SearchPlugin.java

package org.molgenis.mutation.ui.search;

import java.io.OutputStream;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;

import org.apache.commons.collections.CollectionUtils;
import org.apache.commons.lang.StringUtils;
import org.molgenis.framework.db.Database;
import org.molgenis.framework.ui.FreemarkerView;
import org.molgenis.framework.ui.IntegratedPluginController;
import org.molgenis.framework.ui.ScreenController;
import org.molgenis.framework.ui.ScreenMessage;
import org.molgenis.framework.ui.ScreenView;
import org.molgenis.framework.ui.html.AutocompleteInput;
import org.molgenis.framework.ui.html.Container;
import org.molgenis.framework.ui.html.HiddenInput;
import org.molgenis.framework.ui.html.IntInput;
import org.molgenis.framework.ui.html.RadioInput;
import org.molgenis.framework.ui.html.SelectInput;
import org.molgenis.framework.ui.html.TextLineInput;
import org.molgenis.mutation.ServiceLocator;
import org.molgenis.mutation.dto.ExonDTO;
import org.molgenis.mutation.dto.GeneDTO;
import org.molgenis.mutation.dto.MutationSearchCriteriaDTO;
import org.molgenis.mutation.dto.MutationSummaryDTO;
import org.molgenis.mutation.dto.PatientSummaryDTO;
import org.molgenis.mutation.dto.ProteinDomainDTO;
import org.molgenis.mutation.dto.VariantDTO;
import org.molgenis.mutation.service.CmsService;
import org.molgenis.mutation.service.SearchService;
import org.molgenis.mutation.service.StatisticsService;
import org.molgenis.mutation.ui.HtmlFormWrapper;
import org.molgenis.mutation.ui.html.GenePanel;
import org.molgenis.mutation.ui.html.GenomePanel;
import org.molgenis.mutation.ui.html.MBrowse;
import org.molgenis.mutation.ui.search.form.ExpertSearchForm;
import org.molgenis.pheno.service.PhenoService;
import org.molgenis.util.HttpServletRequestTuple;
import org.molgenis.util.Tuple;
import org.molgenis.util.ValueLabel;

public class SearchPlugin extends IntegratedPluginController<SearchModel>
{
	private static final long serialVersionUID = 651270609185006020L;

	protected transient CmsService cmsService;
	protected transient PhenoService phenoService;
	protected transient SearchService searchService;
	protected transient StatisticsService statisticsService;

	public SearchPlugin(String name, ScreenController<?> parent)
	{
		super(name, null, parent);
		this.setModel(new SearchModel(this));
		this.view = new FreemarkerView("init.ftl", getModel());

		this.cmsService = ServiceLocator.instance().getCmsService();
		this.phenoService = ServiceLocator.instance().getPhenoService();
		this.searchService = ServiceLocator.instance().getSearchService();
		this.statisticsService = ServiceLocator.instance().getStatisticsService();

		this.getModel().setPatientPager("/res/mutation/patientPager.jsp");
		this.getModel().setMutationPager("/res/mutation/mutationPager.jsp");
		this.getModel().setPatientViewer("/org/molgenis/mutation/ui/search/patient.ftl");
		this.getModel().setMutationViewer("/org/molgenis/mutation/ui/search/mutation.ftl");
		this.getModel().setExpertSearchFormWrapper(new HtmlFormWrapper(new ExpertSearchForm()));

		this.getModel().setAction("init");

		MBrowse mBrowse = new MBrowse();
		mBrowse.setTarget(this.getName());

		this.getModel().setMbrowse(mBrowse);
		
//		this.getModel().setExpertSearchFormWrapper(new HtmlFormWrapper(new ExpertSearchForm()));
	}

	private ScreenView view;

	public ScreenView getView()
	{
		return view;
	}

	public void setView(ScreenView view)
	{
		this.view = view;
	}

	@Override
	public Show handleRequest(Database db, Tuple request, OutputStream out)
	{
		try
		{
			this.cmsService.setDatabase(db);
			this.phenoService.setDatabase(db);
			this.searchService.setDatabase(db);
			this.statisticsService.setDatabase(db);

			if (StringUtils.isEmpty(request.getAction())) this.getModel().setAction("init");
			else
				this.getModel().setAction(request.getAction());

			if ("1".equals(request.getString("expertSearch"))) this.getModel().getQueryParametersVO()
					.setExpertSearch(true);
			else
				this.getModel().getQueryParametersVO().setExpertSearch(false);

