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ecological-engine-external-algorithms
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Fin TaxaMatch adjustment and Algorithm example 

git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/EcologicalEngineExternalAlgorithms@76848 82a268e6-3cf1-43bd-a215-b396298e98cf
This commit is contained in:
Gianpaolo Coro 2013-06-07 10:15:15 +00:00
parent a975c4c0b4
commit 5a7d0fce26
3 changed files with 2 additions and 118 deletions
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116
src/main/java/org/gcube/dataanalysis/StandardLocalExternalAlgorithm.java
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@ -1,116 +0,0 @@
package org.gcube.dataanalysis;
import java.io.File;
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.DatabaseType;
import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveType;
import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType;
import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.DatabaseParameters;
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 addRemoteDatabaseInput(String runtimeResourceName, String urlParameterName, String userParameterName, String passwordParameterName, String driverParameterName, String dialectParameterName) {
inputs.add(new DatabaseType(DatabaseParameters.REMOTEDATABASERRNAME,runtimeResourceName,"RR name"));
inputs.add(new DatabaseType(DatabaseParameters.REMOTEDATABASEURL,urlParameterName,""));
inputs.add(new DatabaseType(DatabaseParameters.REMOTEDATABASEUSERNAME,userParameterName,""));
inputs.add(new DatabaseType(DatabaseParameters.REMOTEDATABASEPASSWORD,passwordParameterName,""));
inputs.add(new DatabaseType(DatabaseParameters.REMOTEDATABASEDRIVER,driverParameterName,""));
inputs.add(new DatabaseType(DatabaseParameters.REMOTEDATABASEDIALECT,dialectParameterName,""));
}
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();
}

2
src/main/java/org/gcube/dataanalysis/fin/taxamatch/TaxaMatchTransducer.java
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@ -1,7 +1,7 @@
package org.gcube.dataanalysis.fin.taxamatch; package org.gcube.dataanalysis.fin.taxamatch;
import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
import org.gcube.dataanalysis.StandardLocalExternalAlgorithm; import org.gcube.dataanalysis.ecoengine.interfaces.StandardLocalExternalAlgorithm;
import org.gcube.dataanalysis.taxamatch.fin.func_Taxamatch; import org.gcube.dataanalysis.taxamatch.fin.func_Taxamatch;
public class TaxaMatchTransducer extends StandardLocalExternalAlgorithm { public class TaxaMatchTransducer extends StandardLocalExternalAlgorithm {

2
src/main/java/org/gube/examples/MyAlgorithm.java
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@ -5,10 +5,10 @@ import java.io.FileWriter;
import java.util.LinkedHashMap; import java.util.LinkedHashMap;
import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
import org.gcube.dataanalysis.StandardLocalExternalAlgorithm;
import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveType; import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveType;
import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType; import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType;
import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.PrimitiveTypes; import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.PrimitiveTypes;
import org.gcube.dataanalysis.ecoengine.interfaces.StandardLocalExternalAlgorithm;
public class MyAlgorithm extends StandardLocalExternalAlgorithm{ public class MyAlgorithm extends StandardLocalExternalAlgorithm{