From daa7e16fa1815c285bf465b69c8aa1a4ae36c0b9 Mon Sep 17 00:00:00 2001
From: Sasha Sherstnev <a.sherstnev@dundee.ac.uk>
Date: Fri, 20 Dec 2013 08:30:35 +0000
Subject: [PATCH] Add direct link to the job archive file (raw data)

---
 engine/compbio/engine/archive/ArchivedJob.java |   18 +++++++++++++
 server/compbio/controllers/JobController.java  |   33 +++++++++++++++++++++---
 server/compbio/spring/WebConfig.java           |    4 +--
 webapp/view/reportJobLog.jsp                   |    4 +++
 4 files changed, 54 insertions(+), 5 deletions(-)

diff --git a/engine/compbio/engine/archive/ArchivedJob.java b/engine/compbio/engine/archive/ArchivedJob.java
index 94433de..2c2c2ab 100644
--- a/engine/compbio/engine/archive/ArchivedJob.java
+++ b/engine/compbio/engine/archive/ArchivedJob.java
@@ -10,14 +10,20 @@ import java.nio.file.Paths;
 import java.nio.file.Files;
 import java.util.List;
 
+import compbio.engine.ProteoCachePropertyHelperManager;
+import compbio.util.PropertyHelper;
+
 public class ArchivedJob {
 	String path;
 	String id;
+	String jobfilename;
 	int filesize;
 	List<String> files;
+	private static final PropertyHelper ph = ProteoCachePropertyHelperManager.getPropertyHelper();
 
 	public ArchivedJob(String id) {
 		this.id = id;
+		jobfilename = id + ".tar.gz";
 	}
 
 	public boolean copyArchiveFromWeb(String webpath) throws IOException, MalformedURLException {
@@ -25,9 +31,21 @@ public class ArchivedJob {
 		ReadableByteChannel rbc = Channels.newChannel(website.openStream());
 		FileOutputStream fos = new FileOutputStream(path);
 		fos.getChannel().transferFrom(rbc, 0, Long.MAX_VALUE);
+		fos.close();
 		return true;
 	}
 
+	public String prepareJobArchiveToWeb() throws IOException {
+		String resultpath = ph.getProperty("archive.web.dir");
+		String thefile = ph.getProperty("archive.path") + '/' + jobfilename;
+		String finalpath = ProteoCachePropertyHelperManager.getLocalPath() + resultpath + '/' + jobfilename;
+		if (Files.isReadable(Paths.get(thefile))) {
+			Files.copy(Paths.get(thefile), Paths.get(finalpath));
+			return  resultpath + '/' + jobfilename;
+		}
+		return null;
+	}
+
 	public boolean copyArchiveLocaly(String localpath) throws IOException {
 		Files.copy(Paths.get(localpath), Paths.get(path));
 		return true;
diff --git a/server/compbio/controllers/JobController.java b/server/compbio/controllers/JobController.java
index 640dd29..a2b952c 100644
--- a/server/compbio/controllers/JobController.java
+++ b/server/compbio/controllers/JobController.java
@@ -1,6 +1,6 @@
 package compbio.controllers;
 
-import java.security.Principal;
+import java.io.IOException;
 import java.text.SimpleDateFormat;
 import java.util.Calendar;
 import java.util.Date;
@@ -14,14 +14,27 @@ import org.springframework.web.bind.annotation.RequestParam;
 
 import compbio.statistic.CassandraRequester;
 import compbio.cassandra.DataBase;
+import compbio.engine.archive.ArchivedJob;
 
 /**
  * @author Alexander Sherstnev
  * @author Natasha Sherstneva
+ * @version 1.0 Dec 2013
  */
 @Controller
 public class JobController extends BasicController {
 
+	/**
+	 * form a query page for job execution time 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.
+	 * 
+	 * @param model
+	 *            MVC model
+	 * @return link to the JSP query page
+	 */
 	@RequestMapping(value = "/stat/exectime/query", method = RequestMethod.GET)
 	public String initFormExecTime(Map<String, Object> model) {
 		model.put("username", getPrincipalName());
@@ -35,6 +48,13 @@ public class JobController extends BasicController {
 		return "query/JobTimeExecution";
 	}
 
+	/**
+	 * form a query page for a job. The servlet should no be visible to users at all. 
+	 * 
+	 * @param model
+	 *            MVC model
+	 * @return link to the JSP query page
+	 */
 	@RequestMapping(value = "/job/query", method = RequestMethod.GET)
 	public String initFindForm(Map<String, Object> model) {
 		model.put("username", getPrincipalName());
@@ -74,9 +94,16 @@ public class JobController extends BasicController {
 		final long endTime = System.currentTimeMillis();
 		model.put("timeExecution", (endTime - startTime));
 		model.put("IdJob", jobid);
+
+		ArchivedJob aj = new ArchivedJob(jobid);
+		try {
+			model.put("jobarchive", aj.prepareJobArchiveToWeb());
+		} catch (IOException e) {
+			//TODO. what should we do if job is not available???
+		}
 		return "reportJobLog";
 	}
-	
+
 	/*
 	 * convert ???
 	 */
@@ -85,5 +112,5 @@ public class JobController extends BasicController {
 		String dateString = datformat.format(new Date(indate));
 		return dateString;
 	}
-	
+
 }
diff --git a/server/compbio/spring/WebConfig.java b/server/compbio/spring/WebConfig.java
index 0a0de7a..be5e464 100644
--- a/server/compbio/spring/WebConfig.java
+++ b/server/compbio/spring/WebConfig.java
@@ -29,6 +29,6 @@ public class WebConfig extends WebMvcConfigurerAdapter {
 		registry.addResourceHandler("/css/**").addResourceLocations("/css/");
 		registry.addResourceHandler("/images/**").addResourceLocations("/images/");
 		registry.addResourceHandler("/js/**").addResourceLocations("/js/");
+		registry.addResourceHandler("/results/**").addResourceLocations("/results/");
 	}
-
-}
\ No newline at end of file
+}
diff --git a/webapp/view/reportJobLog.jsp b/webapp/view/reportJobLog.jsp
index 3772fbb..da1fcde 100644
--- a/webapp/view/reportJobLog.jsp
+++ b/webapp/view/reportJobLog.jsp
@@ -24,6 +24,10 @@
 <sec:authorize access="hasRole('ROLE_ADMIN')">
 			<p>IP: <a title="Click to view other jobs" href="${ip_query}?ip=${result.ip}">${result.ip}</a></p>
 </sec:authorize>
+			<c:if test='${jobarchive != null}'>
+				<spring:url value="../${jobarchive}" var="jobarchivefile" />
+				<p>Job archive: <a title="Click to get the file" href="${jobarchivefile}">download</a></p>
+			</c:if>
 			<table class="table table-striped table-hover table-bordered">
 			<tbody>
 				<tr>
-- 
1.7.10.2