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ecological-engine-external-algorithms
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Taxamatch List Algorithm 

git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/EcologicalEngineExternalAlgorithms@77387 82a268e6-3cf1-43bd-a215-b396298e98cf
This commit is contained in:
Gianpaolo Coro 2013-06-28 16:21:15 +00:00
parent 5a7d0fce26
commit 2682bf7f4e
5 changed files with 279 additions and 3 deletions
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3
src/main/java/org/gcube/dataanalysis/fin/taxamatch/SimpleTest.java
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@ -18,7 +18,8 @@ public class SimpleTest {
String[] matches = func.func_Taxamatch(genus, species, EQUAL, EQUAL, ip, user, password, db);
System.out.println("Match: "+matches[0]);
System.out.println("Match Number: "+matches[0]);
System.out.println("Match Names:"+matches[1]);
}
}

205
src/main/java/org/gcube/dataanalysis/fin/taxamatch/TaxaMatchListTransducer.java Normal file
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@ -0,0 +1,205 @@
package org.gcube.dataanalysis.fin.taxamatch;
import java.util.ArrayList;
import java.util.List;
import org.apache.bcel.generic.ALOAD;
import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
import org.gcube.dataanalysis.ecoengine.datatypes.ColumnTypesList;
import org.gcube.dataanalysis.ecoengine.datatypes.DatabaseType;
import org.gcube.dataanalysis.ecoengine.datatypes.InputTable;
import org.gcube.dataanalysis.ecoengine.datatypes.OutputTable;
import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveType;
import org.gcube.dataanalysis.ecoengine.datatypes.ServiceType;
import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType;
import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.PrimitiveTypes;
import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.ServiceParameters;
import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.TableTemplates;
import org.gcube.dataanalysis.ecoengine.interfaces.StandardLocalExternalAlgorithm;
import org.gcube.dataanalysis.ecoengine.utils.DatabaseFactory;
import org.gcube.dataanalysis.ecoengine.utils.DatabaseUtils;
import org.gcube.dataanalysis.taxamatch.fin.func_Taxamatch;
import org.hibernate.SessionFactory;
public class TaxaMatchListTransducer extends StandardLocalExternalAlgorithm {
public static enum operators {
EQUAL, NOT_EQUAL, CONTAINS, BEGINS_WITH, ENDS_WITH
};
static String GenusOperator = "ComparisonOperatorforGenus";
static String SpeciesOperator = "ComparisonOperatorforSpecies";
static String Genus = "Genus";
static String Species = "Species";
static String databaseParameterName = "FishBase";
static String userParameterName = "user";
static String passwordParameterName = "password";
static String urlParameterName = "FishBase";
String outputtablename;
String outputtable;
@Override
public String getDescription() {
return "An algorithm for Taxa Matching with respect to the Fishbase database";
}
@Override
public void init() throws Exception {
}
@Override
protected void process() throws Exception {
SessionFactory dbconnection = null;
try{
System.out.println("taxa->USING THE FOLLOWING PARAMETERS FOR DB:");
System.out.println("taxa->driver:"+config.getParam("DatabaseDriver"));
System.out.println("taxa->url:"+config.getParam("DatabaseURL"));
System.out.println("taxa->user:"+config.getParam("DatabaseUserName"));
System.out.println("taxa->password:"+config.getParam("DatabasePassword"));
config.setParam("DatabaseDriver","org.postgresql.Driver");
dbconnection = DatabaseUtils.initDBSession(config);
String tablename = getInputParameter("TaxaTable");
String columnnames = getInputParameter("TaxaColumns");
outputtablename = getInputParameter("OutputTableName");
outputtable = getInputParameter("OutputTable");
String genusOperator = getInputParameter(GenusOperator);
String speciesOperator = getInputParameter(SpeciesOperator);
System.out.println("taxa->got input parameters");
String databaseJdbc = getInputParameter(urlParameterName).replace("//", "");
int separator = databaseJdbc.lastIndexOf("/");
if (separator<0){
