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Posted to commits@taverna.apache.org by st...@apache.org on 2015/06/11 18:35:35 UTC
[16/31] incubator-taverna-language git commit: Test files added
Test files added
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/997f48fc
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/997f48fc
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/997f48fc
Branch: refs/heads/master
Commit: 997f48fcab75cee5399bc2bdd8cd9ef77eb1d73c
Parents: f49db52
Author: menaka121 <me...@gmail.com>
Authored: Thu Jun 11 19:01:29 2015 +0530
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Thu Jun 11 17:33:29 2015 +0100
----------------------------------------------------------------------
.../tavlang/commandline/CommandLineTool.java | 2 +-
.../commandline/tools/convert/ToJson.java | 310 +++++++++++++++++++
.../commandline/tools/convert/ToRobundle.java | 68 ++++
.../commandline/test/CommandLineTest.java | 5 +-
.../commandline/test/Scufl2ConvertTest.java | 14 +
5 files changed, 396 insertions(+), 3 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/997f48fc/taverna-language-commandline/src/main/java/org/apache/tavlang/commandline/CommandLineTool.java
----------------------------------------------------------------------
diff --git a/taverna-language-commandline/src/main/java/org/apache/tavlang/commandline/CommandLineTool.java b/taverna-language-commandline/src/main/java/org/apache/tavlang/commandline/CommandLineTool.java
index 5c0105e..bff8576 100644
--- a/taverna-language-commandline/src/main/java/org/apache/tavlang/commandline/CommandLineTool.java
+++ b/taverna-language-commandline/src/main/java/org/apache/tavlang/commandline/CommandLineTool.java
@@ -39,9 +39,9 @@ import org.apache.taverna.scufl2.api.io.ReaderException;
import org.apache.tavlang.commandline.tools.Tools;
import org.apache.tavlang.commandline.tools.Tools.ConvertionTools;
import org.apache.tavlang.commandline.tools.convert.Scufl2Convert;
+import org.apache.tavlang.commandline.tools.convert.ToRobundle;
import org.apache.tavlang.commandline.tools.inspect.ProcessorNames;
import org.apache.tavlang.commandline.tools.inspect.ServiceTypes;
-import org.apache.tavlang.tools.ToRobundle;
import com.google.common.base.Joiner;
import com.google.common.collect.Lists;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/997f48fc/taverna-language-commandline/src/main/java/org/apache/tavlang/commandline/tools/convert/ToJson.java
----------------------------------------------------------------------
diff --git a/taverna-language-commandline/src/main/java/org/apache/tavlang/commandline/tools/convert/ToJson.java b/taverna-language-commandline/src/main/java/org/apache/tavlang/commandline/tools/convert/ToJson.java
new file mode 100644
index 0000000..4193c30
--- /dev/null
+++ b/taverna-language-commandline/src/main/java/org/apache/tavlang/commandline/tools/convert/ToJson.java
@@ -0,0 +1,310 @@
+package org.apache.tavlang.commandline.tools.convert;
+
+/*
+ * 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 java.io.File;
+import java.io.IOException;
+import java.io.OutputStream;
+import java.net.URI;
+import java.util.Arrays;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import org.apache.taverna.scufl2.api.annotation.Annotation;
+import org.apache.taverna.scufl2.api.annotation.Revision;
+import org.apache.taverna.scufl2.api.common.Child;
+import org.apache.taverna.scufl2.api.common.Ported;
+import org.apache.taverna.scufl2.api.common.Scufl2Tools;
+import org.apache.taverna.scufl2.api.common.URITools;
+import org.apache.taverna.scufl2.api.container.WorkflowBundle;
+import org.apache.taverna.scufl2.api.core.BlockingControlLink;
+import org.apache.taverna.scufl2.api.core.ControlLink;
+import org.apache.taverna.scufl2.api.core.DataLink;
+import org.apache.taverna.scufl2.api.core.Processor;
+import org.apache.taverna.scufl2.api.core.Workflow;
+import org.apache.taverna.scufl2.api.io.ReaderException;
+import org.apache.taverna.scufl2.api.io.WorkflowBundleIO;
+import org.apache.taverna.scufl2.api.io.WorkflowBundleWriter;
+import org.apache.taverna.scufl2.api.io.WriterException;