			if (this.getModel().getAction().equals("findMutationsByTerm"))
			{
				this.handleFindMutationsByTerm(request);
			}
			else if (this.getModel().getAction().equals("findMutations"))
			{
				this.handleFindMutations(request);
			}
			else if (this.getModel().getAction().equals("findPatients"))
			{
				this.handleFindPatients(request);
			}
			else if (this.getModel().getAction().equals("listAllMutations"))
			{
				this.listAllMutations(request);
			}
			else if (this.getModel().getAction().equals("listAllPatients"))
			{
				this.listAllPatients(request);
			}
			else if (this.getModel().getAction().equals("showGene"))
			{
				this.handleShowGene(request);
			}
			else if (this.getModel().getAction().equals("showProteinDomain"))
			{
				this.handleShowProteinDomain(request);
			}
			else if (this.getModel().getAction().equals("showExon"))
			{
				this.handleShowExon(request);
			}
			else if (this.getModel().getAction().equals("showFirstExon"))
			{
				this.handleShowFirstExon(request);
			}
			else if (this.getModel().getAction().equals("showPrevExon"))
			{
				this.handleShowPrevExon(request);
			}
			else if (this.getModel().getAction().equals("showNextExon"))
			{
				this.handleShowNextExon(request);
			}
			else if (this.getModel().getAction().equals("showLastExon"))
			{
				this.handleShowLastExon(request);
			}
			else if (this.getModel().getAction().equals("showMutation"))
			{
				this.handleShowMutation(request);
			}
			else if (this.getModel().getAction().equals("showFirstMutation"))
			{
				this.handleShowFirstMutation(request);
			}
			else if (this.getModel().getAction().equals("showPrevMutation"))
			{
				this.handleShowPrevMutation(request);
			}
			else if (this.getModel().getAction().equals("showNextMutation"))
			{
				this.handleShowNextMutation(request);
			}
			else if (this.getModel().getAction().equals("showLastMutation"))
			{
				this.handleShowLastMutation(request);
			}
			else if (this.getModel().getAction().equals("showPatient"))
			{
				this.handleShowPatient(request);
			}
			else if (this.getModel().getAction().equals("showPhenotypeDetails"))
			{
				this.handleShowPhenotypeDetails(request);
			}
			else if (this.getModel().getAction().startsWith("mutationsFirstPage"))
			{
				this.getModel().getPager().first();
			}
			else if (this.getModel().getAction().startsWith("mutationsPrevPage"))
			{
				this.getModel().getPager().prev();
			}
			else if (this.getModel().getAction().startsWith("mutationsNextPage"))
			{
				this.getModel().getPager().next();
			}
			else if (this.getModel().getAction().startsWith("mutationsLastPage"))
			{
				this.getModel().getPager().last();
			}
			else
			{
				this.setView(new FreemarkerView("init.ftl", this.getModel()));
			}

			this.populateDisplayOptionsForm();

			// for (ScreenController<?> child : this.getChildren())
			// {
			// child.handleRequest(db, request, out);
			// }
		}
		catch (Exception e)
		{
			String message = "Oops, an error occurred. We apologize and will work on fixing it as soon as possible. <a href=\"molgenis.do?__target=SearchPlugin&__action=init&expertSearch=0\">Return to home page</a>";
			this.getModel().getMessages().add(new ScreenMessage(message, false));
			for (StackTraceElement el : e.getStackTrace())
				logger.error(el.toString());
			// this.getMessages().add(new ScreenMessage(el.toString(), false));
		}

		return Show.SHOW_MAIN;
	}

	protected void handleFindMutations(Tuple request)
	{
		this.getModel().setMutationSearchCriteriaVO(new MutationSearchCriteriaDTO());
		if (StringUtils.isNotEmpty(request.getString("variation"))) this.getModel().getMutationSearchCriteriaVO()
				.setVariation(request.getString("variation"));
		if (StringUtils.isNotEmpty(request.getString("consequence"))) this.getModel().getMutationSearchCriteriaVO()
				.setConsequence(request.getString("consequence"));
		if (StringUtils.isNotEmpty(request.getString("mutation_id"))) this.getModel().getMutationSearchCriteriaVO()
				.setMutationId(request.getInt("mutation_id"));
		if (StringUtils.isNotEmpty(request.getString("mid"))) this.getModel().getMutationSearchCriteriaVO()
				.setMid(request.getString("mid"));
		if (StringUtils.isNotEmpty(request.getString("nuclno"))) this.getModel().getMutationSearchCriteriaVO()
				.setCdnaPosition(request.getInt("nuclno"));
		if (StringUtils.isNotEmpty(request.getString("aano"))) this.getModel().getMutationSearchCriteriaVO()
				.setCodonChangeNumber(request.getInt("aano"));
		if (StringUtils.isNotEmpty(request.getString("exon_id"))) this.getModel().getMutationSearchCriteriaVO()
				.setExonId(request.getInt("exon_id"));
		if (StringUtils.isNotEmpty(request.getString("exon"))) this.getModel().getMutationSearchCriteriaVO()
				.setExonName(request.getString("exon"));
		if (StringUtils.isNotEmpty(request.getString("type"))) this.getModel().getMutationSearchCriteriaVO()
				.setType(request.getString("type"));
		if (StringUtils.isNotEmpty(request.getString("domain_id"))) this.getModel().getMutationSearchCriteriaVO()
				.setProteinDomainId(request.getInt("domain_id"));
		if (StringUtils.isNotEmpty(request.getString("phenotype"))) this.getModel().getMutationSearchCriteriaVO()
				.setPhenotypeName(request.getString("phenotype"));
		if (StringUtils.isNotEmpty(request.getString("inheritance"))) this.getModel().getMutationSearchCriteriaVO()
				.setInheritance(request.getString("inheritance"));
		if (StringUtils.isNotEmpty(request.getString("snpbool"))) if (request.getString("snpbool").equals("hide")) this
				.getModel().getMutationSearchCriteriaVO().setReportedAsSNP(false);

