-/* Copyright (c) 2009 Peter Troshin\r
+/* Copyright (c) 2011 Peter Troshin\r
* \r
- * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0 \r
+ * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0 \r
* \r
* This library is free software; you can redistribute it and/or modify it under the terms of the\r
* Apache License version 2 as published by the Apache Software Foundation\r
\r
package compbio.ws.client;\r
\r
-import static compbio.ws.client.Constraints.hostkey;\r
import static compbio.ws.client.Constraints.inputkey;\r
-import static compbio.ws.client.Constraints.limitList;\r
import static compbio.ws.client.Constraints.outputkey;\r
import static compbio.ws.client.Constraints.paramFile;\r
-import static compbio.ws.client.Constraints.paramList;\r
-import static compbio.ws.client.Constraints.presetList;\r
-import static compbio.ws.client.Constraints.presetkey;\r
-import static compbio.ws.client.Constraints.pseparator;\r
-import static compbio.ws.client.Constraints.servicekey;\r
\r
import java.io.Closeable;\r
import java.io.File;\r
import java.io.FileInputStream;\r
import java.io.IOException;\r
-import java.io.OutputStream;\r
+import java.io.PrintWriter;\r
+import java.io.Writer;\r
+import java.net.ConnectException;\r
import java.net.MalformedURLException;\r
import java.net.URL;\r
import java.util.Arrays;\r
+import java.util.Collections;\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 javax.xml.namespace.QName;\r
import javax.xml.ws.Service;\r
import javax.xml.ws.WebServiceException;\r
\r
import compbio.data.msa.JABAService;\r
+import compbio.data.msa.FoldWS;\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
+import compbio.data.sequence.RNAStruct;\r
+import compbio.data.sequence.ScoreManager;\r
+import compbio.data.sequence.ClustalAlignmentUtil;\r
import compbio.data.sequence.SequenceUtil;\r
+import compbio.data.sequence.UnknownFileFormatException;\r
import compbio.metadata.JobSubmissionException;\r
import compbio.metadata.Option;\r
import compbio.metadata.Preset;\r
import compbio.metadata.ResultNotAvailableException;\r
import compbio.metadata.WrongParameterException;\r
+import compbio.util.FileUtil;\r
\r
/**\r
* A command line client for JAva Bioinformatics Analysis Web Services\r
private static final Logger log = Logger.getLogger(Jws2Client.class\r
.getCanonicalName());\r
\r
- // JABAWS version 1.0 service name\r
- static final String QUALIFIED_SERVICE_NAME = "http://msa.data.compbio/01/01/2010/";\r
-\r
- // JABAWS version 2.0 service name\r
- static final String V2_QUALIFIED_SERVICE_NAME = "http://msa.data.compbio/01/12/2010/";\r
-\r
/**\r
* Attempt to construct the URL object from the string\r
* \r
* @throws IOException\r
*/\r
<T> Jws2Client(String[] cmd) throws IOException {\r
+ \r
\r
String hostname = CmdHelper.getHost(cmd);\r
if (hostname == null) {\r
- System.out.println("Host name is not provided!");\r
+ System.err.println("Host name is not provided!");\r
printUsage(1);\r
}\r
\r
if (!validURL(hostname)) {\r
- System.out.println("Host name is not valid!");\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.out.println("Service name is no provided!");\r
+ System.err.println("Service name is no provided!");\r
printUsage(1);\r
}\r
Services service = Services.getService(serviceName);\r
if (service == null) {\r
- System.out.println("Service " + serviceName\r
- + " is no supported! Valid values are: "\r
+ System.err.println("Service " + serviceName\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, new PrintWriter(System.out, true));\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
