Coverage Report

Coverage Report - uk.ac.ebi.intenz.mapper.EnzymeCommentMapper

Classes in this File

Line Coverage

Branch Coverage

Complexity

EnzymeCommentMapper

55%

65/117

28%

30/106

4.133

 package uk.ac.ebi.intenz.mapper;
 
 import java.sql.Connection;
 import java.sql.PreparedStatement;
 import java.sql.ResultSet;
 import java.sql.SQLException;
 import java.util.ArrayList;
 import java.util.List;
 
 import org.apache.log4j.Logger;
 
 import uk.ac.ebi.intenz.domain.constants.EnzymeSourceConstant;
 import uk.ac.ebi.intenz.domain.constants.EnzymeViewConstant;
 import uk.ac.ebi.intenz.domain.constants.Status;
 import uk.ac.ebi.intenz.domain.enzyme.EnzymeComment;
 
 /**
  * Maps link information to the corresponding database tables.
  * <p/>
  *
  * @author Michael Darsow
  * @version $Revision: 1.3 $ $Date: 2009/05/26 14:59:09 $
  */
 public class EnzymeCommentMapper {
 
   private static final String COLUMNS = "enzyme_id, comment_text, order_in, status, source, web_view";
 
   private static final Logger LOGGER =
           Logger.getLogger(EnzymeCommentMapper.class.getName());
 
   public EnzymeCommentMapper() {
   }
 
   private String findStatement() {
     return "SELECT " + COLUMNS +
            " FROM comments" +
            " WHERE enzyme_id = ? ORDER BY order_in";
   }
 
   private String exportSibCommentsStatement() {
     return "SELECT " + COLUMNS +
            " FROM comments WHERE enzyme_id = ?" +
            " AND (web_view = ? OR web_view = ? OR web_view = ? OR web_view = ?)" +
            " FOR UPDATE ORDER BY order_in";
   }
 
   private String insertStatement() {
     return "INSERT INTO comments (enzyme_id, comment_text, order_in, status, source, web_view) VALUES (?, ?, ?, ?, ?, ?)";
   }
 
   private String updateStatement() {
     return "UPDATE comments SET comment_text = ?, order_in = ?, status = ?, source = ?, web_view = ? WHERE enzyme_id = ?";
   }
 
   private String deleteAllStatement() {
     return "DELETE comments WHERE enzyme_id = ?";
   }
 
   /**
    * Tries to find comment information about an enzyme.
    *
    * @param enzymeId Enzyme ID of entry.
    * @param con      The logical connection.
    * @return a <code>String</code> representing the comment.
    * @throws SQLException
    */
   public List<EnzymeComment> find(Long enzymeId, Connection con) throws SQLException {
     if (enzymeId == null) throw new NullPointerException("Parameter 'enzymeId' must not be null.");
     if (con == null) throw new NullPointerException("Parameter 'con' must not be null.");
 
     PreparedStatement findStatement = null;
     ResultSet rs = null;
     List<EnzymeComment> result = new ArrayList<EnzymeComment>();
     boolean noResult = true;
 
     try {
       findStatement = con.prepareStatement(findStatement());
       findStatement.setLong(1, enzymeId.longValue());
       rs = findStatement.executeQuery();
       while (rs.next()) {
         noResult = false;
         EnzymeComment enzymeComment = doLoad(rs);
         result.add(enzymeComment);
       }
     } finally {
             if (rs != null) rs.close();
       if (findStatement != null) findStatement.close();
     }
 
     if (noResult) {
       LOGGER.debug("No comment information found for the enzyme with ID "
               + enzymeId);
       return null;
     }
     return result;
   }
 
