org.glycoinfo.rdf.glycan.wurcs.GlycoSequenceResourceEntryContributorSelectSparql.java Source code

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Here is the source code for org.glycoinfo.rdf.glycan.wurcs.GlycoSequenceResourceEntryContributorSelectSparql.java

Source

package org.glycoinfo.rdf.glycan.wurcs;

import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.glycoinfo.rdf.SparqlException;
import org.glycoinfo.rdf.glycan.Saccharide;
import org.springframework.stereotype.Component;
import org.springframework.util.Assert;

/**
 * 
 * SelectSparql for retrieving various details about a Saccharide. 
 * Includes Mass, Date entered, Contributor, and both GlycoCT and WURCS Sequence Formats.
 * 
 * @author aoki
 *
 * 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/.
 *
 */
@Component
public class GlycoSequenceResourceEntryContributorSelectSparql extends WurcsGlycoSequenceSelectSparql {
    public static final String DateEntered = Saccharide.URI;
    public static final String Mass = "Mass";
    public static final String MassLabel = "MassLabel";
    public static final String Contributor = "Contributor";

    public GlycoSequenceResourceEntryContributorSelectSparql(String sparql) {
        super(sparql);
    }

    public GlycoSequenceResourceEntryContributorSelectSparql() {
        super();
        this.select += "?" + DateEntered + "\n" + "?" + Mass + "\n" + "?" + MassLabel + "\n" + "?" + Contributor
                + "\n" + "?GlycoCTSequence" + "\n" + "?DateRegistered" + "\n";
    }

    @Override
    public String getWhere() throws SparqlException {
        return super.getWhere() + " OPTIONAL {\n" + "?" + SaccharideURI
                + " glycan:has_glycosequence ?GlycanSequenceGlycoCTURI .\n"
                + "?GlycanSequenceGlycoCTURI glycan:in_carbohydrate_format glycan:carbohydrate_format_glycoct .\n"
                + "?GlycanSequenceGlycoCTURI glycan:has_sequence ?GlycoCTSequence .\n" + "}\n" + "?" + SaccharideURI
                + " glycan:has_resource_entry ?resource .\n"
                + "?resource glycan:in_glycan_database glytoucan:database_glytoucan .\n"
                + "?resource glytoucan:contributor ?contributorURI .\n" + "?contributorURI foaf:name ?"
                + Contributor + " .\n" + "?resource glytoucan:date_registered ?DateRegistered .\n" + "OPTIONAL {\n"
                + "?" + SaccharideURI + " glytoucan:has_derivatized_mass ?derivMass .\n"
                + "?derivMass glytoucan:has_mass ?" + Mass + " .\n" + "?derivMass rdfs:label ?" + MassLabel + " .\n"
                + "}\n";
    }

    @Override
    public String getOrderBy() {
        return "DateRegistered";
    }

    protected Log logger = LogFactory.getLog(getClass());

    @Override
    public void afterPropertiesSet() throws Exception {
        Assert.state(getPrefix() != null, "A prefix is required");
        Assert.state(getSelect() != null, "A select is required");
    }
}