unit tests into multiple files.

Author: jcschaff

vcell-native/src/test/java/org/vcell/libvcell/ModelEntrypointsTest.java

@@ -0,0 +1,47 @@
+package org.vcell.libvcell;
+
+import cbit.util.xml.VCLoggerException;
+import cbit.vcell.mapping.MappingException;
+import cbit.vcell.xml.XmlParseException;
+import org.junit.jupiter.api.Test;
+import org.vcell.sbml.SbmlException;
+
+import javax.xml.stream.XMLStreamException;
+import java.io.File;
+import java.io.IOException;
+import java.nio.file.Files;
+
+import static org.vcell.libvcell.ModelUtils.*;
+import static org.vcell.libvcell.TestUtils.getFileContentsAsString;
+
+public class ModelEntrypointsTest {
+
+    @Test
+    public void test_sbml_to_vcml() throws MappingException, IOException, XmlParseException, VCLoggerException {
+        String sbmlContent = getFileContentsAsString("/TinySpatialProject_Application0.xml");
+        File parent_dir = Files.createTempDirectory("sbmlToVcml").toFile();
+        File vcml_temp_file = new File(parent_dir, "temp.vcml");
+        sbml_to_vcml(sbmlContent, vcml_temp_file.toPath());
+        assert(vcml_temp_file.exists());
+    }
+
+    @Test
+    public void test_vcml_to_sbml() throws MappingException, IOException, XmlParseException, XMLStreamException, SbmlException {
+        String vcmlContent = getFileContentsAsString("/TinySpatialProject_Application0.vcml");
+        File parent_dir = Files.createTempDirectory("vcmlToSbml").toFile();
+        File sbml_temp_file = new File(parent_dir, "temp.sbml");
+        String applicationName = "unnamed_spatialGeom";
+        vcml_to_sbml(vcmlContent, applicationName, sbml_temp_file.toPath());
+        assert(sbml_temp_file.exists());
+    }
+
+    @Test
+    public void test_vcml_to_vcml() throws MappingException, IOException, XmlParseException, XMLStreamException, SbmlException {
+        String vcmlContent = getFileContentsAsString("/TinySpatialProject_Application0.vcml");
+        File parent_dir = Files.createTempDirectory("vcmlToVcml").toFile();
+        File vcml_temp_file = new File(parent_dir, "temp.vcml");
+        vcml_to_vcml(vcmlContent, vcml_temp_file.toPath());
+        assert(vcml_temp_file.exists());
+    }
+
+}

…/org/vcell/libvcell/EntrypointsTest.java …cell/libvcell/SolverEntrypointsTest.javavcell-native/src/test/java/org/vcell/libvcell/EntrypointsTest.java renamed to vcell-native/src/test/java/org/vcell/libvcell/SolverEntrypointsTest.java vcell-native/src/test/java/org/vcell/libvcell/EntrypointsTest.java renamed to vcell-native/src/test/java/org/vcell/libvcell/SolverEntrypointsTest.java

@@ -6,30 +6,21 @@
 import cbit.vcell.parser.ExpressionException;
 import cbit.vcell.solver.SolverException;
 import cbit.vcell.xml.XmlParseException;
-import org.apache.commons.compress.archivers.tar.TarArchiveEntry;
-import org.apache.commons.compress.archivers.tar.TarArchiveInputStream;
 import org.junit.jupiter.api.Test;
-import org.vcell.sbml.SbmlException;
 
-import javax.xml.stream.XMLStreamException;
 import java.beans.PropertyVetoException;
-import java.io.*;
-import java.nio.charset.StandardCharsets;
+import java.io.File;
+import java.io.IOException;
 import java.nio.file.Files;
 import java.nio.file.Path;
-import java.util.Objects;
 import java.util.UUID;
-import java.util.stream.Collectors;
-import java.util.zip.GZIPInputStream;
 
 import static org.junit.jupiter.api.Assertions.*;
 import static org.vcell.libvcell.SolverUtils.sbmlToFiniteVolumeInput;
 import static org.vcell.libvcell.SolverUtils.vcmlToFiniteVolumeInput;
-import static org.vcell.libvcell.ModelUtils.sbml_to_vcml;
-import static org.vcell.libvcell.ModelUtils.vcml_to_sbml;
-import static org.vcell.libvcell.ModelUtils.vcml_to_vcml;
+import static org.vcell.libvcell.TestUtils.*;
 
