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

 package org.apache.taverna.robundle.manifest;

 import static org.junit.Assert.assertEquals;
 /*
  * 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 static org.junit.Assert.assertNull;
 import static org.junit.Assert.assertTrue;

 import java.io.InputStream;
 import java.net.URI;
 import java.time.Instant;
 import java.util.Arrays;
 import java.util.Map;
 import java.util.Set;
 import java.util.stream.Collectors;

 import org.apache.taverna.robundle.Bundle;
 import org.apache.taverna.robundle.Bundles;
 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()
 				.loadDocument(CONTEXT).getDocument();
 		// 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);

 	}

 	@Test
 	public void manifestFromSpec() throws Exception {
 		try (Bundle ro = Bundles.createBundle();
 			 InputStream json = getClass().getResourceAsStream("/manifest.json")) {
 			// Make a new, empty manifest we can inspect
 			assertNotNull("Can't find manifest.json", json);
 			Manifest manifest = new Manifest(ro);

 			URI baseURI = ro.getPath(".ro/manifest.json").toUri();
 			new RDFToManifest().readTo(json, manifest, baseURI);

 			assertEquals(Arrays.asList(ro.getPath("/.ro/manifest.json")),
 						manifest.getManifest());

 			assertEquals(URI.create("http://example.com/retrieved"),
 					manifest.getRetrievedFrom());
 			assertEquals(Instant.parse("2013-03-05T17:29:03Z"),
 					manifest.getRetrievedOn().toInstant());

 			Agent retrievedBy = manifest.getRetrievedBy();
 			assertEquals("John P. Smith",
 					retrievedBy.getName());
 			assertEquals(URI.create("http://example.com/foaf#john"),
 					retrievedBy.getUri());
 			assertEquals(URI.create("http://orcid.org/0000-0002-1825-0100"),
 					retrievedBy.getOrcid());

 			assertEquals(Instant.parse("2013-03-05T17:29:03Z"),
 					manifest.getCreatedOn().toInstant());
 			Agent createdBy = manifest.getCreatedBy();
 			assertEquals("Alice W. Land",
 					createdBy.getName());
 			assertEquals(URI.create("http://example.com/foaf#alice"),
 					createdBy.getUri());
 			assertEquals(URI.create("http://orcid.org/0000-0002-1825-0097"),
 					createdBy.getOrcid());

 			assertEquals(Arrays.asList(ro.getPath(".ro/evolution.ttl")),
 						manifest.getHistory());

 			// As manifest.getAggregation() will create non-existing entries
 			// we will check the list of URIs first
 			Set<URI> aggregatedUris = manifest.getAggregates().stream()
 				.map(PathMetadata::getUri)
 				.collect(Collectors.toSet());
 			//System.out.println(aggregatedUris);
 			// Compare as Set as order is not necessarily preserved
 			assertTrue(aggregatedUris.contains(URI.create("/folder/soup.jpeg")));
 			assertTrue(aggregatedUris.contains(URI.create("http://example.com/blog/")));
 			assertTrue(aggregatedUris.contains(URI.create("/README.txt")));
 			assertTrue(aggregatedUris.contains(URI.create("http://example.com/comments.txt")));
 			assertEquals(4, manifest.getAggregates().size());


 			PathMetadata soup = manifest.getAggregation(ro.getPath("folder/soup.jpeg"));
 			assertEquals(URI.create("http://example.com/retrieved/soup.jpeg"),
 					soup.getRetrievedFrom());
 			assertEquals(Instant.parse("2013-03-05T17:29:04Z"),
 					soup.getRetrievedOn().toInstant());
 			Agent peter = soup.getRetrievedBy();
 			assertEquals("Peter L. Jones",
 					peter.getName());
 			assertEquals(URI.create("http://example.com/foaf#peter"),
 					peter.getUri());
 			assertEquals(URI.create("http://orcid.org/0000-0002-1825-0120"),
 					peter.getOrcid());

