From c278475ed30f89bd64dfb0bebc86576defd8061f Mon Sep 17 00:00:00 2001 From: Sasha Sherstnev Date: Thu, 5 Sep 2013 10:52:28 +0100 Subject: [PATCH] New version of the JABAWS client --- webservices/compbio/ws/client/Jws2Client.java | 386 +++++++++++-------------- 1 file changed, 165 insertions(+), 221 deletions(-) diff --git a/webservices/compbio/ws/client/Jws2Client.java b/webservices/compbio/ws/client/Jws2Client.java index 3c62c29..3322b35 100644 --- a/webservices/compbio/ws/client/Jws2Client.java +++ b/webservices/compbio/ws/client/Jws2Client.java @@ -68,11 +68,9 @@ import compbio.util.FileUtil; public class Jws2Client { /* - * Use java.util.Logger instead of log4j logger to reduce the size of the - * client package + * Use java.util.Logger instead of log4j logger to reduce the size of the client package */ - private static final Logger log = Logger.getLogger(Jws2Client.class - .getCanonicalName()); + private static final Logger log = Logger.getLogger(Jws2Client.class.getCanonicalName()); /** * Attempt to construct the URL object from the string @@ -107,96 +105,167 @@ public class Jws2Client { String hostname = CmdHelper.getHost(cmd); if (hostname == null) { System.err.println("Host name is not provided!"); - printUsage(1); + System.out.println(Constraints.help_text); + System.exit(1); } if (!validURL(hostname)) { System.err.println("Host name is not valid!"); - printUsage(1); + System.out.println(Constraints.help_text); + System.exit(1); } - // Just list available services and quit + boolean listServices = CmdHelper.listServices(cmd); if (listServices) { - listServices(hostname); + listAllServices(hostname); System.exit(0); } String serviceName = CmdHelper.getServiceName(cmd); if (serviceName == null) { System.err.println("Service name is no provided!"); - printUsage(1); + System.out.println(Constraints.help_text); + System.exit(1); } + Services service = Services.getService(serviceName); if (service == null) { - System.err.println("Service " + serviceName - + " is no recognized! Valid values are: " - + Arrays.toString(Services.values())); - printUsage(1); + String mess = "Service " + serviceName + " is no available! Valid values are: "; + System.err.println(mess + Arrays.toString(Services.values())); + System.out.println(Constraints.help_text); + System.exit(1); } - // Test service and quit - boolean testService = CmdHelper.testService(cmd); - if (testService) { + + if (CmdHelper.testService(cmd)) { testService(hostname, service, new PrintWriter(System.out, true)); System.exit(0); } - File inputFile = IOHelper.getFile(cmd, inputkey, true); - File outFile = IOHelper.getFile(cmd, outputkey, false); - File parametersFile = IOHelper.getFile(cmd, paramFile, true); - String presetName = CmdHelper.getPresetName(cmd); - - Metadata msaws = (Metadata) connect(hostname, service); + Metadata thews = (Metadata) connect(hostname, service); Preset preset = null; - if (presetName != null) { - preset = MetadataHelper.getPreset(msaws, presetName); + if (null != CmdHelper.getPresetName(cmd)) { + preset = MetadataHelper.getPreset(thews, CmdHelper.getPresetName(cmd)); } + List> customOptions = null; - if (parametersFile != null) { - List prms = IOHelper.loadParameters(parametersFile); - customOptions = MetadataHelper.processParameters(prms, - msaws.getRunnerOptions()); + if (null != IOHelper.getFile(cmd, paramFile, true)) { + List prms = IOHelper.loadParameters(IOHelper.getFile(cmd, paramFile, true)); + customOptions = MetadataHelper.processParameters(prms, thews.getRunnerOptions()); } - Alignment alignment = null; - if (inputFile != null) { + + if (null != IOHelper.getFile(cmd, inputkey, true)) { + File infile = IOHelper.getFile(cmd, inputkey, true); + File outfile = IOHelper.getFile(cmd, outputkey, false); Writer writer = null; - if (outFile != null) { - writer = IOHelper.getWriter(outFile); + if (outfile != null) { + writer = IOHelper.getWriter(outfile); } else { - // this stream is going to be closed later which is fine as - // std.out will not be + // this stream is going to be closed later which is fine as std.out will not be writer = new PrintWriter(System.out, true); } if (service.getServiceType() == SequenceAnnotation.class) { - ScoreManager result = analize(inputFile, - ((SequenceAnnotation) msaws), preset, customOptions); - + ScoreManager result = analize(infile, ((SequenceAnnotation) thews), preset, customOptions); IOHelper.writeOut(writer, result); - } else { - alignment = align(inputFile, (MsaWS) msaws, preset, - customOptions); + } else if (service.getServiceType() == MsaWS.class) { + Alignment alignment = align(infile, (MsaWS) thews, preset, customOptions); IOHelper.writeOut(writer, alignment); } writer.close(); } - boolean listParameters = CmdHelper.listParameters(cmd); - if (listParameters) { - System.out.println(MetadataHelper.getParametersList(msaws)); + if (CmdHelper.listParameters(cmd)) { + System.out.println(MetadataHelper.getParametersList(thews)); } - boolean listPreset = CmdHelper.listPresets(cmd); - if (listPreset) { - System.out.println(MetadataHelper.getPresetList(msaws)); + if (CmdHelper.listPresets(cmd)) { + System.out.println(MetadataHelper.getPresetList(thews)); } - boolean listLimits = CmdHelper.listLimits(cmd); - if (listLimits) { - System.out.println(MetadataHelper.getLimits(msaws)); + if (CmdHelper.listLimits(cmd)) { + System.out.println(MetadataHelper.getLimits(thews)); } log.fine("Disconnecting..."); - ((Closeable) msaws).close(); + ((Closeable) thews).close(); log.fine("Disconnected successfully!"); } /** + * Connects to a web service by the host and the service name web service type + * + * @param host + * the fully qualified name of JABAWS server including JABAWS + * context name e.g + * http://nanna.cluster.lifesci.dundee.ac.uk:8080/jaba + * @param service + * the name of the JABAWS service to connect to + * @return JABAService + * @throws WebServiceException + * @throws ConnectException + * if fails to connect to the service on the host + */ + public static JABAService connect(String host, Services service) + throws WebServiceException, ConnectException { + URL url = null; + log.log(Level.FINE, "Attempting to connect with " + service.toString() + "..."); + System.out.println ("Attempting to connect with " + service.toString() + "..."); + try { + url = new URL(host + "/" + service.toString() + "?wsdl"); + } catch (MalformedURLException e) { + e.printStackTrace(); + // ignore as the host name is already verified + } + Service serv = null; + try { + serv = service.getService(url, service.getServiceNamespace()); + } catch (WebServiceException wse) { + wse.printStackTrace(); + } + if (serv == null) { + throw new ConnectException("Could not connect to " + url + ". Is the server down?"); + } + JABAService serviceIF = service.getInterface(serv); + log.log(Level.INFO, "Connected successfully!"); + + return serviceIF; + } + + /** + * Get a connection of JABAWS registry + * + * @param host + * the fully qualified name of JABAWS server including JABAWS + * context name e.g + * http://nanna.cluster.lifesci.dundee.ac.uk:8080/jaba + * @return compbio.data.msa.RegistryWS - instance of a RegistryWS web + * service + * @throws WebServiceException + * @throws ConnectException + */ + public static compbio.data.msa.RegistryWS connectToRegistry(String host) + throws WebServiceException, ConnectException { + URL url = null; + String service = "RegistryWS"; + log.log(Level.FINE, "Attempting to connect..."); + + try { + url = new URL(host + "/" + service + "?wsdl"); + } catch (MalformedURLException e) { + e.printStackTrace(); + // ignore as the host name is already verified + } + QName qname = new QName(JABAService.V3_SERVICE_NAMESPACE, service); + Service serv = Service.create(url, qname); + + if (serv == null) { + throw new ConnectException("Could not connect to " + url + ". Is the server down?"); + } + + QName portName = new QName(serv.getServiceName().getNamespaceURI(), service + "Port"); + compbio.data.msa.RegistryWS serviceIF = serv.getPort(portName, compbio.data.msa.RegistryWS.class); + log.log(Level.INFO, "Connected to " + service + " successfully!"); + + return serviceIF; + } + + /** * Asks registry to test the service on the host hostname * * @param hostname @@ -205,8 +274,8 @@ public class Jws2Client { * @throws ConnectException * @throws WebServiceException */ - public static void testService(String hostname, Services service, - PrintWriter writer) throws ConnectException, WebServiceException { + public static void testService(String hostname, Services service, PrintWriter writer) + throws ConnectException, WebServiceException { RegistryWS registry = connectToRegistry(hostname); if (registry != null) { String message = registry.testService(service); @@ -217,35 +286,35 @@ public class Jws2Client { writer.flush(); } - public static Set getServices(String hostname) - throws WebServiceException, ConnectException { + private static void listAllServices(String hostname) throws WebServiceException, IOException { RegistryWS registry = connectToRegistry(hostname); - Set services = Collections.EMPTY_SET; + Set func_services = Collections.EMPTY_SET; + Set nonfunc_services = Collections.EMPTY_SET; if (registry != null) { - services = registry.getSupportedServices(); + func_services = registry.getSupportedServices(); + nonfunc_services = registry.getNonoperatedServices(); FileUtil.closeSilently(((Closeable) registry)); - } - return services; - } - - private static void listServices(String hostname) - throws WebServiceException, IOException { - Set services = Jws2Client.getServices(hostname); - if (!services.isEmpty()) { - System.out.println("Supported services are: " - + Services.toString(services)); } else { System.out.println("Failed to connect to the registry! "); + return; + } + if (!func_services.isEmpty()) { + String