http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/316e4a8a/taverna-robundle/src/test/java/org/apache/taverna/robundle/TestExample.java ---------------------------------------------------------------------- diff --git a/taverna-robundle/src/test/java/org/apache/taverna/robundle/TestExample.java b/taverna-robundle/src/test/java/org/apache/taverna/robundle/TestExample.java deleted file mode 100644 index 51767f5..0000000 --- a/taverna-robundle/src/test/java/org/apache/taverna/robundle/TestExample.java +++ /dev/null @@ -1,107 +0,0 @@ -package org.apache.taverna.robundle; - -/* - * Licensed to the Apache Software Foundation (ASF) under one - * or more contributor license agreements. See the NOTICE file - * distributed with this work for additional information - * regarding copyright ownership. The ASF licenses this file - * to you under the Apache License, Version 2.0 (the - * "License"); you may not use this file except in compliance - * with the License. You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, - * software distributed under the License is distributed on an - * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY - * KIND, either express or implied. See the License for the - * specific language governing permissions and limitations - * under the License. - */ - - -import static org.junit.Assert.assertEquals; -import static org.junit.Assert.assertNotNull; -import static org.junit.Assert.assertTrue; - -import java.io.OutputStream; -import java.net.URI; -import java.nio.charset.Charset; -import java.nio.file.Files; -import java.nio.file.Path; -import java.nio.file.StandardCopyOption; -import java.nio.file.StandardOpenOption; - -import org.apache.taverna.robundle.Bundle; -import org.apache.taverna.robundle.Bundles; -import org.junit.Test; - -public class TestExample { - @Test - public void example() throws Exception { - // Create a new (temporary) RO bundle - Bundle bundle = Bundles.createBundle(); - - // Get the inputs - Path inputs = bundle.getRoot().resolve("inputs"); - Files.createDirectory(inputs); - - // Get an input port: - Path in1 = inputs.resolve("in1"); - - // Setting a string value for the input port: - Bundles.setStringValue(in1, "Hello"); - - // And retrieving it - assertTrue(Bundles.isValue(in1)); - assertEquals("Hello", Bundles.getStringValue(in1)); - - // Or just use the regular Files methods: - int lines = 0; - for (String line : Files.readAllLines(in1, Charset.forName("UTF-8"))) { - assertEquals("Hello", line); - lines++; - } - assertEquals(1, lines); - - // Binaries and large files are done through the Files API - try (OutputStream out = Files.newOutputStream(in1, - StandardOpenOption.APPEND)) { - out.write(32); - } - // Or Java 7 style - Path localFile = Files.createTempFile("", ".txt"); - Files.copy(in1, localFile, StandardCopyOption.REPLACE_EXISTING); - //System.out.println("Written to: " + localFile); - - Files.copy(localFile, bundle.getRoot().resolve("out1")); - - // Representing references - URI ref = URI.create("http://example.com/external.txt";); - Path out3 = bundle.getRoot().resolve("out3"); - Bundles.setReference(out3, ref); - if (Bundles.isReference(out3)) { - URI resolved = Bundles.getReference(out3); - assertNotNull(resolved); - //System.out.println(resolved); - } - - // Saving a bundle: - Path zip = Files.createTempFile("bundle", ".zip"); - Bundles.closeAndSaveBundle(bundle, zip); - // NOTE: From now "bundle" and its Path's are CLOSED - // and can no longer be accessed - - //System.out.println("Saved to " + zip); - - // Loading a bundle back from disk - try (Bundle bundle2 = Bundles.openBundle(zip)) { - assertEquals(zip, bundle2.getSource()); - } - - // if (Desktop.isDesktopSupported()) { - // // Open ZIP file for browsing - // Desktop.getDesktop().open(zip.toFile()); - // } - } -}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/316e4a8a/taverna-robundle/src/test/java/org/apache/taverna/robundle/fs/Helper.java ---------------------------------------------------------------------- diff --git a/taverna-robundle/src/test/java/org/apache/taverna/robundle/fs/Helper.java b/taverna-robundle/src/test/java/org/apache/taverna/robundle/fs/Helper.java deleted file mode 100644 index 8538c30..0000000 --- a/taverna-robundle/src/test/java/org/apache/taverna/robundle/fs/Helper.java +++ /dev/null @@ -1,50 +0,0 @@ -package org.apache.taverna.robundle.fs; - -/* - * Licensed to the Apache Software Foundation (ASF) under one - * or more contributor license agreements. See the NOTICE file - * distributed with this work for additional information - * regarding copyright ownership. The ASF licenses this file - * to you under the Apache License, Version 2.0 (the - * "License"); you may not use this file except in compliance - * with the License. You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, - * software distributed under the License is distributed on an - * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY - * KIND, either express or implied. See the License for the - * specific language governing permissions and limitations - * under the License. - */ - - -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; - -import org.apache.taverna.robundle.Bundles; -import org.apache.taverna.robundle.fs.BundleFileSystem; -import org.apache.taverna.robundle.fs.BundleFileSystemProvider; -import org.junit.After; -import org.junit.Before; - -public class Helper { - protected BundleFileSystem fs; - - @Before - public void makeFS() throws IOException { - fs = BundleFileSystemProvider.newFileSystemFromTemporary(); - } - - @After - public void closeAndDeleteFS() throws IOException { - fs.close(); - Path source = fs.getSource(); - Files.deleteIfExists(source); - if (source.getParent().getFileName().toString().startsWith("robundle")) { - Bundles.deleteRecursively(source.getParent()); - } - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/316e4a8a/taverna-robundle/src/test/java/org/apache/taverna/robundle/fs/MemoryEfficiencyIT.java ---------------------------------------------------------------------- diff --git a/taverna-robundle/src/test/java/org/apache/taverna/robundle/fs/MemoryEfficiencyIT.java b/taverna-robundle/src/test/java/org/apache/taverna/robundle/fs/MemoryEfficiencyIT.java deleted file mode 100644 index a0d7ed3..0000000 --- a/taverna-robundle/src/test/java/org/apache/taverna/robundle/fs/MemoryEfficiencyIT.java +++ /dev/null @@ -1,255 +0,0 @@ -package org.apache.taverna.robundle.fs; - -/* - * Licensed to the Apache Software Foundation (ASF) under one - * or more contributor license agreements. See the NOTICE file - * distributed with this work for additional information - * regarding copyright ownership. The ASF licenses this file - * to you under the Apache License, Version 2.0 (the - * "License"); you may not use this file except in compliance - * with the License. You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, - * software distributed under the License is distributed on an - * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY - * KIND, either express or implied. See the License for the - * specific language governing permissions and limitations - * under the License. - */ - - -import static org.junit.Assert.assertTrue; - -import java.io.IOException; -import java.io.OutputStream; -import java.nio.ByteBuffer; -import java.nio.channels.FileChannel; -import java.nio.file.Files; -import java.nio.file.Path; -import java.nio.file.StandardOpenOption; -import java.util.Date; -import java.util.Random; -import java.util.concurrent.ExecutorService; -import java.util.concurrent.Executors; -import java.util.concurrent.TimeUnit; - -import org.apache.taverna.robundle.Bundles; -import org.apache.taverna.robundle.utils.RecursiveCopyFileVisitor.RecursiveCopyOption; -import org.junit.Assume; -import org.junit.Test; - -public class MemoryEfficiencyIT extends Helper { - private static final int MANY_FOLDERS = 100; - private static final int MANY_FILS = 10000; - private Runtime rt = Runtime.getRuntime(); - - // delays to allow garbage collection to run - private static final long GC_DELAY = 300; - private static final int kiB = 1024; - - private static final int MiB = 1024 * 1024; - private static final long GiB = 1024l * 1024l * 1024l; - - Random rand = new Random(); - int MAX_WORKERS = 10; - - @Test - public void writeManyFiles() throws Exception { - - long usedBefore = usedMemory(); - - Path folder = fs.getPath("folder"); - - for (int i = 0; i < MANY_FOLDERS; i++) { - Path dir = folder.resolve("dir" + i); - Files.createDirectories(dir); - } - - final byte[] pattern = new byte[8 * kiB]; - rand.nextBytes(pattern); - - ExecutorService pool = Executors.newFixedThreadPool(MAX_WORKERS); - try { - int numFiles = MANY_FILS; - System.out.println("Writing " + numFiles - + " files in parallell over max " + MAX_WORKERS - + " threads"); - for (int i = 0; i < numFiles; i++) { - int folderNo = i % 100; - Path dir = folder.resolve("dir" + folderNo); - final Path file = dir.resolve("file" + i); - pool.submit(new Runnable() { - @Override - public void run() { - try (OutputStream newOutputStream = Files - .newOutputStream(file)) { - newOutputStream.write(pattern); - } catch (IOException e) { - e.printStackTrace(); - } - }; - }); - } - pool.shutdown(); - assertTrue("Timed out waiting for threads", - pool.awaitTermination(60, TimeUnit.SECONDS)); - System.out.println("Done"); - } finally { - pool.shutdownNow(); - } - long usedAfterCloseFile = usedMemory(); - assertTrue(usedAfterCloseFile - usedBefore < 10 * MiB); - - Date startedRecurse = new Date(); - System.out.println("Recursively copying folder"); - Bundles.copyRecursively(folder, fs.getPath("copy"), - RecursiveCopyOption.IGNORE_ERRORS); - long duration = new Date().getTime() - startedRecurse.getTime(); - System.out.println("Done in " + duration / 1000 + "s"); - - long usedAfterRecursive = usedMemory(); - assertTrue(usedAfterRecursive - usedBefore < 20 * MiB); - - fs.close(); - long zipSize = Files.size(fs.getSource()); - System.out.println("ZIP: " + zipSize / MiB + " MiB"); - long usedAfterCloseFS = usedMemory(); - assertTrue(usedAfterCloseFS - usedBefore < 20 * MiB); - assertTrue(usedAfterCloseFS < zipSize); - - } - - /** - * This file may take a few minutes to complete depending on your OS and - * disk - * - */ - @Test - public void writeGigaFile() throws Exception { - - long usedBefore = usedMemory(); - - Path file = fs.getPath("bigfile"); - long size = 5l * GiB; - Assume.assumeTrue("This test requires at least " + size / GiB - + "GiB free disk space", - fs.getFileStore().getUsableSpace() < size); - System.out.println("Writing " + size / GiB + "GiB to