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

 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.assertNotNull;
 import static org.junit.Assert.assertNull;
 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 java.nio.file.attribute.FileTime;
 import java.time.Instant;

 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_skeleton.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.mirams@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.mirams@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-skeleton.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:fbergman@caltech.edu", createdBy.getUri());
 			//
 		}

 	}

 	@Test
 	public void convertDirectoryMadness() throws Exception {
 		Path file = Files.createTempFile("DirectoryMadness", ".omex");
 		try (InputStream src = getClass().getResourceAsStream(
 				"/combine/DirectoryMadness-skeleton.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-skeleton.omex")) {
 			Files.copy(src, file, StandardCopyOption.REPLACE_EXISTING);
 		}
 		//System.out.println(file);
 		try (Bundle bundle = Bundles.openBundle(file)) {

 		}
 	}

 	@Test
 	public void convertJWSOnlineBroken() throws Exception {
 		Path file = Files.createTempFile("jwsonline-broken", ".omex");
 		try (InputStream src = getClass().getResourceAsStream(
 				"/combine/jwsonline-broken-date.sedx")) {
 			Files.copy(src, file, StandardCopyOption.REPLACE_EXISTING);
 		}
 		//System.out.println(file);
 		try (Bundle bundle = Bundles.openBundle(file)) {
 			Manifest manifest = bundle.getManifest();

 			Path sedml = bundle.getPath("/sedml/testtavernalanguage-user.sedml");
 			assertTrue(Files.isRegularFile(sedml));
 			PathMetadata sedMlAggr = manifest.getAggregation(sedml);
 			assertEquals(URI.create("http://identifiers.org/combine.specifications/sed-ml.level-1.version-3"),
 					sedMlAggr.getConformsTo());

 			Path metadataXml = bundle.getPath("/metadata.rdf");
 			assertTrue(Files.isRegularFile(metadataXml));
 			PathMetadata metadataAggr = manifest.getAggregation(metadataXml);
 			assertEquals(URI.create("http://identifiers.org/combine.specifications/omex-metadata"),
 					metadataAggr.getConformsTo());

 			Path manifestXml = bundle.getRoot().resolve("manifest.xml");
 			assertTrue("manifest.xml not listed in " + manifest.getManifest(),
 					manifest.getManifest().contains(manifestXml));

 			// TAVERNA-1044: Can we still parse dcterms:rreator even if there
 			// is an RDF/XML syntactic error elsewhere?
 			Agent createdBy = manifest.getCreatedBy();
 			assertNotNull("Did not parse dcterms:creator", createdBy);
 			assertEquals(URI.create("mbox:stain@apache.org"),
 					createdBy.getUri());

 			/**
 			 * TAVERNA-1044 - invalid RDF/XML from JWS Online means we can't parse
 			 * dcterms:created correctly
 			 */
 			//FileTime createdOn = manifest.getCreatedOn();
 			//assertEquals(Instant.parse("2018-05-08T07:35:49Z"), createdOn.toInstant());

 		}

 	}


 	@Test
 	public void convertJWSOnlineFixed() throws Exception {
 		Path file = Files.createTempFile("jwsonline-fixed", ".omex");
 		try (InputStream src = getClass().getResourceAsStream(
 				"/combine/jwsonline-fixed-date.sedx")) {
 			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 sedml = bundle.getPath("/sedml/testtavernalanguage-user.sedml");
 			assertTrue(Files.isRegularFile(sedml));
 			PathMetadata sedMlAggr = manifest.getAggregation(sedml);
 			assertEquals(URI.create("http://identifiers.org/combine.specifications/sed-ml.level-1.version-3"),
 					sedMlAggr.getConformsTo());

 			Path metadataXml = bundle.getPath("/metadata.rdf");
 			assertTrue(Files.isRegularFile(metadataXml));
 			PathMetadata metadataAggr = manifest.getAggregation(metadataXml);
 			assertEquals(URI.create("http://identifiers.org/combine.specifications/omex-metadata"),
 					metadataAggr.getConformsTo());


 			// Metadata about the COMBINE archive itself, aka the RO,
 			// correctly parsed from metadata.rdf
 			Agent createdBy = manifest.getCreatedBy();
 			assertNotNull("Did not parse dcterms:creator", createdBy);
 			assertEquals(URI.create("mbox:stain@apache.org"),
 					createdBy.getUri());

 			FileTime createdOn = manifest.getCreatedOn();
 			assertEquals(Instant.parse("2018-05-08T07:35:49Z"), createdOn.toInstant());
 		}

