From e371943c7ba7e4d2efe3c11bca6ed9ad1a94632b Mon Sep 17 00:00:00 2001
From: Natasha Sherstneva <n.shertneva@gmail.com>
Date: Thu, 7 Nov 2013 13:32:02 +0000
Subject: [PATCH] fix data report, protein report

Conflicts:
	.classpath
	datadb/compbio/cassandra/CassandraNativeConnector.java
	website/AllReports.jsp
---
 .classpath                                         |    4 +-
 .../cassandra/CassandraNativeConnector.java        |   26 +++++-
 datadb/compbio/cassandra/DataBase.java             |   10 ++
 .../{QueryServlet.java => ServletJobsByDate.java}  |   13 +--
 ...rotServlet.java => ServletSequenceProtein.java} |   16 ++--
 ...engthServlet.java => ServletTimeExecution.java} |    6 +-
 server/compbio/statistic/CassandraRequester.java   |   97 ++++++++++++++++++++
 website/AllReports.jsp                             |   10 +-
 website/{Sample.jsp => QueryJobsByDate.jsp}        |    2 +-
 website/{Sequence.jsp => QuerySequenceProtein.jsp} |    5 +-
 website/{JobLength.jsp => QueryTimeExecition.jsp}  |    2 +-
 website/{ReportNew.jsp => ReportJobsByDate.jsp}    |    1 -
 .../{ReportProt.jsp => ReportSequenceProtein.jsp}  |    0
 .../{ReportLength.jsp => ReportTimeExecution.jsp}  |    0
 14 files changed, 157 insertions(+), 35 deletions(-)
 rename server/compbio/listeners/{QueryServlet.java => ServletJobsByDate.java} (81%)
 rename server/compbio/listeners/{ProtServlet.java => ServletSequenceProtein.java} (79%)
 rename server/compbio/listeners/{LengthServlet.java => ServletTimeExecution.java} (91%)
 rename website/{Sample.jsp => QueryJobsByDate.jsp} (94%)
 rename website/{Sequence.jsp => QuerySequenceProtein.jsp} (78%)
 rename website/{JobLength.jsp => QueryTimeExecition.jsp} (95%)
 rename website/{ReportNew.jsp => ReportJobsByDate.jsp} (97%)
 rename website/{ReportProt.jsp => ReportSequenceProtein.jsp} (100%)
 rename website/{ReportLength.jsp => ReportTimeExecution.jsp} (100%)

diff --git a/.classpath b/.classpath
index 394889c..bcebc6f 100644
--- a/.classpath
+++ b/.classpath
@@ -16,12 +16,10 @@
 	<classpathentry kind="lib" path="WEB-INF/lib/jackson-mapper-asl-1.9.13.jar"/>
 	<classpathentry kind="lib" path="WEB-INF/lib/displaytag-1.2.jar"/>
 	<classpathentry kind="lib" path="WEB-INF/lib/jabaws-core-2.1.0.jar" sourcepath="WEB-INF/lib/jabaws-core-src-2.1.0.jar"/>
+	<classpathentry kind="lib" path="WEB-INF/lib/jstl-1.2.jar"/>
 	<classpathentry kind="con" path="org.eclipse.jst.server.core.container/org.eclipse.jst.server.tomcat.runtimeTarget/Apache Tomcat v7.0">
 		<attributes>
 			<attribute name="owner.project.facets" value="jst.web"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/jdk1.7.0_45"/>
-	<classpathentry kind="lib" path="WEB-INF/lib/jstl-1.2.jar"/>
-	<classpathentry kind="output" path="WEB-INF/classes"/>
 </classpath>
diff --git a/datadb/compbio/cassandra/CassandraNativeConnector.java b/datadb/compbio/cassandra/CassandraNativeConnector.java
index d87f89e..766c376 100644
--- a/datadb/compbio/cassandra/CassandraNativeConnector.java
+++ b/datadb/compbio/cassandra/CassandraNativeConnector.java
@@ -237,7 +237,7 @@ public class CassandraNativeConnector {
 			return 0;
 		List<Row> rows = results.all();
 		final long endTime = System.currentTimeMillis();
-		System.out.println ("Processing time is " + (endTime - queryTime) + " msec");        
+		System.out.println ("Processing time is " + (endTime - queryTime) + " msec");
 		return rows.size();
 	}
 
