ubic.gemma.web.controller.common.description.bibref.PubMedQueryControllerImpl.java Source code

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Here is the source code for ubic.gemma.web.controller.common.description.bibref.PubMedQueryControllerImpl.java

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/*
 * The Gemma project
 *
 * Copyright (c) 2006 University of British Columbia
 *
 * 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 ubic.gemma.web.controller.common.description.bibref;

import org.apache.commons.lang3.StringUtils;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Controller;
import org.springframework.validation.BindingResult;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestMethod;
import org.springframework.web.bind.support.SessionStatus;
import org.springframework.web.servlet.ModelAndView;
import ubic.gemma.core.annotation.reference.BibliographicReferenceService;
import ubic.gemma.core.loader.entrez.pubmed.PubMedXMLFetcher;
import ubic.gemma.model.common.description.BibliographicReference;
import ubic.gemma.web.controller.BaseController;

import javax.servlet.http.HttpServletRequest;

/**
 * Allow users to search for and view PubMed abstracts from NCBI, or from Gemma.
 *
 * @author pavlidis
 */
@Controller("/bibRefSearch.html")
public class PubMedQueryControllerImpl extends BaseController implements PubMedQueryController {

    @Autowired
    private BibliographicReferenceService bibliographicReferenceService;

    private PubMedXMLFetcher pubMedXmlFetcher = new PubMedXMLFetcher();

    @Override
    @RequestMapping(method = RequestMethod.GET)
    public String getView() {
        return "bibRefSearch";
    }

    @Override
    @RequestMapping(method = RequestMethod.POST)
    public ModelAndView onSubmit(HttpServletRequest request, PubMedSearchCommand command, BindingResult result,
            SessionStatus status) {

        // in the future we can search in other ways.
        String accession = command.getAccession();

        if (StringUtils.isBlank(accession)) {

            result.rejectValue("search", "errors.pubmed.noaccession", "Accession was missing");
            return new ModelAndView("bibRefSearch");
        }

        // first see if we already have it in the system.
        BibliographicReference bibRefFound = bibliographicReferenceService.findByExternalId(accession);
        if (bibRefFound != null) {
            request.setAttribute("existsInSystem", Boolean.TRUE);
            this.saveMessage(request, "bibliographicReference.alreadyInSystem", accession, "Already in Gemma");
        } else {
            request.setAttribute("existsInSystem", Boolean.FALSE);
            try {
                bibRefFound = this.pubMedXmlFetcher.retrieveByHTTP(Integer.parseInt(accession));

                if (bibRefFound == null) {
                    log.debug(accession + " not found in NCBI");

                    result.rejectValue("accession", "bibliographicReference.notfoundInNCBI", "Not found in NCBI");
                    return new ModelAndView("bibRefSearch", result.getModel());
                }

                this.saveMessage(request, "bibliographicReference.found", accession, "Found");

            } catch (NumberFormatException e) {
                result.rejectValue("accession", "error.integer", "Not a number");
                return new ModelAndView("bibRefSearch", result.getModel());
            }
        }

        status.setComplete();
        return new ModelAndView("bibRefView").addObject("bibliographicReference", bibRefFound);
    }

}