Sync the fork to keep it updated with the upstream repository.

README.md

@@ -1,28 +1,28 @@
-#LeoTask
+# LeoTask
 
-LeoTask is a parallel task running and results aggregation framework. It is a free and open-source project designed to facilitate running computational intensive tasks [1]. The framework implements the MapReduce model, allocating tasks to multi-cores of a computer and aggregating results according to a XML based configuration file. The framework includes mechanisms to automatically recover applications from interruptions caused by accidents (e.g. Power Cut). Applications using the framework can continue running after an interruption without losing its calculated results.
+LeoTask is a parallel task running and results aggregation (MapReduce) framework. It is a free and open-source project designed to facilitate running computational intensive tasks [1]. The framework implements the MapReduce model, allocating tasks to multi-cores of a computer and aggregating results according to a XML based configuration file. The framework includes mechanisms to automatically recover applications from interruptions caused by accidents (e.g. Power Cut). Applications using the framework can continue running after an interruption without losing its calculated results.
 
-[**Download the latest version**](leotask/demo/leotask.zip?raw=true)
+[**Download**](leotask/demo/leotask.zip?raw=true) | [**Introduction**](leotask/doc/introduction.pdf?raw=true) | [**Applications**](https://github.com/mleoking/LeoTaskApp) | [**Discussion**](http://groups.google.com/forum/#!forum/leotask) | [**Wiki**](https://github.com/mleoking/LeoTask/wiki)
 
 ## Features:
 
-* Automatic & parallel parameter space exploration
-* Flexible & configuration-based result aggregation
-* Programming model focusing only on the key logic
-* Reliable & automatic interruption recovery
-* ...
+* Automatic & parallel parameter space exploration.
+* Flexible & configuration-based result aggregation.
+* Programming model focusing only on the key logic.
+* Reliable & automatic interruption recovery.
+* Ultra lightweight ~ 300KB Jar.
 
-## Utilities
-* Dynamic & cloneable networks structures: a node, a link, a network, and a network set (within which networks can overlap with each other).
-* Integration with Gnuplot
-* Network generation according to common network models
-* DelimitedReader: a sophisticated reader that explores CSV (Comma-separated values) files like a database
-* Fast random number generator based on the Mersenne Twister algorithm
-* ...
+## Utilities:
+* [All dynamic & cloneable networks structures](leotask/src/app/org/leores/demo/NetDemo.java): a node, a link, a network, a network set (within which networks can overlap with each other), multiplex networks.
+* [Integration with Gnuplot](leotask/src/app/org/leores/demo/JGnuplotDemo.java): hybrid programming with Gnuplot, output statistic results as Gnuplot scripts.
+* [Network generation according to common network models](leotask/src/app/org/leores/demo/ModDemo.java): random networks, scale-free networks, etc.
+* [DelimitedReader](leotask/src/app/org/leores/demo/DelimitedReaderDemo.java): a sophisticated reader that explores CSV (Comma-Separated Values) files like a database.
+* [Fast random number generator based on the Mersenne Twister algorithm](leotask/src/app/org/leores/demo/RandomUtilDemo.java).
+* [Versatile curve fitter and function value optimizer (minimizer)](leotask/src/app/org/leores/demo/MathDemo.java).
 
 ## Example Application:
 
-Please refer to [the introduction](https://github.com/mleoking/leotask/blob/master/leotask/introduction.pdf?raw=true) for building an example application using the framework.
+Please refer to [the introduction](leotask/doc/introduction.pdf?raw=true) for building an example application using the framework.
 
