Coverage Report

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

Classes in this File

Line Coverage

Branch Coverage

Complexity

EnzymeClassMapper

0/64

0/46

4.25

 package uk.ac.ebi.intenz.mapper;
 
 import java.sql.Connection;
 import java.sql.PreparedStatement;
 import java.sql.ResultSet;
 import java.sql.SQLException;
 import java.sql.Statement;
 import java.util.ArrayList;
 import java.util.List;
 
 import org.apache.log4j.Logger;
 
 import uk.ac.ebi.intenz.domain.enzyme.EnzymeClass;
 import uk.ac.ebi.intenz.domain.enzyme.EnzymeCommissionNumber;
 import uk.ac.ebi.intenz.domain.enzyme.EnzymeSubclass;
 import uk.ac.ebi.intenz.domain.exceptions.DomainException;
 import uk.ac.ebi.intenz.domain.exceptions.EcException;
 
 /**
  * Maps enzyme class information to the corresponding database tables.
  *
  * @author Michael Darsow
  * @version $Revision: 1.3 $ $Date: 2009/05/26 14:59:09 $
  */
 public class EnzymeClassMapper {
 
   private static final String COLUMNS = "ec1, name, description";
   
   private static final String SELECT_ALL = "SELECT " + COLUMNS + " FROM classes";
 
   private static final Logger LOGGER =
           Logger.getLogger(EnzymeClassMapper.class.getName());
 
   public EnzymeClassMapper() {
   }
 
   private String findStatement() {
     return "SELECT " + COLUMNS + " FROM classes WHERE ec1 = ?";
   }
 
   private String findNumberOfClassesStatement() {
     return "SELECT count(*) AS count FROM classes";
   }
 
   /**
    * Tries to find Class information about an enzyme.
    *
    * @param ec1 Number of class to search for.
    * @param con The logical connection.
    * @return an <code>EnzymeClass</code> instance or <code>null</code> if nothing has been found.
    * @throws NullPointerException if any of the parameters is <code>null</code>.
    * @throws SQLException         if a database error occurs.
    * @throws DomainException      if any error related to domain information occurs (e.g. <code>ec1</code> is invalid).
    */
   public EnzymeClass find(String ec1, Connection con) throws SQLException, DomainException {
     if (ec1 == null) throw new NullPointerException("Parameter 'ec1' must not be null.");
     if (con == null) throw new NullPointerException("Parameter 'con' must not be null.");
     PreparedStatement findStatement = null;
     ResultSet rs = null;
     EnzymeClass result = null;
     List<EnzymeSubclass> subclasses;
 
     // Get subclasses.
     EnzymeSubclassMapper subclassMapper = new EnzymeSubclassMapper();
     subclasses = subclassMapper.findList(ec1, con);
 
     try {
       findStatement = con.prepareStatement(findStatement());
       findStatement.setString(1, ec1);
       rs = findStatement.executeQuery();
       if (rs.next()) {
         result = doLoad(rs, subclasses);
       } else {
         LOGGER.warn("No class information found for EC " + ec1);
       }
     } finally {
             if (rs != null) rs.close();
       if (findStatement != null) findStatement.close();
     }
 
     return result;
   }
   
   /**
    * 
    * @param con
    * @return A <code>List</code> of all the <code>EnzymeClass</code>es
    *    (without subclass information)
  * @throws SQLException 
  * @throws EcException 
    */
   public List<EnzymeClass> findAll(Connection con) throws SQLException, DomainException{
       List<EnzymeClass> result = new ArrayList<EnzymeClass>();
       Statement stm = null;
       ResultSet rs = null;
       try {
           stm = con.createStatement();
           rs = stm.executeQuery("SELECT ec1 FROM classes");
           while (rs.next()){
               result.add(find(rs.getString(1), con));
           }
       } finally {
               if (rs != null) rs.close();
           if (stm != null) stm.close();
       }
       return result;
   }
 
