import org.springframework.security.core.context.SecurityContextHolder;
import org.springframework.security.core.userdetails.UserDetails;
- import compbio.cassandra.CassandraReader;
import compbio.cassandra.DateFormatter;
+ import compbio.cassandra.readers.CassandraReader;
public class BasicController {
final protected SimpleDateFormat formaterDDMMYY = DateFormatter.getFormatDDMMYY();
protected Calendar cal = Calendar.getInstance();
protected String theEaerlistDate = DateFormatter.DateLongToString(CassandraReader.earliestDate(), formaterYYMMDD);
protected String theCurrentDate = cal.get(Calendar.YEAR) + "/" + (cal.get(Calendar.MONTH) + 1) + "/" + cal.get(Calendar.DAY_OF_MONTH);
-
+
protected String getPrincipalName() {
Object principal = SecurityContextHolder.getContext().getAuthentication().getPrincipal();
if (principal instanceof UserDetails) {
}
return false;
}
-
+
protected String DateChecking(String trimmeddate1, String trimmeddate2, long longDate1, long longDate2) {
Calendar cal2 = Calendar.getInstance();
- if (trimmeddate1.equalsIgnoreCase("") || trimmeddate2.equalsIgnoreCase(""))
+ if (trimmeddate1.equalsIgnoreCase("") || trimmeddate2.equalsIgnoreCase(""))
return "The date cann't be empty";
- else if (!DateFormatter.isThisDateValid(trimmeddate1, formaterYYMMDD) || !DateFormatter.isThisDateValid(trimmeddate2, formaterYYMMDD))
+ 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())
+ else if (longDate2 < CassandraReader.earliestDate())
return "The date2 is after the earlestDate " + theEaerlistDate;
else if (longDate1 > cal2.getTimeInMillis())
return "The date1 is before the current date " + theCurrentDate;
- else if (longDate1 > longDate2)
+ else if (longDate1 > longDate2)
return "Wrong date's diaposon. The date1 is more than date2.";
- else
+ else
return null;
}
}
import org.springframework.web.bind.annotation.RequestParam;
import compbio.engine.JobStatus;
- import compbio.cassandra.CassandraReader;
- import compbio.cassandra.DateBean;
+ import compbio.beans.DateBean;
+ import compbio.beans.TotalJobsStatisticBean;
import compbio.cassandra.DateFormatter;
- import compbio.cassandra.Total;
- import compbio.cassandra.TotalJobsStatisticBean;
- import compbio.statistic.CassandraRequester;
++
++import compbio.beans.Total;
+ import compbio.cassandra.readers.CassandraReader;
+ import compbio.cassandra.readers.DailyStatisticsReader;
-import compbio.cassandra.readers.ProteoDAO;
++
/**
* @author Alexander Sherstnev
* the final date for the report (if option is set, date2 =
* today)
* @param option
- * defined whether the whole time range of jobs is reported
- * (null means date1 and date2 are used)
+ * defined whether the whole time range of jobs is reported (null
+ * means date1 and date2 are used)
* @return link to the report JSP page
*/
@RequestMapping(value = "/stat/jobsdaily/results", method = RequestMethod.GET)
model.put("username", getPrincipalName());
Calendar loccal = Calendar.getInstance();
final long startTime = System.currentTimeMillis();
- CassandraRequester cr = new CassandraRequester();
+ DailyStatisticsReader reader = new DailyStatisticsReader();
if (option.equals("AllDates,off")) {
date1 = theEaerlistDate;
date2 = theCurrentDate;
date2 = DateFormatter.DateLongToString(longDate2, formaterYYMMDD);
model.put("date1", date1);
model.put("date2", date2);
- TotalJobsStatisticBean res = cr.countJobs(date1, date2);
+ TotalJobsStatisticBean res = reader.query(longDate1, longDate2);
model.put("result", res);
+ Map<String, Total> results = res.getDateTotal();
+ String csvline = "\'Date\',\'Total\',\'OK\',\'Stopped\',\'Error\',\'Timeout\'%0A";
+ for (Map.Entry<String, Total> entry : results.entrySet()) {
+ csvline += "\'" + entry.getKey() + "\',\'" + entry.getValue().getTotal() + "\',\'" + entry.getValue().getTotalOK() + "\',\'"
+ + entry.getValue().getTotalStopped() + "\',\'" + entry.getValue().getTotalError() + "\',\'"
+ + entry.getValue().getTotalTimeOut() + "\'%0A";
+ }
+ model.put("csvfile", csvline);
