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Coverage Report

  1. Project Clover database Thu Dec 4 2025 16:11:35 GMT
  2. Package jalview.ws2.client.slivka

File SlivkaWSDiscovererTest.java

 

Code metrics

6
147
38
1
679
633
41
0.28
3.87
38
1.08

Classes

Class Line # Actions
SlivkaWSDiscovererTest 38 147 41
0.9005235490.1%
 

Contributing tests

This file is covered by 71 tests. .

Source view

1    package jalview.ws2.client.slivka;
2   
3    import static org.hamcrest.MatcherAssert.assertThat;
4    import static org.hamcrest.Matchers.*;
5    import static org.mockito.Mockito.mock;
6    import static org.mockito.Mockito.when;
7   
8    import java.io.IOException;
9    import java.net.MalformedURLException;
10    import java.net.URI;
11    import java.net.URL;
12    import java.util.ArrayList;
13    import java.util.Iterator;
14    import java.util.List;
15    import java.util.Map;
16    import java.util.function.Function;
17   
18    import org.hamcrest.Matcher;
19    import org.testng.annotations.BeforeClass;
20    import org.testng.annotations.BeforeMethod;
21    import org.testng.annotations.DataProvider;
22    import org.testng.annotations.Test;
23   
24    import jalview.bin.Cache;
25    import jalview.bin.Console;
26    import jalview.ws.params.ValueConstrainI.ValueType;
27    import jalview.ws.params.simple.BooleanOption;
28    import jalview.ws.params.simple.DoubleParameter;
29    import jalview.ws.params.simple.IntegerParameter;
30    import jalview.ws.params.simple.StringParameter;
31    import jalview.ws2.actions.alignment.AlignmentAction;
32    import jalview.ws2.actions.annotation.AnnotationAction;
33    import jalview.ws2.client.api.WebServiceDiscovererI;
34    import uk.ac.dundee.compbio.slivkaclient.Parameter;
35    import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
36    import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
37   
 
38    public class SlivkaWSDiscovererTest
39    {
40    private static final String URLS_PROPERTY_NAME = "SLIVKAHOSTURLS";
41   
42    SlivkaClient clientMock;
43   
44    Function<URL, SlivkaClient> factoryMock;
45   
 
46  1 toggle @BeforeClass(alwaysRun = true)
47    public void setupProperties()
48    {
49  1 Cache.loadProperties("test/jalview/ws2/client/slivka/default.jvprops");
50  1 Console.initLogger();
51    }
52   
 
53  71 toggle @BeforeMethod(alwaysRun = true)
54    public void setupDiscoverer() throws IOException
55    {
56  71 clientMock = mock(SlivkaClient.class);
57    }
58   
 
59  1 toggle @Test(groups = { "Functional" })
60    public void getStatusForUrl_servicesReturned_statusIsOK() throws Exception
61    {
62  1 when(clientMock.getServices())
63    .thenReturn(List.of(mock(SlivkaService.class)));
64  1 var discoverer = new SlivkaWSDiscoverer(
65  1 url -> url.toString().equals("http://example.org") ? clientMock
66    : null);
67  1 assertThat(discoverer.getStatusForUrl(new URL("http://example.org")),
68    is(WebServiceDiscovererI.STATUS_OK));
69    }
70   
 
71  1 toggle @Test(groups = { "Functional" })
72    public void getStatusForUrl_noServicesReturned_statusIsNoServices()
73    throws Exception
74    {
75  1 when(clientMock.getServices()).thenReturn(List.of());
76  1 var discoverer = new SlivkaWSDiscoverer(
77  1 url -> url.toString().equals("http://example.org") ? clientMock
78    : null);
79  1 assertThat(discoverer.getStatusForUrl(new URL("http://example.org")),
80    is(WebServiceDiscovererI.STATUS_NO_SERVICES));
81    }
82   
 
83  1 toggle @Test(groups = { "Functional" })
84    public void getStatusForUrl_exceptionThrown_statusIsInvalid()
85    throws Exception
86    {
87  1 when(clientMock.getServices()).thenThrow(new IOException());
88  1 var discoverer = new SlivkaWSDiscoverer(
89  1 url -> url.toString().equals("http://example.org") ? clientMock
90    : null);
91  1 assertThat(discoverer.getStatusForUrl(new URL("http://example.org")),
92    is(WebServiceDiscovererI.STATUS_INVALID));
93    }
94   
 
