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package tools; |
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import java.sql.*; |
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import java.util.ArrayList; |
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import java.util.HashMap; |
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/** |
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* ClusterConnection class to wrap the master/node mysql servers so that is transparent to other programs |
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* @author Jose Duarte |
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*/ |
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public class ClusterConnection { |
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private String MASTERDB="key_master"; |
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private final String MASTERHOST="white"; |
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private MySQLConnection nCon; |
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private MySQLConnection mCon; |
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public String keyTable; |
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public String key; |
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public String host; |
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public String db; |
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private String user; |
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private String password; |
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/** |
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* Create a ClusterConnection passing a key. |
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* @param db the database name |
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* @param key the key name: e.g. asu_id |
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* @param user the user name for connection to both master and nodes |
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* @param password the password for connection to both master and nodes |
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*/ |
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public ClusterConnection (String db,String key, String user,String password) { |
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setDb(db); |
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setUser(user); |
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setPassword(password); |
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// For nCon we create a connection to the master too. |
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// This is just a place holder because the actual node connection is not created until we create the statement |
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// If we don't do this then when closing the two connections an exception might occurr because we try to close a non existing object |
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this.nCon = new MySQLConnection(MASTERHOST,user,password,MASTERDB); |
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this.mCon = new MySQLConnection(MASTERHOST,user,password,MASTERDB); |
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this.key=key; //can't use the setKey method here before we've got the db field initialized |
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setKeyTable(db); |
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} |
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/** |
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* Create a ClusterConnection without passing a key. The key will be set later when we call createStatement(key,idx) |
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* @param db the database name |
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* @param user the user name for connection to both master and nodes |
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* @param password the password for connection to both master and nodes |
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*/ |
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public ClusterConnection (String db, String user,String password) { |
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setDb(db); |
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setUser(user); |
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setPassword(password); |
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// For nCon we create a connection to the master too. |
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// This is just a place holder because the actual node connection is not created until we create the statement |
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// If we don't do this then when closing the two connections an exception might occurr because we try to close a non existing object |
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this.nCon = new MySQLConnection(MASTERHOST,user,password,MASTERDB); |
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this.mCon = new MySQLConnection(MASTERHOST,user,password,MASTERDB); |
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} |
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public void close() { |
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this.nCon.close(); |
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this.mCon.close(); |
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} |
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public String getHost4Idx (int idx) { |
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String host=""; |
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String query = "SELECT client_name FROM "+keyTable+" AS m INNER JOIN clients_names AS c "+ |
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"ON (m.client_id=c.client_id) WHERE "+key+"="+idx+";"; |
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host=this.mCon.getStringFromDb(query); |
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return host; |
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} |
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public void setHostFromIdx(int idx){ |
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setHost(getHost4Idx(idx)); |
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} |
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public void setHost(String host) { |
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this.host=host; |
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//Closing previous connection is essential |
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//If we don't close it a lot of connections stay open after using a ClusterConnection object for a while |
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this.nCon.close(); |
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this.nCon = new MySQLConnection(host,user,password,db); |
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} |
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/** |
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* This method is strictly private. We shouldn't call this from another class as a key might not be set when we call it |
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* and thus we can't get the client_id from the master key table. Only to be called from createStatement(key,idx) |
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* @param idx the value of the id for a certain key already set |
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* @return a Stament object with a connection to the node that contains idx for key |
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*/ |
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private Statement createStatement(int idx) { // to use when the field "key" is already set |
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setKeyTable(); |
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Statement S=null; |
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this.setHostFromIdx(idx); |
