TAVERNA-1044: Test combine archive parsing from JWS Online .. and a suggested fix variant
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/repo Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/commit/e33a636e Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/e33a636e Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/e33a636e Branch: refs/heads/master Commit: e33a636ed2d3dfe01df8fb01bafe39fde50f2d76 Parents: 72899c6 Author: Stian Soiland-Reyes <[email protected]> Authored: Thu May 10 11:20:44 2018 +0100 Committer: Stian Soiland-Reyes <[email protected]> Committed: Thu May 10 11:20:44 2018 +0100 ---------------------------------------------------------------------- .../manifest/combine/TestCombineManifest.java | 95 +++++++++++++++++++- 1 file changed, 93 insertions(+), 2 deletions(-) ---------------------------------------------------------------------- http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/e33a636e/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 index 7fc54ed..4ac0dfa 100644 --- 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 @@ -8,9 +8,9 @@ package org.apache.taverna.robundle.manifest.combine; * 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 @@ -21,6 +21,8 @@ package org.apache.taverna.robundle.manifest.combine; 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; @@ -28,6 +30,8 @@ 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; @@ -152,4 +156,91 @@ public class TestCombineManifest { } } + @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:[email protected]"), + 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:[email protected]"), + createdBy.getUri()); + + FileTime createdOn = manifest.getCreatedOn(); + assertEquals(Instant.parse("2018-05-08T07:35:49Z"), createdOn.toInstant()); + } + + } + }
