diff --git a/artemis_sqlmap/Dbxref.xml b/artemis_sqlmap/Dbxref.xml
index 10a4181c1709c1167046bf2cd7edbf4a89645716..43d0f302bc6fa721ac2ef75f21359c8ec9616bea 100644
--- a/artemis_sqlmap/Dbxref.xml
+++ b/artemis_sqlmap/Dbxref.xml
@@ -8,7 +8,7 @@
<sqlMap namespace="Dbxref">
<select id="getDbxref" parameterClass="uk.ac.sanger.artemis.chado.ChadoFeature"
- resultClass="uk.ac.sanger.artemis.chado.Dbxref">
+ resultClass="uk.ac.sanger.artemis.chado.Dbxref">
SELECT
db.name,
dbx.accession,
@@ -25,5 +25,37 @@
</isGreaterThan>
ORDER BY f.type_id, uniquename
</select>
+
+ <select id="getDbId" parameterClass="uk.ac.sanger.artemis.chado.Dbxref"
+ resultClass="java.lang.Integer">
+ SELECT db_id FROM db WHERE name=#name#
+ </select>
+
+ <select id="getDbxrefId" parameterClass="uk.ac.sanger.artemis.chado.Dbxref"
+ resultClass="java.lang.Integer">
+ SELECT dbxref_id FROM dbxref WHERE accession=#accession#
+ AND db_id=db_id;
+ </select>
+
+ <!-- WRITE BACK -->
+ <delete id="deleteFeatureDbxref" parameterClass="uk.ac.sanger.artemis.chado.Dbxref">
+ DELETE FROM $schema$.feature_dbxref
+ WHERE dbxref_id=
+ (SELECT dbxref_id FROM dbxref WHERE accession=#accession#
+ AND db_id=(SELECT db_id FROM db WHERE name=#name#))
+ AND feature_id=$feature_id$
+ </delete>
+
+ <insert id="insertFeatureDbxref" parameterClass="uk.ac.sanger.artemis.chado.Dbxref">
+ INSERT INTO $schema$.feature_dbxref
+ (feature_id, dbxref_id, is_current)
+ VALUES
+ ($feature_id$, $dbxref_id$, $current$)
+ </insert>
+
+ <insert id="insertDbxref" parameterClass="uk.ac.sanger.artemis.chado.Dbxref">
+ INSERT INTO dbxref ( db_id, accession )
+ VALUES ($db_id$, #accession#)
+ </insert>
</sqlMap>
diff --git a/uk/ac/sanger/artemis/chado/ChadoDAO.java b/uk/ac/sanger/artemis/chado/ChadoDAO.java
index a9fdfde433b72998c1a4275c939f6ceb9a312f62..00aaeb944d9c89e19d003e0891c73faeb1f1a4d2 100644
--- a/uk/ac/sanger/artemis/chado/ChadoDAO.java
+++ b/uk/ac/sanger/artemis/chado/ChadoDAO.java
@@ -210,18 +210,20 @@ public interface ChadoDAO
* Insert a dbxref for a feature.
* @param schema schema/organism name or null
* @param tsn the <code>ChadoTransaction</code>
+ * @return number of rows changed
* @throws SQLException
*/
- public void insertFeatureDbxref(final String schema, final ChadoTransaction tsn)
+ public int insertFeatureDbxref(final String schema, final ChadoTransaction tsn)
throws SQLException;
/**
* Delete a dbxref for a feature.
* @param schema schema/organism name or null
* @param tsn the <code>ChadoTransaction</code>
+ * @return number of rows changed
* @throws SQLException
*/
- public void deleteFeatureDbxref(final String schema, final ChadoTransaction tsn)
+ public int deleteFeatureDbxref(final String schema, final ChadoTransaction tsn)
throws SQLException;
/**
diff --git a/uk/ac/sanger/artemis/chado/Dbxref.java b/uk/ac/sanger/artemis/chado/Dbxref.java
index a54aaf818580480b4720733c42b04f296bf9e911..6924e9f900c131b7f10261bffeb0fd4d0146955a 100644
--- a/uk/ac/sanger/artemis/chado/Dbxref.java
+++ b/uk/ac/sanger/artemis/chado/Dbxref.java
@@ -26,7 +26,7 @@ package uk.ac.sanger.artemis.chado;
/**
*
- * Java Object used by ORM to represent the chado dbxref table.
+ * Java Object used by ORM to represent the chado feature_dbxref table.
