#################################################################################
# Cassandra host or IP
# test server is 10.0.115.190
-#cassandra.host=localhost
+cassandra.host=localhost
#cassandra.host=gjb-www-1.cluster.lifesci.dundee.ac.uk
-cassandra.host=c6100-1.cluster.lifesci.dundee.ac.uk
+#cassandra.host=c6100-1.cluster.lifesci.dundee.ac.uk
cassandra.newtables.update=false
cassandra.version.update=false
#################################################################################
# Jpred sources
# real Jpred web-server
-cassandra.jpred.web.update=true
+cassandra.jpred.web.update=false
cassandra.jpred.web.inidelay=0
cassandra.jpred.web.updaterate=30
--- /dev/null
+package compbio.beans;
+
+import java.util.LinkedHashMap;
+import java.util.Map;
+
+ /**
+ * bean for a report of execution time statistics.
+ *
+ * @param dateTotal
+ * Map<String, TotalExecutionTime> where String - a date, Total - total info for
+ * jobs with period of execution time
+ * @param wholeTotal
+ * total sum for each parameter from dateTotal
+ */
+ public class ExecutionTimeBean {
+ private Map<String, TotalExecutionTime> dateTotal;
+ private TotalExecutionTime wholeTotal;
+
+ public ExecutionTimeBean() {
+ this.dateTotal = new LinkedHashMap<String, TotalExecutionTime>();
+ }
+
+ public void setDateTotal(String dat, TotalExecutionTime tot) {
+ if (this.dateTotal == null)
+ dateTotal = new LinkedHashMap<String, TotalExecutionTime>();
+ dateTotal.put(dat, tot);
+ }
+
+ public Map<String, TotalExecutionTime> getDateTotal() {
+ return dateTotal;
+ }
+
+ public void setWholeTotal(TotalExecutionTime tot) {
+ this.wholeTotal = tot;
+ }
+
+ public TotalExecutionTime getWholeTotal() {
+ return wholeTotal;
+ }
+}
--- /dev/null
+package compbio.beans;
+
+ /**
+ * bean is stored Total for a ExecutionTimeBean.
+ *
+ * @param total
+ * total number of jobs for a day
+ * @param total0_30s
+ * number of jobs with execution time 0 - 30 s for a date
+ * @param total30_60s
+ * number of jobs with execution time 30 - 60 s for a date
+ * @param total1_2m
+ * number of jobs with execution time 1-2 min for a date
+ * @param total2_10m
+ * number of jobs with execution time 2 - 10 min for a date
+ * @param total10m
+ * number of jobs with execution time more then 10 min for a date
+ */
+ public class TotalExecutionTime {
+ private long total;
+ private long total0_30s;
+ private long total30_60s;
+ private long total1_2m;
+ private long total2_10m;
+ private long total10m;
+
+ public TotalExecutionTime(long total, long total0_30s, long total30_60s, long total1_2m, long total2_10m, long total10m) {
+ this.total = total;
+ this.total0_30s = total0_30s;
+ this.total30_60s = total30_60s;
+ this.total1_2m = total1_2m;
+ this.total2_10m = total2_10m;
+ this.total10m = total10m;
+ }
+
+ public void setTotal(long tot) {
+ this.total = tot;
+ }
+
+ public long getTotal() {
+ return total;
+ }
+
+ public void setTotal0_30s(long tot) {
+ this.total0_30s = tot;
+ }
+
+ public long getTotal0_30s() {
+ return total0_30s;
+ }
+
+ public void setTotal30_60s(long tot) {
+ this.total30_60s = tot;
+ }
+
+ public long getTotal30_60s() {
+ return total30_60s;
+ }
+
+ public void setTotal1_2m(long tot) {
+ this.total1_2m = tot;
+ }
+
+ public long getTotal1_2m() {
+ return total1_2m;
+ }
+
+ public void setTotal2_10m(long tot) {
+ this.total2_10m = tot;
