--- /dev/null
+package compbio.cassandra;
+
+import java.util.Date;
+import java.util.HashMap;
+import java.util.List;
+import java.util.ArrayList;
+import java.util.Map;
+
+import org.apache.log4j.Logger;
+
+import com.datastax.driver.core.Row;
+import com.datastax.driver.core.Session;
+import com.datastax.driver.core.ResultSet;
+
+import compbio.engine.JobStatus;
+
+public class CassandraReaderOld {
+ private Session session;
+ private static Logger log = Logger.getLogger(CassandraNativeConnector.class);
+
+ public CassandraReaderOld() {
+ Session inis = CassandraNativeConnector.getSession();
+ setSession(inis);
+ }
+
+ public void setSession(Session s) {
+ assert s != null;
+ session = s;
+ }
+
+ /*
+ * getting data from the db
+ */
+ public List<Pair<String, String>> ReadProteinDataTable() {
+ final long startTime = System.currentTimeMillis();
+ String com = "SELECT DataBegin,DataEnd FROM ProteinLog;";
+ System.out.println("Command: " + com);
+ ResultSet results = session.execute(com);
+ final long queryTime = System.currentTimeMillis();
+ List<Row> rows = results.all();
+ System.out.println("Query time is " + (queryTime - startTime) + " msec");
+
+ List<Pair<String, String>> res = new ArrayList<Pair<String, String>>();
+ int c = 0;
+ for (Row r : rows) {
+ Pair<String, String> pair = new Pair<String, String>(r.getString("DataBegin"), r.getString("DataEnd"));
+ res.add(pair);
+ ++c;
+ }
+ final long endTime = System.currentTimeMillis();
+ System.out.println(c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
+ return res;
+ }
+
+ /*
+ * getting data from the db
+ */
+ public DateBean ReadProteinData(long day, String date) {
+ String com = "SELECT JobID, Protein FROM ProteinData WHERE jobtime = " + day + ";";
+ System.out.println("Command: " + com);
+ ResultSet results = session.execute(com);
+ if (results.isExhausted())
+ return null;
+ List<Row> rows = results.all();
+ DateBean res = new DateBean(date);
+ for (Row r : rows) {
+ res.setJobidAndSeq(r.getString("JobID"), r.getString("Protein"));
+ }
+ return res;
+ }
+
+ /**
+ * getting data from the db
+ */
+ public DateBean ReadFailedJobs(long day, String date, JobStatus status) {
+ // FailLog (jobtime, JobID, ExecTime, ip, FinalStatus)
+ String com = "SELECT JobID FROM FailLog WHERE jobtime = " + day + " and FinalStatus = '" + status.name() + "';";
+ ResultSet results = session.execute(com);
+ if (results.isExhausted())
+ return null;
+ List<Row> rows = results.all();
+ DateBean res = new DateBean(date);
+ for (Row r : rows) {
+ String jobid = r.getString("JobID");
+ String com1 = "SELECT Protein FROM ProteinLog WHERE JobID = '" + jobid + "';";
+ System.out.println("Command: " + com1);
+ ResultSet results2 = session.execute(com1);
+ List<Row> jrows = results2.all();
+ if (1 == jrows.size()) {
+ String protein = jrows.get(0).getString("Protein");
+ res.setJobidAndSeq(jobid, protein);
+ }
+ }
+ return res;
+ }
+
+ /*
+ * getting data from the db JobDateInfo
+ */
+ public Total ReadDateTable(long queryDate) {
+ ResultSet results = session.execute("SELECT * FROM JobDateInfo WHERE jobday = " + queryDate + ";");
+ if (results.isExhausted())
+ return null;
+ Row therow = results.one();
+ Total res = new Total(therow.getLong("Total"), therow.getLong("TotalOK"), therow.getLong("TotalStopped"),
+ therow.getLong("TotalError"), therow.getLong("TotalTimeOut"));
+ if (!results.isExhausted()) {
+ Date date = new Date(queryDate);
+ log.warn("CassandraReader.ReadDateTable: date row for " + date.toString() + " (" + queryDate + ") duplicated ");
+ }
+ return res;
+ }
+
+ /*
+ * getting whole protein sequence from the db ProteinRow
+ */
+ public List<ProteinBean> ReadWholeSequence(String queryProtein) {
