Difference between revisions of "How-to Implement Algorithms for the Statistical Manager"

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Line 167: Line 167:
 
producedImages.put("Species Observations", image);
 
producedImages.put("Species Observations", image);
 
…
 
…
 +
}
 +
 +
</source>
 +
 +
==== Timeseries Chart Output ====
 +
 +
In order to create an TimeSeries Chart you have  to fulfill a <code>DafaultCategoryDataser</code> object and use it to create chart.
 +
The second parameter of createStatiChart method is the format of time.
 +
<source lang="java">
 +
 +
DefaultCategoryDataset dataset;
 +
…
 +
dataset.addValue(...);
 +
….
 +
@Override
 +
public StatisticalType getOutput() {
 +
...
 +
HashMap<String, Image> producedImages = new HashMap<String, Image>();
 +
JFreeChart chart = TimeSeriesGraph.createStaticChart(dataset, "yyyy");
 +
Image image = ImageTools.toImage(chart.createBufferedImage(680, 420));
 +
producedImages.put("TimeSeries chart", image);
 +
...
 +
}
 +
 +
 +
</source>
 +
 +
= File of property =
 +
In order to deploy algorithm we must create:
 +
* the war of eclipse project;
 +
* a file of property containing name used to deploy algorithm by statistical manger interface following by classpath of algorithm class.
 +
I-marin will move the algorithm available to the statistical manager and the interface will be automatically generated.
 +
 +
= Complete Example with multiple output =
 +
<source lang="java">
 +
public class SimpleAlgorithm extends StandardLocalExternalAlgorithm{
 +
 +
//case of db used:
 +
// name of urlParameter
 +
static String urlParameterName = "DatabaseURL";
 +
static String userParameterName = "DatabaseUserName";
 +
static String passwordParameterName = "DatabasePassword";
 +
Class driverClass ;
 +
Driver driver ;
 +
Connection connection = null;
 +
 +
LinkedHashMap<String, StatisticalType> map = new LinkedHashMap<String, StatisticalType>();
 +
private DefaultCategoryDataset defaultcategorydataset;
 +
 +
private String species="Species";
 +
 +
@Override
 +
public void init() throws Exception {
 +
AnalysisLogger.getLogger().debug("Initialization");
 +
String driverName = "org.postgresql.Driver";
 +
driverClass = Class.forName(driverName);
 +
  driver = (Driver) driverClass.newInstance();
 +
 +
 +
 +
}
 +
 +
@Override
 +
public String getDescription() {
 +
// TODO Auto-generated method stub
 +
return null;
 +
}
 +
 +
@Override
 +
protected void process() throws Exception {
 +
String userSelectedSp = getInputParameter(species);
 +
 +
String databaseJdbc = getInputParameter(urlParameterName);
 +
String databaseUser = getInputParameter(userParameterName);
 +
String databasePwd = getInputParameter(passwordParameterName);
 +
 +
connection = DriverManager.getConnection(databaseJdbc, databaseUser,
 +
databasePwd);
 +
Statement stmt = connection.createStatement();
 +
String query = "SELECT numberOfObservation FROM public.count_species_per_year WHERE tname ="
 +
+ species;
 +
ResultSet rs = stmt.executeQuery(query);
 +
int i =0;
 +
String s = "Species";
 +
while (rs.next()) {
 +
 +
 +
String count = rs.getString("numberOfObservation");
 +
int countOcc=Integer.parseInt(count);
 +
PrimitiveType val = new PrimitiveType(String.class.getName(), count, PrimitiveTypes.STRING, species, species);
 +
map.put(species, val);
 +
if(i<16)
 +
defaultcategorydataset.addValue(countOcc,s,species);
 +
else
 +
break;
 +
i++;
 +
 +
}
 +
connection.close();
 +
 +
}
 +
 +
@Override
 +
protected void setInputParameters() {
 +
addStringInput(species, "Slected species", "Solea solea");
 +
addRemoteDatabaseInput("Obis2Repository", urlParameterName,
 +
userParameterName, passwordParameterName, "driver", "dialect");
 +
 +
 +
}
 +
 +
@Override
 +
public void shutdown() {
 +
AnalysisLogger.getLogger().debug("Shutdown");
 +
try {
 +
connection.close();
 +
} catch (SQLException e) {
 +
// TODO Auto-generated catch block
 +
e.printStackTrace();
 +
}
 +
}
 +
@Override
 +
public StatisticalType getOutput() {
 +
PrimitiveType p = new PrimitiveType(Map.class.getName(), PrimitiveType.stringMap2StatisticalMap(outputParameters), PrimitiveTypes.MAP, "Discrepancy Analysis","");
 +
AnalysisLogger.getLogger().debug("MapsComparator: Producing Gaussian Distribution for the errors");
 +
//build image:
 +
HashMap<String, Image> producedImages = new HashMap<String, Image>();
 +
 +
JFreeChart chart = HistogramGraph.createStaticChart(defaultcategorydataset);
 +
    Image image = ImageTools.toImage(chart.createBufferedImage(680, 420));
 +
    producedImages.put("Species Observations", image);
 +
   