   /**
    * Exports all comments which are displayed in the ENZYME view.
    *
    * Affected table rows will be locked.
    *
    * @param enzymeId The enzyme ID used to retreive the related comments.
    * @param con The database connection.
    * @return an {@link java.util.ArrayList} of comments or <code>null</code> if no comment could be found.
    * @throws SQLException if a database error occured.
    * @throws NullPointerException if either of the parameters is <code>null</code>.
    */
   public List<EnzymeComment> exportSibComments(Long enzymeId, Connection con) throws SQLException {
     if (enzymeId == null) throw new NullPointerException("Parameter 'enzymeId' must not be null.");
     if (con == null) throw new NullPointerException("Parameter 'con' must not be null.");
 
     PreparedStatement findStatement = null;
     ResultSet rs = null;
     List<EnzymeComment> result = new ArrayList<EnzymeComment>();
     boolean noResult = true;
 
     try {
       findStatement = con.prepareStatement(exportSibCommentsStatement());
       findStatement.setLong(1, enzymeId.longValue());
       findStatement.setString(2, EnzymeViewConstant.INTENZ.toString());
       findStatement.setString(3, EnzymeViewConstant.IUBMB_SIB.toString());
       findStatement.setString(4, EnzymeViewConstant.SIB.toString());
       findStatement.setString(5, EnzymeViewConstant.SIB_INTENZ.toString());
       rs = findStatement.executeQuery();
       while (rs.next()) {
         noResult = false;
         EnzymeComment enzymeComment = doLoad(rs);
         result.add(enzymeComment);
       }
     } finally {
             if (rs != null) rs.close();
         if (findStatement != null) findStatement.close();
     }
 
     if (noResult) return null;
     return result;
   }
 
   public void reload(List<EnzymeComment> comments, Long enzymeId, Status status, Connection con)
           throws SQLException {
     deleteAll(enzymeId, con);
     insert(comments, enzymeId, status, con);
   }
 
   /**
    * Deletes all comments related to an enzyme instance.
    *
    * @param enzymeId Enzyme ID of the enzyme instance.
    * @param con      A database connection.
    * @throws SQLException if a database error occurs.
    * @throws NullPointerException if any of the parameter is <code>null</code>.
    */
   public void deleteAll(Long enzymeId, Connection con) throws SQLException {
     if (enzymeId == null) throw new NullPointerException("Parameter 'enzymeId' must not be null.");
     if (con == null) throw new NullPointerException("Parameter 'con' must not be null.");
 
     PreparedStatement deleteAllStatement = null;
 
     try {
       deleteAllStatement = con.prepareStatement(deleteAllStatement());
       deleteAllStatement.setLong(1, enzymeId.longValue());
       deleteAllStatement.execute();
     } finally {
       if (deleteAllStatement != null) deleteAllStatement.close();
     }
   }
 
   /**
    * Stores the given comment into the database.
    *
    * @param comments The enzyme's comment.
    * @param enzymeId The enzyme ID.
    * @param status   ...
    * @param con      ...
    * @throws SQLException
    */
   public void insert(List<EnzymeComment> comments, Long enzymeId, Status status, Connection con)
           throws SQLException {
     if (comments == null) throw new NullPointerException("Parameter 'comments' must not be null.");
     if (enzymeId == null) throw new NullPointerException("Parameter 'enzymeId' must not be null.");
     if (status == null) throw new NullPointerException("Parameter 'status' must not be null.");
     if (con == null) throw new NullPointerException("Parameter 'con' must not be null.");
 
     PreparedStatement insertStatement = null;
     try {
       insertStatement = con.prepareStatement(insertStatement());
       for (int iii = 0; iii < comments.size(); iii++) {
         EnzymeComment enzymeComment = comments.get(iii);
         doInsert(enzymeComment, enzymeId, (iii+1), status, insertStatement);
         insertStatement.execute();
       }
     } finally {
       if (insertStatement != null) insertStatement.close();
     }
   }
 
   public void update(EnzymeComment comment, Long enzymeId, Status status, int orderIn, Connection con) throws SQLException {
     if (comment == null) throw new NullPointerException("Parameter 'comment' must not be null.");
     if (enzymeId == null) throw new NullPointerException("Parameter 'enzymeId' must not be null.");
     if (status == null) throw new NullPointerException("Parameter 'status' must not be null.");
     if (orderIn < 1) throw new IllegalArgumentException("Parameter 'orderIn' must not be > 0.");
     if (con == null) throw new NullPointerException("Parameter 'con' must not be null.");
 