log("Bad database URL: "+databaseJdbc);
return;
}
System.out.println("taxa->got DB parameters "+databaseJdbc);
String databaseIP = databaseJdbc.substring(0,separator);
String databaseName = databaseJdbc.substring(separator+1);
String databaseUser = getInputParameter(userParameterName);
String databasePwd = getInputParameter(passwordParameterName);
// databaseIP = "biodiversity.db.i-marine.research-infrastructures.eu";
// databaseUser = "postgres";
// databasePwd = "0b1s@d4sc13nc3";
// databaseName = "fishbase";
System.out.println("taxa->Fishbase Database Parameters to use: "+databaseIP+" "+databaseName+" "+databaseUser+" "+databasePwd);
//end inputs recover
String[] columnlist = columnnames.split(AlgorithmConfiguration.getListSeparator());
System.out.println("taxa->got columns: "+columnlist[0]+" and "+columnlist[1]);
System.out.println("taxa->Selecting genus ");
List<Object> genusList = DatabaseFactory.executeSQLQuery("select "+columnlist[0]+" from "+tablename, dbconnection);
System.out.println("taxa->Selecting species");
List<Object> speciesList = DatabaseFactory.executeSQLQuery("select "+columnlist[1]+" from "+tablename, dbconnection);
System.out.println("taxa->creating table "+"create table "+outputtable+" (scientific_name character varying, value real)");
DatabaseFactory.executeSQLUpdate("create table "+outputtable+" (scientific_name character varying, value real)", dbconnection);
//loop
System.out.println("taxa->inserting into table "+"insert into "+outputtable+" (scientific_name,value) values ('Gadus morhua', 3)");
DatabaseFactory.executeSQLUpdate("insert into "+outputtable+" (scientific_name,value) values ('Gadus morhua', 3)", dbconnection);
}catch(Exception e){
e.printStackTrace();
throw e;
}
finally{
DatabaseUtils.closeDBConnection(dbconnection);
}
}
private String doTaxaMatch(){
/*
log("Computing matching for " + genus + " " + species);
log("With operators: " + genusOperator + " " + speciesOperator);
if ((genus == null) || (species == null)) {
log("Void input");
addOutputString("Number of Matches", "0");
} else {
func_Taxamatch func = new func_Taxamatch();
AnalysisLogger.getLogger().trace("TaxaMatcher Initialized");
String[] matches = func.func_Taxamatch(genus, species, genusOperator, speciesOperator, databaseIP, databaseUser, databasePwd, databaseName);
if ((matches == null) || (matches.length == 0)) {
log("No match");
addOutputString("Number of Matches", "0");
} else {
log("Found " + matches[0] + " matches");
addOutputString("Number of Matches", matches[0]);
String[] speciesn = matches[1].split("\n");
if (Integer.parseInt(matches[0]) > 0) {
for (int i = 0; i < speciesn.length; i++) {
addOutputString("Match " + (i + 1), speciesn[i].trim());
}
}
}
}
log(outputParameters);
*/
return null;
}
@Override
public void shutdown() {
}
@Override
protected void setInputParameters() {
addEnumerateInput(operators.values(), GenusOperator, "Comparison Operator for Genus", "" + operators.EQUAL);
addEnumerateInput(operators.values(), SpeciesOperator, "Comparison Operator for Species", "" + operators.EQUAL);
addRemoteDatabaseInput(databaseParameterName,urlParameterName,userParameterName,passwordParameterName,"driver","dialect");
List<TableTemplates> templates = new ArrayList<TableTemplates>();
templates.add(TableTemplates.GENERIC);
InputTable tinput = new InputTable(templates,"TaxaTable","The table containing the taxa information");
ColumnTypesList columns = new ColumnTypesList ("TaxaTable","TaxaColumns", "Select the columns for genus and species", false);
addStringInput("OutputTableName", "The name of the output table", "taxa_");
ServiceType randomstring = new ServiceType(ServiceParameters.RANDOMSTRING, "OutputTable","","taxa");
inputs.add(tinput);
inputs.add(columns);
inputs.add(randomstring);
DatabaseType.addDefaultDBPars(inputs);
}
@Override
public StatisticalType getOutput() {
List<TableTemplates> outtemplate = new ArrayList<TableTemplates>();
outtemplate.add(TableTemplates.GENERIC);
OutputTable out = new OutputTable(outtemplate, outputtablename, outputtable, "The output table containing all the matches");
return out;
}
}