 			PathMetadata blog = manifest.getAggregation(URI.create("http://example.com/blog/"));
 			// No additional metadata
 			assertNull(blog.getRetrievedFrom());
 			assertNull(blog.getRetrievedBy());
 			assertNull(blog.getRetrievedOn());
 			assertNull(blog.getCreatedBy());
 			assertNull(blog.getCreatedOn());
 			// NOTE: bundledAs might be created later when saving the manifest
 			assertNull(blog.getBundledAs());

 			PathMetadata readme = manifest.getAggregation(ro.getPath("/README.txt"));
 			assertEquals("text/plain; charset=\"utf-8\"", readme.getMediatype());
 			assertEquals("Bob Builder", readme.getCreatedBy().getName());
 			assertEquals(URI.create("http://example.com/foaf#bob"), readme.getCreatedBy().getUri());

 			PathMetadata comments = manifest.getAggregation(URI.create("http://example.com/comments.txt"));
 			Proxy bundledAs = comments.getBundledAs();
 			assertEquals(URI.create("urn:uuid:a0cf8616-bee4-4a71-b21e-c60e6499a644"),
 					bundledAs.getURI());
 			// TAVERNA-1043 - should work looking up "folder" even though JSON says "/folder/"
 			assertEquals(ro.getPath("folder"), bundledAs.getFolder());
 			assertEquals("external.txt", bundledAs.getFilename());


 			// Again, these could be in any order
 			assertEquals(3, manifest.getAnnotations().size());
 			// annotation 1
 			PathAnnotation ann1 = manifest.getAnnotation(URI.create("urn:uuid:d67466b4-3aeb-4855-8203-90febe71abdf")).get();
 			assertEquals(URI.create("urn:uuid:d67466b4-3aeb-4855-8203-90febe71abdf"), ann1.getUri());
 			assertEquals(URI.create("/folder/soup.jpeg"), ann1.getAbout());
 			assertEquals(URI.create("annotations/soup-properties.ttl"), ann1.getContent());

 			// annotation 2
 			PathAnnotation ann2 = manifest.getAnnotations(URI.create("urn:uuid:a0cf8616-bee4-4a71-b21e-c60e6499a644")).get(0);
 			assertEquals(URI.create("urn:uuid:a0cf8616-bee4-4a71-b21e-c60e6499a644"), ann2.getAbout());
 			assertEquals(URI.create("http://example.com/blog/they-aggregated-our-file"),
 					ann2.getContent());

 			// annotation 3
 			PathAnnotation ann3 = manifest.getAnnotations(ro.getRoot()).get(0);
 			// Can be retrieved either by Path, relative URI or absolute URI
 			assertEquals(ann3,
 					manifest.getAnnotations(URI.create("/")).get(0));
 			assertEquals(ann3,
 					manifest.getAnnotations(ro.getRoot().toUri()).get(0));
 			// Or by the second 'about' URI
 			assertEquals(ann3,
 					manifest.getAnnotations(URI.create("urn:uuid:d67466b4-3aeb-4855-8203-90febe71abdf")).get(0));
 			// single content
 			assertEquals(URI.create("annotations/a-meta-annotation-in-this-ro.txt"),
 					ann3.getContent());
 			// multiple about
 			assertEquals(2, ann3.getAboutList().size());
 			// ... but order not necessarily preserved
 			assertTrue(ann3.getAboutList().contains(URI.create("urn:uuid:d67466b4-3aeb-4855-8203-90febe71abdf")));
 			assertTrue(ann3.getAboutList().contains(URI.create("/")));
 		}
 	}

 	@Test
 	public void multipleConformsTo() throws Exception {
 		try (Bundle ro = Bundles.createBundle();
 			 InputStream json = getClass().getResourceAsStream("/bag-of-bags-manifest.json")) {
 			// Make a new, empty manifest we can inspect
 			assertNotNull("Can't find bag-of-bags-manifest.json", json);
 			Manifest manifest = new Manifest(ro);

 			// NOTE: Uses RO-BagIt folder metadata/ instead of .ro/
 			URI baseURI = ro.getPath("metadata/manifest.json").toUri();
 			new RDFToManifest().readTo(json, manifest, baseURI);