     PreparedStatement updateStatement = null;
     try {
       updateStatement = con.prepareStatement(updateStatement());
       doUpdate(comment, enzymeId, status, orderIn, updateStatement);
       updateStatement.execute();
     } finally {
       if (updateStatement != null) updateStatement.close();
     }
   }
 
   // ------------------- PRIVATE METHODS ------------------------
 
   /**
    * Creates the <code>EnzymeComment</code> object from the given result set.
    *
    * @param rs The result set object.
    * @return an <code>EnzymeComment</code> instance.
    * @throws SQLException
    */
   private EnzymeComment doLoad(ResultSet rs) throws SQLException {
     assert rs != null : "Parameter 'rs' must not be null.";
 
     String comment = "";
     String source = "";
     String webView = "";
     if (rs.getString("comment_text") != null) comment = rs.getString("comment_text");
     if (rs.getString("source") != null) source = rs.getString("source");
     if (rs.getString("web_view") != null) webView = rs.getString("web_view");
 
     EnzymeComment enzymeComment = new EnzymeComment(comment, EnzymeSourceConstant.valueOf(source),
                                                     EnzymeViewConstant.valueOf(webView));
 
     return enzymeComment;
   }
 
   /**
    * Sets the parameters of the prepared statement.
    *
    * @param comment         ...
    * @param enzymeId        ...
    * @param status          ...
    * @param insertStatement ...
    * @throws SQLException
    */
   private void doInsert(EnzymeComment comment, Long enzymeId, int orderIn, Status status,
                         PreparedStatement insertStatement)
           throws SQLException {
     assert comment != null : "Parameter 'comment' must not be null.";
     assert enzymeId != null : "Parameter 'enzymeId' must not be null.";
     assert status != null : "Parameter 'status' must not be null.";
     assert insertStatement != null : "Parameter 'insertStatement' must not be null.";
 
     insertStatement.setLong(1, enzymeId.longValue());
     insertStatement.setString(2, comment.getCommentText());
     insertStatement.setInt(3, orderIn);
     insertStatement.setString(4, status.getCode());
     insertStatement.setString(5, comment.getSource().toString());
     insertStatement.setString(6, comment.getView().toString());
   }
 
   private void doUpdate(EnzymeComment comment, Long enzymeId, Status status, int orderIn,
                         PreparedStatement updateStatement)
           throws SQLException {
     assert comment != null : "Parameter 'comment' must not be null.";
     assert enzymeId != null : "Parameter 'enzymeId' must not be null.";
     assert status != null : "Parameter 'status' must not be null.";
     assert orderIn > 0 : "Parameter 'orderIn' must not be > 0.";
     assert updateStatement != null : "Parameter 'insertStatement' must not be null.";
 
     updateStatement.setString(1, comment.getCommentText());
     updateStatement.setInt(2, orderIn);
     updateStatement.setString(3, status.getCode());
     updateStatement.setString(4, comment.getSource().toString());
     updateStatement.setString(5, comment.getView().toString());
     updateStatement.setLong(6, enzymeId.longValue());
   }
 }

