-/* 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 java.io.BufferedReader;\r
+import static compbio.ws.client.Constraints.inputkey;\r
+import static compbio.ws.client.Constraints.outputkey;\r
+import static compbio.ws.client.Constraints.paramFile;\r
+\r
import java.io.Closeable;\r
import java.io.File;\r
import java.io.FileInputStream;\r
-import java.io.FileNotFoundException;\r
import java.io.FileOutputStream;\r
-import java.io.FileReader;\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.ArrayList;\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.ws.Service;\r
import javax.xml.ws.WebServiceException;\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.ClustalAlignmentUtil;\r
+import compbio.data.sequence.AlignmentMetadata;\r
+import compbio.data.sequence.JpredAlignment;\r
import compbio.data.sequence.FastaSequence;\r
+import compbio.data.sequence.ScoreManager;\r
import compbio.data.sequence.SequenceUtil;\r
+import compbio.data.sequence.UnknownFileFormatException;\r
import compbio.metadata.JobSubmissionException;\r
-import compbio.metadata.Limit;\r
-import compbio.metadata.LimitsManager;\r
+import compbio.metadata.JobStatus;\r
import compbio.metadata.Option;\r
+import compbio.metadata.Limit;\r
import compbio.metadata.Preset;\r
import compbio.metadata.PresetManager;\r
import compbio.metadata.ResultNotAvailableException;\r
-import compbio.metadata.RunnerConfig;\r
import compbio.metadata.WrongParameterException;\r
+import compbio.util.FileUtil;\r
\r
/**\r
* A command line client for JAva Bioinformatics Analysis Web Services\r
*/\r
public class Jws2Client {\r
\r
- /*\r
- * Use java.util.Logger instead of log4j logger to reduce the size of the\r
- * client package\r
- */\r
- private static final Logger log = Logger.getLogger(Jws2Client.class\r
- .getCanonicalName());\r
-\r
- final static String pseparator = "=";\r
-\r
- // Parameters for required command line options\r
- final static String hostkey = "-h";\r
- final static String servicekey = "-s";\r
-\r
- // Actions\r
- final static String inputkey = "-i";\r
-\r
- final static String paramList = "-parameters";\r
- final static String presetList = "-presets";\r
- final static String limitList = "-limits";\r
-\r
- // Options\r
- final static String paramFile = "-f";\r
- final static String outputkey = "-o";\r
- final static String parameterkey = "-p";\r
- final static String presetkey = "-r";\r
-\r
- //JABAWS version 1.0 service name\r
- static final String qualifiedServiceName = "http://msa.data.compbio/01/01/2010/";\r
-\r
- /**\r
- * Searches the command line keys in the array of parameters\r
- * \r
- * @param cmd\r
- * command line options\r
- * @return true is the list of Parameters is requested, false otherwise\r
- */\r
- private boolean listParameters(String[] cmd) {\r
- return keyFound(cmd, paramList);\r
- }\r
-\r
- /**\r
- * Check whether presetList is set in the command line\r
- * \r
- * @param cmd\r
- * command line options\r
- * @return true if presetList is found, false otherwise\r
- */\r
- boolean listPresets(String[] cmd) {\r
- return keyFound(cmd, presetList);\r
- }\r
-\r
- /**\r
- * Returns {@code Preset} by its name\r
- * \r
- * @see Preset\r
- * @param <T>\r
- * @param msaws\r
- * @param presetName\r
- * @return Return a Preset by its optionName\r
- */\r
- <T> Preset<T> getPreset(MsaWS<T> msaws, String presetName) {\r
- assert presetName != null;\r
- PresetManager<T> presets = getPresetList(msaws);\r
- if (presets == null) {\r
- System.out\r
- .println("No presets are supported by the service! Ignoring -r directive!");\r
- return null;\r
- }\r
- Preset<T> pre = presets.getPresetByName(presetName);\r
- if (pre == null) {\r
- System.out.println("Cannot find preset: " + presetName\r
- + " WARN: ignoring -r directive!");\r
- }\r
