From: Sasha Sherstnev <a.sherstnev@dundee.ac.uk>
Date: Mon, 20 Jan 2014 15:24:16 +0000 (+0000)
Subject: Merge branch 'DAO'
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=6094cb1ef55124629c1862daf9ef9e9b05433a60;hp=0349dbf0d18575d9d35758bc9ced99af202766ce;p=proteocache.git

Merge branch 'DAO'

Conflicts:
	conf/Proteocache.properties
---

diff --git a/.settings/org.eclipse.jdt.core.prefs b/.settings/org.eclipse.jdt.core.prefs
index ef1da3f..02430f4 100644
--- a/.settings/org.eclipse.jdt.core.prefs
+++ b/.settings/org.eclipse.jdt.core.prefs
@@ -1,14 +1,14 @@
 eclipse.preferences.version=1
 org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
-org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.6
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.7
 org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve
-org.eclipse.jdt.core.compiler.compliance=1.6
+org.eclipse.jdt.core.compiler.compliance=1.7
 org.eclipse.jdt.core.compiler.debug.lineNumber=generate
 org.eclipse.jdt.core.compiler.debug.localVariable=generate
 org.eclipse.jdt.core.compiler.debug.sourceFile=generate
 org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
 org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
-org.eclipse.jdt.core.compiler.source=1.6
+org.eclipse.jdt.core.compiler.source=1.7
 org.eclipse.jdt.core.formatter.align_type_members_on_columns=false
 org.eclipse.jdt.core.formatter.alignment_for_arguments_in_allocation_expression=16
 org.eclipse.jdt.core.formatter.alignment_for_arguments_in_annotation=0
diff --git a/conf/Proteocache.properties b/conf/Proteocache.properties
index b5f588f..6ce13ed 100644
--- a/conf/Proteocache.properties
+++ b/conf/Proteocache.properties
@@ -1,8 +1,9 @@
 #################################################################################
 # Cassandra host or IP
 # test server is 10.0.115.190
-cassandra.host=localhost
+#cassandra.host=localhost
 #cassandra.host=gjb-www-1.cluster.lifesci.dundee.ac.uk
+cassandra.host=c6100-1.cluster.lifesci.dundee.ac.uk
 
 cassandra.newtables.update=false
 cassandra.version.update=false
diff --git a/server/compbio/controllers/DailyStatisticsController.java b/server/compbio/controllers/DailyStatisticsController.java
index 9cdf874..322f74e 100644
--- a/server/compbio/controllers/DailyStatisticsController.java
+++ b/server/compbio/controllers/DailyStatisticsController.java
@@ -28,11 +28,13 @@ import compbio.cassandra.readers.DailyStatisticsReader;
 public class DailyStatisticsController extends BasicController {
 
 	/**
-	 * form a query page for daily job statistics. The servlet should be
-	 * available for users and admins only. By defaults the report time range is
-	 * from the earliest day with jobs to today ("Query for all dates" is
-	 * ticked). If the user removes the tick the time range is from today - 3
-	 * days to today. Currently, the input model is empty.
+	 * form a query page for daily job statistics.
+	 * 
+	 * The servlet should be available for users and admins only. By defaults
+	 * the report time range is from the earliest day with jobs to current date
+	 * ("Query for all dates" is ticked). If the user removes the tick the time
+	 * range is from today - 3 days to today. Currently, the input model is
+	 * empty.
 	 * 
 	 * @param model
 	 *            MVC model
diff --git a/server/compbio/controllers/DatabaseController.java b/server/compbio/controllers/DatabaseController.java
index 609ee09..e720a2c 100644
--- a/server/compbio/controllers/DatabaseController.java
+++ b/server/compbio/controllers/DatabaseController.java
@@ -9,6 +9,7 @@ import org.springframework.web.bind.annotation.RequestMethod;
 import org.springframework.web.bind.annotation.RequestParam;
 
 import compbio.cassandra.CassandraRemover;
+import compbio.cassandra.DateFormatter;
 
 /**
  * @author Alexander Sherstnev
@@ -41,39 +42,44 @@ public class DatabaseController extends BasicController {
 		return "support/Denied";
 	}
 