@@ -253,7 +253,7 @@ public class CassandraNativeConnector {
 			return null;
 		final long queryTime = System.currentTimeMillis();
 		List<Row> rows = results.all();
-		System.out.println ("Query time is " + (queryTime - startTime) + " msec");   
+		System.out.println ("Query time is " + (queryTime - startTime) + " msec");
 		System.out.println (" rows analysed,  " + rows.size());
 		List<StructureProteinPrediction> res = new ArrayList<StructureProteinPrediction>();
 		int c = 0;
@@ -268,6 +268,22 @@ public class CassandraNativeConnector {
 	}
 
 	/*
+	 * getting data from the db ProteinData
+	 */
+	public Integer ReadDateTable(long queryDate) {
+		final long startTime = System.currentTimeMillis();
+		String com = "SELECT jobtime, JobID FROM ProteinKeyspace.ProteinData WHERE jobtime = " + queryDate + ";";
+		System.out.println("Command: " + com);
+		ResultSet results = session.execute(com);
+		if (results.isExhausted())
+			return null;
+		final long queryTime = System.currentTimeMillis();
+		List<Row> rows = results.all();
+		System.out.println ("Query time is " + (queryTime - startTime) + " msec");
+		return rows.size();
+	}
+
+	/*
 	 * getting part of protein sequence from the db ProteinRow
 	 */
 	public List<StructureProteinPrediction>  ReadPartOfSequence(String queryProtein) {
@@ -279,7 +295,7 @@ public class CassandraNativeConnector {
 			return null;
 		final long queryTime = System.currentTimeMillis();
 		List<Row> rows = results.all();
-		System.out.println ("Query time is " + (queryTime - startTime) + " msec");   
+		System.out.println ("Query time is " + (queryTime - startTime) + " msec");
 		System.out.println (" rows analysed,  " + rows.size());
 		List<StructureProteinPrediction>  res = new ArrayList<StructureProteinPrediction>();
 		int c = 0;
@@ -308,7 +324,7 @@ public class CassandraNativeConnector {
 			return null;
 		final long queryTime = System.currentTimeMillis();
 		List<Row> rows = results.all();
-		System.out.println ("Query time is " + (queryTime - startTime) + " msec");   
+		System.out.println ("Query time is " + (queryTime - startTime) + " msec");
 		System.out.println (" rows analysed,  " + rows.size());
 		Map<String, Integer> res = new HashMap<String, Integer>();
 		int c = 0;
@@ -354,7 +370,7 @@ public class CassandraNativeConnector {
 	 */
 	public long getEarliestDateInDB() {
 		final long startTime = System.currentTimeMillis();
-		String com = "SELECT jobtime FROM ProteinKeyspace.ProteinData;";
+		String com = "SELECT jobtime,JobID FROM ProteinKeyspace.ProteinData;";
 		System.out.println("Command: " + com);
 		ResultSet results = session.execute(com);
 		final long queryTime = System.currentTimeMillis();
diff --git a/datadb/compbio/cassandra/DataBase.java b/datadb/compbio/cassandra/DataBase.java
index 016a30a..cccf64b 100644
--- a/datadb/compbio/cassandra/DataBase.java
+++ b/datadb/compbio/cassandra/DataBase.java
@@ -7,6 +7,7 @@ import java.util.Collections;
 public class DataBase {
 	private String date;
 	private int total;
+	private int totalJobs;
 	private int totalId;
 	private String id;
 	private String prot;
@@ -39,6 +40,15 @@ public class DataBase {
 		return total;
 	}
 
+	
+	public void setTotalJobs(int totalJobs) {
+		this.totalJobs = totalJobs;
+	}
+
+	public int getTotalJobs() {
+		return totalJobs;
+	}
+
 	public void setTotalId(int totId) {
 		this.totalId = totId;
 	}
diff --git a/server/compbio/listeners/QueryServlet.java b/server/compbio/listeners/ServletJobsByDate.java
similarity index 81%
rename from server/compbio/listeners/QueryServlet.java
rename to server/compbio/listeners/ServletJobsByDate.java
index a69a18f..4aee8be 100644
--- a/server/compbio/listeners/QueryServlet.java
+++ b/server/compbio/listeners/ServletJobsByDate.java
@@ -12,10 +12,11 @@ import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
 import compbio.cassandra.DataBase;
+import compbio.statistic.CassandraRequester;
 import compbio.statistic.StatisticsProt;
 