- return pre;\r
- }\r
-\r
- /**\r
- * Extracts preset name from the command line is any\r
- * \r
- * @param cmd\r
- * command line options\r
- * @return presetName or null if no presets is defined\r
- */\r
- String getPresetName(String[] cmd) {\r
- String preset = null;\r
- for (int i = 0; i < cmd.length; i++) {\r
- String presetPrm = cmd[i];\r
- if (presetPrm.trim().toLowerCase().startsWith(\r
- presetkey + pseparator)) {\r
- preset = presetPrm.substring(presetPrm.indexOf(pseparator) + 1);\r
- break;\r
- }\r
- }\r
- return preset;\r
- }\r
-\r
- /**\r
- * Checks whether limitList parameter is in the command line\r
- * \r
- * @param cmd\r
- * - command line options\r
- * @return true if it is, false otherwise\r
- */\r
- boolean listLimits(String[] cmd) {\r
- return keyFound(cmd, limitList);\r
- }\r
-\r
- /**\r
- * Checks whether the key is in the command line\r
- * \r
- * @param cmd\r
- * @param key\r
- * @return true if it is, false otherwise\r
- */\r
- boolean keyFound(String[] cmd, String key) {\r
- assert cmd != null && cmd.length > 0;\r
- assert key != null;\r
- for (int i = 0; i < cmd.length; i++) {\r
- String listPresets = cmd[i];\r
- if (listPresets.trim().equalsIgnoreCase(key)) {\r
+ /**\r
+ * Use java.util.Logger instead of log4j logger to reduce the size of the client package\r
+ */\r
+ private static final Logger log = Logger.getLogger(Jws2Client.class.getCanonicalName());\r
+\r
+ /**\r
+ * Attempt to construct the URL object from the string\r
+ * \r
+ * @param urlstr\r
+ * @return true if it succeed false otherwise\r
+ */\r
+ public static boolean validURL(String urlstr) {\r
+ try {\r
+ if (urlstr == null || urlstr.trim().length() == 0) {\r
+ return false;\r
+ }\r
+ new URL(urlstr);\r
+ } catch (MalformedURLException e) {\r
+ return false;\r
+ }\r
return true;\r
- }\r
- }\r
- return false;\r
- }\r
-\r
- /**\r
- * Attempt to construct the URL object from the string\r
- * \r
- * @param urlstr\r
- * @return true if it succeed false otherwise\r
- */\r
- public static boolean validURL(String urlstr) {\r
- try {\r
- if (urlstr == null || urlstr.trim().length() == 0) {\r
- return false;\r
- }\r
- new URL(urlstr);\r
- } catch (MalformedURLException e) {\r
- return false;\r
}\r
- return true;\r
- }\r
-\r
- /**\r
- * Extracts service name from the command line\r
- * \r
- * @param cmd\r
- * command line options\r
- * @return service name or null if it is not defined\r
- */\r
- public static String getServiceName(String[] cmd) {\r
- for (int i = 0; i < cmd.length; i++) {\r
- String serv = cmd[i];\r
- if (serv.trim().toLowerCase().startsWith(servicekey + pseparator)) {\r
- return serv.substring(serv.indexOf(pseparator) + 1);\r
- }\r
- }\r
- return null;\r
- }\r
-\r
- /**\r
- * Extracts host name from the command line\r
- * \r
- * @param cmd\r
- * command line options\r
- * @return host name or null if it is not defined\r
- */\r
- public static String getHost(String[] cmd) {\r
- for (int i = 0; i < cmd.length; i++) {\r
- String host = cmd[i];\r
- if (host.trim().toLowerCase().startsWith(hostkey + pseparator)) {\r
- return host.substring(host.indexOf(pseparator) + 1);\r
- }\r
- }\r
- return null;\r
- }\r
-\r
- /**\r
- * Checks -i options and return the File if one was provided, null otherwise\r
- * \r
- * @param cmd\r
- * @param key\r
- * @param mustExist\r
- * @return\r
- * @throws IOException\r
- */\r
- File getFile(String[] cmd, String key, boolean mustExist)\r
- throws IOException {\r
- assert key != null && key.trim().length() != 0;\r
- for (int i = 0; i < cmd.length; i++) {\r
- String filename = cmd[i];\r
- filename = filename.trim();\r
- if (filename.toLowerCase().startsWith(key + pseparator)) {\r
- filename = filename.substring((key + pseparator).length());\r
- File file = new File(filename);\r