bundle"); - - // We'll use FileChannel as it allows calling .position. This should - // be very fast on UNIX which allows zero-padding, but on Windows - // this will still take a while as it writes 5 GiB of \00s to disk. - - // Another downside is that the ZipFileProvider compresses the file - // once the file channel is closed, requiring ~5 GB disk space - try (FileChannel bc = FileChannel.open(file, StandardOpenOption.WRITE, - StandardOpenOption.SPARSE, StandardOpenOption.CREATE_NEW)) { - bc.position(size); - ByteBuffer src = ByteBuffer.allocateDirect(1024); - bc.write(src); - } - - long fileSize = Files.size(file); - assertTrue(fileSize > size); - System.out.println("Written " + fileSize / MiB); - long usedAfterCloseFile = usedMemory(); - assertTrue(usedAfterCloseFile - usedBefore < 10 * MiB); - - fs.close(); - long zipSize = Files.size(fs.getSource()); - System.out.println("ZIP: " + zipSize / MiB + " MiB"); - // Zeros should compress fairly well - assertTrue(zipSize < 10 * MiB); - - long usedAfterCloseFS = usedMemory(); - assertTrue(usedAfterCloseFS - usedBefore < 10 * MiB); - } - - @Test - public void writeBigFile() throws Exception { - - long usedBefore = usedMemory(); - long size = sufficientlyBig(); - long limit = size / 2; - - Path file = fs.getPath("bigfile"); - - // Big enough random bytes to blow ZIP's compression buffer - byte[] pattern = new byte[MiB]; - rand.nextBytes(pattern); - - long written = 0; - try (OutputStream newOutputStream = Files.newOutputStream(file)) { - while (written < size) { - newOutputStream.write(pattern); - written += pattern.length; - } - pattern = null; - rand = null; - long usedAfterWrite = usedMemory(); - assertTrue(usedAfterWrite - usedBefore < limit); - } - long fileSize = Files.size(file); - assertTrue(fileSize >= size); - // System.out.println("Written " + fileSize/MiB + ", needed " + - // size/MiB); - long usedAfterCloseFile = usedMemory(); - assertTrue(usedAfterCloseFile - usedBefore < limit); - - fs.close(); - long zipSize = Files.size(fs.getSource()); - System.out.println("ZIP: " + zipSize / MiB + " MiB"); - assertTrue(zipSize > limit); - - long usedAfterCloseFS = usedMemory(); - assertTrue(usedAfterCloseFS - usedBefore < 10 * MiB); - } - - private long sufficientlyBig() throws IOException { - long usableSpace = fs.getFileStore().getUsableSpace(); - long need = 64 * MiB; - if (need * 2 > usableSpace) { - String msg = "Not enough disk space (%s MiB < %s)"; - long freeSpace = usableSpace / MiB; - long needSpace = need * 2 / MiB; - throw new IllegalStateException(String.format(msg, freeSpace, - needSpace)); - } - return need; - } - - @Test - public void testUsedMemory() throws Exception { - long before = usedMemory(); - byte[] waste = new byte[50 * MiB]; - waste[0] = 13; - waste[waste.length - 1] = 37; - long after = usedMemory(); - - assertTrue((after - before) > 10 * MiB); - waste = null; - long now = usedMemory(); - // and it should have been freed again - assertTrue((after - now) > 10 * MiB); - - } - - public long usedMemory() throws InterruptedException { - runGC(); - long used = rt.totalMemory() - rt.freeMemory(); - System.out.println("Used memory: " + used / MiB + " MiB"); - return used; - } - - public void runGC() { - System.gc(); - try { - Thread.sleep(GC_DELAY); - System.gc(); - Thread.sleep(GC_DELAY); - } catch (InterruptedException e) { - } - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/316e4a8a/taverna-robundle/src/test/java/org/apache/taverna/robundle/fs/TestBundleFileSystem.java ---------------------------------------------------------------------- diff --git a/taverna-robundle/src/test/java/org/apache/taverna/robundle/fs/TestBundleFileSystem.java b/taverna-robundle/src/test/java/org/apache/taverna/robundle/fs/TestBundleFileSystem.java deleted file mode 100644 index 6a4b7bd..0000000 --- a/taverna-robundle/src/test/java/org/apache/taverna/robundle/fs/TestBundleFileSystem.java +++ /dev/null @@ -1,236 +0,0 @@ -package org.apache.taverna.robundle.fs; - -/* - * Licensed to the Apache Software Foundation (ASF) under one - * or more contributor license agreements. See the NOTICE file - * distributed with this work for additional information - * regarding copyright ownership. The ASF licenses this file - * to you under the Apache License, Version 2.0 (the - * "License"); you may not use this file except in compliance - * with the License. You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, - * software distributed under the License is distributed on an - * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY - * KIND, either express or implied. See the License for the - * specific language governing permissions and limitations - * under the License. - */ - - -import static org.junit.Assert.assertEquals; -import static org.junit.Assert.assertFalse; -import static org.junit.Assert.assertTrue; -import static org.junit.Assert.fail; - -import java.io.IOException; -import java.nio.charset.Charset; -import java.nio.file.FileAlreadyExistsException; -import java.nio.file.Files; -import java.nio.file.NoSuchFileException; -import java.nio.file.Path; -import java.nio.file.attribute.BasicFileAttributeView; -import java.nio.file.attribute.FileTime; -import java.util.concurrent.TimeUnit; - -import org.apache.taverna.robundle.Bundle; -import org.apache.taverna.robundle.Bundles; -import org.junit.Test; - -public class TestBundleFileSystem extends Helper { - - @Test - public void writeToNewFile() throws Exception { - Path file = fs.getPath("test.txt"); - Files.newBufferedWriter(file, Charset.defaultCharset()).close(); - } - - @Test - public void reopenNew() throws Exception { - Path x = Files.createTempFile("temp", ".zip"); - Bundle bundle = Bundles.createBundle(x); - Path newFile = Files.createTempFile("temp", ".zip"); - Bundles.closeAndSaveBundle(bundle, newFile); - Bundles.openBundle(newFile); - } - - @Test - public void closeAndSaveToPreserveOriginal() throws Exception { - Path x = Files.createTempFile("temp", ".zip"); - Bundle bundle = Bundles.createBundle(x); - Path newFile = Files.createTempFile("temp", ".zip"); - Bundles.closeAndSaveBundle(bundle, newFile); - Bundles.openBundle(x); - } - - /** - * Test that BundleFileSystem does not allow a ZIP file to also become a - * directory. See http://stackoverflow.com/questions/16588321/ as Java 7'z - * ZIPFS normally allows this (!) - * - * @throws Exception - */ - @Test - public void fileAndDirectory() throws Exception { - Path folder = fs.getPath("folder"); - - // To test on local file system, uncomment next 2 lines: - // Path test = Files.createTempDirectory("test"); - // folder = test.resolve("folder"); - - assertFalse(Files.exists(folder)); - Files.createFile(folder); - assertTrue(Files.exists(folder)); - assertTrue(Files.isRegularFile(folder)); - assertFalse(Files.isDirectory(folder)); - - try { - Files.createDirectory(folder); - fail("Should have thrown FileAlreadyExistsException"); - } catch (FileAlreadyExistsException ex) { - } - assertFalse(Files.isDirectory(folder)); - - try { - Files.createDirectories(folder); - fail("Should have thrown FileAlreadyExistsException"); - } catch (FileAlreadyExistsException ex) { - } - assertFalse(Files.isDirectory(folder)); - - Path child = folder.resolve("child"); - - try { - Files.createFile(child); - fail("Should have thrown NoSuchFileException"); - } catch (NoSuchFileException ex) { - } - assertFalse(Files.exists(child)); - - assertTrue(Files.isRegularFile(folder)); - assertFalse(Files.isDirectory(folder)); - assertFalse(Files.isDirectory(child.getParent())); - assertFalse(Files.isDirectory(fs.getPath("folder/"))); - } - - /** - * Test that BundleFileSystem does not allow a ZIP directory to also become - * a file. See http://stackoverflow.com/questions/16588321/ as Java 7'z - * ZIPFS normally allows this (!) - * - * @throws Exception - */ - @Test - public void directoryAndFile() throws Exception { - Path folderSlash = fs.getPath("folder/"); - Path folder = fs.getPath("folder"); - - // Uncomment next 3 lines to test on local FS - // Path test = Files.createTempDirectory("test"); - // folderSlash = test.resolve("folder/"); - // folder = test.resolve("folder"); - - assertFalse(Files.exists(folderSlash)); - - Files.createDirectory(folderSlash); - assertTrue(Files.exists(folderSlash)); - assertFalse(Files.isRegularFile(folderSlash)); - assertTrue(Files.isDirectory(folderSlash)); - - try { - Files.createDirectory(folderSlash); - fail("Should have thrown FileAlreadyExistsException"); - } catch (FileAlreadyExistsException ex) { - } - - try { - Files.createFile(folderSlash); - fail("Should have thrown IOException"); - } catch (IOException ex) { - } - - try { - Files.createFile(folder); - fail("Should have thrown IOException"); - } catch (IOException ex) { - } - - Path child = folderSlash.resolve("child"); - Files.createFile(child); - - assertTrue(Files.exists(folder)); - assertTrue(Files.exists(folderSlash)); - - assertFalse(Files.isRegularFile(folder)); - assertFalse(Files.isRegularFile(folderSlash)); - - assertTrue(Files.isDirectory(folder)); - assertTrue(Files.isDirectory(folderSlash)); - - } - - @Test - public void setLastModifiedTime() throws Exception { - Path root = fs.getRootDirectories().iterator().next(); - - Path folder = root.resolve("folder"); - Files.createDirectory(folder); - - Path file = root.resolve("file"); - Files.createFile(file); - - int manyDays = 365 * 12; - FileTime someTimeAgo = FileTime.from(manyDays, TimeUnit.DAYS); - Files.setLastModifiedTime(folder, someTimeAgo); - Files.setLastModifiedTime(file, someTimeAgo); - Files.setLastModifiedTime(root, someTimeAgo); - - // Should be equal, +/- 2 seconds (allowing precision loss) - assertEquals((double) someTimeAgo.toMillis(), Files - .getLastModifiedTime(folder).toMillis(), 2001); - assertEquals((double) someTimeAgo.toMillis(), Files - .getLastModifiedTime(file).toMillis(), 2001); - - // Fails as we'll get back -1 instead - // assertEquals((double)someTimeAgo.toMillis(), - // Files.getLastModifiedTime(root).toMillis(), 2001); - } - - @Test - public void creationTime() throws Exception { - Path root = fs.getRootDirectories().iterator().next(); - - Path folder = root.resolve("folder"); - Files.createDirectory(folder); - - Path file = root.resolve("file"); - Files.createFile(file); - - int manyDays = 365 * 12; - FileTime someTimeAgo = FileTime.from(manyDays, TimeUnit.DAYS); - - Files.getFileAttributeView(folder, BasicFileAttributeView.class) - .setTimes(null, null, someTimeAgo); - Files.getFileAttributeView(file, BasicFileAttributeView.class) - .setTimes(null, null, someTimeAgo); - Files.getFileAttributeView(root, BasicFileAttributeView.class) - .setTimes(null, null, someTimeAgo); - - // Should