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try { |
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S=this.nCon.createStatement(); |
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} |
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catch (SQLException e){ |
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System.err.println("SQLException: " + e.getMessage()); |
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System.err.println("SQLState: " + e.getSQLState()); |
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System.err.println("Couldn't create statement for the node connection, idx= "+idx+", exiting."); |
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System.exit(2); |
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} |
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return S; |
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} |
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/** |
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* This method is used to create a statement passing the key and idx. It will create a connection the the right node |
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* and return a Statement for that connection |
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* @param idx the key name |
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* @param idx the id value for that key |
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* @return a Statement object with a connection to the node that contains idx for key |
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*/ |
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public Statement createStatement(String key,int idx) { |
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setKey(key); |
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return createStatement(idx); |
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} |
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/** |
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* To execute a sql update/insert query in the right node given a query, key and idx. Just a shortcut not to have to do the create statement and execute |
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* @param query the SQL query |
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* @param key the name of the key |
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* @param idx the id value for that key |
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*/ |
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public void executeSql(String query,String key, int idx) throws SQLException { |
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Statement stmt; |
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stmt = this.createStatement(key,idx); |
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stmt.execute(query); |
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stmt.close(); |
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} |
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/** |
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* To change the MASTERDB String, i.e. the name of the key master database. To be used in testing. |
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* @param db the name of the key master db we want to use instead of the default defined in the MASTERDB field |
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*/ |
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public void setKeyDb(String db) { |
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this.MASTERDB=db; |
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//Closing previous connection is essential |
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this.mCon.close(); |
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this.mCon = new MySQLConnection(MASTERHOST,user,password,MASTERDB); |
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} |
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/** |
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* To set keyTable field in constructor (i.e. first time). Only to be used in constructor. |
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* @param db the database name |
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*/ |
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public void setKeyTable(String db) { |
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String query="SELECT key_master_table FROM dbs_keys WHERE db=\'"+db+"\' AND key_name=\'"+this.key+"\';"; |
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this.keyTable=this.mCon.getStringFromDb(query); |
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} |
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/** |
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* To set the keyTable field when db is already set |
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* The value of keyTable is taken from the dbs_keys table in the database given the db and key. |
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*/ |
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public void setKeyTable() { |
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String query="SELECT key_master_table FROM dbs_keys WHERE db=\'"+this.db+"\' AND key_name=\'"+this.key+"\';"; |
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this.keyTable=this.mCon.getStringFromDb(query); |
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} |
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public String getKeyTable() { |
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return this.keyTable; |
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} |
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/** |
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* To get the name of the target table where splitted data is stored in nodes, e.g. for keyTable pdbgraph__asu_list, we get asu_list |
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* @return |
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*/ |
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public String getTableOnNode(){ |
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String table=""; |
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if (this.keyTable.contains("__")) { |
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String[] tokens=this.keyTable.split("__"); |
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table=tokens[1]; |
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} |
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else { |
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System.err.println("Error! The keyTable field is not set in this ClusterConnection object."); |
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} |
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return table; |
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} |
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public void setUser(String user) { |
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this.user=user; |
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} |
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public void setPassword(String password) { |
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this.password=password; |
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} |
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public void setDb(String db){ |
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this.db=db; |
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} |
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public void setKey(String key){ |
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this.key=key; |
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setKeyTable(); |
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} |
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public Statement createMasterStatement() { |
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Statement S=null; |
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try { |