1		package uk.ac.ebi.intenz.mapper;
2
3		import java.sql.Connection;
4		import java.sql.PreparedStatement;
5		import java.sql.ResultSet;
6		import java.sql.SQLException;
7		import java.util.ArrayList;
8		import java.util.List;
9
10		import org.apache.log4j.Logger;
11
12		import uk.ac.ebi.intenz.domain.constants.EnzymeSourceConstant;
13		import uk.ac.ebi.intenz.domain.constants.EnzymeViewConstant;
14		import uk.ac.ebi.intenz.domain.constants.Status;
15		import uk.ac.ebi.intenz.domain.enzyme.EnzymeComment;
16
17		/**
18		* Maps link information to the corresponding database tables.
19		* <p/>
20		*
21		* @author Michael Darsow
22		* @version $Revision: 1.3 $ $Date: 2009/05/26 14:59:09 $
23		*/
24	1	public class EnzymeCommentMapper {
25
26		private static final String COLUMNS = "enzyme_id, comment_text, order_in, status, source, web_view";
27
28	1	private static final Logger LOGGER =
29		Logger.getLogger(EnzymeCommentMapper.class.getName());
30
31	2	public EnzymeCommentMapper() {
32	2	}
33
34		private String findStatement() {
35	2	return "SELECT " + COLUMNS +
36		" FROM comments" +
37		" WHERE enzyme_id = ? ORDER BY order_in";
38		}
39
40		private String exportSibCommentsStatement() {
41	0	return "SELECT " + COLUMNS +
42		" FROM comments WHERE enzyme_id = ?" +
43		" AND (web_view = ? OR web_view = ? OR web_view = ? OR web_view = ?)" +
44		" FOR UPDATE ORDER BY order_in";
45		}
46
47		private String insertStatement() {
48	1	return "INSERT INTO comments (enzyme_id, comment_text, order_in, status, source, web_view) VALUES (?, ?, ?, ?, ?, ?)";
49		}
50
51		private String updateStatement() {
52	0	return "UPDATE comments SET comment_text = ?, order_in = ?, status = ?, source = ?, web_view = ? WHERE enzyme_id = ?";
53		}
54
55		private String deleteAllStatement() {
56	2	return "DELETE comments WHERE enzyme_id = ?";
57		}
58
59		/**
60		* Tries to find comment information about an enzyme.
61		*
62		* @param enzymeId Enzyme ID of entry.
63		* @param con The logical connection.
64		* @return a <code>String</code> representing the comment.
65		* @throws SQLException
66		*/
67		public List<EnzymeComment> find(Long enzymeId, Connection con) throws SQLException {
68	2	if (enzymeId == null) throw new NullPointerException("Parameter 'enzymeId' must not be null.");
69	2	if (con == null) throw new NullPointerException("Parameter 'con' must not be null.");
70
71	2	PreparedStatement findStatement = null;
72	2	ResultSet rs = null;
73	2	List<EnzymeComment> result = new ArrayList<EnzymeComment>();
74	2	boolean noResult = true;
75
76		try {
77	2	findStatement = con.prepareStatement(findStatement());
78	2	findStatement.setLong(1, enzymeId.longValue());
79	2	rs = findStatement.executeQuery();
80	5	while (rs.next()) {
81	3	noResult = false;
82	3	EnzymeComment enzymeComment = doLoad(rs);
83	3	result.add(enzymeComment);
84	3	}
85		} finally {
86	2	if (rs != null) rs.close();
87	2	if (findStatement != null) findStatement.close();
88		}
89
90	2	if (noResult) {
91	0	LOGGER.debug("No comment information found for the enzyme with ID "
92		+ enzymeId);
93	0	return null;
94		}
95	2	return result;
96		}
97
98		/**
99		* Exports all comments which are displayed in the ENZYME view.
100		*
101		* Affected table rows will be locked.
102		*
103		* @param enzymeId The enzyme ID used to retreive the related comments.
104		* @param con The database connection.
105		* @return an {@link java.util.ArrayList} of comments or <code>null</code> if no comment could be found.
106		* @throws SQLException if a database error occured.
107		* @throws NullPointerException if either of the parameters is <code>null</code>.
108		*/
109		public List<EnzymeComment> exportSibComments(Long enzymeId, Connection con) throws SQLException {