model.put("ndays", res.getDateTotal().size());
final long endTime = System.currentTimeMillis();
model.put("timeExecution", (endTime - startTime));
final long startTime = System.currentTimeMillis();
String realdate;
+ long thetime = 0;
try {
- long thetime = formaterYYMMDD.parse(date).getTime();
+ thetime = formaterYYMMDD.parse(date).getTime();
if (thetime < 0) {
realdate = date;
} else {
}
} catch (ParseException e) {
realdate = date;
+ thetime = formaterDDMMYY.parse(realdate).getTime();
}
-
+
if (null == JobStatus.getJobStatus(status)) {
return "support/Notimplemented";
}
- CassandraRequester cr = new CassandraRequester();
+ DailyStatisticsReader reader = new DailyStatisticsReader();
// IMPORTANT: input should be suppied in the format: DD/MM/YYYY
- DateBean r = cr.readJobByDay(realdate, JobStatus.getJobStatus(status));
+ DateBean r = reader.readJobByDay(thetime, realdate, JobStatus.getJobStatus(status));
model.put("results", r);
if (r != null)
model.put("njobs", r.getJobidAndSeq().size());
import org.springframework.web.bind.annotation.RequestMethod;
import org.springframework.web.bind.annotation.RequestParam;
- import compbio.cassandra.TotalByCounterBean;
- import compbio.cassandra.UserBean;
+ import compbio.beans.TotalByCounterBean;
+ import compbio.beans.UserBean;
+ import compbio.cassandra.readers.IpReader;
+ import compbio.cassandra.readers.ReaderByCounter;
import compbio.statistic.CassandraRequester;
/**
@RequestMapping(value = "/admin/ip/query", method = RequestMethod.GET)
public String initOneIPForm(Map<String, Object> model) {
model.put("username", getPrincipalName());
- model.put("value", "127.0.0.1");
+ CassandraRequester cr = new CassandraRequester();
+ model.put("value", cr.getExample("ip"));
return "query/IP";
}
}
final long startTime = System.currentTimeMillis();
- CassandraRequester cr = new CassandraRequester();
- List<TotalByCounterBean> r = cr.readIpByCounter(realcounter);
+ ReaderByCounter reader = new ReaderByCounter();
+ List<TotalByCounterBean> r = reader.readIpByCounter(realcounter);
model.put("results", r);
model.put("njobs", 0);
+ String csvline = "";
if (null != r) {
model.put("njobs", r.size());
+ csvline = "\'Job%20 count\', \'IP\'%0A";
}
+ // form line for CSV file
+ for (TotalByCounterBean b : r) {
+ csvline += "\'" + b.getTotaljobs() + "\',\'" + b.getName() + "\'%0A";
+ }
+ model.put("csvfile", csvline);
final long endTime = System.currentTimeMillis();
model.put("timeExecution", (endTime - startTime));
model.put("counter", realcounter);
public String findIP(@RequestParam("ip") String ip, Map<String, Object> model) {
model.put("username", getPrincipalName());
final long startTime = System.currentTimeMillis();
- CassandraRequester cr = new CassandraRequester();
- UserBean r = cr.readIp(ip);
+ IpReader reader = new IpReader();
+ UserBean r = reader.readIp(ip);
model.put("results", r);
model.put("njobs", 0);
if (null != r) {
import java.util.List;
import java.util.Map;
+import org.apache.log4j.Logger;
import org.springframework.stereotype.Controller;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestMethod;
import compbio.statistic.CassandraRequester;
import compbio.cassandra.DataBase;
+ import compbio.cassandra.readers.JobReader;
import compbio.engine.archive.ArchivedJob;
/**
*/
@Controller
public class JobController extends BasicController {
+ private static Logger log = Logger.getLogger(JobController.class);
/**
- * form a query page for job execution time statistics. The servlet should be
- * available for users and admins only. By defaults the report time range is
- * from the earliest day with jobs to today ("Query for all dates" is
+ * form a query page for job execution time statistics. The servlet should
+ * be available for users and admins only. By defaults the report time range
+ * is from the earliest day with jobs to today ("Query for all dates" is
* ticked). If the user removes the tick the time range is from today - 3
* days to today. Currently, the input model is empty.
