more docs and checks

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@4273 ee4ac58c-ac51-4696-9907-e4b3aa274f04

uk/ac/sanger/artemis/chado/ChadoTransactionManager.java

@@ -557,7 +557,8 @@ public class ChadoTransactionManager
    **/
   public void commit(DatabaseDocument dbDoc)
   {
-    dbDoc.commit(sql);
+    int retVal = dbDoc.commit(sql);
+    if(retVal == 0)
       sql = new Vector();
   }
 }

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());
     

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();
@@ -702,13 +697,13 @@ 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>.
    * @param schema      schema/organism name or null
    * @param tsn         the <code>ChadoTransaction</code>
@@ -721,6 +716,7 @@ public class JdbcDAO
   {
     String sql = "DELETE FROM "+schema+".feature WHERE uniquename='"+
                  tsn.getUniqueName()+"'";
+    appendToLogFile(sql, sqlLog);
     
     Statement st = conn.createStatement();
     return st.executeUpdate(sql);
@@ -746,6 +742,12 @@ public class JdbcDAO
     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
     String sqlDbxrefId = "SELECT dbxref_id FROM dbxref WHERE accession='"+

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
   }
 
   /**
-   *
    * 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[])