 			// Check basic metadata
 			assertEquals(URI.create("https://github.com/ini-bdds/bdbag"),
 					manifest.getCreatedBy().getUri());
 			assertEquals(1, manifest.getAuthoredBy().size());
 			Agent author = manifest.getAuthoredBy().get(0);
 			assertEquals("Stian Soiland-Reyes",
 					author.getName());
 			assertEquals(URI.create("mbox:stain@apache.org"),
 					author.getUri());
 			assertEquals(URI.create("https://orcid.org/0000-0001-9842-9718"),
 					author.getOrcid());

 			// FIXME: The BDBag got this wrong and used "uri" instead of "content", and so
 			// data/README accidentally became the ID of the annotation.
 			// That means that we can't find any annotations as we only pick up
 			// on those that have a "content"
 //			assertEquals(1, manifest.getAnnotations().size());
 //			PathAnnotation ann = manifest.getAnnotations().get(0);
 //			assertEquals(ro.getRoot().toUri(),
 //					ann.getAbout());
 //			assertEquals(ro.getPath("data/README").toUri(), ann.getContent());

 			// Now let's check aggregations
 			assertEquals(1, manifest.getAggregates().size());
 			// As aggregates order is not preserved, for simplicity this test
 			// has only one aggregation
 			PathMetadata a1 = manifest.getAggregates().get(0);
 			URI uri = URI.create("http://n2t.net/ark:/57799/b90h3c");
 			assertEquals(uri, a1.getUri());
 			assertEquals(a1, manifest.getAggregation(uri));

 			// FIXME: More than one?
 			assertEquals(URI.create("https://w3id.org/ro/bagit/profile"),
 					a1.getConformsTo());
 //			assertEquals(URI.create("https://tools.ietf.org/html/draft-kunze-bagit-14"),
 //					a1.getConformsTo());


 			Proxy bundledAs = a1.getBundledAs();
 			assertNotNull(bundledAs);
 			// FIXME: Why is there no bundledAs data?
 			assertEquals(ro.getPath("data"),
 					bundledAs.getFolder());
 			assertEquals("bag1.zip", a1.getBundledAs().getFilename());

 			// TODO: Enable fetching based on bundledAs URI?
 			//ro.getRoot().resolve("data/bag1.zip")

 		}
 	}
 }
	package org.apache.taverna.robundle.manifest;

	import static org.junit.Assert.assertEquals;
	/*
	* 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 static org.junit.Assert.assertNull;
	import static org.junit.Assert.assertTrue;

	import java.io.InputStream;
	import java.net.URI;
	import java.time.Instant;
	import java.util.Arrays;
	import java.util.Map;
	import java.util.Set;
	import java.util.stream.Collectors;

	import org.apache.taverna.robundle.Bundle;
	import org.apache.taverna.robundle.Bundles;
	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()
	.loadDocument(CONTEXT).getDocument();
	// 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);

	}

	@Test
	public void manifestFromSpec() throws Exception {
	try (Bundle ro = Bundles.createBundle();
	InputStream json = getClass().getResourceAsStream("/manifest.json")) {
	// Make a new, empty manifest we can inspect
	assertNotNull("Can't find manifest.json", json);
	Manifest manifest = new Manifest(ro);

	URI baseURI = ro.getPath(".ro/manifest.json").toUri();
	new RDFToManifest().readTo(json, manifest, baseURI);

	assertEquals(Arrays.asList(ro.getPath("/.ro/manifest.json")),
	manifest.getManifest());

	assertEquals(URI.create("http://example.com/retrieved"),
	manifest.getRetrievedFrom());
	assertEquals(Instant.parse("2013-03-05T17:29:03Z"),
	manifest.getRetrievedOn().toInstant());

