Merge branch 'master' into servlets

Conflicts:
	server/compbio/listeners/ServletSequenceProtein.java
	server/compbio/statistic/CassandraRequester.java

diff --git a/datadb/compbio/cassandra/CassandraReader.java b/datadb/compbio/cassandra/CassandraReader.java
new file mode 100644 (file)
index 0000000..d2d2e1b
--- /dev/null
+++ b/datadb/compbio/cassandra/CassandraReader.java
@@ -0,0 +1,16 @@
+package compbio.cassandra;
+
+import com.datastax.driver.core.Session;
+
+public interface CassandraReader {
+
+       /*
+        * Defines a source file with metainformation of Jpred Jobs
+        **/
+       void setSession (Session s);
+       
+       /*
+        * Makes real parsing of the source file
+        **/
+       /*void getResults();*/
+}

diff --git a/datadb/compbio/cassandra/readers/CassandraReaderExecutionTime.java b/datadb/compbio/cassandra/readers/CassandraReaderExecutionTime.java
new file mode 100644 (file)
index 0000000..8648aeb
--- /dev/null
+++ b/datadb/compbio/cassandra/readers/CassandraReaderExecutionTime.java
@@ -0,0 +1,104 @@
+package compbio.cassandra.readers;
+
+
+import java.util.Calendar;
+import java.util.List;
+import java.util.ArrayList;
+
+import org.apache.log4j.Logger;
+
+import com.datastax.driver.core.Row;
+import com.datastax.driver.core.Session;
+import com.datastax.driver.core.ResultSet;
+import com.datastax.driver.core.PreparedStatement;
+import com.datastax.driver.core.BoundStatement;
+
+import compbio.cassandra.CassandraReader;
+import compbio.cassandra.Pair;
+import compbio.engine.ProteoCachePropertyHelperManager;
+import compbio.util.PropertyHelper;
+
+public class CassandraReaderExecutionTime implements CassandraReader {
+       private Session session;
+
+       public static String CASSANDRA_HOSTNAME = "localhost";
+       public static boolean READ_WEB_JPRED = false;
+       public static boolean READ_LOCALFILE_JPRED = false;
+
+       public void setSession(Session s) {
+               assert s != null;
+               session = s;
+       }
+
+       private void setConditions() {
+
+       }
+
+       public boolean JobisNotInsterted(String jobid) {
+               ResultSet results1 = session.execute("SELECT * FROM ProteinLog WHERE JobID = '" + jobid + "';");
+               if (results1.isExhausted()) {
+                       return true;
+               }
+               return false;
+       }
+
+       public boolean JobisNotArchived(String jobid) {
+               ResultSet results1 = session.execute("SELECT * FROM JpredArchive WHERE JobID = '" + jobid + "';");
+               if (results1.isExhausted()) {
+                       return true;
+               }
+               return false;
+       }
+
+       /*
+        * getting data from the db
+        */
+       public List<Pair<String, String>> ReadProteinDataTable() {
+               final long startTime = System.currentTimeMillis();
+               String com = "SELECT DataBegin,DataEnd FROM ProteinKeyspace.ProteinLog;";
+               System.out.println("Command: " + com);
+               ResultSet results = session.execute(com);
+               final long queryTime = System.currentTimeMillis();
+               List<Row> rows = results.all();
+               System.out.println("Query time is " + (queryTime - startTime) + " msec");
+
+               List<Pair<String, String>> res = new ArrayList<Pair<String, String>>();
+               int c = 0;
+               for (Row r : rows) {
+                       Pair<String, String> pair = new Pair<String, String>(r.getString("DataBegin"), r.getString("DataEnd"));
+                       res.add(pair);
+                       ++c;
+               }
+               final long endTime = System.currentTimeMillis();
+               System.out.println(c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
+               return res;
+       }
+
+       /*
+        * getting earlest date of jobs from the db
+        */
+       public long getEarliestDateInDB() {
+               final long startTime = System.currentTimeMillis();
+               String com = "SELECT jobtime FROM ProteinKeyspace.ProteinData;";
+               System.out.println("Command: " + com);
+               ResultSet results = session.execute(com);
+               final long queryTime = System.currentTimeMillis();
+               System.out.println("Query time is " + (queryTime - startTime) + " msec");
+
+               Calendar cal = Calendar.getInstance();
+               long res = cal.getTimeInMillis();
+               int c = 0;
+               while (!results.isExhausted()) {
+                       Row r = results.one();
+                       long d1 = r.getLong("jobtime");
+                       if (res > d1) {
+                               res = d1;
+                       }
+                       ++c;
+               }
+               final long endTime = System.currentTimeMillis();
+               System.out.println(c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
+               return res;
+       }
+
+}

diff --git a/doc/packages.odt b/doc/packages.odt
new file mode 100644 (file)
index 0000000..246b4bf
Binary files /dev/null and b/doc/packages.odt differ