+ final long startTime = System.currentTimeMillis();
+ String com = "SELECT JobID, Predictions FROM ProteinRow WHERE Protein = '" + queryProtein + "';";
+ System.out.println("Command: " + com);
+ ResultSet results = session.execute(com);
+ if (results.isExhausted())
+ return null;
+ final long queryTime = System.currentTimeMillis();
+ List<Row> rows = results.all();
+ System.out.println("first size : " + rows.size());
+ System.out.println("Query time is " + (queryTime - startTime) + " msec");
+ System.out.println(" rows analysed, " + rows.size());
+ List<ProteinBean> res = new ArrayList<ProteinBean>();
+ ProteinBean structure = new ProteinBean(queryProtein, rows.get(0).getMap("Predictions", String.class, String.class));
+ System.out.println("second size : " + rows.size());
+ int c = 0;
+ for (Row r : rows) {
+ structure.setJobid(r.getString("JobID"));
+ ++c;
+ }
+ res.add(structure);
+ final long endTime = System.currentTimeMillis();
+ System.out.println(c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
+ return res;
+ }
+
+ /*
+ * getting jobs by ip
+ */
+ public Map<String, String[]> ReadIpWithJobs(String ip) {
+ final long startTime = System.currentTimeMillis();
+ String com = "SELECT JobID, Protein, FinalStatus, DataBegin FROM ProteinLog WHERE ip = '" + ip + "';";
+ System.out.println("Command: " + com);
+ ResultSet results = session.execute(com);
+ if (results.isExhausted())
+ return null;
+ final long queryTime = System.currentTimeMillis();
+ List<Row> rows = results.all();
+ Map<String, String[]> res = new HashMap<String, String[]>();
+ System.out.println("Query time is " + (queryTime - startTime) + " msec");
+ System.out.println(" rows analysed, " + rows.size());
+ int c = 0;
+ for (Row r : rows) {
+ if (r.getString("FinalStatus").equals("OK")) {
+ String date = r.getString("DataBegin");
+ res.put(r.getString("JobID"), new String[] { date.substring(0, date.indexOf(":")), r.getString("Protein") });
+ ++c;
+ }
+ }
+ final long endTime = System.currentTimeMillis();
+ System.out.println(c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
+ return res;
+ }
+
+ /*
+ * getting part of protein sequence from the db ProteinRow
+ */
+ public List<ProteinBean> ReadPartOfSequence(String queryProtein) {
+ final long startTime = System.currentTimeMillis();
+ String com = "SELECT * FROM ProteinRow;";
+ System.out.println("Command: " + com);
+ ResultSet results = session.execute(com);
+ if (results.isExhausted())
+ return null;
+ final long queryTime = System.currentTimeMillis();
+ List<Row> rows = results.all();
+ System.out.println("Query time is " + (queryTime - startTime) + " msec");
+ System.out.println(" rows analysed, " + rows.size());
+ List<ProteinBean> res = new ArrayList<ProteinBean>();
+ int c = 0;
+ for (Row r : rows) {
+ String prot = r.getString("Protein");
+ if (prot.matches("(.*)" + queryProtein + "(.*)")) {
+ ProteinBean structure = new ProteinBean(prot, r.getMap("Predictions", String.class, String.class));
+ structure.setJobid(r.getString("JobID"));
+ res.add(structure);
+ ++c;
+ }
+ }
+ final long endTime = System.currentTimeMillis();
+ System.out.println(c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
+ return res;
+ }
+
+ /*
+ * getting protein sequence from the db ProteinRow
+ */
+ public Map<String, String> ReadProtein() {
+ final long startTime = System.currentTimeMillis();
+ String com = "SELECT * FROM ProteinRow;";
+ System.out.println("Command: " + com);
+ ResultSet results = session.execute(com);
+ if (results.isExhausted())
+ return null;
+ final long queryTime = System.currentTimeMillis();
+ List<Row> rows = results.all();
+ System.out.println("Query time is " + (queryTime - startTime) + " msec");
+ System.out.println(" rows analysed, " + rows.size());