be equal, +/- 2 seconds - assertEquals((double) someTimeAgo.toMillis(), - (double) ((FileTime) Files.getAttribute(file, "creationTime")) - .toMillis(), 2001); - assertEquals( - (double) someTimeAgo.toMillis(), - (double) ((FileTime) Files.getAttribute(folder, "creationTime")) - .toMillis(), 2001); - - // FIXME: FAils with NullPointerException! :( - // assertEquals((double)someTimeAgo.toMillis(), (double) - // ((FileTime)Files.getAttribute(root, "creationTime")).toMillis(), - // 2001); - - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/316e4a8a/taverna-robundle/src/test/java/org/apache/taverna/robundle/fs/TestBundleFileTypeDetector.java ---------------------------------------------------------------------- diff --git a/taverna-robundle/src/test/java/org/apache/taverna/robundle/fs/TestBundleFileTypeDetector.java b/taverna-robundle/src/test/java/org/apache/taverna/robundle/fs/TestBundleFileTypeDetector.java deleted file mode 100644 index ca116b0..0000000 --- a/taverna-robundle/src/test/java/org/apache/taverna/robundle/fs/TestBundleFileTypeDetector.java +++ /dev/null @@ -1,97 +0,0 @@ -package org.apache.taverna.robundle.fs; - -/* - * Licensed to the Apache Software Foundation (ASF) under one - * or more contributor license agreements. See the NOTICE file - * distributed with this work for additional information - * regarding copyright ownership. The ASF licenses this file - * to you under the Apache License, Version 2.0 (the - * "License"); you may not use this file except in compliance - * with the License. You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, - * software distributed under the License is distributed on an - * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY - * KIND, either express or implied. See the License for the - * specific language governing permissions and limitations - * under the License. - */ - - -import static org.junit.Assert.assertEquals; -import static org.junit.Assert.assertNull; -import static org.junit.Assert.assertTrue; - -import java.nio.charset.Charset; -import java.nio.file.Files; -import java.nio.file.Path; -import java.util.Arrays; -import java.util.zip.ZipEntry; -import java.util.zip.ZipOutputStream; - -import org.apache.taverna.robundle.Bundle; -import org.apache.taverna.robundle.Bundles; -import org.apache.taverna.robundle.fs.BundleFileTypeDetector; -import org.junit.Test; - -public class TestBundleFileTypeDetector { - @Test - public void detectRoBundle() throws Exception { - BundleFileTypeDetector detector = new BundleFileTypeDetector(); - try (Bundle bundle = Bundles.createBundle()) { - assertEquals("application/vnd.wf4ever.robundle+zip", - detector.probeContentType(bundle.getSource())); - } - } - - @Test - public void detectEmptyZip() throws Exception { - BundleFileTypeDetector detector = new BundleFileTypeDetector(); - - Path zip = Files.createTempFile("test", ".bin"); - zip.toFile().deleteOnExit(); - try (ZipOutputStream zout = new ZipOutputStream( - Files.newOutputStream(zip))) { - ZipEntry entry = new ZipEntry("e"); - zout.putNextEntry(entry); - zout.closeEntry(); - - } - assertEquals("application/zip", detector.probeContentType(zip)); - } - - @Test - public void detectNonZip() throws Exception { - BundleFileTypeDetector detector = new BundleFileTypeDetector(); - - Path file = Files.createTempFile("test", ".bin"); - file.toFile().deleteOnExit(); - Files.write(file, Arrays.asList("This is just some text", - "added here to make the file", "larger than 38 bytes"), Charset - .forName("UTF8")); - assertTrue(Files.size(file) > 38); - assertNull(detector.probeContentType(file)); - } - - @Test - public void detectEmpty() throws Exception { - BundleFileTypeDetector detector = new BundleFileTypeDetector(); - - Path file = Files.createTempFile("test", ".bin"); - file.toFile().deleteOnExit(); - assertEquals(0, Files.size(file)); - assertNull(detector.probeContentType(file)); - } - - @Test - public void detectorSPI() throws Exception { - try (Bundle bundle = Bundles.createBundle()) { - assertEquals("application/vnd.wf4ever.robundle+zip", - Files.probeContentType(bundle.getSource())); - } - - } - -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/316e4a8a/taverna-robundle/src/test/java/org/apache/taverna/robundle/fs/TestBundlePaths.java ---------------------------------------------------------------------- diff --git a/taverna-robundle/src/test/java/org/apache/taverna/robundle/fs/TestBundlePaths.java b/taverna-robundle/src/test/java/org/apache/taverna/robundle/fs/TestBundlePaths.java deleted file mode 100644 index 93f3cdb..0000000 --- a/taverna-robundle/src/test/java/org/apache/taverna/robundle/fs/TestBundlePaths.java +++ /dev/null @@ -1,58 +0,0 @@ -package org.apache.taverna.robundle.fs; - -/* - * Licensed to the Apache Software Foundation (ASF) under one - * or more contributor license agreements. See the NOTICE file - * distributed with this work for additional information - * regarding copyright ownership. The ASF licenses this file - * to you under the Apache License, Version 2.0 (the - * "License"); you may not use this file except in compliance - * with the License. You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, - * software distributed under the License is distributed on an - * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY - * KIND, either express or implied. See the License for the - * specific language governing permissions and limitations - * under the License. - */ - - -import static org.junit.Assert.assertEquals; -import static org.junit.Assert.assertFalse; -import static org.junit.Assert.assertNull; -import static org.junit.Assert.assertTrue; - -import java.nio.file.Path; - -import org.junit.Test; - -public class TestBundlePaths extends Helper { - - @Test - public void endsWith() throws Exception { - Path root = fs.getRootDirectory(); - Path barBazAbs = root.resolve("bar/baz"); - System.out.println(barBazAbs); - Path barBaz = root.relativize(barBazAbs); - assertEquals("bar/baz", barBaz.toString()); - assertTrue(barBaz.endsWith("bar/baz")); - assertFalse(barBaz.endsWith("bar/../bar/baz")); - Path climber = barBaz.resolve("../baz"); - assertEquals("bar/baz/../baz", climber.toString()); - assertTrue(climber.endsWith("../baz")); - assertFalse(climber.endsWith("bar/baz")); - Path climberNorm = climber.normalize(); - assertFalse(climberNorm.endsWith("../baz")); - assertTrue(climberNorm.endsWith("bar/baz")); - } - - @Test - public void parent() throws Exception { - Path root = fs.getRootDirectory(); - assertNull(root.getParent()); - } - -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/316e4a8a/taverna-robundle/src/test/java/org/apache/taverna/robundle/fs/TestFileSystemProvider.java ---------------------------------------------------------------------- diff --git a/taverna-robundle/src/test/java/org/apache/taverna/robundle/fs/TestFileSystemProvider.java b/taverna-robundle/src/test/java/org/apache/taverna/robundle/fs/TestFileSystemProvider.java deleted file mode 100644 index cdbcae4..0000000 --- a/taverna-robundle/src/test/java/org/apache/taverna/robundle/fs/TestFileSystemProvider.java +++ /dev/null @@ -1,278 +0,0 @@ -package org.apache.taverna.robundle.fs; - -/* - * Licensed to the Apache Software Foundation (ASF) under one - * or more contributor license agreements. See the NOTICE file - * distributed with this work for additional information - * regarding copyright ownership. The ASF licenses this file - * to you under the Apache License, Version 2.0 (the - * "License"); you may not use this file except in compliance - * with the License. You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, - * software distributed under the License is distributed on an - * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY - * KIND, either express or implied. See the License for the - * specific language governing permissions and limitations - * under the License. - */ - - -import static org.junit.Assert.assertEquals; -import static org.junit.Assert.assertSame; -import static org.junit.Assert.assertTrue; -import static org.junit.Assert.fail; - -import java.net.URI; -import java.nio.charset.Charset; -import java.nio.file.FileSystem; -import java.nio.file.FileSystems; -import java.nio.file.Files; -import java.nio.file.InvalidPathException; -import java.nio.file.Path; -import java.nio.file.spi.FileSystemProvider; -import java.util.Collections; -import java.util.HashMap; -import java.util.Map; - -import org.apache.taverna.robundle.fs.BundleFileSystem; -import org.apache.taverna.robundle.fs.BundleFileSystemProvider; -import org.junit.Assume; -import org.junit.Test; - -public class TestFileSystemProvider { - - @Test - public void getInstance() throws Exception { - assertSame(BundleFileSystemProvider.getInstance(), - BundleFileSystemProvider.getInstance()); - } - - @SuppressWarnings("deprecation") - @Test - public void getInstanceEquals() throws Exception { - assertEquals(BundleFileSystemProvider.getInstance(), - new BundleFileSystemProvider()); - } - - @SuppressWarnings("deprecation") - @Test - public void getInstanceHashCode() throws Exception { - assertEquals(BundleFileSystemProvider.getInstance().hashCode(), - new BundleFileSystemProvider().hashCode()); - } - - @SuppressWarnings({ "deprecation", "static-access" }) - @Test - public void sameOpen() throws Exception { - assertSame(BundleFileSystemProvider.getInstance().openFilesystems, - new BundleFileSystemProvider().openFilesystems); - } - - @Test - public void installedProviders() throws Exception { - for (FileSystemProvider provider : FileSystemProvider - .installedProviders()) { - if (provider instanceof BundleFileSystemProvider) { - assertSame(provider, BundleFileSystemProvider.getInstance()); - return; - } - } - fail("Could not find BundleFileSystemProvider as installed provider"); - } - - @Test - public void newByURI() throws Exception { - - Path path = Files.createTempFile("test", "zip"); - path.toFile().deleteOnExit(); - BundleFileSystemProvider.createBundleAsZip(path, null); - - // HACK: Use a opaque version of app: with the file URI as scheme - // specific part - URI w = new URI("app", path.toUri().toASCIIString(), null); - try (FileSystem fs = FileSystems.newFileSystem(w, - Collections.