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
8 import java.io.FileInputStream;
\r
9 import java.io.FileNotFoundException;
\r
10 import java.io.IOException;
\r
11 import java.net.MalformedURLException;
\r
12 import java.net.URL;
\r
13 import java.util.ArrayList;
\r
14 import java.util.HashSet;
\r
15 import java.util.List;
\r
17 import javax.xml.namespace.QName;
\r
18 import javax.xml.ws.Service;
\r
20 import org.testng.annotations.BeforeTest;
\r
21 import org.testng.annotations.Test;
\r
23 import compbio.data.msa.Annotation;
\r
24 import compbio.data.sequence.FastaSequence;
\r
25 import compbio.data.sequence.Method;
\r
26 import compbio.data.sequence.Score;
\r
27 import compbio.data.sequence.SequenceUtil;
\r
28 import compbio.metadata.JobSubmissionException;
\r
29 import compbio.metadata.LimitExceededException;
\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 Annotation<AACon> msaws;
\r
43 void initConnection() {
\r
46 url = new URL("http://localhost:8080/jabaws/AAConWS?wsdl");
\r
47 } catch (MalformedURLException e) {
\r
48 e.printStackTrace();
\r
49 fail(e.getLocalizedMessage());
\r
51 String namespace = "http://msa.data.compbio/01/12/2010/";
\r
52 QName qname = new QName(namespace, "AAConWS");
\r
53 Service serv = Service.create(url, qname);
\r
54 msaws = serv.getPort(new QName(namespace, "AAConWSPort"),
\r
59 public void testAnalize() throws FileNotFoundException, IOException {
\r
62 * MsaWS msaws = serv.getPort(new QName(
\r
63 * "http://msa.data.compbio/01/01/2010/", "ClustalWSPort"),
\r
66 // Annotation<AACon> msaws = serv.getPort(new QName(namespace,
\r
67 // "ClustalWSPort"), Annotation.class);
\r
69 // List<FastaSequence> fsl = SequenceUtil.readFasta(new FileInputStream(
\r
70 // AAConTester.test_alignment_input));
\r
72 String CURRENT_DIRECTORY = SysPrefs.getCurrentDirectory()
\r
75 List<FastaSequence> fsl = SequenceUtil.readFasta(new FileInputStream(
\r
76 CURRENT_DIRECTORY + "testsrc" + File.separator + "testdata"
\r
77 + File.separator + "TO1381.fasta.aln"));
\r
80 System.out.println("Pres: " + msaws.getPresets().getPresets());
\r
81 String jobId = msaws.analize(fsl);
\r
82 System.out.println("J: " + jobId);
\r
83 HashSet<Score> result = msaws.getConservation(jobId);
\r
84 assertNotNull(result);
\r
85 assertEquals(result.size(), 1);
\r
86 assertEquals(result.iterator().next().getMethod(), Method.SHENKIN);
\r
87 List<Float> scores = result.iterator().next().getScores();
\r
88 assertNotNull(scores);
\r
89 assertEquals(scores.size(), 568);
\r
92 PresetManager<AACon> presets = msaws.getPresets();
\r
93 jobId = msaws.presetAnalize(fsl,
\r
94 presets.getPresetByName("Quick conservation"));
\r
95 result = msaws.getConservation(jobId);
\r
96 assertNotNull(result);
\r
97 assertEquals(result.size(), 13);
\r
99 jobId = msaws.presetAnalize(fsl,
\r
100 presets.getPresetByName("Slow conservation"));
\r
101 result = msaws.getConservation(jobId);
\r
102 assertNotNull(result);
\r
103 assertEquals(result.size(), 5);
\r
105 jobId = msaws.presetAnalize(fsl,
\r
106 presets.getPresetByName("Complete conservation"));
\r
107 result = msaws.getConservation(jobId);
\r
108 assertNotNull(result);
\r
109 assertEquals(result.size(), 18);
\r
111 } catch (UnsupportedRuntimeException e) {
\r
112 e.printStackTrace();
\r
113 fail(e.getMessage());
\r
114 } catch (LimitExceededException e) {
\r
115 e.printStackTrace();
\r
116 fail(e.getMessage());
\r
117 } catch (JobSubmissionException e) {
\r
118 e.printStackTrace();
\r
119 fail(e.getMessage());
\r
120 } catch (ResultNotAvailableException e) {