95  1 toggle @Test(groups = { "Functional" })
96    public void testGetUrls_noPropEntry_defaultUrlReturned()
97    throws MalformedURLException
98    {
99  1 var discoverer = SlivkaWSDiscoverer.getInstance();
100  1 assertThat(discoverer.getUrls(),
101    contains(new URL("https://www.compbio.dundee.ac.uk/slivka/")));
102    }
103   
 
104  1 toggle @DataProvider
105    public Object[][] urlPropertyValues() throws MalformedURLException
106    {
107  1 return new Object[][] {
108    { "http://example.org/", List.of(new URL("http://example.org/")) },
109    { "https://example.org/slivka/",
110    List.of(new URL("https://example.org/slivka/")) },
111    { "https://www.compbio.dundee.ac.uk/,http://www.example.org/",
112    List.of(new URL("https://www.compbio.dundee.ac.uk/"),
113    new URL("http://www.example.org/")) },
114    { "http://example.org/,", List.of(new URL("http://example.org/")) },
115    { ",http://example.org", List.of(new URL("http://example.org")) },
116    { "", List.of() },
117    { ",", List.of() },
118    { "example.org", List.of() },
119    { "example.org,http://example.org",
120    List.of(new URL("http://example.org")) } };
121    }
122   
 
123  9 toggle @Test(groups = { "Functional" }, dataProvider = "urlPropertyValues")
124    public void testGetUrls_urlsProperlyParsed(String propValue,
125    List<URL> expected)
126    {
127  9 Cache.setProperty(URLS_PROPERTY_NAME, propValue);
128  9 var discoverer = SlivkaWSDiscoverer.getInstance();
129  9 assertThat(discoverer.getUrls(), equalTo(expected));
130    }
131   
 
132  1 toggle @Test(groups = { "Functional" })
133    public void testSetUrls_emptyList_propertyReset()
134    {
135  1 Cache.setProperty(URLS_PROPERTY_NAME, "http://www.example.org");
136  1 var discoverer = SlivkaWSDiscoverer.getInstance();
137  1 discoverer.setUrls(List.of());
138  1 assertThat(Cache.getProperty(URLS_PROPERTY_NAME), is(nullValue()));
139    }
140   
 
141  1 toggle @Test(groups = { "Functional" })
142    public void testSetUrls_null_propertyReset()
143    {
144  1 Cache.setProperty(URLS_PROPERTY_NAME, "http://www.example.org");
145  1 var discoverer = SlivkaWSDiscoverer.getInstance();
146  1 discoverer.setUrls(null);
147  1 assertThat(Cache.getProperty(URLS_PROPERTY_NAME), is(nullValue()));
148    }
149   
 
150  1 toggle @DataProvider
151    public Object[][] urlsList() throws MalformedURLException
152    {
153  1 return new Object[][] {
154    { List.of(new URL("http://example.org")), "http://example.org" },
155    { List.of(new URL("http://example.org/")), "http://example.org/" },
156    { List.of(new URL("http://example.org/slivka/")),
157    "http://example.org/slivka/" },
158    { List.of(new URL("https://www.compbio.dundee.ac.uk/slivka/"),
159    new URL("http://example.org")),
160    "https://www.compbio.dundee.ac.uk/slivka/,http://example.org" }, };
161    }
162   
 
163  4 toggle @Test(groups = { "Functional" }, dataProvider = "urlsList")
164    public void testSetUrls_urlsPropertySet(List<URL> urls, String expected)
165    throws MalformedURLException
166    {
167  4 var discoverer = SlivkaWSDiscoverer.getInstance();
168  4 discoverer.setUrls(urls);
169  4 assertThat(Cache.getProperty(URLS_PROPERTY_NAME), equalTo(expected));
170    }
171   
 
