uk.ac.ebi.atlas.experimentimport.experimentdesign.magetab.MicroarrayExperimentMageTabParser.java Source code

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Here is the source code for uk.ac.ebi.atlas.experimentimport.experimentdesign.magetab.MicroarrayExperimentMageTabParser.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.experimentimport.experimentdesign.magetab;

import com.google.common.collect.Sets;
import org.springframework.context.annotation.Scope;
import uk.ac.ebi.arrayexpress2.magetab.datamodel.SDRF;
import uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.utils.GraphUtils;
import uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.HybridizationNode;
import uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.SourceNode;
import uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.FactorValueAttribute;
import uk.ac.ebi.atlas.model.ExperimentDesign;

import javax.inject.Named;
import java.util.Collection;
import java.util.List;
import java.util.Set;

@Named
@Scope("prototype")
public class MicroarrayExperimentMageTabParser extends MageTabParser<HybridizationNode> {

    @Override
    protected Set<NamedSdrfNode<HybridizationNode>> getAssayNodes(SDRF sdrf) {
        Set<NamedSdrfNode<HybridizationNode>> namedSdrfNodes = Sets.newLinkedHashSet();

        Collection<? extends HybridizationNode> hybridizationNodes = sdrf.getNodes(HybridizationNode.class);

        if (hybridizationNodes.size() == 0) {
            //this is required because of a bug in limpopo...
            hybridizationNodes = sdrf.getNodes(uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.AssayNode.class);
        }

        for (HybridizationNode node : hybridizationNodes) {
            namedSdrfNodes.add(new NamedSdrfNode<>(node.getNodeName(), node));
        }
        return namedSdrfNodes;

    }

    @Override
    protected Collection<SourceNode> findUpstreamSourceNodes(NamedSdrfNode namedSdrfNode) {
        return GraphUtils.findUpstreamNodes(namedSdrfNode.getSdrfNode(), SourceNode.class);
    }

    @Override
    protected List<FactorValueAttribute> getFactorAttributes(NamedSdrfNode<HybridizationNode> namedSdrfNode) {
        return namedSdrfNode.getSdrfNode().factorValues;
    }

    @Override
    protected void addArrays(ExperimentDesign experimentDesign,
            Set<NamedSdrfNode<HybridizationNode>> namedSdrfNodes) {
        for (NamedSdrfNode<? extends HybridizationNode> namedSdrfNode : namedSdrfNodes) {

            if (namedSdrfNode.getSdrfNode().arrayDesigns.size() != 1) {
                throw new IllegalStateException("Assays with multiple array designs are not supported.");
            }
            experimentDesign.putArrayDesign(namedSdrfNode.getName(),
                    namedSdrfNode.getSdrfNode().arrayDesigns.get(0).getAttributeValue());
        }
    }

}