--- /dev/null
+package jalview.ws2.client.slivka;
+
+import java.io.IOException;
+import java.net.MalformedURLException;
+import java.net.URISyntaxException;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.List;
+
+import jalview.bin.Cache;
+import jalview.ws.params.ParamManager;
+import jalview.ws2.actions.alignment.AlignmentAction;
+import jalview.ws2.actions.annotation.AnnotationAction;
+import jalview.ws2.api.WebService;
+import jalview.ws2.client.api.AbstractWebServiceDiscoverer;
+import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
+import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
+
+public class SlivkaWSDiscoverer extends AbstractWebServiceDiscoverer
+{
+ private static final String SLIVKA_HOST_URLS = "SLIVKAHOSTURLS";
+
+ private static final URL DEFAULT_URL;
+ static
+ {
+ try
+ {
+ DEFAULT_URL = new URL("https://www.compbio.dundee.ac.uk/slivka/");
+ } catch (MalformedURLException e)
+ {
+ throw new AssertionError(e);
+ }
+ }
+
+ private static SlivkaWSDiscoverer instance = null;
+
+ private static ParamManager paramManager = null;
+
+ private SlivkaWSDiscoverer()
+ {
+ }
+
+ public static SlivkaWSDiscoverer getInstance()
+ {
+ if (instance == null)
+ instance = new SlivkaWSDiscoverer();
+ return instance;
+ }
+
+ public static void setParamManager(ParamManager manager)
+ {
+ paramManager = manager;
+ }
+
+ @Override
+ public int getStatusForUrl(URL url)
+ {
+ try
+ {
+ List<?> services = new SlivkaClient(url.toString()).getServices();
+ return services.isEmpty() ? STATUS_NO_SERVICES : STATUS_OK;
+ } catch (IOException e)
+ {
+ Cache.log.error("slivka could not retrieve services from " + url, e);
+ return STATUS_INVALID;
+ }
+ }
+
+ @Override
+ protected String getUrlsPropertyKey()
+ {
+ return SLIVKA_HOST_URLS;
+ }
+
+ @Override
+ protected URL getDefaultUrl()
+ {
+ return DEFAULT_URL;
+ }
+
+ @Override
+ protected List<WebService<?>> fetchServices(URL url) throws IOException
+ {
+ ArrayList<WebService<?>> allServices = new ArrayList<>();
+ SlivkaClient slivkaClient;
+ try
+ {
+ slivkaClient = new SlivkaClient(url.toURI());
+ } catch (URISyntaxException e)
+ {
+ throw new MalformedURLException(e.getMessage());
+ }
+ for (var slivkaService : slivkaClient.getServices())
+ {
+ int serviceClass = getServiceClass(slivkaService);
+ if (serviceClass == SERVICE_CLASS_MSA)
+ {
+ var wsb = WebService.<AlignmentAction> newBuilder();
+ initServiceBuilder(slivkaService, wsb);
+ wsb.category("Alignment");
+ wsb.interactive(false);
+ wsb.actionClass(AlignmentAction.class);
+ var msaService = wsb.build();
+
+ boolean canRealign = msaService.getName().contains("lustal");
+ var client = new SlivkaAlignmentWSClient(slivkaService);
+ var actionBuilder = AlignmentAction.newBuilder(client);
+ actionBuilder.name("Alignment");
+ actionBuilder.webService(msaService);
+ if (canRealign)
+ actionBuilder.subcategory("Align");
+ actionBuilder.minSequences(2);
+ msaService.addAction(actionBuilder.build());
+ if (canRealign)
+ {
+ actionBuilder.name("Re-alignment");
+ actionBuilder.subcategory("Realign");
+ actionBuilder.submitGaps(true);
+ msaService.addAction(actionBuilder.build());
+ }
+ allServices.add(msaService);
+ }
+ else if (serviceClass == SERVICE_CLASS_PROT_SEQ_ANALYSIS)
+ {
+ var wsb = WebService.<AnnotationAction> newBuilder();
+ initServiceBuilder(slivkaService, wsb);
+ wsb.category("Protein Disorder");
+ wsb.interactive(false);
+ wsb.actionClass(AnnotationAction.class);
+ var psaService = wsb.build();
+ var client = new SlivkaAnnotationWSClient(slivkaService);
+ var actionBuilder = AnnotationAction.newBuilder(client);