<String, Object> emptyMap())) { - assertTrue(fs instanceof BundleFileSystem); - } - } - - @Test - public void bundleWithSpaces() throws Exception { - Path path = Files.createTempFile("with several spaces", ".zip"); - path.toFile().deleteOnExit(); - Files.delete(path); - - URI app = new URI("app", path.toUri().toString(), null); - assertTrue(app.toASCIIString().contains("with%2520several%2520spaces")); - - Map<String, Object> env = new HashMap<>(); - env.put("create", "true"); - - try (FileSystem fs = FileSystems.newFileSystem(app, env)) { - } - assertTrue(Files.exists(path)); - // Reopen from now-existing Path to check that the URI is - // escaped in the same way - try (FileSystem fs = BundleFileSystemProvider - .newFileSystemFromExisting(path)) { - } - } - - @Test - public void bundleWithSpacesSource() throws Exception { - Path path = Files.createTempFile("with several spaces", ".zip"); - path.toFile().deleteOnExit(); - Files.delete(path); - - try (BundleFileSystem fs = BundleFileSystemProvider - .newFileSystemFromNew(path)) { - assertTrue(Files.exists(fs.getSource())); - assertEquals(path.toAbsolutePath(), fs.getSource()); - } - assertTrue(Files.exists(path)); - } - - @Test - public void bundleWithUnicode() throws Exception { - Path path; - try { - path = Files.createTempFile("with\u2301unicode\u263bhere", ".zip"); - } catch (InvalidPathException ex) { - Assume.assumeNoException( - "Can't test unicode filename, as -Dfile.encoding=" - + System.getProperty("file.encoding"), ex); - return; - } - path.toFile().deleteOnExit(); - Files.delete(path); - // System.out.println(path); // Should contain a electrical symbol and - // smiley - URI app = new URI("app", path.toUri().toString(), null); - // FIXME: The below passes on Windows 8 but not in Linux!? - // System.out.println(app); - // assertTrue(app.toString().contains("\u2301")); - // assertTrue(app.toString().contains("\u263b")); - - Map<String, Object> env = new HashMap<>(); - env.put("create", "true"); - - try (FileSystem fs = FileSystems.newFileSystem(app, env)) { - } - assertTrue(Files.exists(path)); - // Reopen from now-existing Path to check that the URI is - // escaped in the same way - try (FileSystem fs = BundleFileSystemProvider - .newFileSystemFromExisting(path)) { - } - } - - @Test - public void newFileSystemFromExisting() throws Exception { - Path path = Files.createTempFile("test", null); - path.toFile().deleteOnExit(); - Files.delete(path); - // Make the Bundle first - BundleFileSystemProvider.createBundleAsZip(path, "application/x-test"); - assertTrue(Files.exists(path)); - - try (BundleFileSystem f = BundleFileSystemProvider - .newFileSystemFromExisting(path)) { - assertEquals(path, f.getSource()); - assertEquals( - "application/x-test", - Files.readAllLines( - f.getRootDirectory().resolve("mimetype"), - Charset.forName("ASCII")).get(0)); - } - } - - @Test - public void newFileSystemFromExistingPath() throws Exception { - Path path = Files.createTempFile("test", null); - path.toFile().deleteOnExit(); - Files.delete(path); - // Make the Bundle first as we can't pass inn create=true :/ - BundleFileSystemProvider.createBundleAsZip(path, "application/x-test"); - assertTrue(Files.exists(path)); - - try (FileSystem fs = FileSystems.newFileSystem(path, getClass() - .getClassLoader())) { - assertEquals( - "application/x-test", - Files.readAllLines(fs.getPath("mimetype"), - Charset.forName("ASCII")).get(0)); - } - } - - @Test - public void newFileSystemFromNewDefaultMime() throws Exception { - Path path = Files.createTempFile("test", null); - path.toFile().deleteOnExit(); - Files.delete(path); - BundleFileSystem f = BundleFileSystemProvider - .newFileSystemFromNew(path); - assertTrue(Files.exists(path)); - assertEquals(path, f.getSource()); - assertEquals( - "application/vnd.wf4ever.robundle+zip", - Files.readAllLines(f.getRootDirectory().resolve("mimetype"), - Charset.forName("ASCII")).get(0)); - } - - @Test - public void newFileSystemURI() throws Exception { - Path path = Files.createTempFile("test", null); - path.toFile().deleteOnExit(); - Files.delete(path); - - URI uri = new URI("app", path.toUri().toASCIIString(), (String) null); - - Map<String, String> env = new HashMap<>(); - env.put("create", "true"); - // And the optional mimetype - env.put("mimetype", "application/x-test2"); - FileSystem f = FileSystems.newFileSystem(uri, env, getClass() - .getClassLoader()); - assertTrue(Files.exists(path)); - assertEquals( - "application/x-test2", - Files.readAllLines(f.getPath("mimetype"), - Charset.forName("ASCII")).get(0)); - } - - @Test - public void newFileSystemFromNew() throws Exception { - Path path = Files.createTempFile("test", null); - path.toFile().deleteOnExit(); - Files.delete(path); - path.toUri(); - BundleFileSystem f = BundleFileSystemProvider.newFileSystemFromNew( - path, "application/x-test2"); - assertTrue(Files.exists(path)); - assertEquals(path, f.getSource()); - assertEquals( - "application/x-test2", - Files.readAllLines(f.getRootDirectory().resolve("mimetype"), - Charset.forName("ASCII")).get(0)); - } - - @Test - public void newFileSystemFromTemporary() throws Exception { - Path source; - try (BundleFileSystem f = BundleFileSystemProvider - .newFileSystemFromTemporary()) { - source = f.getSource(); - assertTrue(Files.exists(source)); - assertEquals( - "application/vnd.wf4ever.robundle+zip", - Files.readAllLines( - f.getRootDirectory().resolve("mimetype"), - Charset.forName("ASCII")).get(0)); - } - Files.delete(source); - } - -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/316e4a8a/taverna-robundle/src/test/java/org/apache/taverna/robundle/fs/TestZipFS.java ---------------------------------------------------------------------- diff --git a/taverna-robundle/src/test/java/org/apache/taverna/robundle/fs/TestZipFS.java b/taverna-robundle/src/test/java/org/apache/taverna/robundle/fs/TestZipFS.java deleted file mode 100644 index 95939a8..0000000 --- a/taverna-robundle/src/test/java/org/apache/taverna/robundle/fs/TestZipFS.java +++ /dev/null @@ -1,213 +0,0 @@ -package org.apache.taverna.robundle.fs; - -/* - * Licensed to the Apache Software Foundation (ASF) under one - * or more contributor license agreements. See the NOTICE file - * distributed with this work for additional information - * regarding copyright ownership. The ASF licenses this file - * to you under the Apache License, Version 2.0 (the - * "License"); you may not use this file except in compliance - * with the License. You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, - * software distributed under the License is distributed on an - * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY - * KIND, either express or implied. See the License for the - * specific language governing permissions and limitations - * under the License. - */ - - -import static org.junit.Assert.assertEquals; -import static org.junit.Assert.assertFalse; -import static org.junit.Assert.assertTrue; -import static org.junit.Assert.fail; - -import java.io.IOException; -import java.net.URI; -import java.nio.channels.FileChannel; -import java.nio.file.DirectoryStream; -import java.nio.file.FileAlreadyExistsException; -import java.nio.file.FileSystem; -import java.nio.file.FileSystems; -import java.nio.file.Files; -import java.nio.file.NoSuchFileException; -import java.nio.file.Path; -import java.nio.file.StandardOpenOption; -import java.nio.file.attribute.FileTime; -import java.util.ArrayList; -import java.util.EnumSet; -import java.util.HashMap; -import java.util.List; -import java.util.Map; -import java.util.concurrent.TimeUnit; - -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -public class TestZipFS { - - private static Path zip; - private FileSystem fs; - - @Test - public void fileChannelCreateNew() throws Exception { - Path test = fs.getPath("test.txt"); - EnumSet<StandardOpenOption> options = EnumSet.<StandardOpenOption> of( - StandardOpenOption.CREATE_NEW, StandardOpenOption.WRITE); - fs.provider().newFileChannel(test, options); - } - - @Test - public void fileChannelCreate() throws Exception { - try { - Path test = fs.getPath("test.txt"); - FileChannel.open(test, StandardOpenOption.WRITE, - StandardOpenOption.CREATE).close(); - } catch (NoSuchFileException ex) { - System.err.println("Unexpected exception"); - ex.printStackTrace(); - // Bug in JDK - } - } - - @Test(expected = FileAlreadyExistsException.class) - public void fileChannelCreateFails() throws Exception { - Path test = fs.getPath("test.txt"); - Files.createFile(test); - FileChannel.open(test, StandardOpenOption.WRITE, - StandardOpenOption.CREATE_NEW).close(); - } - - @Test - public void fileChannelTruncate() throws Exception { - Path test = fs.getPath("test.txt"); - Files.write(test, new byte[1024]); - assertEquals(1024, Files.size(test)); - FileChannel.open(test, StandardOpenOption.WRITE, - StandardOpenOption.TRUNCATE_EXISTING).close(); - assertEquals(0, Files.size(test)); - } - - /** - * Verifies http://stackoverflow.com/questions/16588321/ as both ZIP format - * and Java 7 ZIPFS allows a folder and file to have the same name. - * - */ - @Test - public void directoryOrFile() throws Exception { - Path folder = fs.getPath("folder"); - assertFalse(Files.exists(folder)); - Files.createFile(folder); - assertTrue(Files.exists(folder)); - assertTrue(Files.isRegularFile(folder)); - assertFalse(Files.isDirectory(folder)); - - try { - Path folderCreated = Files.createDirectory(folder); - assertEquals(folder, folderCreated); - folder = folderCreated; - System.out.println(folder + " " + folderCreated); - - // Disable for now, just to see where this leads - // fail("Should have thrown FileAlreadyExistsException"); - } catch (FileAlreadyExistsException ex) { - } - - // For some reason the second createDirectory() fails correctly - try { - Files.createDirectory(folder); - fail("Should have thrown FileAlreadyExistsException"); - } catch (FileAlreadyExistsException ex) { - } - - Path child = folder.resolve("child"); - Files.createFile(child); - - // Look, it's both a file and folder! - // Can this be asserted? - assertTrue(Files.isRegularFile(folder)); - // Yes, if you include the final / - assertTrue(Files.isDirectory(fs.getPath("folder/"))); - // But not the parent - // assertTrue(Files.isDirectory(child.getParent())); - // Or the original Path - // assertTrue(Files.isDirectory(folder)); - - fs.close(); - // What if we open it again.. can we find both? - try (FileSystem fs2 = FileSystems.newFileSystem(zip, null)) { - assertTrue(Files.isRegularFile(fs2.getPath("folder"))); - assertTrue(Files.isRegularFile(fs2.getPath("folder/child"))); - assertTrue(Files.isDirectory(fs2.getPath("folder/"))); - - // We can even list the folder - try (DirectoryStream<Path> s = Files.newDirectoryStream(fs2 - .getPath("folder/"))) { - boolean found = false; - for (Path p : s) { - found = p.endsWith("child"); - } - assertTrue("Did not find 'child'", found); - } - // But if we list the root, do we find "folder" or "folder/"? - Path root = fs2.getRootDirectories().iterator().next(); - try (DirectoryStream<Path> s = Files.newDirectoryStream(root)) { - List<String> paths = new ArrayList<>(); - for (Path p : s) { - paths.add(p.toString()); - } - // We find both! - assertEquals(2, paths.size()); - assertTrue(paths.contains("/folder")); - assertTrue(paths.contains("/folder/")); - } - // SO does that mean this is a feature, and not a bug? - // See http://stackoverflow.com/questions/16588321/ for more - } - - } - - @Test - public void setLastModifiedTime() throws Exception { - Path root = fs.getRootDirectories().iterator().next(); - - Path folder = root.resolve("folder"); - Files.createDirectory(folder); - - Path file = root.resolve("file"); - Files.createFile(file); - - FileTime someTimeAgo = FileTime.from(365 * 12, TimeUnit.DAYS); - Files.setLastModifiedTime(folder, someTimeAgo); - Files.setLastModifiedTime(file, someTimeAgo); - try { - Files.setLastModifiedTime(root, someTimeAgo); - } catch (NoSuchFileException ex) { - System.err - .println("Unexpected failure of setLastModifiedTime on root"); - ex.printStackTrace(); - } - } - - @Before - public void tempZipFS() throws Exception { - zip = Files.createTempFile("test", ".zip"); - Files.delete(zip); - System.out.println(zip); - URI jar = new URI("jar", zip.toUri().toString(), null); - Map<String, Object> env = new HashMap<>(); - env.put("create", "true"); - fs = FileSystems.newFileSystem(jar, env); - } - - @After - public void deleteTempFS() throws IOException { - fs.close(); - Files.deleteIfExists(zip); - } - -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/316e4a8a/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/TestManifest.java ---------------------------------------------------------------------- diff --git a/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/TestManifest.java b/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/TestManifest.java deleted file mode 100644 index 3ca4030..0000000 --- a/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/TestManifest.java +++ /dev/null @@ -1,280 +0,0 @@ -package org.apache.taverna.robundle.manifest; - -/* - * Licensed to the Apache Software Foundation (ASF) under one - * or more contributor license agreements. See the NOTICE file - * distributed with this work for additional information - * regarding copyright ownership. The ASF licenses this file - * to you under the Apache License, Version 2.0 (the - * "License"); you may not use this file except in compliance - * with the License. You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, - * software distributed under the License is distributed on an - * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY - * KIND, either express or implied. See the License for the - * specific language governing permissions and limitations - * under the License. - */ - - -import static org.junit.Assert.assertEquals; -import static org.junit.Assert.assertFalse; -import static org.junit.Assert.assertNotNull; -import static org.junit.Assert.assertNull; -import static org.junit.Assert.assertTrue; - -import java.io.ByteArrayOutputStream; -import java.io.IOException; -import java.io.InputStream; -import java.net.URI; -import java.nio.file.Files; -import java.nio.file.Path; -import java.nio.file.Paths; -import java.util.ArrayList; -import java.util.List; -import java.util.UUID; - -import org.apache.taverna.robundle.Bundle; -import org.apache.taverna.robundle.Bundles; -import org.apache.taverna.robundle.manifest.Manifest; -import org.apache.taverna.robundle.manifest.PathMetadata; -import org.apache.taverna.robundle.manifest.RDFToManifest; -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import com.hp.hpl.jena.query.Query; -import com.hp.hpl.jena.query.QueryExecution; -import com.hp.hpl.jena.query.QueryExecutionFactory; -import com.hp.hpl.jena.query.QueryFactory; -import com.hp.hpl.jena.query.QuerySolution; -import com.hp.hpl.jena.query.ResultSet; -import com.hp.hpl.jena.rdf.model.Model; -import com.hp.hpl.jena.rdf.model.Resource; - -@SuppressWarnings({ "deprecation", "unused" }) -public class TestManifest { - private Bundle bundle; - - @Test - public void populateFromBundle() throws Exception { - Path r = bundle.getRoot(); - URI base = r.toUri(); - - Manifest manifest = new Manifest(bundle); - manifest.populateFromBundle(); - - List<String> uris = new ArrayList<>(); - for (PathMetadata s : manifest.getAggregates()) { - uris.add(s.getFile().toString()); - Path path = s.getFile(); - assertNotNull(path.getParent()); - assertEquals(Manifest.withSlash(path.getParent()), s.getFolder()); - if (s.getFile().equals(URI.create("/f/nested/empty/"))) { - continue; - // Folder's don't need proxy and createdOn - } - assertEquals("urn", s.getProxy().getScheme()); - UUID.fromString(s.getProxy().getSchemeSpecificPart() - .replace("uuid:", "")); - assertEquals(s.getCreatedOn(), Files.getLastModifiedTime(path)); - } - //System.out.println(uris); - assertFalse(uris.contains("/mimetype")); - assertFalse(uris.contains("/META-INF")); - assertTrue(uris.remove("/hello.txt")); - assertTrue(uris.remove("/f/file1.txt")); - assertTrue(uris.remove("/f/file2.txt")); - assertTrue(uris.remove("/f/file3.txt")); - assertTrue(uris.remove("/f/nested/file1.txt")); - assertTrue(uris.remove("/f/nested/empty/")); - assertTrue(uris.isEmpty()); - } - - @Test - public void repopulateFromBundle() throws Exception { - Path r = bundle.getRoot(); - URI base = r.toUri(); - - Manifest manifest = new Manifest(bundle); - manifest.populateFromBundle(); - // Second populate should not add additional entries - manifest.populateFromBundle(); - - List<String> uris = new ArrayList<>(); - for (PathMetadata s : manifest.getAggregates()) { - uris.add(s.getFile().toString()); - Path path = s.getFile(); - assertNotNull(path.getParent()); - assertEquals(Manifest.withSlash(path.getParent()), s.getFolder()); - if (s.getFile().equals(URI.create("/f/nested/empty/"))) { - continue; - // Folder's don't need proxy and createdOn - } - assertEquals("urn", s.getProxy().getScheme()); - UUID.fromString(s.getProxy().getSchemeSpecificPart() - .replace("uuid:", "")); - assertEquals(s.getCreatedOn(), Files.getLastModifiedTime(path)); - } - //System.out.println(uris); - assertFalse(uris.contains("/mimetype")); - assertFalse(uris.contains("/META-INF")); - assertTrue(uris.remove("/hello.txt")); - assertTrue(uris.remove("/f/file1.txt")); - assertTrue(uris.remove("/f/file2.txt")); - assertTrue(uris.remove("/f/file3.txt")); - assertTrue(uris.remove("/f/nested/file1.txt")); - assertTrue(uris.remove("/f/nested/empty/")); - assertTrue("Unexpected uri: " + uris, uris.isEmpty()); - } - - private Path uri2path(URI base, URI uri) { - URI fileUri = base.resolve(uri); - return Paths.get(fileUri); - } - - @Test - public void writeAsJsonLD() throws Exception { - Manifest manifest = new Manifest(bundle); - manifest.populateFromBundle(); - PathMetadata helloMeta = null; - for (PathMetadata meta : manifest.getAggregates()) { - if (meta.getFile().endsWith("hello.txt")) { - helloMeta = meta; - } - } - assertNotNull("No metadata for </hello.txt>", helloMeta); - - Path jsonld = manifest.writeAsJsonLD(); - assertEquals(bundle.getFileSystem().getPath("/.ro", "manifest.json"), - jsonld); - assertTrue(Files.exists(jsonld)); - String manifestStr = new String(Files.readAllBytes(jsonld), "UTF8"); - //System.out.println(manifestStr); - - // Rough and ready that somethings are there - // TODO: Read back and check as JSON structure - // TODO: Check as JSON-LD graph - assertTrue(manifestStr.contains("@context")); - assertTrue(manifestStr.contains("https://w3id.org/bundle/context";)); - assertTrue(manifestStr.contains("/f/file2.txt")); - assertTrue(manifestStr.contains("/hello.txt")); - assertTrue(manifestStr.contains(helloMeta.getProxy().toASCIIString())); - - // Parse back as JSON-LD - try (InputStream jsonIn = Files.newInputStream(jsonld)) { - URI baseURI = jsonld.toUri(); - Model model = RDFToManifest.jsonLdAsJenaModel(jsonIn, baseURI); - model.write(new ByteArrayOutputStream(), "TURTLE", baseURI.toString()); - model.write(new ByteArrayOutputStream(), "RDF/XML", baseURI.toString()); - - String queryStr = "PREFIX ore: <http://www.openarchives.org/ore/terms/>" - + "PREFIX bundle: <http://purl.org/wf4ever/bundle#>" - + "SELECT ?file ?proxy " - + "WHERE {" - + " ?ro ore:aggregates ?file ." - + " OPTIONAL { ?file bundle:bundledAs ?proxy . } " + "}"; - Query query = QueryFactory.create(queryStr); - QueryExecution qexec = QueryExecutionFactory.create(query, model); - - try { - ResultSet results = qexec.execSelect(); - int aggregationCount = 0; - for (; results.hasNext(); aggregationCount++) { - QuerySolution soln = results.nextSolution(); - Resource fileRes = soln.getResource("file"); - Resource proxy = soln.getResource("proxy"); - //System.out.println("File: " + fileRes); - //System.out.println(asURI(fileRes)); - - Path file = Paths.get(asURI(fileRes)); - assertTrue(Files.exists(file)); - PathMetadata meta = manifest.getAggregation(file); - assertEquals(meta.getProxy(), asURI(proxy)); - } - assertEquals("Could not find all aggregations from manifest: " - + manifest.getAggregates(), manifest.getAggregates() - .size(), aggregationCount); - } finally { - // WHY is not QueryExecution an instance of Closable? - qexec.close(); - } - } - } - - @Test - public void readManifest() throws Exception { - Manifest manifest = new Manifest(bundle); - - new RDFToManifest().readTo( - getClass().getResourceAsStream("/manifest.json"), manifest, - manifest.getBaseURI().resolve("does/not/exist")); - - Path r = bundle.getRoot(); - assertNotNull(manifest.getAggregation(r.resolve("/README.txt"))); - PathMetadata readme = manifest.getAggregation(r.resolve("/README.txt")); - assertEquals("http://example.com/foaf#bob";, readme.getCreatedBy() - .getUri().toString()); - assertEquals("Bob Builder", - manifest.getAggregation(r.resolve("/README.txt")) - .getCreatedBy().getName()); - assertEquals("text/plain", - manifest.getAggregation(r.resolve("/README.txt")) - .getMediatype()); - - assertNull(manifest.getAggregation(r.resolve("/README.txt")) - .getBundledAs()); - - // Disabled: RO Bundle in flux on how to put external URIs in folders - // assertNotNull(manifest.getAggregation( - // URI.create("http://example.com/comments.txt";)).getProxy()); - - //System.out.println(manifest.getAnnotations()); - - assertEquals(3, manifest.getAnnotations().size()); - - } - - private URI asURI(Resource proxy) { - if (proxy == null) { - return null; - } - String uri = proxy.getURI(); - if (uri == null) { - return null; - } - return bundle.getRoot().toUri().resolve(uri); - } - - @Before - public void exampleBundle() throws IOException { - Path source; - try (Bundle bundle = Bundles.createBundle()) { - source = bundle.getSource(); - Path r = bundle.getRoot(); - Files.createFile(r.resolve("hello.txt")); - Path f = r.resolve("f"); - Files.createDirectory(f); - Files.createFile(f.resolve("file3.txt")); - Files.createFile(f.resolve("file2.txt")); - Files.createFile(f.resolve("file1.txt")); - - Path nested = f.resolve("nested"); - Files.createDirectory(nested); - Files.createFile(nested.resolve("file1.txt")); - - Files.createDirectory(nested.resolve("empty")); - bundle.setDeleteOnClose(false); - } - bundle = Bundles.openBundle(source); - } - - @After - public void closeBundle() throws IOException { - bundle.close(); - - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/316e4a8a/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/TestManifestJSON.java ---------------------------------------------------------------------- diff --git a/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/TestManifestJSON.java b/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/TestManifestJSON.java deleted file mode 100644 index efab8a9..0000000 --- a/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/TestManifestJSON.java +++ /dev/null @@ -1,275 +0,0 @@ -package org.apache.taverna.robundle.manifest; - -/* - * Licensed to the Apache Software Foundation (ASF) under one - * or more contributor license agreements. See the NOTICE file - * distributed with this work for additional information - * regarding copyright ownership. The ASF licenses this file - * to you under the Apache License, Version 2.0 (the - * "License"); you may not use this file except in compliance - * with the License. You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, - * software distributed under the License is distributed on an - * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY - * KIND, either express or implied. See the License for the - * specific language governing permissions and limitations - * under the License. - */ - - -import static org.junit.Assert.assertEquals; -import static org.junit.Assert.assertNotNull; -import static org.junit.Assert.assertNull; -import static org.junit.Assert.assertTrue; - -import java.net.URI; -import java.nio.file.Files; -import java.nio.file.Path; -import java.nio.file.attribute.FileTime; -import java.util.Calendar; -import java.util.Locale; -import java.util.TimeZone; - -import org.apache.taverna.robundle.Bundle; -import org.apache.taverna.robundle.Bundles; -import org.apache.taverna.robundle.manifest.Agent; -import org.apache.taverna.robundle.manifest.Manifest; -import org.apache.taverna.robundle.manifest.PathAnnotation; -import org.apache.taverna.robundle.manifest.PathMetadata; -import org.junit.Test; - -import com.fasterxml.jackson.databind.JsonNode; -import com.fasterxml.jackson.databind.ObjectMapper; - -public class TestManifestJSON { - @Test - public void createBundle() throws Exception { - // Create bundle as in Example 3 of the specification - // http://wf4ever.github.io/ro/bundle/2013-05-21/ - try (Bundle bundle = Bundles.createBundle()) { - Calendar createdOnCal = Calendar.getInstance( - TimeZone.getTimeZone("Z"), Locale.ENGLISH); - // "2013-03-05T17:29:03Z" - // Remember months are 0-based in java.util.Calendar! - createdOnCal.set(2013, 3 - 1, 5, 17, 29, 03); - createdOnCal.set(Calendar.MILLISECOND, 0); - FileTime createdOn = FileTime.fromMillis(createdOnCal - .getTimeInMillis()); - Manifest manifest = bundle.getManifest(); - manifest.setCreatedOn(createdOn); - Agent createdBy = new Agent("Alice W. Land"); - createdBy.setUri(URI.create("http://example.com/foaf#alice";)); - createdBy.setOrcid(URI - .create("http://orcid.org/0000-0002-1825-0097";)); - - manifest.setCreatedBy(createdBy); - - Path evolutionPath = bundle.getPath(".ro/evolution.ttl"); - Files.createDirectories(evolutionPath.getParent()); - Bundles.setStringValue( - evolutionPath, - "<manifest.json> < http://purl.org/pav/retrievedFrom> " - + "<http://wf4ever.github.io/ro/bundle/2013-05-21/example/.ro/manifest.json> ."); - manifest.getHistory().add(evolutionPath); - - Path jpeg = bundle.getPath("folder/soup.jpeg"); - Files.createDirectory(jpeg.getParent()); - Files.createFile(jpeg); - // register in manifest first - bundle.getManifest().getAggregation(jpeg); - - URI blog = URI.create("http://example.com/blog/";); - bundle.getManifest().getAggregation(blog); - - Path readme = bundle.getPath("README.txt"); - Files.createFile(readme); - PathMetadata readmeMeta = bundle.getManifest().getAggregation( - readme); - readmeMeta.setMediatype("text/plain"); - Agent readmeCreatedby = new Agent("Bob Builder"); - readmeCreatedby.setUri(URI.create("http://example.com/foaf#bob";)); - readmeMeta.setCreatedBy(readmeCreatedby); - - // 2013-02-12T19:37:32.939Z - createdOnCal.set(2013, 2 - 1, 12, 19, 37, 32); - createdOnCal.set(Calendar.MILLISECOND, 939); - createdOn = FileTime.fromMillis(createdOnCal.getTimeInMillis()); - Files.setLastModifiedTime(readme, createdOn); - readmeMeta.setCreatedOn(createdOn); - - PathMetadata comments = bundle.getManifest().getAggregation( - URI.create("http://example.com/comments.txt";)); - comments.getOrCreateBundledAs() - .setURI(URI - .create("urn:uuid:a0cf8616-bee4-4a71-b21e-c60e6499a644")); - comments.getOrCreateBundledAs().setFolder( - bundle.getPath("/folder/")); - comments.getOrCreateBundledAs().setFilename("external.txt"); - - PathAnnotation jpegAnn = new PathAnnotation(); - jpegAnn.setAbout(jpeg); - Path soupProps = Bundles.getAnnotations(bundle).resolve( - "soup-properties.ttl"); - Bundles.setStringValue(soupProps, - "</folder/soup.jpeg> <http://xmlns.com/foaf/0.1/depicts> " - + "<http://example.com/menu/tomato-soup> ."); - jpegAnn.setContent(soupProps); - // jpegAnn.setContent(URI.create("annotations/soup-properties.ttl")); - jpegAnn.setUri(URI - .create("urn:uuid:d67466b4-3aeb-4855-8203-90febe71abdf")); - manifest.getAnnotations().add(jpegAnn); - - PathAnnotation proxyAnn = new PathAnnotation(); - proxyAnn.setAbout(comments.getBundledAs().getURI()); - proxyAnn.setContent(URI - .create("http://example.com/blog/they-aggregated-our-file";)); - manifest.getAnnotations().add(proxyAnn); - - Path metaAnn = Bundles.getAnnotations(bundle).resolve( - "a-meta-annotation-in-this-ro.txt"); - Bundles.setStringValue(metaAnn, - "This bundle contains an annotation about /folder/soup.jpeg"); - - PathAnnotation metaAnnotation = new PathAnnotation(); - metaAnnotation.setAbout(bundle.getRoot()); - metaAnnotation - .getAboutList() - .add(URI.create("urn:uuid:d67466b4-3aeb-4855-8203-90febe71abdf")); - - metaAnnotation.setContent(metaAnn); - manifest.getAnnotations().add(metaAnnotation); - - Path jsonPath = bundle.getManifest().writeAsJsonLD(); - ObjectMapper objectMapper = new ObjectMapper(); - String jsonStr = Bundles.getStringValue(jsonPath); - //System.out.println(jsonStr); - JsonNode json = objectMapper.readTree(jsonStr); - checkManifestJson(json); - } - } - - public void checkManifestJson(JsonNode json) { - JsonNode context = json.get("@context"); - assertNotNull("Could not find @context", context); - assertTrue("@context SHOULD be an array", context.isArray()); - assertTrue("@context SHOULD include a context", context.size() > 0); - JsonNode lastContext = context.get(context.size() - 1); - assertEquals( - "@context SHOULD include https://w3id.org/bundle/context as last item", - "https://w3id.org/bundle/context";, lastContext.asText()); - - assertEquals("/", json.get("id").asText()); - - JsonNode manifest = json.get("manifest"); - if (manifest.isValueNode()) { - assertEquals( - "manifest SHOULD be literal value \"manifest.json\" or list", - "manifest.json", manifest.asText()); - } else { - assertTrue("manifest is neither literal or list", - manifest.isArray()); - boolean found = false; - for (JsonNode n : manifest) { - found = n.asText().equals("manifest.json"); - if (found) { - break; - } - } - ; - assertTrue("Could not find 'manifest.json' in 'manifest' list: " - + manifest, found); - } - - assertEquals("2013-03-05T17:29:03Z", json.get("createdOn").asText()); - JsonNode createdBy = json.get("createdBy"); - assertNotNull("Could not find createdBy", createdBy); - assertEquals("http://example.com/foaf#alice";, createdBy.get("uri") - .asText()); - assertEquals("http://orcid.org/0000-0002-1825-0097";, - createdBy.get("orcid").asText()); - assertEquals("Alice W. Land", createdBy.get("name").asText()); - - JsonNode history = json.get("history"); - if (history.isValueNode()) { - assertEquals("evolution.ttl", history.asText()); - } else { - assertEquals("evolution.ttl", history.get(0).asText()); - } - - JsonNode aggregates = json.get("aggregates"); - assertTrue("aggregates not a list", aggregates.isArray()); - JsonNode soup = aggregates.get(0); - if (soup.isValueNode()) { - assertEquals("/folder/soup.jpeg", soup.asText()); - } else { - assertEquals("/folder/soup.jpeg", soup.get("uri").asText()); - } - - JsonNode blog = aggregates.get(1); - if (blog.isValueNode()) { - assertEquals("http://example.com/blog/";, blog.asText()); - } else { - assertEquals("http://example.com/blog/";, blog.get("uri").asText()); - } - - JsonNode readme = aggregates.get(2); - assertEquals("/README.txt", readme.get("uri").asText()); - assertEquals("text/plain", readme.get("mediatype").asText()); - assertEquals("2013-02-12T19:37:32.939Z", readme.get("createdOn") - .asText()); - JsonNode readmeCreatedBy = readme.get("createdBy"); - assertEquals("http://example.com/foaf#bob";, readmeCreatedBy.get("uri") - .asText()); - assertEquals("Bob Builder", readmeCreatedBy.get("name").asText()); - - JsonNode comments = aggregates.get(3); - assertEquals("http://example.com/comments.txt";, comments.get("uri") - .asText()); - JsonNode bundledAs = comments.get("bundledAs"); - assertEquals("urn:uuid:a0cf8616-bee4-4a71-b21e-c60e6499a644", bundledAs - .get("uri").asText()); - assertEquals("/folder/", bundledAs.get("folder").asText()); - assertEquals("external.txt", bundledAs.get("filename").asText()); - - JsonNode annotations = json.get("annotations"); - assertTrue("annotations MUST be a list", annotations.isArray()); - - JsonNode ann0 = annotations.get(0); - assertEquals("urn:uuid:d67466b4-3aeb-4855-8203-90febe71abdf", - ann0.get("uri").asText()); - assertEquals("/folder/soup.jpeg", ann0.get("about").asText()); - assertEquals("annotations/soup-properties.ttl", ann0.get("content") - .asText()); - - JsonNode ann1 = annotations.get(1); - assertNull(ann1.get("annotation")); - assertEquals("urn:uuid:a0cf8616-bee4-4a71-b21e-c60e6499a644", - ann1.get("about").asText()); - assertEquals("http://example.com/blog/they-aggregated-our-file";, ann1 - .get("content").asText()); - - JsonNode ann2 = annotations.get(2); - assertNull(ann2.get("annotation")); - JsonNode about = ann2.get("about"); - assertTrue("about was not a list", about.isArray()); - assertEquals("/", about.get(0).asText()); - assertEquals("urn:uuid:d67466b4-3aeb-4855-8203-90febe71abdf", about - .get(1).asText()); - assertEquals("annotations/a-meta-annotation-in-this-ro.txt", - ann2.get("content").asText()); - - } - - @Test - public void checkJsonFromSpec() throws Exception { - // Verify that our test confirms the existing spec example - ObjectMapper objectMapper = new ObjectMapper(); - JsonNode json = objectMapper.readTree(getClass().getResource( - "/manifest.json")); - checkManifestJson(json); - - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/316e4a8a/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/TestRDFToManifest.java ---------------------------------------------------------------------- diff --git a/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/TestRDFToManifest.java b/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/TestRDFToManifest.java deleted file mode 100644 index 2557973..0000000 --- a/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/TestRDFToManifest.java +++ /dev/null @@ -1,52 +0,0 @@ -package org.apache.taverna.robundle.manifest; - -/* - * Licensed to the Apache Software Foundation (ASF) under one - * or more contributor license agreements. See the NOTICE file - * distributed with this work for additional information - * regarding copyright ownership. The ASF licenses this file - * to you under the Apache License, Version 2.0 (the - * "License"); you may not use this file except in compliance - * with the License. You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, - * software distributed under the License is distributed on an - * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY - * KIND, either express or implied. See the License for the - * specific language governing permissions and limitations - * under the License. - */ - - -import static org.junit.Assert.assertNotNull; - -import java.net.URL; -import java.util.Map; - -import org.junit.Test; - -import com.github.jsonldjava.core.DocumentLoader; - -//import com.github.jsonldjava.core.DocumentLoader; - -public class TestRDFToManifest { - private static final String CONTEXT = "https://w3id.org/bundle/context";; - - @Test - public void contextLoadedFromJarCache() throws Exception { - // RDFToManifest.makeBaseURI(); // trigger static{} block - @SuppressWarnings("unchecked") - Map<String, Object> context = (Map<String, Object>) new DocumentLoader() - .fromURL(new URL(CONTEXT)); - // FIXME: jsonld-java 0.3 and later uses DocumentLoader instead of - // JSONUtils - // Map<String, Object> context = (Map<String, Object>) - // JSONUtils.fromURL(new URL(CONTEXT)); - Object retrievedFrom = context.get("http://purl.org/pav/retrievedFrom";); - assertNotNull("Did not load context from cache: " + CONTEXT, - retrievedFrom); - - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/316e4a8a/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/combine/TestCombineManifest.java ---------------------------------------------------------------------- diff --git a/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/combine/TestCombineManifest.java b/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/combine/TestCombineManifest.java deleted file mode 100644 index 5286d67..0000000 --- a/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/combine/TestCombineManifest.java +++ /dev/null @@ -1,155 +0,0 @@ -package org.apache.taverna.robundle.manifest.combine; - -/* - * Licensed to the Apache Software Foundation (ASF) under one - * or more contributor license agreements. See the NOTICE file - * distributed with this work for additional information - * regarding copyright ownership. The ASF licenses this file - * to you under the Apache License, Version 2.0 (the - * "License"); you may not use this file except in compliance - * with the License. You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, - * software distributed under the License is distributed on an - * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY - * KIND, either express or implied. See the License for the - * specific language governing permissions and limitations - * under the License. - */ - - -import static org.junit.Assert.assertEquals; -import static org.junit.Assert.assertTrue; - -import java.io.InputStream; -import java.net.URI; -import java.nio.file.Files; -import java.nio.file.Path; -import java.nio.file.StandardCopyOption; - -import org.apache.taverna.robundle.Bundle; -import org.apache.taverna.robundle.Bundles; -import org.apache.taverna.robundle.manifest.Agent; -import org.apache.taverna.robundle.manifest.Manifest; -import org.apache.taverna.robundle.manifest.PathMetadata; -import org.junit.Test; - -public class TestCombineManifest { - @Test - public void convertAslanidi() throws Exception { - Path file = Files.createTempFile("aslanidi", ".zip"); - try (InputStream src = getClass().getResourceAsStream( - "/combine/aslanidi_purkinje_model_2009.zip")) { - Files.copy(src, file, StandardCopyOption.REPLACE_EXISTING); - } - System.out.println(file); - try (Bundle bundle = Bundles.openBundle(file)) { - Manifest manifest = bundle.getManifest(); - Path manifestXml = bundle.getRoot().resolve("manifest.xml"); - assertTrue("manifest.xml not listed in " + manifest.getManifest(), - manifest.getManifest().contains(manifestXml)); - - // List<Agent> manifestCreator = manifest.getCreatedBy(); - // Agent createdBy = manifestCreator.get(0); - // assertEquals("Gary Mirams", createdBy.getName()); - // assertEquals("mbox:gary.mir...@cs.ox.ac.uk", createdBy.getUri()); - // assertEquals("2014-02-06T22:01:58Z", - // manifest.getCreatedOn().toString()); - // - Path csvPath = bundle.getRoot().resolve( - "outputs_degree_of_block.csv"); - PathMetadata csv = manifest.getAggregation(csvPath); - assertEquals("text/csv", csv.getMediatype()); - Agent csvCreator = csv.getCreatedBy(); - assertEquals("Gary Mirams", csvCreator.getName()); - assertEquals("mbox:gary.mir...@cs.ox.ac.uk", csvCreator.getUri() - .toString()); - assertEquals("2014-02-06T22:01:58Z", csv.getCreatedOn().toString()); - - } - } - - @Test - public void convertBoris() throws Exception { - Path file = Files.createTempFile("Boris", ".omex"); - try (InputStream src = getClass().getResourceAsStream( - "/combine/Boris.omex")) { - Files.copy(src, file, StandardCopyOption.REPLACE_EXISTING); - } - //System.out.println(file); - try (Bundle bundle = Bundles.openBundle(file)) { - Manifest manifest = bundle.getManifest(); - Path manifestXml = bundle.getRoot().resolve("manifest.xml"); - assertTrue("manifest.xml not listed in " + manifest.getManifest(), - manifest.getManifest().contains(manifestXml)); - - assertEquals("2013-05-28T16:50:43.999Z", manifest.getCreatedOn() - .toString()); - - // Can't test these - as Boris.omex manifest.xml only - // list these as unconnected bnodes - // List<Agent> manifestCreator = manifest.getCreatedBy(); - // Agent createdBy = manifestCreator.get(0); - // assertEquals("Frank Bergmann", createdBy.getName()); - // assertEquals("mbox:fberg...@caltech.edu", createdBy.getUri()); - // - } - - } - - @Test - public void convertDirectoryMadness() throws Exception { - Path file = Files.createTempFile("DirectoryMadness", ".omex"); - try (InputStream src = getClass().getResourceAsStream( - "/combine/DirectoryMadness.omex")) { - Files.copy(src, file, StandardCopyOption.REPLACE_EXISTING); - } - //System.out.println(file); - try (Bundle bundle = Bundles.openBundle(file)) { - Manifest manifest = bundle.getManifest(); - Path manifestXml = bundle.getRoot().resolve("manifest.xml"); - assertTrue("manifest.xml not listed in " + manifest.getManifest(), - manifest.getManifest().contains(manifestXml)); - - Path boris = bundle.getRoot().resolve("BorisEJB.xml"); - PathMetadata borisMeta = bundle.getManifest().getAggregation(boris); - assertEquals( - URI.create("http://identifiers.org/combine.specifications/sbml";), - borisMeta.getConformsTo()); - // dcterms:modified - assertEquals("2013-04-05T12:50:56Z", borisMeta.getCreatedOn() - .toString()); - - Path paperPdf = bundle.getRoot().resolve("paper") - .resolve("Kholodenko2000.pdf"); - PathMetadata paperMeta = bundle.getManifest().getAggregation( - paperPdf); - assertEquals("application/pdf", paperMeta.getMediatype()); - - URI biomd = URI - .create("http://www.ebi.ac.uk/biomodels-main/BIOMD0000000010";); - PathMetadata biomdMeta = bundle.getManifest().getAggregation(biomd); - assertEquals( - URI.create("http://identifiers.org/combine.specifications/sbml";), - biomdMeta.getConformsTo()); - - } - - } - - @Test - public void convertDirectoryMadnessZipped() throws Exception { - Path file = Files.createTempFile("DirectoryMadnessZipped", ".omex"); - try (InputStream src = getClass().getResourceAsStream( - "/combine/DirectoryMadnessZipped.omex")) { - Files.copy(src, file, StandardCopyOption.REPLACE_EXISTING); - } - //System.out.println(file); - try (Bundle bundle = Bundles.openBundle(file)) { - - } - } - -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/316e4a8a/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/odf/TestODFManifest.java ---------------------------------------------------------------------- diff --git a/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/odf/TestODFManifest.java b/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/odf/TestODFManifest.java deleted file mode 100644 index 539c289..0000000 --- a/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/odf/TestODFManifest.java +++ /dev/null @@ -1,74 +0,0 @@ -package org.apache.taverna.robundle.manifest.odf; - -/* - * Licensed to the Apache Software Foundation (ASF) under one - * or more contributor license agreements. See the NOTICE file - * distributed with this work for additional information - * regarding copyright ownership. The ASF licenses this file - * to you under the Apache License, Version 2.0 (the - * "License"); you may not use this file except in compliance - * with the License. You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, - * software distributed under the License is distributed on an - * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY - * KIND, either express or implied. See the License for the - * specific language governing permissions and limitations - * under the License. - */ - - -import static org.junit.Assert.assertEquals; -import static org.junit.Assert.assertNotNull; -import static org.junit.Assert.assertTrue; - -import java.net.URL; -import java.nio.file.Files; -import java.nio.file.Path; - -import org.apache.taverna.robundle.Bundle; -import org.apache.taverna.robundle.Bundles; -import org.apache.taverna.robundle.manifest.Manifest; -import org.apache.taverna.robundle.manifest.PathMetadata; -import org.junit.Test; - -public class TestODFManifest { - @Test - public void openHelloWorld() throws Exception { - URL helloworld = getClass().getResource("/helloworld.wfbundle"); - assertNotNull(helloworld); - try (Bundle bundle = Bundles.openBundle(helloworld)) { - assertEquals("application/vnd.taverna.scufl2.workflow-bundle", - Bundles.getMimeType(bundle)); - Path t2flow = bundle - .getPath("history/8781d5f4-d0ba-48a8-a1d1-14281bd8a917.t2flow"); - assertEquals("application/vnd.taverna.t2flow+xml", bundle - .getManifest().getAggregation(t2flow).getMediatype()); - Path manifestRdf = bundle.getPath("META-INF/manifest.xml"); - assertTrue(Files.exists(manifestRdf)); - assertTrue(bundle.getManifest().getManifest().contains(manifestRdf)); - } - } - - @Test - public void openODTDocument() throws Exception { - URL url = getClass().getResource("/document.odt"); - assertNotNull(url); - try (Bundle bundle = Bundles.openBundle(url)) { - assertEquals("application/vnd.oasis.opendocument.text", - Bundles.getMimeType(bundle)); - - Path contentXml = bundle.getPath("content.xml"); - Manifest manifest = bundle.getManifest(); - assertEquals("text/xml", manifest.getAggregation(contentXml) - .getMediatype()); - PathMetadata rootMeta = manifest.getAggregation(bundle.getRoot()); - assertEquals("1.2", rootMeta.getConformsTo() + ""); - assertEquals("application/vnd.oasis.opendocument.text", - rootMeta.getMediatype()); - } - } - -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/316e4a8a/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/utils/TestRecursiveCopyFileVisitor.java ---------------------------------------------------------------------- diff --git a/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/utils/TestRecursiveCopyFileVisitor.java b/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/utils/TestRecursiveCopyFileVisitor.java deleted file mode 100644 index 84012e9..0000000 --- a/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/utils/TestRecursiveCopyFileVisitor.java +++ /dev/null @@ -1,114 +0,0 @@ -package org.apache.taverna.robundle.manifest.utils; - -/* - * Licensed to the Apache Software Foundation (ASF) under one - * or more contributor license agreements. See the NOTICE file - * distributed with this work for additional information - * regarding copyright ownership. The ASF licenses this file - * to you under the Apache License, Version 2.0 (the - * "License"); you may not use this file except in compliance - * with the License. You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, - * software distributed under the License is distributed on an - * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY - * KIND, either express or implied. See the License for the - * specific language governing permissions and limitations - * under the License. - */ - - -import static org.junit.Assert.assertEquals; -import static org.junit.Assert.assertTrue; - -import java.io.IOException; -import java.nio.charset.Charset; -import java.nio.file.FileAlreadyExistsException; -import java.nio.file.Files; -import java.nio.file.Path; -import java.nio.file.StandardCopyOption; -import java.util.Arrays; -import java.util.LinkedHashSet; -import java.util.List; -import java.util.Set; - -import org.apache.taverna.robundle.Bundles; -import org.junit.After; -import org.junit.Test; - -public class TestRecursiveCopyFileVisitor { - - // TODO: Test NOFOLLOW and follow of symlinks - - private Set<Path> tmps = new LinkedHashSet<>(); - - @After - public void deleteTmps() throws IOException { - IOException lastEx = null; - for (Path p : tmps) { - try { - Bundles.deleteRecursively(p); - } catch (IOException e) { - lastEx = e; - } - } - if (lastEx != null) - throw lastEx; - } - - @Test(expected = FileAlreadyExistsException.class) - public void copyRecursivelyAlreadyExists() throws Exception { - Path orig = tempDir("orig"); - Path dest = tempDir("dest"); - Bundles.copyRecursively(orig, dest); - } - - protected Path tempDir(String name) throws IOException { - Path dir = Files.createTempDirectory(name); - tmps.add(dir); - return dir; - } - - @Test - public void copyRecursivelyReplace() throws Exception { - Path orig = tempDir("orig"); - Files.createFile(orig.resolve("file")); - Path dest = tempDir("dest"); - Bundles.copyRecursively(orig, dest, StandardCopyOption.REPLACE_EXISTING); - assertTrue(Files.isRegularFile(dest.resolve("file"))); - // Second copy should also be OK - Bundles.copyRecursively(orig, dest, StandardCopyOption.REPLACE_EXISTING); - } - - @Test - public void copyRecursively() throws Exception { - Path orig = tempDir("orig"); - Files.createFile(orig.resolve("1")); - Files.createDirectory(orig.resolve("2")); - Files.createFile(orig.resolve("2/1")); - Files.createDirectory(orig.resolve("2/2")); - List<String> hello = Arrays.asList("Hello"); - - Charset ascii = Charset.forName("ASCII"); - Files.write(orig.resolve("2/2/1"), hello, ascii); - - Files.createDirectory(orig.resolve("2/2/2")); - Files.createFile(orig.resolve("3")); - - Path dest = tempDir("dest"); - Files.delete(dest); - Bundles.copyRecursively(orig, dest); - - assertTrue(Files.isDirectory(dest.resolve("2"))); - assertTrue(Files.isDirectory(dest.resolve("2/2"))); - assertTrue(Files.isDirectory(dest.resolve("2/2"))); - assertTrue(Files.isDirectory(dest.resolve("2/2/2"))); - assertTrue(Files.isRegularFile(dest.resolve("1"))); - assertTrue(Files.isRegularFile(dest.resolve("2/1"))); - assertTrue(Files.isRegularFile(dest.resolve("2/2/1"))); - assertTrue(Files.isRegularFile(dest.resolve("3"))); - assertEquals(hello, Files.readAllLines(dest.resolve("2/2/1"), ascii)); - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/316e4a8a/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/utils/TestRecursiveCopyFileVisitorInBundle.java ---------------------------------------------------------------------- diff --git a/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/utils/TestRecursiveCopyFileVisitorInBundle.java b/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/utils/TestRecursiveCopyFileVisitorInBundle.java deleted file mode 100644 index d66c03a..0000000 --- a/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/utils/TestRecursiveCopyFileVisitorInBundle.java +++ /dev/null @@ -1,54 +0,0 @@ -package org.apache.taverna.robundle.manifest.utils; - -/* - * Licensed to the Apache Software Foundation (ASF) under one - * or more contributor license agreements. See the NOTICE file - * distributed with this work for additional information - * regarding copyright ownership. The ASF licenses this file - * to you under the Apache License, Version 2.0 (the - * "License"); you may not use this file except in compliance - * with the License. You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, - * software distributed under the License is distributed on an - * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY - * KIND, either express or implied. See the License for the - * specific language governing permissions and limitations - * under the License. - */ - - -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; - -import org.apache.taverna.robundle.Bundle; -import org.apache.taverna.robundle.Bundles; -import org.junit.After; -import org.junit.Before; - -public class TestRecursiveCopyFileVisitorInBundle extends - TestRecursiveCopyFileVisitor { - - private Bundle bundle; - - @Before - public void createBundle() throws IOException { - bundle = Bundles.createBundle(); - } - - @After - public void closeBundle() throws IOException { - if (bundle != null) { - bundle.close(); - } - bundle = null; - } - - @Override - protected Path tempDir(String name) throws IOException { - return Files.createTempDirectory(bundle.getRoot(), name); - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/316e4a8a/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/utils/TestRecursiveCopyFileVisitorMultipleBundles.java ---------------------------------------------------------------------- diff --git a/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/utils/TestRecursiveCopyFileVisitorMultipleBundles.java b/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/utils/TestRecursiveCopyFileVisitorMultipleBundles.java deleted file mode 100644 index c38c502..0000000 --- a/taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/utils/TestRecursiveCopyFileVisitorMultipleBundles.java +++ /dev/null @@ -1,51 +0,0 @@ -package org.apache.taverna.robundle.manifest.utils; - -/* - * Licensed to the Apache Software Foundation (ASF) under one - * or more contributor license agreements. See the NOTICE file - * distributed with this work for additional information - * regarding copyright ownership. The ASF licenses this file - * to you under the Apache License, Version 2.0 (the - * "License"); you may not use this file except in compliance - * with the License. You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, - * software distributed under the License is distributed on an - * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY - * KIND, either express or implied. See the License for the - * specific language governing permissions and limitations - * under the License. - */ - - -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; -import java.util.ArrayList; -import java.util.List; - -import org.apache.taverna.robundle.Bundle; -import org.apache.taverna.robundle.Bundles; -import org.junit.After; - -public class TestRecursiveCopyFileVisitorMultipleBundles extends - TestRecursiveCopyFileVisitor { - - private List<Bundle> bundles = new ArrayList<>(); - - @After - public void closeBundle() throws IOException { - for (Bundle b : bundles) { - b.close(); - } - } - - @Override - protected Path tempDir(String name) throws IOException { - Bundle bundle = Bundles.createBundle(); - bundles.add(bundle); - return Files.createTempDirectory(bundle.getRoot(), name); - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/316e4a8a/taverna-robundle/src/test/resources/combine/Boris.omex ---------------------------------------------------------------------- diff --git a/taverna-robundle/src/test/resources/combine/Boris.omex b/taverna-robundle/src/test/resources/combine/Boris.omex deleted file mode 100644 index a4d5cf4..0000000 Binary files a/taverna-robundle/src/test/resources/combine/Boris.omex and /dev/null differ
