+++ /dev/null
-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
- <classpathentry kind="src" path="src"/>
- <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.jst.j2ee.internal.web.container"/>
- <classpathentry kind="con" path="org.eclipse.jst.j2ee.internal.module.container"/>
- <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
- <classpathentry kind="lib" path="/home/natasha/Downloads/jamm-0.2.5.jar"/>
- <classpathentry kind="lib" path="/home/natasha/workspace/nosql/jstl-1.2.jar"/>
- <classpathentry kind="lib" path="/home/natasha/workspace/nosql/displaytag-1.2.jar"/>
- <classpathentry kind="output" path="build/classes"/>
-</classpath>
+++ /dev/null
-<?xml version="1.0" encoding="UTF-8"?>
-<projectDescription>
- <name>nosql</name>
- <comment></comment>
- <projects>
- </projects>
- <buildSpec>
- <buildCommand>
- <name>org.eclipse.wst.jsdt.core.javascriptValidator</name>
- <arguments>
- </arguments>
- </buildCommand>
- <buildCommand>
- <name>org.eclipse.jdt.core.javabuilder</name>
- <arguments>
- </arguments>
- </buildCommand>
- <buildCommand>
- <name>org.eclipse.wst.common.project.facet.core.builder</name>
- <arguments>
- </arguments>
- </buildCommand>
- <buildCommand>
- <name>org.eclipse.wst.validation.validationbuilder</name>
- <arguments>
- </arguments>
- </buildCommand>
- </buildSpec>
- <natures>
- <nature>org.eclipse.jem.workbench.JavaEMFNature</nature>
- <nature>org.eclipse.wst.common.modulecore.ModuleCoreNature</nature>
- <nature>org.eclipse.wst.common.project.facet.core.nature</nature>
- <nature>org.eclipse.jdt.core.javanature</nature>
- <nature>org.eclipse.wst.jsdt.core.jsNature</nature>
- </natures>
-</projectDescription>
+++ /dev/null
-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
- <classpathentry kind="src" path="WebContent"/>
- <classpathentry kind="con" path="org.eclipse.wst.jsdt.launching.JRE_CONTAINER"/>
- <classpathentry kind="con" path="org.eclipse.wst.jsdt.launching.WebProject">
- <attributes>
- <attribute name="hide" value="true"/>
- </attributes>
- </classpathentry>
- <classpathentry kind="con" path="org.eclipse.wst.jsdt.launching.baseBrowserLibrary"/>
- <classpathentry kind="output" path=""/>
-</classpath>
+++ /dev/null
-eclipse.preferences.version=1
-org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
-org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.7
-org.eclipse.jdt.core.compiler.compliance=1.7
-org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
-org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
-org.eclipse.jdt.core.compiler.source=1.7
+++ /dev/null
-<?xml version="1.0" encoding="UTF-8"?><project-modules id="moduleCoreId" project-version="1.5.0">
- <wb-module deploy-name="nosql">
- <wb-resource deploy-path="/" source-path="/WebContent" tag="defaultRootSource"/>
- <wb-resource deploy-path="/WEB-INF/classes" source-path="/src"/>
- <property name="java-output-path" value="/nosql/build/classes"/>
- <property name="context-root" value="nosql"/>
- </wb-module>
-</project-modules>
+++ /dev/null
-<?xml version="1.0" encoding="UTF-8"?>
-<faceted-project>
- <runtime name="Apache Tomcat v7.0"/>
- <fixed facet="java"/>
- <fixed facet="jst.web"/>
- <fixed facet="wst.jsdt.web"/>
- <installed facet="java" version="1.7"/>
- <installed facet="jst.web" version="3.0"/>
- <installed facet="wst.jsdt.web" version="1.0"/>
-</faceted-project>
+++ /dev/null
-org.eclipse.wst.jsdt.launching.baseBrowserLibrary
\ No newline at end of file
+++ /dev/null
-Window
\ No newline at end of file
+++ /dev/null
-eclipse.preferences.version=1
-org.jboss.ide.eclipse.as.core.singledeployable.deployableList=
+++ /dev/null
-<%
- String query = request.getParameter("query");
- if (query.equals("date"))
- response.sendRedirect("Sample.jsp");
- else if (query.equals("length"))
- response.sendRedirect("JobLength.jsp");
- else if (query.equals("protein"))
- response.sendRedirect("Sequence.jsp");
-%>
\ 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">
-<html>
-<head>
-<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<title>Cassandra report</title>
-</head>
-<body>
- <form method="post" action="AllReports.jsp">
- <h3>Choose query type</h3>
- <input type="radio" name="query" value="date" Checked>Search by date<br/>
- <input type="radio" name="query" value="length">Search by time interval<br/>
- <input type="radio" name="query" value="protein">Search by protein sequence<br/>