- if (mustExist && !file.exists()) {\r
- System.out.println(key + " file " + file.getAbsolutePath()\r
- + " does not exist");\r
- return null;\r
+\r
+ /**\r
+ * Connects to the service and do the job as requested, if something goes\r
+ * wrong reports or/and prints usage help.\r
+ * \r
+ * @param <T>\r
+ * web service type\r
+ * @param cmd\r
+ * command line options\r
+ * @throws IOException\r
+ */\r
+ @SuppressWarnings("unchecked")\r
+ <T> Jws2Client(String[] cmd) throws IOException {\r
+ \r
+\r
+ String hostname = CmdHelper.getHost(cmd);\r
+ if (hostname == null) {\r
+ System.err.println("Host name is not provided!");\r
+ System.out.println(Constraints.help_text);\r
+ System.exit(1);\r
}\r
- if (!mustExist && !file.exists()) {\r
- file.createNewFile();\r
+\r
+ if (!validURL(hostname)) {\r
+ System.err.println("Host name is not valid!");\r
+ System.out.println(Constraints.help_text);\r
+ System.exit(1);\r
}\r
- if (!file.canRead()) {\r
- System.out.println("Cannot read " + key + " file "\r
- + file.getAbsolutePath());\r
- return null;\r
+\r
+ boolean listServices = CmdHelper.listServices(cmd);\r
+ if (listServices) {\r
+ listAllServices(hostname);\r
+ System.exit(0);\r
}\r
- return file;\r
- }\r
- }\r
- return null;\r
- }\r
-\r
- /**\r
- * Connects to the service and do the job as requested, if something goes\r
- * wrong reports or/and prints usage help.\r
- * \r
- * @param <T>\r
- * web service type\r
- * @param cmd\r
- * command line options\r
- * @throws IOException\r
- */\r
- <T> Jws2Client(String[] cmd) throws IOException {\r
-\r
- String hostname = getHost(cmd);\r
- if (hostname == null) {\r
- System.out.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
- printUsage(1);\r
- }\r
- String serviceName = getServiceName(cmd);\r
- if (serviceName == null) {\r
- System.out.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
- + Arrays.toString(Services.values()));\r
- printUsage(1);\r
- }\r
- File inputFile = getFile(cmd, inputkey, true);\r
- File outFile = getFile(cmd, outputkey, false);\r
- File parametersFile = getFile(cmd, paramFile, true);\r
- String presetName = getPresetName(cmd);\r
-\r
- MsaWS<T> msaws = connect(hostname, service);\r
- Preset<T> preset = null;\r
- if (presetName != null) {\r
- preset = getPreset(msaws, presetName);\r
- }\r
- List<Option<T>> customOptions = null;\r
- if (parametersFile != null) {\r
- List<String> prms = loadParameters(parametersFile);\r
- customOptions = processParameters(prms, msaws.getRunnerOptions());\r
- }\r
- Alignment alignment = null;\r
- if (inputFile != null) {\r
- alignment = align(inputFile, msaws, preset, customOptions);\r
- OutputStream outStream = null;\r
- if (outFile != null) {\r
- outStream = 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
- writeOut(outStream, alignment);\r
- // stream is closed in the method no need to close it here\r
+ String serviceName = CmdHelper.getServiceName(cmd);\r
+ if (serviceName == null) {\r
+ System.err.println("Service name is no provided!");\r
+ System.out.println(Constraints.help_text);\r
+ System.exit(1);\r
+ }\r
+\r
+ Services service = Services.getService(serviceName);\r
+ if (service == null) {\r
+ String mess = "Service " + serviceName + " is no available! Valid values are: ";\r
+ System.err.println(mess + Arrays.toString(Services.values()));\r
+ System.out.println(Constraints.help_text);\r
+ System.exit(1);\r
+ }\r
+\r
+ if (CmdHelper.testService(cmd)) {\r
+ testService(hostname, service, new PrintWriter(System.out, true));\r
+ System.exit(0);\r
+ }\r
+\r
+ Metadata<T> thews = (Metadata<T>) connect(hostname, service);\r
+ Preset<T> preset = null;\r
+ if (null != CmdHelper.getPresetName(cmd)) {\r
+ preset = MetadataHelper.getPreset(thews, CmdHelper.getPresetName(cmd));\r
+ }\r
+\r