*
}
/**
- * form a query page for a job. The servlet should no be visible to users at all.
+ * form a query page for a job. The servlet should no be visible to users at
+ * all.
*
* @param model
* MVC model
@RequestMapping(value = "/job/query", method = RequestMethod.GET)
public String initFindForm(Map<String, Object> model) {
model.put("username", getPrincipalName());
- model.put("value", "jp_NzBOJKo");
+ CassandraRequester cr = new CassandraRequester();
+ model.put("value", cr.getExample("jobid"));
return "query/JobLog";
}
+ /**
+ * form a report page for a job execution time statistics.
+ *
+ * @param model
+ * MVC model
+ * @return link to the JSP query page
+ */
@RequestMapping(value = "/stat/exectime/results", method = RequestMethod.GET)
public String findExecTimeData(@RequestParam("date1") String date1, @RequestParam("date2") String date2,
@RequestParam(value = "option", required = false) String option, Map<String, Object> model) {
model.put("option", option);
List<DataBase> res = sp.extractExecutionTime(date1, date2);
model.put("result", res);
+ String csvline = "";
+ if (0 < res.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";
+ }
+ }
+ model.put("csvfile", csvline);
model.put("ndays", res.size() - 1);
final long endTime = System.currentTimeMillis();
model.put("timeExecution", (endTime - startTime));
return "/reportTimeExecution";
}
+ /**
+ * form a query page for a job. The servlet should no be visible to users at
+ * all.
+ *
+ * @param model
+ * MVC model
+ * @return link to the JSP query page
+ */
@RequestMapping(value = "/job/results", method = RequestMethod.GET)
public String findJob(@RequestParam("IdJob") String jobid, Map<String, Object> model) {
model.put("username", getPrincipalName());
final long startTime = System.currentTimeMillis();
- CassandraRequester cr = new CassandraRequester();
- model.put("result", cr.readJobLog(jobid));
+ JobReader reader = new JobReader();
+ model.put("result", reader.readJobLog(jobid));
final long endTime = System.currentTimeMillis();
model.put("timeExecution", (endTime - startTime));
model.put("IdJob", jobid);
try {
model.put("jobarchive", aj.prepareJobArchiveToWeb());
} catch (IOException e) {
- //TODO. what should we do if job is not available???
+ log.error("JobController.prepareJobArchiveToWeb: IO exception with job archive file");
+ log.error(e.getLocalizedMessage(), e.getCause());
}
return "reportJobLog";
}
- /*
- * convert ???
+ /**
+ * convert date from the standard long representation (milliseconds from 1
+ * Jan 1970) to yyyy/mm/dd
+ *
+ * @param indate
+ * date in milliseconds from 1 Jan 1970
+ * @return date in the form of yyyy/mm/dd
*/
private String DateFormatYYMMDD(long indate) {
SimpleDateFormat datformat = new SimpleDateFormat("yyyy/MM/dd");
package compbio.controllers;
+import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import java.util.regex.Pattern;
import org.springframework.web.bind.annotation.RequestMethod;
import org.springframework.web.bind.annotation.RequestParam;
- import compbio.cassandra.DataBase;
- import compbio.cassandra.ProteinBean;
- import compbio.cassandra.Total;
- import compbio.cassandra.TotalByCounterBean;
- import compbio.statistic.CassandraRequester;
+ import compbio.beans.ProteinBean;
+ import compbio.beans.TotalByCounterBean;
+ import compbio.cassandra.readers.ReaderByCounter;
+ import compbio.cassandra.readers.SequenceReader;
-import compbio.statistic.CassandraRequester;
/**
* Spring controller for sequence queries. This version works in the servlet
*/
private final Pattern NONPROTEIN = Pattern.compile("[^ARNDCQEGHILKMFPSTWYV]+", Pattern.CASE_INSENSITIVE);
+ /**
+ * form a query page for search protein sequence. The servlet should be
+ * available for users and admins only.