- <input type="submit" name="Search" value="Search"/>
- </form>
-</body>
-</html>
\ No newline at end of file
+++ /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">
-<html>
-<head>
-<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<title>Date interval</title>
-</head>
-<body>
- <form method="post" action="LengthServlet">
- <h3>Enter time period</h3>
- <% Calendar cal = Calendar.getInstance();
- String datecalBegin = cal.get(Calendar.YEAR) + "/" + cal.get(Calendar.MONTH) + "/1";
- String datecalEnd = cal.get(Calendar.YEAR) + "/" + cal.get(Calendar.MONTH) + "/" + cal.get(Calendar.DAY_OF_MONTH);
- %>
- <p>from <input type="text" name="data1" value = <%= datecalBegin%> style=" width : 145px;"/>
- to <input type="text" name="data2" value = <%= datecalEnd%> style=" width : 145px;"/></p>
- <input type="submit" name="Search" value="Search"/>
- </form>
-</body>
-</html>
\ No newline at end of file
+++ /dev/null
-Manifest-Version: 1.0\r
-Class-Path: \r
-\r
+++ /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">
-<html>
-<head>
-<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<title>Report</title>
-</head>
-<body>
-<h3>Report Results</h3>
-<% String rez = request.getAttribute("result").toString();
- String[] rezLines = rez.split(";");
- for (int i = 0; i < rezLines.length; i++) {
-%>
-<%= rezLines[i]+"<br/>" %>
-<%
-}
-%>
-<a href="javascript:history.back()">Click here to go Back</a>
-</body>
-</html>
\ No newline at end of file
+++ /dev/null
-<%@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" %>
-
-<h3>Time execution for the interval: ${data1} - ${data2}</h3>
-<table border="1" style = "border-collapse: collapse; white-space: nowrap">
-<thead>
-<tr>
-<th style="text-align: centre">Date</th>
-<th style="text-align: centre">less then 1s</th>
-<th style="text-align: centre">less then 10s</th>
-<th style="text-align: centre">less then 20s</th>
-<th style="text-align: centre">more then 20s</th>
-</tr>
-</thead>
-<tbody>
-<c:forEach items="${result}" var="res">
-<tr>
-<td>${res.date}</td>
-<c:forEach items="${res.timeRez}" var="time">
-<td>${time}</td>
-</c:forEach>
-</c:forEach>
-</tbody>
-</table>
+++ /dev/null
-<%@page import="java.util.ArrayList"%>
-<%@ taglib uri="http://java.sun.com/jsp/jstl/core" prefix="c" %>
-<%@ taglib uri="http://java.sun.com/jsp/jstl/functions" prefix="fn" %>
-<%@ taglib uri="http://java.sun.com/jsp/jstl/fmt" prefix="fmt" %>
-<%@ taglib uri="http://displaytag.sf.net" prefix="dt" %>
-
-<h3>Jobs statistics for the Period:
-<c:out value = "${data1}"/> to <c:out value = "${data2}"/> </h3>
-<table class="its" style="width:800px" border="1">
-<thead>
-<tr>
-<th rowspan="2"style="text-align: centre">Date</th>
-<th colspan="4" style="text-align: centre">Number of Proteins</th>
-</tr>
-<tr>
-<th style="text-align: centre">Total</th>
-<th style="text-align: centre">Failed</th>
-<th style="text-align: centre">Cancelled</th>
-<th style="text-align: centre">Abandoned</th>
-</tr>
-</thead>
-<tbody>
-<c:set var="sum" value="0" />
-<c:forEach items="${result}" var="res">
-<tr>
-<td>${res.date}</td>
-<c:set var="tot" value="${res.total}" />
-<c:set var="sum" value="${sum + tot}" />
-<td style="text-align: right"><c:out value = "${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>
-<tr style="font-weight: bolder;">
-<td>Total:</td>
-<td style="text-align: right">${sum}</td>
-<td style="text-align: right">0</td>
-<td style="text-align: right">0</td>
-<td style="text-align: right">0</td>
-</tr>
-</tbody>
-</table>
\ No newline at end of file
+++ /dev/null
-<%@page import="java.util.ArrayList"%>
-<%@ page trimDirectiveWhitespaces="true" %>
-<%@ taglib uri="http://java.sun.com/jsp/jstl/core" prefix="c" %>
-<%@ taglib uri="http://java.sun.com/jsp/jstl/functions" prefix="fn" %>
-<%@ taglib uri="http://java.sun.com/jsp/jstl/fmt" prefix="fmt" %>
-<%@ taglib uri="http://displaytag.sf.net" prefix="dt" %>
-
-<h3>Dundee ProteoCache query result</h3>
-<table border="1" style = "border-collapse: collapse; white-space: nowrap">
-<thead>
-<tr>
-<th style="text-align: centre">ID</th>
-<th style="text-align: centre">Prediction</th>
-</tr>
-</thead>
-<tbody>
-<c:forEach items="${result}" var="res">
-<tr>
-<td rowspan="2">${res.id}</td>
-<c:if test ="${flag == 'whole'}">
-<td style=" text-align: left; border-buttom: dotted; font-family: monospace"><c:out value = "${res.prot}" /></td>
-</c:if>
-<c:if test ="${flag == 'part'}">