+ List<Option<T>> customOptions = null;\r
+ if (null != IOHelper.getFile(cmd, paramFile, true)) {\r
+ List<String> prms = IOHelper.loadParameters(IOHelper.getFile(cmd, paramFile, true));\r
+ customOptions = MetadataHelper.processParameters(prms, thews.getRunnerOptions());\r
+ }\r
+\r
+ if (null != IOHelper.getFile(cmd, inputkey, true)) {\r
+ File infile = IOHelper.getFile(cmd, inputkey, true);\r
+ File outfile = IOHelper.getFile(cmd, outputkey, false);\r
+ Writer writer = null;\r
+ if (outfile != null) {\r
+ writer = IOHelper.getWriter(outfile);\r
+ } else {\r
+ writer = new PrintWriter(System.out, true);\r
+ }\r
+ if (service.getServiceType() == SequenceAnnotation.class) {\r
+ ScoreManager result = analize(infile, ((SequenceAnnotation<T>) thews), preset, customOptions);\r
+ IOHelper.writeOut(writer, result);\r
+ writer.close();\r
+ } else if (service.getServiceType() == MsaWS.class) {\r
+ Alignment alignment = align(infile, (MsaWS<T>) thews, preset, customOptions);\r
+ if (serviceName.equalsIgnoreCase("JpredWS")) {\r
+ writer.close();\r
+ JpredAlignment jpred = (JpredAlignment)alignment;\r
+ if (outfile != null) {\r
+ FileOutputStream fout = new FileOutputStream(outfile);\r
+ SequenceUtil.writeFastaKeepTheStream(fout, jpred.getJpredSequences(), 60);\r
+ fout.close();\r
+ } else {\r
+ SequenceUtil.writeFasta(System.out, jpred.getJpredSequences());\r
+ }\r
+ } else {\r
+ IOHelper.writeOut(writer, alignment);\r
+ writer.close();\r
+ }\r
+ AlignmentMetadata md = alignment.getMetadata();\r
+ System.out.println("Output has been prepared with " + md.getProgram());\r
+ }\r
+ }\r
+\r
+ if (CmdHelper.listParameters(cmd)) {\r
+ List<Option<T>> opts = MetadataHelper.getParametersList(thews, hostname);\r
+ for (Option<T> o : opts) {\r
+ System.out.println("##############################################################################\n" + o.toString());\r
+ }\r
+ }\r
+ if (CmdHelper.listPresets(cmd)) {\r
+ PresetManager<T> psm = MetadataHelper.getPresetList(thews);\r
+ if (null != psm) {\r
+ System.out.print(psm);\r
+ } else {\r
+ System.out.println("No presets are defined for the Web service");\r
+ }\r
+ }\r
+ if (CmdHelper.listLimits(cmd)) {\r
+ List<Limit<T>> lims = MetadataHelper.getLimits(thews);\r
+ for (Limit<T> l : lims) {\r
+ System.out.println("##############################################################################\n" + l.toString());\r
+ }\r
+ }\r
+ log.fine("Disconnecting...");\r
+ ((Closeable) thews).close();\r
+ log.fine("Disconnected successfully!");\r
}\r
\r
- boolean listParameters = listParameters(cmd);\r
- if (listParameters) {\r
- System.out.println(getParametersList(msaws));\r
+ /**\r
+ * Connects to a web service by the host and the service name web service type\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
+ * @param service\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, ConnectException {\r
+ URL url = null;\r
+ log.log(Level.FINE, "Attempting to connect with " + service.toString() + "...");\r
+ System.out.println ("Attempting to connect with " + service.toString() + "...");\r
+ try {\r
+ url = new URL(host + "/" + service.toString() + "?wsdl");\r
+ } catch (MalformedURLException e) {\r
+ e.printStackTrace();\r
+ // ignore as the host name is already verified\r
+ }\r
+ Service serv = null;\r
+ try {\r
+ serv = service.getService(url, service.getServiceNamespace());\r
+ } catch (WebServiceException wse) {\r
+ wse.printStackTrace();\r
+ }\r
+ if (serv == null) {\r
+ throw new ConnectException("Could not connect to " + url + ". Is the server down?");\r
+ }\r
+ JABAService serviceIF = service.getInterface(serv);\r
+ log.log(Level.INFO, "Connected successfully!");\r
+\r
+ return serviceIF;\r
}\r
- boolean listPreset = listPresets(cmd);\r
- if (listPreset) {\r