		this.getModel().setMutationSummaryDTOList(
				searchService.findMutations(this.getModel().getMutationSearchCriteriaVO()));
		((HttpServletRequestTuple) request).getRequest().setAttribute("mutationSummaryDTOList",
				this.getModel().getMutationSummaryDTOList());
		this.getModel().setRawOutput(this.include(request, this.getModel().getMutationPager()));

		this.getModel().setHeader(this.getModel().getMutationSummaryDTOList().size() + " results.");

		this.setView(new FreemarkerView("included.ftl", this.getModel()));
	}

	protected void handleShowMutation(Tuple request)
	{
		if (StringUtils.isNotEmpty(request.getString("mid")))
		{
			String mutationIdentifier = request.getString("mid");

			// if (StringUtils.isNotEmpty(request.getString("snpbool")))
			// if (request.getString("snpbool").equals("hide"))
			// this.getModel().getMutationSearchCriteriaVO().setReportedAsSNP(false);

			MutationSummaryDTO mutationSummaryDTO = searchService.findMutationByIdentifier(mutationIdentifier);

			this.getModel().setMutationSummaryVO(mutationSummaryDTO);

			this.getModel().setPositionMutations(searchService.findPositionMutations(mutationSummaryDTO));
			this.getModel().setCodonMutations(searchService.findCodonMutations(mutationSummaryDTO));

			this.getModel().setHeader("Details for mutation " + mutationIdentifier);

			this.setView(new FreemarkerView(this.getModel().getMutationViewer(), this.getModel()));
		}
	}

	protected void handleFindPatients(Tuple request)
	{
		if (StringUtils.isNotEmpty(request.getString("mid")))
		{
			String mutationIdentifier = request.getString("mid");

			List<PatientSummaryDTO> patientSummaryVOList = searchService
					.findPatientsByMutationIdentifier(mutationIdentifier);

			((HttpServletRequestTuple) request).getRequest().setAttribute("patientSummaryVOs", patientSummaryVOList);
			this.getModel().setRawOutput(this.include(request, this.getModel().getPatientPager()));
			this.getModel().setHeader(patientSummaryVOList.size() + " results for " + mutationIdentifier);

			this.setView(new FreemarkerView("included.ftl", this.getModel()));
		}
	}

	protected void handleFindMutationsByTerm(Tuple request)
	{
		// if (StringUtils.isNotEmpty(request.getString("term")) &&
		// request.getString("term").length() < 3)
		// throw new
		// SearchException("Search term is too general. Please use a more specific one.");

		if (StringUtils.isNotEmpty(request.getString("result"))) this.getModel().setResult(request.getString("result"));
		else
			this.getModel().setResult("mutations"); // Default: Show mutations

		this.getModel().setMutationSummaryVOHash(new HashMap<String, String>());
		this.getModel().setPatientSummaryVOHash(new HashMap<String, String>());

		if (this.getModel().getResult().equals("patients"))
		{
			HashMap<String, List<PatientSummaryDTO>> result = searchService.findPatientsByTerm(request
					.getString("term"));

			int numPatients = 0;

			for (String key : result.keySet())
			{
				if (CollectionUtils.isNotEmpty(result.get(key)))
				{
					((HttpServletRequestTuple) request).getRequest().setAttribute("patientSummaryVOs", result.get(key));
					this.getModel().getPatientSummaryVOHash()
							.put(" " + key + " ", this.include(request, this.getModel().getPatientPager()));
					numPatients += result.get(key).size();
				}
			}

			this.getModel().setHeader(numPatients + " patients found.");
		}
		else if (this.getModel().getResult().equals("mutations"))
		{
			HashMap<String, List<MutationSummaryDTO>> result = searchService.findMutationsByTerm(request
					.getString("term"));

			int numMutations = 0;