-<td style=" text-align: left; border-buttom: dotted; font-family: monospace">
-<c:forEach items="${res.subProt}" var="seq">
-<c:choose>
-<c:when test="${fn:contains(seq, prot)}"><span style="color:blue">${seq}</span></c:when>
-<c:otherwise>${seq}</c:otherwise>
-</c:choose>
-</c:forEach>
-</td>
-</c:if>
-</tr>
-<tr>
-<td style="text-align: left; border-top: hidden; font-family: monospace"><c:out value = "${res.jpred}" /></td>
-</tr>
-</c:forEach>
-</tbody>
-</table>
+++ /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">
-<html>
-<head>
-<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<title>Date period</title>
-</head>
-<body>
- <form method="post" action="QueryServlet">
- <h3>Enter time period</h3>
- <% Calendar cal = Calendar.getInstance();
- String datecalBegin = cal.get(Calendar.YEAR) + "/" + cal.get(Calendar.MONTH) + "/1";
- String datecalEnd = cal.get(Calendar.YEAR) + "/" + cal.get(Calendar.MONTH) + "/" + cal.get(Calendar.DAY_OF_MONTH);
- %>
- <p>from <input type="text" name="data1" value = <%= datecalBegin%> style=" width : 145px;"/>
- to <input type="text" name="data2" value = <%= datecalEnd%> style=" width : 145px;"/></p>
- <input type="submit" name="Full report" value="Full Search"/>
- </form>
-</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">
-<html>
-<head>
-<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<title>Sequence of protein</title>
-</head>
-<body>
- <br/>
- <form method="post" action="ProtServlet">
- <h3>Enter protein sequence</h3>
- <p><textarea rows="2" cols="100" name="prot">MPIDYSKWKDIEVSDDEDDTHPNIDTPSLFRWRHQARLERMAEKKMEQEKIDKEKGTTSKKMEELEKKLAAADVTDKSDIQKQIDEVKAQEEAWRKKEAELEEKERLEPWNVDTIGHEAFSTSRINKI</textarea></p>
- <input type="radio" name="protein" value="whole" Checked>search by the whole sequence
- <input type="radio" name="protein" value="part">search by a part of sequence<br/>
- <input type="submit" name="Search" value="Search"/>
- </form>
-</body>
-</html>
\ No newline at end of file
+++ /dev/null
-<%@ 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" %>
-
-<table class="its" style="width:800px" border="1">
-<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>
-<c:set var="sum" value="0" />
-<c:forEach items="${statistics}" var="res">
-<tr>
-<td>${res.date}</td>
-<c:set var="tot" value="${res.total}" />
-<c:set var="sum" value="${sum + tot}" />
-<td style="text-align: right"><c:out value = "${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>
-<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>
-</tbody>
-</table>
+++ /dev/null
-<?xml version="1.0" encoding="UTF-8"?>
-<web-app xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://java.sun.com/xml/ns/javaee" xsi:schemaLocation="http://java.sun.com/xml/ns/javaee http://java.sun.com/xml/ns/javaee/web-app_3_0.xsd" id="WebApp_ID" version="3.0">
- <display-name>nosql</display-name>
- <listener>
- <listener-class>combio.listeners.ContextListener</listener-class>
- </listener>
-</web-app>
\ No newline at end of file
+++ /dev/null
-package combio.cassandra;
-
-import java.util.Arrays;
-
-import me.prettyprint.cassandra.serializers.LongSerializer;
-import me.prettyprint.cassandra.serializers.StringSerializer;
-import me.prettyprint.cassandra.service.ThriftKsDef;
-import me.prettyprint.hector.api.Cluster;
-import me.prettyprint.hector.api.Keyspace;
-import me.prettyprint.hector.api.beans.ColumnSlice;
-import me.prettyprint.hector.api.ddl.ColumnFamilyDefinition;
-import me.prettyprint.hector.api.ddl.ComparatorType;
-import me.prettyprint.hector.api.ddl.KeyspaceDefinition;
-import me.prettyprint.hector.api.factory.HFactory;
-import me.prettyprint.hector.api.mutation.Mutator;
-import me.prettyprint.hector.api.query.QueryResult;
-import me.prettyprint.hector.api.query.SliceQuery;
-
-public class CassandraCreate {
- private static Keyspace ksp;
- private static Cluster cluster;
- private static Mutator<Long> mutatorLong;
- private static Mutator<String> mutatorString;
- private static Mutator<String> mutatorLog;
- StringSerializer ss = StringSerializer.get();
- LongSerializer ls = LongSerializer.get();
-
-
- // connect to cluster
- public void Connection() {
- cluster = HFactory.getOrCreateCluster("Protein Cluster", "127.0.0.1:9160");
- KeyspaceDefinition keyspaceDef = cluster.describeKeyspace("ProteinKeyspace");
- // If keyspace does not exist, the CFs don't exist either. => create them.
