return res;
}
+
+ /*
+ * getting jobs by ip
+ */
+ public List<Pair<String, String>> ReadIpWithJobs(String ip) {
+ final long startTime = System.currentTimeMillis();
+ String com = "SELECT JobID, Protein, FinalStatus FROM ProteinLog WHERE ip = '" + ip + "';";
+ 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();
+ List<Pair<String, String>> res = new ArrayList<Pair<String, String>>();
+ System.out.println("Query time is " + (queryTime - startTime) + " msec");
+ System.out.println(" rows analysed, " + rows.size());
+ int c = 0;
+ for (Row r : rows) {
+ if (r.getString("FinalStatus").equals("OK")) {
+ Pair<String, String> pair = new Pair<String, String>(r.getString("JobID"), r.getString("Protein"));
+ System.out.println(pair.getElement0());
+ System.out.println(pair.getElement1());
+ res.add(pair);
+ ++c;
+ }
+ }
+ final long endTime = System.currentTimeMillis();
+ System.out.println(c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
+ return res;
+ }
+
/*
* getting part of protein sequence from the db ProteinRow
*/
}
/*
+ * getting ip by counter
+ */
+ public Map<String, Integer> ReadIpByCounter() {
+ final long startTime = System.currentTimeMillis();
+ String com = "SELECT JobID, ip FROM ProteinLog;";
+ 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");
+ System.out.println(" rows analysed, " + rows.size());
+ Map<String, Integer> res = new HashMap<String, Integer>();
+ int c = 0;
+ for (Row r : rows) {
+ String protein = r.getString("ip");
+ String id = r.getString("JobID");
+ if (res.containsKey(protein))
+ res.put(protein, res.get(protein) + 1);
+ else
+ res.put(protein, 1);
+ }
+ final long endTime = System.currentTimeMillis();
+ System.out.println(c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
+ return res;
+ }
+
+ /*
* getting log info for jobid
*/
public StructureJobLog ReadJobLog(String jobid) {
private int totalJobs;
private int totalId; // total jobs for current protein sequence
private String id;
+ private String ip;
private String prot; // protein sequence
private String jpred;
private List<String> subProt; // protein sequence divided by several parts for highlighting the particular part
public String getId() {
return id;
}
+
+ public void setIp(String ip) {
+ this.ip = ip;
+ }
+
+ public String getIp() {
+ return ip;
+ }
public void setSubProt(List<String> subProt) {
this.subProt = subProt;
--- /dev/null
+package compbio.controllers;
+
+import java.util.List;
+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;
+
+import compbio.cassandra.DataBase;
+import compbio.statistic.CassandraRequester;
+
+/**
+ * @author Alexander Sherstnev
+ * @author Natasha Sherstneva
+ */
+@Controller
+public class IPStatisticsController {
+
+ @RequestMapping(value = "/ip/stat", method = RequestMethod.GET)
+ public String initStatisticsForm(Map<String, Object> model) {
+ return "queryIPStatistics";
+ }
+
+ @RequestMapping(value = "/ip", method = RequestMethod.GET)
+ public String initOneIPForm(Map<String, Object> model) {
+ return "queryIP";
+ }
+
+ @RequestMapping(value = "/ip/stat/querycounter", method = RequestMethod.GET)
+ public String findIPwithCounter(@RequestParam("JobCounter") int counter, Map<String, Object> model) {
+ final long startTime = System.currentTimeMillis();
+ CassandraRequester cr = new CassandraRequester();
+ List<DataBase> r = cr.readIpByCounter(counter);
+ model.put("results", r);
+ model.put("njobs", 0);
+ if (null != r) {
+ model.put("njobs", r.size());
+ }
+ final long endTime = System.currentTimeMillis();
+ model.put("timeExecution", (endTime - startTime));
+ model.put("counter", counter);
+ return "reportIPstatistics";
+ }
+
+ @RequestMapping(value = "/ip/query", method = RequestMethod.GET)
+ public String findIP(@RequestParam("ip") String ip, Map<String, Object> model) {
+ final long startTime = System.currentTimeMillis();
+ CassandraRequester cr = new CassandraRequester();
+ List<DataBase> r = cr.readIp(ip);
+ model.put("results", r);
+ model.put("njobs", 0);
+ if (null != r) {
+ model.put("njobs", r.size());
+ }
+ final long endTime = System.currentTimeMillis();
+ model.put("timeExecution", (endTime - startTime));
+ model.put("ip", ip);
+ return "reportIP";
+ }
+}
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
*/
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;
*/
--- /dev/null
+<%@ page language="java" contentType="text/html; charset=UTF-8" pageEncoding="UTF-8"%>
+<%@page import="java.util.Calendar"%>
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+
+<%@ taglib prefix="spring" uri="http://www.springframework.org/tags"%>
+<%@ taglib prefix="fmt" uri="http://java.sun.com/jsp/jstl/fmt"%>
