Description: Removing tests which depend on not yet packaged Java stuff. Author: Andrius Merkys --- a/mmtf-serialization/src/test/java/org/rcsb/mmtf/dataholders/TestDataHolders.java +++ /dev/null @@ -1,66 +0,0 @@ -package org.rcsb.mmtf.dataholders; - - -import static org.junit.Assert.assertNotNull; - -import java.beans.IntrospectionException; -import java.beans.Introspector; -import java.beans.PropertyDescriptor; -import java.lang.reflect.InvocationTargetException; - -import org.junit.Test; -import org.unitils.reflectionassert.ReflectionAssert; - -import uk.co.jemos.podam.api.PodamFactory; -import uk.co.jemos.podam.api.PodamFactoryImpl; - -/** - * A class to test the dataholders. - * @author Anthony Bradley - * - */ -public class TestDataHolders { - - /** - * Test the available beans - * @throws IllegalAccessException related to Jackson conversion - * @throws IllegalArgumentException related to Jackson conversion - * @throws InvocationTargetException related to Jackson conversion - * @throws IntrospectionException related to Jackson conversion - */ - @Test - public void testBeans() throws IllegalAccessException, IllegalArgumentException, InvocationTargetException, IntrospectionException{ - PodamFactory factory = new PodamFactoryImpl(); - // Tests if setters are set appropriately - ReflectionAssert.assertPropertiesNotNull("Some properties null.", - factory.manufacturePojo(MmtfStructure.class)); - testData(MmtfStructure.class, factory.manufacturePojo(MmtfStructure.class)); - - ReflectionAssert.assertPropertiesNotNull("Some properties null.", - factory.manufacturePojo(BioAssemblyData.class)); - testData(BioAssemblyData.class, factory.manufacturePojo(BioAssemblyData.class)); - - ReflectionAssert.assertPropertiesNotNull("Some properties null.", - factory.manufacturePojo(BioAssemblyTransformation.class)); - testData(BioAssemblyTransformation.class, factory.manufacturePojo(BioAssemblyTransformation.class)); - - ReflectionAssert.assertPropertiesNotNull("Some properties null.", - factory.manufacturePojo(Entity.class)); - testData(Entity.class, factory.manufacturePojo(Entity.class)); - - ReflectionAssert.assertPropertiesNotNull("Some properties null.", - factory.manufacturePojo(Group.class)); - testData(Group.class, factory.manufacturePojo(Group.class)); - - } - - - private void testData(@SuppressWarnings("rawtypes") Class beanClass, Object object) throws IllegalAccessException, IllegalArgumentException, InvocationTargetException, IntrospectionException { - for(PropertyDescriptor propertyDescriptor : - Introspector.getBeanInfo(beanClass).getPropertyDescriptors()){ - assertNotNull(propertyDescriptor.getReadMethod().invoke(object)); - } - } - - -} --- a/mmtf-serialization/src/test/java/org/rcsb/mmtf/serialization/TestMessagePack.java +++ /dev/null @@ -1,48 +0,0 @@ -package org.rcsb.mmtf.serialization; - -import static org.junit.Assert.assertNotNull; - -import java.io.ByteArrayInputStream; -import java.io.ByteArrayOutputStream; -import java.io.IOException; -import java.text.ParseException; - -import org.junit.Test; -import org.rcsb.mmtf.dataholders.MmtfStructure; - -import uk.co.jemos.podam.api.PodamFactory; -import uk.co.jemos.podam.api.PodamFactoryImpl; - -/** - * Class to test the message pack serializer and deserializer. - * @author Anthony Bradley - * - */ -public class TestMessagePack { - - - /** - * Test the deserialize. - */ - @Test - public void testDeserialize() throws ParseException, IOException { - MessagePackSerialization mmtfBeanSeDeMessagePackImpl = new MessagePackSerialization(); - byte[] source = new byte[] {(byte) (char) 129, (byte) (char)162, (byte) (char)100, (byte) (char)111, (byte) (char)1}; - ByteArrayInputStream bis = new ByteArrayInputStream(source); - MmtfStructure mmtfBean = mmtfBeanSeDeMessagePackImpl.deserialize(bis); - assertNotNull(mmtfBean); - } - - /** - * Test the serialize. - */ - @Test - public void testSerialize() throws IOException { - MessagePackSerialization mmtfBeanSeDeMessagePackImpl = new MessagePackSerialization(); - PodamFactory factory = new PodamFactoryImpl(); - MmtfStructure mmtfBean = factory.manufacturePojo(MmtfStructure.class); - ByteArrayOutputStream bos = new ByteArrayOutputStream(); - mmtfBeanSeDeMessagePackImpl.serialize(mmtfBean, bos); - assertNotNull(bos.toByteArray()); - } -} --- a/mmtf-codec/src/test/java/org/rcsb/mmtf/decoder/TestGenericDecoder.java +++ /dev/null @@ -1,62 +0,0 @@ -package org.rcsb.mmtf.decoder; - -import static org.junit.Assert.assertNotNull; - -import java.beans.IntrospectionException; -import