package jalview.ws2.client.slivka;
+import static org.hamcrest.MatcherAssert.assertThat;
+import static org.hamcrest.Matchers.*;
+import static org.mockito.Mockito.mock;
+import static org.mockito.Mockito.when;
+
import java.io.IOException;
+import java.net.MalformedURLException;
+import java.net.URI;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+import java.util.function.Function;
import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
+import jalview.bin.Cache;
+import jalview.bin.Console;
+import jalview.ws2.actions.alignment.AlignmentAction;
+import jalview.ws2.actions.annotation.AnnotationAction;
+import jalview.ws2.client.api.WebServiceDiscovererI;
+import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
+import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
+
public class SlivkaWSDiscovererTest
{
- @BeforeClass
- public void setupClass() throws IOException
+ private static final String URLS_PROPERTY_NAME = "SLIVKAHOSTURLS";
+
+ SlivkaClient clientMock;
+
+ Function<URL, SlivkaClient> factoryMock;
+
+ @BeforeClass(alwaysRun = true)
+ public void setupProperties()
+ {
+ Cache.loadProperties("test/jalview/ws2/client/slivka/default.jvprops");
+ Console.initLogger();
+ }
+
+ @BeforeMethod
+ public void setupDiscoverer() throws IOException
+ {
+ clientMock = mock(SlivkaClient.class);
+ }
+
+ @Test
+ public void getStatusForUrl_servicesReturned_statusIsOK() throws Exception
+ {
+ when(clientMock.getServices())
+ .thenReturn(List.of(mock(SlivkaService.class)));
+ var discoverer = new SlivkaWSDiscoverer(
+ url -> url.toString().equals("http://example.org") ? clientMock
+ : null);
+ assertThat(discoverer.getStatusForUrl(new URL("http://example.org")),
+ is(WebServiceDiscovererI.STATUS_OK));
+ }
+
+ @Test
+ public void getStatusForUrl_noServicesReturned_statusIsNoServices()
+ throws Exception
+ {
+ when(clientMock.getServices()).thenReturn(List.of());
+ var discoverer = new SlivkaWSDiscoverer(
+ url -> url.toString().equals("http://example.org") ? clientMock
+ : null);
+ assertThat(discoverer.getStatusForUrl(new URL("http://example.org")),
+ is(WebServiceDiscovererI.STATUS_NO_SERVICES));
+ }
+
+ @Test
+ public void getStatusForUrl_exceptionThrown_statusIsInvalid()
+ throws Exception
+ {
+ when(clientMock.getServices()).thenThrow(new IOException());
+ var discoverer = new SlivkaWSDiscoverer(
+ url -> url.toString().equals("http://example.org") ? clientMock
+ : null);
+ assertThat(discoverer.getStatusForUrl(new URL("http://example.org")),
+ is(WebServiceDiscovererI.STATUS_INVALID));
+ }
+
+ @Test
+ public void testGetUrls_noPropEntry_defaultUrlReturned()
+ throws MalformedURLException
{
var discoverer = SlivkaWSDiscoverer.getInstance();
-
+ assertThat(discoverer.getUrls(),
+ contains(new URL("https://www.compbio.dundee.ac.uk/slivka/")));
}
-
+
+ @DataProvider
+ public Object[][] urlPropertyValues() throws MalformedURLException
+ {
+ return new Object[][] {
+ { "http://example.org/", List.of(new URL("http://example.org/")) },
+ { "https://example.org/slivka/",
+ List.of(new URL("https://example.org/slivka/")) },
+ { "https://www.compbio.dundee.ac.uk/,http://www.example.org/",
+ List.of(new URL("https://www.compbio.dundee.ac.uk/"),
+ new URL("http://www.example.org/")) },
+ { "http://example.org/,", List.of(new URL("http://example.org/")) },
+ { ",http://example.org", List.of(new URL("http://example.org")) },
+ { "", List.of() },
+ { ",", List.of() },
+ { "example.org", List.of() },
+ { "example.org,http://example.org",
+ List.of(new URL("http://example.org")) } };
+ }
+
+ @Test(dataProvider = "urlPropertyValues")
+ public void testGetUrls_urlsProperlyParsed(String propValue,
+ List<URL> expected)
+ {
+ Cache.setProperty(URLS_PROPERTY_NAME, propValue);
+ var discoverer = SlivkaWSDiscoverer.getInstance();
+ assertThat(discoverer.getUrls(), equalTo(expected));
+ }
+
@Test
- public void testServiceFetch() throws IOException
+ public void testSetUrls_emptyList_propertyReset()
{
+ Cache.setProperty(URLS_PROPERTY_NAME, "http://www.example.org");