3
src/main/java/org/gcube/dataanalysis/fin/taxamatch/TaxaMatchTransducer.java
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@ -55,7 +55,8 @@ public class TaxaMatchTransducer extends StandardLocalExternalAlgorithm {
String databaseUser = getInputParameter(userParameterName);
String databasePwd = getInputParameter(passwordParameterName);
log("Database Parameters to use: "+databaseIP+" "+databaseName+" "+databaseUser+" "+databasePwd);
log("Computing matching for " + genus + " " + species);
log("With operators: " + genusOperator + " " + speciesOperator);
if ((genus == null) || (species == null)) {

2
src/main/java/org/gcube/dataanalysis/test/TestFinTaxaMatch.java
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@ -28,7 +28,7 @@ public static void main(String[] args) throws Exception {
config.setAgent("FIN_TAXA_MATCH");
config.setParam("Genus", "gadus");
config.setParam("Species", "");
config.setParam("ComparisonOperatorforGenus", "EQUAL");
config.setParam("ComparisonOperatorforSpecies", "EQUAL");

69
src/main/java/org/gcube/dataanalysis/test/TestFinTaxaMatchList.java Normal file
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@ -0,0 +1,69 @@
package org.gcube.dataanalysis.test;
import java.util.ArrayList;
import java.util.List;
import java.util.UUID;
import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
import org.gcube.dataanalysis.ecoengine.datatypes.ColumnTypesList;
import org.gcube.dataanalysis.ecoengine.datatypes.InputTable;
import org.gcube.dataanalysis.ecoengine.datatypes.ServiceType;
import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType;
import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.ServiceParameters;
import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.TableTemplates;
import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent;
import org.gcube.dataanalysis.ecoengine.processing.factories.TransducerersFactory;
import org.gcube.dataanalysis.ecoengine.test.regression.Regressor;
import org.gcube.dataanalysis.fin.taxamatch.TaxaMatchListTransducer.operators;
public class TestFinTaxaMatchList {
public static void main(String[] args) throws Exception {
System.out.println("TEST 1");
List<ComputationalAgent> trans = null;
trans = TransducerersFactory.getTransducerers(testConfig());
trans.get(0).init();
Regressor.process(trans.get(0));
StatisticalType st = trans.get(0).getOutput();
trans = null;
}
private static AlgorithmConfiguration testConfig() {
AlgorithmConfiguration config = Regressor.getConfig();
config.setConfigPath("./cfg/");
config.setPersistencePath("./");
String databaseURL = "//biodiversity.db.i-marine.research-infrastructures.eu/fishbase";
String databaseUser = "postgres";
String databasePwd = "0b1s@d4sc13nc3";
config.setParam("FishBase", databaseURL);
config.setParam("user", databaseUser);
config.setParam("password", databasePwd);
config.setAgent("FIN_TAXA_MATCH_LIST");
config.setParam("ComparisonOperatorforGenus", "EQUAL");
config.setParam("ComparisonOperatorforSpecies", "EQUAL");
config.setParam("DatabaseUserName","utente");
config.setParam("DatabasePassword","d4science");
config.setParam("DatabaseURL","jdbc:postgresql://dbtest.research-infrastructures.eu/testdb");
config.setParam("DatabaseDriver","org.postgresql.Driver");
config.setParam("TaxaTable","generic_id1098fa80_aa83_4441_8ff1_28c4b8e09630");
config.setParam("TaxaColumns","genus"+AlgorithmConfiguration.listSeparator+"species");
String tablename = "testtaxa"+(UUID.randomUUID());
config.setParam("OutputTableName","Test Casey");
config.setParam("OutputTable", tablename.replace("-", ""));
return config;
}
}