uk.ac.ebi.atlas.model.ExperimentConfiguration.java Source code

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Here is the source code for uk.ac.ebi.atlas.model.ExperimentConfiguration.java

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/*
 * Copyright 2008-2013 Microarray Informatics Team, EMBL-European Bioinformatics Institute
 *
 * 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.
 *
 *
 * For further details of the Gene Expression Atlas project, including source code,
 * downloads and documentation, please see:
 *
 * http://gxa.github.com/gxa
 */

package uk.ac.ebi.atlas.model;

import com.google.common.base.Joiner;
import com.google.common.collect.ImmutableSet;
import com.google.common.collect.Sets;
import org.apache.commons.configuration.Configuration;
import org.apache.commons.configuration.XMLConfiguration;
import org.apache.commons.lang3.StringUtils;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
import uk.ac.ebi.atlas.model.differential.Contrast;

import javax.xml.xpath.*;
import java.util.EnumSet;
import java.util.Set;

public class ExperimentConfiguration {

    public static final String EXPERIMENT_TYPE = "experimentType";
    private XMLConfiguration xmlConfiguration;

    private Document document;

    private XPath xpath = XPathFactory.newInstance().newXPath();

    public ExperimentConfiguration(XMLConfiguration xmlConfiguration, Document document) {
        this.xmlConfiguration = xmlConfiguration;
        this.document = document;
    }

    public Set<Contrast> getContrasts() {

        Set<Contrast> contrasts = Sets.newLinkedHashSet();

        NodeList arrayDesigns = document.getElementsByTagName("array_design");
        for (int i = 0; i < arrayDesigns.getLength(); i++) {
            Node currentArrayDesign = arrayDesigns.item(i);
            String arrayDesignAccession = currentArrayDesign.getFirstChild().getTextContent().trim();
            parseContrastConfiguration("analytics[" + (i + 1) + "]/contrasts/contrast/@id", arrayDesignAccession,
                    contrasts);
        }

        // in case no array designs (case of RNA-seq)
        if (arrayDesigns.getLength() == 0) {
            parseContrastConfiguration("analytics/contrasts/contrast/@id", null, contrasts);
        }

        return contrasts;
    }

    private void parseContrastConfiguration(String query, String arrayDesignAccession, Set<Contrast> contrasts) {
        String[] ids = xmlConfiguration.getStringArray(query);
        for (String id : ids) {
            Contrast contrast = getContrast(id, arrayDesignAccession);
            contrasts.add(contrast);
        }
    }

    Contrast getContrast(String id, String arrayDesignAccession) {
        Configuration configuration = xmlConfiguration
                .configurationAt("analytics/contrasts/contrast[@id=\'" + id + "\']");
        String name = configuration.getString("name");
        String reference = configuration.getString("reference_assay_group");
        String test = configuration.getString("test_assay_group");
        return new Contrast(id, arrayDesignAccession, getAssayGroup(reference), getAssayGroup(test), name);
    }

    AssayGroup getAssayGroup(String id) {
        try {

            XPathExpression expr = xpath
                    .compile("/configuration/analytics/assay_groups/assay_group[@id='" + id + "']/assay");

            NodeList nl = (NodeList) expr.evaluate(document, XPathConstants.NODESET);
            String[] assayAccessions = new String[nl.getLength()];

            ImmutableSet.Builder<String> builder = ImmutableSet.builder();
            for (int i = 0; i < nl.getLength(); i++) {
                Node node = nl.item(i);
                String technicalReplicateId = getAttribute(node, "technical_replicate_id");
                if (technicalReplicateId != null) {
                    builder.add(technicalReplicateId);
                }
                assayAccessions[i] = node.getTextContent();
            }

            int technicalReplicates = builder.build().size();
            int biologicalReplicates = (technicalReplicates == 0) ? assayAccessions.length : technicalReplicates;
            return new AssayGroup(id, biologicalReplicates, assayAccessions);

        } catch (XPathExpressionException e) {
            throw new IllegalStateException("Problem parsing configuration file.", e);
        }
    }

    private String getAttribute(Node node, String name) {
        Node attribute = node.getAttributes().getNamedItem(name);
        return (attribute == null) ? null : attribute.getNodeValue();
    }

    public Set<String> getAssayAccessions() {
        try {

            XPathExpression expr = xpath.compile("/configuration/analytics/assay_groups/assay_group/assay");

            Set<String> assayAccessions = Sets.newHashSet();

            NodeList nl = (NodeList) expr.evaluate(document, XPathConstants.NODESET);
            for (int i = 0; i < nl.getLength(); i++) {
                Node node = nl.item(i);
                assayAccessions.add(node.getTextContent());
            }

            return assayAccessions;

        } catch (XPathExpressionException e) {
            throw new IllegalStateException("Problem parsing configuration file.", e);
        }
    }

    public AssayGroups getAssayGroups() {
        Set<AssayGroup> assayGroups = Sets.newHashSet();

        String[] assayGoupIds = xmlConfiguration.getStringArray("/analytics/assay_groups/assay_group/@id");

        for (String assayGoupId : assayGoupIds) {
            assayGroups.add(getAssayGroup(assayGoupId));
        }

        return new AssayGroups(assayGroups);
    }

    public ExperimentType getExperimentType() {
        Element configuration = document.getDocumentElement();

        String type = configuration.getAttribute(EXPERIMENT_TYPE);

        if (StringUtils.isEmpty(type)) {
            throw new IllegalStateException(String.format("Missing %s attribute on root element of %s",
                    EXPERIMENT_TYPE, xmlConfiguration.getFileName()));
        }

        ExperimentType experimentType = ExperimentType.get(type);

        if (experimentType == null) {
            throw new IllegalStateException(String.format("Unknown %s attribute: \"%s\". Must be one of: [%s]",
                    EXPERIMENT_TYPE, type, Joiner.on(", ").join(EnumSet.allOf(ExperimentType.class))));
        }

        return experimentType;
    }
}