-@WebServlet("/QueryServlet")
-public class QueryServlet extends HttpServlet {
+@WebServlet("/ServletJobsByDate")
+public class ServletJobsByDate extends HttpServlet {
 	private static final long serialVersionUID = 1L;
 
 	/**
@@ -26,21 +27,21 @@ public class QueryServlet extends HttpServlet {
 		final long startTime = System.currentTimeMillis();
 		String date1 = request.getParameter("data1");
 		String date2 = request.getParameter("data2");
-		StatisticsProt sp = new StatisticsProt();
+		CassandraRequester cr = new CassandraRequester();
 		if (null != request.getParameter("option")) {
 			Calendar cal = Calendar.getInstance();
-			date1 = StatisticsProt.DateFormatYYMMDD(sp.earliestDate());
+			date1 = StatisticsProt.DateFormatYYMMDD(cr.earliestDate());
 			date2 = cal.get(Calendar.YEAR) + "/" + (cal.get(Calendar.MONTH) + 1) + "/" + cal.get(Calendar.DAY_OF_MONTH);
 		}
 		request.setAttribute("data1", date1);
 		request.setAttribute("data2", date2);
-		List<DataBase> res = sp.readDetails(date1, date2);
+		List<DataBase> res = cr.countJobs(date1, date2);
 		request.setAttribute("result", res);
 		final long endTime = System.currentTimeMillis();
 		request.setAttribute("timeExecution", (endTime - startTime));
 		System.out.println ("QueryServlet.doGet: total number of dates = " + res.size());
 		request.setAttribute("flag", request.getParameter("option"));
-		RequestDispatcher rd = request.getRequestDispatcher("/ReportNew.jsp");
+		RequestDispatcher rd = request.getRequestDispatcher("/ReportJobsByDate.jsp");
 		rd.forward(request, response);
 	}
 
diff --git a/server/compbio/listeners/ProtServlet.java b/server/compbio/listeners/ServletSequenceProtein.java
similarity index 79%
rename from server/compbio/listeners/ProtServlet.java
rename to server/compbio/listeners/ServletSequenceProtein.java
index d567106..6a10b94 100644
--- a/server/compbio/listeners/ProtServlet.java
+++ b/server/compbio/listeners/ServletSequenceProtein.java
@@ -9,13 +9,14 @@ import javax.servlet.http.HttpServlet;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
+import compbio.statistic.CassandraRequester;
 import compbio.statistic.StatisticsProt;
 
 /**
  * Servlet implementation class ProtServlet
  */
-@WebServlet("/ProtServlet")
-public class ProtServlet extends HttpServlet {
+@WebServlet("/ServletSequenceProtein")
+public class ServletSequenceProtein extends HttpServlet {
 	private static final long serialVersionUID = 1L;
 
 	/**
@@ -28,14 +29,11 @@ public class ProtServlet extends HttpServlet {
 		String prot = request.getParameter("prot");
 		String search = request.getParameter("Search");
 		int counter = Integer.parseInt(request.getParameter("counterJob"));
-		StatisticsProt sp = new StatisticsProt();
+		CassandraRequester cr = new CassandraRequester();
 		if (search.equals("Search counter")) {
-			request.setAttribute("result", sp.readProtID(counter));
+	//		request.setAttribute("result", sp.readProtID(counter));
 		} else {
-			if (flag.equals("whole"))
-				request.setAttribute("result", sp.readProteins(prot));
-			else
-				request.setAttribute("result", sp.readPart(prot));
+				request.setAttribute("result", cr.readProteins(prot, flag));
 		}
 		final long endTime = System.currentTimeMillis();
 		request.setAttribute("timeExecution", (endTime - startTime));
@@ -43,7 +41,7 @@ public class ProtServlet extends HttpServlet {
 		request.setAttribute("flag", flag);
 		request.setAttribute("search", search);
 		request.setAttribute("counter", counter);
-		RequestDispatcher rd = request.getRequestDispatcher("/ReportProt.jsp");
+		RequestDispatcher rd = request.getRequestDispatcher("/ReportSequenceProtein.jsp");
 		rd.forward(request, response);
 	}
 
diff --git a/server/compbio/listeners/LengthServlet.java b/server/compbio/listeners/ServletTimeExecution.java
similarity index 91%
rename from server/compbio/listeners/LengthServlet.java
rename to server/compbio/listeners/ServletTimeExecution.java
index 76d0462..c380604 100644
--- a/server/compbio/listeners/LengthServlet.java
+++ b/server/compbio/listeners/ServletTimeExecution.java
@@ -16,8 +16,8 @@ import compbio.statistic.CassandraRequester;
 /**
  * Servlet implementation class LengthServlet
  */
-@WebServlet("/LengthServlet")
-public class LengthServlet extends HttpServlet {
+@WebServlet("/ServletTimeExecution")
+public class ServletTimeExecution extends HttpServlet {
 	private static final long serialVersionUID = 1L;
 
