1 package compbio.cassandra;
4 import java.util.HashMap;
6 import java.util.ArrayList;
9 import org.apache.log4j.Logger;
11 import com.datastax.driver.core.Row;
12 import com.datastax.driver.core.Session;
13 import com.datastax.driver.core.ResultSet;
15 public class CassandraReader {
16 private Session session;
17 private static Logger log = Logger.getLogger(CassandraNativeConnector.class);
19 public CassandraReader() {
20 Session inis = CassandraNativeConnector.getSession();
24 public void setSession(Session s) {
30 * getting data from the db
32 public List<Pair<String, String>> ReadProteinDataTable() {
33 final long startTime = System.currentTimeMillis();
34 String com = "SELECT DataBegin,DataEnd FROM ProteinLog;";
35 System.out.println("Command: " + com);
36 ResultSet results = session.execute(com);
37 final long queryTime = System.currentTimeMillis();
38 List<Row> rows = results.all();
39 System.out.println("Query time is " + (queryTime - startTime) + " msec");
41 List<Pair<String, String>> res = new ArrayList<Pair<String, String>>();
44 Pair<String, String> pair = new Pair<String, String>(r.getString("DataBegin"), r.getString("DataEnd"));
48 final long endTime = System.currentTimeMillis();
49 System.out.println(c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
54 * getting data from the db
56 public List<Pair<String, String>> ReadProteinData(long day) {
57 final long startTime = System.currentTimeMillis();
58 String com = "SELECT JobID, Protein FROM ProteinData WHERE jobtime = " + day + ";";
59 System.out.println("Command: " + com);
60 ResultSet results = session.execute(com);
61 if (results.isExhausted())
63 final long queryTime = System.currentTimeMillis();
64 List<Row> rows = results.all();
65 System.out.println("Query time is " + (queryTime - startTime) + " msec");
66 List<Pair<String, String>> res = new ArrayList<Pair<String, String>>();
69 Pair<String, String> pair = new Pair<String, String>(r.getString("JobID"), r.getString("Protein"));
73 final long endTime = System.currentTimeMillis();
74 System.out.println(c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
78 * getting data from the db JobDateInfo
80 public List<Long> ReadDateTable(long queryDate) {
81 ResultSet results = session.execute("SELECT * FROM JobDateInfo WHERE jobday = " + queryDate + ";");
82 if (results.isExhausted())
84 Row therow = results.one();
85 List<Long> res = new ArrayList<Long>();
86 res.add(therow.getLong("Total"));
87 res.add(therow.getLong("TotalOK"));
88 res.add(therow.getLong("TotalStopped"));
89 res.add(therow.getLong("TotalError"));
90 res.add(therow.getLong("TotalTimeOut"));
91 if (!results.isExhausted()) {
92 Date date = new Date (queryDate);
93 log.warn("CassandraReader.ReadDateTable: date row for " + date.toString () + " ("+ queryDate + ") duplicated ");
99 * getting whole protein sequence from the db ProteinRow
101 public List<AnnotatedProteinSequenceBean> ReadWholeSequence(String queryProtein) {
102 final long startTime = System.currentTimeMillis();
103 String com = "SELECT JobID, Predictions FROM ProteinRow WHERE Protein = '" + queryProtein + "';";
104 System.out.println("Command: " + com);
105 ResultSet results = session.execute(com);
106 if (results.isExhausted())
108 final long queryTime = System.currentTimeMillis();
109 List<Row> rows = results.all();
110 System.out.println("Query time is " + (queryTime - startTime) + " msec");
111 System.out.println(" rows analysed, " + rows.size());
112 List<AnnotatedProteinSequenceBean> res = new ArrayList<AnnotatedProteinSequenceBean>();
115 AnnotatedProteinSequenceBean structure = new AnnotatedProteinSequenceBean(queryProtein, r.getString("JobID"), r.getMap(
116 "Predictions", String.class, String.class));
120 final long endTime = System.currentTimeMillis();
121 System.out.println(c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
129 public List<Pair<String, String>> ReadIpWithJobs(String ip) {
130 final long startTime = System.currentTimeMillis();
131 String com = "SELECT JobID, Protein, FinalStatus FROM ProteinLog WHERE ip = '" + ip + "';";
132 System.out.println("Command: " + com);
133 ResultSet results = session.execute(com);
134 if (results.isExhausted())
136 final long queryTime = System.currentTimeMillis();
137 List<Row> rows = results.all();
138 List<Pair<String, String>> res = new ArrayList<Pair<String, String>>();
139 System.out.println("Query time is " + (queryTime - startTime) + " msec");