*
*/
public class Dbxref
@@ -34,6 +34,12 @@ public class Dbxref
private String name;
private String accession;
private int feature_id;
+ /** database id */
+ private int db_id;
+ /** database cross reference id */
+ private int dbxref_id;
+ private boolean current = true;
+ private String schema;
public Dbxref()
{
@@ -69,5 +75,46 @@ public class Dbxref
this.feature_id = feature_id;
}
+ public boolean isCurrent()
+ {
+ return current;
+ }
+
+ public void setCurrent(boolean current)
+ {
+ this.current = current;
+ }
+
+ public String getSchema()
+ {
+ return schema;
+ }
+
+ public void setSchema(String schema)
+ {
+ this.schema = schema;
+ }
+
+ public int getDb_id()
+ {
+ return db_id;
+ }
+
+ public void setDb_id(int db_id)
+ {
+ this.db_id = db_id;
+ }
+
+ public int getDbxref_id()
+ {
+ return dbxref_id;
+ }
+
+ public void setDbxref_id(int dbxref_id)
+ {
+ this.dbxref_id = dbxref_id;
+ }
+
+
}
diff --git a/uk/ac/sanger/artemis/chado/IBatisDAO.java b/uk/ac/sanger/artemis/chado/IBatisDAO.java
index 31db1e3bf5c17f4bd4ad3253fedf827f2afbde0f..9df0b7a3a8b3978a2025c08be08601ab60728710 100644
--- a/uk/ac/sanger/artemis/chado/IBatisDAO.java
+++ b/uk/ac/sanger/artemis/chado/IBatisDAO.java
@@ -287,7 +287,6 @@ public class IBatisDAO implements ChadoDAO
}
/**
- *
* Insert attributes defined by the <code>ChadoTransaction</code>.
* @param schema schema/organism name or null
* @param tsn the <code>ChadoTransaction</code>
@@ -311,7 +310,6 @@ public class IBatisDAO implements ChadoDAO
}
/**
- *
* Delete attributes defined by the <code>ChadoTransaction</code>.
* @param schema schema/organism name or null
* @param tsn the <code>ChadoTransaction</code>
@@ -335,7 +333,6 @@ public class IBatisDAO implements ChadoDAO
}
/**
- *
* Insert a feature into the database defined by the <code>ChadoTransaction</code>.
* @param schema schema/organism name or null
* @param tsn the <code>ChadoTransaction</code>
@@ -398,28 +395,63 @@ public class IBatisDAO implements ChadoDAO
* Insert a dbxref for a feature.
* @param schema schema/organism name or null
* @param tsn the <code>ChadoTransaction</code>
+ * @return number of rows changed
* @throws SQLException
*/
- public void insertFeatureDbxref(final String schema, final ChadoTransaction tsn)
+ public int insertFeatureDbxref(final String schema, final ChadoTransaction tsn)
throws SQLException
{
Dbxref dbxref = tsn.getFeatureDbxref();
+ SqlMapClient sqlMap = DbSqlConfig.getSqlMapInstance();
+ Integer db_id = (Integer)sqlMap.queryForObject("getDbId", dbxref);
+
+ dbxref.setDb_id(db_id.intValue());
+
+ Integer dbxref_id = (Integer)sqlMap.queryForObject("getDbxrefId", dbxref);
+ if(dbxref_id == null)
+ {
+ // create a new accession entry in dbxref
+ sqlMap.insert("insertDbxref", dbxref);
+ // now get the new dbxref_id
+ dbxref_id = (Integer)sqlMap.queryForObject("getDbxrefId", dbxref);
+ }
+
+ dbxref.setDbxref_id(dbxref_id.intValue());
+
+ // get the feature id's
+ tsn.setSchema(schema);
+ List feature_ids = sqlMap.queryForList("getFeatureID", tsn);
+ dbxref.setFeature_id( ((Integer)feature_ids.get(0)).intValue() );
+
+ dbxref.setSchema(schema);
+ sqlMap.insert("insertFeatureDbxref", dbxref);
+
+ return 1;
}
/**
* Delete a dbxref for a feature.
* @param schema schema/organism name or null
* @param tsn the <code>ChadoTransaction</code>
+ * @return number of rows changed
* @throws SQLException
*/
- public void deleteFeatureDbxref(final String schema, final ChadoTransaction tsn)
+ public int deleteFeatureDbxref(final String schema, final ChadoTransaction tsn)
throws SQLException
{
Dbxref dbxref = tsn.getFeatureDbxref();
+
+ SqlMapClient sqlMap = DbSqlConfig.getSqlMapInstance();
+ tsn.setSchema(schema);
+ dbxref.setSchema(schema);
+ // get the feature id's
+ List feature_ids = sqlMap.queryForList("getFeatureID", tsn);
+
+ dbxref.setFeature_id( ((Integer)feature_ids.get(0)).intValue() );
+ return sqlMap.delete("deleteFeatureDbxref", dbxref);
}
/**
- *
* Write the time a feature was last modified
* @param schema schema/organism name or null
* @param uniquename the unique name of the feature
@@ -437,7 +469,6 @@ public class IBatisDAO implements ChadoDAO
}
/**
- *
* Write the time a feature was last accessed
* @param schema schema/organism name or null
* @param uniquename the unique name of the feature
diff --git a/uk/ac/sanger/artemis/chado/JdbcDAO.java b/uk/ac/sanger/artemis/chado/JdbcDAO.java
index 4c71b56ded073a1cc4b1e16b5577375ce1663ebe..151d89880cb5fb76352b83fdae5dc88664c8e7b3 100644
--- a/uk/ac/sanger/artemis/chado/JdbcDAO.java
+++ b/uk/ac/sanger/artemis/chado/JdbcDAO.java
@@ -730,24 +730,66 @@ public class JdbcDAO
* Insert a dbxref for a feature.
