diff --git a/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java b/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java
index 2e2582de675201d6027559f1c92bcc3c03b01977..70a08e2bcc6297c403064c053d64d2723d897d52 100644
--- a/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java
+++ b/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java
@@ -557,8 +557,9 @@ public class ChadoTransactionManager
**/
public void commit(DatabaseDocument dbDoc)
{
- dbDoc.commit(sql);
- sql = new Vector();
+ int retVal = dbDoc.commit(sql);
+ if(retVal == 0)
+ sql = new Vector();
}
}
diff --git a/uk/ac/sanger/artemis/chado/IBatisDAO.java b/uk/ac/sanger/artemis/chado/IBatisDAO.java
index 9df0b7a3a8b3978a2025c08be08601ab60728710..e313e049cbe0cbff9d0b02d8abe39782d3d6caaa 100644
--- a/uk/ac/sanger/artemis/chado/IBatisDAO.java
+++ b/uk/ac/sanger/artemis/chado/IBatisDAO.java
@@ -42,12 +42,10 @@ import javax.swing.JPasswordField;
public class IBatisDAO implements ChadoDAO
{
/**
- *
* Define a iBatis data access object. This uses <code>DbSqlConfig</code>
* to read the configuration in. The system property <quote>chado</quote>
* can be used to define the database location <i>e.g.</i>
* -Dchado=host:port/database?user
- *
*/
public IBatisDAO(final JPasswordField pfield)
{
@@ -372,7 +370,6 @@ public class IBatisDAO implements ChadoDAO
/**
- *
* Delete a feature from the database defined by the <code>ChadoTransaction</code>.
* @param schema schema/organism name or null
* @param tsn the <code>ChadoTransaction</code>
@@ -404,6 +401,11 @@ public class IBatisDAO implements ChadoDAO
Dbxref dbxref = tsn.getFeatureDbxref();
SqlMapClient sqlMap = DbSqlConfig.getSqlMapInstance();
Integer db_id = (Integer)sqlMap.queryForObject("getDbId", dbxref);
+ if(db_id == null)
+ throw new SQLException("No database called "+
+ dbxref.getName()+" found (for "+
+ tsn.getUniqueName()+
+ ") check the spelling!");
dbxref.setDb_id(db_id.intValue());
diff --git a/uk/ac/sanger/artemis/chado/JdbcDAO.java b/uk/ac/sanger/artemis/chado/JdbcDAO.java
index 151d89880cb5fb76352b83fdae5dc88664c8e7b3..8ad1db6c72ac153bc6ff2033d7c65f9a1aa901a8 100644
--- a/uk/ac/sanger/artemis/chado/JdbcDAO.java
+++ b/uk/ac/sanger/artemis/chado/JdbcDAO.java
@@ -636,19 +636,15 @@ public class JdbcDAO
//
// get the organism_id
Statement st = conn.createStatement();
- String str_sql = "SELECT organism_id from " + schema +
+ String sql = "SELECT organism_id from " + schema +
".feature where feature_id = '" + srcfeature_id + "'";
- System.out.println(str_sql);
- appendToLogFile(str_sql, sqlLog);
-
- ResultSet rs = st.executeQuery(str_sql);
+ appendToLogFile(sql, sqlLog);
+ ResultSet rs = st.executeQuery(sql);
rs.next();
final int organism_id = rs.getInt("organism_id");
- //
- // insert feature into feature table
ChadoFeature chadoFeature = tsn.getChadoFeature();
// insert new feature into feature table
StringBuffer sql_buff = new StringBuffer();
@@ -666,21 +662,20 @@ public class JdbcDAO
sql_buff.append(Long.toString(chadoFeature.getType_id()));
sql_buff.append(" )");
- System.out.println(new String(sql_buff));
+ sql = new String(sql_buff);
+ appendToLogFile(sql, sqlLog);
st = conn.createStatement();
- int rowCount = st.executeUpdate(new String(sql_buff));
+ int rowCount = st.executeUpdate(sql);
//
// get the current feature_id sequence value
- String sql = "SELECT currval('"+schema+".feature_feature_id_seq')";
- System.out.println(sql);
+ sql = "SELECT currval('"+schema+".feature_feature_id_seq')";
+ appendToLogFile(sql, sqlLog);
rs = st.executeQuery(sql);
rs.next();
final int feature_id = rs.getInt("currval");
-
-// System.out.println("SELECT currval('"+schema+".featureprop_featureprop_id_seq')");
-
+
//
// insert feature location into featureloc
sql_buff = new StringBuffer();
@@ -702,14 +697,14 @@ public class JdbcDAO
sql_buff.append(chadoFeature.getPhase());
sql_buff.append(" )");
- System.out.println(new String(sql_buff));
+ sql = new String(sql_buff);
+ appendToLogFile(sql, sqlLog);
st = conn.createStatement();
- rowCount = st.executeUpdate(new String(sql_buff));
+ rowCount = st.executeUpdate(sql);
}
/**
- *
- * Delete a feature from the database defined by the <code>ChadoTransaction</code>.
+ * Delete a feature from the database defined by the <code>ChadoTransaction</code>.
