1 package compbio.ws.client;
\r
3 import static org.testng.Assert.assertEquals;
\r
4 import static org.testng.Assert.assertNotNull;
\r
5 import static org.testng.Assert.fail;
\r
6 import static org.testng.Assert.assertTrue;
\r
8 import java.io.FileInputStream;
\r
9 import java.io.FileNotFoundException;
\r
10 import java.io.IOException;
\r
11 import java.net.ConnectException;
\r
12 import java.util.List;
\r
14 import javax.xml.ws.WebServiceException;
\r
16 import org.testng.annotations.BeforeTest;
\r
17 import org.testng.annotations.Test;
\r
19 import compbio.data.msa.JABAService;
\r
20 import compbio.data.msa.SequenceAnnotation;
\r
21 import compbio.data.sequence.ConservationMethod;
\r
22 import compbio.data.sequence.FastaSequence;
\r
23 import compbio.data.sequence.ScoreManager;
\r
24 import compbio.data.sequence.SequenceUtil;
\r
25 import compbio.metadata.AllTestSuit;
\r
26 import compbio.metadata.JobSubmissionException;
\r
27 import compbio.metadata.LimitExceededException;
\r
28 import compbio.metadata.Option;
\r
29 import compbio.metadata.Preset;
\r
30 import compbio.metadata.PresetManager;
\r
31 import compbio.metadata.ResultNotAvailableException;
\r
32 import compbio.metadata.RunnerConfig;
\r
33 import compbio.metadata.UnsupportedRuntimeException;
\r
34 import compbio.metadata.WrongParameterException;
\r
35 import compbio.runner.conservation.AACon;
\r
36 import compbio.util.SysPrefs;
\r
38 public class TestAAConWS {
\r
40 SequenceAnnotation<AACon> msaws;
\r
42 @BeforeTest(groups = {AllTestSuit.test_group_webservices})
\r
43 void initConnection() {
\r
45 * URL url = null; try { url = new
\r
46 * URL("http://localhost:8080/jabaws/AAConWS?wsdl"); } catch
\r
47 * (MalformedURLException e) { e.printStackTrace();
\r
48 * fail(e.getLocalizedMessage()); } String namespace =
\r
49 * "http://msa.data.compbio/01/12/2010/"; QName qname = new
\r
50 * QName(namespace, "AAConWS"); Service serv = Service.create(url,
\r
51 * qname); msaws = serv.getPort(new QName(namespace, "AAConWSPort"),
\r
52 * Annotation.class);
\r
54 JABAService client = Jws2Client.connect(
\r
55 "http://localhost:8080/jabaws", Services.AAConWS);
\r
56 msaws = (SequenceAnnotation<AACon>) client;
\r
57 } catch (ConnectException e) {
\r
58 e.printStackTrace();
\r
59 fail(e.getMessage());
\r
60 } catch (WebServiceException e) {
\r
61 e.printStackTrace();
\r
62 fail(e.getMessage());
\r
66 @Test(groups = {AllTestSuit.test_group_webservices})
\r
67 public void testAnalize() throws FileNotFoundException, IOException {
\r
70 * MsaWS msaws = serv.getPort(new QName(
\r
71 * "http://msa.data.compbio/01/01/2010/", "ClustalWSPort"),
\r
74 // Annotation<AACon> msaws = serv.getPort(new QName(namespace,
\r
75 // "ClustalWSPort"), Annotation.class);
\r
77 // List<FastaSequence> fsl = SequenceUtil.readFasta(new FileInputStream(
\r
78 // AAConTester.test_alignment_input));
\r
80 String CURRENT_DIRECTORY = SysPrefs.getCurrentDirectory()
\r
83 List<FastaSequence> fsl = SequenceUtil.readFasta(new FileInputStream(
\r
84 CURRENT_DIRECTORY + "testsrc" + File.separator + "testdata"
\r
85 + File.separator + "TO1381.fasta.aln"));
\r
88 System.out.println("Pres: " + msaws.getPresets().getPresets());
\r
89 String jobId = msaws.analize(fsl);
\r
90 System.out.println("J: " + jobId);
\r
91 ScoreManager result = msaws.getAnnotation(jobId);
\r
92 assertNotNull(result);
\r
93 assertEquals(result.asSet().size(), 1);
\r
95 assertEquals(result.asSet().iterator().next().getMethod(),
\r
96 ConservationMethod.SHENKIN.toString());
\r
97 List<Float> scores = result.asSet().iterator().next().getScores();
\r
98 assertNotNull(scores);
\r
99 assertEquals(scores.size(), 568);
\r
102 PresetManager<AACon> presets = msaws.getPresets();
\r
103 jobId = msaws.presetAnalize(fsl,
\r
104 presets.getPresetByName("Quick conservation"));
\r
105 result = msaws.getAnnotation(jobId);
\r
106 assertNotNull(result);
\r
107 assertEquals(result.asSet().size(), 13);
\r
109 jobId = msaws.presetAnalize(fsl,
\r
110 presets.getPresetByName("Slow conservation"));
\r
111 result = msaws.getAnnotation(jobId);
\r
112 assertNotNull(result);
\r
113 assertEquals(result.asSet().size(), 5);
\r
115 jobId = msaws.presetAnalize(fsl,
\r
116 presets.getPresetByName("Complete conservation"));
\r
117 result = msaws.getAnnotation(jobId);
\r
118 assertNotNull(result);
\r
119 assertEquals(result.asSet().size(), 18);
\r
121 } catch (UnsupportedRuntimeException e) {
\r
122 e.printStackTrace();
\r
123 fail(e.getMessage());
\r
124 } catch (LimitExceededException e) {
\r
