1 /*

2 * GDPC: The Genomic Diversity and Phenotype Connection

3 * for more information: http://www.maizegenetics.net/gdpc/index.html

4 *

6 *

7 * This library is free software; you can redistribute it and/or

8 * modify it under the terms of the GNU Lesser General Public

9 * License as published by the Free Software Foundation; either

10 * version 2.1 of the License, or (at your option) any later version.

11 *

12 * This library is distributed in the hope that it will be useful,

13 * but WITHOUT ANY WARRANTY; without even the implied warranty of

14 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU

15 * Lesser General Public License for more details.

16 */

18 /*

19 * TestGDPC.java

20 *

21 * Created on October 11, 2003

22 */

24 package gov.usda.gdpc.test;

26 import gov.usda.gdpc.*;

27 import gov.usda.gdpc.axis.DBConnectionProxy;

28 import java.util.List;

32 /**

33 * This class demonstrates the use of The Genomic

34 * Diversity and Phenotype Connection (GDPC) API.

35 *

36 * @author terryc

37 */

38 public class TestGDPC {

40 /** The GDPC gateway */

41 private final DBGateway myDBGateway = DefaultDBGateway.getInstance();

43 /** Creates a new instance of TestGDPC */

44 public TestGDPC() {

45 }

47 /** main */

48 public static void main(String[] args) {

50 // create test object

51 TestGDPC test = new TestGDPC();

53 // make data source connections to gateway

54 test.makeConnections();

56 // test gateway methods

57 test.testGetGenotypeExperimentGroup();

58 test.testGetEnvironmentExperimentGroup();

59 test.testGetLocusGroup();

60 test.testGetPhenotypeOntologyGroup();

61 test.testGetPhenotypetable();

62 test.testGetGenotypetable();

64 // Get and print out list of taxa received

65 TaxonGroup group = test.testGetTaxonGroup();

66 for (int i=0, n=group.size(); i<n; i++) {

67 System.out.println(group.get(i));

68 }

70 }

73 /**

74 * This creates and adds a database connection

75 * (Panzea database) to the GDPC gateway.

76 */

77 public void makeConnections() {

79 // this shows how you could connect to a private database

80 // DBConnection connection = new PanzeaDBConnection(

81 // "oracle.jdbc.driver.OracleDriver", "Panzea database",

82 // "oracle.jdbc.driver.OracleDriver",

83 // "jdbc:oracle:thin:@gaut.statgen.ncsu.edu:1521:panzea", "??", "??");

85 // instantiate connection to web service for the panzea database

86 DBConnection connection = new DBConnectionProxy("PanzeaConnection",

87 "http://152.14.14.27:8080/axis/services/PanzeaConnection");

89 // add connection to gateway

90 myDBGateway.addDBConnection(connection);

92 }

95 /**

96 * Tests the gateway method to get a taxon group.

97 *

98 * @return taxon group

99 */

100 public TaxonGroup testGetTaxonGroup() {

101

102 // taxon properties

103 TaxonProperty [] props = new TaxonProperty[2];

104 props[0] = TaxonProperty.SUBSPECIES;

105 props[1] = TaxonProperty.GENUS;

106

107 // get distinct values for given taxon properties

108 DistinctPropertyValues values = myDBGateway.getDistinctProperties(props);

109

110 // get distinct values for specified property

111 // from previously return object

112 List distinctSubspecies = values.getValues(TaxonProperty.SUBSPECIES);

113 List distinctGenus = values.getValues(TaxonProperty.GENUS);

114

115 // create taxon filter

116 TaxonFilter filter = new TaxonFilter();

117

118 // add values to the filter

119 filter.addValue(new FilterSingleValue(TaxonProperty.SUBSPECIES, "mexicana"));

120 filter.addValue(new FilterSingleValue(TaxonProperty.SUBSPECIES, distinctSubspecies.get(2)));

121 filter.addValue(new FilterSingleValue(TaxonProperty.GENUS, distinctGenus.get(1)));

122 filter.addValue(new FilterSingleValue(TaxonProperty.GENUS, "genus"));

123

124 // retrieve taxon group using filter

125 TaxonGroup group = myDBGateway.getTaxonGroup(filter);

126

127 return group;

128

129 }

130

131

132 /**

133 * Tests the gateway method to get a locus group.

134 *

135 * @return locus group

136 */

137 public LocusGroup testGetLocusGroup() {

138

139 // locus properties

140 LocusProperty [] props = new LocusProperty[2];

141 props[0] = LocusProperty.CHROMOSOME_NUMBER;

142 props[1] = LocusProperty.LOCUS_TYPE;

143

144 // get distinct values for specified locus properties

145 DistinctPropertyValues values = myDBGateway.getDistinctProperties(props);

146

147 // get distinct values for specified property

148 // from previously return object

149 List distinctChromosomeNumbers = values.getValues(LocusProperty.CHROMOSOME_NUMBER);

150 List distinctTypes = values.getValues(LocusProperty.LOCUS_TYPE);

151

152 // create locus filter

153 LocusFilter filter = new LocusFilter();

154

155 // add values to the filter

156 filter.addValue(new FilterSingleValue(LocusProperty.CHROMOSOME_NUMBER, distinctChromosomeNumbers.get(1)));

157 filter.addValue(new FilterSingleValue(LocusProperty.CHROMOSOME_NUMBER, new Integer(5)));

158 filter.addValue(new FilterSingleValue(LocusProperty.LOCUS_TYPE, distinctTypes.get(1)));

159 filter.addValue(new FilterSingleValue(LocusProperty.LOCUS_TYPE, distinctTypes.get(2)));

160

161 // retrieve locus group using filter

162 LocusGroup group = myDBGateway.getLocusGroup(filter);

163

164 return group;

165

166 }

167

168

169 /**

170 * Tests the gateway method to get an environment experiment group.