-	@RequestMapping(value = "/database/remove/goreal", method = RequestMethod.GET)
-	public String findIPwithCounter(@RequestParam("byId") String flagId, @RequestParam("id") String jobId,
-			@RequestParam("byDate") String flagDate, @RequestParam("date1") String date1, @RequestParam("date2") String date2,
-			@RequestParam("byIp") String flagIp, @RequestParam("ip") String ip, @RequestParam("bySequence") String flagSeq,
-			@RequestParam("seq") String seq, Map<String, Object> model) {
+	@RequestMapping(value = "/database/remove/go", method = RequestMethod.GET)
+	public String findIPwithCounter(@RequestParam("byId") String byId, @RequestParam("id") String jobid,
+			@RequestParam("byDate") String byDate, @RequestParam("date1") String date1, @RequestParam("date2") String date2,
+			@RequestParam("byIp") String byIp, @RequestParam("ip") String ip, @RequestParam("bySequence") String bySequence,
+			@RequestParam("seq") String sequence, Map<String, Object> model) {
 		model.put("username", getPrincipalName());
+
+		model.put("byDate", byDate);
+		model.put("date1", date1);
+		model.put("date2", date2);
+
+		model.put("byId", byId);
+		model.put("id", jobid);
+
+		model.put("byIp", byIp);
+		model.put("ip", ip);
+
+		model.put("bySequence", bySequence);
+		model.put("seq", sequence);
+
 		CassandraRemover cr = new CassandraRemover();
-		int numberRemover = 0;
-		if (flagId != null)
-			numberRemover = cr.RemoveJobById(jobId);
-		if (flagDate != null)
-			numberRemover = cr.RemoveJobByDate(date1, date2);
-		if (flagIp != null)
-			numberRemover = cr.RemoveJobByIp(ip);
-		if (flagSeq != null)
-			numberRemover = cr.RemoveJobBySequence(seq);
-		model.put("result", numberRemover);
-		return "reports/RemoveDBrecords";
-	}
+		int njobs = 0;
+		if (byId.equals("on,off"))
+			njobs = cr.RemoveJobById(jobid);
+		if (byDate.equals("on,off")) {
+			long longDate1 = DateFormatter.DateParsing(date1, formaterYYMMDD) / 1000;
+			long longDate2 = DateFormatter.DateParsing(date2, formaterYYMMDD) / 1000;
+			int timerange = (int)(longDate2 - longDate1) /24 / 3600 + 1;
+			model.put("ndays", timerange);
+			njobs = cr.RemoveJobByDate(date1, date2);
+		}
+		if (byIp.equals("on,off"))
+			njobs = cr.RemoveJobByIp(ip);
+		if (bySequence.equals("on,off"))
+			njobs = cr.RemoveJobBySequence(sequence);
+		model.put("njobs", njobs);
 
-	@RequestMapping(value = "/database/remove/go", method = RequestMethod.GET)
-	public String findIPwithCounter(@RequestParam("id") String jobId, @RequestParam("date1") String date1,
-			@RequestParam("date2") String date2, @RequestParam("ip") String ip, @RequestParam("seq") String seq, Map<String, Object> model) {
-		model.put("username", getPrincipalName());
-		/*
-		 * CassandraRemover cr = new CassandraRemover(); int numberRemover = 0;
-		 * if (flagId != null) numberRemover = cr.RemoveJobById(jobId); if
-		 * (flagDate != null) numberRemover = cr.RemoveJobByDate(date1, date2);
-		 * if (flagIp != null) numberRemover = cr.RemoveJobByIp(ip); if (flagSeq
-		 * != null) numberRemover = cr.RemoveJobBySequence(seq);
-		 * model.put("result", numberRemover); return "reportRemoveData";
-		 */
-		return "support/Blocked";
+		return "reports/RemoveJobs";
 	}
 
 }
diff --git a/webapp/view/query/JobLog.jsp b/webapp/view/query/JobLog.jsp
index 2afcf3f..9310f25 100644
--- a/webapp/view/query/JobLog.jsp
+++ b/webapp/view/query/JobLog.jsp
@@ -18,9 +18,9 @@
 		</div>
 		<div class="panel-body">
 			<form method="get" action="${query}">
-			<p><input type="text" name="IdJob" value="${value}"></p>
-			<input type="submit" name="Search" value="Search"/>
-		</form>
+				<p><input type="text" name="IdJob" value="${value}"></p>
+				<input type="submit" name="Search" value="Search"/>
+			</form>
 		</div>
 	</div>
 
diff --git a/webapp/view/query/RemoveJobs.jsp b/webapp/view/query/RemoveJobs.jsp
index cf3459f..d5c138f 100644
--- a/webapp/view/query/RemoveJobs.jsp
+++ b/webapp/view/query/RemoveJobs.jsp
@@ -22,6 +22,7 @@
 				<p>
 					<input type="checkbox" name="byId" onclick="show(this, 'id');" /> Job with the job Id
 					<div id='id' style="visibility:hidden;">Job Id: <input type="text" name="id" value="${samplejobid}" /></div>
+					<input type="hidden" name="byId" value="off" />
 				</p>
 