+import org.apache.taverna.scufl2.api.port.DepthPort;
+import org.apache.taverna.scufl2.api.port.GranularDepthPort;
+import org.apache.taverna.scufl2.api.port.Port;
+import org.apache.taverna.scufl2.api.profiles.Profile;
+
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.SerializationFeature;
+import com.fasterxml.jackson.databind.node.ArrayNode;
+import com.fasterxml.jackson.databind.node.ObjectNode;
+import com.fasterxml.jackson.databind.util.ISO8601DateFormat;
+
+public class ToJson {
+ public class JsonWriter implements WorkflowBundleWriter {
+
+ @Override
+ public Set<String> getMediaTypes() {
+ return new HashSet<String>(Arrays.asList("application/ld+json",
+ "application/json"));
+ }
+ @Override
+ public void writeBundle(WorkflowBundle wfBundle, File destination,
+ String mediaType) throws WriterException, IOException {
+ ObjectNode json = toJson(wfBundle);
+ mapper.writeValue(destination, json);
+ }
+
+ @Override
+ public void writeBundle(WorkflowBundle wfBundle,
+ OutputStream output, String mediaType)
+ throws WriterException, IOException {
+ ObjectNode json = toJson(wfBundle);
+ mapper.writeValue(output, json);
+ }
+
+ }
+
+ public static void main(String[] args) throws ReaderException, IOException,
+ WriterException {
+ String[] args2 = {"/home/menaka/conv/aaa/as.wfbundle"};
+ new ToJson().convert(args2);
+ }
+
+
+ private WorkflowBundleIO io = new WorkflowBundleIO();;
+
+ private WorkflowBundleWriter jsonWriter = new JsonWriter();
+
+ private ObjectMapper mapper = new ObjectMapper();
+
+ private Scufl2Tools scufl2Tools = new Scufl2Tools();
+
+ private URITools uriTools = new URITools();
+
+ public ToJson() {
+ mapper.enable(SerializationFeature.INDENT_OUTPUT);
+ mapper.disable(SerializationFeature.FAIL_ON_EMPTY_BEANS);
+ mapper.disable(SerializationFeature.WRITE_DATES_AS_TIMESTAMPS);
+
+ mapper.setDateFormat(new ISO8601DateFormat());
+
+ // Adding custom writer dynamically
+ List<WorkflowBundleWriter> writers = io.getWriters();
+ writers.add(jsonWriter);
+ io.setWriters(writers);
+ }
+
+ protected void addPorts(Ported ported, ObjectNode p) {
+ ArrayNode inputs = mapper.createArrayNode();
+ for (Port port : ported.getInputPorts()) {
+ inputs.add(toJson(port));
+ }
+ p.put("inputs", inputs);
+
+ ArrayNode outputs = mapper.createArrayNode();
+ for (Port port : ported.getOutputPorts()) {
+ outputs.add(toJson(port));
+ // FIXME: Do we need the id for ports? Needed if we add datalinks
+ }
+ p.put("outputs", outputs);
+ }
+
+ protected ObjectNode annotations(Child<?> bean) {
+ ObjectNode node = mapper.createObjectNode();
+ for (Annotation ann : scufl2Tools.annotationsFor(bean)) {
+ URI annUri = uriTools.uriForBean(ann);
+
+ // TODO: include annotation body?
+ }
+ return node;
+ }
+
+ public void convert(String[] filepaths) throws ReaderException,
+ IOException, WriterException {
+ if (filepaths[0].equals("-")) {
+ // Do piped Stdin/Stdout instead
+ WorkflowBundle wfBundle = io.readBundle(System.in, null);
+ io.writeBundle(wfBundle, System.err, "application/ld+json");
+ return;
+ }
+
+ for (String filepath : filepaths) {
+ File workflow = new File(filepath);
+
+ String filename = workflow.getName();
+ filename = filename.replaceFirst("\\..*", ".json");
+ File workflowFile = new File(workflow.getParentFile(), filename);
+
+ WorkflowBundle wfBundle = io.readBundle(workflow, null);
+ io.writeBundle(wfBundle, workflowFile, "application/ld+json");
+ System.out.println(workflowFile);
+ }
+ }
+
+ protected ObjectNode toJson(Port port) {
+ ObjectNode p = mapper.createObjectNode();
+ p.put("name", port.getName());
+ p.putPOJO("id", uriTools.relativeUriForBean(port,
+ scufl2Tools.findParent(WorkflowBundle.class, ((Child<?>)port))));
+
+ if (port instanceof DepthPort) {
+ DepthPort depthPort = (DepthPort) port;
+ if (depthPort.getDepth() != null) {
+ p.put("depth", depthPort.getDepth());
+ }
+ }
+ if (port instanceof GranularDepthPort) {
+ GranularDepthPort granularDepthPort = (GranularDepthPort) port;
+ if (granularDepthPort.getGranularDepth() != null &&
+ ! granularDepthPort.getGranularDepth().equals(granularDepthPort.getDepth())) {
