org.glytoucan.api.soap.endpoint.GlycoSequenceEndpoint.java Source code

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Here is the source code for org.glytoucan.api.soap.endpoint.GlycoSequenceEndpoint.java

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package org.glytoucan.api.soap.endpoint;

import java.math.BigInteger;

import org.apache.commons.lang.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.glycoinfo.convert.error.ConvertException;
import org.glycoinfo.rdf.SparqlException;
import org.glycoinfo.rdf.dao.SparqlEntity;
import org.glycoinfo.rdf.glycan.DerivatizedMass;
import org.glycoinfo.rdf.glycan.GlycoSequence;
import org.glycoinfo.rdf.glycan.ResourceEntry;
import org.glycoinfo.rdf.glycan.Saccharide;
import org.glycoinfo.rdf.service.GlycanProcedure;
import org.glycoinfo.rdf.service.exception.InvalidException;
import org.glytoucan.api.soap.GlycoSequenceCountRequest;
import org.glytoucan.api.soap.GlycoSequenceCountResponse;
import org.glytoucan.api.soap.GlycoSequenceDetailRequest;
import org.glytoucan.api.soap.GlycoSequenceDetailResponse;
import org.glytoucan.api.soap.GlycoSequenceSearchResponse;
import org.glytoucan.api.soap.GlycoSequenceTextSearchRequest;
import org.glytoucan.api.soap.ResponseMessage;
import org.glytoucan.api.soap.util.ResponseMessageGenerator;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.util.Assert;
import org.springframework.ws.server.endpoint.annotation.Endpoint;
import org.springframework.ws.server.endpoint.annotation.PayloadRoot;
import org.springframework.ws.server.endpoint.annotation.RequestPayload;
import org.springframework.ws.server.endpoint.annotation.ResponsePayload;

/**
 * 
 * @author aoki
 * 
 *         The specification for this can be found at
 *         http://code.glytoucan.org/system/api_list/.
 *
 *         This work is licensed under the Creative Commons Attribution 4.0
 *         International License. To view a copy of this license, visit
 *         http://creativecommons.org/licenses/by/4.0/.
 *
 */
@Endpoint
public class GlycoSequenceEndpoint {
    private static final Log logger = LogFactory.getLog(GlycoSequenceEndpoint.class);
    private static final String NAMESPACE_URI = "http://soap.api.glytoucan.org/";

    private GlycanProcedure glycanProcedure;

    @Autowired
    public GlycoSequenceEndpoint(GlycanProcedure glycanProcedure) {
        this.glycanProcedure = glycanProcedure;
    }

    /**
     * 
     * Query entry using accession number.
     * 
     * @param accessionNumber
     * @return
     */
    @PayloadRoot(namespace = NAMESPACE_URI, localPart = "glycoSequenceDetailRequest")
    @ResponsePayload
    public GlycoSequenceDetailResponse queryEntry(@RequestPayload GlycoSequenceDetailRequest request) {
        Assert.notNull(request);
        Assert.notNull(request.getAccessionNumber());

        SparqlEntity se = null;
        ResponseMessage rm = new ResponseMessage();
        GlycoSequenceDetailResponse gsdr = new GlycoSequenceDetailResponse();
        try {
            se = glycanProcedure.getDescription(request.getAccessionNumber());
        } catch (InvalidException e) {
            // invalid data in se, return with errorcode.
            rm.setMessage("Invalid Accession Number");
            rm.setErrorCode(new BigInteger("-100"));
            gsdr.setAccessionNumber(request.getAccessionNumber());
            gsdr.setResponseMessage(rm);
            return gsdr;
        }

        rm.setMessage(se.getValue(GlycanProcedure.Description));
        rm.setErrorCode(new BigInteger("0"));

        gsdr.setAccessionNumber(se.getValue(ResourceEntry.Identifier));
        gsdr.setDescription(se.getValue(GlycanProcedure.Description));
        gsdr.setIupac(se.getValue(GlycoSequence.Sequence));
        gsdr.setMass(se.getValue(DerivatizedMass.MassLabel));
        gsdr.setSequence(se.getValue(GlycoSequence.Sequence));
        gsdr.setResponseMessage(rm);
        return gsdr;
    }

    /**
     * 
     * Search for entry using sequence text.
     * 
     * @param sequence
     *          text
     * @return glycosequencesearchresponse
     * 
     */
    @PayloadRoot(namespace = NAMESPACE_URI, localPart = "glycoSequenceTextSearchRequest")
    @ResponsePayload
    public GlycoSequenceSearchResponse searchSequence(@RequestPayload GlycoSequenceTextSearchRequest request) {
        Assert.notNull(request);
        Assert.notNull(request.getSequence());
        GlycoSequenceSearchResponse gssr = new GlycoSequenceSearchResponse();

        SparqlEntity se;
        try {
            se = glycanProcedure.searchBySequence(request.getSequence());
        } catch (SparqlException | ConvertException e) {
            ResponseMessage rm = ResponseMessageGenerator.extractException(e);
            rm.setErrorCode(new BigInteger(GlycanProcedure.CouldNotConvertErrorCode));
            gssr.setResponseMessage(rm);
            return gssr;
        }

        ResponseMessage rm = new ResponseMessage();
        rm.setMessage(se.getValue(GlycanProcedure.FromSequence));
        rm.setErrorCode(new BigInteger("0"));

        gssr.setAccessionNumber(se.getValue(GlycanProcedure.AccessionNumber));
        gssr.setSequence(se.getValue(GlycanProcedure.Sequence));
        gssr.setImage(se.getValue(GlycanProcedure.Image));
        gssr.setResponseMessage(rm);
        return gssr;
    }

    /**
     * 
     * Query for total count.
     * 
     * @return glycosequencecountresponse
     * 
     */
    @PayloadRoot(namespace = NAMESPACE_URI, localPart = "glycoSequenceCountRequest")
    @ResponsePayload
    public GlycoSequenceCountResponse countSequence(@RequestPayload GlycoSequenceCountRequest request) {
        Assert.notNull(request);
        GlycoSequenceCountResponse gscr = new GlycoSequenceCountResponse();

        SparqlEntity se = glycanProcedure.getCount();

        ResponseMessage rm = new ResponseMessage();
        rm.setMessage(se.getValue("total"));
        rm.setErrorCode(new BigInteger("0"));

        gscr.setCount(se.getValue("total"));
        gscr.setResponseMessage(rm);
        return gscr;
    }
}