org.obolibrary.obo2owl.IdTranslator Maven / Gradle / Ivy

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A java library for converting obo format documents to OWL, and for converting (a subset of) OWL to obo format. This version has been slightly modified to be included directly in the OWL API. The upstream code for this module and its authors can be found at https://code.google.com/p/oboformat/.

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package org.obolibrary.obo2owl;

import java.util.HashMap;
import java.util.Map;

import javax.annotation.Nonnull;
import javax.annotation.Nullable;

import org.semanticweb.owlapi.model.IRI;

/**
 * This class will eventually replace the id to uri translation in Owl2Obo and
 * OboO2Owl 

 * It is currently in-progress.
 * 
 * @author cjm
 */
public class IdTranslator {

    @Nonnull
    static final String OBO_IRI_PREFIX = "http://purl.obolibrary.org/obo/";
    @Nonnull
    private final Map idspaceMap = new HashMap<>();

    /**
     * @param iri
     *        iri
     * @return string for iri
     */
    @Nullable
    public static String translateIRI(@SuppressWarnings("unused") IRI iri) {
        return null;
    }

    /**
     * @param id
     *        id
     * @return string for id
     */
    @Nullable
    public String translateIdToIRIString(@Nonnull String id) {
        if (isURI(id)) {
            return id;
        }
        if (id.contains(":")) {
            // PREFIXED ID
            int p = id.lastIndexOf(':');
            String prefix = id.substring(0, p);
            String localId = id.substring(p + 1);
            if (!localId.isEmpty() && localId.replaceAll("[0-9]", "").isEmpty()) {
                // CANONICAL
                return expandPrefix(prefix) + localId;
            }
        }
        return null;
    }

    /**
     * True if id starts with a standard URI prefix (http, ftp, https) followed
     * by a ":". Does not check if it actually conforms to URI syntax.
     * 
     * @param id
     *        id
     * @return boolean
     */
    public static boolean isURI(@Nonnull String id) {
        if (id.startsWith("http:") || id.startsWith("ftp:") || id.startsWith("https:")) {
            return true;
        }
        return false;
    }

    /**
     * Expands an OBO prefix such as "GO" to
     * "http://purl.obolibrary.org/obo/GO_". By default a prefix XX maps to
     * http://purl.obolibrary.org/obo/XX_
     * 
     * @param prefix
     *        prefix
     * @return expanded prefix
     */
    public String expandPrefix(String prefix) {
        if (idspaceMap.containsKey(prefix)) {
            return idspaceMap.get(prefix);
        }
        return OBO_IRI_PREFIX + prefix + '_';
    }
}