var discoverer = SlivkaWSDiscoverer.getInstance();
- var services = discoverer.fetchServices(discoverer.getDefaultUrl());
- for (var service : services)
+ discoverer.setUrls(List.of());
+ assertThat(Cache.getProperty(URLS_PROPERTY_NAME), is(nullValue()));
+ }
+
+ @Test
+ public void testSetUrls_null_propertyReset()
+ {
+ Cache.setProperty(URLS_PROPERTY_NAME, "http://www.example.org");
+ var discoverer = SlivkaWSDiscoverer.getInstance();
+ discoverer.setUrls(null);
+ assertThat(Cache.getProperty(URLS_PROPERTY_NAME), is(nullValue()));
+ }
+
+ @DataProvider
+ public Object[][] urlsList() throws MalformedURLException
+ {
+ return new Object[][] {
+ { List.of(new URL("http://example.org")), "http://example.org" },
+ { List.of(new URL("http://example.org/")), "http://example.org/" },
+ { List.of(new URL("http://example.org/slivka/")),
+ "http://example.org/slivka/" },
+ { List.of(new URL("https://www.compbio.dundee.ac.uk/slivka/"),
+ new URL("http://example.org")),
+ "https://www.compbio.dundee.ac.uk/slivka/,http://example.org" }, };
+ }
+
+ @Test(dataProvider = "urlsList")
+ public void testSetUrls_urlsPropertySet(List<URL> urls, String expected)
+ throws MalformedURLException
+ {
+ var discoverer = SlivkaWSDiscoverer.getInstance();
+ discoverer.setUrls(urls);
+ assertThat(Cache.getProperty(URLS_PROPERTY_NAME), equalTo(expected));
+ }
+
+ @Test
+ public void testFetchServices_oneService_basicDataMatches()
+ throws IOException
+ {
+ var service = new SlivkaService(
+ URI.create("http://example.org/api/services/example"),
+ "example", "Example name", "Example service description",
+ "John Smith", "1.0", "MIT License",
+ List.of("operation::analysis::multiple sequence alignment"),
+ List.of(), List.of(), null);
+ when(clientMock.getServices()).thenReturn(List.of(service));
+ when(clientMock.getUrl()).thenReturn(URI.create("http://example.org/"));
+ var discoverer = new SlivkaWSDiscoverer(url -> clientMock);
+ var webServices = discoverer
+ .fetchServices(new URL("http://example.org/"));
+ assertThat(webServices, hasSize(1));
+ var webService = webServices.get(0);
+ assertThat(webService.getUrl(),
+ equalTo(new URL("http://example.org/")));
+ assertThat(webService.getClientName(), equalTo("slivka"));
+ assertThat(webService.getName(), equalTo("Example name"));
+ assertThat(webService.getDescription(),
+ equalTo("Example service description"));
+ }
+
+ @DataProvider
+ public String[] validMultipleSequenceAlignmentClassifiers()
+ {
+ return new String[] {
+ "Operation :: Analysis :: Multiple sequence alignment",
+ "operation :: analysis :: multiple sequence alignment",
+ "Operation\t::\tAnalysis\t::\tMultiple sequence alignment",
+ "Operation::Analysis::Multiple sequence alignment",
+ "Operation :: Analysis :: Multiple Sequence Alignment",
+ "OPERATION :: ANALYSIS :: MULTIPLE SEQUENCE ALIGNMENT",
+ "Operation :: Analysis :: Sequence alignment :: Multiple sequence alignment",
+ "Operation :: Analysis :: Sequence analysis :: Sequence alignment :: Multiple sequence alignment",
+ "Operation :: Alignment :: Multiple sequence alignment",
+ "Operation :: Alignment :: Sequence alignment :: Multiple sequence alignment",
+ "Operation :: Comparison :: Multiple sequence alignment",
+ "Operation :: Comparison :: Sequence comparison :: Sequence alignment :: Multiple sequence alignment" };
+
+ }
+
+ @Test(dataProvider = "validMultipleSequenceAlignmentClassifiers")
+ public void testFetchServices_multipleSequenceAlignmentClassifier_serviceTypeIsMSA(
+ String classifier) throws IOException
+ {
+ var service = new SlivkaService(URI.create("http://example.org/"),
+ "example", "name", "description", "author", "1.0", "MIT",
+ List.of(classifier), List.of(), List.of(), null);
+ when(clientMock.getServices()).thenReturn(List.of(service));
+ when(clientMock.getUrl()).thenReturn(URI.create("http://example.org/"));
+ var discoverer = new SlivkaWSDiscoverer(url -> clientMock);
+ var webServices = discoverer
+ .fetchServices(new URL("http://example.org/"));
+ assertThat(webServices, hasSize(1));