-/* if (keyspaceDef != null) {
- cluster.dropColumnFamily("ProteinKeyspace", "ProteinRow", true);
- cluster.dropColumnFamily("ProteinKeyspace", "ProteinData", true);
- cluster.dropKeyspace("ProteinKeyspace", true);
- System.out.println("ProteinKeyspace has been dropped");
- } else*/ if (keyspaceDef == null) { // create column family
- System.out.println("ProteinKeyspace has been null");
- ColumnFamilyDefinition cfProtein = HFactory.createColumnFamilyDefinition("ProteinKeyspace", "ProteinRow", ComparatorType.ASCIITYPE);
- ColumnFamilyDefinition cfLog = HFactory.createColumnFamilyDefinition("ProteinKeyspace", "ProteinLog", ComparatorType.ASCIITYPE);
- ColumnFamilyDefinition cfData = HFactory.createColumnFamilyDefinition("ProteinKeyspace", "ProteinData", ComparatorType.ASCIITYPE);
-
- KeyspaceDefinition newKeyspace = HFactory.createKeyspaceDefinition("ProteinKeyspace",
- ThriftKsDef.DEF_STRATEGY_CLASS, 1, Arrays.asList(cfProtein, cfLog, cfData));
- //Add the schema to the cluster.
- //"true" as the second param means that Hector will block until all nodes see the change.
- cluster.addKeyspace(newKeyspace, true);
- cluster.addColumnFamily(cfProtein, true);
- cluster.addColumnFamily(cfLog, true);
- cluster.addColumnFamily(cfData, true);
- }
- ksp = HFactory.createKeyspace("ProteinKeyspace", cluster);
- System.out.println("Cassantra has been connected");
- }
-
- // parsing data from http://www.compbio.dundee.ac.uk/www-jpred/results/usage-new/alljobs.dat
- public void Parsing() {
- mutatorString = HFactory.createMutator(ksp, ss); // CF ProteinRow store protein and prediction
- mutatorLog = HFactory.createMutator(ksp, ss); // CF ProteinLog store log informations (ip, id, dates start and dates of end)
- mutatorLong = HFactory.createMutator(ksp, ls); // CF ProteinData store id and protein per data
- System.out.println("Parsing......");
- String in = "http://www.compbio.dundee.ac.uk/www-jpred/results/usage-new/alljobs.dat";
- DataParsing datParsing = new DataParsing();
- datParsing.ParsingTest(in);
- mutatorString.execute();
- mutatorLong.execute();
- mutatorLog.execute();
- System.out.println("Data Inserted");
- }
-
- public void Closing() {
- cluster.getConnectionManager().shutdown();
- System.out.println("Cassantra has been closed");
- }
-
- // check whether this id exists in the cassandra DB
- public boolean CheckIP(String ip) {
- SliceQuery<String, String, String> sliceQuery = HFactory.createSliceQuery(ksp, ss, ss, ss);
- sliceQuery.setColumnFamily("ProteinLog").setKey(ip).setRange("", "", false, 100);
- QueryResult<ColumnSlice<String, String>> result = sliceQuery.execute();
- if (result.get().getColumns().size() > 0)
- return true;
- else
- return false;
- }
-
- public void InsertData(long dataWork, String dataBegin, String dataEnd, String ip, String id, String statusEx, String statusFinal, String protein, String jnetpred) {
- mutatorLog.addInsertion(id, "ProteinLog", HFactory.createColumn("ip", ip, ss, ss))
- .addInsertion(id, "ProteinLog", HFactory.createColumn("DataBegin", dataBegin, ss, ss))
- .addInsertion(id, "ProteinLog", HFactory.createColumn("DataEnd", dataEnd, ss, ss))
- .addInsertion(id, "ProteinLog", HFactory.createColumn("Status ex", statusEx, ss, ss))
- .addInsertion(id, "ProteinLog", HFactory.createColumn("Status final", statusFinal, ss, ss))
- .addInsertion(id, "ProteinLog", HFactory.createColumn("Protein", protein, ss, ss));
- mutatorString.addInsertion(protein, "ProteinRow", HFactory.createColumn(id, jnetpred, ss, ss));
- mutatorLong.addInsertion(dataWork, "ProteinData", HFactory.createColumn(id, protein, ss, ss));
- }
-
- public Keyspace GetKeyspace() {
- return ksp;
- }
-}
+++ /dev/null
-package combio.cassandra;
-
-import java.util.List;
-
-public class DataBase {
- String date;
- int total;
- String id;
- String prot;
- String jpred;
- List<String> subProt;
- List<Integer> timeRez;
-
-
- public DataBase() {}
-
- public DataBase(String dat, int total) {
- this.date = dat;
- this.total = total;
- }
-
- public void setDate(String dat) {
- this.date = dat;
- }
-
- public String getDate() {
- return date;
- }
-
- public void setTotal(int tot) {
- this.total = tot;
- }
- public int getTotal() {
- return total;
- }
-
- public void setProt(String prot) {
- this.prot = prot;
- }
-
- public String getProt() {
- return prot;
- }
-
- public void setJpred(String jpred) {
- this.jpred = jpred;
- }
-
- public String getJpred() {
- return jpred;
- }
-