* @param schema schema/organism name or null
* @param tsn the <code>ChadoTransaction</code>
* @return number of rows deleted
@@ -721,7 +716,8 @@ public class JdbcDAO
{
String sql = "DELETE FROM "+schema+".feature WHERE uniquename='"+
tsn.getUniqueName()+"'";
-
+ appendToLogFile(sql, sqlLog);
+
Statement st = conn.createStatement();
return st.executeUpdate(sql);
}
@@ -745,6 +741,12 @@ public class JdbcDAO
Statement st = conn.createStatement();
ResultSet rs = st.executeQuery(sql);
boolean exists = rs.next();
+
+ if(!exists)
+ throw new SQLException("No database called "+
+ dbxref.getName()+
+ " found (for "+uniquename+
+ ") check the spelling!");
final int db_id = rs.getInt("db_id");
// find if accession exists already
diff --git a/uk/ac/sanger/artemis/util/DatabaseDocument.java b/uk/ac/sanger/artemis/util/DatabaseDocument.java
index 45886b76390b0829852f98d4d67ac046ebcc88bc..f1de62bfced081f5326ab065bcdf93c70cf21151 100644
--- a/uk/ac/sanger/artemis/util/DatabaseDocument.java
+++ b/uk/ac/sanger/artemis/util/DatabaseDocument.java
@@ -346,9 +346,12 @@ public class DatabaseDocument extends Document
}
/**
- *
- * Create an array of GFF-like lines
- *
+ * Create an array of GFF lines.
+ * @param dao the data access object
+ * @param parentFeatureID the parent identifier for the features to
+ * extract
+ * @return the <code>ByteBuffer</code> array of GFF lines
+ * @throws java.sql.SQLException
*/
private ByteBuffer[] getGff(ChadoDAO dao, String parentFeatureID)
throws java.sql.SQLException
@@ -433,9 +436,6 @@ public class DatabaseDocument extends Document
this_buff.append("timelastmodified=" + timelastmodified + ";");
-// String value = "";
-// if(feat.getValue() != null)
-// value = GFFStreamFeature.encode(feat.getValue());
// attributes
Hashtable qualifiers = feat.getQualifiers();
@@ -481,6 +481,11 @@ public class DatabaseDocument extends Document
}
+ /**
+ * Look up the cvterm_id for a controlled vocabulary name.
+ * @param name
+ * @return
+ */
public static Long getCvtermID(String name)
{
Enumeration enum_cvterm = cvterm.keys();
@@ -495,9 +500,9 @@ public class DatabaseDocument extends Document
}
/**
- *
- * Lookup a cvterm name from the collection of cvterms.
- *
+ * Look up a cvterm name from the collection of cvterms.
+ * @param id a cvterm_id
+ * @return the cvterm name
*/
private String getCvtermName(long id)
{
@@ -521,9 +526,9 @@ public class DatabaseDocument extends Document
}
/**
- *
* Look up cvterms names and id and return in a hashtable.
- *
+ * @param dao the data access object
+ * @return the cvterm <code>Hashtable</code>
*/
private Hashtable getCvterm(ChadoDAO dao)
{
@@ -549,6 +554,13 @@ public class DatabaseDocument extends Document
return cvterm;
}
+ /**
+ * Get the sequence for a feature.
+ * @param dao the data access object
+ * @param buff the buffer to add the sequence to
+ * @return the resulting buffer
+ * @throws java.sql.SQLException
+ */
private ByteBuffer getSequence(ChadoDAO dao, ByteBuffer buff)
throws java.sql.SQLException
{
@@ -572,12 +584,10 @@ public class DatabaseDocument extends Document
}
/**
- *
* Create a hashtable of the available entries with residues.
* @return a <code>Hashtable</code> of the <code>String</code>
* representation (schema-type-feature_name) and the
* corresponding feature_id
- *
*/
public Hashtable getDatabaseEntries()
{
@@ -629,9 +639,10 @@ public class DatabaseDocument extends Document
/**
*
* Make a connetion with the jdbc
- * jdbc:postgresql://localhost:13001/chadoCVS?user=es2
+ * jdbc:postgresql://host:port/database?user
*
*/
+ /**
public Connection getConnection() throws java.sql.SQLException,
java.net.ConnectException
{
@@ -645,12 +656,11 @@ public class DatabaseDocument extends Document
location.substring(index + 6),
new String(pfield.getPassword()));
}
-
+ */
+
/**
- *
* Get the data access object (DAO).
* @return data access object
- *
*/
private ChadoDAO getDAO()
throws java.net.ConnectException, SQLException
@@ -695,14 +705,20 @@ public class DatabaseDocument extends Document
return file_output_stream;
}
-
- public void commit(Vector sql)
+ /**
+ * Commit the <code>ChadoTransaction</code> SQL back to the
+ * database.
+ * @param sql the collection of <code>ChadoTransaction</code> objects
+ * @return
+ */
+ public int commit(Vector sql)
{
+ int i = 0;
try
{
ChadoDAO dao = getDAO();
- for(int i = 0; i < sql.size(); i++)
+ for(i = 0; i < sql.size(); i++)
{
ChadoTransaction tsn = (ChadoTransaction) sql.get(i);
@@ -730,9 +746,9 @@ public class DatabaseDocument extends Document
}
catch (java.sql.SQLException sqlExp)
{
- JOptionPane.showMessageDialog(null, "Problems Writing",
- "Problems Writing to Database "+
+ JOptionPane.showMessageDialog(null, "Problems Writing...\n" +
sqlExp.getMessage(),
+ "Problems Writing to Database ",
JOptionPane.ERROR_MESSAGE);
sqlExp.printStackTrace();
}
@@ -744,7 +760,7 @@ public class DatabaseDocument extends Document
JOptionPane.ERROR_MESSAGE);
conn_ex.printStackTrace();
}
-
+ return i;
}
public static void main(String args[])