 ### Code (RollDice.java):
 ```java
@@ -44,7 +44,7 @@ public class RollDice extends Task {
     public boolean step() {
         boolean rtn = iStep <= nDice;
         if (rtn) {
-            sum += (int) (rand.nextDouble() * nSide);
+            sum += (int) (rand.nextDouble() * nSide + 1);
         }
         return rtn;
     }
@@ -54,33 +54,32 @@ public class RollDice extends Task {
 ### Configuration (rolldice.xml):
 ```xml
 <Tasks>
-    <name val="task-rolldice"/><usage val="0.5"/><nRepeats val="5"/><checkInterval val="4"/>
+    <name val="task-rolldice"/><usage val="0.9"/><nRepeats val="2000"/><checkInterval val="4"/>
     <variables class="org.leores.task.app.RollDice">    
         <nSide val="2;4;6"/>
         <nDice val="2:1:5"/><!--from 2 to 5 with a step of 1, i.e. 2;3;4;5 -->
     </variables>
     <statistics>
         <members>
-            <i><info val="Fig1%pltm+@afterRept@"/><valVar val="sum;#$sum$/$nDice$#"/>
-               <parVars val="nSide;nDice"/></i>
-            <i><info val="Fig2%plt+@afterRept@"/><valVar val="sum"/><parVars val="nSide"/></i>
-            <i><info val="Fig3%plt+@afterRept@"/><valVar val="sum"/><parVars val="nDice"/></i> 
+            <i><info val="afterRept@"/><valVar val="sum;#$sum$/$nDice$#"/><parVars val="nSide;nDice"/></i>
+            <i><info val="afterRept@"/><valVar val="sum"/><parVars val="nSide"/></i>
+            <i><info val="afterRept@"/><valVar val="sum"/><parVars val="nDice"/></i> 
         </members>
     </statistics>
 </Tasks>
 ```
 
-Before running the example application, please install [Java](http://www.oracle.com/technetwork/java/javase/downloads/jdk7-downloads-1880260.html) and include the the directory of the command _java_ in the system's _PATH_ environment variable.
+Before running the example application, please install [Java](http://www.oracle.com/technetwork/java/javase/downloads/jdk7-downloads-1880260.html) and include the the directory of the command _java_ in the system's _PATH_ environment variable. Windows system users can alternatively download and install (_install.bat_) the all-in-one runtime environment package: [LeoTaskRunEnv](https://github.com/mleoking/LeoTaskApp/releases/download/v1.0.0/LeoTaskRunEnv.zip)
 
 Chang the current directory to the "Demo" folder and then execute the following commnad
 
     java -jar leotask.jar -load=rolldice.xml
 
 If you are using a MS windows system, you can also execute "rolldice.bat".
 
-Additional applications using the framework can be found in [LeoTaskApp](https://github.com/mleoking/LeoTaskApp).
-
 ## References:
 
-[1] Changwang Zhang, Shi Zhou, Benjamin M. Chain (January 2015). "[LeoTask: a fast, flexible and reliable framework for computational research](http://arxiv.org/abs/1501.01678)" (arXiv:1501.01678). Cornell University. [(PDF)](http://arxiv-web3.library.cornell.edu/pdf/1501.01678v1)
+[1] Changwang Zhang, Shi Zhou, Benjamin M. Chain (2015). "[LeoTask: a fast, flexible and reliable framework for computational research](http://arxiv.org/abs/1501.01678)", arXiv:1501.01678. [(PDF)](http://arxiv-web3.library.cornell.edu/pdf/1501.01678v1)
+
+
 

leotask/.gitignore

@@ -0,0 +1,8 @@
+/bin/
+
+# Windows image file caches
+Thumbs.db
+ehthumbs.db
+
+# Folder config file
+Desktop.ini

leotask/demo/dreader.csv

@@ -1,26 +1,38 @@
-Test file for csv reader,,,
-----,,,
-1,2,3,4
-5,6,7,8
-data,end,,
----,,,
----,,,
-data,start1,,
-c1,c2,c3,c4
-1,10,100,1000
-2,20,200,1100
-,,,
-data,end,,
-data,start2,,
-c1,c2,c3,c4
-1,30,300,2000
-4,40,400,9000
-1,50,500
-data,start3,,
-c1,c2,c3,c4
-1,30,300,3000
-1,40,400,4000
-2,50,500,
-2,50,500,
-1,30,300,5000
-1,40,400,6000
+Test file for csv reader,,,,
+----,,,,
+1,2,3,4,