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S=this.mCon.createStatement(); |
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} |
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catch (SQLException e){ |
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System.err.println("SQLException: " + e.getMessage()); |
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System.err.println("SQLState: " + e.getSQLState()); |
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System.err.println("Couldn't create statement for the master connection, exiting."); |
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System.exit(2); |
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} |
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return S; |
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} |
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public int[] getAllIdxFromMaster(String key) { |
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this.setKey(key); |
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int[] ids=null; |
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ArrayList<Integer> idsAL=new ArrayList<Integer>(); |
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try { |
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String query="SELECT "+key+" FROM "+keyTable+";"; |
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Statement S=this.mCon.createStatement(); |
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ResultSet R=S.executeQuery(query); |
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while (R.next()){ |
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idsAL.add(R.getInt(1)); |
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} |
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R.close(); |
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S.close(); |
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} |
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catch (SQLException e){ |
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System.err.println("SQLException: " + e.getMessage()); |
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System.err.println("SQLState: " + e.getSQLState()); |
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System.err.println("Couldn't get all indices from columnn "+key+" in table "+keyTable+" from "+MASTERDB+" database in "+MASTERHOST+", exiting."); |
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System.exit(2); |
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} |
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ids=new int[idsAL.size()]; |
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for (int i=0;i<idsAL.size();i++){ |
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ids[i]=idsAL.get(i); |
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} |
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return ids; |
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} |
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/** |
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* To get all ids and clients_names pairs for a certain key. Useful when need to submit to all hosts using qsub -q |
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* @param key the name of the key |
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* @return HashMap with keys = indices, and values = node names where the corresponding index is stored |
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*/ |
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public HashMap<Integer,String> getAllIdxAndClients (String key){ |
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this.setKey(key); |
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HashMap<Integer,String> idsAndClients=new HashMap<Integer,String>(); |
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try { |
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String query="SELECT a."+key+",c.client_name FROM "+keyTable+" AS a INNER JOIN clients_names AS c ON (a.client_id=c.client_id);"; |
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Statement S=this.mCon.createStatement(); |
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ResultSet R=S.executeQuery(query); |
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while (R.next()){ |
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idsAndClients.put(R.getInt(1),R.getString(2)); |
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} |
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R.close(); |
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S.close(); |
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} |
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catch (SQLException e){ |
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System.err.println("SQLException: " + e.getMessage()); |
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System.err.println("SQLState: " + e.getSQLState()); |
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System.err.println("Couldn't get all indices/client_names pairs from table "+keyTable+" from "+MASTERDB+" database in "+MASTERHOST+", exiting."); |
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System.exit(2); |
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} |
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return idsAndClients; |
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} |
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/** |
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* To get client_id for a certain idx and key |
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* @param key the key name |
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* @param idx the id value for that key |
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* @return the client_id for node that has the data for the idx for that key |
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*/ |
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//TODO will need to change the query. In general this method would return more than 1 client_id if the idx is not unique |
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public int getHostId4Idx (String key,int idx) { |
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int hostId=0; |
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this.setKey(key); |
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String query; |
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int countCids=0; |
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query="SELECT count(client_id) FROM "+keyTable+" WHERE "+key+"="+idx+";"; |
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countCids=this.mCon.getIntFromDb(query); |
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if (countCids!=1){ |
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System.err.println("the query was: "+query); |
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System.err.println("Error! the count of client_ids for idx "+key+"= "+idx+" is " +countCids+ |
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". It must be 1! The values were taken from host: "+MASTERHOST+", database: "+MASTERDB+", table: "+keyTable+". Check what's wrong! Exiting now."); |
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System.exit(2); |
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} |
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else { |
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query="SELECT client_id FROM "+keyTable+" WHERE "+key+"="+idx+";"; |
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hostId=this.mCon.getIntFromDb(query); |
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} |
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return hostId; |
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} |
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public void insertIdxInMaster(String key, int clientId) { |
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String query; |
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this.setKey(key); |