- public void setId(String id) {
- this.id = id;
- }
-
- public String getId() {
- return id;
- }
-
- public void setSubProt(List<String> subProt) {
- this.subProt = subProt;
- }
-
- public List<String> getSubProt() {
- return subProt;
- }
-
- public void setTimeRez(List<Integer> timeRez) {
- this.timeRez = timeRez;
- }
-
- public List<Integer> getTimeRez() {
- return timeRez;
- }
-}
+++ /dev/null
-package combio.cassandra;
-
-import java.io.BufferedReader;
-import java.io.IOException;
-import java.io.InputStreamReader;
-import java.net.HttpURLConnection;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.net.URLConnection;
-import java.text.ParseException;
-import java.text.SimpleDateFormat;
-import java.util.Calendar;
-import java.util.Date;
-
-public class DataParsing {
- private CassandraCreate cc = new CassandraCreate();
-
- public void ParsingTest(String input) {
- System.out.println("Inserting.....");
- URL url, urltable;
-// int count = 0;
-// int countNotM = 0;
-// int countEr = 0;
-// int countEmp = 0;
- Calendar cal = Calendar.getInstance();
- String date = cal.get(Calendar.YEAR) + "/" + cal.get(Calendar.MONTH) + "/" + cal.get(Calendar.DAY_OF_MONTH);
- try {
- url = new URL(input);
- URLConnection conn = url.openConnection();
- BufferedReader br = new BufferedReader(new InputStreamReader(conn.getInputStream()));
- String line;
-
- while ((line = br.readLine()) != null) {
- if (line.matches(date + "(.*)jp_[^\\s]+")) {
- String[] table;
- table = line.split("\\s+");
- // count++;
- if (!cc.CheckIP(table[table.length - 1])) {
- // countNotM++;
- urltable = new URL("http://www.compbio.dundee.ac.uk/www-jpred/results/" +table[table.length - 1]+"/"+table[table.length - 1]+".concise.fasta");
- HttpURLConnection httpConnection = (HttpURLConnection) urltable.openConnection();
- if (httpConnection.getResponseCode() > 200) {
-// countEr++;
- continue;
- }
- try {
- BufferedReader br1 = new BufferedReader(new InputStreamReader(httpConnection.getInputStream()));
- String lineNext;
- String newProt = "";
- String jnetpred = "";
- while ((lineNext = br1.readLine()) != null) {
- if (lineNext.equals(">QUERY")) {
- while (!(lineNext = br1.readLine()).matches(">[^\\s]+"))
- newProt += lineNext;
- } else if (lineNext.equals(">jnetpred")) {
- while (!(lineNext = br1.readLine()).matches(">[^\\s]+"))
- jnetpred += lineNext;
- }
- }
- br1.close();
- if (newProt.length() <= 1) {
- // countEmp++;
- continue;
- }
-
- SimpleDateFormat formatter = new SimpleDateFormat("yyyy/MM/dd");
-
- String dateInString1 = table[0].substring(0, table[0].indexOf(":"));
-
- long dateWork1 = 0;
-
- try {
- Date dat1 = formatter.parse(dateInString1);
- dateWork1 = dat1.getTime();
-
- } catch (ParseException e) {
- e.printStackTrace();
- }
- cc.InsertData(dateWork1, table[0], table[1], table[2], table[table.length - 1], "OK", "OK", newProt, jnetpred);
- } catch (IOException e) {
- // e.printStackTrace();
- }
- // }
- }
- }
- }
- br.close();
-// System.out.println("Match " + count);
-// System.out.println("Not Match " + countNotM);
-// System.out.println("Error " + countEr);
-// System.out.println("No protein " + countEmp);
- } catch (MalformedURLException e) {
- e.printStackTrace();
- } catch (IOException e) {
- e.printStackTrace();
- }
- }
-}
+++ /dev/null
-package combio.listeners;
-
-import java.util.concurrent.Executors;
-import java.util.concurrent.ScheduledExecutorService;
-import java.util.concurrent.TimeUnit;
-
-import javax.servlet.ServletContextEvent;
-import javax.servlet.ServletContextListener;
-import javax.servlet.annotation.WebListener;
-
-import combio.cassandra.CassandraCreate;
-
-/**
- * Application Lifecycle Listener implementation class ContextListener
- *
- */
-@WebListener
-public class ContextListener implements ServletContextListener {
- private ScheduledExecutorService scheduler;
- CassandraCreate cc = new CassandraCreate();
- /**
- * @see ServletContextListener#contextInitialized(ServletContextEvent)
- */
- public void contextInitialized(ServletContextEvent arg0) {
- System.out.println("Session start ...........................................");
- cc.Connection();
-
-
- scheduler = Executors.newSingleThreadScheduledExecutor();
- scheduler.scheduleAtFixedRate(new Runnable() {
- @Override
- public void run() { cc.Parsing();}}
- , 0, 30, TimeUnit.SECONDS);
- }
-
- /**
- * @see ServletContextListener#contextDestroyed(ServletContextEvent)
- */
- public void contextDestroyed(ServletContextEvent arg0) {