			for (String key : result.keySet())
			{
				if (CollectionUtils.isNotEmpty(result.get(key)))
				{
					((HttpServletRequestTuple) request).getRequest().setAttribute("mutationSummaryDTOList",
							result.get(key));
					this.getModel().getMutationSummaryVOHash()
							.put(" " + key + " ", this.include(request, this.getModel().getMutationPager()));
					numMutations += result.get(key).size();
				}
			}

			this.getModel().setHeader(numMutations + " mutations found.");
		}

		this.setView(new FreemarkerView("freetext.ftl", this.getModel()));
	}

	protected void handleShowNextMutation(Tuple request)
	{
		MutationSummaryDTO mutationSummaryDTO = searchService.findNextMutation(request.getString("mid"));
		request.set("mid", mutationSummaryDTO.getIdentifier());
		this.handleShowMutation(request);
	}

	protected void handleShowPrevMutation(Tuple request)
	{
		MutationSummaryDTO mutationSummaryVO = searchService.findPrevMutation(request.getString("mid"));
		request.set("mid", mutationSummaryVO.getIdentifier());
		this.handleShowMutation(request);
	}

	protected void handleShowLastMutation(Tuple request)
	{
		MutationSummaryDTO mutationSummaryVO = searchService.findLastMutation();
		request.set("mid", mutationSummaryVO.getIdentifier());
		this.handleShowMutation(request);
	}

	protected void handleShowFirstMutation(Tuple request)
	{
		MutationSummaryDTO mutationSummaryVO = searchService.findFirstMutation();
		request.set("mid", mutationSummaryVO.getIdentifier());
		this.handleShowMutation(request);
	}

	protected void listAllMutations(Tuple request)
	{
		this.getModel().setMutationSummaryDTOList(searchService.findAllMutationSummaries());
		((HttpServletRequestTuple) request).getRequest().setAttribute("mutationSummaryDTOList",
				this.getModel().getMutationSummaryDTOList());
		this.getModel().setRawOutput(this.include(request, this.getModel().getMutationPager()));

		this.getModel().setHeader(
				this.getModel().getMutationSummaryDTOList().size() + " results for \"Display all mutations\".");
		this.setView(new FreemarkerView("included.ftl", getModel()));
	}

	protected void handleShowPatient(Tuple request)
	{
		if (StringUtils.isNotEmpty(request.getString("pid")))
		{
			String patientIdentifier = request.getString("pid");

			PatientSummaryDTO patientSummaryVO = searchService.findPatientByPatientIdentifier(patientIdentifier);

			this.getModel().setPatientSummaryVO(patientSummaryVO);

			this.getModel().setHeader("Details for patient " + patientIdentifier);

			this.setView(new FreemarkerView(this.getModel().getPatientViewer(), getModel()));
		}
	}

	protected void listAllPatients(Tuple request)
	{
		// MolgenisUser user = new MolgenisUser();
		// user.setId(this.getLogin().getUserId());
		// this.getModel().setPatientSummaryVOs(this.patientService.find(user));
		List<PatientSummaryDTO> patientSummaryVOs = searchService.findAllPatientSummaries();
		this.getModel().setPatientSummaryVOs(patientSummaryVOs);
		((HttpServletRequestTuple) request).getRequest().setAttribute("patientSummaryVOs",
				this.getModel().getPatientSummaryVOs());
		this.getModel().setRawOutput(this.include(request, this.getModel().getPatientPager()));
		this.getModel().setHeader(
				this.getModel().getPatientSummaryVOs().size() + " results for \"Display all patients\".");

		this.setView(new FreemarkerView("included.ftl", this.getModel()));
	}

	protected void handleShowPhenotypeDetails(Tuple request) throws Exception
	{
		if (StringUtils.isNotEmpty(request.getString("pid")))
		{
			String patientIdentifier = request.getString("pid");

			PatientSummaryDTO patientSummaryVO = searchService.findPatientByPatientIdentifier(patientIdentifier);

			this.getModel().setIndividualDTO(phenoService.findPhenotypeDetails(patientSummaryVO.getPatientId()));

			this.getModel().setHeader("Phenotypic details for Patient " + patientIdentifier);

			this.setView(new FreemarkerView("phenotypedetails.ftl", getModel()));
		}
	}

	protected void handleShowGene(Tuple request) throws Exception
	{
		if (StringUtils.isNotEmpty(request.getString("gene_id")))
		{
			Integer geneId  = request.getInt("gene_id");
			
