session = cluster.connect();
session.execute("CREATE KEYSPACE IF NOT EXISTS ProteinKeyspace WITH replication = {'class':'SimpleStrategy', 'replication_factor':3};");
- session.execute("CREATE COLUMNFAMILY IF NOT EXISTS ProteinKeyspace.ProteinRow (Protein ascii PRIMARY KEY, Predictions map<ascii,ascii>);");
+ session.execute("CREATE COLUMNFAMILY IF NOT EXISTS ProteinKeyspace.ProteinRow (Protein ascii, JobID ascii, Predictions map<ascii,ascii>, PRIMARY KEY(JobID));");
session.execute("CREATE COLUMNFAMILY IF NOT EXISTS ProteinKeyspace.ProteinLog "
- + "(JobID ascii PRIMARY KEY, DataBegin ascii, DataEnd ascii, ip ascii, FinalStatus ascii, ExecutionStatus ascii, Protein ascii);");
- session.execute("CREATE COLUMNFAMILY IF NOT EXISTS ProteinKeyspace.ProteinData (jobtime bigint PRIMARY KEY, JobID ascii, Protein ascii);");
+ + "(JobID ascii, DataBegin ascii, DataEnd ascii, ip ascii, FinalStatus ascii, ExecutionStatus ascii, Protein ascii, PRIMARY KEY(JobID));");
+ session.execute("CREATE COLUMNFAMILY IF NOT EXISTS ProteinKeyspace.ProteinData (jobtime bigint, JobID ascii, Protein ascii, PRIMARY KEY(JobID));");
+
+ session.execute("CREATE INDEX ProteinSeq ON ProteinKeyspace.ProteinRow (protein);");
+ session.execute("CREATE INDEX JobDateStamp ON ProteinKeyspace.ProteinData (jobtime);");
System.out.println("Cassandra connected");
}
}
/*
- * check whether the job id exists in the DB
- */
- public boolean CheckID(String jobid) {
- String com = "SELECT * FROM ProteinKeyspace.ProteinData WHERE jobid = '" + jobid + "';";
- System.out.println(com);
- ResultSet results = session.execute(com);
- if (null != results) {
- return true;
- }
- return false;
- }
-
- /*
* prepare data for insertion into the db
*/
public void InsertData(long jobtime, String startdate, String enddate, String ip, String jobid, String statusEx, String statusFinal,
String protein, List<FastaSequence> predictions) {
- String check1 = "SELECT count(*) FROM ProteinKeyspace.ProteinLog WHERE JobID = '" + jobid + "';";
+ String check1 = "SELECT * FROM ProteinKeyspace.ProteinLog WHERE JobID = '" + jobid + "';";
//System.out.println(check1);
ResultSet results1 = session.execute(check1);
- if (!results1.isExhausted()) {
+ if (results1.isExhausted()) {
String com1 = "INSERT INTO ProteinKeyspace.ProteinLog "
+ "(JobID, IP, DataBegin, DataEnd, FinalStatus, ExecutionStatus, Protein)" + " VALUES ('" + jobid + "','" + ip + "','"
+ startdate + "','" + enddate + "','" + statusFinal + "','" + statusEx + "','" + protein + "');";
- // System.out.println(com1);
+ //System.out.println(com1);
session.execute(com1);
String com2 = "INSERT INTO ProteinKeyspace.ProteinData " + "(jobtime, JobID, Protein)" + " VALUES (" + jobtime + ",'" + jobid
+ "','" + protein + "');";
- // System.out.println(com2);
- // session.execute(com2);
+ //System.out.println(com2);
+ session.execute(com2);
String allpredictions = "";
for (FastaSequence pred : predictions) {
final_prediction = allpredictions.substring(0, allpredictions.length() - 1);
}
- String check2 = "SELECT count(*) FROM ProteinKeyspace.ProteinRow WHERE Protein = '" + protein + "';";
- //System.out.println(check1);
+ String check2 = "SELECT * FROM ProteinKeyspace.ProteinRow WHERE JobID = '" + jobid + "';";
+ //System.out.println(check2);
ResultSet results2 = session.execute(check2);
-
- if (results1.isExhausted()) {
- String com3 = "INSERT INTO ProteinKeyspace.ProteinRow " + "(Protein, " + jobid + ")" + " VALUES ('" + protein + "'," + "{"
- + final_prediction + "}" + ");";
- System.out.println(com3);
- session.execute(com3);
- } else {
- String com4 = "ALTER TABLE ProteinKeyspace.ProteinRow ADD " + jobid + ");";
- System.out.println(com4);
- session.execute(com4);
- String com3 = "INSERT INTO ProteinKeyspace.ProteinRow " + "(" + jobid + ")" + " VALUES ({" + final_prediction + "}" + ")"
- + " WHERE Protein = '" + protein + "';";
- System.out.println(com3);
+ if (results2.isExhausted()) {
+ String com3 = "INSERT INTO ProteinKeyspace.ProteinRow " + "(Protein, JobID, Predictions)" + " VALUES ('"
+ + protein + "','" + jobid + "',{" + final_prediction + "});";
+ //System.out.println(com3);
session.execute(com3);
}
}