- cc.Closing();
- System.out.println("Shut down");
- scheduler.shutdownNow();
- }
-
-
-
-
-}
+++ /dev/null
-package combio.listeners;
-
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.servlet.ServletException;
-import javax.servlet.annotation.WebServlet;
-import javax.servlet.http.HttpServlet;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
-
-import combio.cassandra.*;
-import combio.statistic.StatisticsProt;
-
-/**
- * Servlet implementation class DetailList
- */
-@WebServlet("/DetailList")
-public class DetailList extends HttpServlet {
- private static final long serialVersionUID = 1L;
-
- /**
- * @see HttpServlet#HttpServlet()
- */
-
- /**
- * @see HttpServlet#doGet(HttpServletRequest request, HttpServletResponse response)
- */
- protected void doGet(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException {
- List<DataBase> result;
- String date1 = request.getParameter("data1");
- String date2 = request.getParameter("data2");
- StatisticsProt sp = new StatisticsProt();
-// result = sp.readDetail(date1, date2);
- }
-
- /**
- * @see HttpServlet#doPost(HttpServletRequest request, HttpServletResponse response)
- */
- protected void doPost(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException {
- // TODO Auto-generated method stub
- }
-
-}
+++ /dev/null
-package combio.listeners;
-
-import java.io.IOException;
-import java.util.List;
-
-import javax.servlet.RequestDispatcher;
-import javax.servlet.ServletException;
-import javax.servlet.annotation.WebServlet;
-import javax.servlet.http.HttpServlet;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
-
-import combio.cassandra.DataBase;
-import combio.statistic.StatisticsProt;
-
-/**
- * Servlet implementation class LengthServlet
- */
-@WebServlet("/LengthServlet")
-public class LengthServlet extends HttpServlet {
- private static final long serialVersionUID = 1L;
- /**
- * @see HttpServlet#doGet(HttpServletRequest request, HttpServletResponse response)
- */
- protected void doGet(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException {
- List<DataBase> result;
- String date1 = request.getParameter("data1");
- String date2 = request.getParameter("data2");
- StatisticsProt sp = new StatisticsProt();
- result = sp.readLength(date1, date2);
- request.setAttribute("data1", date1);
- request.setAttribute("data2", date2);
- request.setAttribute("result", result);
- RequestDispatcher rd = request.getRequestDispatcher("/ReportLength.jsp");
- rd.forward(request, response);
- }
-
- /**
- * @see HttpServlet#doPost(HttpServletRequest request, HttpServletResponse response)
- */
- protected void doPost(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException {
- doGet(request, response);
- }
-}
+++ /dev/null
-package combio.listeners;
-
-import java.io.IOException;
-import java.util.List;
-
-import javax.servlet.RequestDispatcher;
-import javax.servlet.ServletException;
-import javax.servlet.annotation.WebServlet;
-import javax.servlet.http.HttpServlet;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
-
-import combio.cassandra.DataBase;
-import combio.statistic.StatisticsProt;
-
-/**
- * Servlet implementation class ProtServlet
- */
-@WebServlet("/ProtServlet")
-public class ProtServlet extends HttpServlet {
- private static final long serialVersionUID = 1L;
- /**
- * @see HttpServlet#doGet(HttpServletRequest request, HttpServletResponse response)
- */
- protected void doGet(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException {
- List<DataBase> result;
- String flag = request.getParameter("protein");
- String prot = request.getParameter("prot");
- StatisticsProt sp = new StatisticsProt();
- if (flag.equals("whole")) {
- result = sp.readProt(prot);
- } else {
- result = sp.readPart(prot);
- }
- request.setAttribute("prot", prot);
- request.setAttribute("flag", flag);
- request.setAttribute("result", result);
- RequestDispatcher rd = request.getRequestDispatcher("/ReportProt.jsp");
- rd.forward(request, response);
- }
-
- /**
- * @see HttpServlet#doPost(HttpServletRequest request, HttpServletResponse response)
- */
- protected void doPost(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException {
- doGet(request, response);
- }
-
-}
+++ /dev/null
-package combio.listeners;
-
-import java.io.IOException;
-import java.util.List;
-
-import javax.servlet.RequestDispatcher;
-import javax.servlet.ServletException;
-import javax.servlet.annotation.WebServlet;
