X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=server%2Fcompbio%2Fstatistic%2FCassandraRequester.java;h=f4c4c18fa37105fc947a86d0a3e9580efc866784;hb=b154a542bd08371e3bcc7d92d0ded1c638399087;hp=2da38e76f54cccc193061a232e8801c4c959b3b8;hpb=ae38ab4dc7b6e22731c1d57765605304d36ccfa2;p=proteocache.git

diff --git a/server/compbio/statistic/CassandraRequester.java b/server/compbio/statistic/CassandraRequester.java
index 2da38e7..f4c4c18 100755
--- a/server/compbio/statistic/CassandraRequester.java
+++ b/server/compbio/statistic/CassandraRequester.java
@@ -9,18 +9,20 @@ import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 
+import compbio.cassandra.AnnotatedProteinSequenceBean;
 import compbio.cassandra.CassandraNativeConnector;
 import compbio.cassandra.CassandraReader;
 import compbio.cassandra.DataBase;
 import compbio.cassandra.Pair;
 import compbio.cassandra.StructureJobLog;
-import compbio.cassandra.StructureProteinPrediction;
 
 public class CassandraRequester {
 	private CassandraReader db = new CassandraReader();
 	private ArrayList<DataBase> query;
 	private static long currentDate = 0;
 	private static long earlestDate = 0;
+	private final static SimpleDateFormat formatYYMMDD = new SimpleDateFormat("yyyy/MM/dd");
+	private final static SimpleDateFormat formatDDMMYY = new SimpleDateFormat("dd/MM/yyyy");
 
 	/*
 	 * query: execution time for the period from date1 till date2
@@ -32,14 +34,14 @@ public class CassandraRequester {
 		if (null == date2) {
 			date1 = "2100/1/1";
 		}
-		if (!isThisDateValid(date1) || !isThisDateValid(date2)) {
+		if (!isThisDateValid(date1,formatYYMMDD) || !isThisDateValid(date2,formatYYMMDD)) {
 			System.out.println("Wrong date: point 3");
 			return null;
 		}
 		SetDateRange();
 		int nbins = 5;
-		long dateStart = DateParsing(date1);
-		long dateEnd = DateParsing(date2);
+		long dateStart = DateParsing(date1, formatYYMMDD);
+		long dateEnd = DateParsing(date2, formatYYMMDD);
 		if (dateEnd < earlestDate || dateStart > currentDate || dateStart > dateEnd)
 			return null;
 		if (dateStart < earlestDate)
@@ -121,13 +123,13 @@ public class CassandraRequester {
 		if (null == date2) {
 			date1 = "2100/1/1";
 		}
-		if (!isThisDateValid(date1) || !isThisDateValid(date2)) {
+		if (!isThisDateValid(date1, formatYYMMDD) || !isThisDateValid(date2, formatYYMMDD)) {
 			System.out.println("Wrong date: point 3");
 			return null;
 		}
 		SetDateRange();
-		long dateStart = DateParsing(date1);
-		long dateEnd = DateParsing(date2);
+		long dateStart = DateParsing(date1, formatYYMMDD);
+		long dateEnd = DateParsing(date2, formatYYMMDD);
 		if (dateEnd < earlestDate || dateStart > currentDate || dateStart > dateEnd)
 			return null;
 		if (dateStart < earlestDate)
@@ -141,42 +143,81 @@ public class CassandraRequester {
 		end.setTime(new Date(dateEnd));
 		query = new ArrayList<DataBase>();
 		for (Date date = start.getTime(); !start.after(end); start.add(Calendar.DATE, 1), date = start.getTime()) {
-			long res = db.ReadDateTable(date.getTime());
-			DataBase db = new DataBase();
-			db.setTotal((int)res);
-			db.setDate(DateFormat(date.getTime()));
-			query.add(db);
+			List<Long> res = db.ReadDateTable(date.getTime());
+			if (res == null)
+				continue;
+			DataBase bean = new DataBase();
+			bean.setTotal((int)(long)res.get(0));
+			bean.setTotalOK((int)(long)res.get(1));
+			bean.setTotalStopped((int)(long)res.get(2));
+			bean.setTotalError((int)(long)res.get(3));
+			bean.setTotalTimeOut((int)(long)res.get(4));
+			bean.setDate(DateFormat(date.getTime()));
+			query.add(bean);
+		}
+		System.out.println("StatisticsProt.readLength: total number of dates = " + query.size());
+		return query;
+	}
+
+	/*
+	 * query: jobs and sequence at date
+	 */
+	public List<DataBase> readJobByDay (String date) {
+		System.out.println(date);
+		if (null == date) {
+			return null;
+		}
+		if (!isThisDateValid(date, formatDDMMYY)) {
+			System.out.println("Wrong date: point 3");
+			return null;
+		}
+		SetDateRange();
+		long day = DateParsing(date, formatDDMMYY);
+		System.out.println(day);
+		if (day < earlestDate || day > currentDate)
+			return null;	
+		List<Pair<String, String>>	res = db.ReadProteinData(day);
+		if (res == null)
+			return null;
+		query = new ArrayList<DataBase>();
+		for (Pair<String, String> entry : res) {		
+			DataBase bean = new DataBase();
+			bean.setDate(date);
+			bean.setId(entry.getElement0());
+			bean.setProt(entry.getElement1());
+			query.add(bean);
 		}
 		System.out.println("StatisticsProt.readLength: total number of dates = " + query.size());
 		return query;
 	}
+
+
 	/* 
 	 * query: protein sequence
 	 * */
 	public List<DataBase> readProteins(String protIn, String flag) {
 		query = new ArrayList<DataBase>();
-		List<StructureProteinPrediction> res;
+		List<AnnotatedProteinSequenceBean> res;
 		if (flag.equals("whole")) 
 			res = db.ReadWholeSequence(protIn);
 		 else 
 			res = db.ReadPartOfSequence(protIn);
-		for (StructureProteinPrediction entry : res) {
-			Map<String,String> pred = entry.getPrediction();
-			Iterator it = pred.entrySet().iterator();
-			while (it.hasNext()) {
-				DataBase db = new DataBase();
-				db.setProt(entry.getSequence());
-				Map.Entry pairs = (Map.Entry)it.next();
-				db.setId(entry.getJobid());
-				db.setJpred(pairs.getValue().toString());
-				if (flag.equals("part"))
-					db.setSubProt(CreateSubprot (entry.getSequence(), protIn));				
-				query.add(db);
+		if (res == null)
+			return null;
+		for (AnnotatedProteinSequenceBean entry : res) {
+			DataBase db = new DataBase();
+			db.setProt(entry.getSequence());
+			db.setPredictions(entry);
+			db.setId(entry.getJobid());
+			if (flag.equals("part")) {
+				db.setSubProt(CreateSubprot (entry.getSequence(), protIn));
 			}
+			query.add(db);
 		}
 		return query;
 	}
 	
