net.sf.taverna.t2.activities.biomart.BiomartActivityFactory.java Source code

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Here is the source code for net.sf.taverna.t2.activities.biomart.BiomartActivityFactory.java

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package net.sf.taverna.t2.activities.biomart;
/*
 * 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.IOException;
import java.io.StringReader;
import java.net.URI;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;

import net.sf.taverna.t2.reference.ExternalReferenceSPI;
import net.sf.taverna.t2.workflowmodel.Edit;
import net.sf.taverna.t2.workflowmodel.Edits;
import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityFactory;
import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityInputPort;
import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityOutputPort;

import org.apache.log4j.Logger;
import org.biomart.martservice.MartQuery;
import org.biomart.martservice.MartServiceXMLHandler;
import org.biomart.martservice.query.Attribute;
import org.biomart.martservice.query.Filter;
import org.biomart.martservice.query.Query;
import org.jdom.Document;
import org.jdom.JDOMException;
import org.jdom.input.SAXBuilder;

import com.fasterxml.jackson.databind.JsonNode;
import com.fasterxml.jackson.databind.ObjectMapper;

/**
 * An {@link ActivityFactory} for creating <code>BiomartActivity</code>.
 *
 * @author David Withers
 */
public class BiomartActivityFactory implements ActivityFactory {

    private static Logger logger = Logger.getLogger(BiomartActivityFactory.class);

    private Edits edits;
    private SAXBuilder builder = new SAXBuilder();

    @Override
    public BiomartActivity createActivity() {
        return new BiomartActivity();
    }

    @Override
    public URI getActivityType() {
        return URI.create(BiomartActivity.URI);
    }

    @Override
    public JsonNode getActivityConfigurationSchema() {
        ObjectMapper objectMapper = new ObjectMapper();
        try {
            return objectMapper.readTree(getClass().getResource("/schema.json"));
        } catch (IOException e) {
            return objectMapper.createObjectNode();
        }
    }

    @Override
    public Set<ActivityInputPort> getInputPorts(JsonNode configuration) {
        Set<ActivityInputPort> inputPorts = new HashSet<>();
        try {
            Query query = getQuery(configuration);
            for (Filter filter : query.getFilters()) {
                String name = filter.getQualifiedName() + "_filter";
                inputPorts.add(edits.createActivityInputPort(name, filter.isList() ? 1 : 0, true,
                        new ArrayList<Class<? extends ExternalReferenceSPI>>(), String.class));
            }
        } catch (JDOMException | IOException e) {
            logger.warn("Error caluculating input ports from BioMart configuration", e);
        }
        return inputPorts;
    }

    @Override
    public Set<ActivityOutputPort> getOutputPorts(JsonNode configuration) {
        Set<ActivityOutputPort> outputPorts = new HashSet<>();
        try {
            Query query = getQuery(configuration);
            List<Attribute> attributes = query.getAttributes();
            if (query.getFormatter() == null) {
                // Create new output ports corresponding to attributes
                for (Attribute attribute : attributes) {
                    String name = attribute.getQualifiedName();
                    ActivityOutputPort outputPort = null;
                    if (attribute.getAttributes() != null) {
                        outputPorts.add(
                                edits.createActivityOutputPort(name, 2, BiomartActivity.STREAM_RESULTS ? 1 : 2));
                    } else {
                        outputPorts.add(
                                edits.createActivityOutputPort(name, 1, BiomartActivity.STREAM_RESULTS ? 0 : 1));
                    }
                }
            } else if (attributes.size() > 0) {
                // create one port using the dataset name
                Attribute attribute = attributes.get(0);
                String name = attribute.getContainingDataset().getName();
                outputPorts.add(edits.createActivityOutputPort(name, 0, 0));
            }
        } catch (JDOMException | IOException e) {
            logger.warn("Error caluculating output ports from BioMart configuration", e);
        }
        return outputPorts;
    }

    public void setEdits(Edits edits) {
        this.edits = edits;
    }

    private Query getQuery(JsonNode configuration) throws JDOMException, IOException {
        String martQueryText = configuration.get("martQuery").asText();
        Document document = builder.build(new StringReader(martQueryText));
        MartQuery martQuery = MartServiceXMLHandler.elementToMartQuery(document.getRootElement(), null);
        return martQuery.getQuery();
    }

}