-import javax.servlet.http.HttpServlet;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
-
-import combio.cassandra.*;
-import combio.statistic.StatisticsProt;
-
-
-@WebServlet("/QueryServlet")
-public class QueryServlet extends HttpServlet {
- private static final long serialVersionUID = 1L;
-
- /**
- * @see HttpServlet#doPost(HttpServletRequest request, HttpServletResponse response)
- */
- protected void doGet(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException {
- List<DataBase> result;
- String date1 = request.getParameter("data1");
- String date2 = request.getParameter("data2");
- StatisticsProt sp = new StatisticsProt();
- result = sp.readDetail(date1, date2);
- request.setAttribute("data1", date1);
- request.setAttribute("data2", date2);
- request.setAttribute("result", result);
- RequestDispatcher rd = request.getRequestDispatcher("/ReportNew.jsp");
- rd.forward(request, response);
- }
-
- protected void doPost(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException {
- doGet(request, response);
- }
-
-}
+++ /dev/null
-package combio.statistic;
-
-import java.text.ParseException;
-import java.text.SimpleDateFormat;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.Date;
-import java.util.Iterator;
-import java.util.List;
-
-import me.prettyprint.cassandra.serializers.LongSerializer;
-import me.prettyprint.cassandra.serializers.StringSerializer;
-import me.prettyprint.hector.api.beans.ColumnSlice;
-import me.prettyprint.hector.api.beans.HColumn;
-import me.prettyprint.hector.api.beans.OrderedRows;
-import me.prettyprint.hector.api.beans.Row;
-import me.prettyprint.hector.api.factory.HFactory;
-import me.prettyprint.hector.api.query.QueryResult;
-import me.prettyprint.hector.api.query.RangeSlicesQuery;
-import me.prettyprint.hector.api.query.SliceQuery;
-import combio.cassandra.CassandraCreate;
-import combio.cassandra.DataBase;
-
-public class StatisticsProt {
- private final static long MILLISECONDS_PER_DAY = 1000L * 60 * 60 * 24;
- private CassandraCreate cc = new CassandraCreate();
- private ArrayList<DataBase> query;
-
- // query for the period from date1 till date2
- public List<DataBase> readDetail(String dateInStringSt, String dateInStringEnd) {
- long dateWorkSt = DateParsing(dateInStringSt);
- long dateWorkEnd = DateParsing(dateInStringEnd);
- query = new ArrayList<DataBase>();
- while (dateWorkSt <= dateWorkEnd) {
- SliceQuery<Long, String, String> result = HFactory.createSliceQuery(cc.GetKeyspace(), LongSerializer.get(), StringSerializer.get(), StringSerializer.get());
- result.setColumnFamily("ProteinData");
- result.setKey(dateWorkSt);
- result.setRange(null, null, false, Integer.MAX_VALUE);
- QueryResult <ColumnSlice<String, String>> columnSlice = result.execute();
- DataBase db = new DataBase(DateFormat(dateWorkSt), columnSlice.get().getColumns().size());
- query.add(db);
- dateWorkSt += MILLISECONDS_PER_DAY ;
- }
- return query;
- }
-
- // query jobs for the period from dateInStringSt till dateInStringEnd
- public List<DataBase> readLength(String dateInStringSt, String dateInStringEnd) {
- query = new ArrayList<DataBase>();
- long dateWorkSt = DateParsing(dateInStringSt);
- long dateWorkEnd = DateParsing(dateInStringEnd);
- while (dateWorkSt <= dateWorkEnd) {
- List<Integer> timeResult = new ArrayList<Integer>();
- SliceQuery<Long, String, String> result = HFactory.createSliceQuery(cc.GetKeyspace(), LongSerializer.get(), StringSerializer.get(), StringSerializer.get());
- result.setColumnFamily("ProteinData");
- result.setKey(dateWorkSt);
- result.setRange(null, null, false, Integer.MAX_VALUE);
- QueryResult <ColumnSlice<String, String>> columnSlice = result.execute();
- List<HColumn<String, String>> col = columnSlice.get().getColumns();
- Iterator<HColumn<String, String>> itCol = col.iterator();
- for (int i = 0; i < 4; i++)
- timeResult.add(i, 0);
- while (itCol.hasNext()) {
- String id = itCol.next().getName();
- long lenResult = CountID(id);
- if (lenResult <= 1)
- timeResult.set(0, timeResult.get(0) + 1);
- else if (lenResult > 1 && lenResult <= 10)
- timeResult.set(1, timeResult.get(1) + 1);
- else if (lenResult > 10 && lenResult <= 20)
- timeResult.set(2, timeResult.get(2) + 1);
- else
- timeResult.set(3, timeResult.get(3) + 1);
- }
- DataBase db = new DataBase();
- db.setTimeRez(timeResult);
- db.setDate(DateFormat(dateWorkSt));
- query.add(db);
- List<Integer> test = query.get(0).getTimeRez();
- dateWorkSt += MILLISECONDS_PER_DAY ;
