/*
 * GDPC: The Genomic Diversity and Phenotype Connection
 * for more information: http://www.maizegenetics.net/gdpc/index.html
 *
 * Copyright (C) 2003  Terry Casstevens
 *
 * This library is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public
 * License as published by the Free Software Foundation; either
 * version 2.1 of the License, or (at your option) any later version.
 *
 * This library is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
 * Lesser General Public License for more details.
 */

/*
 * TestGDPC.java
 *
 * Created on October 11, 2003
 */

package gov.usda.gdpc.test;

import gov.usda.gdpc.*;
import gov.usda.gdpc.axis.DBConnectionProxy;
import java.util.List;



/**
 * This class demonstrates the use of The Genomic
 * Diversity and Phenotype Connection (GDPC) API.
 *
 * @author  terryc
 */
public class TestGDPC {
    
    /** The GDPC gateway */
    private final DBGateway myDBGateway = DefaultDBGateway.getInstance();
    
    /** Creates a new instance of TestGDPC */
    public TestGDPC() {
    }
    
    /** main */
    public static void main(String[] args) {
        
        // create test object
        TestGDPC test = new TestGDPC();
        
        // make data source connections to gateway
        test.makeConnections();
        
        // test gateway methods
        test.testGetGenotypeExperimentGroup();
        test.testGetEnvironmentExperimentGroup();
        test.testGetLocusGroup();
        test.testGetPhenotypeOntologyGroup();
        test.testGetPhenotypetable();
        test.testGetGenotypetable();
        
        // Get and print out list of taxa received
        TaxonGroup group = test.testGetTaxonGroup();
        for (int i=0, n=group.size(); i<n; i++) {
            System.out.println(group.get(i));
        }
        
    }
    
    
    /**
     * This creates and adds a database connection
     * (Panzea database) to the GDPC gateway.
     */
    public void makeConnections() {
        
        // this shows how you could connect to a private database
        // DBConnection connection = new PanzeaDBConnection(
        // "oracle.jdbc.driver.OracleDriver", "Panzea database",
        // "oracle.jdbc.driver.OracleDriver",
        // "jdbc:oracle:thin:@gaut.statgen.ncsu.edu:1521:panzea", "??", "??");
        
        // instantiate connection to web service for the panzea database
        DBConnection connection = new DBConnectionProxy("PanzeaConnection",
        "http://152.14.14.27:8080/axis/services/PanzeaConnection");
        
        // add connection to gateway
        myDBGateway.addDBConnection(connection);
        
    }
    
    
    /**
     * Tests the gateway method to get a taxon group.
     *
     * @return taxon group
     */
    public TaxonGroup testGetTaxonGroup() {
        
        // taxon properties
        TaxonProperty [] props = new TaxonProperty[2];
        props[0] = TaxonProperty.SUBSPECIES;
        props[1] = TaxonProperty.GENUS;
        
        // get distinct values for given taxon properties
        DistinctPropertyValues values = myDBGateway.getDistinctProperties(props);
        
        // get distinct values for specified property
        // from previously return object
        List distinctSubspecies = values.getValues(TaxonProperty.SUBSPECIES);
        List distinctGenus = values.getValues(TaxonProperty.GENUS);
        
        // create taxon filter
        TaxonFilter filter = new TaxonFilter();
        
        // add values to the filter
        filter.addValue(new FilterSingleValue(TaxonProperty.SUBSPECIES, "mexicana"));
        filter.addValue(new FilterSingleValue(TaxonProperty.SUBSPECIES, distinctSubspecies.get(2)));
        filter.addValue(new FilterSingleValue(TaxonProperty.GENUS, distinctGenus.get(1)));
        filter.addValue(new FilterSingleValue(TaxonProperty.GENUS, "genus"));
        
        // retrieve taxon group using filter
        TaxonGroup group = myDBGateway.getTaxonGroup(filter);
        
        return group;
        
    }
    
    
    /**
     * Tests the gateway method to get a locus group.
     *
     * @return locus group
     */
    public LocusGroup testGetLocusGroup() {
        
        // locus properties
        LocusProperty [] props = new LocusProperty[2];
        props[0] = LocusProperty.CHROMOSOME_NUMBER;
        props[1] = LocusProperty.LOCUS_TYPE;
        
        // get distinct values for specified locus properties
        DistinctPropertyValues values = myDBGateway.getDistinctProperties(props);
        
        // get distinct values for specified property
        // from previously return object
        List distinctChromosomeNumbers = values.getValues(LocusProperty.CHROMOSOME_NUMBER);
        List distinctTypes = values.getValues(LocusProperty.LOCUS_TYPE);
        
        // create locus filter
        LocusFilter filter = new LocusFilter();
        
        // add values to the filter
        filter.addValue(new FilterSingleValue(LocusProperty.CHROMOSOME_NUMBER, distinctChromosomeNumbers.get(1)));
        filter.addValue(new FilterSingleValue(LocusProperty.CHROMOSOME_NUMBER, new Integer(5)));
        filter.addValue(new FilterSingleValue(LocusProperty.LOCUS_TYPE, distinctTypes.get(1)));
        filter.addValue(new FilterSingleValue(LocusProperty.LOCUS_TYPE, distinctTypes.get(2)));
        