 +
PrimitiveType images = new PrimitiveType(HashMap.class.getName(), producedImages, PrimitiveTypes.IMAGES, "ErrorRepresentation", "Graphical representation of the error spread");
 +
 +
//end build image
 +
AnalysisLogger.getLogger().debug("Bar Charts Species Occurrences Produced");
 +
//collect all the outputs
 +
 +
map.put("Result", p);
 +
map.put("Images", images);
 +
 +
//generate a primitive type for the collection
 +
PrimitiveType output = new PrimitiveType(HashMap.class.getName(), map, PrimitiveTypes.MAP, "ResultsMap", "Results Map");
 +
 +
 +
return output;
 +
}
 +
 +
 
}
 
}
  
 
</source>
 
</source>

Revision as of 11:44, 21 June 2013

Prerequisites

IDE: Eclipse Java EE IDE for Web Developers. Version: 3.7+

Step by Step

Let's start creating a project using the eclipse IDE that is mavenized. After having mavenized the project in eclipse you have to put dependencies.

Maven coordinates

The maven artifact coordinates are: 

<dependency>
	<groupId>org.gcube.dataanalysis</groupId>
	<artifactId>ecological-engine</artifactId>
	<version>1.6.1-SNAPSHOT</version>
</dependency>

Let's start creating a new call which implements basic algorithm; it will be executed by Statistical Manager. Next step is to extend basic interface StandardLocalExternalAlgorithm. The following snippet shows unimplemented interface methods that we are going to fulfill. 

public class SimpleAlgorithm extends StandardLocalExternalAlgorithm{
 
	@Override
	public void init() throws Exception {
		// TODO Auto-generated method stub		
	}
	@Override
	public String getDescription() {
		// TODO Auto-generated method stub
		return null;
	}
	@Override
	protected void process() throws Exception {
		// TODO Auto-generated method stub
 
	}
	@Override
	protected void setInputParameters() {
		// TODO Auto-generated method stub
 
	}
	@Override
	public void shutdown() {
		// TODO Auto-generated method stub		
	}
	@Override
	public StatisticalType getOutput() {
		return null;
	}
}

The init() is the initialization method. In this simple example we need to initialize log and we use logger from ecological engine library. In case algorithm uses database, we have to open its connection in this method. The shutdown() closes database connection. In the getDescription() method we add a simple description for the algorithm.

Customize input visualization

String input parameters

User input is obtained calling from setInputParameters() the method addStringInput with following parameters:

  • name of the variable ;
  • description for the variable;
  • default value;

User input is retrieved using getInputParameter() passing name used as parameter into setInputParameters(). 

protected void setInputParameters() {
		addStringInput(NameOfVariable, "Description", "DefaultInput");
 
}

The input parameter will be automatically passed by Statistical Manager to the procedure. In particular, to process method we can retrieve such parameter by name that we set in addStringInput method. 