 				<!-- remove jobs executed on the dates: -->
@@ -30,18 +31,21 @@
 					<div id='date' style="visibility:hidden;">
 					From <input type="text" name="date1" value = "${date1}" style=" width : 145px;" />
 					to <input type="text" name="date2" value = "${date2}" /></div>
+					<input type="hidden" name="byDate" value="off" />
 				</p>
 
 				<!-- remove jobs executed from particular IP: -->
 				<p>
 					<input type="checkbox" name="byIp" onclick="show(this, 'ip');" /> Jobs executed from the IP
 					<div id='ip' style="visibility:hidden;">IP: <input type="text" name="ip" value = '${sampleip}'/></div>
+					<input type="hidden" name="byIp" value="off" />
 				</p>
 				
 				<!-- remove jobs with a particular protein subsiquence: -->
 				<p>
 					<input type="checkbox" name="bySequence"  onclick="show(this, 'seq');"> Jobs with the protein subsequence
 					<div id='seq' style="visibility:hidden;"> Sequence: <input type="text" name="seq" value = "${sampleseq}"/></div>
+					<input type="hidden" name="bySequence" value="off" />
 				</p>
 				
 				<p><input type="submit" name="Delete" value="Delete"/></p>
diff --git a/webapp/view/reports/RemoveDBrecords.jsp b/webapp/view/reports/RemoveDBrecords.jsp
deleted file mode 100644
index 67e120d..0000000
--- a/webapp/view/reports/RemoveDBrecords.jsp
+++ /dev/null
@@ -1,10 +0,0 @@
-<!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>Jobs have been removed from ProteoCache</title>
-</head>
-<body>
-<h1>ProteoCache removed : ${result} jobs</h1>
-</body>
-</html>
\ No newline at end of file
diff --git a/webapp/view/reports/RemoveJobs.jsp b/webapp/view/reports/RemoveJobs.jsp
new file mode 100644
index 0000000..b1d62fa
--- /dev/null
+++ b/webapp/view/reports/RemoveJobs.jsp
@@ -0,0 +1,42 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+
+<%@ taglib uri="http://www.springframework.org/tags" prefix="spring"%>
+<%@ taglib uri="http://java.sun.com/jsp/jstl/core" prefix="c"%>
+<%@ taglib uri="http://java.sun.com/jsp/jstl/functions" prefix="fn"%>
+<%@ taglib uri="http://java.sun.com/jsp/jstl/fmt" prefix="fmt"%>
+<%@ taglib prefix="sec" uri="http://www.springframework.org/security/tags"%>
+
+<html>
+<jsp:include page="../fragments/header.jsp" />
+<body>
+	<div class="container">
+		<jsp:include page="../fragments/mainmenu.jsp" />
+		<spring:url value="/sequence/sequence/results" var="sequence_query" />
+		<spring:url value="/admin/ip/results" var="ip_query" />
+
+		<div class="panel panel-default">
+		<div class="panel-heading">
+			<p style="font-weight:bold;">Information for removed jobs</p>
+		</div>
+		<div class="panel-body">
+			<!-- <div class="grid-wrapper-div">-->
+			<c:if test="${byDate != 'off'}">
+				<p>${njobs} jobs have been removed for time period: <c:out value="${date1}" /> to <c:out value="${date2}"/> (${ndays} days)</p>
+			</c:if>
+			<c:if test="${byId != 'off'}">
+				<p>Job ${id} has been removed.</p>
+			</c:if>
+			<c:if test="${byIp != 'off'}">
+				<p>Jobs launched from ${ip} have been removed. ${njobs} jobs have been removed.</p>
+			</c:if>
+			<c:if test="${bySequence != 'off'}">
+				<p>Jobs launched with sequence ${seq} have been removed. ${njobs} jobs have been removed.</p>
+			</c:if>
+			<!-- </div>-->
+		</div>
+		</div>
+
+		<jsp:include page="../fragments/footer.jsp" />
+	</div>
+</body>
+</html>
\ No newline at end of file