gov.nih.nci.caintegrator.web.action.analysis.biodbnet.BioDbNetSearchAction.java Source code

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Here is the source code for gov.nih.nci.caintegrator.web.action.analysis.biodbnet.BioDbNetSearchAction.java

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/**
 * Copyright 5AM Solutions Inc, ESAC, ScenPro & SAIC
 *
 * Distributed under the OSI-approved BSD 3-Clause License.
 * See http://ncip.github.com/caintegrator/LICENSE.txt for details.
 */
package gov.nih.nci.caintegrator.web.action.analysis.biodbnet;

import gov.nih.nci.caintegrator.external.biodbnet.BioDbNetService;
import gov.nih.nci.caintegrator.external.biodbnet.enums.SearchType;
import gov.nih.nci.caintegrator.external.biodbnet.search.GeneResults;
import gov.nih.nci.caintegrator.external.biodbnet.search.PathwayResults;
import gov.nih.nci.caintegrator.external.biodbnet.search.SearchParameters;
import gov.nih.nci.caintegrator.web.action.AbstractCaIntegrator2Action;

import java.util.Set;

import org.apache.commons.collections.CollectionUtils;
import org.apache.commons.lang3.StringUtils;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.config.BeanDefinition;
import org.springframework.context.annotation.Scope;
import org.springframework.stereotype.Component;

import com.google.common.collect.Sets;

/**
 * Actions for dealing with bioDbNet searches.
 *
 * @author Abraham J. Evans-EL <aevansel@5amsolutions.com>
 */
@Component
@Scope(value = BeanDefinition.SCOPE_PROTOTYPE)
public class BioDbNetSearchAction extends AbstractCaIntegrator2Action {
    private static final long serialVersionUID = 1L;
    private static final String GENE_RESULT = "genes";
    private static final String PATHWAY_RESULT = "pathways";
    private BioDbNetService bioDbNetService;
    private SearchParameters searchParameters;
    private Set<GeneResults> geneResults;
    private Set<PathwayResults> pathwayResults;

    /**
     * {@inheritDoc}
     */
    @Override
    public void prepare() {
        super.prepare();
        setSearchParameters(new SearchParameters());
        geneResults = Sets.newHashSet();
        pathwayResults = Sets.newHashSet();
    }

    /**
     * Default input method.
     * @return the struts result
     */
    @Override
    public String input() {
        return SUCCESS;
    }

    /**
     * Performs the bioDbNet search.
     * @return the struts results
     */
    public String search() {
        try {
            getSearchParameters().setStudy(getCurrentStudy());
            if (getSearchParameters().getSearchType() == SearchType.PATHWAY_BY_GENE) {
                setPathwayResults(handlePathwaySearch());
                if (CollectionUtils.isEmpty(getPathwayResults())) {
                    addActionError(getText("bioDbNet.noPathwayResultsFound"));
                }
                return PATHWAY_RESULT;
            } else {
                setGeneResults(handleGeneSearch(getSearchParameters().getSearchType()));
                if (CollectionUtils.isEmpty(getGeneResults())) {
                    addActionError(getText("bioDbNet.noGeneResultsFound"));
                }
                return GENE_RESULT;
            }
        } catch (Exception e) {
            addActionError(getText("bioDbNet.error"));
            LOG.error("Unabled to access the bioDbNet Web Service.", e);
            return INPUT;
        }
    }

    private Set<PathwayResults> handlePathwaySearch() {
        Set<String> newInputs = handleCaseSensitivity(getSearchParameters());
        return bioDbNetService.retrievePathwaysByGeneSymbols(generateNewParams(newInputs));
    }

    private Set<GeneResults> handleGeneSearch(SearchType searchType) {
        Set<GeneResults> results = Sets.newHashSet();
        Set<String> newInputs = handleCaseSensitivity(getSearchParameters());
        if (searchType == SearchType.GENE_ID) {
            results = bioDbNetService.retrieveGenesById(generateNewParams(newInputs));
        } else if (searchType == SearchType.GENE_ALIAS) {
            Set<String> geneIds = bioDbNetService.retrieveGeneIdsByAlias(generateNewParams(newInputs));
            results = bioDbNetService.retrieveGenesById(generateNewParams(geneIds));
        } else if (searchType == SearchType.GENE_SYMBOL) {
            Set<String> geneIds = bioDbNetService.retrieveGeneIds(generateNewParams(newInputs));
            results = bioDbNetService.retrieveGenesById(generateNewParams(geneIds));
        } else if (searchType == SearchType.PATHWAY) {
            results = bioDbNetService.retrieveGenesByPathway(generateNewParams(newInputs));
        }
        return results;
    }

    private SearchParameters generateNewParams(Set<String> input) {
        SearchParameters params = new SearchParameters();
        params.setFilterGenesOnStudy(getSearchParameters().isFilterGenesOnStudy());
        params.setTaxon(getSearchParameters().getTaxon());
        params.setInputValues(StringUtils.join(input, ','));
        params.setStudy(getCurrentStudy());
        return params;
    }

    /**
     * Generates the search inputs in the following manner if case insensitivity has been selected.
     *  - the original inputs
     *  - inputs are transformed to all upper case
     *  - inputs are transformed to all lower case
     *  - inputs are transformed to 1st letter upper case, all others lower case
     * @return the transformed input strings as comma separated values
     */
    private Set<String> handleCaseSensitivity(SearchParameters searchParams) {
        Set<String> inputs = Sets.newTreeSet();
        if (searchParams.isCaseSensitiveSearch() || searchParams.getSearchType() == SearchType.GENE_ID) {
            CollectionUtils.addAll(inputs, StringUtils.split(searchParams.getInputValues(), ','));
            return inputs;
        }
        String[] splitInputs = StringUtils.split(searchParams.getInputValues(), ',');
        for (String input : splitInputs) {
            inputs.add(input);
            inputs.add(StringUtils.upperCase(input));
            inputs.add(StringUtils.lowerCase(input));
            inputs.add(StringUtils.capitalize(input));
        }
        return inputs;
    }

    /**
     * {@inheritDoc}
     */
    @Override
    public void validate() {
        super.validate();
        if (StringUtils.isEmpty(getSearchParameters().getInputValues())) {
            addActionError(getText("struts.messages.error.must.enter.keywords"));
        }
    }

    /**
     * @return the searchParameters
     */
    public SearchParameters getSearchParameters() {
        return searchParameters;
    }

    /**
     * @param searchParameters the searchParameters to set
     */
    public void setSearchParameters(SearchParameters searchParameters) {
        this.searchParameters = searchParameters;
    }

    /**
     * @return the geneResults
     */
    public Set<GeneResults> getGeneResults() {
        return geneResults;
    }

    /**
     * @param geneResults the geneResults to set
     */
    public void setGeneResults(Set<GeneResults> geneResults) {
        this.geneResults = geneResults;
    }

    /**
     * @return the pathwayResults
     */
    public Set<PathwayResults> getPathwayResults() {
        return pathwayResults;
    }

    /**
     * @param pathwayResults the pathwayResults to set
     */
    public void setPathwayResults(Set<PathwayResults> pathwayResults) {
        this.pathwayResults = pathwayResults;
    }

    /**
     * Sets the bioDbNet service.
     * @param svc the service to set
     */
    @Autowired
    public void setBioDbNetService(BioDbNetService svc) {
        this.bioDbNetService = svc;
    }
}