			GeneDTO geneDTO = this.searchService.findGene(geneId);
			
			this.getModel().setGeneDTO(geneDTO);
			GenePanel genePanel = this.getModel().getMbrowse().createGenePanel(geneDTO.getProteinDomainDTOList());
			genePanel.setLabel("Browse the " + geneDTO.getName() + " gene");
			this.getModel().setMBrowsePanel(genePanel);

			this.setView(new FreemarkerView("init.ftl", this.getModel()));
		}
	}

	protected void handleShowProteinDomain(Tuple request) throws Exception
	{
		if (StringUtils.isNotEmpty(request.getString("domain_id"))) this.getModel().getMutationSearchCriteriaVO()
				.setProteinDomainId(request.getInt("domain_id"));
		if (StringUtils.isNotEmpty(request.getString("snpbool"))) if (request.getString("snpbool").equals("hide")) this
				.getModel().getMutationSearchCriteriaVO().setReportedAsSNP(false);

		this.getModel().setProteinDomainDTO(searchService.findProteinDomain(request.getInt("domain_id"), false));
		this.getModel().setMutationSummaryDTOList(searchService.findMutationsByDomainId(request.getInt("domain_id")));
		((HttpServletRequestTuple) request).getRequest().setAttribute("mutationSummaryDTOList",
				this.getModel().getMutationSummaryDTOList());
		this.getModel().setRawOutput(this.include(request, this.getModel().getMutationPager()));

		this.getModel().setHeader((this.getModel().getProteinDomainDTO() == null) ? "Unknown id." : "");

		this.getModel().setMBrowsePanel(this.getModel().getMbrowse().createExonIntronPanel(searchService.findAllExons()));
//		this.getModel().setMBrowsePanel(this.getModel().getMbrowse().createProteinDomainPanel(this.getModel().getProteinDomainDTO()));
		this.setView(new FreemarkerView("proteindomain.ftl", getModel()));
	}

	protected void handleShowExon(Tuple request)
	{
		Integer exonId = request.getInt("exon_id");

		this.getModel().setExonDTO(searchService.findExonById(exonId));

		if (this.getModel().getQueryParametersVO().getShowMutations())
		{
			this.getModel().setMutationSummaryDTOList(searchService.findMutationsByExonId(exonId));
			((HttpServletRequestTuple) request).getRequest().setAttribute("mutationSummaryDTOList",
					this.getModel().getMutationSummaryDTOList());
			this.getModel().setRawOutput(this.include(request, this.getModel().getMutationPager()));
		}
		this.getModel().setHeader("");
		this.getModel().setMBrowsePanel(this.getModel().getMbrowse().createSequencePanel(this.getModel().getExonDTO(), this.getModel().getMutationSummaryDTOList()));
		this.setView(new FreemarkerView("exon.ftl", getModel()));
	}

	protected void handleShowNextExon(Tuple request)
	{
		ExonDTO exonDTO = searchService.findNextExon(request.getInt("exon_id"));
		request.set("__action", "showExon");
		request.set("exon_id", exonDTO.getId());
		this.handleShowExon(request);
	}

	protected void handleShowPrevExon(Tuple request)
	{
		ExonDTO exonDTO = searchService.findPrevExon(request.getInt("exon_id"));
		request.set("__action", "showExon");
		request.set("exon_id", exonDTO.getId());
		this.handleShowExon(request);
	}

	protected void handleShowLastExon(Tuple request)
	{
		ExonDTO exonDTO = searchService.findLastExon();
		request.set("exon_id", exonDTO.getId());
		this.handleShowExon(request);
	}

	protected void handleShowFirstExon(Tuple request)
	{
		ExonDTO exonDTO = searchService.findFirstExon();
		request.set("exon_id", exonDTO.getId());
		this.handleShowExon(request);
	}

	@Override
	public void reload(Database db)
	{
		try
		{
			this.cmsService.setDatabase(db);
			this.phenoService.setDatabase(db);
			this.searchService.setDatabase(db);
			this.statisticsService.setDatabase(db);

			if (this.getModel().getGeneDTO() == null)
			{
				this.getModel().setGeneDTO(searchService.findGene());
			}

			this.initTopPanel();

			this.getModel().setTextRemarks(cmsService.findContentByName("remarks"));
			this.getModel().setTextCollaborations(cmsService.findContentByName("collaborators"));

			if (this.getModel().getQueryParametersVO().getExpertSearch())
			{
				this.populateExpertSearchForm();
				this.populateShowMutationForm();
				this.populateToSimpleSearchForm();
			}
			else
			{
				this.getModel().setTextWelcome(cmsService.findContentByName("welcome"));
				this.getModel().setTextSearch(cmsService.findContentByName("search"));

				this.getModel().setNumMutations(statisticsService.getNumMutations());
				this.getModel().setNumPatients(statisticsService.getNumPatients());
				this.getModel().setNumUnpublished(statisticsService.getNumUnpublishedPatients());
				this.getModel().setNumMutationsByPathogenicity(statisticsService.getNumMutationsByPathogenicity());
				this.getModel().setNumPatientsByPathogenicity(statisticsService.getNumPatientsByPathogenicity());

