taverna-robundle/src/test/java/org/apache/taverna/robundle/manifest/TestManifest.java - incubator-taverna-language - Git at Google

 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 org.apache.jena.query.Query;
 import org.apache.jena.query.QueryExecution;
 import org.apache.jena.query.QueryExecutionFactory;
 import org.apache.jena.query.QueryFactory;
 import org.apache.jena.query.QuerySolution;
 import org.apache.jena.query.ResultSet;
 import org.apache.jena.rdf.model.Model;
 import org.apache.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(path.getParent(), s.getBundledAs().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> paths = new ArrayList<>();
 		for (PathMetadata s : manifest.getAggregates()) {
 			Path path = s.getFile();
 			paths.add(s.toString());
 			assertNotNull(path.getParent());
 			assertEquals(path.getParent(), s.getBundledAs().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(paths.contains("/mimetype"));
 		assertFalse(paths.contains("/META-INF"));
 		assertTrue(paths.remove("/hello.txt"));
 		assertTrue(paths.remove("/f/file1.txt"));
 		assertTrue(paths.remove("/f/file2.txt"));
 		assertTrue(paths.remove("/f/file3.txt"));
 		assertTrue(paths.remove("/f/nested/file1.txt"));
 		assertTrue(paths.remove("/f/nested/empty/"));
 		assertTrue("Unexpected path: " + paths, paths.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();

 		assertEquals("http://example.com/retrieved", manifest.getRetrievedFrom().toString());
 		assertEquals("2013-03-05T17:29:03Z", manifest.getRetrievedOn().toString());
 		assertEquals("http://example.com/foaf#john", manifest.getRetrievedBy().getUri().toString());

 		PathMetadata soupAggregation = manifest.getAggregation(r.resolve("/folder/soup.jpeg"));
 		assertEquals("http://example.com/retrieved/soup.jpeg", soupAggregation.getRetrievedFrom().toString());
 		assertEquals("2013-03-05T17:29:04Z", soupAggregation.getRetrievedOn().toString());
 		assertEquals("http://example.com/foaf#peter", soupAggregation.getRetrievedBy().getUri().toString());

 		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; charset=\"utf-8\"",
 				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();

 	}
 }
	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 org.apache.jena.query.Query;
	import org.apache.jena.query.QueryExecution;
	import org.apache.jena.query.QueryExecutionFactory;
	import org.apache.jena.query.QueryFactory;
	import org.apache.jena.query.QuerySolution;
	import org.apache.jena.query.ResultSet;
	import org.apache.jena.rdf.model.Model;
	import org.apache.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(path.getParent(), s.getBundledAs().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> paths = new ArrayList<>();
	for (PathMetadata s : manifest.getAggregates()) {
	Path path = s.getFile();
	paths.add(s.toString());
	assertNotNull(path.getParent());
	assertEquals(path.getParent(), s.getBundledAs().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(paths.contains("/mimetype"));
	assertFalse(paths.contains("/META-INF"));
	assertTrue(paths.remove("/hello.txt"));
	assertTrue(paths.remove("/f/file1.txt"));
	assertTrue(paths.remove("/f/file2.txt"));
	assertTrue(paths.remove("/f/file3.txt"));
	assertTrue(paths.remove("/f/nested/file1.txt"));
	assertTrue(paths.remove("/f/nested/empty/"));
	assertTrue("Unexpected path: " + paths, paths.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();

	assertEquals("http://example.com/retrieved", manifest.getRetrievedFrom().toString());
	assertEquals("2013-03-05T17:29:03Z", manifest.getRetrievedOn().toString());
	assertEquals("http://example.com/foaf#john", manifest.getRetrievedBy().getUri().toString());

	PathMetadata soupAggregation = manifest.getAggregation(r.resolve("/folder/soup.jpeg"));
	assertEquals("http://example.com/retrieved/soup.jpeg", soupAggregation.getRetrievedFrom().toString());
	assertEquals("2013-03-05T17:29:04Z", soupAggregation.getRetrievedOn().toString());
	assertEquals("http://example.com/foaf#peter", soupAggregation.getRetrievedBy().getUri().toString());

	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; charset=\"utf-8\"",
	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();

	}
	}