java.beans.Introspector; -import java.beans.PropertyDescriptor; -import java.io.IOException; -import java.lang.reflect.InvocationTargetException; -import java.text.ParseException; - -import org.junit.Test; -import org.rcsb.mmtf.codec.Utils; -import org.rcsb.mmtf.dataholders.MmtfStructure; -import org.unitils.reflectionassert.ReflectionAssert; - -/** - * Test that the {@link GenericDecoder} works. - * @author Anthony Bradley - * - */ -public class TestGenericDecoder { - - /** - * Check that we decode all fields and that all getters are not null. - * @throws IOException an error reading in data - * @throws IntrospectionException an error with introspection - * @throws InvocationTargetException an error with introspection - * @throws IllegalArgumentException an error with introspection - * @throws IllegalAccessException an error with introspection - */ - @Test - public void testDecodeAllFields() throws IOException, ParseException, IllegalAccessException, - IllegalArgumentException, InvocationTargetException, IntrospectionException { - ClassLoader classLoader = getClass().getClassLoader(); - MmtfStructure mmtfBean = ReaderUtils.getDataFromFile(Utils.getResource("/mmtf/4CUP.mmtf")); - GenericDecoder genericDecoder = new GenericDecoder(mmtfBean); - ReflectionAssert.assertPropertiesNotNull("Some properties null after decoding", - genericDecoder); - for(PropertyDescriptor propertyDescriptor : - Introspector.getBeanInfo(MmtfStructure.class).getPropertyDescriptors()){ - assertNotNull(propertyDescriptor.getReadMethod().invoke(mmtfBean)); - } - // Check the decoder has been populated to - for(PropertyDescriptor propertyDescriptor : - Introspector.getBeanInfo(GenericDecoder.class).getPropertyDescriptors()){ - if(propertyDescriptor.getReadMethod()!=null){ - assertNotNull(propertyDescriptor.getReadMethod().invoke(genericDecoder)); - } - } - } - - /** - * Test that we can pass data into the inflator. - */ - @Test - public void testReader() { - DummyApiImpl dummyApiImpl = new DummyApiImpl(); - new StructureDataToAdapter(dummyApiImpl, new DummyTransferImpl()); - } - -} --- a/mmtf-codec/src/test/java/org/rcsb/mmtf/encoder/TestEncoder.java +++ /dev/null @@ -1,96 +0,0 @@ -package org.rcsb.mmtf.encoder; - -import static org.junit.Assert.assertNotNull; - -import java.beans.IntrospectionException; -import java.beans.Introspector; -import java.beans.PropertyDescriptor; -import java.io.File; -import java.io.IOException; -import java.lang.reflect.InvocationTargetException; - -import org.junit.Rule; -import org.junit.Test; -import org.junit.rules.TemporaryFolder; -import org.rcsb.mmtf.api.StructureAdapterInterface; -import org.unitils.reflectionassert.ReflectionAssert; - -/** - * A class to test the encoding of data using the encoders. - * @author Anthony Bradley - * - */ -public class TestEncoder { - - /** - * A test folder for testing writing files. - */ - @Rule - public TemporaryFolder testFolder = new TemporaryFolder(); - - /** - * Test whether calling all the set methods gives a none null get. - * @throws IOException an error converting byte arrays - */ - @Test - public void testGenricEncoder() throws IOException { - DummyApiImpl dummyApiImpl = new DummyApiImpl(); - EncoderInterface encoder = new GenericEncoder(dummyApiImpl); - ReflectionAssert.assertPropertiesNotNull("Some properties null after encoding", encoder.getMmtfEncodedStructure()); - } - - - /** - * Test the writer of data. - * @throws IllegalAccessException reflection based error - * @throws IllegalArgumentException reflection based error - * @throws InvocationTargetException reflection based error - * @throws IntrospectionException reflection based error - */ - @Test - public void testWriter() throws IllegalAccessException, IllegalArgumentException, InvocationTargetException, IntrospectionException { - AdapterToStructureData adapterToStructureData = getWriterEncoder(); - ReflectionAssert.assertPropertiesNotNull("Some properties null after writing", adapterToStructureData); - for(PropertyDescriptor propertyDescriptor : - Introspector.getBeanInfo(AdapterToStructureData.class).getPropertyDescriptors()){ - if(propertyDescriptor.getReadMethod()!