Difference between revisions of "Cholera MapReduce Application"

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=Background=
 
=Background=
  
<youtube>TLpzHHbFrHY</youtube>
+
{{CollapsibleYouTube|Extra History: The Broad Street Pump|<youtube>TLpzHHbFrHY</youtube>
  
 
<youtube>1jlsyucUwpo</youtube>
 
<youtube>1jlsyucUwpo</youtube>
  
<youtube>9NVT6iZP2qg</youtube>
+
<youtube>9NVT6iZP2qg</youtube>}}
  
 
Imagine you are [https://en.wikipedia.org/wiki/John_Snow a physician] in [https://en.wikipedia.org/wiki/1854_Broad_Street_cholera_outbreak 1854 London in the midst of a cholera outbreak].  Your theory that contaminated water is the cause meets resistance from the medical establishment which holds that it is spread via the air.
 
Imagine you are [https://en.wikipedia.org/wiki/John_Snow a physician] in [https://en.wikipedia.org/wiki/1854_Broad_Street_cholera_outbreak 1854 London in the midst of a cholera outbreak].  Your theory that contaminated water is the cause meets resistance from the medical establishment which holds that it is spread via the air.
  
Imagine further that your friend [https://en.wikipedia.org/wiki/Ada_Lovelace Ada] has left you access to computing.
+
Imagine further that your friend [https://en.wikipedia.org/wiki/Ada_Lovelace Ada] has taught you to program.
 +
 
 +
=Lecture=
 +
{{CollapsibleYouTube|CSE 231s Lecture: Cholera|<youtube>Ny5sjWGVuy0</youtube>}}
  
 
=Code To Use=
 
=Code To Use=
We have made the data from [https://www1.udel.edu/johnmack/frec682/cholera/cholera2.html this GIS Analysis] available via methods:
+
You will be asked to produce evidence from CholeraDeath locations and WaterPump locations.  The CholeraDeath data is from [https://www1.udel.edu/johnmack/frec682/cholera/cholera2.html this GIS Analysis] and made available in Java in [https://www.cse.wustl.edu/~dennis.cosgrove/courses/cse231/current/apidocs/mapreduce/apps/cholera/util/SohoCholeraOutbreak1854.html SohoCholeraOutbreak1854]. source: [https://web.archive.org/web/20160822002253/http://www1.udel.edu/johnmack/frec682/cholera/deaths.txt deaths.txt].
  
* [https://www1.udel.edu/johnmack/frec682/cholera/deaths.txt SohoCholeraOutbreak1854.getDeaths()]
+
The WaterPump data is available via [https://www.cse.wustl.edu/~dennis.cosgrove/courses/cse231/current/apidocs/mapreduce/apps/cholera/core/WaterPump.html WaterPump.values()]<br/>source: [https://web.archive.org/web/20160822002256/http://www1.udel.edu/johnmack/frec682/cholera/pumps.txt pumps.txt].
* [https://www1.udel.edu/johnmack/frec682/cholera/pumps.txt WaterPump.values()]
 
  
 
[https://www.cse.wustl.edu/~cosgroved/courses/cse231/current/apidocs/mapreduce/apps/cholera/core/Location.html class Location]
 
[https://www.cse.wustl.edu/~cosgroved/courses/cse231/current/apidocs/mapreduce/apps/cholera/core/Location.html class Location]
: [https://www.cse.wustl.edu/~cosgroved/courses/cse231/current/apidocs/mapreduce/apps/cholera/core/Location.html#getDistanceTo-mapreduce.apps.cholera.core.Location- double getDistanceTo( Location other )]
+
: [https://www.cse.wustl.edu/~cosgroved/courses/cse231/current/apidocs/mapreduce/apps/cholera/core/Location.html#distanceTo-mapreduce.apps.cholera.core.Location- double distanceTo( Location other )]
 +
: [https://www.cse.wustl.edu/~cosgroved/courses/cse231/current/apidocs/mapreduce/apps/cholera/core/Location.html#x double x()]
 +
: [https://www.cse.wustl.edu/~cosgroved/courses/cse231/current/apidocs/mapreduce/apps/cholera/core/Location.html#y double y()]
  
 
[https://www.cse.wustl.edu/~cosgroved/courses/cse231/current/apidocs/mapreduce/apps/cholera/core/CholeraDeath.html class CholeraDeath]
 