customOptions = MetadataHelper.processParameters(prms,\r
msaws.getRunnerOptions());\r
}\r
+// System.out.println("The Options read from the command line: " + customOptions);\r
+ \r
Alignment alignment = null;\r
if (inputFile != null) {\r
- if (service == Services.AAConWS) {\r
- System.out.println("calc conserv!");\r
+ Writer writer = null;\r
+ if (outFile != null) {\r
+ writer = IOHelper.getWriter(outFile);\r
} else {\r
+ // this stream is going to be closed later which is fine as\r
+ // std.out will not be\r
+ writer = new PrintWriter(System.out, true);\r
+ }\r
+ if (service.getServiceType() == SequenceAnnotation.class) {\r
+ ScoreManager result = analize(inputFile,\r
+ ((SequenceAnnotation<T>) msaws), preset, customOptions);\r
\r
+ IOHelper.writeOut(writer, result);\r
+ } else if (service.getServiceType() == MsaWS.class) {\r
alignment = align(inputFile, (MsaWS<T>) msaws, preset,\r
customOptions);\r
- OutputStream outStream = null;\r
- if (outFile != null) {\r
- outStream = IOHelper.getOutStream(outFile);\r
- } else {\r
- // this stream is going to be closed later which is fine as\r
- // std.out will not be\r
- outStream = System.out;\r
- }\r
- IOHelper.writeOut(outStream, alignment);\r
- // stream is closed in the method no need to close it here\r
+ IOHelper.writeOut(writer, alignment);\r
}\r
+ writer.close();\r
}\r
\r
boolean listParameters = CmdHelper.listParameters(cmd);\r
}\r
\r
/**\r
- * Connects to a web service by the host and the service name\r
+ * Asks registry to test the service on the host hostname\r
+ * \r
+ * @param hostname\r
+ * @param service\r
+ * @param writer\r
+ * @throws ConnectException\r
+ * @throws WebServiceException\r
+ */\r
+ public static void testService(String hostname, Services service,\r
+ PrintWriter writer) throws ConnectException, WebServiceException {\r
+ RegistryWS registry = connectToRegistry(hostname);\r
+ if (registry != null) {\r
+ String message = registry.testService(service);\r
+ writer.println("Service " + service + " testing results: ");\r
+ writer.println(message);\r
+ FileUtil.closeSilently(((Closeable) registry));\r
+ }\r
+ writer.flush();\r
+ }\r
+\r
+ public static Set<Services> getServices(String hostname)\r
+ throws WebServiceException, ConnectException {\r
+ RegistryWS registry = connectToRegistry(hostname);\r
+ Set<Services> services = Collections.EMPTY_SET;\r
+ if (registry != null) {\r
+ services = registry.getSupportedServices();\r
+ FileUtil.closeSilently(((Closeable) registry));\r
+ }\r
+ return services;\r
+ }\r
+\r
+ private static void listServices(String hostname)\r
+ throws WebServiceException, IOException {\r
+ Set<Services> services = Jws2Client.getServices(hostname);\r
+ if (!services.isEmpty()) {\r
+ System.out.println("Supported services are: "\r
+ + Services.toString(services));\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
+ * @param wsproxy\r
+ * a web service proxy\r
+ * @param file\r
+ * the file to read the results from\r
+ * @param preset\r
+ * Preset to use optional\r
+ * @param customOptions\r
+ * the list of options\r
+ * @return Set<Score> the conservation scores\r
+ * @throws UnknownFileFormatException\r
+ */\r
+ static <T> ScoreManager analize(List<FastaSequence> fastalist,\r
+ SequenceAnnotation<T> wsproxy, Preset<T> preset,\r
+ List<Option<T>> customOptions) {\r
+\r
+ ScoreManager scores = null;\r
+ try {\r
+ String jobId = null;\r
+ if (customOptions != null && preset != null) {\r
+ System.out\r
+ .println("WARN: Parameters (-f) are defined together with a preset (-r) ignoring preset!");\r
+ }\r