@Override
protected void process() throws Exception {
....
String userInputValue = getInputParameter(NameOfVariable);
}

Combo box input parameter

In order to obtain a combo box we have to define enumerator that contains the possible choice that could be selected in the combo box and you have to pass it to the method addEnumerateInput as follow: 

public enum Enum {
FIRST_ENUM,
SECOND_ENUM
}
 
protected void setInputParameters() {
addEnumerateInput(Enum.values(), variableName, "Description",
					Enum.FIRST_ENUM.name());
}

addEnumerateInput parameters are rispectivly:

  • values of declared enumerator;
  • name of variable used to extract value insert by user;
  • description of value;
  • default value visualized in comboBox

Case of algorithm use database

In order to use database it is required to call into setInputParameters() the method addRemoteDatabaseInput(). An important step is to pass as first parameters the name of Runtime Resource addressing database. Statistical manager automatically retrieves from runtime resource: url ,user and password. Into process method ,before database connection, url,user and password will be retrieve using getInputParameter. Each of them are retrieved using the name and passing it into addRemoteDatabaseInput as parameters. 

@Override
protected void setInputParameters() {	
...	
addRemoteDatabaseInput("Obis2Repository", urlParameterName,userParameterName, passwordParameterName, "driver", "dialect");
 
@Override
protected void process() throws Exception {
...
 
String databaseJdbc = getInputParameter(urlParameterName);
String databaseUser = getInputParameter(userParameterName);
String databasePwd = getInputParameter(passwordParameterName);
 
connection = DriverManager.getConnection(databaseJdbc, databaseUser,databasePwd);
...
 
}

Customize output

The last step is to set and to specify output of procedure. For this purpose we override the method getOutput() which return StatisticalType. First output parameter we instantiate is a PrimitiveType object that wraps a string; so, we set type as string. We associate name and description to the output value. We can istantiate a second output as an another PrimitiveType We set them as a map which will keep the order of the parameter used to store both output. We add both the output object into the map.

getOutput() procedure which will invoke Statistical Manager to understand type of the output object and at this point in the ecological engine library the algorithm will be indexed with the name set in the file of property.

String Output

In ordert to have a string as output you have to create a PrimitiveType as follows: 

@Override
public StatisticalType getOutput() {
….
PrimitiveType val = new PrimitiveType(String.class.getName(), myString , PrimitiveTypes.STRING, stringName, defaultValue);
return val;
 
}

Bar Chart Output

In order to create an Histogram Chart you have to fulfill a DafaultCategoryDataser object and use it to create chart 

DefaultCategoryDataset dataset;
…
dataset.addValue(...);	
….
 
 
@Override
public StatisticalType getOutput() {
….
HashMap<String, Image> producedImages = new HashMap<String, Image>();
JFreeChart chart = HistogramGraph.createStaticChart(dataset);
Image image = ImageTools.toImage(chart.createBufferedImage(680, 420));
producedImages.put("Species Observations", image);
…
}

Timeseries Chart Output

In order to create an TimeSeries Chart you have to fulfill a DafaultCategoryDataser object and use it to create chart. The second parameter of createStatiChart method is the format of time. 

DefaultCategoryDataset dataset;
…
dataset.addValue(...);	
….
@Override
public StatisticalType getOutput() {
...
HashMap<String, Image> producedImages = new HashMap<String, Image>();
JFreeChart chart = TimeSeriesGraph.createStaticChart(dataset, "yyyy");
Image image = ImageTools.toImage(chart.createBufferedImage(680, 420));
producedImages.put("TimeSeries chart", image);
... 
}

File of property

In order to deploy algorithm we must create:

  • the war of eclipse project;
  • a file of property containing name used to deploy algorithm by statistical manger interface following by classpath of algorithm class.