[https://www.cse.wustl.edu/~cosgroved/courses/cse231/current/apidocs/mapreduce/apps/cholera/core/CholeraDeath.html class CholeraDeath]
: [https://www.cse.wustl.edu/~cosgroved/courses/cse231/current/apidocs/mapreduce/apps/cholera/core/CholeraDeath.html#getLocation-- Location getLocation()]
+
: [https://www.cse.wustl.edu/~cosgroved/courses/cse231/current/apidocs/mapreduce/apps/cholera/core/CholeraDeath.html#location-- Location location()]
  
 
[https://www.cse.wustl.edu/~cosgroved/courses/cse231/current/apidocs/mapreduce/apps/cholera/core/WaterPump.html enum WaterPump]
 
[https://www.cse.wustl.edu/~cosgroved/courses/cse231/current/apidocs/mapreduce/apps/cholera/core/WaterPump.html enum WaterPump]
: [https://www.cse.wustl.edu/~cosgroved/courses/cse231/current/apidocs/mapreduce/apps/cholera/core/WaterPump.html#getLocation-- Location getLocation()]
+
: [https://www.cse.wustl.edu/~cosgroved/courses/cse231/current/apidocs/mapreduce/apps/cholera/core/WaterPump.html#location-- Location location()]
 +
 
 +
=Code To Implement=
 +
In order to provide a more open-ended assignment, we have abstracted out different aspects of the studio. In particular, <code>getValueRepresentation()</code>  allows you to specify whether your CholeraApp sees high or low numbers as suspects. For example, if you return <code>ValueRepresentation.HIGH_NUMBERS_SUSPECT</code>, you are indicating that a higher number is more likely to indicate that the water pump is the source of the cholera outbreak.  This will aid the [[#Visualization]] in presenting your findings.
  
[https://www.cse.wustl.edu/~cosgroved/courses/cse231/current/apidocs/mapreduce/apps/cholera/core/SohoCholeraOutbreak1854.html class SohoCholeraOutbreak1854]
+
We have anticipated two basic approaches to this problem (with a variation^2 on one of the approaches). You may choose to implement an integer-based or a double-based CholeraApp. If you take a different approach than one we have anticipated, that is fine. Get it checked out by an instructor.
: [https://www.cse.wustl.edu/~cosgroved/courses/cse231/current/apidocs/mapreduce/apps/cholera/core/SohoCholeraOutbreak1854.html#getDeaths-- <nowiki>static CholeraDeath[] getDeaths()</nowiki>]
 
  
=Code To Implement=
+
==CholeraOutbreak==
In order to provide a more open-ended assignment, we have abstracted out different aspects of the studio.  Of particular note is <code>getValueRepresentation()</code> which allows you to specify whether high or low numbers are suspect.  That is: if you return <code>CholeraAppValueRepresentation.HIGH_NUMBERS_SUSPECT</code> you are indicating that a higher number is more likely to indicate that the water pump is the source of the cholera outbreak.  This will aid the [[#Visualization]] in presenting your findings.  We have anticipated two basic approaches to this problem (with a variation^2 on one of the approaches). If you take a different approach than one we have anticipated, that is fine.  Get it checked out by an instructor.
+
 
 +
{{CodeToImplement|CholeraOutbreak|produceEvidence|mapreduce.apps.cholera.exercise}}
 +
 
 +
===valueRepresentation===
 +
{{Sequential|public static ValueRepresentation valueRepresentation()}}
 +
 
 +
You have been provided with this implementation which should be sufficient:
 +
<syntaxhighlight lang="java">
 +
public static ValueRepresentation valueRepresentation() {
 +
    return ValueRepresentation.AUTO_DETECT;
 +
}
 +
</syntaxhighlight>
 +
 
 +
===thresholdIfApplicable===
 +
{{Sequential|public static Optional<Double> thresholdIfApplicable()}}
 +
 
 +
For the vast majority of students, a threshold value will not be applicable to their solution and thus this method need not to be changed:
 +
 
 +
<syntaxhighlight lang="java">
 +
public static Optional<Double> thresholdIfApplicable() {
 +
final boolean IS_THRESHOLD_APPLICABLE = true;
 +
if (IS_THRESHOLD_APPLICABLE) {
 +
throw new NotYetImplementedException();
 +
} else {
 +
return Optional.empty();
 +
}
 +
}
 +
</syntaxhighlight>
 +
 
 +
However, if your solution has a threshold value which would be necessary for visualization and testing, return it here via Optional.of(threshold).
 +
 
 +
Again, you need not concern yourself with this method if you are going with a threshold-less strategy.
  