140 System.out.println(" rows analysed, " + rows.size());
143 if (r.getString("FinalStatus").equals("OK")) {
144 Pair<String, String> pair = new Pair<String, String>(r.getString("JobID"), r.getString("Protein"));
145 System.out.println(pair.getElement0());
146 System.out.println(pair.getElement1());
151 final long endTime = System.currentTimeMillis();
152 System.out.println(c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
157 * getting part of protein sequence from the db ProteinRow
159 public List<AnnotatedProteinSequenceBean> ReadPartOfSequence(String queryProtein) {
160 final long startTime = System.currentTimeMillis();
161 String com = "SELECT * FROM ProteinRow;";
162 System.out.println("Command: " + com);
163 ResultSet results = session.execute(com);
164 if (results.isExhausted())
166 final long queryTime = System.currentTimeMillis();
167 List<Row> rows = results.all();
168 System.out.println("Query time is " + (queryTime - startTime) + " msec");
169 System.out.println(" rows analysed, " + rows.size());
170 List<AnnotatedProteinSequenceBean> res = new ArrayList<AnnotatedProteinSequenceBean>();
173 String prot = r.getString("Protein");
174 if (prot.matches("(.*)" + queryProtein + "(.*)")) {
175 AnnotatedProteinSequenceBean structure = new AnnotatedProteinSequenceBean(prot, r.getString("JobID"), r.getMap("Predictions",
176 String.class, String.class));
181 final long endTime = System.currentTimeMillis();
182 System.out.println(c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
187 * getting protein sequences by counter
189 public Map<String, Integer> ReadProteinSequenceByCounter() {
190 final long startTime = System.currentTimeMillis();
191 String com = "SELECT Protein, JobID FROM ProteinRow;";
192 System.out.println("Command: " + com);
193 ResultSet results = session.execute(com);
194 if (results.isExhausted())
196 final long queryTime = System.currentTimeMillis();
197 List<Row> rows = results.all();
198 System.out.println("Query time is " + (queryTime - startTime) + " msec");
199 System.out.println(" rows analysed, " + rows.size());
200 Map<String, Integer> res = new HashMap<String, Integer>();
203 String protein = r.getString("Protein");
204 String id = r.getString("JobID");
205 if (res.containsKey(protein))
206 res.put(protein, res.get(protein) + 1);
210 final long endTime = System.currentTimeMillis();
211 System.out.println(c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
216 * getting ip by counter
218 public Map<String, Integer> ReadIpByCounter() {
219 final long startTime = System.currentTimeMillis();
220 String com = "SELECT JobID, ip FROM ProteinLog;";
221 System.out.println("Command: " + com);
222 ResultSet results = session.execute(com);
223 if (results.isExhausted())
225 final long queryTime = System.currentTimeMillis();
226 List<Row> rows = results.all();
227 System.out.println("Query time is " + (queryTime - startTime) + " msec");
228 System.out.println(" rows analysed, " + rows.size());
229 Map<String, Integer> res = new HashMap<String, Integer>();
232 String protein = r.getString("ip");
233 String id = r.getString("JobID");
234 if (res.containsKey(protein))
235 res.put(protein, res.get(protein) + 1);
239 final long endTime = System.currentTimeMillis();
240 System.out.println(c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
245 * getting log info for jobid
247 public StructureJobLog ReadJobLog(String jobid) {
248 final long startTime = System.currentTimeMillis();
249 String com = "SELECT * FROM ProteinLog WHERE JobID = '" + jobid + "';";
250 System.out.println("Command: " + com);
251 ResultSet results = session.execute(com);
252 if (results.isExhausted())
254 final long queryTime = System.currentTimeMillis();
255 Row row = results.one();
256 String com1 = "SELECT * FROM ProteinRow WHERE JobID = '" + jobid + "' ALLOW FILTERING;";
257 System.out.println("Command: " + com1);
258 ResultSet results1 = session.execute(com1);
259 if (results1.isExhausted())
261 Row row1 = results1.one();
262 StructureJobLog res = new StructureJobLog(row.getString("Protein"), row.getString("JobID"), row.getString("DataBegin"),
263 row.getString("DataEnd"), row.getString("ip"), row1.getMap("Predictions", String.class, String.class));
264 System.out.println("Query time is " + (queryTime - startTime) + " msec");
265 final long endTime = System.currentTimeMillis();
266 System.out.println(" rows analysed, execution time is " + (endTime - startTime) + " msec");