Repository: incubator-taverna-language Updated Branches: refs/heads/master 13283c9a9 -> 8eb242fba
Added resolve() Adapted from org.apache.taverna.platform.execution.impl.local.T2ReferenceConverter 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/74d014f6 Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/74d014f6 Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/74d014f6 Branch: refs/heads/master Commit: 74d014f6b15c894ba75c8fb16980d8044996e5a7 Parents: 13283c9 Author: Stian Soiland-Reyes <[email protected]> Authored: Sun Aug 28 23:28:29 2016 +0100 Committer: Stian Soiland-Reyes <[email protected]> Committed: Sun Aug 28 23:28:29 2016 +0100 ---------------------------------------------------------------------- .../apache/taverna/databundle/DataBundles.java | 82 ++++++++++++++++++-- .../taverna/databundle/TestDataBundles.java | 54 ++++++++++++- 2 files changed, 127 insertions(+), 9 deletions(-) ---------------------------------------------------------------------- http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/74d014f6/taverna-databundle/src/main/java/org/apache/taverna/databundle/DataBundles.java ---------------------------------------------------------------------- diff --git a/taverna-databundle/src/main/java/org/apache/taverna/databundle/DataBundles.java b/taverna-databundle/src/main/java/org/apache/taverna/databundle/DataBundles.java index c491d13..0598e10 100644 --- a/taverna-databundle/src/main/java/org/apache/taverna/databundle/DataBundles.java +++ b/taverna-databundle/src/main/java/org/apache/taverna/databundle/DataBundles.java @@ -1,6 +1,4 @@ -package org.apache.taverna.databundle; /* - * * 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 @@ -18,8 +16,8 @@ package org.apache.taverna.databundle; * specific language governing permissions and limitations * under the License. * -*/ - + */ +package org.apache.taverna.databundle; import static java.nio.file.Files.createDirectories; import static java.nio.file.Files.delete; @@ -33,10 +31,12 @@ import static java.nio.file.Files.write; import static java.nio.file.StandardOpenOption.CREATE; import static java.nio.file.StandardOpenOption.TRUNCATE_EXISTING; +import java.io.File; import java.io.IOException; import java.io.InputStream; import java.io.OutputStream; import java.net.URI; +import java.net.URL; import java.nio.charset.Charset; import java.nio.file.DirectoryIteratorException; import java.nio.file.DirectoryStream; @@ -49,15 +49,15 @@ import java.util.List; import java.util.NavigableMap; import java.util.TreeMap; import java.util.UUID; -import java.util.logging.Logger; import java.util.logging.Level; +import java.util.logging.Logger; +import org.apache.taverna.robundle.Bundle; +import org.apache.taverna.robundle.Bundles; import org.apache.taverna.scufl2.api.container.WorkflowBundle; import org.apache.taverna.scufl2.api.io.ReaderException; import org.apache.taverna.scufl2.api.io.WorkflowBundleIO; import org.apache.taverna.scufl2.api.io.WriterException; -import org.apache.taverna.robundle.Bundle; -import org.apache.taverna.robundle.Bundles; import com.fasterxml.jackson.databind.JsonNode; import com.fasterxml.jackson.databind.ObjectMapper; @@ -68,7 +68,6 @@ import com.fasterxml.jackson.databind.ObjectMapper; * The style of using this class is similar to that of {@link Files}. In fact, a * data bundle is implemented as a set of {@link Path}s. * - * @author Stian Soiland-Reyes */ public class DataBundles extends Bundles { private static final class OBJECT_MAPPER { @@ -440,6 +439,73 @@ public class DataBundles extends Bundles { throw ex.getCause(); } } + + /** + * Deeply resolve a {@link Path} to JVM objects. + * <p> + * This method is intended for use with a particular input/output port from + * {@link #getPorts(Path)} or {@link #getPort(Path, String)}. + * <p> + * If the path is <code>null</code> or {@link #isMissing(Path)}, + * <code>null</code> is returned. + * <p> + * If the path {@link #isValue(Path)}, its {@link #getStringValue(Path)} is + * returned (assuming an UTF-8 encoding). NOTE: Binary formats (e.g. PNG) + * will NOT be represented correctly as such a String and should be read + * directly with + * {@link Files#newInputStream(Path, java.nio.file.OpenOption...)