{{CodeToImplement|CholeraApp|getValueRepresentation<br>createMapper<br>createCollector|mapreduce.apps.cholera.studio}}
 
  
==getValueRepresentation==
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===produceEvidence(choleraDeaths)===
{{Sequential|public static CholeraAppValueRepresentation getValueRepresentation()}}
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{{Sequential|public static Map<WaterPump, ? extends Number> produceEvidence(CholeraDeath[] choleraDeaths)}}
  
return one of the three values to aid the visualization and testing:
+
Note: [https://docs.oracle.com/javase/8/docs/api/java/lang/Integer.html Integer] and [https://docs.oracle.com/javase/8/docs/api/java/lang/Double.html Double] extend [https://docs.oracle.com/javase/8/docs/api/java/lang/Number.html Number].
  
<nowiki>public enum CholeraAppValueRepresentation {
+
How to leverage map reduce to solve this problem.
HIGH_NUMBERS_SUSPECT, LOW_NUMBERS_SUSPECT, LOW_NUMBERS_SUSPECT_SQUARED
 
}</nowiki>
 
  
==createMapper==
+
If going the Integer route:
{{Sequential|public static Mapper<CholeraDeath, WaterPump, Number> createMapper()}}
 
  
We have implemented WaterPump as an enum.  You can access the enum constants of any enum [https://docs.oracle.com/javase/tutorial/java/javaOO/enum.html via its values() method]. For example:
+
<syntaxhighlight lang="java">
 +
Mapper<CholeraDeath, WaterPump, Integer> mapper = null; // TODO
 +
AccumulatorCombinerReducer<Integer, ?, Integer> accumulatorCombinerReducer = null; // TODO: note you have already created a class which will suffice here.
 +
MapReduceFramework<CholeraDeath, WaterPump, Integer, ?, Integer> framework = new StreamMapReduceFramework<>(mapper, accumulatorCombinerReducer);
 +
return framework.mapReduceAll(choleraDeaths);
 +
</syntaxhighlight>
  
<nowiki>for (WaterPump pump : WaterPump.values()) {
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If going the Double route:
}</nowiki>
 
  
==createCollector==
+
<syntaxhighlight lang="java">
Depending on your approach, you may be able to reuse one of your existing Collectors.  Otherwise, implement one to go with your Mapper.
+
Mapper<CholeraDeath, WaterPump, Double> mapper = null; // TODO
 +
AccumulatorCombinerReducer<Double, ?, Double> accumulatorCombinerReducer = null; // TODO
 +
MapReduceFramework<CholeraDeath, WaterPump, Double, ?, Double> framework = new StreamMapReduceFramework<>(mapper, accumulatorCombinerReducer);
 +
return framework.mapReduceAll(choleraDeaths);
 +
</syntaxhighlight>
  
{{Sequential|public static Collector<? extends Number, ?, ? extends Number> createCollector()}}
+
{{Alert|You are allowed to and encouraged to create additional class file(s) and/or use code from previous exercises.}}
  
 
=Testing Your Solution=
 
=Testing Your Solution=
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Original Map Drawn By John Snow:
 
Original Map Drawn By John Snow:
  
[[File:Snow-cholera-map-1.jpg||400px]]
+
[[File:Snow-cholera-map-1.jpg|400px]]
  
 
Our Visualization App:
 
Our Visualization App:
  
{{Viz|CholeraOutbreakVisualizationApp|mapreduce.apps.cholera.viz}}
+
{{Viz|CholeraOutbreakViz|mapreduce.apps.cholera.viz|main}}
 
[[File:CholeraOutbreak.png|600px]]
 
[[File:CholeraOutbreak.png|600px]]
  
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If you have chosen to go a different route than the ones we anticipated, do not worry about passing the test suite.  Demo your work to an instructor in class and we can discuss its fitness.
 
If you have chosen to go a different route than the ones we anticipated, do not worry about passing the test suite.  Demo your work to an instructor in class and we can discuss its fitness.
  
{{TestSuite|CholeraStudioTestSuite|mapreduce}}
+
{{TestSuite|_CholeraOutbreakTestSuite|mapreduce.apps.cholera.exercise}}
 +
 
 +
=Pledge, Acknowledgments, Citations=
 +
{{Pledge|map-reduce-cholera-app}}

Latest revision as of 03:35, 18 March 2024

John Snow memorial and pub.jpg

Motivation

Epidemiology is the important study of "why certain people are getting ill."

We get a chance to make sense of the data in a relatively open-ended studio.

