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;
+import com.datastax.driver.core.Session;
public class CassandraReader {
+ private static long earlestDate = 0;
private Session session;
private static Logger log = Logger.getLogger(CassandraNativeConnector.class);
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;";
+
+ public ResultSet CassandraQuery(String column, String table, String condition) {
+ String com = "SELECT " + column + " FROM " + table + ";";
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;
+ return results;
}
-
+
/*
- * 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
+ * find the earliest date in the database
*/
- 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;
+ public static long earliestDate() {
+ earlestDate = CassandraNativeConnector.getEarliestDateInDB();
+ return earlestDate;
}
- /*
- * 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;
- }
+
}
--- /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;
+ }
+}
--- /dev/null
+package compbio.cassandra;
+
+import java.text.ParseException;
+import java.text.SimpleDateFormat;
+import java.util.Date;
+
+public class DateFormatter {
+ private final static SimpleDateFormat formatYYMMDD = new SimpleDateFormat("yyyy/MM/dd");
+ private final static SimpleDateFormat formatDDMMYY = new SimpleDateFormat("dd/MM/yyyy");
+
+ /*
+ * convert String date into long date (miliseconds since the epoch start)
+ */
+ public static long DateParsing(String datInput, SimpleDateFormat formatter) {
+ if (datInput == null) {
+ return 0;
+ }
+ long dateWorkSt = 0;
+
+ try {
+ dateWorkSt = formatter.parse(datInput).getTime();
+ } catch (ParseException e) {
+ e.printStackTrace();
+ }
+ return dateWorkSt;
+ }
+
+ /*
+ * date validator
+ * true - if valid date, false - if invalid
+ */
+ public static boolean isThisDateValid(String dateToValidate, SimpleDateFormat sdf) {
+ if (dateToValidate == null || dateToValidate.equals("")) {
+ return false;
+ }
+ try {
+ // if not valid, this will throw ParseException
+ sdf.setLenient(false);
+ Date date = sdf.parse(dateToValidate);
+ } catch (ParseException e) {
+ e.printStackTrace();
+ return false;
+ }
+ return true;
+ }
+
+ /*
+ * convert date from long to String
+ */
+ public static String DateLongToString(long indate, SimpleDateFormat formatter) {
+ String dateString = formatter.format(new Date(indate));
+ return dateString;
+ }
+
+ public static SimpleDateFormat getFormatYYMMDD() {
+ return formatYYMMDD;
+ }
+
+ public static SimpleDateFormat getFormatDDMMYY() {
+ return formatDDMMYY;
+ }
+}
import com.datastax.driver.core.PreparedStatement;
import com.datastax.driver.core.BoundStatement;
-import compbio.cassandra.CassandraReader;
+import compbio.cassandra.CassandraReaderOld;
import compbio.cassandra.Pair;
import compbio.engine.ProteoCachePropertyHelperManager;
import compbio.util.PropertyHelper;
import org.springframework.web.bind.annotation.RequestParam;
import compbio.engine.JobStatus;
+import compbio.cassandra.CassandraReader;
import compbio.cassandra.DateBean;
+import compbio.cassandra.DateFormatter;
import compbio.cassandra.TotalJobsStatisticBean;
import compbio.statistic.CassandraRequester;
-import compbio.statistic.StatisticsProt;
+
/**
* @author Alexander Sherstnev
*/
@Controller
public class DailyStatisticsController extends BasicController {
-
+ Calendar cal = Calendar.getInstance();
+ final SimpleDateFormat formaterDDMMYY = DateFormatter.getFormatDDMMYY();
+ final SimpleDateFormat formaterYYMMDD = DateFormatter.getFormatYYMMDD();
+ String theEaerlistDate = DateFormatter.DateLongToString(CassandraReader.earliestDate(), formaterYYMMDD);