\r
121 e.printStackTrace();
\r
122 fail(e.getMessage());
\r
123 } catch (WrongParameterException e) {
\r
124 e.printStackTrace();
\r
125 fail(e.getMessage());
\r
131 public void testPresetAnalize() throws FileNotFoundException, IOException {
\r
133 String CURRENT_DIRECTORY = SysPrefs.getCurrentDirectory()
\r
136 List<FastaSequence> fsl = SequenceUtil.readFasta(new FileInputStream(
\r
137 CURRENT_DIRECTORY + "testsrc" + File.separator + "testdata"
\r
138 + File.separator + "TO1381.fasta.aln"));
\r
141 System.out.println("Pres: " + msaws.getPresets().getPresets());
\r
144 PresetManager<AACon> presets = msaws.getPresets();
\r
145 String jobId = msaws.presetAnalize(fsl,
\r
146 presets.getPresetByName("Quick conservation"));
\r
147 HashSet<Score> result = msaws.getConservation(jobId);
\r
148 assertNotNull(result);
\r
149 assertEquals(result.size(), 13);
\r
151 jobId = msaws.presetAnalize(fsl,
\r
152 presets.getPresetByName("Slow conservation"));
\r
153 result = msaws.getConservation(jobId);
\r
154 assertNotNull(result);
\r
155 assertEquals(result.size(), 5);
\r
157 jobId = msaws.presetAnalize(fsl,
\r
158 presets.getPresetByName("Complete conservation"));
\r
159 result = msaws.getConservation(jobId);
\r
160 assertNotNull(result);
\r
161 assertEquals(result.size(), 18);
\r
163 } catch (UnsupportedRuntimeException e) {
\r
164 e.printStackTrace();
\r
165 fail(e.getMessage());
\r
166 } catch (LimitExceededException e) {
\r
167 e.printStackTrace();
\r
168 fail(e.getMessage());
\r
169 } catch (JobSubmissionException e) {
\r
170 e.printStackTrace();
\r
171 fail(e.getMessage());
\r
172 } catch (ResultNotAvailableException e) {
\r
173 e.printStackTrace();
\r
174 fail(e.getMessage());
\r
175 } catch (WrongParameterException e) {
\r
176 e.printStackTrace();
\r
177 fail(e.getMessage());
\r
183 public void testCustomAnalize() throws FileNotFoundException, IOException {
\r
185 String CURRENT_DIRECTORY = SysPrefs.getCurrentDirectory()
\r
188 List<FastaSequence> fsl = SequenceUtil.readFasta(new FileInputStream(
\r
189 CURRENT_DIRECTORY + "testsrc" + File.separator + "testdata"
\r
190 + File.separator + "TO1381.fasta.aln"));
\r
193 RunnerConfig<AACon> options = msaws.getRunnerOptions();
\r
194 // System.out.println(options.getArguments());
\r
197 options.getArgument("Calculation method").setDefaultValue("SMERFS");
\r
198 String jobId = msaws.customAnalize(fsl, options.getArguments());
\r
199 HashSet<Score> result = msaws.getConservation(jobId);
\r
200 assertNotNull(result);
\r
201 assertEquals(result.size(), 1);
\r
203 new ArrayList<Score>(result).get(0).getScores().get(0),
\r
206 options.getArgument("Calculation method").setDefaultValue("SMERFS");
\r
207 options.removeArgument("Normalize");
\r
208 System.out.println(options);
\r
209 jobId = msaws.customAnalize(fsl, options.getArguments());
\r
210 result = msaws.getConservation(jobId);
\r
211 assertNotNull(result);
\r
212 assertEquals(result.size(), 1);
\r
214 new ArrayList<Score>(result).get(0).getScores().get(0),
\r
217 } catch (WrongParameterException e) {
\r
218 e.printStackTrace();
\r
219 fail(e.getMessage());
\r
220 } catch (UnsupportedRuntimeException e) {
\r
221 e.printStackTrace();
\r
222 fail(e.getMessage());
\r
223 } catch (LimitExceededException e) {
\r
224 e.printStackTrace();
\r
225 fail(e.getMessage());
\r
226 } catch (JobSubmissionException e) {
\r
227 e.printStackTrace();
\r
228 fail(e.getMessage());
\r
229 } catch (ResultNotAvailableException e) {
\r
230 e.printStackTrace();
\r
231 fail(e.getMessage());
\r