				this.populateSimpleSearchForm();
				this.populateListAllMutationsForm();
				this.populateListAllPatientsForm();
				this.populateToExpertSearchForm();
			}
		}
		catch (Exception e)
		{
			String message = "Oops, an error occurred. We apologize and will work on fixing it as soon as possible. <a href=\"molgenis.do?__target=SearchPlugin&select=SearchPlugin&__action=init&expertSearch=0\">Return to home page</a>";
			this.getModel().getMessages().add(new ScreenMessage(message, false));
			for (StackTraceElement el : e.getStackTrace())
				logger.error(el.toString());
		}

		for (ScreenController<?> child : this.getChildren())
			try
			{
				child.reload(db);
			}
			catch (Exception e)
			{
				e.printStackTrace();
			}
	}

	// private void convert2eav(Database db) throws DatabaseException,
	// ParseException
	// {
	// List<Patient> patients = db.query(Patient.class).find();
	// for (Patient patient : patients)
	// {
	// PhenotypeDetails details = db.findById(PhenotypeDetails.class,
	// patient.getPhenotype_Details_Id());
	// for (String field : details.getFields())
	// {
	// if ("id".equals(field))
	// continue;
	// if (details.get(field) == null)
	// continue;
	// String value = details.get(field).toString();
	// System.out.println("INSERT INTO ObservedValue (Investigation, Feature, Target, __Type, value) SELECT 1, f.id, "
	// + patient.getId() + ", 'ObservedValue', '" + value +
	// "' FROM ObservationElement f WHERE name = '" + field + "';");
	// }
	//
	// List<I_F> ifs = db.query(I_F.class).equals(I_F.PATIENT,
	// patient.getId()).find();
	// for (I_F if_ : ifs)
	// {
	// String field = "Amount of type VII collagen";
	// String value = if_.getValue();
	// System.out.println("INSERT INTO ObservedValue (Investigation, Feature, Target, __Type, value) SELECT 1, f.id, "
	// + patient.getId() + ", 'ObservedValue', '" + value +
	// "' FROM ObservationElement f WHERE name = '" + field + "';");
	// String field2 = "IF Retention of type VII Collagen in basal cells";
	// String value2 = if_.getRetention();
	// System.out.println("INSERT INTO ObservedValue (Investigation, Feature, Target, __Type, value) SELECT 1, f.id, "
	// + patient.getId() + ", 'ObservedValue', '" + value2 +
	// "' FROM ObservationElement f WHERE name = '" + field2 + "';");
	// }
	//
	// List<E_M> ems = db.query(E_M.class).equals(E_M.PATIENT,
	// patient.getId()).find();
	// for (E_M em_ : ems)
	// {
	// String field = "Anchoring fibrils Number";
	// String value = em_.getNumber();
	// System.out.println("INSERT INTO ObservedValue (Investigation, Feature, Target, __Type, value) SELECT 1, f.id, "
	// + patient.getId() + ", 'ObservedValue', '" + value +
	// "' FROM ObservationElement f WHERE name = '" + field + "';");
	// String field2 = "Anchoring fibrils Ultrastructure";
	// String value2 = em_.getAppearance();
	// System.out.println("INSERT INTO ObservedValue (Investigation, Feature, Target, __Type, value) SELECT 1, f.id, "
	// + patient.getId() + ", 'ObservedValue', '" + value2 +
	// "' FROM ObservationElement f WHERE name = '" + field2 + "';");
	// String field3 = "EM Retention of type VII Collagen in basal cells";
	// String value3 = em_.getRetention();
	// System.out.println("INSERT INTO ObservedValue (Investigation, Feature, Target, __Type, value) SELECT 1, f.id, "
	// + patient.getId() + ", 'ObservedValue', '" + value3 +
	// "' FROM ObservationElement f WHERE name = '" + field3 + "';");
	// }
	// }
	//
	// }

	private void initTopPanel()
	{
		if (this.getModel().getMbrowse().getIsVisible())
		{
			List<GeneDTO> geneDTOList = this.searchService.findAllGenes();
			if (geneDTOList.size() == 1)
			{
				GeneDTO geneDTO = geneDTOList.get(0);
				GenePanel genePanel = this.getModel().getMbrowse().createGenePanel(geneDTO.getProteinDomainDTOList());
				genePanel.setLabel("Browse the " + geneDTO.getName() + " gene");
				this.getModel().setTopPanel(genePanel);
			}
			else
			{
				GenomePanel genomePanel = this.getModel().getMbrowse().createGenomePanel(geneDTOList);
				genomePanel.setLabel("Browse the genome");
				this.getModel().setTopPanel(genomePanel);
			}
		}
	}

