import java.net.URL;\r
import java.util.Arrays;\r
import java.util.List;\r
+import java.util.Set;\r
import java.util.logging.Level;\r
import java.util.logging.Logger;\r
\r
import compbio.data.msa.JABAService;\r
import compbio.data.msa.Metadata;\r
import compbio.data.msa.MsaWS;\r
+import compbio.data.msa.RegistryWS;\r
import compbio.data.msa.SequenceAnnotation;\r
import compbio.data.sequence.Alignment;\r
import compbio.data.sequence.FastaSequence;\r
System.err.println("Host name is not valid!");\r
printUsage(1);\r
}\r
+ // Just list available services and quit\r
+ boolean listServices = CmdHelper.listServices(cmd);\r
+ if (listServices) {\r
+ listServices(hostname);\r
+ System.exit(0);\r
+ }\r
+\r
String serviceName = CmdHelper.getServiceName(cmd);\r
if (serviceName == null) {\r
System.err.println("Service name is no provided!");\r
Services service = Services.getService(serviceName);\r
if (service == null) {\r
System.err.println("Service " + serviceName\r
- + " is no supported! Valid values are: "\r
+ + " is no recognized! Valid values are: "\r
+ Arrays.toString(Services.values()));\r
printUsage(1);\r
}\r
+ // Test service and quit\r
+ boolean testService = CmdHelper.testService(cmd);\r
+ if (testService) {\r
+ testService(hostname, service);\r
+ System.exit(0);\r
+ }\r
+\r
File inputFile = IOHelper.getFile(cmd, inputkey, true);\r
File outFile = IOHelper.getFile(cmd, outputkey, false);\r
File parametersFile = IOHelper.getFile(cmd, paramFile, true);\r
((Closeable) msaws).close();\r
log.fine("Disconnected successfully!");\r
}\r
+\r
+ private void testService(String hostname, Services service)\r
+ throws IOException {\r
+ RegistryWS registry = connectToRegistry(hostname);\r
+ if (registry != null) {\r
+ String message = registry.testService(service);\r
+ System.out.println("Service " + service + " testing results: ");\r
+ System.out.println(message);\r
+ ((Closeable) registry).close();\r
+ }\r
+ }\r
+\r
+ private void listServices(String hostname) throws IOException {\r
+ RegistryWS registry = connectToRegistry(hostname);\r
+ if (registry != null) {\r
+ Set<Services> services = registry.getSupportedServices();\r
+ System.out.println("Supported services are: "\r
+ + Services.toString(services));\r
+ ((Closeable) registry).close();\r
+ } else {\r
+ System.out.println("Failed to connect to the registry! ");\r
+ }\r
+ }\r
+\r
/**\r
* Calculate conservation for sequences loaded from the file\r
* \r