From: Sasha Sherstnev Date: Fri, 10 Jan 2014 15:15:38 +0000 (+0000) Subject: Merge branch 'DAO' X-Git-Url: http://source.jalview.org/gitweb/?p=proteocache.git;a=commitdiff_plain;h=6823d2f36ff55b7ab11d674e3fe4d04dc57d6bbf Merge branch 'DAO' Conflicts: server/compbio/controllers/DailyStatisticsController.java server/compbio/controllers/SequenceController.java --- 6823d2f36ff55b7ab11d674e3fe4d04dc57d6bbf diff --cc server/compbio/controllers/DailyStatisticsController.java index a9b51f1,75ab67a..403c220 --- a/server/compbio/controllers/DailyStatisticsController.java +++ b/server/compbio/controllers/DailyStatisticsController.java @@@ -11,12 -11,12 +11,14 @@@ import org.springframework.web.bind.ann 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 @@@ -100,16 -100,8 +102,16 @@@ public class DailyStatisticsController 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 results = res.getDateTotal(); + String csvline = "\'Date\',\'Total\',\'OK\',\'Stopped\',\'Error\',\'Timeout\'%0A"; + for (Map.Entry 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)); diff --cc server/compbio/controllers/IPDataController.java index 86f752e,b01caa7..d66b7cc --- a/server/compbio/controllers/IPDataController.java +++ b/server/compbio/controllers/IPDataController.java @@@ -59,20 -60,13 +61,20 @@@ public class IPDataController extends B } final long startTime = System.currentTimeMillis(); - CassandraRequester cr = new CassandraRequester(); - List r = cr.readIpByCounter(realcounter); + ReaderByCounter reader = new ReaderByCounter(); + List 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); diff --cc server/compbio/controllers/SequenceController.java index 738e2d8,105ef2f..76903f8 --- a/server/compbio/controllers/SequenceController.java +++ b/server/compbio/controllers/SequenceController.java @@@ -10,11 -9,11 +10,10 @@@ import org.springframework.web.bind.ann 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 @@@ -71,33 -97,18 +97,33 @@@ public class SequenceController extend model.put("njobs", 0); model.put("prot", trimmedsequence); model.put("searchtype", searchtype); - + String csvline = ""; if (0 < trimmedsequence.length()) { - CassandraRequester cr = new CassandraRequester(); - List r = cr.readProteins(trimmedsequence, searchtype); - model.put("results", r); - if (null != r) { + SequenceReader reader = new SequenceReader(); + List 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 jobs = entry.getJobid(); + String protein = entry.getSequence(); + LinkedHashMap predictions = entry.getPredictions(); + for (String job : jobs) { + csvline += "\'" + job + "\',\'Sequence\',\'" + protein + "\',\'%0A"; + for (Map.Entry 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"; @@@ -129,29 -149,14 +164,31 @@@ return "query/SequenceCounts"; } - CassandraRequester cr = new CassandraRequester(); - List r = cr.readProteinByCounter(realcounter); - ReaderByCounter reader = new ReaderByCounter(); + ++ ReaderByCounter reader = new ReaderByCounter(); + List 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); diff --cc server/compbio/statistic/CassandraRequester.java index 892fd8e,0d2ffc0..ca59844 --- a/server/compbio/statistic/CassandraRequester.java +++ b/server/compbio/statistic/CassandraRequester.java @@@ -122,15 -120,18 +122,15 @@@ public class CassandraRequester /* * 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);