- System.out.println(getPresetList(msaws));\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 + ". Is the server down?");\r
+ }\r
+\r
+ QName portName = new QName(serv.getServiceName().getNamespaceURI(), service + "Port");\r
+ compbio.data.msa.RegistryWS serviceIF = serv.getPort(portName, compbio.data.msa.RegistryWS.class);\r
+ log.log(Level.INFO, "Connected to " + service + " successfully!");\r
+\r
+ return serviceIF;\r
}\r
- boolean listLimits = listLimits(cmd);\r
- if (listLimits) {\r
- System.out.println(getLimits(msaws));\r
+\r
+ /**\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, PrintWriter writer)\r
+ 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
- log.fine("Disconnecting...");\r
- ((Closeable) msaws).close();\r
- log.fine("Disconnected successfully!");\r
- }\r
-\r
- /**\r
- * Load parameters from file\r
- * \r
- * @throws IOException\r
- */\r
- List<String> loadParameters(File paramsfile) throws IOException {\r
- assert paramsfile != null && paramsfile.exists();\r
- BufferedReader reader = new BufferedReader(new FileReader(paramsfile));\r
- String line = null;\r
- ArrayList<String> params = new ArrayList<String>();\r
- while ((line = reader.readLine()) != null) {\r
- line = line.trim();\r
- if (line.length() == 0)\r
- continue;\r
- params.add(line);\r
+\r
+ private static void listAllServices(String hostname) throws WebServiceException, IOException {\r
+ RegistryWS registry = connectToRegistry(hostname);\r
+ Set<Services> func_services = Collections.emptySet();\r
+ //Set<Services> nonfunc_services = Collections.emptySet();\r
+ if (registry != null) {\r
+ func_services = registry.getSupportedServices();\r
+ //nonfunc_services = registry.getNonoperatedServices();\r
+ FileUtil.closeSilently(((Closeable) registry));\r
+ } else {\r
+ System.out.println("Failed to connect to the registry! ");\r
+ return;\r
+ }\r
+ if (!func_services.isEmpty()) {\r
+ System.out.println("There are " + func_services.size() + " services at " + hostname + ":");\r
+ String mess = "\n\rThe list:\n";\r
+ System.out.println(mess + Services.toString(func_services));\r
+ }\r
+ /*\r
+ if (!nonfunc_services.isEmpty()) {\r
+ System.out.println("There are " + nonfunc_services.size() + " non-available services at " + hostname + ":");\r
+ String mess = "The list (internal tests failed): ";\r
+ System.out.println(mess + Services.toString(nonfunc_services));\r
+ }\r
+ */\r
}\r
- return params;\r
- }\r
-\r
- /**\r
- * Converts options supplied via parameters file into {@code Option} objects\r
- * \r
- * @param <T>\r
- * web service type\r
- * @param params\r
- * @param options\r
- * @return List of Options of type T\r
- */\r
- <T> List<Option<T>> processParameters(List<String> params,\r
- RunnerConfig<T> options) {\r
- List<Option<T>> chosenOptions = new ArrayList<Option<T>>();\r
- for (String param : params) {\r
- String oname = null;\r
- if (isParameter(param)) {\r
- oname = this.getParamName(param);\r
- } else {\r
- oname = param;\r
- }\r
- Option<T> o = options.getArgumentByOptionName(oname);\r
- if (o == null) {\r
- System.out.println("WARN ignoring unsuppoted parameter: "\r
- + oname);\r
- continue;\r
- }\r
- if (isParameter(param)) {\r
+\r
+ /**\r
+ * Calculate conservation for sequences loaded from a FASTA record list structure \r
+ * \r
+ * @param fastalist\r
+ * the list of FASTA records\r
+ * @param wsproxy\r
+ * a web service proxy\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, SequenceAnnotation<T> wsproxy, Preset<T> preset, List<Option<T>> customOptions) {\r
+ ScoreManager scores = null;\r
try {\r
- o.setValue(getParamValue(param));\r
+ String jobId = null;\r
+ if (customOptions != null && preset != null) {\r
+ System.out.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\rcalling predictor.........");\r
+ Thread.sleep(100);\r