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try { |
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query="INSERT INTO "+this.keyTable+" (client_id) VALUES ("+clientId+");"; |
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this.mCon.executeSql(query); |
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} |
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catch (SQLException E) { |
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System.err.println("SQLException: " + E.getMessage()); |
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System.err.println("SQLState: " + E.getSQLState()); |
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System.err.println("Couldn't insert new "+this.key+" in master table "+this.getKeyTable()+". The client_id for it was "+clientId+". Exiting."); |
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System.exit(2); |
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} |
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} |
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public void insertIdxInMaster(String keySrc,String keyDest,int idxSrc) { |
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this.setKey(keySrc); |
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int clientId=0; |
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clientId=this.getHostId4Idx(keySrc,idxSrc); |
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insertIdxInMaster(keyDest,clientId); |
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} |
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public int getLastInsertId(String key) { |
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int lastIdx=0; |
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this.setKey(key); |
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String query = ""; |
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query = "SELECT LAST_INSERT_ID() FROM "+this.keyTable+" LIMIT 1;"; |
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lastIdx=this.mCon.getIntFromDb(query); |
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return lastIdx; |
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} |
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public int[][] getIdxSet(String key) { |
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int[][] indMatrix=null; |
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this.setKey(key); |
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String query; |
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Statement S; |
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ResultSet R; |
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try { |
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// STEP 1 -- getting set of all client_ids |
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query="SELECT count(distinct client_id) FROM "+keyTable+";"; |
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int count=0; |
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count=this.mCon.getIntFromDb(query); |
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S=this.mCon.createStatement(); |
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query="SELECT DISTINCT client_id FROM "+keyTable+" ORDER BY client_id;"; |
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R=S.executeQuery(query); |
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// STEP 2 -- putting sets of indices counts into temp tables c_<client_id> with a serial auto_increment field |
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int[] clids=new int[count]; //array to store all client_ids. To be used in loops later |
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int i=0; |
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while (R.next()){ |
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Statement Sloop=this.mCon.createStatement(); |
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int clid=R.getInt(1); |
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query="CREATE TEMPORARY TABLE c_"+clid+" (serial int(11) NOT NULL AUTO_INCREMENT,"+key+" int(11),client_id int(11), PRIMARY KEY(serial));"; |
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Sloop.executeUpdate(query); |
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query="INSERT INTO c_"+clid+" ("+key+",client_id) SELECT "+key+",client_id FROM "+keyTable+" WHERE client_id="+clid+";"; |
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Sloop.executeUpdate(query); |
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clids[i]=clid; |
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i++; |
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Sloop.close(); |
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} |
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// STEP3 -- merging all c_<client_id> tables into a temp table tmp_allcs and selecting the client_id with the maximum count |
355 |
|
|
//query="SELECT client_id,count(*) as c FROM c_34 GROUP BY client_id UNION SELECT client_id,count(*) as c FROM c_32 GROUP BY client_id;"; |
356 |
|
|
query="DROP TABLE IF EXISTS tmp_allcs;"; |
357 |
|
|
S.executeUpdate(query); |
358 |
|
|
//this table must be permanent! otherwise cannot do the select max(c) later |
359 |
|
|
query="CREATE TABLE IF NOT EXISTS tmp_allcs (client_id int(11), c int(11)) ENGINE=MEMORY;"; |
360 |
|
|
S.executeUpdate(query); |
361 |
|
|
String unionStr="SELECT client_id,count(*) AS c FROM c_"+clids[0]+" GROUP BY client_id"; |
362 |
|
|
for (i=1;i<clids.length;i++) { |
363 |
|
|
unionStr+=" UNION SELECT client_id,count(*) AS c FROM c_"+clids[i]+" GROUP BY client_id"; |
364 |
|
|
} |
365 |
|
|
query="INSERT INTO tmp_allcs "+unionStr+";"; |
366 |
|
|
S.executeUpdate(query); |
367 |
|
|
query="SELECT client_id,c FROM tmp_allcs WHERE c=(SELECT max(c) FROM tmp_allcs);"; |
368 |
|
|
R=S.executeQuery(query); |
369 |
|
|
int clidMaxIdxCount=0; |
370 |
|
|
int maxIdxCount=0; |
371 |
|
|
if (R.next()) { |
372 |
|
|
clidMaxIdxCount=R.getInt(1); |
373 |
|
|
maxIdxCount=R.getInt(2); |
374 |
|
|
} |
375 |
|
|
query="DROP TABLE tmp_allcs;"; |
376 |
|
|
S.executeUpdate(query); |
377 |
|
|
|
378 |
|
|
// STEP 4 -- join all c_<client_id> tables into a table with a serial column, and c_<client_id> columns each of them with the indices for each client_id |
379 |
|
|
//query="SELECT c_34.serial,c_34.asu_id AS c_34,c_32.asu_id AS c_32,c_36.asu_id AS c_36 FROM c_34 LEFT JOIN c_32 ON (c_34.serial=c_32.serial) LEFT JOIN c_36 ON (c_34.serial=c_36.serial);"; |
380 |
duarte |
72 |
String selectStr="c_"+clidMaxIdxCount+".serial, c_"+clidMaxIdxCount+"."+key+" AS c_"+clidMaxIdxCount; |
381 |
duarte |
21 |
String fromStr="c_"+clidMaxIdxCount; |
382 |
|
|
for (i=0;i<clids.length;i++) { |
383 |
|
|
if (clids[i]!=clidMaxIdxCount){ |
384 |
duarte |
72 |
selectStr+=", c_"+clids[i]+"."+key+" AS c_"+clids[i]; |
385 |
duarte |
21 |
fromStr+=" LEFT JOIN c_"+clids[i]+" ON (c_"+clidMaxIdxCount+".serial=c_"+clids[i]+".serial)"; |
386 |
|
|
} |
387 |
|
|
} |
388 |
|
|
query="CREATE TEMPORARY TABLE indices_matrix "+"SELECT "+selectStr+" FROM "+fromStr+";"; |
389 |
|
|
S.executeUpdate(query); |
390 |
|
|
|
391 |
|
|
// STEP 5 -- put the table into a 2-dimensional array and return it |
392 |
|
|
indMatrix = new int[maxIdxCount][clids.length]; |
393 |
|
|
query="SELECT * FROM indices_matrix"; |
394 |
|
|
R=S.executeQuery(query); |
395 |
|
|
i=0; |
396 |
|
|
while (R.next()) { |
397 |
|
|
for (int j=0;j<clids.length;j++){ |
398 |
duarte |
22 |
indMatrix[i][j]=R.getInt(j+2); |
399 |
duarte |
21 |
} |
400 |
|
|
i++; |
401 |
|
|
} |
402 |
|
|
R.close(); |
403 |
|
|
S.close(); |
404 |
|
|
} |
405 |
|
|
catch (SQLException e){ |
406 |
duarte |
33 |
System.err.println("SQLException: " + e.getMessage()); |
407 |
|
|
System.err.println("SQLState: " + e.getSQLState()); |
408 |
duarte |
72 |
System.err.println("Couldn't get the indices set from columnn "+key+" in table "+keyTable+" from "+MASTERDB+" database in "+MASTERHOST+", exiting."); |
409 |
duarte |
21 |
System.exit(2); |
410 |
|
|
} |
411 |
|
|
return indMatrix; |
412 |
|
|
} |
413 |
|
|
|
414 |
|
|
|
415 |
duarte |
15 |
} |