 	/**
@@ -40,7 +40,7 @@ public class LengthServlet extends HttpServlet {
 		request.setAttribute("flag", request.getParameter("option"));
 		final long endTime = System.currentTimeMillis();
 		request.setAttribute("timeExecution", (endTime - startTime));
-		RequestDispatcher rd = request.getRequestDispatcher("/ReportLength.jsp");
+		RequestDispatcher rd = request.getRequestDispatcher("/ReportTimeExecution.jsp");
 		rd.forward(request, response);
 	}
 
diff --git a/server/compbio/statistic/CassandraRequester.java b/server/compbio/statistic/CassandraRequester.java
index 83c8a7a..5335023 100755
--- a/server/compbio/statistic/CassandraRequester.java
+++ b/server/compbio/statistic/CassandraRequester.java
@@ -5,11 +5,14 @@ import java.text.SimpleDateFormat;
 import java.util.ArrayList;
 import java.util.Calendar;
 import java.util.Date;
+import java.util.Iterator;
 import java.util.List;
+import java.util.Map;
 
 import compbio.cassandra.CassandraNativeConnector;
 import compbio.cassandra.DataBase;
 import compbio.cassandra.Pair;
+import compbio.cassandra.StructureProteinPrediction;
 
 public class CassandraRequester {
 	private CassandraNativeConnector DBInstance = new CassandraNativeConnector();
@@ -105,7 +108,100 @@ public class CassandraRequester {
 		System.out.println("StatisticsProt.readLength: total number of dates = " + query.size());
 		return query;
 	}
+	
+	/*
+	 * query: total number of jobs  for the period from date1 till date2
+	 */
+	public List<DataBase> countJobs(String date1, String date2) {
+		if (null == date1) {
+			date1 = "1970/1/1";
+		}
+		if (null == date2) {
+			date1 = "2100/1/1";
+		}
+		if (!isThisDateValid(date1) || !isThisDateValid(date2)) {
+			System.out.println("Wrong date: point 3");
+			return null;
+		}
+		SetDateRange();
+		long dateStart = DateParsing(date1);
+		long dateEnd = DateParsing(date2);
+		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();
+		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()) {
+			Integer res = DBInstance.ReadDateTable(date.getTime());
+			if (res == null)
+				continue;
+			DataBase db = new DataBase();
+			db.setTotal(res);
+			db.setDate(DateFormat(date.getTime()));
+			query.add(db);
+		}			
+		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;
+		if (flag.equals("whole")) 
+			res = DBInstance.ReadWholeSequence(protIn);
+		 else 
+			res = DBInstance.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);
+			}
+		}
+		return query;
+	}
+	
+	/* 
+	 * query  protein sequences with number of jobs
+	 * */
+	public List<DataBase> readProteinByCounter(int counter) {
+		query = new ArrayList<DataBase>();
+	//	List<Pair<String, String>> res = DBInstance.ReadProteinDataByCounter(counter);
+		
+		return query;
+	}
+	
+	
+	private static List<String> CreateSubprot (String protein, String subprot) {
+		List<String> sub = new ArrayList<String>();
+		String subStr = protein;
+		while (subStr.length() > 0 && subStr.contains(subprot)) {
+			String first = subStr.substring(0, subStr.indexOf(subprot));
+			if (first.length() > 0)
+				sub.add(first);
+			sub.add(subprot);
+			subStr = subStr.substring(subStr.indexOf(subprot) + subprot.length(), subStr.length());
+		}
+		if (subStr.length() > 0)
+			sub.add(subStr);
+		return sub;
+	}
 	/*
 	 * convert String date into long date (miliseconds since the epoch start)
 	 */
@@ -167,4 +263,5 @@ public class CassandraRequester {
 		earlestDate = DBInstance.getEarliestDateInDB();
 		return earlestDate;
 	}