+ *
+ * @param model
+ * MVC model
+ * @return link to the JSP query page
+ */
@RequestMapping(value = "query", method = RequestMethod.GET)
public String formSequenceQuery(Map<String, Object> model) {
model.put("username", getPrincipalName());
return "query/Sequence";
}
+ /**
+ * form a query page for statistics: Protein by job count. The servlet should be
+ * available for users and admins only.
+ *
+ * @param model
+ * MVC model
+ * @return link to the JSP query page
+ */
@RequestMapping(value = "counts/query", method = RequestMethod.GET)
public String formCounterQuery(Map<String, Object> model) {
model.put("username", getPrincipalName());
return "query/SequenceCounts";
}
+ /**
+ * form a report page for search protein sequence.
+ *
+ * @param model
+ * MVC model object
+ * @param sequence
+ * protein sequence or part of sequence
+ * @param searchtype
+ * defined whether the whole sequence or part of sequence would be searched
+ * @return link to the report JSP page
+ */
@RequestMapping(value = "sequence/results", method = RequestMethod.GET)
public String findSequence(@RequestParam("sequence") String sequence, @RequestParam("searchtype") String searchtype,
Map<String, Object> model) {
model.put("njobs", 0);
model.put("prot", trimmedsequence);
model.put("searchtype", searchtype);
-
+ String csvline = "";
if (0 < trimmedsequence.length()) {
- CassandraRequester cr = new CassandraRequester();
- List<ProteinBean> r = cr.readProteins(trimmedsequence, searchtype);
- model.put("results", r);
- if (null != r) {
+ SequenceReader reader = new SequenceReader();
+ List<ProteinBean> result = reader.readProteins(trimmedsequence, searchtype);
+ model.put("results", result);
+ if (null != result) {
if (searchtype.equals("whole"))
- model.put("njobs", r.get(0).getJobid().size());
+ model.put("njobs", result.get(0).getJobid().size());
else
- model.put("njobs", r.size());
+ model.put("njobs", result.size());
+ csvline = "\'Job\',\'Annotation\',\'Sequence\'%0A";
+ }
+ // form CSV file string
- for (ProteinBean entry : r) {
++ for (ProteinBean entry : result) {
+ List<String> jobs = entry.getJobid();
+ String protein = entry.getSequence();
+ LinkedHashMap<String, String> predictions = entry.getPredictions();
+ for (String job : jobs) {
+ csvline += "\'" + job + "\',\'Sequence\',\'" + protein + "\',\'%0A";
+ for (Map.Entry<String, String> pr : predictions.entrySet()) {
+ csvline += "\'\',\'" + pr.getKey() + "\',\'" + pr.getValue() + "\'%0A";
+ }
+ }
}
}
+ model.put("csvfile", csvline);
+
final long endTime = System.currentTimeMillis();
model.put("timeExecution", (endTime - startTime));
return "reportProteinSequences";
}
+ /**
+ * form a report page for statistics: Protein by job count.
+ *
+ * @param model
+ * MVC model object
+ * @param counter
+ *
+ * @return link to the report JSP page
+ */
@RequestMapping(value = "counts/results", method = RequestMethod.GET)
public String countSequences(@RequestParam("counterJob") String counter, Map<String, Object> model) {
model.put("username", getPrincipalName());
return "query/SequenceCounts";
}
- CassandraRequester cr = new CassandraRequester();
- List<TotalByCounterBean> r = cr.readProteinByCounter(realcounter);
- ReaderByCounter reader = new ReaderByCounter();
+
++ ReaderByCounter reader = new ReaderByCounter();
+ List<TotalByCounterBean> r = reader.readProteinByCounter(realcounter);
+ model.put("results", r);
model.put("njobs", 0);
+ String csvline = "";
if (null != r) {
model.put("njobs", r.size());
+ csvline = "\'Job%20 count\', \'Protein%20Sequence\'%0A";
}
+ // form line for CSV file
+
+ for (TotalByCounterBean b : r) {
+ if (b.getName().equals("")) {
+ csvline += "\'" + b.getTotaljobs() + "\',\'Alignment%20job\'%0A";
+ // fix problem with records without protein sequence (alignment
+ // jobs)
+ b.setName("Alignment job");
+ } else {
+ csvline += "\'" + b.getTotaljobs() + "\',\'" + b.getName() + "\'%0A";
+ }
+ }
+ model.put("csvfile", csvline);
+
+ model.put("results", r);
final long endTime = System.currentTimeMillis();
model.put("timeExecution", (endTime - startTime));
model.put("counter", realcounter);
import java.util.List;
import java.util.Map;
- import compbio.cassandra.DateBean;
- import compbio.cassandra.ProteinBean;
+ import compbio.beans.DateBean;
+ import compbio.beans.JobBean;
+ import compbio.beans.ProteinBean;
+ import compbio.beans.Total;
+ import compbio.beans.TotalByCounterBean;
+ import compbio.beans.TotalJobsStatisticBean;
+ import compbio.beans.UserBean;
import compbio.cassandra.CassandraNativeConnector;
import compbio.cassandra.CassandraReaderOld;
import compbio.cassandra.DataBase;
import compbio.cassandra.Pair;
- import compbio.cassandra.JobBean;
- import compbio.cassandra.Total;
- import compbio.cassandra.TotalByCounterBean;
- import compbio.cassandra.TotalJobsStatisticBean;
- import compbio.cassandra.UserBean;
import compbio.engine.JobStatus;
public class CassandraRequester {
query.add(db);
}
+ /* ???? Very strange code...
