/*
* EuroCarbDB, a framework for carbohydrate bioinformatics
*
* Copyright (c) 2006-2009, Eurocarb project, or third-party contributors as
* indicated by the @author tags or express copyright attribution
* statements applied by the authors.
*
* This copyrighted material is made available to anyone wishing to use, modify,
* copy, or redistribute it subject to the terms and conditions of the GNU
* Lesser General Public License, as published by the Free Software Foundation.
* A copy of this license accompanies this distribution in the file LICENSE.txt.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
* or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
* for more details.
*
* Last commit: $Rev: 1870 $ by $Author: david@nixbioinf.org $ on $Date:: 2010-02-23 #$
*/
package org.eurocarbdb.action.core;
// stdlib imports
import java.util.*;
import java.io.*;
import java.net.*;
// 3rd party imports
import org.apache.log4j.Logger;
import org.hibernate.*;
import org.hibernate.criterion.*;
// eurocarb imports
import org.eurocarbdb.action.EurocarbAction;
import org.eurocarbdb.action.RequiresLogin;
import org.eurocarbdb.dataaccess.EntityManager;
import org.eurocarbdb.dataaccess.core.*;
import org.eurocarbdb.application.glycoworkbench.GlycanWorkspace;
import org.eurocarbdb.application.glycanbuilder.GlycanDocument;
import org.eurocarbdb.application.glycanbuilder.Glycan;
import org.eurocarbdb.application.glycanbuilder.FileUtils;
import org.eurocarbdb.application.glycanbuilder.LogUtils;
import org.eurocarbdb.application.glycanbuilder.TextUtils;
// static imports
import static org.eurocarbdb.dataaccess.Eurocarb.getEntityManager;
import static org.eurocarbdb.dataaccess.Eurocarb.getHqlQuery;
import org.eurocarbdb.dataaccess.hibernate.*;
/* class ContributeStructure ***********************************
*
* Action for entering/creating a glycan structure with biological
* context
*
* @author ac [a.ceroni@imperial.ac.uk]
* @version $Rev: 1870 $
*/
@org.eurocarbdb.action.ParameterChecking(whitelist={"taxonomySearch","tissueTaxonomySearch","diseaseSearch","perturbationSearch"}, blacklist={"biologicalContextId"})
public class CreateBiologicalContext extends EurocarbAction implements RequiresLogin
{
//~~~~~~~~~~~~~~~~~~~~~~ STATIC FIELDS ~~~~~~~~~~~~~~~~~~~~~~~~//
/** Logging handle. */
protected static final Logger log = Logger.getLogger( ContributeStructure.class.getName() );
private Taxonomy taxonomy = null;
private TissueTaxonomy tissueTaxonomy = null;
private Set<Disease> diseases = null;
private Set<Perturbation> perturbations = null;
private BiologicalContext biologicalContext = null;
private String comment = null;
//~~~~~~~~~~~~~~~~~~~~~~~~~ METHODS ~~~~~~~~~~~~~~~~~~~~~~~~~~~//
public void setParameters(Map params)
{
comment=(String) params.get("bc_comment");
super.setParameters(params);
}
public void setBiologicalContext(BiologicalContext bc)
{
biologicalContext = bc;
}
public BiologicalContext getBiologicalContext()
{
return biologicalContext;
}
public void setTaxonomySearch(String text)
{
text = text.toLowerCase();
log.debug("Searching for taxonomy with name "+text);
// exact search by taxon
if( text!=null && text.length()>0 )
{
log.debug("In first!");
//Criteria crit = getEntityManager().createQuery(Taxonomy.class).add(Restrictions.eq("taxon",text));
Query hqlQuery=getHqlQuery("SELECT t FROM Taxonomy t WHERE lower(t.taxon)=?");
hqlQuery.setString(0, text);
java.util.Collection<Taxonomy> list = hqlQuery.list();
if( list!=null && list.size()>0 )
{
log.debug("In second!");
taxonomy = list.iterator().next();
log.debug("Found a taxonomy "+taxonomy.getTaxonomyId());
return;
}
}
log.debug("In third!");
taxonomy = null;
}
public void setTissueTaxonomySearch(String text)
{
log.debug("Searching for tissue with name "+text);
// exact search by taxon
if( text!=null && text.length()>0 )
{
Criteria crit = getEntityManager().createQuery(TissueTaxonomy.class).add(Restrictions.eq("tissueTaxon",text));