+ if (customOptions != null) {\r
+ jobId = wsproxy.customAnalize(fastalist, customOptions);\r
+ } else if (preset != null) {\r
+ jobId = wsproxy.presetAnalize(fastalist, preset);\r
+ } else {\r
+ jobId = wsproxy.analize(fastalist);\r
+ }\r
+ System.out.println("\n\ncalling analise.........");\r
+ Thread.sleep(1000);\r
+ scores = wsproxy.getAnnotation(jobId);\r
+\r
+ } catch (JobSubmissionException e) {\r
+ System.err\r
+ .println("Exception while submitting job to a web server. "\r
+ + "Exception details are below:");\r
+ e.printStackTrace();\r
+ } catch (ResultNotAvailableException e) {\r
+ System.err.println("Exception while waiting for results. "\r
+ + "Exception details are below:");\r
+ e.printStackTrace();\r
+ } catch (InterruptedException e) {\r
+ // ignore and propagate an interruption\r
+ Thread.currentThread().interrupt();\r
+ System.err.println("Exception while waiting for results. "\r
+ + "Exception details are below:");\r
+ e.printStackTrace();\r
+ } catch (WrongParameterException e) {\r
+ System.err\r
+ .println("Exception while parsing the web method input parameters. "\r
+ + "Exception details are below:");\r
+ e.printStackTrace();\r
+ }\r
+ return scores;\r
+\r
+ }\r
+\r
+ /**\r
+ * Calculate conservation for sequences loaded from the file\r
+ * \r
+ * @param wsproxy\r
+ * a web service proxy\r
+ * @param file\r
+ * the file to read the results from\r
+ * @param preset\r
+ * Preset to use optional\r
+ * @param customOptions\r
+ * the list of options\r
+ * @return Set<Score> the conservation scores\r
+ * @throws IOException\r
+ * @throws UnknownFileFormatException\r
+ */\r
+ static <T> ScoreManager analize(File file, SequenceAnnotation<T> wsproxy,\r
+ Preset<T> preset, List<Option<T>> customOptions) {\r
+ List<FastaSequence> fastalist = null;\r
+ try {\r
+ fastalist = SequenceUtil.openInputStream(file.getAbsolutePath());\r
+ assert !fastalist.isEmpty() : "Input is empty!";\r
+ } catch (IOException e) {\r
+ System.err\r
+ .println("Exception while reading the input file. "\r
+ + "Check that the input file contains a list of fasta formatted sequences! "\r
+ + "Exception details are below:");\r
+ e.printStackTrace();\r
+ } catch (UnknownFileFormatException e) {\r
+ System.err\r
+ .println("Exception while attempting to read the input file "\r
+ + "Exception details are below:");\r
+ System.out.println(e.getMessage());\r
+ e.printStackTrace();\r
+ }\r
+ return analize(fastalist, wsproxy, preset, customOptions);\r
+ }\r
+ /**\r
+ * Connects to a web service by the host and the service name web service\r
+ * type\r
* \r
- * @param <T>\r
- * web service type\r
* @param host\r
+ * the fully qualified name of JABAWS server including JABAWS\r
+ * context name e.g\r
+ * http://nanna.cluster.lifesci.dundee.ac.uk:8080/jaba\r
* @param service\r
- * @return MsaWS<T>\r
+ * the name of the JABAWS service to connect to\r
+ * @return JABAService<T>\r
* @throws WebServiceException\r
+ * @throws ConnectException\r
+ * if fails to connect to the service on the host\r
*/\r
public static JABAService connect(String host, Services service)\r
- throws WebServiceException {\r
+ throws WebServiceException, ConnectException {\r
URL url = null;\r
log.log(Level.FINE, "Attempting to connect...");\r
try {\r
}\r
Service serv = null;\r
try {\r
- serv = service.getService(url, QUALIFIED_SERVICE_NAME);\r
+ serv = service.getService(url, JABAService.SERVICE_NAMESPACE);\r
} catch (WebServiceException wse) {\r
- System.out.println("Conecting to JABAWS version 2 service");\r
+ System.out.println("Connecting to JABAWS version 2 service");\r