mess = "\n\rAvailable services: "; + System.out.println(mess + Services.toString(func_services)); + } + if (!nonfunc_services.isEmpty()) { + String mess = "Non-available services (internal tests failed): "; + System.out.println(mess + Services.toString(nonfunc_services)); } } /** - * Calculate conservation for sequences loaded from the file + * Calculate conservation for sequences loaded from a FASTA record list structure * + * @param fastalist + * the list of FASTA records * @param wsproxy * a web service proxy - * @param file - * the file to read the results from * @param preset * Preset to use optional * @param customOptions @@ -253,16 +322,12 @@ public class Jws2Client { * @return Set the conservation scores * @throws UnknownFileFormatException */ - static ScoreManager analize(List fastalist, - SequenceAnnotation wsproxy, Preset preset, - List> customOptions) { - + static ScoreManager analize(List fastalist, SequenceAnnotation wsproxy, Preset preset, List> customOptions) { ScoreManager scores = null; try { String jobId = null; if (customOptions != null && preset != null) { - System.out - .println("WARN: Parameters (-f) are defined together with a preset (-r) ignoring preset!"); + System.out.println("WARN: Parameters (-f) are defined together with a preset (-r) ignoring preset!"); } if (customOptions != null) { jobId = wsproxy.customAnalize(fastalist, customOptions); @@ -271,29 +336,22 @@ public class Jws2Client { } else { jobId = wsproxy.analize(fastalist); } - System.out.println("\n\ncalling analise........."); - Thread.sleep(1000); + System.out.println("\n\rcalling predictor........."); + Thread.sleep(100); scores = wsproxy.getAnnotation(jobId); - } catch (JobSubmissionException e) { - System.err - .println("Exception while submitting job to a web server. " - + "Exception details are below:"); + System.err.println("Exception while submitting job to a web server. Exception details are below:"); e.printStackTrace(); } catch (ResultNotAvailableException e) { - System.err.println("Exception while waiting for results. " - + "Exception details are below:"); + System.err.println("Exception while waiting for results. Exception details are below:"); e.printStackTrace(); } catch (InterruptedException e) { - // ignore and propagate an interruption Thread.currentThread().interrupt(); - System.err.println("Exception while waiting for results. " - + "Exception details are below:"); + System.err.println("Exception while waiting for results. Exception details are below:"); e.printStackTrace(); } catch (WrongParameterException e) { - System.err - .println("Exception while parsing the web method input parameters. " - + "Exception details are below:"); + String mess = "Parsing the web method input parameters failed Exception details are below:"; + System.err.println(mess); e.printStackTrace(); } return scores; @@ -315,125 +373,23 @@ public class Jws2Client { * @throws IOException * @throws UnknownFileFormatException */ - static ScoreManager analize(File file, SequenceAnnotation wsproxy, - Preset preset, List> customOptions) { + static ScoreManager analize(File file, SequenceAnnotation wsproxy, Preset preset, List> customOptions) { List fastalist = null; try { fastalist = SequenceUtil.openInputStream(file.getAbsolutePath()); assert !fastalist.isEmpty() : "Input is empty!"; } catch (IOException e) { - System.err - .println("Exception while reading the input file. " - + "Check that the input file contains a list of fasta formatted sequences! " - + "Exception details are below:"); + String mess = "Reading the input file failed. Check that the file contains a list of FASTA records!\n"; + System.err.println(mess + "Exception details are below:"); e.printStackTrace(); } catch (UnknownFileFormatException e) { - System.err - .println("Exception while attempting to read the input file " - + "Exception details are below:"); + String mess = "Reading the input file failed. Exception details are below:"; + System.err.println(mess); System.out.println(e.getMessage()); e.printStackTrace(); } return analize(fastalist, wsproxy, preset, customOptions); } - /** - * Connects to a web service by the host and the service name web service - * type - * - * @param host - * the fully qualified name of JABAWS server including JABAWS - * context name e.g - * http://nanna.cluster.lifesci.dundee.ac.uk:8080/jaba - * @param service - * the name of the JABAWS service to connect to - * @return JABAService - * @throws WebServiceException - * @throws ConnectException - * if fails to connect to the service on the host - */ - public static JABAService connect(String host, Services service) - throws WebServiceException, ConnectException { - URL url = null; - log.log(Level.FINE, "Attempting to connect..."); - try { - url = new URL(host + "/" + service.toString() + "?wsdl"); - } catch (MalformedURLException e) { - e.printStackTrace(); - // ignore as the