110	0	if (enzymeId == null) throw new NullPointerException("Parameter 'enzymeId' must not be null.");
111	0	if (con == null) throw new NullPointerException("Parameter 'con' must not be null.");
112
113	0	PreparedStatement findStatement = null;
114	0	ResultSet rs = null;
115	0	List<EnzymeComment> result = new ArrayList<EnzymeComment>();
116	0	boolean noResult = true;
117
118		try {
119	0	findStatement = con.prepareStatement(exportSibCommentsStatement());
120	0	findStatement.setLong(1, enzymeId.longValue());
121	0	findStatement.setString(2, EnzymeViewConstant.INTENZ.toString());
122	0	findStatement.setString(3, EnzymeViewConstant.IUBMB_SIB.toString());
123	0	findStatement.setString(4, EnzymeViewConstant.SIB.toString());
124	0	findStatement.setString(5, EnzymeViewConstant.SIB_INTENZ.toString());
125	0	rs = findStatement.executeQuery();
126	0	while (rs.next()) {
127	0	noResult = false;
128	0	EnzymeComment enzymeComment = doLoad(rs);
129	0	result.add(enzymeComment);
130	0	}
131		} finally {
132	0	if (rs != null) rs.close();
133	0	if (findStatement != null) findStatement.close();
134		}
135
136	0	if (noResult) return null;
137	0	return result;
138		}
139
140		public void reload(List<EnzymeComment> comments, Long enzymeId, Status status, Connection con)
141		throws SQLException {
142	0	deleteAll(enzymeId, con);
143	0	insert(comments, enzymeId, status, con);
144	0	}
145
146		/**
147		* Deletes all comments related to an enzyme instance.
148		*
149		* @param enzymeId Enzyme ID of the enzyme instance.
150		* @param con A database connection.
151		* @throws SQLException if a database error occurs.
152		* @throws NullPointerException if any of the parameter is <code>null</code>.
153		*/
154		public void deleteAll(Long enzymeId, Connection con) throws SQLException {
155	2	if (enzymeId == null) throw new NullPointerException("Parameter 'enzymeId' must not be null.");
156	2	if (con == null) throw new NullPointerException("Parameter 'con' must not be null.");
157
158	2	PreparedStatement deleteAllStatement = null;
159
160		try {
161	2	deleteAllStatement = con.prepareStatement(deleteAllStatement());
162	2	deleteAllStatement.setLong(1, enzymeId.longValue());
163	2	deleteAllStatement.execute();
164		} finally {
165	2	if (deleteAllStatement != null) deleteAllStatement.close();
166		}
167	2	}
168
169		/**
170		* Stores the given comment into the database.
171		*
172		* @param comments The enzyme's comment.
173		* @param enzymeId The enzyme ID.
174		* @param status ...
175		* @param con ...
176		* @throws SQLException
177		*/
178		public void insert(List<EnzymeComment> comments, Long enzymeId, Status status, Connection con)
179		throws SQLException {
180	1	if (comments == null) throw new NullPointerException("Parameter 'comments' must not be null.");
181	1	if (enzymeId == null) throw new NullPointerException("Parameter 'enzymeId' must not be null.");
182	1	if (status == null) throw new NullPointerException("Parameter 'status' must not be null.");
183	1	if (con == null) throw new NullPointerException("Parameter 'con' must not be null.");
184
185	1	PreparedStatement insertStatement = null;
186		try {
187	1	insertStatement = con.prepareStatement(insertStatement());
188	2	for (int iii = 0; iii < comments.size(); iii++) {
189	1	EnzymeComment enzymeComment = comments.get(iii);
190	1	doInsert(enzymeComment, enzymeId, (iii+1), status, insertStatement);
191	1	insertStatement.execute();
192		}
193		} finally {
194	1	if (insertStatement != null) insertStatement.close();
195		}
196	1	}
197
198		public void update(EnzymeComment comment, Long enzymeId, Status status, int orderIn, Connection con) throws SQLException {