diff --git a/website/ReportLength.jsp b/website/ReportLength.jsp
deleted file mode 100644 (file)
index e68dc64..0000000
--- a/website/ReportLength.jsp
+++ /dev/null
@@ -1,68 +0,0 @@
-<%@page import="java.util.ArrayList"%>
-<%@ page trimDirectiveWhitespaces="true"%>
-<%@ taglib uri="http://java.sun.com/jsp/jstl/core" prefix="c"%>
-<%@ taglib uri="http://java.sun.com/jsp/jstl/functions" prefix="fn"%>
-<%@ taglib uri="http://java.sun.com/jsp/jstl/fmt" prefix="fmt"%>
-<%@ taglib uri="http://displaytag.sf.net" prefix="dt"%>
-<c:choose>
-       <c:when test="${flag == 'AllDate'}">
-               <h3>Time execution for the whole period</h3>
-       </c:when>
-       <c:otherwise>
-               <h3>Time execution for the interval: ${data1} - ${data2}</h3>
-       </c:otherwise>
-</c:choose>
-<h3>Time execution: ${timeExecution} ms</h3>
-
-<c:set var="sum" value="0" />
-<c:forEach items="${result}" var="res" varStatus="loop">
-       <c:choose>
-               <c:when test="${loop.last}">
-                       <c:forEach items="${res.timeTotalExec}" var="total">
-                               <c:set var="sum" value="${sum + total}" />
-                       </c:forEach>
-               </c:when>
-       </c:choose>
-</c:forEach>
-
-<h3>Total number of jobs: ${sum}</h3>
-
-<table border="1" style="border-collapse: collapse; white-space: nowrap">
-       <thead>
-               <tr>
-                       <th style="text-align: centre; width: 150px">Date</th>
-                       <th style="text-align: centre; width: 150px">less then 30 s</th>
-                       <th style="text-align: centre; width: 150px">30 s - 60 s</th>
-                       <th style="text-align: centre; width: 150px">1 min - 2 min</th>
-                       <th style="text-align: centre; width: 150px">2 min - 10 min</th>
-                       <th style="text-align: centre; width: 150px">more then 10 min</th>
-               </tr>
-       </thead>
-       <tbody>
-               <c:forEach items="${result}" var="res" varStatus="loop">
-                       <c:choose>
-                               <c:when test="${loop.last}">
-                                       <tr style="font-weight: bolder;">
-                                               <td>Total:</td>
-                                               <c:forEach items="${res.timeTotalExec}" var="total">
-                                                       <td style="text-align: right">${total}</td>
-                                               </c:forEach>
-                                       </tr>
-                               </c:when>
-                       </c:choose>
-               </c:forEach>
-
-               <c:forEach items="${result}" var="res" varStatus="loop">
-                       <c:choose>
-                               <c:when test="${not loop.last}">
-                                       <tr>
-                                               <td>${res.date}</td>
-                                               <c:forEach items="${res.timeRez}" var="time">
-                                                       <td style="text-align: right">${time}</td>
-                                               </c:forEach>
-                                       </tr>
-                               </c:when>
-                       </c:choose>
-               </c:forEach>
-       </tbody>
-</table>

diff --git a/website/ReportNew.jsp b/website/ReportNew.jsp
deleted file mode 100644 (file)
index 969cad7..0000000
--- a/website/ReportNew.jsp
+++ /dev/null
@@ -1,63 +0,0 @@
-<%@page import="java.util.ArrayList"%>
-<%@ taglib uri="http://java.sun.com/jsp/jstl/core" prefix="c"%>
-<%@ taglib uri="http://java.sun.com/jsp/jstl/functions" prefix="fn"%>
-<%@ taglib uri="http://java.sun.com/jsp/jstl/fmt" prefix="fmt"%>
-<%@ taglib uri="http://displaytag.sf.net" prefix="dt"%>
-<c:choose>
-       <c:when test="${flag == 'AllDate'}">
-               <h3>Jobs statistics for the whole period</h3>
-       </c:when>
-       <c:otherwise>
-               <h3>
-                       Jobs statistics for the Period:
-                       <c:out value="${data1}" />
-                       to
-                       <c:out value="${data2}" />
-               </h3>
-       </c:otherwise>
-</c:choose>
-<h3>Time execution: ${timeExecution} ms</h3>
-
-<c:set var="sum" value="0" />
-<c:forEach items="${result}" var="res">
-       <c:set var="tot" value="${res.total}" />
-       <c:set var="sum" value="${sum + tot}" />
-</c:forEach>
-
-
-<table border="1" style="border-collapse: collapse; white-space: nowrap">
-       <thead>
-               <tr>
-                       <th rowspan="2" style="text-align: centre">Date</th>
-                       <th colspan="4" style="text-align: centre">Number of Proteins</th>
-               </tr>
-               <tr>
-                       <th style="text-align: centre">Total</th>
-                       <th style="text-align: centre">Failed</th>
-                       <th style="text-align: centre">Cancelled</th>
-                       <th style="text-align: centre">Abandoned</th>
-               </tr>
-       </thead>
-       <tbody>
-
-               <tr style="font-weight: bolder;">
-                       <td>Total:</td>
-                       <td style="text-align: right">${sum}</td>
-                       <td style="text-align: right">0</td>
-                       <td style="text-align: right">0</td>
-                       <td style="text-align: right">0</td>
-               </tr>
-
-               <c:set var="sum" value="0" />
-               <c:forEach items="${result}" var="res">
-                       <tr>
-                               <td>${res.date}</td>
-                               <td style="text-align: right"><c:out value="${res.total}" /></td>
-                               <td style="text-align: right">0</td>
-                               <td style="text-align: right">0</td>
-                               <td style="text-align: right">0</td>
-                       </tr>
-               </c:forEach>
-
-       </tbody>
-</table>
\ No newline at end of file