+ }
+
+ public long getTotal2_10m() {
+ return total2_10m;
+ }
+
+ public void setTotal10m(long tot) {
+ this.total10m = tot;
+ }
+
+ public long getTotal10m() {
+ return total10m;
+ }
+}
Calendar endcal = Calendar.getInstance();
long endTime = endcal.getTime().getTime();
for (Date date = runnicCal.getTime(); date.getTime() < endTime; runnicCal.add(Calendar.DATE, 1), date = runnicCal.getTime()) {
- try {
+ try {
String com = "SELECT JobID, Protein FROM ProteinData WHERE jobtime = " + date.getTime() + ";";
System.out.println(com);
ResultSet results = session.execute(com);
continue;
List<Row> rows = results.all();
System.out.println(rows.size());
+ int k=0;
for (Row r : rows) {
session.execute("UPDATE ProteinLog SET ProgramName = 'Jpred', ProgramVersion = '3.0.1' WHERE JobID = '"
+ r.getString("JobID") + "';");
session.execute("UPDATE JpredArchive SET ProgramName = 'Jpred', ProgramVersion = '3.0.1' WHERE JobID = '"
- + r.getString("JobID") + "';");
+ + r.getString("JobID") + "';");
}
} catch (QueryExecutionException e) {
e.printStackTrace();
--- /dev/null
+package compbio.cassandra.readers;
+
+import java.text.ParseException;
+import java.text.SimpleDateFormat;
+import java.util.ArrayList;
+import java.util.Calendar;
+import java.util.Date;
+import java.util.List;
+
+import com.datastax.driver.core.ResultSet;
+import com.datastax.driver.core.Row;
+
+import compbio.beans.ExecutionTimeBean;
+import compbio.beans.Total;
+import compbio.beans.TotalExecutionTime;
+import compbio.beans.TotalJobsStatisticBean;
+import compbio.cassandra.DataBase;
+import compbio.cassandra.DateFormatter;
+import compbio.cassandra.Pair;
+
+public class ExecutionTimeReader extends CassandraReader {
+
+ public ExecutionTimeReader() {
+ super();
+ }
+
+ /**
+ * query: execution time statistics for the period from date1 till date2
+ *
+ * @param dateStart
+ * the first date in the period
+ * @param dateEnd
+ * the last date in the period
+ *
+ * @return TotalJobsStatisticBean to the controller
+ * JobController
+ **/
+ public ExecutionTimeBean query(long dateStart, long dateEnd) {
+ Calendar start = Calendar.getInstance();
+ start.setTime(new Date(dateStart));
+ Calendar end = Calendar.getInstance();
+ end.setTime(new Date(dateEnd));
+ ExecutionTimeBean query = new ExecutionTimeBean();
+ TotalExecutionTime wholeTotal = new TotalExecutionTime(0, 0, 0, 0, 0, 0);
+
+ for (Date date = end.getTime(); !end.before(start); end.add(Calendar.DATE, -1), date = end.getTime()) {
+ ResultSet results = CassandraQuery("SELECT ExecTime FROM ProteinData WHERE jobtime = " + date.getTime() + ";");
+ if (results == null)
+ return null;
+ if (results.isExhausted())
+ continue;
+ List<Row> rows = results.all();
+ TotalExecutionTime currentTotal = new TotalExecutionTime(0, 0, 0, 0, 0, 0);
+ for (Row r : rows) {
+ long timeExec = r.getInt("ExecTime")/1000;
+ if (timeExec <= 30)
+ currentTotal.setTotal0_30s(currentTotal.getTotal0_30s() + 1);
+ else if (timeExec > 30 && timeExec <= 60)
+ currentTotal.setTotal30_60s(currentTotal.getTotal30_60s() + 1);
+ else if (timeExec > 60 && timeExec <= 120)
+ currentTotal.setTotal1_2m(currentTotal.getTotal1_2m() + 1);
+ else if (timeExec > 120 && timeExec <= 600)
+ currentTotal.setTotal2_10m(currentTotal.getTotal2_10m() + 1);
+ else
+ currentTotal.setTotal10m(currentTotal.getTotal10m() + 1);
+
+ }