DataBase db = new DataBase();
db.setTimeTotalExec(totalTime);
query.add(db);
+ */
return query;
}
/*
* query: total number of jobs for the period from date1 till date2
- */
+ */
public TotalJobsStatisticBean countJobs(String date1, String date2) {
- /* if (null == date1) {
- date1 = "1970/1/1";
- }
- if (null == date2) {
- date1 = "2100/1/1";
- }
- if (!isThisDateValid(date1, formatYYMMDD) || !isThisDateValid(date2, formatYYMMDD)) {
- System.out.println("CassandraRequester.countJobs: wrong format for date1 " + date1 + "or date2 " + date2);
- return null;
- }*/
+ /*
+ * if (null == date1) { date1 = "1970/1/1"; } if (null == date2) { date1
+ * = "2100/1/1"; } 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)
- return null;
- if (dateStart < earlestDate)
- dateStart = earlestDate;
- if (dateEnd > currentDate)
- dateStart = currentDate;*/
+ /*
+ * if (dateEnd < earlestDate || dateStart > currentDate || dateStart >
+ * dateEnd) return null; if (dateStart < earlestDate) dateStart =
+ * earlestDate; if (dateEnd > currentDate) dateStart = currentDate;
+ */
Calendar start = Calendar.getInstance();
start.setTime(new Date(dateStart));
Calendar end = Calendar.getInstance();
long day = DateParsing(date, formatDDMMYY);
if (day < earlestDate || day > currentDate)
return null;
-
+
if (status == JobStatus.OK) {
return db.ReadProteinData(day, date);
}
}
return result;
}
-
+
/*
* query: protein feature
*/
public Map<String, String> readProteinsPrediction(String feature, int percent) {
- Map<String, String> result = db.ReadProtein();;
+ Map<String, String> result = db.ReadProtein();
+ ;
if (result == null)
return null;
Map<String, String> query = new HashMap<String, String>();
for (Map.Entry<String, String> entry : result.entrySet()) {
- String pred = entry.getValue();
- if (pred.replaceAll("[^"+feature+"]", "").length() > pred.length() * percent / 100 && (!entry.getKey().equals(""))) {
- // if (!entry.getKey().equals(""))
- query.put(entry.getKey(), pred);
- }
+ String pred = entry.getValue();
+ if (pred.replaceAll("[^" + feature + "]", "").length() > pred.length() * percent / 100 && (!entry.getKey().equals(""))) {
+ // if (!entry.getKey().equals(""))
+ query.put(entry.getKey(), pred);
+ }
}
return query;
}
return earlestDate;
}
+ /**
+ * prepares an example of either job id or IP for the DB
+ *
+ * @param exampletype
+ * defines which example you need (an existing job from the DB -
+ * jobid, an IP - "ip")
+ * @return a string representation of the requested example, if the example
+ * type is not known empty string is returned
+ */
+ public String getExample(String exampletype) {
+ if (exampletype.equals("jobid")) {
+ return "jp_NzBOJKo";
+ } else if (exampletype.equals("ip")) {
+ return "127.0.0.1";
+ }
+ return "";
+ }
+
}
git://source.jalview.org / proteocache.git / commitdiff