[Obo-svn-commit] SF.net SVN: obo:[2974] OBD-WS/trunk/src/org/phenoscape

[<car...@us...>]

Revision: 2974
          http://obo.svn.sourceforge.net/obo/?rev=2974&view=rev
Author:   cartik73
Date:     2009-12-21 20:48:22 +0000 (Mon, 21 Dec 2009)

Log Message:
-----------
New class to invoke stored procedures for summarize phenotypes by gene and taxon

Added Paths:
-----------
    OBD-WS/trunk/src/org/phenoscape/dw/
    OBD-WS/trunk/src/org/phenoscape/dw/queries/
    OBD-WS/trunk/src/org/phenoscape/dw/queries/StoredProceduresForPhenotypeSummaries.java

Added: OBD-WS/trunk/src/org/phenoscape/dw/queries/StoredProceduresForPhenotypeSummaries.java
===================================================================
--- OBD-WS/trunk/src/org/phenoscape/dw/queries/StoredProceduresForPhenotypeSummaries.java	                        (rev 0)
+++ OBD-WS/trunk/src/org/phenoscape/dw/queries/StoredProceduresForPhenotypeSummaries.java	2009-12-21 20:48:22 UTC (rev 2974)
@@ -0,0 +1,82 @@
+package org.phenoscape.dw.queries;
+
+import java.sql.CallableStatement;
+import java.sql.Connection;
+import java.sql.ResultSet;
+import java.sql.SQLException;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import org.obd.query.impl.OBDSQLShard;
+import org.obd.ws.util.dto.PhenotypeDTO;
+
+public class StoredProceduresForPhenotypeSummaries {
+
+	public static final String invokeStoredProcedureForTaxonSummary = "SELECT * FROM get_phenotype_summary_for_taxon(?)";
+	public static final String invokeStoredProcedureForGeneSummary = "SELECT * FROM get_phenotype_summary_for_gene(?)";
+	
+	private OBDSQLShard shard;
+	private Connection conn; 
+	
+	public StoredProceduresForPhenotypeSummaries(OBDSQLShard shard){
+		this.shard = shard;
+		this.conn = shard.getConnection();
+	}
+	
+	public Collection<PhenotypeDTO> executeStoredProcedureAndAssembleResults(String storedProc, String parameter) throws SQLException{
+		
+		/** <a> annotationToReifsMap </a> 
+		 * This new map has been added tp consolidate reif ids for a TAXON to PHENOTYPE assertion*/
+		Map<PhenotypeDTO, Set<String>> annotationToReifsMap = new HashMap<PhenotypeDTO, Set<String>>();
+		Collection<PhenotypeDTO> results = new ArrayList<PhenotypeDTO>();
+		
+		CallableStatement cs = conn.prepareCall(storedProc);
+		cs.setString(1, parameter);
+		ResultSet rs = cs.executeQuery();
+		
+		PhenotypeDTO pdto;
+		
+		while(rs.next()){
+			pdto = new PhenotypeDTO(rs.getString(1));
+			pdto.setTaxonId(rs.getString(2));
+			pdto.setTaxon(rs.getString(3));
+			pdto.setQualityId(rs.getString(4));
+			pdto.setQuality(rs.getString(5));
+			pdto.setCharacterId(rs.getString(6));			
+			pdto.setCharacter(rs.getString(7));
+			pdto.setEntityId(rs.getString(8));
+			pdto.setEntity(rs.getString(9));
+			pdto.setNumericalCount(rs.getString(11));
+			String reif = rs.getString(10);
+			
+			pdto.setRelatedEntityId(rs.getString(12));
+			pdto.setRelatedEntity(rs.getString(13));
+			pdto.setPublication(rs.getString(14));
+			
+			//we collect all the reif ids associated with each DTO object
+			Set<String> reifs = annotationToReifsMap.get(pdto);
+			if(reifs == null)
+				reifs = new HashSet<String>();
+			reifs.add(reif);
+			annotationToReifsMap.put(pdto, reifs);
+		}
+		
+		for(PhenotypeDTO dto : annotationToReifsMap.keySet()){
+			//here we reassign the reif ids to the DTO
+			String reifString = "";
+			for(String reif : annotationToReifsMap.get(dto)){
+				reifString += reif + ",";
+			}
+			//we trim out the last comma
+			reifString = reifString.substring(0, reifString.lastIndexOf(","));
+			dto.setReifId(reifString);
+			results.add(dto);
+		}
+		return results;
+	}
+}


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