+ JobStatus status = wsproxy.getJobStatus(jobId);\r
+ System.out.println("\njob " + jobId + " status: " + status);\r
+ scores = wsproxy.getAnnotation(jobId);\r
+ } catch (JobSubmissionException e) {\r
+ System.err.println("Exception while submitting job to a web server. Exception details are below:");\r
+ e.printStackTrace();\r
+ } catch (ResultNotAvailableException e) {\r
+ System.err.println("Exception while waiting for results. Exception details are below:");\r
+ e.printStackTrace();\r
+ } catch (InterruptedException e) {\r
+ Thread.currentThread().interrupt();\r
+ System.err.println("Exception while waiting for results. Exception details are below:");\r
+ e.printStackTrace();\r
} catch (WrongParameterException e) {\r
- System.out\r
- .println("Problem setting value for the parameter: "\r
- + param);\r
- e.printStackTrace();\r
+ String mess = "Parsing the web method input parameters failed Exception details are below:";\r
+ System.err.println(mess);\r
+ e.printStackTrace();\r
}\r
- }\r
- chosenOptions.add(o);\r
- }\r
- return chosenOptions;\r
- }\r
-\r
- String getParamName(String fullName) {\r
- assert isParameter(fullName);\r
- return fullName.substring(0, fullName.indexOf(pseparator));\r
- }\r
-\r
- String getParamValue(String fullName) {\r
- assert isParameter(fullName);\r
- return fullName.substring(fullName.indexOf(pseparator) + 1);\r
- }\r
-\r
- boolean isParameter(String param) {\r
- return param.contains(pseparator);\r
- }\r
-\r
- OutputStream getOutStream(File file) {\r
- assert file != null && file.exists();\r
- try {\r
- return new FileOutputStream(file);\r
- } catch (FileNotFoundException e) {\r
- e.printStackTrace();\r
+ return scores;\r
+\r
}\r
- return null;\r
- }\r
-\r
- /**\r
- * Outputs clustal formatted alignment into the file represented by the\r
- * outStream\r
- * \r
- * @param outStream\r
- * @param align\r
- * the alignment to output\r
- */\r
- void writeOut(OutputStream outStream, Alignment align) {\r
- try {\r
- ClustalAlignmentUtil.writeClustalAlignment(outStream, align);\r
- } catch (IOException e) {\r
- System.err\r
- .println("Problems writing output file! Stack trace is below: ");\r
- e.printStackTrace();\r
- } finally {\r
- if (outStream != null) {\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, Preset<T> preset, List<Option<T>> customOptions) {\r
+ List<FastaSequence> fastalist = null;\r
try {\r
- outStream.close();\r
- } catch (IOException ignored) {\r
- // e.printStackTrace();\r
+ fastalist = SequenceUtil.openInputStream(file.getAbsolutePath());\r
+ assert !fastalist.isEmpty() : "Input is empty!";\r
+ } catch (IOException e) {\r
+ String mess = "Reading the input file failed. Check that the file contains a list of FASTA records!\n";\r
+ System.err.println(mess + "Exception details are below:");\r
+ e.printStackTrace();\r
+ } catch (UnknownFileFormatException e) {\r
+ String mess = "Reading the input file failed. Exception details are below:";\r
+ System.err.println(mess);\r
+ System.out.println(e.getMessage());\r
+ e.printStackTrace();\r
}\r
- }\r
+ return analize(fastalist, wsproxy, preset, customOptions);\r
}\r
- }\r
-\r
- /**\r
- * Connects to a web service by the host and the service name\r
- * \r
- * @param <T>\r
- * web service type\r
- * @param host\r
- * @param service\r
- * @return MsaWS<T>\r
- * @throws WebServiceException\r
- */\r
- public static <T> MsaWS<T> connect(String host, Services service)\r
- throws WebServiceException {\r
- URL url = null;\r
- log.log(Level.FINE, "Attempt to connect...");\r
- try {\r
- url = new URL(host + "/" + service.toString() + "?wsdl");\r
- } catch (MalformedURLException e) {\r
- e.printStackTrace();\r
- // ignore as the host name is already verified\r
- }\r
- QName qname = new QName(qualifiedServiceName, service.toString());\r