if (isV2service(wse)) {\r
- serv = service.getService(url, V2_QUALIFIED_SERVICE_NAME);\r
+ serv = service\r
+ .getService(url, JABAService.V2_SERVICE_NAMESPACE);\r
}\r
}\r
+ if (serv == null) {\r
+ throw new ConnectException("Could not connect to " + url\r
+ + " the server is down?");\r
+ }\r
JABAService serviceIF = service.getInterface(serv);\r
- log.log(Level.FINE, "Connected successfully!");\r
+ log.log(Level.INFO, "Connected successfully!");\r
\r
return serviceIF;\r
}\r
String message = wse.getMessage();\r
int idx = message.indexOf("not a valid service");\r
if (idx > 0) {\r
- if (message.substring(idx).contains(V2_QUALIFIED_SERVICE_NAME)) {\r
+ if (message.substring(idx).contains(\r
+ JABAService.V2_SERVICE_NAMESPACE)) {\r
return true;\r
}\r
}\r
}\r
\r
/**\r
+ * Get a connection of JABAWS registry\r
+ * \r
+ * @param host\r
+ * the fully qualified name of JABAWS server including JABAWS\r
+ * context name e.g\r
+ * http://nanna.cluster.lifesci.dundee.ac.uk:8080/jaba\r
+ * @return compbio.data.msa.RegistryWS - instance of a RegistryWS web\r
+ * service\r
+ * @throws WebServiceException\r
+ * @throws ConnectException\r
+ */\r
+ public static compbio.data.msa.RegistryWS connectToRegistry(String host)\r
+ throws WebServiceException, ConnectException {\r
+ URL url = null;\r
+ String service = "RegistryWS";\r
+ log.log(Level.FINE, "Attempting to connect...");\r
+\r
+ try {\r
+ url = new URL(host + "/" + service + "?wsdl");\r
+ } catch (MalformedURLException e) {\r
+ e.printStackTrace();\r
+ // ignore as the host name is already verified\r
+ }\r
+ QName qname = new QName(JABAService.V2_SERVICE_NAMESPACE, service);\r
+ Service serv = Service.create(url, qname);\r
+\r
+ if (serv == null) {\r
+ throw new ConnectException("Could not connect to " + url\r
+ + " the server is down?");\r
+ }\r
+\r
+ QName portName = new QName(serv.getServiceName().getNamespaceURI(),\r
+ service + "Port");\r
+ compbio.data.msa.RegistryWS serviceIF = serv.getPort(portName,\r
+ compbio.data.msa.RegistryWS.class);\r
+\r
+ log.log(Level.INFO, "Connected to " + service + " successfully!");\r
+\r
+ return serviceIF;\r
+ }\r
+\r
+ /**\r
* Align sequences from the file using MsaWS\r
* \r
* @param <T>\r
} else {\r
jobId = msaws.align(fastalist);\r
}\r
+ System.out.println("\n\ncalling align.........");\r
Thread.sleep(1000);\r
alignment = msaws.getResult(jobId);\r
\r
}\r
return alignment;\r
}\r
-\r
+ \r
+ /**\r
+ * Return RNA secondary structure from a file using FoldWS\r
+ * \r
+ * @param <T>\r
+ * web service type e.g. Clustal\r
+ * @param file\r
+ * to read the results from\r
+ * @param foldws\r
+ * FoldWS required\r
+ * @param preset\r
+ * Preset to use optional\r
+ * @param customOptions\r
+ * file which contains new line separated list of options\r
+ * @return String\r
+ */\r
+ \r
+ static <T> String fold(File file, FoldWS<T> foldws, Preset<T> preset,\r
+ List<Option<T>> customOptions) {\r
+ FileInputStream instream = null;\r
+ Alignment alignment = null;\r
+ String rnastruct = null;\r
+ try {\r
+ instream = new FileInputStream(file);\r
+ alignment = ClustalAlignmentUtil.readClustalFile(instream);\r
+ instream.close();\r
+ String jobId = null;\r
+ if (customOptions != null && preset != null) {\r
+ System.out.println("WARN: Parameters (-f) are defined together"\r
+ + "with a preset (-r), ignoring preset! ");\r
+ }\r
+ if (customOptions != null) {\r
+ jobId = foldws.customFold(alignment, customOptions);\r
+ } else if (preset != null) {\r
+ jobId = foldws.presetFold(alignment, preset);\r
+ } else {\r
+ jobId = foldws.fold(alignment);\r