199	0	if (comment == null) throw new NullPointerException("Parameter 'comment' must not be null.");
200	0	if (enzymeId == null) throw new NullPointerException("Parameter 'enzymeId' must not be null.");
201	0	if (status == null) throw new NullPointerException("Parameter 'status' must not be null.");
202	0	if (orderIn < 1) throw new IllegalArgumentException("Parameter 'orderIn' must not be > 0.");
203	0	if (con == null) throw new NullPointerException("Parameter 'con' must not be null.");
204
205	0	PreparedStatement updateStatement = null;
206		try {
207	0	updateStatement = con.prepareStatement(updateStatement());
208	0	doUpdate(comment, enzymeId, status, orderIn, updateStatement);
209	0	updateStatement.execute();
210		} finally {
211	0	if (updateStatement != null) updateStatement.close();
212		}
213	0	}
214
215		// ------------------- PRIVATE METHODS ------------------------
216
217		/**
218		* Creates the <code>EnzymeComment</code> object from the given result set.
219		*
220		* @param rs The result set object.
221		* @return an <code>EnzymeComment</code> instance.
222		* @throws SQLException
223		*/
224		private EnzymeComment doLoad(ResultSet rs) throws SQLException {
225	3	assert rs != null : "Parameter 'rs' must not be null.";
226
227	3	String comment = "";
228	3	String source = "";
229	3	String webView = "";
230	3	if (rs.getString("comment_text") != null) comment = rs.getString("comment_text");
231	3	if (rs.getString("source") != null) source = rs.getString("source");
232	3	if (rs.getString("web_view") != null) webView = rs.getString("web_view");
233
234	3	EnzymeComment enzymeComment = new EnzymeComment(comment, EnzymeSourceConstant.valueOf(source),
235		EnzymeViewConstant.valueOf(webView));
236
237	3	return enzymeComment;
238		}
239
240		/**
241		* Sets the parameters of the prepared statement.
242		*
243		* @param comment ...
244		* @param enzymeId ...
245		* @param status ...
246		* @param insertStatement ...
247		* @throws SQLException
248		*/
249		private void doInsert(EnzymeComment comment, Long enzymeId, int orderIn, Status status,
250		PreparedStatement insertStatement)
251		throws SQLException {
252	1	assert comment != null : "Parameter 'comment' must not be null.";
253	1	assert enzymeId != null : "Parameter 'enzymeId' must not be null.";
254	1	assert status != null : "Parameter 'status' must not be null.";
255	1	assert insertStatement != null : "Parameter 'insertStatement' must not be null.";
256
257	1	insertStatement.setLong(1, enzymeId.longValue());
258	1	insertStatement.setString(2, comment.getCommentText());
259	1	insertStatement.setInt(3, orderIn);
260	1	insertStatement.setString(4, status.getCode());
261	1	insertStatement.setString(5, comment.getSource().toString());
262	1	insertStatement.setString(6, comment.getView().toString());
263	1	}
264
265		private void doUpdate(EnzymeComment comment, Long enzymeId, Status status, int orderIn,
266		PreparedStatement updateStatement)
267		throws SQLException {
268	0	assert comment != null : "Parameter 'comment' must not be null.";
269	0	assert enzymeId != null : "Parameter 'enzymeId' must not be null.";
270	0	assert status != null : "Parameter 'status' must not be null.";
271	0	assert orderIn > 0 : "Parameter 'orderIn' must not be > 0.";
272	0	assert updateStatement != null : "Parameter 'insertStatement' must not be null.";
273
274	0	updateStatement.setString(1, comment.getCommentText());
275	0	updateStatement.setInt(2, orderIn);
276	0	updateStatement.setString(3, status.getCode());
277	0	updateStatement.setString(4, comment.getSource().toString());
278	0	updateStatement.setString(5, comment.getView().toString());
279	0	updateStatement.setLong(6, enzymeId.longValue());
280	0	}
281		}