	private void populateSimpleSearchForm()
	{
		((HiddenInput) this.getModel().getSimpleSearchForm().get("__target")).setValue(this.getName());
		((HiddenInput) this.getModel().getSimpleSearchForm().get("select")).setValue(this.getName());
		((RadioInput) this.getModel().getSimpleSearchForm().get("result")).setValue(this.getModel().getResult());
		((AutocompleteInput) this.getModel().getSimpleSearchForm().get("term")).setValue(this.getModel()
				.getSearchTerm());
	}

	private void populateListAllMutationsForm()
	{
		((HiddenInput) this.getModel().getListAllMutationsForm().get("__target")).setValue(this.getName());
		((HiddenInput) this.getModel().getListAllMutationsForm().get("select")).setValue(this.getName());
	}

	private void populateListAllPatientsForm()
	{
		((HiddenInput) this.getModel().getListAllPatientsForm().get("__target")).setValue(this.getName());
		((HiddenInput) this.getModel().getListAllMutationsForm().get("select")).setValue(this.getName());
	}

	private void populateToSimpleSearchForm()
	{
		((HiddenInput) this.getModel().getToSimpleSearchForm().get("__target")).setValue(this.getName());
	}

	private void populateToExpertSearchForm()
	{
		((HiddenInput) this.getModel().getToExpertSearchForm().get("__target")).setValue(this.getName());
	}

	private void populateShowMutationForm()
	{
		((HiddenInput) this.getModel().getShowMutationForm().get("__target")).setValue(this.getName());
		((HiddenInput) this.getModel().getListAllMutationsForm().get("select")).setValue(this.getName());
		List<ValueLabel> mutationIdOptions = new ArrayList<ValueLabel>();
		mutationIdOptions.add(new ValueLabel("", "Select mutation"));
		for (VariantDTO variantDTO : searchService.getAllVariants())
			mutationIdOptions.add(new ValueLabel(variantDTO.getIdentifier(), variantDTO.getCdnaNotation() + " ("
					+ variantDTO.getAaNotation() + ")"));
		((SelectInput) this.getModel().getShowMutationForm().get("mid")).setOptions(mutationIdOptions);
		((SelectInput) this.getModel().getShowMutationForm().get("mid")).setValue("Select mutation");
	}

	@SuppressWarnings("unchecked")
	protected void populateExpertSearchForm()
	{
		Container expertSearchForm = this.getModel().getExpertSearchFormWrapper().getForm();

		((HiddenInput) expertSearchForm.get("__target")).setValue(this.getName());
		((HiddenInput) expertSearchForm.get("select")).setValue(this.getName());

		if (this.getModel().getMutationSearchCriteriaVO().getVariation() != null) ((TextLineInput<String>) expertSearchForm
				.get("variation")).setValue(this.getModel().getMutationSearchCriteriaVO().getVariation());

		if (this.getModel().getMutationSearchCriteriaVO().getCdnaPosition() != null) ((IntInput) expertSearchForm
				.get("nuclno")).setValue(this.getModel().getMutationSearchCriteriaVO().getCdnaPosition());

		if (this.getModel().getMutationSearchCriteriaVO().getCodonNumber() != null) ((IntInput) expertSearchForm
				.get("aano")).setValue(this.getModel().getMutationSearchCriteriaVO().getCodonNumber());

		List<ValueLabel> exonIdOptions = new ArrayList<ValueLabel>();
		exonIdOptions.add(new ValueLabel("", "Select"));
		for (ExonDTO exonSummaryVO : searchService.findAllExons())
			exonIdOptions.add(new ValueLabel(exonSummaryVO.getId(), exonSummaryVO.getName()));
		((SelectInput) expertSearchForm.get("exon_id")).setOptions(exonIdOptions);
		if (this.getModel().getMutationSearchCriteriaVO().getExonId() != null) ((SelectInput) expertSearchForm
				.get("exon_id")).setValue(this.getModel().getMutationSearchCriteriaVO().getExonId());
		else
			((SelectInput) expertSearchForm.get("exon_id")).setValue("Select");

		List<ValueLabel> typeOptions = new ArrayList<ValueLabel>();
		typeOptions.add(0, new ValueLabel("", "Select"));
		for (String mutationType : phenoService.findObservedValues("Type of mutation"))
			typeOptions.add(new ValueLabel(mutationType, mutationType));
		((SelectInput) expertSearchForm.get("type")).setOptions(typeOptions);
		if (this.getModel().getMutationSearchCriteriaVO().getType() != null) ((SelectInput) expertSearchForm
				.get("type")).setValue(this.getModel().getMutationSearchCriteriaVO().getType());
		else
			((SelectInput) expertSearchForm.get("type")).setValue("Select");