+ Map<String, String> res = new HashMap<String, String>();
+ int c = 0;
+ for (Row r : rows) {
+ String prot = r.getString("Protein");
+ String prediction = findJnetpred(r.getMap("Predictions", String.class, String.class));
+ if (prot != null || prediction != null)
+ res.put(prot, prediction);
+ }
+ final long endTime = System.currentTimeMillis();
+ System.out.println(c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
+ return res;
+ }
+
+ private String findJnetpred (Map<String,String> pred) {
+ if (pred != null) {
+ if (pred.containsKey("jnetpred"))
+ return pred.get("jnetpred");
+ }
+ return null;
+ }
+ /*
+ * getting protein sequences by counter
+ */
+ public Map<String, Integer> ReadProteinSequenceByCounter() {
+ final long startTime = System.currentTimeMillis();
+ String com = "SELECT Protein, JobID FROM ProteinRow;";
+ System.out.println("Command: " + com);
+ ResultSet results = session.execute(com);
+ if (results.isExhausted())
+ return null;
+ final long queryTime = System.currentTimeMillis();
+ List<Row> rows = results.all();
+ System.out.println("Query time is " + (queryTime - startTime) + " msec");
+ System.out.println(" rows analysed, " + rows.size());
+ Map<String, Integer> res = new HashMap<String, Integer>();
+ int c = 0;
+ for (Row r : rows) {
+ String protein = r.getString("Protein");
+ String id = r.getString("JobID");
+ if (res.containsKey(protein))
+ res.put(protein, res.get(protein) + 1);
+ else
+ res.put(protein, 1);
+ }
+ final long endTime = System.currentTimeMillis();
+ System.out.println(c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
+ return res;
+ }
+
+ /*
+ * getting ip by counter
+ */
+ public Map<String, Integer> ReadIpByCounter() {
+ final long startTime = System.currentTimeMillis();
+ String com = "SELECT JobID, ip FROM ProteinLog;";
+ System.out.println("Command: " + com);
+ ResultSet results = session.execute(com);
+ if (results.isExhausted())
+ return null;
+ final long queryTime = System.currentTimeMillis();
+ List<Row> rows = results.all();
+ System.out.println("Query time is " + (queryTime - startTime) + " msec");
+ System.out.println(" rows analysed, " + rows.size());
+ Map<String, Integer> res = new HashMap<String, Integer>();
+ int c = 0;
+ for (Row r : rows) {
+ String ip = r.getString("ip");
+ String id = r.getString("JobID");
+ if (res.containsKey(ip))
+ res.put(ip, res.get(ip) + 1);
+ else
+ res.put(ip, 1);
+ }
+ final long endTime = System.currentTimeMillis();
+ System.out.println(c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
+ return res;
+ }
+
+ /*
+ * getting log info for jobid
+ */
+ public JobBean ReadJobLog(String jobid) {
+ final long startTime = System.currentTimeMillis();
+ String com = "SELECT * FROM ProteinLog WHERE JobID = '" + jobid + "';";
+ System.out.println("Command: " + com);
+ ResultSet results = session.execute(com);
+ if (results.isExhausted())
+ return null;
+ final long queryTime = System.currentTimeMillis();
+ Row row = results.one();
+ String com1 = "SELECT * FROM ProteinRow WHERE JobID = '" + jobid + "' ALLOW FILTERING;";
+ System.out.println("Command: " + com1);
+ ResultSet results1 = session.execute(com1);
+ if (results1.isExhausted())
+ return null;
+ Row row1 = results1.one();
+ JobBean res = new JobBean(row.getString("Protein"), row.getString("JobID"), row.getString("DataBegin"), row.getString("DataEnd"),
+ row.getString("ip"), row1.getMap("Predictions", String.class, String.class));
+ System.out.println("Query time is " + (queryTime - startTime) + " msec");
+ final long endTime = System.currentTimeMillis();
+ System.out.println(" rows analysed, execution time is " + (endTime - startTime) + " msec");
+ return res;
+ }
+}
git://source.jalview.org / proteocache.git / blobdiff