+ String theCurrentDate = cal.get(Calendar.YEAR) + "/" + (cal.get(Calendar.MONTH) + 1) + "/" + cal.get(Calendar.DAY_OF_MONTH);
+
@RequestMapping(value = "/stat/jobs/query", method = RequestMethod.GET)
public String initFindForm(Map<String, Object> model) {
model.put("username", getPrincipalName());
- Calendar cal = Calendar.getInstance();
String date2 = cal.get(Calendar.YEAR) + "/" + (cal.get(Calendar.MONTH) + 1) + "/" + cal.get(Calendar.DATE);
cal.add(Calendar.DATE, -3);
String date1 = cal.get(Calendar.YEAR) + "/" + (cal.get(Calendar.MONTH) + 1) + "/" + cal.get(Calendar.DATE);
-
model.put("date1", date1);
model.put("date2", date2);
-
return "query/JobStatistics";
}
public String findJobsInPeriod(@RequestParam("date1") String date1, @RequestParam("date2") String date2,
@RequestParam("option") String option, Map<String, Object> model) {
model.put("username", getPrincipalName());
- final long startTime = System.currentTimeMillis();
-
+ final long startTime = System.currentTimeMillis();
CassandraRequester cr = new CassandraRequester();
if (option.equals("AllDates,off")) {
- Calendar cal = Calendar.getInstance();
- date1 = StatisticsProt.DateFormatYYMMDD(cr.earliestDate());
- date2 = cal.get(Calendar.YEAR) + "/" + (cal.get(Calendar.MONTH) + 1) + "/" + cal.get(Calendar.DAY_OF_MONTH);
+ date1 = theEaerlistDate;
+ date2 = theCurrentDate;
+ }
+
+ // dates in string format
+ String trimmeddate1 = date1.replaceAll("\\s", "");
+ String trimmeddate2 = date2.replaceAll("\\s", "");
+ // dates in long format
+ long longDate1 = DateFormatter.DateParsing(date1,formaterYYMMDD);
+ long longDate2 = DateFormatter.DateParsing(date2, formaterYYMMDD);
+ String error = DateChecking(trimmeddate1, trimmeddate2, longDate1, longDate2);
+ if (error != null) {
+ model.put("error", error);
+ model.put("date1", date1);
+ model.put("date2", date2);
+ return "query/JobStatistics";
}
+
+ if (longDate1 < CassandraReader.earliestDate())
+ longDate1 = CassandraReader.earliestDate();
+ if (longDate2 > cal.getTimeInMillis())
+ longDate2 = cal.getTimeInMillis();
+
+ date1 = DateFormatter.DateLongToString(longDate1, formaterYYMMDD);
+ date2 = DateFormatter.DateLongToString(longDate2, formaterYYMMDD);
model.put("date1", date1);
model.put("date2", date2);
TotalJobsStatisticBean res = cr.countJobs(date1, date2);
final long startTime = System.currentTimeMillis();
String realdate;
- final SimpleDateFormat formaterDDMMYY = new SimpleDateFormat("dd/MM/yyyy");
- final SimpleDateFormat formaterYYMMDD = new SimpleDateFormat("yyyy/MM/dd");
try {
long thetime = formaterYYMMDD.parse(date).getTime();
if (thetime < 0) {
model.put("timeExecution", (endTime - startTime));
return "/reportJobStatisticsOneDay";
}
+
+ private String DateChecking(String trimmeddate1, String trimmeddate2, long longDate1, long longDate2) {
+
+ if (trimmeddate1.equalsIgnoreCase("") || trimmeddate2.equalsIgnoreCase(""))
+ return "The date cann't be empty";
+ else if (!DateFormatter.isThisDateValid(trimmeddate1, formaterYYMMDD) || !DateFormatter.isThisDateValid(trimmeddate2, formaterYYMMDD))
+ return "The date format in invalid. Try format yyyy/mm/dd";
+ else if (longDate2 < CassandraReader.earliestDate())
+ return "The date2 is after the earlestDate " + theEaerlistDate;
+ else if (longDate1 > cal.getTimeInMillis())
+ return "The date1 is before the current date " + theCurrentDate;
+ else if (longDate1 > longDate2)
+ return "Wrong date's diaposon. The date1 is more than date2.";
+ else
+ return null;
+ }
}
import compbio.cassandra.DateBean;
import compbio.cassandra.ProteinBean;
import compbio.cassandra.CassandraNativeConnector;
-import compbio.cassandra.CassandraReader;