host name is already verified - } - Service serv = null; - try { - serv = service.getService(url, JABAService.SERVICE_NAMESPACE); - } catch (WebServiceException wse) { - System.out.println("Connecting to JABAWS version 2 service"); - if (isV2service(wse)) { - serv = service - .getService(url, JABAService.V2_SERVICE_NAMESPACE); - } - } - if (serv == null) { - throw new ConnectException("Could not connect to " + url - + " the server is down?"); - } - JABAService serviceIF = service.getInterface(serv); - log.log(Level.INFO, "Connected successfully!"); - - return serviceIF; - } - - static boolean isV2service(WebServiceException wse) { - String message = wse.getMessage(); - int idx = message.indexOf("not a valid service"); - if (idx > 0) { - if (message.substring(idx).contains( - JABAService.V2_SERVICE_NAMESPACE)) { - return true; - } - } - return false; - } - - /** - * Get a connection of JABAWS registry - * - * @param host - * the fully qualified name of JABAWS server including JABAWS - * context name e.g - * http://nanna.cluster.lifesci.dundee.ac.uk:8080/jaba - * @return compbio.data.msa.RegistryWS - instance of a RegistryWS web - * service - * @throws WebServiceException - * @throws ConnectException - */ - public static compbio.data.msa.RegistryWS connectToRegistry(String host) - throws WebServiceException, ConnectException { - URL url = null; - String service = "RegistryWS"; - log.log(Level.FINE, "Attempting to connect..."); - - try { - url = new URL(host + "/" + service + "?wsdl"); - } catch (MalformedURLException e) { - e.printStackTrace(); - // ignore as the host name is already verified - } - QName qname = new QName(JABAService.V2_SERVICE_NAMESPACE, service); - Service serv = Service.create(url, qname); - - if (serv == null) { - throw new ConnectException("Could not connect to " + url - + " the server is down?"); - } - - QName portName = new QName(serv.getServiceName().getNamespaceURI(), - service + "Port"); - compbio.data.msa.RegistryWS serviceIF = serv.getPort(portName, - compbio.data.msa.RegistryWS.class); - - log.log(Level.INFO, "Connected to " + service + " successfully!"); - - return serviceIF; - } /** * Align sequences from the file using MsaWS @@ -461,8 +417,7 @@ public class Jws2Client { instream.close(); String jobId = null; if (customOptions != null && preset != null) { - System.out - .println("WARN: Parameters (-f) are defined together with a preset (-r) ignoring preset!"); + System.out.println("WARN: Parameters (-f) are defined together with a preset (-r) ignoring preset!"); } if (customOptions != null) { jobId = msaws.customAlign(fastalist, customOptions); @@ -471,20 +426,18 @@ public class Jws2Client { } else { jobId = msaws.align(fastalist); } - System.out.println("\n\ncalling align........."); + System.out.println("\ncalling aligner........."); Thread.sleep(1000); alignment = msaws.getResult(jobId); } catch (IOException e) { - System.err - .println("Exception while reading the input file. " - + "Check that the input file contains a list of fasta formatted sequences! " - + "Exception details are below:"); + System.err.println("Exception while reading the input file. " + + "Check that the input file contains a list of fasta formatted sequences! " + + "Exception details are below:"); e.printStackTrace(); } catch (JobSubmissionException e) { - System.err - .println("Exception while submitting job to a web server. " - + "Exception details are below:"); + System.err.println("Exception while submitting job to a web server. " + + "Exception details are below:"); e.printStackTrace(); } catch (ResultNotAvailableException e) { System.err.println("Exception while waiting for results. " @@ -508,16 +461,6 @@ public class Jws2Client { } /** - * Prints Jws2Client usage information to standard out - * - * @param exitStatus - */ - static void printUsage(int exitStatus) { - System.out.println(Constraints.help_text); - System.exit(exitStatus); - } - - /** * Starts command line client, if no parameter are supported print help. Two * parameters are required for successful call the JWS2 host name and a * service name. @@ -556,18 +499,19 @@ public class Jws2Client { public static void main(String[] args) { if (args == null) { - printUsage(1); + System.out.println(Constraints.help_text); + System.exit(1); } if (args.length < 2) { - System.err.println("Host and service names are required!"); - printUsage(1); + System.err.println("Host (-h=, e.g. -h=http://www.compbio.dundee.ac.uk/jabaws) and service (-s=, e.g. -s=Jpred) are required!"); + System.out.println(Constraints.help_text); + System.exit(1); } try { new Jws2Client(args); } catch (IOException e) { - log.log(Level.SEVERE, "IOException in client! " + e.getMessage(), - e.getCause()); + log.log(Level.SEVERE, "IOException in client! " + e.getMessage(), e.getCause()); System.err.println("Cannot write output file! Stack trace: "); e.printStackTrace(); } -- 1.7.10.2