+ assertThat(webServices.get(0).getCategory(), equalTo("Alignment"));
+ assertThat(webServices.get(0).getActionClass(),
+ typeCompatibleWith(AlignmentAction.class));
+ }
+
+ @DataProvider
+ public SlivkaService[] multipleSequenceAlignmentService()
+ {
+ return new SlivkaService[] { new SlivkaService(
+ URI.create("http://example.org/"), "example", "Examaple name",
+ "Example description", "John Smith", "1.0", "MIT",
+ List.of("Operation :: Analysis :: Multiple sequence alignment"),
+ List.of(), List.of(), null),
+ new SlivkaService(
+ URI.create("http://example.org/api/services/muscle"),
+ "muscle", "MUSCLE",
+ "MUltiple Sequence Comparison by Log- Expectation",
+ "Robert C. Edgar", "3.8.31", "Public domain",
+ List.of("Topic :: Computational biology :: Sequence analysis",
+ "Operation :: Analysis :: Sequence analysis :: Sequence alignment :: Multiple sequence alignment"),
+ List.of(), List.of(), null),
+ new SlivkaService(
+ URI.create("http://example.org/api/services/tcoffee"),
+ "tcoffee", "TCoffee",
+ "Tree-based Consistency Objective Function for Alignment Evaluation",
+ "Cedric Notredame", "13.41.0", "GNU GPL",
+ List.of("Topic :: Computational biology :: Sequence analysis",
+ "Operation :: Analysis :: Sequence analysis :: Sequence alignment :: Multiple sequence alignment"),
+ List.of(), List.of(), null) };
+ }
+
+ @Test(dataProvider = "multipleSequenceAlignmentService")
+ public void testFetchServices_multipleSequenceAlignmentService_actionTypeIsAlignment(
+ SlivkaService service) throws IOException
+ {
+ when(clientMock.getServices()).thenReturn(List.of(service));
+ when(clientMock.getUrl()).thenReturn(URI.create("http://example.org/"));
+ var discoverer = new SlivkaWSDiscoverer(url -> clientMock);
+ var webServices = discoverer
+ .fetchServices(new URL("http://example.org/"));
+ assertThat(webServices.get(0).getCategory(), equalTo("Alignment"));
+ assertThat(webServices.get(0).getActionClass(),
+ typeCompatibleWith(AlignmentAction.class));
+ }
+
+ @Test(dataProvider = "multipleSequenceAlignmentService")
+ public void testFetchServices_multipleSequenceAlignmentService_serviceIsNonInteractive(
+ SlivkaService service) throws IOException
+ {
+ when(clientMock.getServices()).thenReturn(List.of(service));
+ when(clientMock.getUrl()).thenReturn(URI.create("http://example.org/"));
+ var discoverer = new SlivkaWSDiscoverer(url -> clientMock);
+ var webServices = discoverer
+ .fetchServices(new URL("http://example.org/"));
+ assertThat(webServices.get(0).isInteractive(), is(false));
+ }
+
+ @DataProvider
+ public SlivkaService[] clustalFamilyService()
+ {
+ return new SlivkaService[] { new SlivkaService(
+ URI.create("http://example.org/api/services/clustalo"),
+ "clustalo", "ClustalO",
+ "Clustal Omega is the latest addition to the Clustal family.",
+ "Fabian Sievers, et al.", "1.2.4", "GNU GPL ver. 2",
+ List.of("Topic :: Computational biology :: Sequence analysis",
+ "Operation :: Analysis :: Sequence analysis :: Sequence alignment :: Multiple sequence alignment"),
+ List.of(), List.of(), null),
+ new SlivkaService(
+ URI.create("http://example.org/api/services/clustalw"),
+ "clustalw", "ClustalW",
+ "ClustalW is a general purpose multiple alignment program.",
+ "Larkin MA, et al.", "2.1", "GNU GPL ver. 3",
+ List.of("Topic :: Computation biology :: Sequence analysis",
+ "Operation :: Analysis :: Multiple sequence alignment"),
+ List.of(), List.of(), null),
+ new SlivkaService(
+ URI.create("http://example.org/api/services/clustalw2"),
+ "clustalw2", "ClustalW2",
+ "ClustalW is a general purpose multiple alignment program.",
+ "Larkin MA, et al.", "2.1", "GNU GPL ver. 3",
+ List.of("Topic :: Computation biology :: Sequence analysis",
+ "Operation :: Analysis :: Multiple sequence alignment"),
+ List.of(), List.of(), null), };
+ }
+
+ @Test(dataProvider = "clustalFamilyService")
+ public void testFetchService_clustalFamilyService_containsTwoActions(
+ SlivkaService service) throws IOException
+ {
+ when(clientMock.getServices()).thenReturn(List.of(service));