=null){ - assertNotNull(propertyDescriptor.getReadMethod().invoke(adapterToStructureData)); - } - } - } - - - /** - * Test writing the data to a file. - * @throws IOException an error accessing the file system - */ - @Test - public void testWriteToFile() throws IOException { - AdapterToStructureData AdapterToStructureData = getWriterEncoder(); - File tempFile = testFolder.newFile("tmpfile"); - WriterUtils.writeDataToFile(AdapterToStructureData, tempFile.toPath()); - } - - - /** - * Utility function for getting the base data into the {@link AdapterToStructureData} - * implementation of the {@link StructureAdapterInterface}. - * @return the {@link AdapterToStructureData} instance - */ - private AdapterToStructureData getWriterEncoder() { - AdapterToStructureData adapterToStructureData = new AdapterToStructureData(); - adapterToStructureData.initStructure(1, 1, 1, 1, 1, "ABC"); - adapterToStructureData.setModelInfo(0, 1); - adapterToStructureData.setChainInfo("A","A",10); - adapterToStructureData.setGroupInfo("HET", 1, 'a', "D", 1, 1, 'A', 0, -1); - adapterToStructureData.setAtomInfo("A", 1, 'a', 1.0f, 1.0f, 1.0f,1.0f, 1.0f, "A", 1); - adapterToStructureData.setEntityInfo(new int[1], "A", "A", "A"); - adapterToStructureData.setGroupBond(0, 0, 1); - adapterToStructureData.setHeaderInfo(1.0f, 1.0f, 1.0f, "A", "A", "A", new String[1]); - adapterToStructureData.setInterGroupBond(0, 0, 1); - adapterToStructureData.setBioAssemblyTrans(0, new int[1], new double[6], "1"); - adapterToStructureData.setXtalInfo("A", new float[6], new double[16][16]); - adapterToStructureData.finalizeStructure(); - return adapterToStructureData; - } -} --- a/mmtf-codec/src/test/java/org/rcsb/mmtf/serialization/mp/MessagePackSerializationTest.java +++ /dev/null @@ -1,107 +0,0 @@ -package org.rcsb.mmtf.serialization.mp; - -import org.rcsb.mmtf.utils.Lines; -import java.io.ByteArrayInputStream; -import java.io.ByteArrayOutputStream; -import java.io.IOException; -import java.io.InputStream; -import java.net.URL; -import java.text.ParseException; -import java.util.ArrayList; -import java.util.List; -import java.util.Random; - -import org.junit.Test; -import org.rcsb.mmtf.api.StructureDataInterface; -import org.rcsb.mmtf.dataholders.MmtfStructure; -import org.rcsb.mmtf.decoder.GenericDecoder; -import org.rcsb.mmtf.decoder.ReaderUtils; -import org.rcsb.mmtf.serialization.MessagePackSerialization; - -import org.unitils.reflectionassert.ReflectionAssert; - -/** - * Tests if both MessagePack decoding methods, Jackson and the manual object - * creation gives identical data. - * - */ -public class MessagePackSerializationTest { - - private final int n = 10; // how many structures should be tested - private final List testCodes; - - public MessagePackSerializationTest() throws IOException { - testCodes = getTestCodes(); - } - - private List getTestCodes() throws IOException { - List result = new ArrayList<>(); - Random random = new Random(); - int seed = random.nextInt(); - System.out.println("Using seed " + seed + " to select " + n + " random " - + "structures for MessagePack testing."); - random = new Random(seed); - List codes = getAllPdbCodes(); - for (int i = 0; i < Math.min(n, codes.size()); i++) { - int r = random.nextInt(codes.size()); - String code = codes.get(r); - codes.remove(r); - result.add(code); - } - return result; - } - - public List getAllPdbCodes() throws IOException { - List codes = new ArrayList<>(); - for (String line : Lines.readResource("/mmtf/pdb_codes.gz")) { - String code = line.trim().substring(0, 4); - codes.add(code); - } - return codes; - } - - /** - * Decodes the MMTF from the MessagePack data. - */ - private StructureDataInterface parse(byte[] bytes) throws IOException, ParseException { - MmtfStructure mmtf = ReaderUtils.getDataFromInputStream( - new ByteArrayInputStream(bytes)); - GenericDecoder gd = new GenericDecoder(mmtf); - return gd; - } - - private byte[] fetchMmtf(String code) throws IOException { - ByteArrayOutputStream outputStream = new ByteArrayOutputStream(); - String url = "http://mmtf.rcsb.org/v1.0/full/" + code + ".mmtf.gz"; - try (InputStream is = new URL(url).openStream()) { - byte[] chunk = new byte[4096]; - int bytesRead; - while ((bytesRead = is.read(chunk)) > 0) { - outputStream.write(chunk, 0, bytesRead); - } - } - return outputStream.toByteArray(); - } - - @Test - public void testByComparisonWithJackson() throws IOException { - - for (String code : testCodes) { - try { - byte[] zipped = fetchMmtf(code); - byte[] bytes = ReaderUtils.deflateGzip(zipped); - - MessagePackSerialization.setJackson(false); - StructureDataInterface sdiJmol = parse(bytes); - - MessagePackSerialization.setJackson(true); - StructureDataInterface sdiJackson = parse(bytes); - - ReflectionAssert.assertReflectionEquals(sdiJackson, sdiJmol); - } catch (Exception ex) { - throw new RuntimeException(code, ex); - } - } - } - -}