From: Sasha Sherstnev Date: Thu, 5 Dec 2013 09:44:49 +0000 (+0000) Subject: Fix problem due to new internal java beans X-Git-Url: http://source.jalview.org/gitweb/?p=proteocache.git;a=commitdiff_plain;h=68377f711516ef7566fac3371eb4962b86b3ba19 Fix problem due to new internal java beans --- diff --git a/server/compbio/controllers/DailyStatisticsController.java b/server/compbio/controllers/DailyStatisticsController.java index 5731b96..0fdd4b8 100644 --- a/server/compbio/controllers/DailyStatisticsController.java +++ b/server/compbio/controllers/DailyStatisticsController.java @@ -34,7 +34,7 @@ public class DailyStatisticsController { model.put("date1", date1); model.put("date2", date2); - + return "queryJobStatistics"; } @@ -53,13 +53,13 @@ public class DailyStatisticsController { model.put("date2", date2); TotalJobsStatisticBean res = cr.countJobs(date1, date2); model.put("result", res); - model.put("ndays", res.size()); + model.put("ndays", res.getDateTotal().size()); final long endTime = System.currentTimeMillis(); model.put("timeExecution", (endTime - startTime)); model.put("option", option); return "/reportJobStatistics"; } - + @RequestMapping(value = "/stat/oneday", method = RequestMethod.GET) public String findJobsInOneDay(@RequestParam("date") String date, Map model) throws ParseException { final long startTime = System.currentTimeMillis(); diff --git a/server/compbio/controllers/HelpController.java b/server/compbio/controllers/HelpController.java index cd16fff..e0345b1 100644 --- a/server/compbio/controllers/HelpController.java +++ b/server/compbio/controllers/HelpController.java @@ -5,6 +5,7 @@ import java.util.Map; import org.springframework.stereotype.Controller; import org.springframework.web.bind.annotation.RequestMapping; import org.springframework.web.bind.annotation.RequestMethod; + //import org.springframework.web.bind.annotation.RequestParam; /** @@ -24,12 +25,10 @@ public class HelpController { return "support/Notimplemented"; } - @RequestMapping(value = "/help/doc", method = RequestMethod.GET) public String formDocPage(Map model) { return "support/Notimplemented"; } - @RequestMapping(value = "/help/javadoc", method = RequestMethod.GET) public String formJavadoc(Map model) { diff --git a/server/compbio/controllers/SequenceController.java b/server/compbio/controllers/SequenceController.java index 62ec81e..4bb9271 100644 --- a/server/compbio/controllers/SequenceController.java +++ b/server/compbio/controllers/SequenceController.java @@ -16,7 +16,8 @@ import compbio.cassandra.TotalByCounterBean; import compbio.statistic.CassandraRequester; /** - * Spring controller for sequence search. This version works in the servlet style. + * Spring controller for sequence search. This version works in the servlet + * style. * * @author Alexander Sherstnev * @author Natasha Sherstneva @@ -26,9 +27,9 @@ import compbio.statistic.CassandraRequester; */ @Controller public class SequenceController { - + /** - * pattern for NON-protein alphabet symbols + * pattern for NON-protein alphabet symbols */ private final Pattern NONPROTEIN = Pattern.compile("[^ARNDCQEGHILKMFPSTWYV]+", Pattern.CASE_INSENSITIVE); @@ -43,7 +44,7 @@ public class SequenceController { model.put("value", 5); return "queryProteinSequenceCounter"; } - + @RequestMapping(value = "/sequence/querysequence", method = RequestMethod.GET) public String findSequence(@RequestParam("sequence") String sequence, @RequestParam("protein") String flag, Map model) { final long startTime = System.currentTimeMillis(); @@ -71,7 +72,7 @@ public class SequenceController { model.put("results", r); if (null != r) { if (flag.equals("whole")) - model.put("njobs",r.get(0).getJobid().size()); + model.put("njobs", r.get(0).getJobid().size()); else model.put("njobs", r.size()); } diff --git a/server/compbio/statistic/CassandraRequester.java b/server/compbio/statistic/CassandraRequester.java index c150d9d..5ed9398 100755 --- a/server/compbio/statistic/CassandraRequester.java +++ b/server/compbio/statistic/CassandraRequester.java @@ -39,7 +39,7 @@ public class CassandraRequester { if (null == date2) { date1 = "2100/1/1"; } - if (!isThisDateValid(date1,formatYYMMDD) || !isThisDateValid(date2,formatYYMMDD)) { + if (!isThisDateValid(date1, formatYYMMDD) || !isThisDateValid(date2, formatYYMMDD)) { System.out.println("CassandraRequester.extractExecutionTime: wrong format for date1 " + date1 + "or date2 " + date2); return null; } @@ -116,9 +116,9 @@ public class CassandraRequester { query.add(db); return query; } - + /* - * query: total number of jobs for the period from date1 till date2 + * query: total number of jobs for the period from date1 till date2 */ public TotalJobsStatisticBean countJobs(String date1, String date2) { if (null == date1) { @@ -146,7 +146,7 @@ public class CassandraRequester { Calendar end = Calendar.getInstance(); end.setTime(new Date(dateEnd)); TotalJobsStatisticBean query = new TotalJobsStatisticBean(); - Total wholeTotal = new Total(0,0,0,0,0); + Total wholeTotal = new Total(0, 0, 0, 0, 0); for (Date date = start.getTime(); !start.after(end); start.add(Calendar.DATE, 1), date = start.getTime()) { Total res = db.ReadDateTable(date.getTime()); if (res == null) @@ -165,7 +165,7 @@ public class CassandraRequester { /* * query: jobs and sequence at date */ - public DateBean readJobByDay (String date) { + public DateBean readJobByDay(String date) { if (!isThisDateValid(date, formatDDMMYY)) { System.out.println("CassandraRequester.readJobByDay: Wrong date format for " + date); return null; @@ -173,36 +173,34 @@ public class CassandraRequester { SetDateRange(); long day = DateParsing(date, formatDDMMYY); if (day < earlestDate || day > currentDate) - return null; + return null; return db.ReadProteinData(day, date); } - - /* + /* * query: protein sequence - **/ + */ public List readProteins(String protIn, String flag) { List result; - if (flag.equals("whole")) + if (flag.equals("whole")) result = db.ReadWholeSequence(protIn); - else - result = db.ReadPartOfSequence(protIn); + else + result = db.ReadPartOfSequence(protIn); if (result == null) return null; - + if (flag.equals("part")) { for (ProteinBean entry : result) { entry.setSubProt(CreateSubprot(entry.getSequence(), protIn)); } - } + } return result; } - - /* + /* * query protein sequences with number of jobs */ - public List readProteinByCounter(int minimalcounter) { + public List readProteinByCounter(int minimalcounter) { List query = new ArrayList(); Map map = db.ReadProteinSequenceByCounter(); if (map == null) @@ -217,8 +215,8 @@ public class CassandraRequester { } return query; } - - /* + + /* * query ip with number of jobs */ public List readIpByCounter(Integer minimalcounter) { @@ -238,6 +236,7 @@ public class CassandraRequester { } return query; } + /* * query jobs log info */ @@ -246,8 +245,7 @@ public class CassandraRequester { return null; return db.ReadJobLog(jobid); } - - + /* * query jobs by ipStructureJobLog */ @@ -255,17 +253,17 @@ public class CassandraRequester { if (ip == null) return null; Map res = db.ReadIpWithJobs(ip); - if (res == null) + if (res == null) return null; UserBean query = new UserBean(ip); query.setMainInfo(res); return query; } - + /* * create list of parts of protein sequence; */ - private static List CreateSubprot (String protein, String subprot) { + private static List CreateSubprot(String protein, String subprot) { List sub = new ArrayList(); String subStr = protein; while (subStr.length() > 0 && subStr.contains(subprot)) { @@ -279,6 +277,7 @@ public class CassandraRequester { sub.add(subStr); return sub; } + /* * convert String date into long date (miliseconds since the epoch start) */ @@ -287,7 +286,7 @@ public class CassandraRequester { return 0; } long dateWorkSt = 0; - + try { dateWorkSt = formatter.parse(datInput).getTime(); } catch (ParseException e) { @@ -308,7 +307,8 @@ public class CassandraRequester { */ private static void SetDateRange() { Calendar cal = Calendar.getInstance(); - currentDate = DateParsing(cal.get(Calendar.YEAR) + "/" + (cal.get(Calendar.MONTH) + 1) + "/" + cal.get(Calendar.DAY_OF_MONTH), formatYYMMDD); + currentDate = DateParsing(cal.get(Calendar.YEAR) + "/" + (cal.get(Calendar.MONTH) + 1) + "/" + cal.get(Calendar.DAY_OF_MONTH), + formatYYMMDD); if (0 == earlestDate) { CassandraRequester cr = new CassandraRequester(); earlestDate = cr.earliestDate(); @@ -337,5 +337,5 @@ public class CassandraRequester { earlestDate = CassandraNativeConnector.getEarliestDateInDB(); return earlestDate; } - + }