/*
* getting data from the db
*/
- public List<Pair<String, String>> ReadProteinData(long day) {
+ public DateBean ReadProteinData(long day, String date) {
final long startTime = System.currentTimeMillis();
String com = "SELECT JobID, Protein FROM ProteinData WHERE jobtime = " + day + ";";
System.out.println("Command: " + 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>>();
+ DateBean res = new DateBean(date);
int c = 0;
for (Row r : rows) {
- Pair<String, String> pair = new Pair<String, String>(r.getString("JobID"), r.getString("Protein"));
- res.add(pair);
+ res.setJobidAndSeq(r.getString("JobID"), r.getString("Protein"));
++c;
}
final long endTime = System.currentTimeMillis();
/*
* getting data from the db JobDateInfo
*/
- public List<Long> ReadDateTable(long queryDate) {
+ public Total 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"));
+ 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<AnnotatedProteinSequenceBean> ReadWholeSequence(String queryProtein) {
+ 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);
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<AnnotatedProteinSequenceBean> res = new ArrayList<AnnotatedProteinSequenceBean>();
+ 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) {
- AnnotatedProteinSequenceBean structure = new AnnotatedProteinSequenceBean(queryProtein, r.getString("JobID"), r.getMap(
- "Predictions", String.class, String.class));
- if (structure.getPrediction().containsKey("jnetpred"))
- structure.setJnetpred(structure.getPrediction().get("jnetpred"));
- else
- structure.setJnetpred("");
- res.add(structure);
+ 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<AnnotatedProteinSequenceBean> ReadPartOfSequence(String queryProtein) {
+ public List<ProteinBean> ReadPartOfSequence(String queryProtein) {
final long startTime = System.currentTimeMillis();
String com = "SELECT * FROM ProteinRow;";
System.out.println("Command: " + com);
List<Row> rows = results.all();
System.out.println("Query time is " + (queryTime - startTime) + " msec");
System.out.println(" rows analysed, " + rows.size());
- List<AnnotatedProteinSequenceBean> res = new ArrayList<AnnotatedProteinSequenceBean>();
+ List<ProteinBean> res = new ArrayList<ProteinBean>();
int c = 0;
for (Row r : rows) {
String prot = r.getString("Protein");
if (prot.matches("(.*)" + queryProtein + "(.*)")) {
- AnnotatedProteinSequenceBean structure = new AnnotatedProteinSequenceBean(prot, r.getString("JobID"), r.getMap("Predictions",
- String.class, String.class));
+ ProteinBean structure = new ProteinBean(prot, r.getMap("Predictions", String.class, String.class));
+ structure.setJobid(r.getString("JobID"));
res.add(structure);
++c;
}
}
/*
+ * 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 StructureJobLog ReadJobLog(String jobid) {
+ public JobBean ReadJobLog(String jobid) {
final long startTime = System.currentTimeMillis();
String com = "SELECT * FROM ProteinLog WHERE JobID = '" + jobid + "';";
System.out.println("Command: " + com);
if (results1.isExhausted())
return null;
Row row1 = results1.one();
- StructureJobLog res = new StructureJobLog(row.getString("Protein"), row.getString("JobID"), row.getString("DataBegin"),
+ 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();
git://source.jalview.org / proteocache.git / blobdiff