+ when(clientMock.getUrl()).thenReturn(URI.create("http://example.org"));
+ var discoverer = new SlivkaWSDiscoverer(url -> clientMock);
+ var webServices = discoverer
+ .fetchServices(new URL("http://example.org"));
+ var actions = webServices.get(0).getActions();
+ assertThat(actions, hasSize(2));
+ assertThat(actions.get(0), allOf(hasProperty("name", is("Alignment")),
+ hasProperty("subcategory", is("Align"))));
+ assertThat(actions.get(1),
+ allOf(hasProperty("name", is("Re-alignment")),
+ hasProperty("subcategory", is("Realign"))));
+ }
+
+ @DataProvider
+ public String[] validRNASecondaryStructurePredictionClassifiers()
+ {
+ return new String[] {
+ "Operation :: Analysis :: RNA secondary structure prediction",
+ "operation :: analysis :: rna secondary structure prediction",
+ "OPERATION :: ANALYSIS :: RNA SECONDARY STRUCTURE PREDICTION",
+ "Operation\t::\tAnalysis\t::\tRNA secondary structure prediction",
+ "Operation::Analysis::RNA secondary structure prediction",
+ "Operation :: Analysis :: Structure analysis :: RNA secondary structure prediction",
+ "Operation :: Analysis :: Structure analysis :: Nucleic acid structure analysis :: RNA secondary structure analysis :: RNA secondary structure prediction",
+ "Operation :: Analysis :: Structure analysis :: Nucleic acid structure analysis :: Nucleic acid structure prediction :: RNA secondary structure prediction",
+ "Operation :: Analysis :: Sequence analysis :: Nucleic acid sequence analysis :: Nucleic acid feature detection :: RNA secondary structure prediction",
+ "Operation :: Prediction and recognition :: RNA secondary structure prediction",
+ "Operation :: Prediction and recognition :: Nucleic acid feature detection :: RNA secondary structure prediction",
+ "Operation :: Prediction and recignition :: Nucleic acid structure prediction :: RNA secondary structure prediction", };
+ }
+
+ @DataProvider
+ public Iterator<Object> RNASecondaryStructurePredictionService()
+ {
+ var services = new ArrayList<>();
+ for (var classifier : validRNASecondaryStructurePredictionClassifiers())
{
- System.out.format("Service(%s>%s @%s)%n", service.getCategory(),
- service.getName(), service.getUrl());
- var datastore = service.getParamDatastore();
- for (var param : datastore.getServiceParameters())
- {
- System.out.format(" %s :%s%n", param.getName(), param.getClass().getSimpleName());
- }
+ services.add(new SlivkaService(URI.create("http://example.org/"),
+ "example", "name", "description", "author", "1.0", "MIT",
+ List.of(classifier), List.of(), List.of(), null));
}
+ return services.iterator();
+ }
+
+ @Test(dataProvider = "RNASecondaryStructurePredictionService")
+ public void testFetchServices_RNASecStrPredClassifier_serviceTypeIsRNASecStrPred(
+ SlivkaService service) throws IOException
+ {
+ when(clientMock.getServices()).thenReturn(List.of(service));
+ when(clientMock.getUrl()).thenReturn(URI.create("http://example.org/"));
+ var discoverer = new SlivkaWSDiscoverer(url -> clientMock);
+ var webServices = discoverer
+ .fetchServices(new URL("http://example.org/"));
+ assertThat(webServices, hasSize(1));
+ assertThat(webServices.get(0).getCategory(),
+ equalTo("Secondary Structure Prediction"));
+ assertThat(webServices.get(0).getActionClass(),
+ typeCompatibleWith(AnnotationAction.class));
+ }
+
+ @DataProvider
+ public String[] validConservationAnalysisClassifiers()
+ {
+ return new String[] {
+ "Operation :: Analysis :: Sequence alignment analysis (conservation)",
+ "Operation::Analysis::Sequence alignment analysis (conservation)",
+ "Operation\t::\tAnalysis\t::\tSequence alignment analysis (conservation)",
+ "Operation :: Analysis :: Sequence analysis :: Sequence alignment analysis (conservation)",
+ "Operation :: Analysis :: Sequence analysis :: Sequence alignment analysis :: Sequence alignment analysis (conservation)", };
+ }
+
+ @DataProvider
+ public Iterator<Object> ConservationAnalysisService()
+ {
+ var services = new ArrayList<>();
+ for (var classifier : validConservationAnalysisClassifiers())