171 *

172 * @return environment experiment group

173 */

174 public EnvironmentExperimentGroup testGetEnvironmentExperimentGroup() {

175

176 // environment experiment properties

177 EnvironmentExperimentProperty [] props = new EnvironmentExperimentProperty[1];

178 props[0] = EnvironmentExperimentProperty.PLANT_DATE;

179

180 // get distinct values for specified environment experiment properties

181 DistinctPropertyValues values = myDBGateway.getDistinctProperties(props);

182

183 // get distinct values for specified property

184 // from previously return object

185 List properties = values.getValues(EnvironmentExperimentProperty.PLANT_DATE);

186

187 // create environment experiment filter

188 EnvironmentExperimentFilter filter = new EnvironmentExperimentFilter();

189

190 // add values to the filter

191 filter.addValue(new FilterSingleValue(EnvironmentExperimentProperty.PLANT_DATE, properties.get(1)));

192 filter.addValue(new FilterSingleValue(EnvironmentExperimentProperty.PLANT_DATE, properties.get(2)));

193 filter.addValue(new FilterRangeValue(EnvironmentExperimentProperty.PLANT_DATE, (Comparable)properties.get(3), (Comparable)properties.get(5)));

194

195 // retrieve environment experiment group using filter

196 EnvironmentExperimentGroup group = myDBGateway.getEnvironmentExperimentGroup(filter);

197

198 return group;

199

200 }

201

202

203 /**

204 * Tests the gateway method to get a genotype experiment group.

205 *

206 * @return genotype experiment group

207 */

208 public GenotypeExperimentGroup testGetGenotypeExperimentGroup() {

209

210 // genotype experiment properties

211 GenotypeExperimentProperty [] props = new GenotypeExperimentProperty[1];

212 props[0] = GenotypeExperimentProperty.ID;

213

214 // get distinct values for specified genotype experiment properties

215 DistinctPropertyValues values = myDBGateway.getDistinctProperties(props);

216

217 // get distinct values for specified property

218 // from previously return object

219 List properties = values.getValues(GenotypeExperimentProperty.ID);

220

221 // create genotype experiment filter

222 GenotypeExperimentFilter filter = new GenotypeExperimentFilter();

223

224 // add values to the filter

225 filter.addValue(new FilterSingleValue(GenotypeExperimentProperty.ID, properties.get(1)));

226 filter.addValue(new FilterSingleValue(GenotypeExperimentProperty.ID, properties.get(2)));

227

228 // retrieve genotype experiment group using filter

229 GenotypeExperimentGroup group = myDBGateway.getGenotypeExperimentGroup(filter);

230

231 return group;

232

233 }

234

235

236 /**

237 * Tests the gateway method to get a phenotype ontology group.

238 *

239 * @return phenotype ontology group

240 */

241 public PhenotypeOntologyGroup testGetPhenotypeOntologyGroup() {

242

243 // create phenotype ontology filter

244 PhenotypeOntologyFilter filter = new PhenotypeOntologyFilter();

245

246 // add value to filter

247 filter.addValue(new FilterSingleValue(PhenotypeOntologyProperty.NAME, "DSILK"));

248

249 // retrieve phenotype ontology group using filter

250 PhenotypeOntologyGroup group = myDBGateway.getPhenotypeOntologyGroup(filter);

251

252 return group;

253 }

254

255

256 /**

257 * Tests the gateway method to get a phenotype table.

258 *

259 * @return phenotype table

260 */

261 public PhenotypeTable testGetPhenotypetable() {

262

263 // use other test methods to get an environment experiment group,

264 // a taxon group, and phenotype ontology group

265 EnvironmentExperimentGroup envGroup = testGetEnvironmentExperimentGroup();

266 TaxonGroup taxonGroup = testGetTaxonGroup();

267 PhenotypeOntologyGroup ontologyGroup = testGetPhenotypeOntologyGroup();

268

269 // get the phenotype group

270 PhenotypeGroup group = myDBGateway.getPhenotypeGroup(envGroup, taxonGroup, ontologyGroup);

271

272 // create a phenotype table based on phenotype group and

273 // particular phenotype ontology

274 PhenotypeOntology ontology = (PhenotypeOntology) ontologyGroup.get(0);

275 PhenotypeTable table = PhenotypeTable.getInstance(group, ontology);

276

277 return table;

278

279 }

280

281

282 /**

283 * Tests the gateway method to get a genotype table.

284 *

285 * @return genotype table

286 */

287 public GenotypeTable testGetGenotypetable() {

288

289 // use other test methods to get an genotype experiment group

290 // and a taxon group.

291 GenotypeExperimentGroup expGroup = testGetGenotypeExperimentGroup();

292 TaxonGroup taxonGroup = testGetTaxonGroup();

293

294 // get genotype group

295 GenotypeGroup group = myDBGateway.getGenotypeGroup(expGroup, taxonGroup);

296

297 // create genotype table

298 GenotypeTable table = GenotypeTable.getInstance(group);

299

300 return table;

301

302 }

303

304 }