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manage standard local algorithms executions 

git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/EcologicalEngine@93133 82a268e6-3cf1-43bd-a215-b396298e98cf
This commit is contained in:
Gianpaolo Coro 2014-03-14 13:53:37 +00:00
parent a9579a12af
commit 678a68060d
4 changed files with 34 additions and 21 deletions
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3
src/main/java/org/gcube/dataanalysis/ecoengine/configuration/INFRASTRUCTURE.java
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@ -4,6 +4,7 @@ public enum INFRASTRUCTURE {
RAINY_CLOUD, RAINY_CLOUD,
D4SCIENCE, D4SCIENCE,
LOCAL LOCAL,
EXTERNAL_WPS
} }

44
src/main/java/org/gcube/dataanalysis/ecoengine/interfaces/StandardLocalExternalAlgorithm.java
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@ -23,49 +23,55 @@ public abstract class StandardLocalExternalAlgorithm implements Transducerer {
protected List<StatisticalType> inputs = new ArrayList<StatisticalType>(); protected List<StatisticalType> inputs = new ArrayList<StatisticalType>();
protected ResourceFactory resourceManager; protected ResourceFactory resourceManager;
public LinkedHashMap<String, String> outputParameters = new LinkedHashMap<String, String>(); public LinkedHashMap<String, String> outputParameters = new LinkedHashMap<String, String>();
protected void addEnumerateInput(Object itemsList, String name, String description, String defaultvalue) { protected void addEnumerateInput(Object itemsList, String name, String description, String defaultvalue) {
inputs.add(new PrimitiveType(Enum.class.getName(), itemsList, PrimitiveTypes.ENUMERATED, name, description, 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) { 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.REMOTEDATABASERRNAME, runtimeResourceName, "RR name"));
inputs.add(new DatabaseType(DatabaseParameters.REMOTEDATABASEURL,urlParameterName,"")); inputs.add(new DatabaseType(DatabaseParameters.REMOTEDATABASEURL, urlParameterName, ""));
inputs.add(new DatabaseType(DatabaseParameters.REMOTEDATABASEUSERNAME,userParameterName,"")); inputs.add(new DatabaseType(DatabaseParameters.REMOTEDATABASEUSERNAME, userParameterName, ""));
inputs.add(new DatabaseType(DatabaseParameters.REMOTEDATABASEPASSWORD,passwordParameterName,"")); inputs.add(new DatabaseType(DatabaseParameters.REMOTEDATABASEPASSWORD, passwordParameterName, ""));
inputs.add(new DatabaseType(DatabaseParameters.REMOTEDATABASEDRIVER,driverParameterName,"")); inputs.add(new DatabaseType(DatabaseParameters.REMOTEDATABASEDRIVER, driverParameterName, ""));
inputs.add(new DatabaseType(DatabaseParameters.REMOTEDATABASEDIALECT,dialectParameterName,"")); inputs.add(new DatabaseType(DatabaseParameters.REMOTEDATABASEDIALECT, dialectParameterName, ""));
} }
protected void addStringInput(String name, String description, String defaultvalue) { protected void addStringInput(String name, String description, String defaultvalue) {
inputs.add(new PrimitiveType(String.class.getName(), null, PrimitiveTypes.STRING, name, description, defaultvalue)); inputs.add(new PrimitiveType(String.class.getName(), null, PrimitiveTypes.STRING, name, description, defaultvalue));
} }
protected void addIntegerInput(String name, String description, String defaultvalue) { protected void addIntegerInput(String name, String description, String defaultvalue) {
inputs.add(new PrimitiveType(Integer.class.getName(), null, PrimitiveTypes.NUMBER, name,description,defaultvalue)); inputs.add(new PrimitiveType(Integer.class.getName(), null, PrimitiveTypes.NUMBER, name, description, defaultvalue));
} }
protected void addDoubleInput(String name, String description, String defaultvalue) { protected void addDoubleInput(String name, String description, String defaultvalue) {
inputs.add(new PrimitiveType(Double.class.getName(), null, PrimitiveTypes.NUMBER, name,description,defaultvalue)); inputs.add(new PrimitiveType(Double.class.getName(), null, PrimitiveTypes.NUMBER, name, description, defaultvalue));
} }
protected void addOutputString(String name, String value) { protected void addOutputString(String name, String value) {
outputParameters.put(name, value); outputParameters.put(name, value);
} }
@Override @Override
public void compute() throws Exception { public void compute() throws Exception {
AnalysisLogger.setLogger(config.getConfigPath() + AlgorithmConfiguration.defaultLoggerFile); AnalysisLogger.setLogger(config.getConfigPath() + AlgorithmConfiguration.defaultLoggerFile);
status = 0; status = 0;
process(); try {
status = 100; process();
} catch (Exception e) {
e.printStackTrace();
AnalysisLogger.getLogger().debug("StandardLocalExternalAlgorithm->Error in processing");
throw e;
} finally {
status = 100;
}
} }
protected void log(Object message){ protected void log(Object message) {
AnalysisLogger.getLogger().debug(message); AnalysisLogger.getLogger().debug(message);
} }
@Override @Override
public abstract void init() throws Exception; public abstract void init() throws Exception;
@ -89,7 +95,7 @@ public abstract class StandardLocalExternalAlgorithm implements Transducerer {
@Override @Override
public StatisticalType getOutput() { public StatisticalType getOutput() {
PrimitiveType p = new PrimitiveType(Map.class.getName(), PrimitiveType.stringMap2StatisticalMap(outputParameters), PrimitiveTypes.MAP, "Species Match",""); PrimitiveType p = new PrimitiveType(Map.class.getName(), PrimitiveType.stringMap2StatisticalMap(outputParameters), PrimitiveTypes.MAP, "Species Match", "");
return p; return p;
} }

3
src/main/java/org/gcube/dataanalysis/ecoengine/signals/PeriodicityDetector.java
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@ -172,7 +172,10 @@ public class PeriodicityDetector {
power = MathFunctions.incrementPerc(power, (float)powers[i], counter); power = MathFunctions.incrementPerc(power, (float)powers[i], counter);
counter++; counter++;
} }
this.periodicityStrength=power; this.periodicityStrength=power;
if (this.periodicityStrength==-0.0)
this.periodicityStrength=0;
// reconstruct the F // reconstruct the F
double meanF = MathFunctions.mean(maxfrequencies); double meanF = MathFunctions.mean(maxfrequencies);

5
src/main/java/org/gcube/dataanalysis/ecoengine/utils/DatabaseUtils.java
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@ -177,7 +177,10 @@ public class DatabaseUtils {
for (int j=0;j<row.length;j++){ for (int j=0;j<row.length;j++){
String preprow = row[j].replaceAll("^'", "").replaceAll("'$", ""); String preprow = row[j].replaceAll("^'", "").replaceAll("'$", "");
preprow=preprow.replace("'", ""+(char)96); preprow=preprow.replace("'", ""+(char)96);
sb.append("'"+preprow+"'"); if (preprow.equalsIgnoreCase("NULL"))
sb.append(preprow);
else
sb.append("'"+preprow+"'");
if (j<row.length-1) if (j<row.length-1)
sb.append(","); sb.append(",");
} }