+ currentTotal.setTotal(currentTotal.getTotal0_30s() + currentTotal.getTotal30_60s() + currentTotal.getTotal1_2m() +
+ currentTotal.getTotal2_10m() + currentTotal.getTotal10m());
+ query.setDateTotal(DateFormatter.DateLongToString(date.getTime(), DateFormatter.getFormatDDMMYY()), currentTotal);
+ wholeTotal.setTotal(currentTotal.getTotal() + wholeTotal.getTotal());
+ wholeTotal.setTotal0_30s(currentTotal.getTotal0_30s() + wholeTotal.getTotal0_30s());
+ wholeTotal.setTotal30_60s(currentTotal.getTotal30_60s() + wholeTotal.getTotal30_60s());
+ wholeTotal.setTotal1_2m(currentTotal.getTotal1_2m() + wholeTotal.getTotal1_2m());
+ wholeTotal.setTotal2_10m(currentTotal.getTotal2_10m() + wholeTotal.getTotal2_10m());
+ wholeTotal.setTotal10m(currentTotal.getTotal10m() + wholeTotal.getTotal10m());
+ }
+ query.setWholeTotal(wholeTotal);
+ return query;
+
+ }
+}
import org.springframework.web.bind.annotation.RequestParam;
import compbio.statistic.CassandraRequester;
+import compbio.beans.ExecutionTimeBean;
+import compbio.beans.Total;
+import compbio.beans.TotalExecutionTime;
+import compbio.beans.TotalJobsStatisticBean;
import compbio.cassandra.DataBase;
+import compbio.cassandra.DateFormatter;
+import compbio.cassandra.readers.CassandraReader;
+import compbio.cassandra.readers.ExecutionTimeReader;
import compbio.cassandra.readers.JobReader;
import compbio.engine.archive.ArchivedJob;
@RequestParam(value = "option", required = false) String option, Map<String, Object> model) {
model.put("username", getPrincipalName());
final long startTime = System.currentTimeMillis();
-
- CassandraRequester sp = new CassandraRequester();
+ Calendar loccal = Calendar.getInstance();
+ ExecutionTimeReader reader = new ExecutionTimeReader();
if (option.equals("AllDates,off")) {
- Calendar cal = Calendar.getInstance();
- date1 = DateFormatYYMMDD(sp.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/JobTimeExecution";
}
+
+ if (longDate1 < CassandraReader.earliestDate())
+ longDate1 = CassandraReader.earliestDate();
+ if (longDate2 > loccal.getTimeInMillis())
+ longDate2 = loccal.getTimeInMillis();
+
+ date1 = DateFormatter.DateLongToString(longDate1, formaterYYMMDD);
+ date2 = DateFormatter.DateLongToString(longDate2, formaterYYMMDD);
model.put("date1", date1);
model.put("date2", date2);
model.put("option", option);
- List<DataBase> res = sp.extractExecutionTime(date1, date2);
+ ExecutionTimeBean res = reader.query(longDate1, longDate2);;
model.put("result", res);
+ Map<String, TotalExecutionTime> results = res.getDateTotal();
String csvline = "";
- if (0 < res.size()) {
+ if (0 < res.getDateTotal().size()) {
csvline = "\'Date\',\'Total\',\'0-30 sec\',\'30-60 sec\',\'1-2 min\',\'2-10 min\',\'more 10 min\'%0A";
- for (DataBase entry : res) {
- List<Integer> counts = entry.getTimeRez();
- int total = 0;
- for (int i = 0; i < counts.size(); ++i) {
- total += counts.get(i);
- }
- csvline += "\'" + entry.getDate() + "\',\'" + total;
- for (int i = 0; i < counts.size(); ++i) {
- csvline += "\',\'" + counts.get(i);
- }
- csvline += "\'%0A";
+ for (Map.Entry<String, TotalExecutionTime> entry : results.entrySet()) {
+ csvline += "\'" + entry.getKey() + "\',\'" + entry.getValue().getTotal() + "\',\'" + entry.getValue().getTotal0_30s() + "\',\'"
+ + entry.getValue().getTotal30_60s() + "\',\'" + entry.getValue().getTotal1_2m() + "\',\'"