Background

Video: Extra History: The Broad Street Pump  

Imagine you are a physician in 1854 London in the midst of a cholera outbreak. Your theory that contaminated water is the cause meets resistance from the medical establishment which holds that it is spread via the air.

Imagine further that your friend Ada has taught you to program.

Lecture

Video: CSE 231s Lecture: Cholera  

Code To Use

You will be asked to produce evidence from CholeraDeath locations and WaterPump locations. The CholeraDeath data is from this GIS Analysis and made available in Java in SohoCholeraOutbreak1854. source: deaths.txt.

The WaterPump data is available via WaterPump.values()
source: pumps.txt.

class Location

double distanceTo( Location other )
double x()
double y()

class CholeraDeath

Location location()

enum WaterPump

Location location()

Code To Implement

In order to provide a more open-ended assignment, we have abstracted out different aspects of the studio. In particular, getValueRepresentation() allows you to specify whether your CholeraApp sees high or low numbers as suspects. For example, if you return ValueRepresentation.HIGH_NUMBERS_SUSPECT, you are indicating that a higher number is more likely to indicate that the water pump is the source of the cholera outbreak. This will aid the #Visualization in presenting your findings.

We have anticipated two basic approaches to this problem (with a variation^2 on one of the approaches). You may choose to implement an integer-based or a double-based CholeraApp. If you take a different approach than one we have anticipated, that is fine. Get it checked out by an instructor.

CholeraOutbreak

class: CholeraOutbreak.java Java.png
methods: produceEvidence
package: mapreduce.apps.cholera.exercise
source folder: student/src/main/java

valueRepresentation

method: public static ValueRepresentation valueRepresentation() Sequential.svg (sequential implementation only)

You have been provided with this implementation which should be sufficient:

public static ValueRepresentation valueRepresentation() {
    return ValueRepresentation.AUTO_DETECT;
}

thresholdIfApplicable

method: public static Optional<Double> thresholdIfApplicable() Sequential.svg (sequential implementation only)

For the vast majority of students, a threshold value will not be applicable to their solution and thus this method need not to be changed:

public static Optional<Double> thresholdIfApplicable() {
	final boolean IS_THRESHOLD_APPLICABLE = true;
	if (IS_THRESHOLD_APPLICABLE) {
		throw new NotYetImplementedException();
	} else {
		return Optional.empty();
	}
}

However, if your solution has a threshold value which would be necessary for visualization and testing, return it here via Optional.of(threshold).

Again, you need not concern yourself with this method if you are going with a threshold-less strategy.


produceEvidence(choleraDeaths)

method: public static Map<WaterPump, ? extends Number> produceEvidence(CholeraDeath[] choleraDeaths) Sequential.svg (sequential implementation only)

Note: Integer and Double extend Number.

How to leverage map reduce to solve this problem.

If going the Integer route:

		Mapper<CholeraDeath, WaterPump, Integer> mapper = null; // TODO
		AccumulatorCombinerReducer<Integer, ?, Integer> accumulatorCombinerReducer = null; // TODO: note you have already created a class which will suffice here.
		MapReduceFramework<CholeraDeath, WaterPump, Integer, ?, Integer> framework = new StreamMapReduceFramework<>(mapper, accumulatorCombinerReducer);
		return framework.mapReduceAll(choleraDeaths);

If going the Double route:

		Mapper<CholeraDeath, WaterPump, Double> mapper = null; // TODO
		AccumulatorCombinerReducer<Double, ?, Double> accumulatorCombinerReducer = null; // TODO
		MapReduceFramework<CholeraDeath, WaterPump, Double, ?, Double> framework = new StreamMapReduceFramework<>(mapper, accumulatorCombinerReducer);
		return framework.mapReduceAll(choleraDeaths);
Attention niels epting.svg Alert:You are allowed to and encouraged to create additional class file(s) and/or use code from previous exercises.

Testing Your Solution

Visualization

Original Map Drawn By John Snow:

Snow-cholera-map-1.jpg

Our Visualization App:

class: CholeraOutbreakViz.java VIZ
package: mapreduce.apps.cholera.viz
source folder: student/src/main/java

CholeraOutbreak.png

Correctness

If you have chosen to go a different route than the ones we anticipated, do not worry about passing the test suite. Demo your work to an instructor in class and we can discuss its fitness.

class: _CholeraOutbreakTestSuite.java Junit.png
package: mapreduce.apps.cholera.exercise
source folder: testing/src/test/java

Pledge, Acknowledgments, Citations

file: map-reduce-cholera-app-pledge-acknowledgments-citations.txt

More info about the Honor Pledge