		List<ValueLabel> domainOptions = new ArrayList<ValueLabel>();
		domainOptions.add(new ValueLabel("", "Select"));
		for (ProteinDomainDTO domainVO : searchService.findAllProteinDomains())
			domainOptions.add(new ValueLabel(domainVO.getDomainId(), domainVO.getDomainName()));
		((SelectInput) expertSearchForm.get("domain_id")).setOptions(domainOptions);
		if (this.getModel().getMutationSearchCriteriaVO().getProteinDomainId() != null) ((SelectInput) expertSearchForm
				.get("domain_id")).setValue(this.getModel().getMutationSearchCriteriaVO().getProteinDomainId());
		else
			((SelectInput) expertSearchForm.get("domain_id")).setValue("Select");

		List<ValueLabel> phenotypeOptions = new ArrayList<ValueLabel>();
		phenotypeOptions.add(new ValueLabel("", "Select"));
		for (String phenotypeName : phenoService.findObservedValues("Phenotype"))
			phenotypeOptions.add(new ValueLabel(phenotypeName, phenotypeName));
		((SelectInput) expertSearchForm.get("phenotype")).setOptions(phenotypeOptions);
		if (this.getModel().getMutationSearchCriteriaVO().getPhenotypeId() != null) ((SelectInput) expertSearchForm
				.get("phenotype")).setValue(this.getModel().getMutationSearchCriteriaVO().getPhenotypeId());
		else
			((SelectInput) expertSearchForm.get("phenotype")).setValue("Select");
	}

	private void populateDisplayOptionsForm()
	{
		((HiddenInput) this.getModel().getDisplayOptionsForm().get("__target")).setValue(this.getName());
		((HiddenInput) this.getModel().getDisplayOptionsForm().get("__action")).setValue(this.getModel().getAction());

		if (this.getModel().getMutationSearchCriteriaVO().getProteinDomainId() != null) ((HiddenInput) this.getModel()
				.getDisplayOptionsForm().get("domain_id")).setValue(this.getModel().getMutationSearchCriteriaVO()
				.getProteinDomainId().toString());
		if (this.getModel().getMutationSearchCriteriaVO().getExonId() != null) ((HiddenInput) this.getModel()
				.getDisplayOptionsForm().get("exon_id")).setValue(this.getModel().getMutationSearchCriteriaVO()
				.getExonId().toString());
		if (this.getModel().getMutationSearchCriteriaVO().getMid() != null) ((HiddenInput) this.getModel()
				.getDisplayOptionsForm().get("mid")).setValue(this.getModel().getMutationSearchCriteriaVO().getMid());

		if (this.getModel().getQueryParametersVO().getShowSNP()) ((SelectInput) this.getModel().getDisplayOptionsForm()
				.get("snpbool")).setValue("show");
		else
			((SelectInput) this.getModel().getDisplayOptionsForm().get("snpbool")).setValue("hide");

		if (this.getModel().getQueryParametersVO().getShowIntrons()) ((SelectInput) this.getModel()
				.getDisplayOptionsForm().get("showIntrons")).setValue("show");
		else
			((SelectInput) this.getModel().getDisplayOptionsForm().get("showIntrons")).setValue("hide");

		if (this.getModel().getQueryParametersVO().getShowNames()) ((SelectInput) this.getModel()
				.getDisplayOptionsForm().get("showNames")).setValue("show");
		else
			((SelectInput) this.getModel().getDisplayOptionsForm().get("showNames")).setValue("hide");

		if (this.getModel().getQueryParametersVO().getShowNumbering()) ((SelectInput) this.getModel()
				.getDisplayOptionsForm().get("showNumbering")).setValue("show");
		else
			((SelectInput) this.getModel().getDisplayOptionsForm().get("showNumbering")).setValue("hide");

		if (this.getModel().getQueryParametersVO().getShowMutations()) ((SelectInput) this.getModel()
				.getDisplayOptionsForm().get("showMutations")).setValue("show");
		else
			((SelectInput) this.getModel().getDisplayOptionsForm().get("showMutations")).setValue("hide");
	}

	// private CmsService getCmsService(Database db)
	// {
	// CmsService cmsService = ServiceLocator.instance().getCmsService();
	// cmsService.setDatabase(db);
	// return cmsService;
	// }
	//
	// private PhenoService getPhenoService(Database db)
	// {
	// PhenoService phenoService = ServiceLocator.instance().getPhenoService();
	// phenoService.setDatabase(db);
	// return phenoService;
	// }
	//
	// private SearchService getSearchService(Database db)
	// {
	// SearchService searchService =
	// ServiceLocator.instance().getSearchService();
	// searchService.setDatabase(db);
	// return searchService;
	// }
	//
	// private StatisticsService getStatisticsService(Database db)
	// {
	// StatisticsService statisticsService =
	// ServiceLocator.instance().getStatisticsService();
	// statisticsService.setDatabase(db);
	// return statisticsService;
	// }
}