git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/EcologicalEngineExternalAlgorithms@71571 82a268e6-3cf1-43bd-a215-b396298e98cf

src/main/java/org/gcube/dataanalysis/StandardLocalExternalAlgorithm.java

@@ -0,0 +1,104 @@
+package org.gcube.dataanalysis;
+
+import java.util.ArrayList;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+
+import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
+import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
+import org.gcube.dataanalysis.ecoengine.configuration.INFRASTRUCTURE;
+import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveType;
+import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType;
+import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.PrimitiveTypes;
+import org.gcube.dataanalysis.ecoengine.interfaces.Transducerer;
+import org.gcube.dataanalysis.ecoengine.utils.ResourceFactory;
+
+public abstract class StandardLocalExternalAlgorithm implements Transducerer {
+	protected AlgorithmConfiguration config;
+	protected float status = 0;
+	protected List<StatisticalType> inputs = new ArrayList<StatisticalType>();
+	protected ResourceFactory resourceManager;
+	protected LinkedHashMap<String, String> outputParameters = new LinkedHashMap<String, String>();
+	
+	
+	protected void addEnumerateInput(Object itemsList, String name, String description, String defaultvalue) {
+		inputs.add(new PrimitiveType(Enum.class.getName(), itemsList, PrimitiveTypes.ENUMERATED, name, description, defaultvalue));
+	}
+
+	protected void addStringInput(String name, String description, String defaultvalue) {
+		inputs.add(new PrimitiveType(String.class.getName(), null, PrimitiveTypes.STRING, name, description, defaultvalue));
+	}
+
+	protected void addOutputString(String name, String value) {
+		outputParameters.put(name, value);
+	}
+	
+	@Override
+	public void compute() throws Exception {
+		AnalysisLogger.setLogger(config.getConfigPath() + AlgorithmConfiguration.defaultLoggerFile);
+		status = 0;
+		process();
+		status = 100;
+	}
+
+	protected void log(Object message){
+		AnalysisLogger.getLogger().trace(message);
+	}
+	
+	@Override
+	public abstract void init() throws Exception;
+
+	@Override
+	public abstract String getDescription();
+
+	@Override
+	public INFRASTRUCTURE getInfrastructure() {
+		return INFRASTRUCTURE.LOCAL;
+	}
+
+	@Override
+	public List<StatisticalType> getInputParameters() {
+		setInputParameters();
+		return inputs;
+	}
+
+	protected String getInputParameter(String paramName) {
+		return config.getParam(paramName);
+	}
+
+	@Override
+	public StatisticalType getOutput() {
+		PrimitiveType p = new PrimitiveType(Map.class.getName(), PrimitiveType.stringMap2StatisticalMap(outputParameters), PrimitiveTypes.MAP, "Species Match","");
+		return p;
+	}
+
+	public String getResourceLoad() {
+		if (resourceManager == null)
+			resourceManager = new ResourceFactory();
+		return resourceManager.getResourceLoad(1);
+	}
+
+	@Override
+	public String getResources() {
+		return ResourceFactory.getResources(100f);
+	}
+
+	@Override
+	public float getStatus() {
+		return status;
+	}
+
+	protected abstract void process() throws Exception;
+
+	@Override
+	public void setConfiguration(AlgorithmConfiguration config) {
+		this.config = config;
+	}
+
+	protected abstract void setInputParameters();
+
+	@Override
+	public abstract void shutdown();
+
+}

src/main/java/org/gcube/dataanalysis/fin/taxamatch/Test.java

@@ -1,24 +0,0 @@
-package org.gcube.dataanalysis.fin.taxamatch;
-import org.gcube.dataanalysis.taxamatch.fin.func_Taxamatch;
-
-
-
-public class Test {
-
-	public static void main(String[] args) throws Exception{
-		func_Taxamatch func = new func_Taxamatch();
-		
-		String EQUAL = "EQUAL";
-		String genus = "Gadus";
-		String species = "morhua";
-		String ip = "biodiversity.db.i-marine.research-infrastructures.eu";
-		String user = "postgres";
-		String password = "0b1s@d4sc13nc3";
-		String db = "fishbase";
-		
-		String[] matches = func.func_Taxamatch(genus, species, EQUAL, EQUAL, ip, user, password, db);
-		
-		System.out.println("Match: "+matches[0]);
-	}
-	
-}