edu.mayo.cts2.framework.plugin.service.bprdf.model.modifier.NamespaceModifier.java Source code

Introduction

Here is the source code for edu.mayo.cts2.framework.plugin.service.bprdf.model.modifier.NamespaceModifier.java

Source

/*
 * Copyright: (c) 2004-2011 Mayo Foundation for Medical Education and 
 * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the
 * triple-shield Mayo logo are trademarks and service marks of MFMER.
 *
 * Except as contained in the copyright notice above, or as used to identify 
 * MFMER as the author of this software, the trade names, trademarks, service
 * marks, or product names of the copyright holder shall not be used in
 * advertising, promotion or otherwise in connection with this software without
 * prior written authorization of the copyright holder.
 *
 * 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.
 */
package edu.mayo.cts2.framework.plugin.service.bprdf.model.modifier;

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

import javax.annotation.Resource;

import org.apache.commons.lang.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.springframework.beans.factory.InitializingBean;
import org.springframework.stereotype.Component;

import edu.mayo.cts2.framework.plugin.service.bprdf.dao.id.IdService;
import edu.mayo.cts2.framework.plugin.service.bprdf.dao.namespace.NamespaceLookupService;
import edu.mayo.twinkql.context.TwinkqlContext;
import edu.mayo.twinkql.model.NamespaceDefinition;
import edu.mayo.twinkql.model.TwinkqlConfig;
import edu.mayo.twinkql.model.TwinkqlConfigItem;
import edu.mayo.twinkql.result.callback.Modifier;

/**
 * The Class NamespaceModifier.
 *
 * @author <a href="mailto:kevin.peterson@mayo.edu">Kevin Peterson</a>
 */
@Component("namespaceModifier")
public class NamespaceModifier implements Modifier<String>, InitializingBean {

    protected final Log log = LogFactory.getLog(getClass().getName());

    private Map<String, String> knownNamespaces;

    @Resource
    private TwinkqlContext twinkqlContext;

    @Resource
    private IdService idService;

    @Resource
    private NamespaceLookupService namespaceLookupService;

    /* (non-Javadoc)
     * @see org.springframework.beans.factory.InitializingBean#afterPropertiesSet()
     */
    @Override
    public void afterPropertiesSet() throws Exception {
        if (this.knownNamespaces == null) {
            this.knownNamespaces = this.setUpDefaultKnownNamespaces();
        }
    }

    /* (non-Javadoc)
     * @see edu.mayo.twinkql.result.callback.Modifier#beforeSetting(java.lang.Object)
     */
    @Override
    public String beforeSetting(String object) {
        return this.getNamespace(object);
    }

    /**
     * Gets the namespace.
     *
     * @param uri the uri
     * @return the namespace
     */
    public String getNamespace(String uri) {

        String acronym = this.idService.getAcronymForUri(uri);
        if (acronym != null) {
            return acronym;
        }

        if (!this.knownNamespaces.containsKey(uri)) {

            String prefix = this.namespaceLookupService.getPreferredPrefixForUri(uri);

            if (StringUtils.isNotBlank(prefix)) {
                this.knownNamespaces.put(uri, prefix);

            } else {
                String hashString = Integer.toString(uri.hashCode());

                hashString = "ns" + hashString;

                this.knownNamespaces.put(uri, hashString);

                log.warn("Generating prefix for Namespace URI: " + uri);
            }
        }

        return this.knownNamespaces.get(uri);
    }

    /**
     * Sets the up default known namespaces.
     *
     * @return the map
     */
    protected Map<String, String> setUpDefaultKnownNamespaces() {
        Map<String, String> namespaces = new HashMap<String, String>();

        namespaces.put("http://purl.bioontology.org/ontology/bioportal/", "bioportal");
        namespaces.put("http://www.w3.org/1999/02/22-rdf-syntax-ns#", "rdfs");
        namespaces.put("http://www.w3.org/2002/07/owl#", "owl");
        namespaces.put("http://bioportal.bioontology.org/ontologies/umls/", "bioportal_umls");

        TwinkqlConfig twinkqlConfig = this.twinkqlContext.getTwinkqlConfig();
        if (twinkqlConfig != null && twinkqlConfig.getTwinkqlConfigItem() != null) {
            for (TwinkqlConfigItem item : twinkqlConfig.getTwinkqlConfigItem()) {
                if (item.getNamespace() != null) {
                    NamespaceDefinition def = item.getNamespace();
                    namespaces.put(def.getUri(), def.getPrefix());
                }
            }
        }

        return namespaces;

    }
}