I-marin will move the algorithm available to the statistical manager and the interface will be automatically generated.

Complete Example with multiple output

public class SimpleAlgorithm extends StandardLocalExternalAlgorithm{
 
	//case of db used:
	// name of urlParameter
	static String urlParameterName = "DatabaseURL";
	static String userParameterName = "DatabaseUserName";
	static String passwordParameterName = "DatabasePassword";
	Class driverClass ;
	Driver driver ;
	Connection connection = null;
 
	LinkedHashMap<String, StatisticalType> map = new LinkedHashMap<String, StatisticalType>();
	private DefaultCategoryDataset defaultcategorydataset;
 
	private String species="Species";
 
	@Override
	public void init() throws Exception {
		AnalysisLogger.getLogger().debug("Initialization");
		String driverName = "org.postgresql.Driver";
		driverClass = Class.forName(driverName);
	  driver = (Driver) driverClass.newInstance();
 
 
 
	}
 
	@Override
	public String getDescription() {
		// TODO Auto-generated method stub
		return null;
	}
 
	@Override
	protected void process() throws Exception {
		String userSelectedSp = getInputParameter(species);
 
		String databaseJdbc = getInputParameter(urlParameterName);
		String databaseUser = getInputParameter(userParameterName);
		String databasePwd = getInputParameter(passwordParameterName);
 
		connection = DriverManager.getConnection(databaseJdbc, databaseUser,
				databasePwd);
		Statement stmt = connection.createStatement();
		String query = "SELECT numberOfObservation FROM public.count_species_per_year WHERE tname ="
				+ species;
		ResultSet rs = stmt.executeQuery(query);
		int i =0;
		String s = "Species";
			while (rs.next()) {
 
 
				String count = rs.getString("numberOfObservation");
				int countOcc=Integer.parseInt(count);
				PrimitiveType val = new PrimitiveType(String.class.getName(), count, PrimitiveTypes.STRING, species, species);
				map.put(species, val);	
				if(i<16)
				defaultcategorydataset.addValue(countOcc,s,species);	
				else
					break;
				i++;
 
		}
		connection.close();
 
	}
 
	@Override
	protected void setInputParameters() {
		addStringInput(species, "Slected species", "Solea solea");
		addRemoteDatabaseInput("Obis2Repository", urlParameterName,
				userParameterName, passwordParameterName, "driver", "dialect");
 
 
	}
 
	@Override
	public void shutdown() {
		AnalysisLogger.getLogger().debug("Shutdown");	
		try {
			connection.close();
		} catch (SQLException e) {
			// TODO Auto-generated catch block
			e.printStackTrace();
		}
	}
	@Override
	public StatisticalType getOutput() {
		PrimitiveType p = new PrimitiveType(Map.class.getName(), PrimitiveType.stringMap2StatisticalMap(outputParameters), PrimitiveTypes.MAP, "Discrepancy Analysis","");
		AnalysisLogger.getLogger().debug("MapsComparator: Producing Gaussian Distribution for the errors");	
		//build image:
		HashMap<String, Image> producedImages = new HashMap<String, Image>();
 
		JFreeChart chart = HistogramGraph.createStaticChart(defaultcategorydataset);
	     Image image = ImageTools.toImage(chart.createBufferedImage(680, 420));
	     producedImages.put("Species Observations", image);
 
		PrimitiveType images = new PrimitiveType(HashMap.class.getName(), producedImages, PrimitiveTypes.IMAGES, "ErrorRepresentation", "Graphical representation of the error spread");
 
		//end build image
		AnalysisLogger.getLogger().debug("Bar Charts Species Occurrences Produced");
		//collect all the outputs
 
		map.put("Result", p);
		map.put("Images", images);
 
		//generate a primitive type for the collection
		PrimitiveType output = new PrimitiveType(HashMap.class.getName(), map, PrimitiveTypes.MAP, "ResultsMap", "Results Map");
 
 
		return output;
	}
 
 
}
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