}. + * <p> + * If the path {@link #isError(Path)}, the corresponding + * {@link ErrorDocument} is returned. + * <p> + * If the path {@link #isReference(Path)}, either a {@link File} or a + * {@link URL} is returned, depending on its protocol. + * <p> + * If the path {@link #isList(Path)}, a {@link List} is returned + * corresponding to resolving the paths from {@link #getList(Path)}. using + * this method. Thus a depth 2 path which elements are lists of values will + * effectively be returned as a <code>List<List<String>></code>, + * assuming no references, errors or empty slots. + * <p> + * If the path is neither of the above, the {@link Path} itself is returned. + * + * @param path Data bundle path to resolve + * @return <code>null</code>, a {@link String}, {@link ErrorDocument}, + * {@link URL}, {@link File}, {@link Path} or {@link List} + * (containing any of these). + * @throws IOException + * If the path (or any of the path in a contained list) can't be + * accessed + */ + public static Object resolve(Path path) throws IOException { + if (path == null) { + return null; + } + if (isMissing(path)) { + return null; + } else if (isValue(path)) { + return getStringValue(path); + } else if (isReference(path)) { + URI reference = getReference(path); + String scheme = reference.getScheme(); + if ("file".equals(scheme)) { + return new File(reference); + } else { + return reference.toURL(); + } + } else if (isList(path)) { + List<Path> list = getList(path); + List<Object> objectList = new ArrayList<Object>(list.size()); + for (Path pathElement : list) { + objectList.add(resolve(pathElement)); + } + return objectList; + } else if (isError(path)) { + return getError(path); + } else { + return path; + } + } public static WorkflowBundleIO getWfBundleIO() { if (wfBundleIO == null) http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/74d014f6/taverna-databundle/src/test/java/org/apache/taverna/databundle/TestDataBundles.java ---------------------------------------------------------------------- diff --git a/taverna-databundle/src/test/java/org/apache/taverna/databundle/TestDataBundles.java b/taverna-databundle/src/test/java/org/apache/taverna/databundle/TestDataBundles.java index c5d692d..ed87bc7 100644 --- a/taverna-databundle/src/test/java/org/apache/taverna/databundle/TestDataBundles.java +++ b/taverna-databundle/src/test/java/org/apache/taverna/databundle/TestDataBundles.java @@ -23,9 +23,11 @@ package org.apache.taverna.databundle; import static org.junit.Assert.*; +import java.io.File; import java.io.IOException; import java.io.InputStream; import java.net.URI; +import java.net.URL; import java.nio.charset.Charset; import java.nio.file.DirectoryStream; import java.nio.file.FileAlreadyExistsException; @@ -185,7 +187,7 @@ public class TestDataBundles { public void getInputs() throws Exception { Path inputs = DataBundles.getInputs(dataBundle); assertTrue(Files.isDirectory(inputs)); - // Second time should not fail because it already exists + // Second time should not fail because it alreadresolvy exists inputs = DataBundles.getInputs(dataBundle); assertTrue(Files.isDirectory(inputs)); assertEquals(dataBundle.getRoot(), inputs.getParent()); @@ -523,6 +525,55 @@ public class TestDataBundles { } @Test + public void resolve() throws Exception { + Path inputs = DataBundles.getInputs(dataBundle); + Path list = DataBundles.getPort(inputs, "in1"); + DataBundles.createList(list); + // 0 string value + DataBundles.setStringValue(DataBundles.newListItem(list), "test0"); + // 1 http:// reference + URI reference = URI.create("http://example.com/";); + DataBundles.setReference(DataBundles.newListItem(list), reference); + // 2 file:/// reference + Path tmpFile = Files.createTempFile("test", ".txt"); + URI fileRef = tmpFile.toUri(); + assertEquals("file", fileRef.getScheme()); + DataBundles.setReference(DataBundles.newListItem(list), fileRef); + // 3 empty (null) + // 4 error + DataBundles.setError(DataBundles.getListItem(list, 4), "Example error", "1. Tried it\n2. Didn't work"); + + + + + Object resolved = DataBundles.resolve(list); + assertTrue("Didn't resolve to a list", resolved instanceof List); + + List resolvedList = (List) resolved; + assertEquals("Unexpected list size", 5, resolvedList.size()); + + assertTrue(resolvedList.get(0) instanceof String); + assertEquals("test0", resolvedList.get(0)); + + assertTrue(resolvedList.get(1) instanceof URL); + assertEquals(reference, ((URL)resolvedList.get(1)).toURI()); + + assertTrue(resolvedList.get(2) instanceof File); + assertEquals(tmpFile.toFile(), resolvedList.get(2)); + + assertNull(resolvedList.get(3)); + assertTrue(resolvedList.get(4) instanceof ErrorDocument); + assertEquals("Example error", ((ErrorDocument)resolvedList.get(4)).getMessage()); + + } + + @Test + public void resolveBreaksOnBinaries() throws Exception { + Path inputs = DataBundles.getInputs(dataBundle); + Path list = DataBundles.getPort(inputs, "in1"); + } + + @Test public void setErrorArgs() throws Exception { Path inputs = DataBundles.getInputs(dataBundle); Path portIn1 = DataBundles.getPort(inputs, "in1"); @@ -765,6 +816,7 @@ public class TestDataBundles { Files.probeContentType(wf)); } + // TODO: Why was this ignored? Check with taverna-language-0.15.x RC emails @Ignore @Test public void getWorkflowBundle() throws Exception {