java.util.Collection<TissueTaxonomy> list = crit.list();
if( list!=null && list.size()>0 )
{
tissueTaxonomy = list.iterator().next();
log.debug("Found a tissueTaxonomy "+tissueTaxonomy.getId());
return;
}
}
tissueTaxonomy = null;
}
public void setDiseaseSearch(String[] values)
{
log.debug("Searching for disease with names in array size of "+values.length);
diseases = new HashSet<Disease>();
if( values!=null )
{
for( int i=0; i<values.length; i++ )
{
String text = values[i];
// exact search by disease name
if( text!=null && text.length()>0 )
{
Criteria crit = getEntityManager().createQuery(Disease.class).add(Restrictions.eq("diseaseName",text));
java.util.Collection<Disease> list = crit.list();
if( list!=null && list.size()>0 )
{
log.debug("Found a disease");
diseases.add(list.iterator().next());
}
}
}
}
}
public void setPerturbationSearch(String[] values)
{
perturbations = new HashSet<Perturbation>();
if( values!=null )
{
for( int i=0; i<values.length; i++ )
{
String text = values[i];
// exact search by disease name
if( text!=null && text.length()>0 )
{
Criteria crit = getEntityManager().createQuery(Perturbation.class).add(Restrictions.eq("perturbationName",text));
java.util.Collection<Perturbation> list = crit.list();
if( list!=null && list.size()>0 )
{
perturbations.add(list.iterator().next());
}
}
}
}
}
protected BiologicalContext createBiologicalContext() throws Exception
{
BiologicalContext bc=null;
log.debug("--FIND ME--");
// log.debug("Tissue taxonomy id is: "+tissueTaxonomy.getTissueTaxonomyId());
Query checkForExistingBiologicalContext=getHqlQuery("SELECT bc FROM BiologicalContext bc where bc.taxonomy.taxonomyId=?");
checkForExistingBiologicalContext.setInteger(0, taxonomy.getTaxonomyId());
List<BiologicalContext> bcList=checkForExistingBiologicalContext.list();
if(bcList.size()!=0){
for(BiologicalContext bcItem:bcList){
log.debug("Matched contexts based on taxonomyId");
if(tissueTaxonomy==null){
if(bcItem.getTissueTaxonomy().getTissueTaxonomyId()==1){
log.debug("Found matching bc");
bc=bcItem;
break;
}
}else if(bcItem.getTissueTaxonomy().getTissueTaxonomyId()==tissueTaxonomy.getTissueTaxonomyId()){
log.debug("Found matching bc");
bc=bcItem;
break;
}
}
}
if(bc==null){
bc=new BiologicalContext();
// set taxonomy & tissue taxonomy
bc.setTaxonomy( taxonomy );
bc.setTissueTaxonomy( tissueTaxonomy );
// add disease associations, if any
if( diseases!=null )
{
Set<DiseaseContext> dcSet = new HashSet<DiseaseContext>(); //bc.getDiseaseContexts();
for ( Disease d : diseases ) {
dcSet.add( new DiseaseContext( bc, d ) );
}
bc.setDiseaseContexts( dcSet );
}
// add perturbation associations, if any
if( perturbations!=null )
{
Set<PerturbationContext> pcSet = new HashSet<PerturbationContext>(); //bc.getDiseaseContexts();
for ( Perturbation p : perturbations )
pcSet.add( new PerturbationContext( bc, p ) );
bc.setPerturbationContexts( pcSet );
}
}//else{
//bc=null;
//}
return bc;
}
public String execute() throws Exception
{
log.debug("---Creating biological context---");
if ( taxonomy == null ) {
log.debug("Taxonomy is null!");
return "input";
}
try {
biologicalContext = createBiologicalContext();
if( biologicalContext !=null){
//if(biologicalContext.getBiologicalContextContributor(Contributor.getCurrentContributor().getContributorId())==null){
//biologicalContext.addContributor(Contributor.getCurrentContributor(), comment);
//}else{
// addActionError("You have already contributed this association...");
// return "input";
// }
getEntityManager().store( biologicalContext );
return "success";
}else{
addActionError("An unexpected error has occured");
return "input";
}
}
catch(Exception e) {
StringWriter sw = new StringWriter();
e.printStackTrace(new PrintWriter(sw));
String stacktrace = sw.toString();
log.debug("Exception storing new bc: "+stacktrace);
return "input";
}
}
} // end class