* @param schema schema/organism name or null
* @param tsn the <code>ChadoTransaction</code>
+ * @return number of rows changed
* @throws SQLException
*/
- public void insertFeatureDbxref(final String schema, final ChadoTransaction tsn)
+ public int insertFeatureDbxref(final String schema, final ChadoTransaction tsn)
throws SQLException
{
- Dbxref dbxref = tsn.getFeatureDbxref();
+ final Dbxref dbxref = tsn.getFeatureDbxref();
+ final String uniquename = tsn.getUniqueName();
+
+ // find database id
+ String sql = "SELECT db_id FROM db WHERE name='"+dbxref.getName()+"'";
+
+ Statement st = conn.createStatement();
+ ResultSet rs = st.executeQuery(sql);
+ boolean exists = rs.next();
+
+ final int db_id = rs.getInt("db_id");
+ // find if accession exists already
+ String sqlDbxrefId = "SELECT dbxref_id FROM dbxref WHERE accession='"+
+ dbxref.getAccession()+"' AND db_id="+db_id;
+ appendToLogFile(sqlDbxrefId, sqlLog);
+ rs = st.executeQuery(sqlDbxrefId);
+ exists = rs.next();
+
+ if(!exists)
+ {
+ // create a new accession entry in dbxref
+ sql = "INSERT INTO dbxref ( db_id, accession ) "+
+ "VALUES ("+db_id+", "+dbxref.getAccession()+" )";
+ appendToLogFile(sql, sqlLog);
+ int rowCount = st.executeUpdate(new String(sql));
+
+ // now get the new dbxref_id
+ appendToLogFile(sqlDbxrefId, sqlLog);
+ rs = st.executeQuery(sqlDbxrefId);
+ rs.next();
+ }
+
+ final int dbxref_id = rs.getInt("dbxref_id");
+ sql = "INSERT INTO "+schema+".feature_dbxref "+
+ "(feature_id, dbxref_id, is_current)"+
+ " VALUES "+
+ "( (SELECT feature_id FROM "+schema+
+ ".feature WHERE uniquename='"+uniquename+"'), "+
+ dbxref_id+", "+ Boolean.toString(dbxref.isCurrent())+")";
+ appendToLogFile(sql, sqlLog);
+ return st.executeUpdate(new String(sql));
}
/**
* Delete a dbxref for a feature.
* @param schema schema/organism name or null
* @param tsn the <code>ChadoTransaction</code>
+ * @return number of rows changed
* @throws SQLException
*/
- public void deleteFeatureDbxref(final String schema, final ChadoTransaction tsn)
+ public int deleteFeatureDbxref(final String schema, final ChadoTransaction tsn)
throws SQLException
{
- Dbxref dbxref = tsn.getFeatureDbxref();
+ final Dbxref dbxref = tsn.getFeatureDbxref();
final String uniquename = tsn.getUniqueName();
final String sql =
@@ -757,8 +799,9 @@ public class JdbcDAO
"AND db_id=(SELECT db_id FROM db WHERE name='"+dbxref.getName()+"'))"+
"AND feature_id=(SELECT feature_id FROM "+schema+
".feature WHERE uniquename='"+uniquename+"')";
-
- System.out.println(sql);
+
+ Statement st = conn.createStatement();
+ return st.executeUpdate(sql);
}
/**
diff --git a/uk/ac/sanger/artemis/util/DatabaseDocument.java b/uk/ac/sanger/artemis/util/DatabaseDocument.java
index 0ee5c1304750258aef8b843b0a60bf54a7502133..f4cafbdd63985e8f8218889cb40d6424e873a9dc 100644
--- a/uk/ac/sanger/artemis/util/DatabaseDocument.java
+++ b/uk/ac/sanger/artemis/util/DatabaseDocument.java
@@ -712,6 +712,8 @@ public class DatabaseDocument extends Document
dao.deleteFeature(schema, tsn);
else if(tsn.getType() == ChadoTransaction.DELETE_DBXREF)
dao.deleteFeatureDbxref(schema, tsn);
+ else if(tsn.getType() == ChadoTransaction.INSERT_DBXREF)
+ dao.insertFeatureDbxref(schema, tsn);
}
}
catch (java.sql.SQLException sqlExp)