edu.sdsc.scigraph.services.jersey.writers.BbopJsGraphWriter.java Source code

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Here is the source code for edu.sdsc.scigraph.services.jersey.writers.BbopJsGraphWriter.java

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/**
 * Copyright (C) 2014 The SciGraph authors
 *
 * Licensed 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.
 */
package edu.sdsc.scigraph.services.jersey.writers;

import static com.google.common.collect.Lists.newArrayList;
import io.dropwizard.jackson.Jackson;

import java.io.IOException;
import java.io.OutputStream;
import java.lang.annotation.Annotation;
import java.lang.reflect.Array;
import java.lang.reflect.Type;
import java.util.Collection;
import java.util.HashSet;

import javax.ws.rs.Produces;
import javax.ws.rs.core.MediaType;
import javax.ws.rs.core.MultivaluedMap;
import javax.ws.rs.ext.Provider;

import jersey.repackaged.com.google.common.collect.Iterables;

import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.common.base.Optional;
import com.tinkerpop.blueprints.Direction;
import com.tinkerpop.blueprints.Edge;
import com.tinkerpop.blueprints.Graph;
import com.tinkerpop.blueprints.Vertex;

import edu.sdsc.scigraph.frames.CommonProperties;
import edu.sdsc.scigraph.frames.Concept;
import edu.sdsc.scigraph.frames.NodeProperties;
import edu.sdsc.scigraph.services.api.graph.BbopGraph;

@Produces(MediaType.APPLICATION_JSON)
@Provider
public class BbopJsGraphWriter extends GraphWriter {

    private static final ObjectMapper MAPPER = Jackson.newObjectMapper();

    // TODO: Move these next three methods someplace common
    String getCurieOrFragment(Vertex vertex) {
        String property = vertex.getPropertyKeys().contains(CommonProperties.CURIE) ? CommonProperties.CURIE
                : CommonProperties.FRAGMENT;
        return (String) vertex.getProperty(property);
    }

    static Optional<String> getLabel(Vertex vertex) {
        Optional<String> label = Optional.absent();
        if (vertex.getPropertyKeys().contains(NodeProperties.LABEL)) {
            Object value = vertex.getProperty(NodeProperties.LABEL);
            if (value.getClass().isArray()) {
                label = Optional.of((String) Array.get(value, 0));
            } else if (value instanceof Iterable) {
                label = Optional.of((String) Iterables.getFirst((Iterable<?>) value, null));
            } else {
                label = Optional.of((String) value);
            }
        }
        return label;
    }

    static Collection<String> getCategories(Vertex vertex) {
        Collection<String> categories = new HashSet<>();
        if (vertex.getPropertyKeys().contains(Concept.CATEGORY)) {
            Object value = vertex.getProperty(Concept.CATEGORY);
            if (value.getClass().isArray()) {
                for (int i = 0; i < Array.getLength(value); i++) {
                    categories.add((String) Array.get(value, i));
                }
            } else if (value instanceof Iterable) {
                categories.addAll(newArrayList((Iterable<String>) value));
            } else {
                categories.add((String) value);
            }
        }
        return categories;
    }

    @Override
    public void writeTo(Graph data, Class<?> type, Type genericType, Annotation[] annotations, MediaType mediaType,
            MultivaluedMap<String, Object> headers, OutputStream out) throws IOException {
        BbopGraph bbopGraph = new BbopGraph();
        for (Vertex vertex : data.getVertices()) {
            BbopGraph.BbopNode bbopNode = new BbopGraph.BbopNode();
            bbopNode.setId(getCurieOrFragment(vertex));
            Optional<String> label = getLabel(vertex);
            if (label.isPresent()) {
                bbopNode.setLbl(label.get());
            }
            bbopNode.getMeta().put(Concept.CATEGORY, getCategories(vertex));
            bbopGraph.getNodes().add(bbopNode);
        }
        for (Edge edge : data.getEdges()) {
            BbopGraph.BbopEdge bbopEdge = new BbopGraph.BbopEdge();
            Vertex subject = edge.getVertex(Direction.OUT);
            Vertex object = edge.getVertex(Direction.IN);
            bbopEdge.setSub(getCurieOrFragment(subject));
            bbopEdge.setObj(getCurieOrFragment(object));
            bbopEdge.setPred(edge.getLabel());
            bbopGraph.getEdges().add(bbopEdge);
        }
        MAPPER.writeValue(out, bbopGraph);
        out.flush();
    }

}