taverna-scufl2-examples/src/main/java/org/apache/taverna/examples/JsonExport.java - incubator-taverna-language - Git at Google

 package org.apache.taverna.examples;

 /*
  * 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 JsonExport {
     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 {
         new JsonExport().convert(args);
     }


     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 JsonExport() {
         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.length == 0  || filepaths[0].equals("-h")) {
             System.out.println("Export workflow structore as JSON.");
             System.out.println("Usage: jsonexport [filename] ...");
             System.out.println("If the filename is - the workflow will be read from STDIN and");
             System.out.println("JSON written to STDOUT. ");
             System.out.println("Otherwise, the file is read as a workflow (t2flow, workflow bundle)");
             System.out.println("and written as JSON to a file with the .json extension.");
             System.out.println("Multiple filenames can be given. JSON filenames are written to STDOUT");
             return;
         }
         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;
     }
 }
	package org.apache.taverna.examples;

	/*
	* 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 JsonExport {
	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 {
	new JsonExport().convert(args);
	}


	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 JsonExport() {
	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.length == 0 \|\| filepaths[0].equals("-h")) {
	System.out.println("Export workflow structore as JSON.");
	System.out.println("Usage: jsonexport [filename] ...");
	System.out.println("If the filename is - the workflow will be read from STDIN and");
	System.out.println("JSON written to STDOUT. ");
	System.out.println("Otherwise, the file is read as a workflow (t2flow, workflow bundle)");
	System.out.println("and written as JSON to a file with the .json extension.");
	System.out.println("Multiple filenames can be given. JSON filenames are written to STDOUT");
	return;
	}
	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;
	}
	}