+
 	/* 
 	 * query protein sequences with number of jobs
 	 */
@@ -184,27 +225,75 @@ public class CassandraRequester {
 		query = new ArrayList<DataBase>();
 		Map<String, Integer> map = db.ReadProteinSequenceByCounter();
 		for (Map.Entry<String, Integer> entry : map.entrySet()) {
-			if (entry.getValue() > minimalcounter) {
-				DataBase db = new DataBase();
-				db.setTotalId(entry.getValue());
-				db.setProt(entry.getKey());
-				query.add(db);
+			if (entry.getValue() > minimalcounter && entry.getKey().length() > 0) {
+				DataBase bean = new DataBase();
+				bean.setTotalId(entry.getValue());
+				bean.setProt(entry.getKey());
+				query.add(bean);
 			}
 		}
 		return query;
 	}
 	
+	/* 
+	 * query ip with number of jobs
+	 */
+	public List<DataBase> readIpByCounter(Integer minimalcounter) {
+		query = new ArrayList<DataBase>();
+		Map<String, Integer> map = db.ReadIpByCounter();
+		if (minimalcounter == null)
+			minimalcounter = 0;
+		if (map == null)
+			return null;
+		for (Map.Entry<String, Integer> entry : map.entrySet()) {
+			if (entry.getValue() > minimalcounter) {
+				DataBase bean = new DataBase();
+				bean.setTotalId(entry.getValue());
+				bean.setIp(entry.getKey());
+				query.add(bean);
+			}
+		}
+		return query;
+	}
 	/*
 	 * query jobs log info
 	 */
 	public DataBase readJobLog(String jobid) {
-	//	query = new ArrayList<DataBase>();
+		if (jobid == null)
+			return null;
 		StructureJobLog res = db.ReadJobLog(jobid);
+		if (res == null)
+			return null;
 		DataBase query = new DataBase();
 		query.setLogInfo(res);
-	//	query.setres);
 		return query;
 	}
+	
+	
+	/*
+	 * query jobs by ipStructureJobLog
+	 */
+	public List<DataBase> readIp(String ip) {
+		if (ip == null)
+			return null;
+		List<Pair<String, String>> res = db.ReadIpWithJobs(ip);
+	//	System.out.println(res.size());
+		if (res == null) 
+			return null;
+		query = new ArrayList<DataBase>();
+		for (Pair<String, String> entry : res) {	
+			System.out.println("ip " + ip);
+			System.out.println("id " + entry.getElement0());
+			DataBase bean = new DataBase();
+			bean.setIp(ip);
+			bean.setId(entry.getElement0());
+			bean.setProt(entry.getElement1());
+			query.add(bean);
+		}
+		System.out.println(query.size());
+		return query;
+	}
+	
 	/*
 	 * create list of parts of protein sequence;
 	 */
@@ -225,12 +314,12 @@ public class CassandraRequester {
 	/*
 	 * convert String date into long date (miliseconds since the epoch start)
 	 */
-	private static long DateParsing(String datInput) {
+	private static long DateParsing(String datInput, SimpleDateFormat formatter) {
 		if (datInput == null) {
 			return 0;
 		}
 		long dateWorkSt = 0;
-		SimpleDateFormat formatter = new SimpleDateFormat("yyyy/MM/dd");
+		
 		try {
 			dateWorkSt = formatter.parse(datInput).getTime();
 		} catch (ParseException e) {
@@ -251,7 +340,7 @@ 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));
+		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();
@@ -259,12 +348,11 @@ public class CassandraRequester {
 		}
 	}
 
-	public boolean isThisDateValid(String dateToValidate) {
+	public boolean isThisDateValid(String dateToValidate, SimpleDateFormat sdf) {
 		if (dateToValidate == null || dateToValidate.equals("")) {
 			System.out.println("Undefined date");
 			return false;
 		}
-		SimpleDateFormat sdf = new SimpleDateFormat("yyyy/MM/dd");
 		try {
 			// if not valid, this will throw ParseException
 			sdf.setLenient(false);