   /**
    * Finds the number of classes.
    *
    * @param con The logical connection.
    * @return the number of classes.
    * @throws SQLException
    */
   public int findNumberOfClasses(Connection con) throws SQLException {
     if (con == null) throw new NullPointerException("Parameter 'con' must not be null.");
     PreparedStatement findStatement = null;
     ResultSet rs = null;
     int number = 0;
 
     try {
       findStatement = con.prepareStatement(findNumberOfClassesStatement());
       rs = findStatement.executeQuery();
       if (rs.next()) {
         number = Integer.parseInt(rs.getString("count"));
       }
     } finally {
               if (rs != null) rs.close();
               if (findStatement != null) findStatement.close();
     }
 
     return number;
   }
 
   /**
    * Checks if the given class number is valid.
    *
    * @param ec1 The class number.
    * @param con The connection.
    * @return <code>true</code> if the class exists.
    * @throws SQLException
    */
   public boolean classExists(String ec1, Connection con) throws SQLException {
     if (ec1 == null) throw new NullPointerException("Parameter 'ec1' must not be null.");
     if (con == null) throw new NullPointerException("Parameter 'con' must not be null.");
     PreparedStatement findStatement = null;
     ResultSet rs = null;
     try {
       findStatement = con.prepareStatement(findStatement());
       findStatement.setString(1, ec1);
       rs = findStatement.executeQuery();
       if (rs.next()) {
         return true;
       }
     } finally {
               if (rs != null) rs.close();
               if (findStatement != null) findStatement.close();
     }
 
     return false;
   }
 
   // ------------------- PRIVATE METHODS ------------------------
 
   /**
    * Creates the <code>EnzymeClass</code> object.
    *
    * @param rs The result set object.
    * @return an <code>EnzymeClass</code> instance.
    * @throws SQLException
    */
   private EnzymeClass doLoad(ResultSet rs, List<EnzymeSubclass> subclasses)
   throws SQLException, EcException {
     assert rs != null;
     
     int ec1 = 0;
     String name = "";
     String description = "";
 
     if (rs.getInt("ec1") > 0) ec1 = rs.getInt("ec1");
     if (rs.getString("name") != null) name = rs.getString("name");
     if (rs.getString("description") != null) description = rs.getString("description");
 
     EnzymeCommissionNumber ec = EnzymeCommissionNumber.valueOf(ec1);
     return EnzymeClass.valueOf(ec, name, description, subclasses);
   }
 }

