-
- /*
- * 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 JobDateInfo
- */
- public List<Long> ReadDateTable(long queryDate) {
- ResultSet results = session.execute("SELECT * FROM JobDateInfo WHERE jobday = " + queryDate + ";");
- if (results.isExhausted())
- return null;
- Row therow = results.one();
- List<Long> res = new ArrayList<Long>();
- res.add(therow.getLong("Total"));
- res.add(therow.getLong("TotalOK"));
- res.add(therow.getLong("TotalStopped"));
- res.add(therow.getLong("TotalError"));
- res.add(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<StructureProteinPrediction> 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("Query time is " + (queryTime - startTime) + " msec");
- System.out.println(" rows analysed, " + rows.size());
- List<StructureProteinPrediction> res = new ArrayList<StructureProteinPrediction>();
- int c = 0;
- for (Row r : rows) {
- StructureProteinPrediction structure = new StructureProteinPrediction(queryProtein, r.getString("JobID"), r.getMap(
- "Predictions", String.class, String.class));
- res.add(structure);
- ++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<StructureProteinPrediction> ReadPartOfSequence(String queryProtein) {
- final long startTime = System.currentTimeMillis();
- String com = "SELECT * FROM ProteinRow;";