	Agent retrievedBy = manifest.getRetrievedBy();
	assertEquals("John P. Smith",
	retrievedBy.getName());
	assertEquals(URI.create("http://example.com/foaf#john"),
	retrievedBy.getUri());
	assertEquals(URI.create("http://orcid.org/0000-0002-1825-0100"),
	retrievedBy.getOrcid());

	assertEquals(Instant.parse("2013-03-05T17:29:03Z"),
	manifest.getCreatedOn().toInstant());
	Agent createdBy = manifest.getCreatedBy();
	assertEquals("Alice W. Land",
	createdBy.getName());
	assertEquals(URI.create("http://example.com/foaf#alice"),
	createdBy.getUri());
	assertEquals(URI.create("http://orcid.org/0000-0002-1825-0097"),
	createdBy.getOrcid());

	assertEquals(Arrays.asList(ro.getPath(".ro/evolution.ttl")),
	manifest.getHistory());

	// As manifest.getAggregation() will create non-existing entries
	// we will check the list of URIs first
	Set<URI> aggregatedUris = manifest.getAggregates().stream()
	.map(PathMetadata::getUri)
	.collect(Collectors.toSet());
	//System.out.println(aggregatedUris);
	// Compare as Set as order is not necessarily preserved
	assertTrue(aggregatedUris.contains(URI.create("/folder/soup.jpeg")));
	assertTrue(aggregatedUris.contains(URI.create("http://example.com/blog/")));
	assertTrue(aggregatedUris.contains(URI.create("/README.txt")));
	assertTrue(aggregatedUris.contains(URI.create("http://example.com/comments.txt")));
	assertEquals(4, manifest.getAggregates().size());


	PathMetadata soup = manifest.getAggregation(ro.getPath("folder/soup.jpeg"));
	assertEquals(URI.create("http://example.com/retrieved/soup.jpeg"),
	soup.getRetrievedFrom());
	assertEquals(Instant.parse("2013-03-05T17:29:04Z"),
	soup.getRetrievedOn().toInstant());
	Agent peter = soup.getRetrievedBy();
	assertEquals("Peter L. Jones",
	peter.getName());
	assertEquals(URI.create("http://example.com/foaf#peter"),
	peter.getUri());
	assertEquals(URI.create("http://orcid.org/0000-0002-1825-0120"),
	peter.getOrcid());

	PathMetadata blog = manifest.getAggregation(URI.create("http://example.com/blog/"));
	// No additional metadata
	assertNull(blog.getRetrievedFrom());
	assertNull(blog.getRetrievedBy());
	assertNull(blog.getRetrievedOn());
	assertNull(blog.getCreatedBy());
	assertNull(blog.getCreatedOn());
	// NOTE: bundledAs might be created later when saving the manifest
	assertNull(blog.getBundledAs());

	PathMetadata readme = manifest.getAggregation(ro.getPath("/README.txt"));
	assertEquals("text/plain; charset=\"utf-8\"", readme.getMediatype());
	assertEquals("Bob Builder", readme.getCreatedBy().getName());
	assertEquals(URI.create("http://example.com/foaf#bob"), readme.getCreatedBy().getUri());

	PathMetadata comments = manifest.getAggregation(URI.create("http://example.com/comments.txt"));
	Proxy bundledAs = comments.getBundledAs();
	assertEquals(URI.create("urn:uuid:a0cf8616-bee4-4a71-b21e-c60e6499a644"),
	bundledAs.getURI());
	// TAVERNA-1043 - should work looking up "folder" even though JSON says "/folder/"
	assertEquals(ro.getPath("folder"), bundledAs.getFolder());
	assertEquals("external.txt", bundledAs.getFilename());


	// Again, these could be in any order
	assertEquals(3, manifest.getAnnotations().size());
	// annotation 1
	PathAnnotation ann1 = manifest.getAnnotation(URI.create("urn:uuid:d67466b4-3aeb-4855-8203-90febe71abdf")).get();
	assertEquals(URI.create("urn:uuid:d67466b4-3aeb-4855-8203-90febe71abdf"), ann1.getUri());
	assertEquals(URI.create("/folder/soup.jpeg"), ann1.getAbout());
	assertEquals(URI.create("annotations/soup-properties.ttl"), ann1.getContent());

