RecordManager.java

package edu.ucsf.mousedatabase.admin;

import java.util.ArrayList;

import javax.servlet.http.HttpServletRequest;

import edu.ucsf.mousedatabase.DBConnect;
import edu.ucsf.mousedatabase.HTMLGeneration;
import edu.ucsf.mousedatabase.MGIConnect;
import edu.ucsf.mousedatabase.objects.Gene;
import edu.ucsf.mousedatabase.objects.MGIResult;
import edu.ucsf.mousedatabase.objects.MouseHolder;
import edu.ucsf.mousedatabase.objects.MouseRecord;

public class RecordManager {

  public static class PopulateMouseResult
  {
    public boolean Success;
    public String Message;
    public PopulateMouseResult(boolean success, String message) {
      super();
      Success = success;
      Message = message;
    }


  }

  public static class GeneInfo
  {
    public String mgiGeneID;
    public String targetMgiGeneID;
    public String manualGeneName;
    public String manualGeneSymbol;
    public String manualTargetGeneName;
    public String manualTargetGeneSymbol;
  }

  public static class AddGeneResult
  {
    public boolean Success;
    public String Message;

    public AddGeneResult(boolean success, String message) {
      Success = success;
      Message = message;
    }
  }

  public static PopulateMouseResult PopulateMouseDataFromRequest(MouseRecord newMouse, HttpServletRequest request)
  {
    PopulateMouseResult result = new PopulateMouseResult(true, null);

    GeneInfo geneInfo = new GeneInfo();
    geneInfo.manualGeneName = request.getParameter("geneManualName");
    geneInfo.manualGeneSymbol = request.getParameter("geneManualSymbol");
    geneInfo.manualTargetGeneName = request.getParameter("targetGeneManualName");
    geneInfo.manualTargetGeneSymbol = request.getParameter("targetGeneManualSymbol");
    geneInfo.mgiGeneID = request.getParameter("geneMGIID");
    geneInfo.targetMgiGeneID = request.getParameter("targetGeneMGIID");

    AddGeneResult geneResult = CreateAndAddGenes(newMouse,geneInfo);
    if (!geneResult.Success)
    {
      result.Message += result.Message + "<br/>";
      result.Success = false;
    }

    AddHolders(newMouse,request);
      AddPubMedIds(newMouse,request);

    return new PopulateMouseResult(true, null);
  }

  public static AddGeneResult CreateAndAddGenes(MouseRecord newMouse, GeneInfo geneInfo)
  {
    //convert MGI Gene IDs into mouse db gene IDs

    if(geneInfo.mgiGeneID != null && !geneInfo.mgiGeneID.isEmpty())
    {
      String geneID;
      Gene geneObj = DBConnect.findGene(geneInfo.mgiGeneID);
      if (geneObj == null)
      {
        MGIResult result = MGIConnect.doMGIQuery(geneInfo.mgiGeneID,MGIConnect.MGI_MARKER,"This ID is not a valid MGI Gene Accession ID",false);
        if(result.isValid())
        {
          geneID = DBConnect.addGeneManually(result.getAccessionID(),result.getName(),result.getSymbol());
        }
        else if (geneInfo.manualGeneName == null || geneInfo.manualGeneName.isEmpty() || geneInfo.manualGeneSymbol == null || geneInfo.manualGeneSymbol.isEmpty())
        {
          String message = "Unable to automatically add gene because: " + result.getErrorString()
          + "<br>.Please go back and manually enter the symbol and full name for the gene at MGI ID: " + geneInfo.mgiGeneID;
          return new AddGeneResult(false,message);
        }
        else
        {
          geneID = DBConnect.addGeneManually(result.getAccessionID(),geneInfo.manualGeneName,geneInfo.manualGeneSymbol);
        }
      }
      else
      {
        geneID = Integer.toString(geneObj.getGeneRecordID());
      }
      newMouse.setGeneID(geneID);
    }
    //mgiGeneID = request.getParameter("targetGeneMGIID");
    if(geneInfo.targetMgiGeneID != null && !geneInfo.targetMgiGeneID.isEmpty())
    {
      String geneID;
      Gene geneObj = DBConnect.findGene(geneInfo.targetMgiGeneID);
      if (geneObj == null)
      {
        MGIResult result = MGIConnect.doMGIQuery(geneInfo.targetMgiGeneID,MGIConnect.MGI_MARKER,"This ID is not a valid MGI Gene Accession ID",false);
        if(result.isValid())
        {
          geneID = DBConnect.addGeneManually(result.getAccessionID(),result.getName(),result.getSymbol());
        }
        else if (geneInfo.manualTargetGeneName == null || geneInfo.manualTargetGeneName.isEmpty() || geneInfo.manualTargetGeneSymbol == null || geneInfo.manualTargetGeneSymbol.isEmpty())
        {
          String message = "Unable to automatically add gene because: " + result.getErrorString()
          + "<br>.Please go back and manually enter the symbol and full name for the gene at MGI ID: " + geneInfo.targetMgiGeneID;
          return new AddGeneResult(false,message);
        }
        else
        {
          geneID = DBConnect.addGeneManually(result.getAccessionID(),geneInfo.manualTargetGeneName,geneInfo.manualTargetGeneSymbol);
        }
      }
      else
      {
        geneID = Integer.toString(geneObj.getGeneRecordID());
      }
      newMouse.setTargetGeneID(geneID);
    }
    return new AddGeneResult(true, null);
  }

  public static int RecordExists(MouseRecord newMouse)
  {
    if (newMouse.getRepositoryCatalogNumber() != null && !(newMouse.getRepositoryCatalogNumber().trim().equalsIgnoreCase("none")))
    {
      try
      {
        int mID = -1;
        String recordIDString = newMouse.getMouseID();
        if (recordIDString != null && !recordIDString.isEmpty() && !recordIDString.equalsIgnoreCase("null"))
        {
          mID = Integer.parseInt(newMouse.getMouseID());
        }

        return DBConnect.checkForDuplicates(Integer.parseInt(newMouse.getRepositoryCatalogNumber()), mID);

      }
      catch (NumberFormatException ex)
      {
        //ignore these exceptions, caused by abnormal mgi id
      }
    }
    return -1;
  }

  public static void AddHolders(MouseRecord newMouse, HttpServletRequest request)
  {
    //create nice and neat ArrayList of holders
    ArrayList<MouseHolder> holders = new ArrayList<MouseHolder>();

      String holderIDStr;
      int k = 0;
      while ((holderIDStr = request.getParameter("holder_id-" + k)) != null) {
        int holderID = HTMLGeneration.stringToInt(holderIDStr);
        if(holderID > 1)
        {
           MouseHolder holder = new MouseHolder();
           holder.setFacilityID(HTMLGeneration.stringToInt(request.getParameter("facility_id-" + k)));
          holder.setCovert(request.getParameter("covertHolder_-" + k) != null);
          holder.setCryoLiveStatus(request.getParameter("cryoLiveStatus-" + k));
        holder.setHolderID(holderID);
        holders.add(holder);
        }
          k++;
      }

      newMouse.setHolders(holders);

  }

  public static void AddPubMedIds(MouseRecord newMouse, HttpServletRequest request)
  {
    //create nice and neat ArrayList of PM IDs
      ArrayList<String> pmIDs = new ArrayList<String>();

      String pmID;
      int k = 1;
      while((pmID = request.getParameter("pmid" + k)) != null)
      {
        pmIDs.add(pmID);
        k++;
      }
       newMouse.setPubmedIDs(pmIDs);
  }

}