+ + entry.getValue().getTotal2_10m() + "\',\'" + entry.getValue().getTotal10m() + "\'%0A";
}
}
model.put("csvfile", csvline);
- model.put("ndays", res.size() - 1);
+ model.put("ndays", res.getDateTotal().size() - 1);
final long endTime = System.currentTimeMillis();
model.put("timeExecution", (endTime - startTime));
return "/reports/TimeExecution";
</div>
<div class="panel-body">
- <c:set var="sum" value="0" />
- <c:forEach items="${result}" var="res" varStatus="loop">
- <c:choose>
- <c:when test="${loop.last}">
- <c:forEach items="${res.timeTotalExec}" var="total">
- <c:set var="sum" value="${sum + total}" />
- </c:forEach>
- </c:when>
- </c:choose>
- </c:forEach>
-
- <p>There are ${sum} jobs in total</p>
-
- <table class="table table-striped table-hover table-bordered">
- <thead>
+ <c:choose>
+ <c:when test="${result == null}">
+ <p>No jobs for this period</p>
+ </c:when>
+ <c:otherwise>
+ <div class="table-responsive">
+ <table class="table table-striped table-hover table-bordered">
+ <thead>
<tr>
<th style="text-align: center; width: 150px">Date</th>
<th style="text-align: center; width: 150px">Total</th>
</tr>
</thead>
<tbody>
- <c:forEach items="${result}" var="res" varStatus="loop">
- <c:choose>
- <c:when test="${loop.last}">
- <tr style="font-weight: bolder;">
- <td style="text-align: right">Total numbers:</td>
- <c:set var="alldaytotal" value="0"/>
- <c:forEach items="${res.timeTotalExec}" var="total">
- <c:set var="alldaytotal" value="${alldaytotal + total}"/>
- </c:forEach>
- <td style="text-align: right">${alldaytotal}</td>
- <c:forEach items="${res.timeTotalExec}" var="total">
- <td style="text-align: right">${total}</td>
- </c:forEach>
- </tr>
- </c:when>
- </c:choose>
- </c:forEach>
+ <tr style="font-weight: bolder;">
+ <td style="text-align: center">Total:</td>
+ <c:set var="total" value="${result.wholeTotal}"/>
+ <td style="text-align: right">${total.total}</td>
+ <td style="text-align: right">${total.total0_30s}</td>
+ <td style="text-align: right">${total.total30_60s}</td>
+ <td style="text-align: right">${total.total1_2m}</td>
+ <td style="text-align: right">${total.total2_10m}</td>
+ <td style="text-align: right">${total.total10m}</td>
+ </tr>
- <c:forEach items="${result}" var="res" varStatus="loop">
- <c:choose>
- <c:when test="${not loop.last}">
+ <c:forEach items="${result.dateTotal}" var="res">
<tr>
- <td style="text-align: center">${res.date}</td>
- <c:set var="daytotal" value="0"/>
- <c:forEach items="${res.timeRez}" var="time">
- <c:set var="daytotal" value="${daytotal + time}"/>
- </c:forEach>
- <td style="text-align: right">${daytotal}</td>
- <c:forEach items="${res.timeRez}" var="time">
- <td style="text-align: right">${time}</td>
- </c:forEach>
+ <td style="text-align: center">${res.key}</td>
+ <c:set var="value" value="${res.value}"/>
+ <td style="text-align: right">${value.total}</td>
+ <td style="text-align: right">${value.total0_30s}</td>
+ <td style="text-align: right">${value.total30_60s}</td>
+ <td style="text-align: right">${value.total1_2m}</td>
+ <td style="text-align: right">${value.total2_10m}</td>
+ <td style="text-align: right">${value.total10m}</td>
</tr>
- </c:when>
- </c:choose>
- </c:forEach>
+ </c:forEach>
</tbody>
</table>
+ </div>
+ </c:otherwise>
+ </c:choose>
</div>
</div>
git://source.jalview.org / proteocache.git / commitdiff