- }
- return query;
- }
-
- //query by a protein name
- public List<DataBase> readProt(String protIn) {
- query = new ArrayList<DataBase>();
- SliceQuery<String, String, String> result = HFactory.createSliceQuery(cc.GetKeyspace(), StringSerializer.get(), StringSerializer.get(), StringSerializer.get());
- result.setColumnFamily("ProteinRow");
- result.setKey(protIn);
- result.setRange(null, null, false, Integer.MAX_VALUE);
- QueryResult <ColumnSlice<String, String>> columnSlice = result.execute();
- Iterator <HColumn<String, String>> it = columnSlice.get().getColumns().iterator();
- while (it.hasNext()) {
- HColumn<String, String> col = it.next();
- DataBase db = new DataBase();
- db.setProt(protIn);
- db.setId(col.getName());
- db.setJpred(col.getValue());
- query.add(db);
- }
- return query;
- }
-
-
- //query by a sequence (whether exists proteins contains this sequence in the name)
- public List<DataBase> readPart(String protIn) {
- int row_count = 10000;
- query = new ArrayList<DataBase>();
- RangeSlicesQuery<String, String, String> result = HFactory.createRangeSlicesQuery(cc.GetKeyspace(), StringSerializer.get(), StringSerializer.get(), StringSerializer.get());
- result.setColumnFamily("ProteinRow");
- result.setRange(null, null, false, Integer.MAX_VALUE);
- result.setRowCount(row_count);
- String last_key = null;
- while (true) {
- result.setKeys(last_key, null);
- QueryResult <OrderedRows<String,String, String>> columnSlice = result.execute();
- OrderedRows<String, String, String> rows = columnSlice.get();
- Iterator<Row<String, String, String>> rowsIterator = rows.iterator();
- while (rowsIterator.hasNext()) {
- Row<String, String, String> row = rowsIterator.next();
- last_key = row.getKey();
- if (last_key.matches("(.*)" + protIn + "(.*)")) {
- Iterator <HColumn<String, String>> it = row.getColumnSlice().getColumns().iterator();
- while (it.hasNext()) {
- HColumn<String, String> col = it.next();
- List<String> subProt = new ArrayList<String>();
- String subStr = last_key;
- while (subStr.length() > 0 && subStr.contains(protIn)) {
- String first = subStr.substring(0, subStr.indexOf(protIn));
- if (first.length() > 0)
- subProt.add(first);
- subProt.add(protIn);
- subStr = subStr.substring(subStr.indexOf(protIn) + protIn.length(), subStr.length());
- }
- if (subStr.length() > 0)
- subProt.add(subStr);
- DataBase db = new DataBase();
- db.setProt(last_key);
- db.setId(col.getName());
- db.setJpred(col.getValue());
- db.setSubProt(subProt);
- query.add(db);
- }
- }
- }
- if (rows.getCount() < row_count)
- break;
- }
- return query;
- }
-
- // convert String to Date
- private static long DateParsing(String datInput) {
- long dateWorkSt = 0;
- SimpleDateFormat formatter = new SimpleDateFormat("yyyy/MM/dd");
- try {
- dateWorkSt = formatter.parse(datInput).getTime();
- } catch (ParseException e) {
- e.printStackTrace();
- }
- return dateWorkSt;
- }
-
- // convert String to Date
- private static long TimeConvert(String datInput) {
- long dateWorkSt = 0;
- SimpleDateFormat formatter = new SimpleDateFormat("yyyy/MM/dd:hh:mm:ss");
- try {
- dateWorkSt = formatter.parse(datInput).getTime();
- } catch (ParseException e) {
- e.printStackTrace();
- }
- // System.out.println("start reverce" + DateFormat1(dateWorkSt));
- return dateWorkSt;
- }
-
- // convert long to date in string format
- private static String DateFormat(long inDate){
- SimpleDateFormat datformat = new SimpleDateFormat("dd/MM/yyyy");
- String dateString = datformat.format(new Date(inDate));
- return dateString;
- }
-
- private static String DateFormat1(long inDate){
- SimpleDateFormat datformat = new SimpleDateFormat("dd/MM/yyyy:hh:mm:ss");
- String dateString = datformat.format(new Date(inDate));
- return dateString;
- }
-
- public long CountID(String id) {
- SliceQuery<String, String, String> sliceQuery = HFactory.createSliceQuery(cc.GetKeyspace(), StringSerializer.get(), StringSerializer.get(), StringSerializer.get());
- sliceQuery.setColumnFamily("ProteinLog").setKey(id).setRange("", "", false, 100);
- QueryResult<ColumnSlice<String, String>> result = sliceQuery.execute();
- String datBegin = result.get().getColumnByName("DataBegin").getValue();
- String datEnd = result.get().getColumnByName("DataEnd").getValue();
- long datBeginLong = TimeConvert(datBegin);
- long datEndLong = TimeConvert(datEnd);
- return datEndLong-datBeginLong;
-
- }
-
-}
git://source.jalview.org / jabaws.git / commitdiff