-public class EntrypointsTest {
+public class SolverEntrypointsTest {
 
     @Test
     public void testSbmlToFiniteVolumeInput() throws PropertyVetoException, SolverException, ExpressionException, MappingException, VCLoggerException, IOException {
@@ -66,7 +57,7 @@ public void testVcmlToFiniteVolumeInput_field_data() throws SolverException, Exp
         File output_dir = new File(parent_dir, "output_dir");
         File ext_data_dir = new File(parent_dir, "test2_lsm_DEMO");
         assertEquals(0, countFiles(ext_data_dir));
-        extractTgz(EntrypointsTest.class.getResourceAsStream("/test2_lsm_DEMO.tgz"), parent_dir);
+        extractTgz(SolverEntrypointsTest.class.getResourceAsStream("/test2_lsm_DEMO.tgz"), parent_dir);
         listFilesInDirectory(ext_data_dir);
         assertEquals(10, countFiles(ext_data_dir));
 
@@ -87,7 +78,7 @@ public void testVcmlToFiniteVolumeInput_field_data_not_found() throws SolverExce
         File ext_data_dir_MISSPELLED = new File(parent_dir, "test2_lsm_DEMO_MISSPELLED");
         assertEquals(0, countFiles(ext_data_dir));
         assertEquals(0, countFiles(ext_data_dir_MISSPELLED));
-        extractTgz(EntrypointsTest.class.getResourceAsStream("/test2_lsm_DEMO.tgz"), parent_dir);
+        extractTgz(SolverEntrypointsTest.class.getResourceAsStream("/test2_lsm_DEMO.tgz"), parent_dir);
         Files.move(ext_data_dir.toPath(), ext_data_dir_MISSPELLED.toPath()).toFile();
         assertEquals(0, countFiles(ext_data_dir));
         listFilesInDirectory(ext_data_dir_MISSPELLED);
@@ -112,34 +103,6 @@ public void testVcmlToFiniteVolumeInput() throws SolverException, ExpressionExce
         assertEquals(4, countFiles(output_dir));
     }
 
-    @Test
-    public void test_sbml_to_vcml() throws MappingException, IOException, XmlParseException, VCLoggerException {
-        String sbmlContent = getFileContentsAsString("/TinySpatialProject_Application0.xml");
-        File parent_dir = Files.createTempDirectory("sbmlToVcml").toFile();
-        File vcml_temp_file = new File(parent_dir, "temp.vcml");
-        sbml_to_vcml(sbmlContent, vcml_temp_file.toPath());
-        assert(vcml_temp_file.exists());
-    }
-
-    @Test
-    public void test_vcml_to_sbml() throws MappingException, IOException, XmlParseException, XMLStreamException, SbmlException {
-        String vcmlContent = getFileContentsAsString("/TinySpatialProject_Application0.vcml");
-        File parent_dir = Files.createTempDirectory("vcmlToSbml").toFile();
-        File sbml_temp_file = new File(parent_dir, "temp.sbml");
-        String applicationName = "unnamed_spatialGeom";
-        vcml_to_sbml(vcmlContent, applicationName, sbml_temp_file.toPath());
-        assert(sbml_temp_file.exists());
-    }
-
-    @Test
-    public void test_vcml_to_vcml() throws MappingException, IOException, XmlParseException, XMLStreamException, SbmlException {
-        String vcmlContent = getFileContentsAsString("/TinySpatialProject_Application0.vcml");
-        File parent_dir = Files.createTempDirectory("vcmlToVcml").toFile();
-        File vcml_temp_file = new File(parent_dir, "temp.vcml");
-        vcml_to_vcml(vcmlContent, vcml_temp_file.toPath());
-        assert(vcml_temp_file.exists());
-    }
-
     @Test
     public void testVcmlToFiniteVolumeInput_bad_simname() throws IOException {
         String vcmlContent = getFileContentsAsString("/TinySpatialProject_Application0.vcml");
@@ -177,75 +140,4 @@ public void testVcmlToFiniteVolumeInput_sbml_instead() throws IOException {
         assertEquals("expecting VCML content, not SBML", exc.getMessage());
     }
 