+ p.put("granularDepth", granularDepthPort.getGranularDepth());
+ }
+ }
+ p.putAll(annotations((Child<?>)port));
+ return p;
+ }
+
+ protected JsonNode toJson(Processor proc) {
+ ObjectNode p = mapper.createObjectNode();
+ p.putPOJO("id", uriTools.relativeUriForBean(proc, proc.getParent().getParent()));
+ p.put("name", proc.getName());
+ addPorts(proc, p);
+ p.putAll(annotations(proc));
+
+ List<Workflow> nested = scufl2Tools.nestedWorkflowsForProcessor(proc,
+ proc.getParent().getParent().getMainProfile());
+ if (! nested.isEmpty()) {
+ if (nested.size() == 1) {
+ p.put("nestedWorkflow", toJson(nested.iterator().next()));
+ } else {
+ ArrayNode list = mapper.createArrayNode();
+ for (Workflow w : nested) {
+ list.add(toJson(w));
+ }
+ p.put("nestedWorkflow", list);
+ }
+ }
+ return p;
+ }
+
+ protected JsonNode toJson(Revision currentRevision) {
+ ArrayNode revisions = mapper.createArrayNode();
+ while (currentRevision != null) {
+ ObjectNode rev = mapper.createObjectNode();
+ rev.putPOJO("id", currentRevision.getIdentifier());
+ if (currentRevision.getGeneratedAtTime() != null) {
+ rev.putPOJO("generatedAtTime", currentRevision.getGeneratedAtTime());
+ }
+ currentRevision = currentRevision.getPreviousRevision();
+ if (currentRevision != null) {
+ rev.putPOJO("wasRevisionOf", currentRevision.getIdentifier());
+ }
+ revisions.add(rev);
+ }
+ return revisions;
+ }
+
+ protected ObjectNode toJson(Workflow workflow) {
+ ObjectNode wf = mapper.createObjectNode();
+
+ wf.putPOJO("id", uriTools.relativeUriForBean(workflow, workflow.getParent()));
+
+ wf.put("name", workflow.getName());
+ wf.put("revisions", toJson(workflow.getCurrentRevision()));
+
+ ArrayNode processors = mapper.createArrayNode();
+ for (Processor p : workflow.getProcessors()) {
+ processors.add(toJson(p));
+ }
+ addPorts(workflow, wf);
+ wf.put("processors", processors);
+
+ ArrayNode datalinks = mapper.createArrayNode();
+ for (DataLink link : workflow.getDataLinks()) {
+ datalinks.add(toJson(link));
+ }
+ wf.put("datalinks", datalinks);
+
+ ArrayNode controlLinks = mapper.createArrayNode();
+ for (ControlLink link : workflow.getControlLinks()) {
+ controlLinks.add(toJson(link));
+ }
+ wf.put("controllinks", controlLinks);
+
+
+ wf.putAll(annotations(workflow));
+
+ return wf;
+ }
+
+ protected JsonNode toJson(ControlLink link) {
+ ObjectNode l = mapper.createObjectNode();
+ if (link instanceof BlockingControlLink) {
+ BlockingControlLink controlLink = (BlockingControlLink) link;
+ l.putPOJO("block", uriTools.relativeUriForBean(controlLink.getBlock(),
+ link.getParent().getParent()));
+ l.putPOJO("untilFinished", uriTools.relativeUriForBean(controlLink.getUntilFinished(),
+ link.getParent().getParent()));
+ }
+ return l;
+ }
+
+ protected JsonNode toJson(DataLink link) {
+ ObjectNode l = mapper.createObjectNode();
+ l.putPOJO("receivesFrom", uriTools.relativeUriForBean(link.getReceivesFrom(),
+ link.getParent().getParent()));
+ l.putPOJO("sendsTo", uriTools.relativeUriForBean(link.getSendsTo(),
+ link.getParent().getParent()));
+ if (link.getMergePosition() != null) {
+ l.put("mergePosition", link.getMergePosition());
+ }
+ return l;
+ }
+
+ public ObjectNode toJson(WorkflowBundle wfBundle) {
+
+ ObjectNode root = mapper.createObjectNode();
+ ArrayNode contextList = root.arrayNode();
+ root.put("@context", contextList);
+ ObjectNode context = root.objectNode();
+ contextList.add("https://w3id.org/scufl2/context");
+ contextList.add(context);
+ URI base = wfBundle.getGlobalBaseURI();
+ context.put("@base", base.toASCIIString());
+ root.put("id", base.toASCIIString());
+
+// root.put("name", wfBundle.getName());
+// root.put("revisions", toJson(wfBundle.getCurrentRevision()));
+
+ root.put("workflow", toJson(wfBundle.getMainWorkflow()));
+ root.put("profile", toJson(wfBundle.getMainProfile()));
+
+ return root;
+ }
+
+ private JsonNode toJson(Profile profile) {
+ ObjectNode pf = mapper.createObjectNode();
+
+ pf.putPOJO("id", uriTools.relativeUriForBean(profile, profile.getParent()));
+ // TODO: Activities and configurations
+ return pf;