172  1 toggle @Test(groups = { "Functional" })
173    public void testFetchServices_oneService_basicDataMatches()
174    throws IOException
175    {
176  1 var service = new SlivkaService(
177    URI.create("http://example.org/api/services/example"),
178    "example", "Example name", "Example service description",
179    "John Smith", "1.0", "MIT License",
180    List.of("operation::analysis::multiple sequence alignment"),
181    List.of(), List.of(), null);
182  1 when(clientMock.getServices()).thenReturn(List.of(service));
183  1 when(clientMock.getUrl()).thenReturn(URI.create("http://example.org/"));
184  1 var discoverer = new SlivkaWSDiscoverer(url -> clientMock);
185  1 var webServices = discoverer
186    .fetchServices(new URL("http://example.org/"));
187  1 assertThat(webServices, hasSize(1));
188  1 var webService = webServices.get(0);
189  1 assertThat(webService.getUrl(),
190    equalTo(new URL("http://example.org/")));
191  1 assertThat(webService.getClientName(), equalTo("slivka"));
192  1 assertThat(webService.getName(), equalTo("Example name"));
193  1 assertThat(webService.getDescription(),
194    equalTo("Example service description"));
195    }
196   
 
197  1 toggle @DataProvider
198    public String[] validMultipleSequenceAlignmentClassifiers()
199    {
200  1 return new String[] {
201    "Operation :: Analysis :: Multiple sequence alignment",
202    "operation :: analysis :: multiple sequence alignment",
203    "Operation\t::\tAnalysis\t::\tMultiple sequence alignment",
204    "Operation::Analysis::Multiple sequence alignment",
205    "Operation :: Analysis :: Multiple Sequence Alignment",
206    "OPERATION :: ANALYSIS :: MULTIPLE SEQUENCE ALIGNMENT",
207    "Operation :: Analysis :: Sequence alignment :: Multiple sequence alignment",
208    "Operation :: Analysis :: Sequence analysis :: Sequence alignment :: Multiple sequence alignment",
209    "Operation :: Alignment :: Multiple sequence alignment",
210    "Operation :: Alignment :: Sequence alignment :: Multiple sequence alignment",
211    "Operation :: Comparison :: Multiple sequence alignment",
212    "Operation :: Comparison :: Sequence comparison :: Sequence alignment :: Multiple sequence alignment" };
213   
214    }
215   
 
216  12 toggle @Test(
217    groups = { "Functional" },
218    dataProvider = "validMultipleSequenceAlignmentClassifiers")
219    public void testFetchServices_multipleSequenceAlignmentClassifier_serviceTypeIsMSA(
220    String classifier) throws IOException
221    {
222  12 var service = new SlivkaService(URI.create("http://example.org/"),
223    "example", "name", "description", "author", "1.0", "MIT",
224    List.of(classifier), List.of(), List.of(), null);
225  12 when(clientMock.getServices()).thenReturn(List.of(service));
226  12 when(clientMock.getUrl()).thenReturn(URI.create("http://example.org/"));
227  12 var discoverer = new SlivkaWSDiscoverer(url -> clientMock);
228  12 var webServices = discoverer
229    .fetchServices(new URL("http://example.org/"));
230  12 assertThat(webServices, hasSize(1));
231  12 assertThat(webServices.get(0).getCategory(), equalTo("Alignment"));
232  12 assertThat(webServices.get(0).getActionClass(),
233    typeCompatibleWith(AlignmentAction.class));
234    }
235   
 
236  2 toggle @DataProvider
237    public SlivkaService[] multipleSequenceAlignmentService()
238    {
239  2 return new SlivkaService[] {
240    new SlivkaService(
241    URI.create("http://example.org/"), "example", "Examaple name",
242    "Example description", "John Smith", "1.0", "MIT",
243    List.of("Operation :: Analysis :: Multiple sequence alignment"),
244    List.of(), List.of(), null),
245    new SlivkaService(
246    URI.create("http://example.org/api/services/muscle"),
247    "muscle", "MUSCLE",
248    "MUltiple Sequence Comparison by Log- Expectation",
249    "Robert C. Edgar", "3.8.31", "Public domain",
250    List.of("Topic :: Computational biology :: Sequence analysis",
251    "Operation :: Analysis :: Sequence analysis :: Sequence alignment :: Multiple sequence alignment"),
252    List.of(), List.of(), null),
253    new SlivkaService(
254    URI.create("http://example.org/api/services/tcoffee"),
255    "tcoffee", "TCoffee",
256    "Tree-based Consistency Objective Function for Alignment Evaluation",
257    "Cedric Notredame", "13.41.0", "GNU GPL",
258    List.of("Topic :: Computational biology :: Sequence analysis",
259    "Operation :: Analysis :: Sequence analysis :: Sequence alignment :: Multiple sequence alignment"),
260    List.of(), List.of(), null) };
261    }
262   
 