-    private static String getFileContentsAsString(String filename) throws IOException {
-        try (InputStream inputStream = EntrypointsTest.class.getResourceAsStream(filename)) {
-            if (inputStream == null) {
-                throw new FileNotFoundException("file not found! " + filename);
-            }
-            return new BufferedReader(new InputStreamReader(inputStream, StandardCharsets.UTF_8))
-                    .lines().collect(Collectors.joining("\n"));
-        }
-    }
-
-    private static byte[] getFileContentsAsBytes(String filename) throws IOException {
-        try (InputStream inputStream = EntrypointsTest.class.getResourceAsStream(filename)) {
-            if (inputStream == null) {
-                throw new FileNotFoundException("file not found! " + filename);
-            }
-            try (ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream()) {
-                byte[] buffer = new byte[1024];
-                int length;
-                while ((length = inputStream.read(buffer)) != -1) {
-                    byteArrayOutputStream.write(buffer, 0, length);
-                }
-                return byteArrayOutputStream.toByteArray();
-            }
-        }
-    }
-
-    private int countFiles(File dir) {
-        File[] files = dir.listFiles();
-        if (files == null) {
-            return 0;
-        }
-        return Objects.requireNonNull(dir.listFiles()).length;
-    }
-
-    private void listFilesInDirectory(File dir) {
-        File[] files = dir.listFiles();
-        if (files != null) {
-            for (File file : files) {
-                System.out.println(file.getAbsolutePath());
-            }
-        }
-    }
-
-    public static void extractTgz(InputStream tgzFileStream, File outputDir) throws IOException {
-        try (GZIPInputStream gis = new GZIPInputStream(tgzFileStream);
-             TarArchiveInputStream tis = new TarArchiveInputStream(gis)) {
-
-            TarArchiveEntry entry;
-            while ((entry = tis.getNextTarEntry()) != null) {
-                File outputFile = new File(outputDir, entry.getName());
-                if (entry.isDirectory()) {
-                    if (!outputFile.exists()) {
-                        outputFile.mkdirs();
-                    }
-                } else {
-                    File parent = outputFile.getParentFile();
-                    if (!parent.exists()) {
-                        parent.mkdirs();
-                    }
-                    try (OutputStream os = Files.newOutputStream(outputFile.toPath())) {
-                        byte[] buffer = new byte[1024];
-                        int len;
-                        while ((len = tis.read(buffer)) != -1) {
-                            os.write(buffer, 0, len);
-                        }
-                    }
-                }
-            }
-        }
-    }
-
 }

vcell-native/src/test/java/org/vcell/libvcell/TestUtils.java

@@ -0,0 +1,86 @@
+package org.vcell.libvcell;
+
+import org.apache.commons.compress.archivers.tar.TarArchiveEntry;
+import org.apache.commons.compress.archivers.tar.TarArchiveInputStream;
+
+import java.io.*;
+import java.nio.charset.StandardCharsets;
+import java.nio.file.Files;
+import java.util.Objects;
+import java.util.stream.Collectors;
+import java.util.zip.GZIPInputStream;
+
+public class TestUtils {
+    public static String getFileContentsAsString(String filename) throws IOException {
+        try (InputStream inputStream = ModelEntrypointsTest.class.getResourceAsStream(filename)) {
+            if (inputStream == null) {
+                throw new FileNotFoundException("file not found! " + filename);
+            }
+            return new BufferedReader(new InputStreamReader(inputStream, StandardCharsets.UTF_8))
+                    .lines().collect(Collectors.joining("\n"));
+        }
+    }
+
+    public static byte[] getFileContentsAsBytes(String filename) throws IOException {
+        try (InputStream inputStream = SolverEntrypointsTest.class.getResourceAsStream(filename)) {
+            if (inputStream == null) {
+                throw new FileNotFoundException("file not found! " + filename);
+            }
+            try (ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream()) {
+                byte[] buffer = new byte[1024];
+                int length;
+                while ((length = inputStream.read(buffer)) != -1) {
+                    byteArrayOutputStream.write(buffer, 0, length);
+                }
+                return byteArrayOutputStream.toByteArray();
+            }
+        }
+    }
+
+    public static int countFiles(File dir) {
+        File[] files = dir.listFiles();
+        if (files == null) {
+            return 0;
+        }
+        return Objects.requireNonNull(dir.listFiles()).length;
+    }
+
+    public static void listFilesInDirectory(File dir) {
+        File[] files = dir.listFiles();
+        if (files != null) {
+            for (File file : files) {
+                System.out.println(file.getAbsolutePath());
+            }
+        }
+    }
+
+    public static void extractTgz(InputStream tgzFileStream, File outputDir) throws IOException {
+        try (GZIPInputStream gis = new GZIPInputStream(tgzFileStream);
+             TarArchiveInputStream tis = new TarArchiveInputStream(gis)) {
+
+            TarArchiveEntry entry;
+            while ((entry = tis.getNextTarEntry()) != null) {
+                File outputFile = new File(outputDir, entry.getName());
+                if (entry.isDirectory()) {
+                    if (!outputFile.exists()) {
+                        outputFile.mkdirs();
+                    }
+                } else {
+                    File parent = outputFile.getParentFile();
+                    if (!parent.exists()) {
+                        parent.mkdirs();
+                    }
+                    try (OutputStream os = Files.newOutputStream(outputFile.toPath())) {
+                        byte[] buffer = new byte[1024];
+                        int len;
+                        while ((len = tis.read(buffer)) != -1) {
+                            os.write(buffer, 0, len);
+                        }
+                    }
+                }
+            }
+        }
+    }
+
+
+}