125 e.printStackTrace();
\r
126 fail(e.getMessage());
\r
127 } catch (JobSubmissionException e) {
\r
128 e.printStackTrace();
\r
129 fail(e.getMessage());
\r
130 } catch (ResultNotAvailableException e) {
\r
131 e.printStackTrace();
\r
132 fail(e.getMessage());
\r
133 } catch (WrongParameterException e) {
\r
134 e.printStackTrace();
\r
135 fail(e.getMessage());
\r
139 @Test(groups = {AllTestSuit.test_group_webservices})
\r
140 public void testRecoverArgsForPreset() throws Exception {
\r
141 PresetManager<AACon> presets = msaws.getPresets();
\r
142 for (Preset<AACon> preset:presets.getPresets())
\r
144 List<Option<AACon>> args = preset.getArguments(msaws.getRunnerOptions());
\r
145 List opts = preset.getOptions();
\r
146 assertTrue(args.size()>=opts.size(),"Couldn't recover all Option items for preset "+preset.getName());
\r
149 @Test(groups = {AllTestSuit.test_group_webservices})
\r
150 public void testPresetAnalize() throws FileNotFoundException, IOException {
\r
152 String CURRENT_DIRECTORY = SysPrefs.getCurrentDirectory()
\r
155 List<FastaSequence> fsl = SequenceUtil.readFasta(new FileInputStream(
\r
156 CURRENT_DIRECTORY + "testsrc" + File.separator + "testdata"
\r
157 + File.separator + "TO1381.fasta.aln"));
\r
160 System.out.println("Pres: " + msaws.getPresets().getPresets());
\r
163 PresetManager<AACon> presets = msaws.getPresets();
\r
164 String jobId = msaws.presetAnalize(fsl,
\r
165 presets.getPresetByName("Quick conservation"));
\r
166 ScoreManager result = msaws.getAnnotation(jobId);
\r
167 assertNotNull(result);
\r
168 assertEquals(result.asSet().size(), 13);
\r
170 jobId = msaws.presetAnalize(fsl,
\r
171 presets.getPresetByName("Slow conservation"));
\r
172 result = msaws.getAnnotation(jobId);
\r
173 assertNotNull(result);
\r
174 assertEquals(result.asSet().size(), 5);
\r
176 jobId = msaws.presetAnalize(fsl,
\r
177 presets.getPresetByName("Complete conservation"));
\r
178 result = msaws.getAnnotation(jobId);
\r
179 assertNotNull(result);
\r
180 assertEquals(result.asSet().size(), 18);
\r
182 } catch (UnsupportedRuntimeException e) {
\r
183 e.printStackTrace();
\r
184 fail(e.getMessage());
\r
185 } catch (LimitExceededException e) {
\r
186 e.printStackTrace();
\r
187 fail(e.getMessage());
\r
188 } catch (JobSubmissionException e) {
\r
189 e.printStackTrace();
\r
190 fail(e.getMessage());
\r
191 } catch (ResultNotAvailableException e) {
\r
192 e.printStackTrace();
\r
193 fail(e.getMessage());
\r
194 } catch (WrongParameterException e) {
\r
195 e.printStackTrace();
\r
196 fail(e.getMessage());
\r
201 @Test(groups = {AllTestSuit.test_group_webservices})
\r
202 public void testCustomAnalize() throws FileNotFoundException, IOException {
\r
204 String CURRENT_DIRECTORY = SysPrefs.getCurrentDirectory()
\r
207 List<FastaSequence> fsl = SequenceUtil.readFasta(new FileInputStream(
\r
208 CURRENT_DIRECTORY + "testsrc" + File.separator + "testdata"
\r
209 + File.separator + "TO1381.fasta.aln"));
\r
212 RunnerConfig<AACon> options = msaws.getRunnerOptions();
\r
213 // System.out.println(options.getArguments());
\r
216 options.getArgument("Calculation method").setDefaultValue("SMERFS");
\r
217 // options.getArgument("SMERFS Column Scoring Method")
\r
218 // .setDefaultValue("MAX_SCORE");
\r
219 // options.getArgument("SMERFS Gap Threshhold").setDefaultValue("1");
\r
220 String jobId = msaws.customAnalize(fsl, options.getArguments());
\r
221 ScoreManager result = msaws.getAnnotation(jobId);
\r
222 assertNotNull(result);
\r
223 assertEquals(result.asSet().size(), 1);
\r
224 assertEquals(result.asSet().iterator().next().getScores().get(0),
\r
227 options.getArgument("Calculation method").setDefaultValue("SMERFS");
\r
228 options.removeArgument("Normalize");
\r
229 System.out.println(options);
\r
230 jobId = msaws.customAnalize(fsl, options.getArguments());
\r
231 result = msaws.getAnnotation(jobId);
\r
232 assertNotNull(result);
\r
233 assertEquals(result.asSet().size(), 1);
\r
234 assertEquals(result.asSet().iterator().next().getScores().get(0),
\r
237 } catch (WrongParameterException e) {
\r
238 e.printStackTrace();
\r
239 fail(e.getMessage());
\r
240 } catch (UnsupportedRuntimeException e) {
\r
241 e.printStackTrace();
\r
242 fail(e.getMessage());
\r
243 } catch (LimitExceededException e) {
\r
244 e.printStackTrace();
\r
245 fail(e.getMessage());
\r
246 } catch (JobSubmissionException e) {
\r
247 e.printStackTrace();
\r
248 fail(e.getMessage());
\r
249 } catch (ResultNotAvailableException e) {
\r
250 e.printStackTrace();
\r
251 fail(e.getMessage());
\r