        // retrieve locus group using filter
        LocusGroup group = myDBGateway.getLocusGroup(filter);
        
        return group;
        
    }
    
    
    /**
     * Tests the gateway method to get an environment experiment group.
     *
     * @return environment experiment group
     */
    public EnvironmentExperimentGroup testGetEnvironmentExperimentGroup() {
        
        // environment experiment properties
        EnvironmentExperimentProperty [] props = new EnvironmentExperimentProperty[1];
        props[0] = EnvironmentExperimentProperty.PLANT_DATE;
        
        // get distinct values for specified environment experiment properties
        DistinctPropertyValues values = myDBGateway.getDistinctProperties(props);
        
        // get distinct values for specified property
        // from previously return object
        List properties = values.getValues(EnvironmentExperimentProperty.PLANT_DATE);
        
        // create environment experiment filter
        EnvironmentExperimentFilter filter = new EnvironmentExperimentFilter();
        
        // add values to the filter
        filter.addValue(new FilterSingleValue(EnvironmentExperimentProperty.PLANT_DATE, properties.get(1)));
        filter.addValue(new FilterSingleValue(EnvironmentExperimentProperty.PLANT_DATE, properties.get(2)));
        filter.addValue(new FilterRangeValue(EnvironmentExperimentProperty.PLANT_DATE, (Comparable)properties.get(3),  (Comparable)properties.get(5)));
        
        // retrieve environment experiment group using filter
        EnvironmentExperimentGroup group = myDBGateway.getEnvironmentExperimentGroup(filter);
        
        return group;
        
    }
    
    
    /**
     * Tests the gateway method to get a genotype experiment group.
     *
     * @return genotype experiment group
     */
    public GenotypeExperimentGroup testGetGenotypeExperimentGroup() {
        
        // genotype experiment properties
        GenotypeExperimentProperty [] props = new GenotypeExperimentProperty[1];
        props[0] = GenotypeExperimentProperty.ID;
        
        // get distinct values for specified genotype experiment properties
        DistinctPropertyValues values = myDBGateway.getDistinctProperties(props);
        
        // get distinct values for specified property
        // from previously return object
        List properties = values.getValues(GenotypeExperimentProperty.ID);
        
        // create genotype experiment filter
        GenotypeExperimentFilter filter = new GenotypeExperimentFilter();
        
        // add values to the filter
        filter.addValue(new FilterSingleValue(GenotypeExperimentProperty.ID, properties.get(1)));
        filter.addValue(new FilterSingleValue(GenotypeExperimentProperty.ID, properties.get(2)));
        
        // retrieve genotype experiment group using filter
        GenotypeExperimentGroup group = myDBGateway.getGenotypeExperimentGroup(filter);
        
        return group;
        
    }
    
    
    /**
     * Tests the gateway method to get a phenotype ontology group.
     *
     * @return phenotype ontology group
     */
    public PhenotypeOntologyGroup testGetPhenotypeOntologyGroup() {
        
        // create phenotype ontology filter
        PhenotypeOntologyFilter filter = new PhenotypeOntologyFilter();
        
        // add value to filter
        filter.addValue(new FilterSingleValue(PhenotypeOntologyProperty.NAME, "DSILK"));
        
        // retrieve phenotype ontology group using filter
        PhenotypeOntologyGroup group = myDBGateway.getPhenotypeOntologyGroup(filter);
        
        return group;
    }
    
    
    /**
     * Tests the gateway method to get a phenotype table.
     *
     * @return phenotype table
     */
    public PhenotypeTable testGetPhenotypetable() {
        
        // use other test methods to get an environment experiment group,
        // a taxon group, and phenotype ontology group
        EnvironmentExperimentGroup envGroup = testGetEnvironmentExperimentGroup();
        TaxonGroup taxonGroup = testGetTaxonGroup();
        PhenotypeOntologyGroup ontologyGroup = testGetPhenotypeOntologyGroup();
        
        // get the phenotype group
        PhenotypeGroup group = myDBGateway.getPhenotypeGroup(envGroup, taxonGroup, ontologyGroup);
        
        // create a phenotype table based on phenotype group and
        // particular phenotype ontology
        PhenotypeOntology ontology = (PhenotypeOntology) ontologyGroup.get(0);
        PhenotypeTable table = PhenotypeTable.getInstance(group, ontology);
        
        return table;
        
    }
    
    
    /**
     * Tests the gateway method to get a genotype table.
     *
     * @return genotype table
     */
    public GenotypeTable testGetGenotypetable() {
        
        // use other test methods to get an genotype experiment group
        // and a taxon group.
        GenotypeExperimentGroup expGroup = testGetGenotypeExperimentGroup();
        TaxonGroup taxonGroup = testGetTaxonGroup();
        
        // get genotype group
        GenotypeGroup group = myDBGateway.getGenotypeGroup(expGroup, taxonGroup);
        
        // create genotype table
        GenotypeTable table = GenotypeTable.getInstance(group);
        
        return table;
        
    }
    
}