+ actionBuilder.webService(psaService);
+ actionBuilder.name("Analysis");
+ psaService.addAction(actionBuilder.build());
+ allServices.add(psaService);
+ }
+ else if (serviceClass == SERVICE_CLASS_CONSERVATION)
+ {
+ var wsb = WebService.<AnnotationAction> newBuilder();
+ initServiceBuilder(slivkaService, wsb);
+ wsb.category("Conservation");
+ wsb.interactive(true);
+ wsb.actionClass(AnnotationAction.class);
+ var conService = wsb.build();
+ var client = new SlivkaAnnotationWSClient(slivkaService);
+ var actionBuilder = AnnotationAction.newBuilder(client);
+ actionBuilder.webService(conService);
+ actionBuilder.name("");
+ actionBuilder.alignmentAnalysis(true);
+ actionBuilder.requireAlignedSequences(true);
+ actionBuilder.filterSymbols(true);
+ conService.addAction(actionBuilder.build());
+ allServices.add(conService);
+ }
+ else if (serviceClass == SERVICE_CLASS_RNA_SEC_STR_PRED)
+ {
+ var wsb = WebService.<AnnotationAction> newBuilder();
+ initServiceBuilder(slivkaService, wsb);
+ wsb.category("Secondary Structure Prediction");
+ wsb.interactive(true);
+ wsb.actionClass(AnnotationAction.class);
+ var predService = wsb.build();
+ var client = new SlivkaAnnotationWSClient(slivkaService);
+ var actionBuilder = AnnotationAction.newBuilder(client);
+ actionBuilder.webService(predService);
+ actionBuilder.name("Prediction");
+ actionBuilder.minSequences(2);
+ actionBuilder.allowNucleotide(true);
+ actionBuilder.allowProtein(false);
+ actionBuilder.alignmentAnalysis(true);
+ actionBuilder.requireAlignedSequences(true);
+ actionBuilder.filterSymbols(false);
+ predService.addAction(actionBuilder.build());
+ allServices.add(predService);
+ }
+ else
+ {
+ continue;
+ }
+ }
+ return allServices;
+ }
+
+ private void initServiceBuilder(SlivkaService service, WebService.Builder<?> wsBuilder)
+ {
+ try
+ {
+ wsBuilder.url(service.getClient().getUrl().toURL());
+ } catch (MalformedURLException e)
+ {
+ e.printStackTrace();
+ }
+ wsBuilder.clientName("slivka");
+ wsBuilder.name(service.getName());
+ wsBuilder.description(service.getDescription());
+ var storeBuilder = new SlivkaParamStoreFactory(service, paramManager);
+ wsBuilder.paramDatastore(storeBuilder.createParamDatastore());
+ }
+
+ static final int SERVICE_CLASS_UNSUPPORTED = -1;
+
+ static final int SERVICE_CLASS_MSA = 1;
+
+ static final int SERVICE_CLASS_RNA_SEC_STR_PRED = 2;
+
+ static final int SERVICE_CLASS_CONSERVATION = 3;
+
+ static final int SERVICE_CLASS_PROT_SEQ_ANALYSIS = 4;
+
+ static final int SERVICE_CLASS_PROT_SEC_STR_PRED = 5;
+
+ /**
+ * Scan service classifiers starting with operation :: analysis to decide the
+ * operation class.
+ *
+ * @return service class flag
+ */
+ private static int getServiceClass(SlivkaService service)
+ {
+ for (String classifier : service.getClassifiers())
+ {
+ String[] path = classifier.split("\\s*::\\s*");
+ if (path.length < 3 || !path[0].equalsIgnoreCase("operation") ||
+ !path[1].equalsIgnoreCase("analysis"))
+ continue;
+ // classifier is operation :: analysis :: *
+ var tail = path[path.length - 1].toLowerCase();
+ switch (tail)
+ {
+ case "multiple sequence alignment":
+ return SERVICE_CLASS_MSA;
+ case "rna secondary structure prediction":
+ return SERVICE_CLASS_RNA_SEC_STR_PRED;
+ case "sequence alignment analysis (conservation)":
+ return SERVICE_CLASS_CONSERVATION;
+ case "protein sequence analysis":
+ return SERVICE_CLASS_PROT_SEQ_ANALYSIS;
+ case "protein secondary structure prediction":
+ return SERVICE_CLASS_PROT_SEC_STR_PRED;
+ }
+ }
+ return SERVICE_CLASS_UNSUPPORTED;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff