org.caleydo.data.importer.tcga.regular.TCGAPostprocessingTask.java Source code

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Here is the source code for org.caleydo.data.importer.tcga.regular.TCGAPostprocessingTask.java

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/*******************************************************************************
 * Caleydo - Visualization for Molecular Biology - http://caleydo.org
 * Copyright (c) The Caleydo Team. All rights reserved.
 * Licensed under the new BSD license, available at http://caleydo.org/license
 ******************************************************************************/
package org.caleydo.data.importer.tcga.regular;

import java.util.ArrayList;
import java.util.Collection;
import java.util.concurrent.RecursiveAction;
import java.util.logging.Logger;

import org.apache.commons.lang.StringUtils;
import org.caleydo.core.data.datadomain.ATableBasedDataDomain;
import org.caleydo.core.data.perspective.table.TablePerspective;
import org.caleydo.data.importer.tcga.model.ClinicalMapping;
import org.caleydo.data.importer.tcga.model.TCGADataSet;

/**
 * utility task to create the initial table perspectives for the clinical data domain
 *
 */
public class TCGAPostprocessingTask extends RecursiveAction {
    private static final Logger log = Logger.getLogger(TCGAPostprocessingTask.class.getName());
    private static final long serialVersionUID = 7378867458430247164L;

    private final TCGADataSet dataSet;

    public TCGAPostprocessingTask(TCGADataSet dataSet) {
        this.dataSet = dataSet;
    }

    @Override
    protected void compute() {
        if (dataSet.getDataDomain() == null)
            return;

        switch (dataSet.getType()) {
        case clinical:
            updateClinicalNames(dataSet.getDataDomain());
            break;
        default:
            // nothing to do up to now
        }
    }

    /**
     * create initial table perspectives per column
     *
     * @param dataDomain
     */
    private void updateClinicalNames(ATableBasedDataDomain dataDomain) {
        log.info(dataSet.getType() + " updating clinicial tableperspective names");
        Collection<String> done = new ArrayList<>();
        for (TablePerspective p : dataDomain.getAllTablePerspectives()) {
            if (p.getDimensionPerspective().isDefault())
                continue;
            String name = p.getLabel();
            ClinicalMapping mapping = ClinicalMapping.byName(name);
            if (mapping != null) {
                done.add("updating " + p.getLabel() + "->" + mapping.getLabel());
                p.setLabel(mapping.getLabel());
                p.getDimensionPerspective().setLabel(mapping.getLabel());
                if (!p.getRecordPerspective().isDefault())
                    p.getRecordPerspective().setLabel(mapping.getLabel());
            }
        }
        log.info(dataSet.getType() + " updated: " + StringUtils.join(done, ", "));

    }

}