263  3 toggle @Test(
264    groups = { "Functional" },
265    dataProvider = "multipleSequenceAlignmentService")
266    public void testFetchServices_multipleSequenceAlignmentService_actionTypeIsAlignment(
267    SlivkaService service) throws IOException
268    {
269  3 when(clientMock.getServices()).thenReturn(List.of(service));
270  3 when(clientMock.getUrl()).thenReturn(URI.create("http://example.org/"));
271  3 var discoverer = new SlivkaWSDiscoverer(url -> clientMock);
272  3 var webServices = discoverer
273    .fetchServices(new URL("http://example.org/"));
274  3 assertThat(webServices.get(0).getCategory(), equalTo("Alignment"));
275  3 assertThat(webServices.get(0).getActionClass(),
276    typeCompatibleWith(AlignmentAction.class));
277    }
278   
 
279  3 toggle @Test(
280    groups = { "Functional" },
281    dataProvider = "multipleSequenceAlignmentService")
282    public void testFetchServices_multipleSequenceAlignmentService_serviceIsNonInteractive(
283    SlivkaService service) throws IOException
284    {
285  3 when(clientMock.getServices()).thenReturn(List.of(service));
286  3 when(clientMock.getUrl()).thenReturn(URI.create("http://example.org/"));
287  3 var discoverer = new SlivkaWSDiscoverer(url -> clientMock);
288  3 var webServices = discoverer
289    .fetchServices(new URL("http://example.org/"));
290  3 assertThat(webServices.get(0).isInteractive(), is(false));
291    }
292   
 
293  1 toggle @DataProvider
294    public SlivkaService[] clustalFamilyService()
295    {
296  1 return new SlivkaService[] {
297    new SlivkaService(
298    URI.create("http://example.org/api/services/clustalo"),
299    "clustalo", "ClustalO",
300    "Clustal Omega is the latest addition to the Clustal family.",
301    "Fabian Sievers, et al.", "1.2.4", "GNU GPL ver. 2",
302    List.of("Topic :: Computational biology :: Sequence analysis",
303    "Operation :: Analysis :: Sequence analysis :: Sequence alignment :: Multiple sequence alignment"),
304    List.of(), List.of(), null),
305    new SlivkaService(
306    URI.create("http://example.org/api/services/clustalw"),
307    "clustalw", "ClustalW",
308    "ClustalW is a general purpose multiple alignment program.",
309    "Larkin MA, et al.", "2.1", "GNU GPL ver. 3",
310    List.of("Topic :: Computation biology :: Sequence analysis",
311    "Operation :: Analysis :: Multiple sequence alignment"),
312    List.of(), List.of(), null),
313    new SlivkaService(
314    URI.create("http://example.org/api/services/clustalw2"),
315    "clustalw2", "ClustalW2",
316    "ClustalW is a general purpose multiple alignment program.",
317    "Larkin MA, et al.", "2.1", "GNU GPL ver. 3",
318    List.of("Topic :: Computation biology :: Sequence analysis",
319    "Operation :: Analysis :: Multiple sequence alignment"),
320    List.of(), List.of(), null), };
321    }
322   
 
323  3 toggle @Test(groups = { "Functional" }, dataProvider = "clustalFamilyService")
324    public void testFetchService_clustalFamilyService_containsTwoActions(
325    SlivkaService service) throws IOException
326    {
327  3 when(clientMock.getServices()).thenReturn(List.of(service));
328  3 when(clientMock.getUrl()).thenReturn(URI.create("http://example.org"));
329  3 var discoverer = new SlivkaWSDiscoverer(url -> clientMock);
330  3 var webServices = discoverer
331    .fetchServices(new URL("http://example.org"));
332  3 var actions = webServices.get(0).getActions();
333  3 assertThat(actions, hasSize(2));
334  3 assertThat(actions.get(0), allOf(hasProperty("name", is("Alignment")),
335    hasProperty("subcategory", is("Align"))));
336  3 assertThat(actions.get(1),
337    allOf(hasProperty("name", is("Re-alignment")),
338    hasProperty("subcategory", is("Realign"))));
339    }
340   
 