	// annotation 2
	PathAnnotation ann2 = manifest.getAnnotations(URI.create("urn:uuid:a0cf8616-bee4-4a71-b21e-c60e6499a644")).get(0);
	assertEquals(URI.create("urn:uuid:a0cf8616-bee4-4a71-b21e-c60e6499a644"), ann2.getAbout());
	assertEquals(URI.create("http://example.com/blog/they-aggregated-our-file"),
	ann2.getContent());

	// annotation 3
	PathAnnotation ann3 = manifest.getAnnotations(ro.getRoot()).get(0);
	// Can be retrieved either by Path, relative URI or absolute URI
	assertEquals(ann3,
	manifest.getAnnotations(URI.create("/")).get(0));
	assertEquals(ann3,
	manifest.getAnnotations(ro.getRoot().toUri()).get(0));
	// Or by the second 'about' URI
	assertEquals(ann3,
	manifest.getAnnotations(URI.create("urn:uuid:d67466b4-3aeb-4855-8203-90febe71abdf")).get(0));
	// single content
	assertEquals(URI.create("annotations/a-meta-annotation-in-this-ro.txt"),
	ann3.getContent());
	// multiple about
	assertEquals(2, ann3.getAboutList().size());
	// ... but order not necessarily preserved
	assertTrue(ann3.getAboutList().contains(URI.create("urn:uuid:d67466b4-3aeb-4855-8203-90febe71abdf")));
	assertTrue(ann3.getAboutList().contains(URI.create("/")));
	}
	}

	@Test
	public void multipleConformsTo() throws Exception {
	try (Bundle ro = Bundles.createBundle();
	InputStream json = getClass().getResourceAsStream("/bag-of-bags-manifest.json")) {
	// Make a new, empty manifest we can inspect
	assertNotNull("Can't find bag-of-bags-manifest.json", json);
	Manifest manifest = new Manifest(ro);

	// NOTE: Uses RO-BagIt folder metadata/ instead of .ro/
	URI baseURI = ro.getPath("metadata/manifest.json").toUri();
	new RDFToManifest().readTo(json, manifest, baseURI);

	// Check basic metadata
	assertEquals(URI.create("https://github.com/ini-bdds/bdbag"),
	manifest.getCreatedBy().getUri());
	assertEquals(1, manifest.getAuthoredBy().size());
	Agent author = manifest.getAuthoredBy().get(0);
	assertEquals("Stian Soiland-Reyes",
	author.getName());
	assertEquals(URI.create("mbox:stain@apache.org"),
	author.getUri());
	assertEquals(URI.create("https://orcid.org/0000-0001-9842-9718"),
	author.getOrcid());

	// FIXME: The BDBag got this wrong and used "uri" instead of "content", and so
	// data/README accidentally became the ID of the annotation.
	// That means that we can't find any annotations as we only pick up
	// on those that have a "content"
	// assertEquals(1, manifest.getAnnotations().size());
	// PathAnnotation ann = manifest.getAnnotations().get(0);
	// assertEquals(ro.getRoot().toUri(),
	// ann.getAbout());
	// assertEquals(ro.getPath("data/README").toUri(), ann.getContent());

	// Now let's check aggregations
	assertEquals(1, manifest.getAggregates().size());
	// As aggregates order is not preserved, for simplicity this test
	// has only one aggregation
	PathMetadata a1 = manifest.getAggregates().get(0);
	URI uri = URI.create("http://n2t.net/ark:/57799/b90h3c");
	assertEquals(uri, a1.getUri());
	assertEquals(a1, manifest.getAggregation(uri));

	// FIXME: More than one?
	assertEquals(URI.create("https://w3id.org/ro/bagit/profile"),
	a1.getConformsTo());
	// assertEquals(URI.create("https://tools.ietf.org/html/draft-kunze-bagit-14"),
	// a1.getConformsTo());


	Proxy bundledAs = a1.getBundledAs();
	assertNotNull(bundledAs);
	// FIXME: Why is there no bundledAs data?
	assertEquals(ro.getPath("data"),
	bundledAs.getFolder());
	assertEquals("bag1.zip", a1.getBundledAs().getFilename());

	// TODO: Enable fetching based on bundledAs URI?
	//ro.getRoot().resolve("data/bag1.zip")

	}
	}
	}