+ }\r
+ System.out.println("\n\ncalling fold.........");\r
+ Thread.sleep(1000);\r
+ rnastruct = foldws.getResult(jobId);\r
+ \r
+ } catch (IOException e) {\r
+ System.err.println("Exception while reading the input file. Exception details: ");\r
+ e.printStackTrace();\r
+ } catch (UnknownFileFormatException e) {\r
+ System.err.println("Exception while reading input file. Doesnt look like a Clustal format file");\r
+ e.printStackTrace();\r
+ } catch (JobSubmissionException e) {\r
+ System.err.println("Exception while submitting job to the web server. ");\r
+ e.printStackTrace();\r
+ } catch (ResultNotAvailableException e) {\r
+ System.err.println("Exception while waiting for results. Exception details: ");\r
+ e.printStackTrace();\r
+ } catch (InterruptedException ignored) {\r
+ // ignore and propagate an interruption\r
+ Thread.currentThread().interrupt();\r
+ } catch (WrongParameterException e) {\r
+ e.printStackTrace();\r
+ } finally {\r
+ if (instream != null) {\r
+ try {\r
+ instream.close();\r
+ } catch (IOException ignored) {\r
+ // ignore\r
+ }\r
+ }\r
+ }\r
+ return rnastruct;\r
+ }\r
+ \r
/**\r
* Prints Jws2Client usage information to standard out\r
* \r
* @param exitStatus\r
*/\r
static void printUsage(int exitStatus) {\r
- System.out.println();\r
- System.out.println("Usage: <Class or Jar file name> " + hostkey\r
- + pseparator + "host_and_context " + servicekey + pseparator\r
- + "serviceName ACTION [OPTIONS] ");\r
- System.out.println();\r
- System.out\r
- .println(hostkey\r
- + pseparator\r
- + "<host_and_context> - a full URL to the JWS2 web server including context path e.g. http://10.31.1.159:8080/ws");\r
- System.out.println(servicekey + pseparator + "<ServiceName> - one of "\r
- + Arrays.toString(Services.values()));\r
- System.out.println();\r
- System.out.println("ACTIONS: ");\r
- System.out\r
- .println(inputkey\r
- + pseparator\r
- + "<inputFile> - full path to fasta formatted sequence file, from which to align sequences");\r
- System.out.println(paramList\r
- + " - lists parameters supported by web service");\r
- System.out.println(presetList\r
- + " - lists presets supported by web service");\r
- System.out.println(limitList + " - lists web services limits");\r
- System.out\r
- .println("Please note that if input file is specified other actions are ignored");\r
-\r
- System.out.println();\r
- System.out.println("OPTIONS (only for use with -i action):");\r
-\r
- System.out.println(presetkey + pseparator\r
- + "<presetName> - name of the preset to use");\r
- System.out\r
- .println(outputkey\r
- + pseparator\r
- + "<outputFile> - full path to the file where to write an alignment");\r
- System.out\r
- .println("-f=<parameterInputFile> - the name of the file with the list of parameters to use.");\r
- System.out\r
- .println("Please note that -r and -f options cannot be used together. "\r
- + "Alignment is done with either preset or a parameters from the file, but not both!");\r
-\r
+ System.out.println(Constraints.help_text);\r
System.exit(exitStatus);\r
}\r
\r
/**\r
* Starts command line client, if no parameter are supported print help. Two\r
- * parameters are required for successfull call the JWS2 host name and a\r
+ * parameters are required for successful call the JWS2 host name and a\r
* service name.\r
* \r
* @param args\r
printUsage(1);\r
}\r
if (args.length < 2) {\r
- System.out.println("Host and service names are required!");\r
+ System.err.println("Host and service names are required!");\r
printUsage(1);\r
}\r
\r
git://source.jalview.org / jabaws.git / blobdiff