+ {
+ services.add(new SlivkaService(URI.create("http://example.org/"),
+ "example", "name", "description", "author", "1.0", "MIT",
+ List.of(classifier), List.of(), List.of(), null));
+ }
+ return services.iterator();
+ }
+
+ @Test(dataProvider = "validConservationAnalysisClassifiers")
+ public void testFetchServices_conservationAnalysisClassifier_serviceTypeIsConservation(
+ String classifier) throws IOException
+ {
+ var service = new SlivkaService(URI.create("http://example.org/"),
+ "example", "name", "description", "author", "1.0", "MIT",
+ List.of(classifier), List.of(), List.of(), null);
+ when(clientMock.getServices()).thenReturn(List.of(service));
+ when(clientMock.getUrl()).thenReturn(URI.create("http://example.org/"));
+ var discoverer = new SlivkaWSDiscoverer(url -> clientMock);
+ var webServices = discoverer
+ .fetchServices(new URL("http://example.org/"));
+ assertThat(webServices, hasSize(1));
+ assertThat(webServices.get(0).getCategory(), equalTo("Conservation"));
+ assertThat(webServices.get(0).getActionClass(),
+ typeCompatibleWith(AnnotationAction.class));
+ }
+
+ @DataProvider
+ public Object[] validProteinSequenceAnalysisClassifiers()
+ {
+ return new Object[] {
+ "Operation :: Analysis :: Sequence analysis :: Protein sequence analysis", };
+ }
+
+ @Test(dataProvider = "validProteinSequenceAnalysisClassifiers")
+ public void testFetchServices_proteinSequenceAnalysisClassifier_serviceTypeIsProtSeqAnalysis(
+ String classifier) throws IOException
+ {
+ var service = new SlivkaService(URI.create("http://example.org/"),
+ "example", "name", "description", "author", "1.0", "MIT",
+ List.of(classifier), List.of(), List.of(), null);
+ when(clientMock.getServices()).thenReturn(List.of(service));
+ when(clientMock.getUrl()).thenReturn(URI.create("http://example.org/"));
+ var discoverer = new SlivkaWSDiscoverer(url -> clientMock);
+ var webServices = discoverer
+ .fetchServices(new URL("http://example.org/"));
+ assertThat(webServices, hasSize(1));
+ assertThat(webServices.get(0).getCategory(),
+ equalTo("Protein Disorder"));
+ assertThat(webServices.get(0).getActionClass(),
+ typeCompatibleWith(AnnotationAction.class));
+ }
+
+ @DataProvider
+ public Object[] validProteinSecondaryStructurePredictionClassifiers()
+ {
+ return new Object[] {
+ "Operation ;: Analysis :: Protein secondary structure prediction",
+ "Operation :: Analysis :: Structure analysis :: Protein structure analysis :: Protein secondary structure analysis :: Protein secondary structure prediction",
+ "Operation :: Analysis :: Sequence analysis :: Protein sequence analysis :: Protein feature detection :: Protein secondary structure prediction",
+ "Operation :: Analysis :: Sequence analysis :: Protein sequence analysis :: Protein secondary structure prediction",
+ "Operation :: Prediction and recognition :: Protein secondary structure prediction",
+ "Operation :: Prediction and recognition :: Protein feature detection :: Protein secondary structure prediction", };
+ }
+
+ @Test(
+ enabled = false, // sec. str. pred. not implemented for slivka
+ dataProvider = "validProteinSecondaryStructurePredictionClassifiers")
+ public void testFetchServices_proteinSecStrPredClassifier_serviceTypeIsProtSecStrPred(
+ String classifier) throws IOException
+ {
+ var service = new SlivkaService(URI.create("http://example.org/"),
+ "example", "name", "description", "author", "1.0", "MIT",
+ List.of(classifier), List.of(), List.of(), null);
+ when(clientMock.getServices()).thenReturn(List.of(service));
+ when(clientMock.getUrl()).thenReturn(URI.create("http://example.org/"));
+ var discoverer = new SlivkaWSDiscoverer(url -> clientMock);
+ var webServices = discoverer
+ .fetchServices(new URL("http://example.org/"));
+ assertThat(webServices, hasSize(1));
+ assertThat(webServices.get(0).getCategory(),
+ equalTo("Protein Disorder"));
+ assertThat(webServices.get(0).getActionClass(),
+ typeCompatibleWith(AnnotationAction.class));
}
}
git://source.jalview.org / jalview.git / commitdiff