341  1 toggle @DataProvider
342    public String[] validRNASecondaryStructurePredictionClassifiers()
343    {
344  1 return new String[] {
345    "Operation :: Analysis :: RNA secondary structure prediction",
346    "operation :: analysis :: rna secondary structure prediction",
347    "OPERATION :: ANALYSIS :: RNA SECONDARY STRUCTURE PREDICTION",
348    "Operation\t::\tAnalysis\t::\tRNA secondary structure prediction",
349    "Operation::Analysis::RNA secondary structure prediction",
350    "Operation :: Analysis :: Structure analysis :: RNA secondary structure prediction",
351    "Operation :: Analysis :: Structure analysis :: Nucleic acid structure analysis :: RNA secondary structure analysis :: RNA secondary structure prediction",
352    "Operation :: Analysis :: Structure analysis :: Nucleic acid structure analysis :: Nucleic acid structure prediction :: RNA secondary structure prediction",
353    "Operation :: Analysis :: Sequence analysis :: Nucleic acid sequence analysis :: Nucleic acid feature detection :: RNA secondary structure prediction",
354    "Operation :: Prediction and recognition :: RNA secondary structure prediction",
355    "Operation :: Prediction and recognition :: Nucleic acid feature detection :: RNA secondary structure prediction",
356    "Operation :: Prediction and recignition :: Nucleic acid structure prediction :: RNA secondary structure prediction", };
357    }
358   
 
359  1 toggle @DataProvider
360    public Iterator<Object> RNASecondaryStructurePredictionService()
361    {
362  1 var services = new ArrayList<>();
363  1 for (var classifier : validRNASecondaryStructurePredictionClassifiers())
364    {
365  12 services.add(new SlivkaService(URI.create("http://example.org/"),
366    "example", "name", "description", "author", "1.0", "MIT",
367    List.of(classifier), List.of(), List.of(), null));
368    }
369  1 return services.iterator();
370    }
371   
 
372  12 toggle @Test(
373    groups = { "Functional" },
374    dataProvider = "RNASecondaryStructurePredictionService")
375    public void testFetchServices_RNASecStrPredClassifier_serviceTypeIsRNASecStrPred(
376    SlivkaService service) throws IOException
377    {
378  12 when(clientMock.getServices()).thenReturn(List.of(service));
379  12 when(clientMock.getUrl()).thenReturn(URI.create("http://example.org/"));
380  12 var discoverer = new SlivkaWSDiscoverer(url -> clientMock);
381  12 var webServices = discoverer
382    .fetchServices(new URL("http://example.org/"));
383  12 assertThat(webServices, hasSize(1));
384  12 assertThat(webServices.get(0).getCategory(),
385    equalTo("Secondary Structure Prediction"));
386  12 assertThat(webServices.get(0).getActionClass(),
387    typeCompatibleWith(AnnotationAction.class));
388    }
389   
 
390  1 toggle @DataProvider
391    public String[] validConservationAnalysisClassifiers()
392    {
393  1 return new String[] {
394    "Operation :: Analysis :: Sequence alignment analysis (conservation)",
395    "Operation::Analysis::Sequence alignment analysis (conservation)",
396    "Operation\t::\tAnalysis\t::\tSequence alignment analysis (conservation)",
397    "Operation :: Analysis :: Sequence analysis :: Sequence alignment analysis (conservation)",
398    "Operation :: Analysis :: Sequence analysis :: Sequence alignment analysis :: Sequence alignment analysis (conservation)", };
399    }
400   
 
401  0 toggle @DataProvider
402    public Iterator<Object> ConservationAnalysisService()
403    {
404  0 var services = new ArrayList<>();
405  0 for (var classifier : validConservationAnalysisClassifiers())
406    {
407  0 services.add(new SlivkaService(URI.create("http://example.org/"),
408    "example", "name", "description", "author", "1.0", "MIT",
409    List.of(classifier), List.of(), List.of(), null));
410    }
411  0 return services.iterator();
412    }
413   
 