+<%@ taglib prefix="fn" uri="http://java.sun.com/jsp/jstl/functions" %>
+<%@ taglib prefix="form" uri="http://www.springframework.org/tags/form" %>
+
+<html>
+<jsp:include page="fragments/header.jsp" />
+<body>
+ <div class="container">
+ <jsp:include page="fragments/mainmenu.jsp" />
+
+ <spring:url value="/ip/query" var="formurl"/>
+ <form method="get" action="${fn:escapeXml(formurl)}">
+ <h3>Enter IP</h3>
+ <input type="text" name="ip"><br/>
+ <input type="submit" name="Search" value="Search"/><br/><br/>
+ </form>
+ <jsp:include page="fragments/footer.jsp"/>
+ </div>
+</body>
+</html>
\ No newline at end of file
--- /dev/null
+<%@ page language="java" contentType="text/html; charset=UTF-8" pageEncoding="UTF-8"%>
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+
+<%@ taglib prefix="spring" uri="http://www.springframework.org/tags"%>
+<%@ taglib prefix="fmt" uri="http://java.sun.com/jsp/jstl/fmt"%>
+<%@ taglib prefix="fn" uri="http://java.sun.com/jsp/jstl/functions" %>
+<%@ taglib prefix="form" uri="http://www.springframework.org/tags/form" %>
+
+<html>
+<jsp:include page="fragments/header.jsp" />
+<body>
+ <div class="container">
+ <jsp:include page="fragments/mainmenu.jsp" />
+
+ <spring:url value="/ip/stat/querycounter" var="formurl"/>
+ <form method="get" action="${fn:escapeXml(formurl)}">
+ <h3>Enter minimum number of jobs executed from a given IP</h3>
+ <input type="text" name="JobCounter" value = 3>
+ <input type="submit" name="Search" value="Search"/>
+ </form>
+ <jsp:include page="fragments/footer.jsp"/>
+ </div>
+</body>
+</html>
--- /dev/null
+<%@ page language="java" contentType="text/html; charset=UTF-8"
+ pageEncoding="UTF-8"%>
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+
+<%@ taglib uri="http://www.springframework.org/tags" prefix="spring"%>
+<%@ 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"%>
+<%@page import="java.util.ArrayList"%>
+
+<html>
+<jsp:include page="fragments/header.jsp" />
+<body>
+ <div class="container">
+ <jsp:include page="fragments/mainmenu.jsp" />
+ <spring:url value="/sequence/querysequence" var="searchquery" />
+ <spring:url value="/joblog/query" var="jobquery" />
+
+ <p style="font-weight:bold;">Job statistics for ${res.ip}</p>
+ <!-- <h3>Time execution: ${timeExecution} ms</h3>-->
+
+ <c:choose>
+ <c:when test="${results == null}">
+ <p>No jobs found...</p>
+ </c:when>
+ <c:otherwise>
+ <p>${njobs} jobs found:</p>
+ <div class="table-responsive">
+ <table class="table table-striped table-hover table-bordered">
+ <thead>
+ <tr>
+ <th style="text-align: centre">ID</th>
+ <th style="text-align: left">IP</th>
+ <th style="text-align: left">Sequence</th>
+ </tr>
+ </thead>
+ <tbody>
+ <c:forEach items="${results}" var="res" varStatus="status">
+ <tr>
+ <td><a href="{jobquery}?IdJob=${res.id}">${res.id}</a></td>
+ <td style="text-align: left; border-buttom: dotted; font-family: monospace">${res.ip}</td>
+ <td style="text-align: left; border-buttom: dotted; font-family: monospace">${res.prot}</td>
+ </tr>
+ </c:forEach>
+ </tbody>
+ </table>
+ </div>
+ </c:otherwise>
+ </c:choose>
+
+ <jsp:include page="fragments/footer.jsp" />
+ </div>
+</body>
+</html>
\ No newline at end of file
--- /dev/null
+<%@ page language="java" contentType="text/html; charset=UTF-8"
+ pageEncoding="UTF-8"%>
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+
+<%@ taglib uri="http://www.springframework.org/tags" prefix="spring"%>
+<%@ 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"%>
+<%@page import="java.util.ArrayList"%>
+
+<html>
+<jsp:include page="fragments/header.jsp" />
+<body>
+ <div class="container">
+ <jsp:include page="fragments/mainmenu.jsp" />
+ <spring:url value="/ip/query" var="ipquery" />
+
+ <!-- <h3>Time execution: ${timeExecution} ms</h3>-->
+ <c:choose>
+ <c:when test="${njobs == 0}">
+ <p>No IP with at least ${counter} jobs found</p>
+ </c:when>
+ <c:otherwise>
+ <p>${njobs} IP with at least ${counter} jobs found</p>
+ <div class="table-responsive">
+ <table class="table table-striped table-hover table-bordered">
+ <thead>
+ <tr>
+ <th style="text-align: centre">Number of jobs</th>
+ <th style="text-align: left">IP</th>
+ </tr>
+ </thead>
+ <tbody>
+ <c:forEach items="${results}" var="res">
+ <tr>
+ <td>${res.totalId}</td>
+ <td><a title="Click to view other jobs" href="${ipquery}?ip=${res.ip}&Search=Search">${res.ip}</a></td>
+ </tr>
+ </c:forEach>
+ </tbody>
+ </table>
+ </div>
+ </c:otherwise>
+ </c:choose>
+
+ <jsp:include page="fragments/footer.jsp" />
+ </div>
+</body>
+</html>
\ No newline at end of file
git://source.jalview.org / proteocache.git / commitdiff