+ }
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/997f48fc/taverna-language-commandline/src/main/java/org/apache/tavlang/commandline/tools/convert/ToRobundle.java
----------------------------------------------------------------------
diff --git a/taverna-language-commandline/src/main/java/org/apache/tavlang/commandline/tools/convert/ToRobundle.java b/taverna-language-commandline/src/main/java/org/apache/tavlang/commandline/tools/convert/ToRobundle.java
new file mode 100644
index 0000000..9c788ff
--- /dev/null
+++ b/taverna-language-commandline/src/main/java/org/apache/tavlang/commandline/tools/convert/ToRobundle.java
@@ -0,0 +1,68 @@
+package org.apache.tavlang.commandline.tools.convert;
+
+/*
+ * 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 java.io.File;
+import java.io.IOException;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.List;
+import java.util.logging.ConsoleHandler;
+import java.util.logging.Level;
+import java.util.logging.Logger;
+
+import org.apache.taverna.robundle.Bundle;
+import org.apache.taverna.robundle.Bundles;
+
+public class ToRobundle{
+
+ public ToRobundle(List<String> files, String out) throws Exception{
+
+ Logger logger = Logger.getLogger("");
+ //logger.setLevel(Level.FINER);
+ ConsoleHandler console = new ConsoleHandler();
+ console.setLevel(Level.FINEST);
+ logger.addHandler(console);
+ Logger.getLogger("org.researchobject").setLevel(Level.FINEST);
+
+ for(String f : files){
+ Path file = Paths.get(f);
+ convert(file);
+ }
+ }
+
+ //Recursive conversion
+ public ToRobundle(String type, String in, String out) {
+ // TODO Auto-generated constructor stub
+
+ }
+
+ public void convert(Path file) throws IOException{
+ try (Bundle bundle = Bundles.openBundle(file)) {
+
+ System.out.println(bundle.getManifest().toString());
+// bundle.getManifest().writeAsJsonLD();
+// bundle.getManifest().writeAsCombineManifest();
+ }
+ }
+
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/997f48fc/taverna-language-commandline/src/test/java/org/apache/tavlang/commandline/test/CommandLineTest.java
----------------------------------------------------------------------
diff --git a/taverna-language-commandline/src/test/java/org/apache/tavlang/commandline/test/CommandLineTest.java b/taverna-language-commandline/src/test/java/org/apache/tavlang/commandline/test/CommandLineTest.java
index e97c715..6e03c88 100644
--- a/taverna-language-commandline/src/test/java/org/apache/tavlang/commandline/test/CommandLineTest.java
+++ b/taverna-language-commandline/src/test/java/org/apache/tavlang/commandline/test/CommandLineTest.java
@@ -42,10 +42,11 @@ public class CommandLineTest {
@Test
public void testConvert(){
+
// CommandLineTool tool = new CommandLineTool();
- commandLineTool.parse("convert", "-r", "-wfbundle", "-o", "/files/dir", "-i", "/files0/dir");
+// commandLineTool.parse("convert", "-r", "-wfbundle", "-o", "/files/dir", "-i", "/files0/dir");
// CommandLineTool tool2 = new CommandLineTool();
- commandLineTool.parse("convert", "-r", "-wfdesc", "-o", "/files/dir", "-i", "/files0/dir");
+// commandLineTool.parse("convert", "-r", "-wfdesc", "-o", "/files/dir", "-i", "/files0/dir");
// commandLineTool.parse();
// commandLineTool.parse();
// commandLineTool.parse();
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/997f48fc/taverna-language-commandline/src/test/java/org/apache/tavlang/commandline/test/Scufl2ConvertTest.java
----------------------------------------------------------------------
diff --git a/taverna-language-commandline/src/test/java/org/apache/tavlang/commandline/test/Scufl2ConvertTest.java b/taverna-language-commandline/src/test/java/org/apache/tavlang/commandline/test/Scufl2ConvertTest.java
new file mode 100644
index 0000000..c838549
--- /dev/null
+++ b/taverna-language-commandline/src/test/java/org/apache/tavlang/commandline/test/Scufl2ConvertTest.java
@@ -0,0 +1,14 @@
+package org.apache.tavlang.commandline.test;
+
+import static org.junit.Assert.*;
+
+import org.junit.Test;
+
+public class Scufl2ConvertTest{
+
+ @Test
+ public void test() {
+ fail("Not yet implemented");
+ }
+
+}