414  5 toggle @Test(
415    groups = { "Functional" },
416    dataProvider = "validConservationAnalysisClassifiers")
417    public void testFetchServices_conservationAnalysisClassifier_serviceTypeIsConservation(
418    String classifier) throws IOException
419    {
420  5 var service = new SlivkaService(URI.create("http://example.org/"),
421    "example", "name", "description", "author", "1.0", "MIT",
422    List.of(classifier), List.of(), List.of(), null);
423  5 when(clientMock.getServices()).thenReturn(List.of(service));
424  5 when(clientMock.getUrl()).thenReturn(URI.create("http://example.org/"));
425  5 var discoverer = new SlivkaWSDiscoverer(url -> clientMock);
426  5 var webServices = discoverer
427    .fetchServices(new URL("http://example.org/"));
428  5 assertThat(webServices, hasSize(1));
429  5 assertThat(webServices.get(0).getCategory(), equalTo("Conservation"));
430  5 assertThat(webServices.get(0).getActionClass(),
431    typeCompatibleWith(AnnotationAction.class));
432    }
433   
 
434  1 toggle @DataProvider
435    public Object[] validProteinSequenceAnalysisClassifiers()
436    {
437  1 return new Object[] {
438    "Operation :: Analysis :: Sequence analysis :: Protein sequence analysis", };
439    }
440   
 
441  1 toggle @Test(
442    groups = { "Functional" },
443    dataProvider = "validProteinSequenceAnalysisClassifiers")
444    public void testFetchServices_proteinSequenceAnalysisClassifier_serviceTypeIsProtSeqAnalysis(
445    String classifier) throws IOException
446    {
447  1 var service = new SlivkaService(URI.create("http://example.org/"),
448    "example", "name", "description", "author", "1.0", "MIT",
449    List.of(classifier), List.of(), List.of(), null);
450  1 when(clientMock.getServices()).thenReturn(List.of(service));
451  1 when(clientMock.getUrl()).thenReturn(URI.create("http://example.org/"));
452  1 var discoverer = new SlivkaWSDiscoverer(url -> clientMock);
453  1 var webServices = discoverer
454    .fetchServices(new URL("http://example.org/"));
455  1 assertThat(webServices, hasSize(1));
456  1 assertThat(webServices.get(0).getCategory(),
457    equalTo("Protein Disorder"));
458  1 assertThat(webServices.get(0).getActionClass(),
459    typeCompatibleWith(AnnotationAction.class));
460    }
461   
 
462  0 toggle @DataProvider
463    public Object[] validProteinSecondaryStructurePredictionClassifiers()
464    {
465  0 return new Object[] {
466    "Operation ;: Analysis :: Protein secondary structure prediction",
467    "Operation :: Analysis :: Structure analysis :: Protein structure analysis :: Protein secondary structure analysis :: Protein secondary structure prediction",
468    "Operation :: Analysis :: Sequence analysis :: Protein sequence analysis :: Protein feature detection :: Protein secondary structure prediction",
469    "Operation :: Analysis :: Sequence analysis :: Protein sequence analysis :: Protein secondary structure prediction",
470    "Operation :: Prediction and recognition :: Protein secondary structure prediction",
471    "Operation :: Prediction and recognition :: Protein feature detection :: Protein secondary structure prediction", };
472    }
473   
 
474  0 toggle @Test(
475    enabled = false, // sec. str. pred. not implemented for slivka
476    groups = { "Functional" },
477    dataProvider = "validProteinSecondaryStructurePredictionClassifiers")
478    public void testFetchServices_proteinSecStrPredClassifier_serviceTypeIsProtSecStrPred(
479    String classifier) throws IOException
480    {
481  0 var service = new SlivkaService(URI.create("http://example.org/"),
482    "example", "name", "description", "author", "1.0", "MIT",
483    List.of(classifier), List.of(), List.of(), null);
484  0 when(clientMock.getServices()).thenReturn(List.of(service));
485  0 when(clientMock.getUrl()).thenReturn(URI.create("http://example.org/"));
486  0 var discoverer = new SlivkaWSDiscoverer(url -> clientMock);
487  0 var webServices = discoverer
488    .fetchServices(new URL("http://example.org/"));
489  0 assertThat(webServices, hasSize(1));
490  0 assertThat(webServices.get(0).getCategory(),
491    equalTo("Protein Disorder"));
492  0 assertThat(webServices.get(0).getActionClass(),
493    typeCompatibleWith(AnnotationAction.class));
494    }
495   
 
