From 5aec34fb583587602104757aaadc13e7a32ca75c Mon Sep 17 00:00:00 2001
From: Alexander Sherstnev <sherstnv@gmail.com>
Date: Wed, 6 Aug 2014 09:32:14 +0100
Subject: [PATCH] Add mode comments to the classes

---
 .../cassandra/CassandraNativeConnector.java        |    2 +-
 .../compbio/cassandra/readers/CassandraReader.java |   26 ++++++++++++++++---
 server/compbio/controllers/DatabaseController.java |    2 ++
 server/compbio/controllers/IPDataController.java   |   27 ++++++++++++++++++--
 4 files changed, 51 insertions(+), 6 deletions(-)

diff --git a/datadb/compbio/cassandra/CassandraNativeConnector.java b/datadb/compbio/cassandra/CassandraNativeConnector.java
index 6deed99..6b63a57 100644
--- a/datadb/compbio/cassandra/CassandraNativeConnector.java
+++ b/datadb/compbio/cassandra/CassandraNativeConnector.java
@@ -37,7 +37,7 @@ public class CassandraNativeConnector {
 		return session;
 	}
 
-	/*
+	/**
 	 * connect to the cluster and look whether all tables exist
 	 */
 	public void Connect() {
diff --git a/datadb/compbio/cassandra/readers/CassandraReader.java b/datadb/compbio/cassandra/readers/CassandraReader.java
index f970659..a4561be 100644
--- a/datadb/compbio/cassandra/readers/CassandraReader.java
+++ b/datadb/compbio/cassandra/readers/CassandraReader.java
@@ -9,11 +9,22 @@ import com.datastax.driver.core.exceptions.QueryValidationException;
 
 import compbio.cassandra.CassandraNativeConnector;
 
+/**
+ * basic reader of the ProteoCache database. It depends on open
+ * CassandraNativeConnector, which should provide an open session to the
+ * ProteoCache DB (in the default constructor)
+ * 
+ * @author as373024
+ *
+ */
 public class CassandraReader {
 	protected static long earlestDate = 0;
 	protected Session session;
 	protected static Logger log = Logger.getLogger(CassandraNativeConnector.class);
 
+	/**
+	 * default constructor.
+	 */
 	public CassandraReader() {
 		Session inis = CassandraNativeConnector.getSession();
 		setSession(inis);
@@ -24,6 +35,13 @@ public class CassandraReader {
 		session = s;
 	}
 
+	/**
+	 * Basic query to the DB. The method throws exception if the input command
+	 * is not valid or if there is a problem with execution of the command
+	 * 
+	 * @param command - reading CQL command
+	 * @return resulting outout of the command
+	 */
 	protected ResultSet CassandraQuery(String command) {
 		try {
 			ResultSet results = session.execute(command);
@@ -44,14 +62,16 @@ public class CassandraReader {
 
 	}
 
-	/*
-	 * find the earliest date in the database
+	/**
+	 * finds the earliest date in the database
+	 * 
+	 * @return the earliest date (long)
 	 */
 	public static long earliestDate() {
 		earlestDate = CassandraNativeConnector.getEarliestDateInDB();
 		return earlestDate;
 	}
-	
+
 	/**
 	 * prepares an example of either job id or IP for the DB
 	 * 
diff --git a/server/compbio/controllers/DatabaseController.java b/server/compbio/controllers/DatabaseController.java
index c7d6155..f49572d 100644
--- a/server/compbio/controllers/DatabaseController.java
+++ b/server/compbio/controllers/DatabaseController.java
@@ -13,6 +13,8 @@ import compbio.cassandra.DateFormatter;
 
 /**
  * MVC controller for direct interaction with the internal DB
+ * A really dangerous controller since it can change data in the DB
+ * Should be available to administrators only
  * 
  * @author Alexander Sherstnev
  * @author Natasha Sherstneva
diff --git a/server/compbio/controllers/IPDataController.java b/server/compbio/controllers/IPDataController.java
index 2b06e39..a9d25b9 100644
--- a/server/compbio/controllers/IPDataController.java
+++ b/server/compbio/controllers/IPDataController.java
@@ -15,19 +15,36 @@ import compbio.cassandra.readers.IpReader;
 import compbio.cassandra.readers.ReaderByCounter;
 
 /**
+ * The controller 
+ * 
  * @author Alexander Sherstnev
  * @author Natasha Sherstneva
+ * @version 1.0
  */
 @Controller
 public class IPDataController extends BasicController {
-
+	/**
+	 * default minimal jobs to consider a user "heavy user"
+	 */
+	private int minimalJobsFromIP = 5;
+	
+	/**
+	 * for initial page for request "heavy users"
+	 * 
+	 */
 	@RequestMapping(value = "/admin/ip/counts/query", method = RequestMethod.GET)
 	public String initStatisticsForm(Map<String, Object> model) {
 		model.put("username", getPrincipalName());
-		model.put("value", 5);
+		model.put("value", minimalJobsFromIP);
 		return "query/IPStatistics";
 	}
 
+	/**
+	 * form query page for requesting a single IP
+	 * 
+	 * @param model - MVC abstract model
+	 * @return
+	 */
 	@RequestMapping(value = "/admin/ip/query", method = RequestMethod.GET)
 	public String initOneIPForm(Map<String, Object> model) {
 		model.put("username", getPrincipalName());
@@ -36,6 +53,12 @@ public class IPDataController extends BasicController {
 		return "query/IP";
 	}
 
+	/**
+	 * Form output model with statistics on "heavy users"
+	 * @param counter - the number of jobs for requested "heavy users"
+	 * @param model - abstract MVC model
+	 * @return
+	 */
 	@RequestMapping(value = "/admin/ip/counts/results", method = RequestMethod.GET)
 	public String findIPwithCounter(@RequestParam("JobCounter") String counter, Map<String, Object> model) {
 		model.put("username", getPrincipalName());
-- 
1.7.10.2