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.sql.Statement;
8		import java.util.ArrayList;
9		import java.util.List;
10
11		import org.apache.log4j.Logger;
12
13		import uk.ac.ebi.intenz.domain.enzyme.EnzymeClass;
14		import uk.ac.ebi.intenz.domain.enzyme.EnzymeCommissionNumber;
15		import uk.ac.ebi.intenz.domain.enzyme.EnzymeSubclass;
16		import uk.ac.ebi.intenz.domain.exceptions.DomainException;
17		import uk.ac.ebi.intenz.domain.exceptions.EcException;
18
19		/**
20		* Maps enzyme class information to the corresponding database tables.
21		*
22		* @author Michael Darsow
23		* @version $Revision: 1.3 $ $Date: 2009/05/26 14:59:09 $
24		*/
25	0	public class EnzymeClassMapper {
26
27		private static final String COLUMNS = "ec1, name, description";
28
29		private static final String SELECT_ALL = "SELECT " + COLUMNS + " FROM classes";
30
31	0	private static final Logger LOGGER =
32		Logger.getLogger(EnzymeClassMapper.class.getName());
33
34	0	public EnzymeClassMapper() {
35	0	}
36
37		private String findStatement() {
38	0	return "SELECT " + COLUMNS + " FROM classes WHERE ec1 = ?";
39		}
40
41		private String findNumberOfClassesStatement() {
42	0	return "SELECT count(*) AS count FROM classes";
43		}
44
45		/**
46		* Tries to find Class information about an enzyme.
47		*
48		* @param ec1 Number of class to search for.
49		* @param con The logical connection.
50		* @return an <code>EnzymeClass</code> instance or <code>null</code> if nothing has been found.
51		* @throws NullPointerException if any of the parameters is <code>null</code>.
52		* @throws SQLException if a database error occurs.
53		* @throws DomainException if any error related to domain information occurs (e.g. <code>ec1</code> is invalid).
54		*/
55		public EnzymeClass find(String ec1, Connection con) throws SQLException, DomainException {
56	0	if (ec1 == null) throw new NullPointerException("Parameter 'ec1' must not be null.");
57	0	if (con == null) throw new NullPointerException("Parameter 'con' must not be null.");
58	0	PreparedStatement findStatement = null;
59	0	ResultSet rs = null;
60	0	EnzymeClass result = null;
61		List<EnzymeSubclass> subclasses;
62
63		// Get subclasses.
64	0	EnzymeSubclassMapper subclassMapper = new EnzymeSubclassMapper();
65	0	subclasses = subclassMapper.findList(ec1, con);
66
67		try {
68	0	findStatement = con.prepareStatement(findStatement());
69	0	findStatement.setString(1, ec1);
70	0	rs = findStatement.executeQuery();
71	0	if (rs.next()) {
72	0	result = doLoad(rs, subclasses);
73		} else {
74	0	LOGGER.warn("No class information found for EC " + ec1);
75		}
76		} finally {
77	0	if (rs != null) rs.close();
78	0	if (findStatement != null) findStatement.close();
79		}
80
81	0	return result;
82		}
83
84		/**
85		*
86		* @param con
87		* @return A <code>List</code> of all the <code>EnzymeClass</code>es
88		* (without subclass information)
89		* @throws SQLException
90		* @throws EcException
91		*/
92		public List<EnzymeClass> findAll(Connection con) throws SQLException, DomainException{
93	0	List<EnzymeClass> result = new ArrayList<EnzymeClass>();
94	0	Statement stm = null;
95	0	ResultSet rs = null;
96		try {
97	0	stm = con.createStatement();
98	0	rs = stm.executeQuery("SELECT ec1 FROM classes");
99	0	while (rs.next()){
100	0	result.add(find(rs.getString(1), con));
101		}
102		} finally {
103	0	if (rs != null) rs.close();
104	0	if (stm != null) stm.close();
105		}
106	0	return result;
107		}
108
109		/**
110		* Finds the number of classes.
111		*
112		* @param con The logical connection.
113		* @return the number of classes.
114		* @throws SQLException
115		*/
116		public int findNumberOfClasses(Connection con) throws SQLException {
117	0	if (con == null) throw new NullPointerException("Parameter 'con' must not be null.");
118	0	PreparedStatement findStatement = null;
119	0	ResultSet rs = null;
120	0	int number = 0;
121
122		try {
123	0	findStatement = con.prepareStatement(findNumberOfClassesStatement());
124	0	rs = findStatement.executeQuery();
125	0	if (rs.next()) {
126	0	number = Integer.parseInt(rs.getString("count"));
127		}
128		} finally {
129	0	if (rs != null) rs.close();
130	0	if (findStatement != null) findStatement.close();
131		}
132
133	0	return number;
134		}
135
136		/**
137		* Checks if the given class number is valid.
138		*
139		* @param ec1 The class number.
140		* @param con The connection.
141		* @return <code>true</code> if the class exists.
142		* @throws SQLException
143		*/
144		public boolean classExists(String ec1, Connection con) throws SQLException {
145	0	if (ec1 == null) throw new NullPointerException("Parameter 'ec1' must not be null.");
146	0	if (con == null) throw new NullPointerException("Parameter 'con' must not be null.");
147	0	PreparedStatement findStatement = null;
148	0	ResultSet rs = null;
149		try {
150	0	findStatement = con.prepareStatement(findStatement());
151	0	findStatement.setString(1, ec1);
152	0	rs = findStatement.executeQuery();
153	0	if (rs.next()) {
154	0	return true;
155		}
156		} finally {
157	0	if (rs != null) rs.close();
158	0	if (findStatement != null) findStatement.close();
159		}
160
161	0	return false;
162		}
163
164		// ------------------- PRIVATE METHODS ------------------------
165
166		/**
167		* Creates the <code>EnzymeClass</code> object.
168		*
169		* @param rs The result set object.
170		* @return an <code>EnzymeClass</code> instance.
171		* @throws SQLException
172		*/
173		private EnzymeClass doLoad(ResultSet rs, List<EnzymeSubclass> subclasses)
174		throws SQLException, EcException {
175	0	assert rs != null;
176
177	0	int ec1 = 0;
178	0	String name = "";
179	0	String description = "";
180
181	0	if (rs.getInt("ec1") > 0) ec1 = rs.getInt("ec1");
182	0	if (rs.getString("name") != null) name = rs.getString("name");
183	0	if (rs.getString("description") != null) description = rs.getString("description");
184
185	0	EnzymeCommissionNumber ec = EnzymeCommissionNumber.valueOf(ec1);
186	0	return EnzymeClass.valueOf(ec, name, description, subclasses);
187		}
188		}