496  1 toggle @DataProvider
497    public SlivkaService[] unrecognisedService()
498    {
499  1 return new SlivkaService[] {
500    new SlivkaService(URI.create("http://example.org/"), "example",
501    "Example name", "Example description", "John Smith",
502    "1.0.0", "Apache License, version 2.0",
503    List.of("This :: Classifier :: Does not exist"), List.of(),
504    List.of(), null) };
505    }
506   
 
507  1 toggle @Test(groups = { "Functional" }, dataProvider = "unrecognisedService")
508    public void testFetchServices_unrecognisedService_noServiceDiscovered(
509    SlivkaService service) throws IOException
510    {
511  1 when(clientMock.getServices()).thenReturn(List.of(service));
512  1 when(clientMock.getUrl()).thenReturn(URI.create("http://example.org"));
513  1 var discoverer = new SlivkaWSDiscoverer(url -> clientMock);
514  1 var webServices = discoverer
515    .fetchServices(new URL("http://example.org"));
516  1 assertThat(webServices, hasSize(0));
517    }
518   
 
519  1 toggle @DataProvider
520    public Object[] serviceParameterAndMappedClass()
521    {
522  1 return new Object[][] {
523    {
524    new Parameter.IntegerParameter("param", "Parameter", "Description",
525    true, false, null, Map.of(), null, null),
526    IntegerParameter.class
527    },
528    {
529    new Parameter.DecimalParameter("param", "Parameter",
530    "Description", true, false, null, Map.of(), null, null,
531    false, false),
532    DoubleParameter.class
533    },
534    {
535    new Parameter.TextParameter("param", "Parameter", "Description",
536    true, false, null, Map.of(), 0, null),
537    StringParameter.class
538    },
539    {
540    new Parameter.FlagParameter("param", "Parameter", "Description",
541    true, false, null, Map.of()),
542    BooleanOption.class
543    },
544    {
545    new Parameter.ChoiceParameter("param", "Parameter", "Description",
546    true, false, null, Map.of(), List.of()),
547    StringParameter.class
548    },
549    };
550    }
551   
 
552  5 toggle @Test(
553    groups = { "Functional" },
554    dataProvider = "serviceParameterAndMappedClass")
555    public void testServiceParameter_slivkaParameterMappedToJalviewParameter(
556    Parameter slivkaParameter, Class<?> expectedClass)
557    throws IOException
558    {
559  5 var service = new SlivkaService(URI.create("http://example.org"),
560    "example", "name", "description", "author", "1.0",
561    "MIT License",
562    List.of("Operation :: Analysis :: Multiple sequence alignment"),
563    List.of(slivkaParameter), List.of(), null);
564  5 when(clientMock.getServices()).thenReturn(List.of(service));
565  5 when(clientMock.getUrl()).thenReturn(URI.create("http://example.org"));
566  5 var discoverer = new SlivkaWSDiscoverer(url -> clientMock);
567  5 var webServices = discoverer
568    .fetchServices(new URL("http://example.org"));
569  5 var paramDatastore = webServices.get(0).getParamDatastore();
570  5 var arguments = paramDatastore.getServiceParameters();
571  5 assertThat(arguments.get(0), instanceOf(expectedClass));
572    }
573   
 