+	
 }
diff --git a/website/AllReports.jsp b/website/AllReports.jsp
index 110bc3e..b470feb 100644
--- a/website/AllReports.jsp
+++ b/website/AllReports.jsp
@@ -1,9 +1,11 @@
 <%
 	String query = request.getParameter("query");
 	if (query.equals("date"))
-		response.sendRedirect("Sample.jsp");
+		response.sendRedirect("QueryJobsByDate.jsp");
 	else if (query.equals("length"))
-		response.sendRedirect("JobLength.jsp");
+		response.sendRedirect("QueryTimeExecition.jsp");
 	else if (query.equals("protein"))
-		response.sendRedirect("Sequence.jsp");
-%>
\ No newline at end of file
+		response.sendRedirect("QuerySequenceProtein.jsp");
+	else if (query.equals("log"))
+		response.sendRedirect("LogQuery.jsp");
+%>
diff --git a/website/Sample.jsp b/website/QueryJobsByDate.jsp
similarity index 94%
rename from website/Sample.jsp
rename to website/QueryJobsByDate.jsp
index 0116ba7..ae667fd 100644
--- a/website/Sample.jsp
+++ b/website/QueryJobsByDate.jsp
@@ -9,7 +9,7 @@
 <title>Date period</title>
 </head>
 <body>
-	<form method="post" action="QueryServlet">
+	<form method="post" action="ServletJobsByDate">
 		<h3>Enter time period</h3>	
 		 <% Calendar cal = Calendar.getInstance();
 			String datecalBegin = cal.get(Calendar.YEAR) + "/" + (cal.get(Calendar.MONTH) + 1) + "/1";
diff --git a/website/Sequence.jsp b/website/QuerySequenceProtein.jsp
similarity index 78%
rename from website/Sequence.jsp
rename to website/QuerySequenceProtein.jsp
index 1cccbb2..3d86bd6 100644
--- a/website/Sequence.jsp
+++ b/website/QuerySequenceProtein.jsp
@@ -9,10 +9,11 @@
 </head>
 <body>
 	<br/>
-	<form method="get" action="ProtServlet">
+	<form method="get" action="ServletSequenceProtein">
 		<h3>Enter protein sequence</h3>	
 		<p><textarea rows="14" cols="80" name="prot">ABCDE</textarea></p>
-		<input type="radio" name="protein" value="part" Checked>search<br/>
+		<input type="radio" name="protein" value="whole" Checked>search whole<br/>
+		<input type="radio" name="protein" value="part">search part<br/>
 		<input type="submit" name="Search" value="Search sequence"/><br/><br/>
 		<h3>Enter minimum number of jobs per protein</h3>
 		<input type="text" name="counterJob" value = 3><br/>
diff --git a/website/JobLength.jsp b/website/QueryTimeExecition.jsp
similarity index 95%
rename from website/JobLength.jsp
rename to website/QueryTimeExecition.jsp
index c64ec3c..aaf925f 100644
--- a/website/JobLength.jsp
+++ b/website/QueryTimeExecition.jsp
@@ -9,7 +9,7 @@
 <title>Date interval</title>
 </head>
 <body>
-	<form method="post" action="LengthServlet">
+	<form method="post" action="ServletTimeExecution">
 		<h3>Enter time period</h3>
 		<%
 			Calendar cal = Calendar.getInstance();
diff --git a/website/ReportNew.jsp b/website/ReportJobsByDate.jsp
similarity index 97%
rename from website/ReportNew.jsp
rename to website/ReportJobsByDate.jsp
index 969cad7..261a11b 100644
--- a/website/ReportNew.jsp
+++ b/website/ReportJobsByDate.jsp
@@ -48,7 +48,6 @@
 			<td style="text-align: right">0</td>
 		</tr>
 
-		<c:set var="sum" value="0" />
 		<c:forEach items="${result}" var="res">
 			<tr>
 				<td>${res.date}</td>
diff --git a/website/ReportProt.jsp b/website/ReportSequenceProtein.jsp
similarity index 100%
rename from website/ReportProt.jsp
rename to website/ReportSequenceProtein.jsp
diff --git a/website/ReportLength.jsp b/website/ReportTimeExecution.jsp
similarity index 100%
rename from website/ReportLength.jsp
rename to website/ReportTimeExecution.jsp
-- 
1.7.10.2