[Obo-svn-commit] SF.net SVN: obo:[2575] OBDAPI/trunk

[<ba...@us...>]

Revision: 2575
          http://obo.svn.sourceforge.net/obo/?rev=2575&view=rev
Author:   balhoff
Date:     2009-05-19 15:57:25 +0000 (Tue, 19 May 2009)

Log Message:
-----------
Changed database name env variable for Phenoscape build.  Changes to OBDSQLShard to comply with Java 1.5.

Modified Paths:
--------------
    OBDAPI/trunk/phenoscape/build.xml
    OBDAPI/trunk/src/org/obd/query/impl/OBDSQLShard.java

Modified: OBDAPI/trunk/phenoscape/build.xml
===================================================================
--- OBDAPI/trunk/phenoscape/build.xml	2009-05-18 20:08:21 UTC (rev 2574)
+++ OBDAPI/trunk/phenoscape/build.xml	2009-05-19 15:57:25 UTC (rev 2575)
@@ -15,13 +15,13 @@
 	<property name="nexml-repo" value="https://phenoscape.svn.sourceforge.net/svnroot/phenoscape/trunk/data/phenex-files"/>
 	
 	<property environment="environment"/>
-	<property name="db-name" value="${environment.DBNAME}"/>
 <!-- Environment variables to set for database connections:
 DBNAME sets the name of the database
 PGUSER sets the user name used to connect to the database.
 PGPASSWORD sets the password used if the server demands password authentication. Use of this environment variable is not recommended for security reasons (some operating systems allow non-root users to see process environment variables via ps); instead consider using the ~/.pgpass file.
 PGHOST sets the database server name.
 -->
+	<property name="db-name" value="${environment.PGDATABASE}"/>
 	<property name="db-user" value="${environment.PGUSER}"/>
 	<property name="db-password" value="${environment.PGPASSWORD}"/>
 	<property name="db-host" value="${environment.PGHOST}"/>

Modified: OBDAPI/trunk/src/org/obd/query/impl/OBDSQLShard.java
===================================================================
--- OBDAPI/trunk/src/org/obd/query/impl/OBDSQLShard.java	2009-05-18 20:08:21 UTC (rev 2574)
+++ OBDAPI/trunk/src/org/obd/query/impl/OBDSQLShard.java	2009-05-19 15:57:25 UTC (rev 2575)
@@ -19,7 +19,6 @@
 import java.util.Set;
 import java.util.logging.Logger;
 
-import org.bbop.rdbms.FromClause;
 import org.bbop.rdbms.GroupByClause;
 import org.bbop.rdbms.RelationalQuery;
 import org.bbop.rdbms.SelectClause;
@@ -27,8 +26,6 @@
 import org.bbop.rdbms.impl.SqlQueryImpl;
 import org.bbop.rdbms.impl.SqlSelectClauseImpl;
 import org.bbop.rdbms.impl.SqlWhereClauseImpl;
-import org.obd.model.CompositionalDescription;
-import org.obd.model.Graph;
 import org.obd.model.LinkStatement;
 import org.obd.model.LiteralStatement;
 import org.obd.model.Node;
@@ -39,7 +36,6 @@
 import org.obd.model.rule.RelationCompositionRule;
 import org.obd.model.stats.AggregateStatisticCollection;
 import org.obd.model.stats.ScoredNode;
-import org.obd.model.stats.SimilarityPair;
 import org.obd.model.stats.AggregateStatistic.AggregateType;
 import org.obd.model.vocabulary.TermVocabulary;
 import org.obd.query.AnnotationLinkQueryTerm;
@@ -49,7 +45,6 @@
 import org.obd.query.ComparisonQueryTerm;
 import org.obd.query.CompositionalDescriptionQueryTerm;
 import org.obd.query.ExistentialQueryTerm;
-import org.obd.query.GraphQuery;
 import org.obd.query.LabelQueryTerm;
 import org.obd.query.LinkQueryTerm;
 import org.obd.query.LiteralQueryTerm;
@@ -59,16 +54,11 @@
 import org.obd.query.Shard;
 import org.obd.query.SourceQueryTerm;
 import org.obd.query.SubsetQueryTerm;
-import org.obd.query.AnalysisCapableRepository.SimilaritySearchParameters;
 import org.obd.query.BooleanQueryTerm.BooleanOperator;
 import org.obd.query.ComparisonQueryTerm.Operator;
 import org.obd.query.LabelQueryTerm.AliasType;
 import org.obd.query.QueryTerm.Aspect;
-import org.obd.query.Shard.EntailmentUse;
-import org.obd.query.Shard.GraphTranslation;
 import org.obd.query.exception.ShardExecutionException;
-import org.obo.dataadapter.OBDSQLDatabaseAdapter;
-import org.obo.dataadapter.OBDSQLDatabaseAdapter.OBDSQLDatabaseAdapterConfiguration;
 import org.obo.datamodel.IdentifiedObject;
 import org.obo.datamodel.Link;
 import org.obo.datamodel.LinkedObject;
@@ -498,7 +488,7 @@
 		}
 		catch(SQLException sqle){
 			logger.severe("SqlException");
-			throw new SQLException(sqle);
+			throw sqle;
 			
 		}
 		
@@ -564,7 +554,7 @@
 		} catch (SQLException e) {
 			System.err.println("Error fetching nodes: "
 					+ e.getMessage());
-			throw new SQLException(e);
+			throw e;
 		}
 
 		return results;
@@ -614,7 +604,7 @@
 			System.err.println("Error fetching nodes: "
 					+ e.getMessage());
 			e.printStackTrace();
-			throw new SQLException(e);
+			throw e;
 		}
 		
 		return results;
@@ -665,7 +655,7 @@
 			System.err.println("Error fetching nodes: "
 					+ e.getMessage());
 			e.printStackTrace();
-			throw new SQLException(e);
+			throw e;
 		}
 
 		return results;
@@ -712,7 +702,7 @@
 			System.err.println("Error fetching nodes: "
 					+ e.getMessage());
 			e.printStackTrace();
-			throw new SQLException(e);
+			throw e;
 		}
 
 		return results;


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.