574  1 toggle @DataProvider
575    public Object[][] serviceParametersAndPropertyMatcher()
576    {
577  1 return new Object[][] {
578    {
579    new Parameter.IntegerParameter("param1", "Parameter 1",
580    "Description of parameter 1", true, false, null, Map.of(),
581    null, null),
582    allOf(
583    hasProperty("name", equalTo("param1")),
584    hasProperty("label", equalTo("Parameter 1")),
585    hasProperty("description", equalTo("Description of parameter 1")),
586    hasProperty("required", is(true)),
587    hasProperty("value", nullValue()))
588    },
589    {
590    new Parameter.IntegerParameter("param2", null, null, true, false,
591    null, Map.of(), null, null),
592    allOf(
593    hasProperty("name", equalTo("param2")),
594    hasProperty("label", equalTo("param2")),
595    hasProperty("description", nullValue()),
596    hasProperty("required", is(true)),
597    hasProperty("value", nullValue()))
598    },
599    {
600    new Parameter.IntegerParameter("param3", "Parameter 3", "", false,
601    false, 12, Map.of(), null, null),
602    allOf(
603    hasProperty("name", equalTo("param3")),
604    hasProperty("label", equalTo("Parameter 3")),
605    hasProperty("description", equalTo("")),
606    hasProperty("required", is(false)),
607    hasProperty("value", equalTo("12")))
608    },
609    };
610    }
611   
 
612  3 toggle @Test(
613    groups = { "Functional" },
614    dataProvider = "serviceParametersAndPropertyMatcher")
615    public void testServiceParameters_testBasicParameterProperties(
616    Parameter parameter, Matcher<Object> matcher) throws IOException
617    {
618  3 var service = new SlivkaService(URI.create("http://example.org/"),
619    "example", "Example name", "Example description", "John Smith",
620    "1.0", "MIT",
621    List.of("Operation :: Analysis :: Multiple sequence alignment"),
622    List.of(parameter), List.of(), null);
623  3 when(clientMock.getServices()).thenReturn(List.of(service));
624  3 when(clientMock.getUrl()).thenReturn(URI.create("http://example.org/"));
625  3 var discoverer = new SlivkaWSDiscoverer(url -> clientMock);
626  3 var webServices = discoverer
627    .fetchServices(new URL("http://example.org/"));
628  3 var paramDatastore = webServices.get(0).getParamDatastore();
629  3 var arguments = paramDatastore.getServiceParameters();
630  3 assertThat(arguments.get(0), matcher);
631    }
632   
 
633  1 toggle @DataProvider
634    public Object[][] integerParametersAndPropertyMatcher()
635    {
636  1 return new Object[][] {
637    {
638    new Parameter.IntegerParameter("param", null, null, true, false,
639    null, Map.of(), null, null),
640    hasProperty("validValue", hasProperty("type", is(ValueType.Integer)))
641    },
642    {
643    new Parameter.IntegerParameter("param", null, null, true, false,
644    null, Map.of(), null, null),
645    hasProperty("validValue", allOf(
646    hasProperty("min", nullValue()),
647    hasProperty("max", nullValue()))),
648    },
649    {
650    new Parameter.IntegerParameter("param", null, null, true, false,
651    null, Map.of(), -12, 42),
652    hasProperty("validValue", allOf(
653    hasProperty("min", is(-12)),
654    hasProperty("max", is(42))))
655    },
656    };
657    }
658   
 
659  3 toggle @Test(
660    groups = { "Functional" },
661    dataProvider = "integerParametersAndPropertyMatcher")
662    public void testServiceParameters_testIntegerProperties(
663    Parameter parameter, Matcher<Object> matcher) throws IOException
664    {
665  3 var service = new SlivkaService(URI.create("http://example.org"),
666    "example", "Example name", "Example description", "John Smith",
667    "1.0", "MIT",
668    List.of("Operation :: Analysis :: Multiple Sequence Alignment"),
669    List.of(parameter), List.of(), null);
670  3 when(clientMock.getServices()).thenReturn(List.of(service));
671  3 when(clientMock.getUrl()).thenReturn(URI.create("http://example.org/"));
672  3 var discoverer = new SlivkaWSDiscoverer(url -> clientMock);
673  3 var webServices = discoverer
674    .fetchServices(new URL("http://example.org/"));
675  3 var paramDatastore = webServices.get(0).getParamDatastore();
676  3 var arguments = paramDatastore.getServiceParameters();
677  3 assertThat(arguments.get(0), matcher);
678    }
679    }
  • Report generated by OpenClover v 4.4.1 on Thu Dec 4 2025 16:21:53 GMT using coverage data from Thu Dec 4 2025 16:21:39 GMT.
  • OpenClover is free and open-source software.