 	}

 }
	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.assertNotNull;
	import static org.junit.Assert.assertNull;
	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 java.nio.file.attribute.FileTime;
	import java.time.Instant;

	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_skeleton.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.mirams@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.mirams@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-skeleton.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:fbergman@caltech.edu", createdBy.getUri());
	//
	}

	}

	@Test
	public void convertDirectoryMadness() throws Exception {
	Path file = Files.createTempFile("DirectoryMadness", ".omex");
	try (InputStream src = getClass().getResourceAsStream(
	"/combine/DirectoryMadness-skeleton.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-skeleton.omex")) {
	Files.copy(src, file, StandardCopyOption.REPLACE_EXISTING);
	}
	//System.out.println(file);
	try (Bundle bundle = Bundles.openBundle(file)) {

	}
	}

	@Test
	public void convertJWSOnlineBroken() throws Exception {
	Path file = Files.createTempFile("jwsonline-broken", ".omex");
	try (InputStream src = getClass().getResourceAsStream(
	"/combine/jwsonline-broken-date.sedx")) {
	Files.copy(src, file, StandardCopyOption.REPLACE_EXISTING);
	}
	//System.out.println(file);
	try (Bundle bundle = Bundles.openBundle(file)) {
	Manifest manifest = bundle.getManifest();

	Path sedml = bundle.getPath("/sedml/testtavernalanguage-user.sedml");
	assertTrue(Files.isRegularFile(sedml));
	PathMetadata sedMlAggr = manifest.getAggregation(sedml);
	assertEquals(URI.create("http://identifiers.org/combine.specifications/sed-ml.level-1.version-3"),
	sedMlAggr.getConformsTo());

	Path metadataXml = bundle.getPath("/metadata.rdf");
	assertTrue(Files.isRegularFile(metadataXml));
	PathMetadata metadataAggr = manifest.getAggregation(metadataXml);
	assertEquals(URI.create("http://identifiers.org/combine.specifications/omex-metadata"),
	metadataAggr.getConformsTo());

	Path manifestXml = bundle.getRoot().resolve("manifest.xml");
	assertTrue("manifest.xml not listed in " + manifest.getManifest(),
	manifest.getManifest().contains(manifestXml));

	// TAVERNA-1044: Can we still parse dcterms:rreator even if there
	// is an RDF/XML syntactic error elsewhere?
	Agent createdBy = manifest.getCreatedBy();
	assertNotNull("Did not parse dcterms:creator", createdBy);
	assertEquals(URI.create("mbox:stain@apache.org"),
	createdBy.getUri());

	/**
	* TAVERNA-1044 - invalid RDF/XML from JWS Online means we can't parse
	* dcterms:created correctly
	*/
	//FileTime createdOn = manifest.getCreatedOn();
	//assertEquals(Instant.parse("2018-05-08T07:35:49Z"), createdOn.toInstant());

	}

	}


	@Test
	public void convertJWSOnlineFixed() throws Exception {
	Path file = Files.createTempFile("jwsonline-fixed", ".omex");
	try (InputStream src = getClass().getResourceAsStream(
	"/combine/jwsonline-fixed-date.sedx")) {
	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 sedml = bundle.getPath("/sedml/testtavernalanguage-user.sedml");
	assertTrue(Files.isRegularFile(sedml));
	PathMetadata sedMlAggr = manifest.getAggregation(sedml);
	assertEquals(URI.create("http://identifiers.org/combine.specifications/sed-ml.level-1.version-3"),
	sedMlAggr.getConformsTo());

	Path metadataXml = bundle.getPath("/metadata.rdf");
	assertTrue(Files.isRegularFile(metadataXml));
	PathMetadata metadataAggr = manifest.getAggregation(metadataXml);
	assertEquals(URI.create("http://identifiers.org/combine.specifications/omex-metadata"),
	metadataAggr.getConformsTo());


	// Metadata about the COMBINE archive itself, aka the RO,
	// correctly parsed from metadata.rdf
	Agent createdBy = manifest.getCreatedBy();
	assertNotNull("Did not parse dcterms:creator", createdBy);
	assertEquals(URI.create("mbox:stain@apache.org"),
	createdBy.getUri());

	FileTime createdOn = manifest.getCreatedOn();
	assertEquals(Instant.parse("2018-05-08T07:35:49Z"), createdOn.toInstant());
	}

	}

	}