+5,6,7,8,
+data,end,,,
+---,,,,
+---,,,,
+data,start1,,,
+c1,c2,c3,c4,
+1,10,100,1000,
+2,20,200,1100,
+,,,,
+data,end,,,
+data,start2,,,
+c1,c2,c3,c4,
+1,30,300,2000,
+4,40,400,9000,
+1,50,500,,
+data,start3,,,
+c1,c2,c3,c4,
+1,30,300,3000,
+1,40,400,4000,
+2,50,500,,
+2,50,500,,
+1,30,300,5000,
+1,40,400,6000,
+data,end,,,
+,,,,
+id,name,age,,
+mm1,Leo,25,,
+mm2,Emily,18,,
+,,,,
+id,date,blood pressure,heart rate,mood
+mm1,01-Apr,100,50,Happy
+mm1,05-Apr,120,60,Sad
+mm2,01-Apr,80,40, 
+mm2,03-Apr,90,,Sad
+mm2,05-Apr,,50,Happy

leotask/demo/rolldice#.xml

@@ -1,5 +1,5 @@
 <Taskss>
-  <name val="rolldices"/><usage val="0.5"/><nRepeats val="5"/><!--<dataLevels val="SA"/>-->
+  <name val="rolldices"/><usage val="0.9"/><nRepeats val="2000"/><!--<dataLevels val="SA"/>-->
   <sNameToRun val="setX;set1"/><!--<sPatNameToRun val=".*set\d"/>--><!--<bAggregateFile val="false"/>-->
   <vMap val="~ls=info=rolldices $id$ nSide:$nSide$ nDice:$nDice$;logInfo=~afterRept@$sum$;}"/>
   <members>

leotask/demo/rolldice.xml

@@ -1,5 +1,5 @@
 <Tasks>
-  <name val="task-rolldice"/><usage val="0.5"/><nRepeats val="5"/><checkInterval val="4"/>
+  <name val="rolldice"/><usage val="0.9"/><nRepeats val="2000"/><checkInterval val="4"/>
   <!--<sTaskMethodEnd val="mDrawPDF"/>--><!-- Uncomment this line if you have installed gnuplot4.6.5 and included its directory in the system variable PATH -->
   <variables class="org.leores.task.app.RollDice">    
     <nSide val="2;4;6"/>

leotask/src/app/org/leores/demo/DelimitedReaderDemo.java

@@ -7,11 +7,12 @@
 import org.leores.util.Logger;
 import org.leores.util.U;
 import org.leores.util.able.Processable1;
+import org.leores.util.data.DataTable;
 
 public class DelimitedReaderDemo extends Demo {
+	String sFile = "dreader.csv";
 
 	public void delimitedReader() {
-		String sFile = "dreader.csv";
 		String[] rowToStart1 = { "data", "start1" };
 		String[] columnsToRead = { "c4", "c1" };
 		String[] rowToEnd = { "data", "end" };
@@ -90,8 +91,6 @@ public void delimitedReader() {
 	}
 
 	protected void _readRowPatterns(String[] rowPattern, String[] rowToStart, String[] columnsToRead, String[] rowToEnd) {
-		String sFile = "dreader.csv";
-
 		DelimitedReader dr;
 		String[] row;
 		List<String[]> lrow;
@@ -174,10 +173,32 @@ public void readRowPatterns() {
 		_readRowPatterns(rowPatterns, rowToStartEnd, columnsToRead, rowToStartEnd);
 	}
 
+	public void readRelatedData() {
+		log("Read from related data:");
+		try {
+			DelimitedReader dr = new DelimitedReader(sFile);
+			dr.prep(null, new String[] { "id", "name" });
+			dr.setValidRowPattern(new String[] { null, "Emily" });
+			String[] row = dr.readValidRow();
+			String id = row[0];
+			dr.prep(null, new String[] { "id", "date", "mood", "blood pressure", "heart rate" });
+			dr.setValidRowPattern(new String[] { id });
+			DataTable dt = dr.readValidDataTable();
+
+			log(dt.getColNames());
+			for (int i = 0, mi = dt.nRows(); i < mi; i++) {
+				log(dt.getRow(i));
+			}
+		} catch (FileNotFoundException e) {
+			log(e);
+		}
+	}
+
 	public static void demo() {
 		DelimitedReaderDemo drd = new DelimitedReaderDemo();
-		//drd.delimitedReader();
+		drd.delimitedReader();
 		drd.readRowPatterns();
+		drd.readRelatedData();
 	}
 
 }

leotask/src/app/org/leores/demo/Demo.java

@@ -23,14 +23,14 @@ public static void main(String[] args) {
 		//DelimitedReaderDemo.demo();
 		//EpidemicDemo.demo();
 		//FileUtilDemo.demo();
-		//JGnuplotDemo.demo();
+		JGnuplotDemo.demo();
 		//MathDemo.demo();
 		//ModDemo.demo();
 		//NetDemo.demo();
 		//ObjUtilDemo.demo();
 		//ProcessableDemo.demo();
 		//RandomUtilDemo.demo();
-		TaskDemo.demo();
+		//TaskDemo.demo();
 		//UtilDemo.demo();
 	}
 }