+import compbio.cassandra.CassandraReaderOld;
import compbio.cassandra.DataBase;
import compbio.cassandra.Pair;
import compbio.cassandra.JobBean;
import compbio.engine.JobStatus;
public class CassandraRequester {
- private CassandraReader db = new CassandraReader();
+ private CassandraReaderOld db = new CassandraReaderOld();
private ArrayList<DataBase> query;
private static long currentDate = 0;
private static long earlestDate = 0;
* query: total number of jobs for the period from date1 till date2
*/
public TotalJobsStatisticBean countJobs(String date1, String date2) {
- if (null == date1) {
+ /* if (null == date1) {
date1 = "1970/1/1";
}
if (null == date2) {
if (!isThisDateValid(date1, formatYYMMDD) || !isThisDateValid(date2, formatYYMMDD)) {
System.out.println("CassandraRequester.countJobs: wrong format for date1 " + date1 + "or date2 " + date2);
return null;
- }
+ }*/
SetDateRange();
long dateStart = DateParsing(date1, formatYYMMDD);
long dateEnd = DateParsing(date2, formatYYMMDD);
- if (dateEnd < earlestDate || dateStart > currentDate || dateStart > dateEnd)
+/* if (dateEnd < earlestDate || dateStart > currentDate || dateStart > dateEnd)
return null;
if (dateStart < earlestDate)
dateStart = earlestDate;
if (dateEnd > currentDate)
- dateStart = currentDate;
-
+ dateStart = currentDate;*/
Calendar start = Calendar.getInstance();
start.setTime(new Date(dateStart));
Calendar end = Calendar.getInstance();
<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
<%@ taglib prefix="spring" uri="http://www.springframework.org/tags"%>
+<%@ taglib prefix="c" uri="http://java.sun.com/jsp/jstl/core" %>
<%@ taglib prefix="fmt" uri="http://java.sun.com/jsp/jstl/fmt"%>
<%@ taglib prefix="fn" uri="http://java.sun.com/jsp/jstl/functions"%>
<%@ taglib prefix="form" uri="http://www.springframework.org/tags/form"%>
</div>
<div class="panel-body">
<form method="get" action="${query}">
- <p><input type="checkbox" name="option" value="AllDates" checked="checked" onclick="hide(this, 'date');"> Query for all dates<br>
- <div id='date' style="visibility:hidden;">
- <p>
- Jobs executed
- from <input type="text" name="date1" value="${date1}" style="width: 145px;" />
- to <input type="text" name="date2" value="${date2}" style="width: 145px;" />
- </p>
- </div>
- <input type="hidden" name="option" value="off" />
- <input type="submit" name="Search" value="Search" />
+ <c:choose>
+ <c:when test="${error == null}">
+ <div class="form-group">
+ <p><input type="checkbox" name="option" value="AllDates" checked="checked" onclick="hide(this, 'date');"> Query for all dates<br>
+ <div id='date' style="visibility:hidden;">
+ <p>
+ Jobs executed
+ from <input type="text" name="date1" value="${date1}" style="width: 145px;" />
+ to <input type="text" name="date2" value="${date2}" style="width: 145px;" />
+ </p>
+ </div>
+ <input type="hidden" name="option" value="off" />
+ <input type="submit" name="Search" value="Search" />
+ </div>
+ </c:when>
+ <c:otherwise>
+ <div class="form-group has-error">
+ <p><input type="checkbox" name="option" value="AllDates" onclick="hide(this, 'dateError');"> Query for all dates<br>
+ <div id='dateError' style="visibility:visible;">
+ <p>
+ Jobs executed
+ from <input type="text" name="date1" value="${date1}" style="width: 145px;" />
+ to <input type="text" name="date2" value="${date2}" style="width: 145px;" />
+ </p>
+ <p class="help-block">${error}</p>
+ </div>
+ <input type="hidden" name="option" value="off" />
+ <input type="submit" name="Search" value="Search" />
+ </div>
+ </c:otherwise>
+ </c:choose>
</form>
</div>
</div>
git://source.jalview.org / proteocache.git / commitdiff