- Service serv = Service.create(url, qname);\r
- MsaWS<T> msaws = serv.getPort(new QName(qualifiedServiceName, service\r
- + "Port"), MsaWS.class);\r
- log.log(Level.FINE, "Connected successfully!");\r
- return msaws;\r
- }\r
-\r
- /**\r
- * Align sequences from the file using MsaWS\r
- * \r
- * @param <T>\r
- * web service type e.g. Clustal\r
- * @param file\r
- * to write the resulting alignment to\r
- * @param msaws\r
- * MsaWS required\r
- * @param preset\r
- * Preset to use optional\r
- * @param customOptions\r
- * file which contains new line separated list of options\r
- * @return Alignment\r
- */\r
- static <T> Alignment align(File file, MsaWS<T> msaws, Preset<T> preset,\r
- List<Option<T>> customOptions) {\r
- FileInputStream instream = null;\r
- List<FastaSequence> fastalist = null;\r
- Alignment alignment = null;\r
- try {\r
- instream = new FileInputStream(file);\r
- fastalist = SequenceUtil.readFasta(instream);\r
- instream.close();\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 = msaws.customAlign(fastalist, customOptions);\r
- } else if (preset != null) {\r
- jobId = msaws.presetAlign(fastalist, preset);\r
- } else {\r
- jobId = msaws.align(fastalist);\r
- }\r
- Thread.sleep(1000);\r
- alignment = msaws.getResult(jobId);\r
-\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 (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 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
+\r
+ /**\r
+ * Align sequences from the file using MsaWS\r
+ * \r
+ * @param <T>\r
+ * web service type e.g. Clustal\r
+ * @param file\r
+ * to write the resulting alignment to\r
+ * @param msaws\r
+ * MsaWS required\r
+ * @param preset\r
+ * Preset to use optional\r
+ * @param customOptions\r
+ * file which contains new line separated list of options\r
+ * @return Alignment\r
+ */\r
+ static <T> Alignment align(File file, MsaWS<T> msaws, Preset<T> preset,\r
+ List<Option<T>> customOptions) {\r
+ FileInputStream instream = null;\r
+ Alignment alignment = null;\r
try {\r
- instream.close();\r
- } catch (IOException ignored) {\r
- // ignore\r
+ instream = new FileInputStream(file);\r
+ List<FastaSequence> fastalist = SequenceUtil.readFasta(instream);\r
+ instream.close();\r
+ String jobId = null;\r
+ if (customOptions != null && preset != null) {\r
+ System.out.println("WARN: Parameters (-f) are defined together with a preset (-r) ignoring preset!");\r
+ }\r
+ if (customOptions != null) {\r
+ jobId = msaws.customAlign(fastalist, customOptions);\r
+ } else if (preset != null) {\r
+ jobId = msaws.presetAlign(fastalist, preset);\r
+ } else {\r
+ jobId = msaws.align(fastalist);\r
+ }\r
+ System.out.println("\ncalling program.........");\r
+ long startTime = System.nanoTime();\r
+ while (JobStatus.RUNNING == msaws.getJobStatus(jobId)) {\r
+ Thread.sleep(1000);\r
+ long endTime = System.nanoTime();\r
+ System.out.println("job " + jobId + " time executing: "+ (endTime - startTime) / 1000000 +" msec, status: " + msaws.getJobStatus(jobId));\r
+ }\r
+ alignment = msaws.getResult(jobId);\r
+ } catch (IOException e) {\r
+ System.err.println("Exception while reading the input file. Check that the input file is a FASTA file! "\r
+ + "Exception details are below:");\r
+ e.printStackTrace();\r
+ } catch (JobSubmissionException e) {\r
+ System.err.println("Exception while submitting job to a web server. Exception details are below:");\r
+ e.printStackTrace();\r
+ } catch (ResultNotAvailableException e) {\r
+ System.err.println("Exception while waiting for results. Exception details are below:");\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
- }\r
- }\r
- return alignment;\r
- }\r
-\r
- /**\r
- * Returns a list of options supported by web service\r
- * \r
- * @param <T>\r
- * web service type\r
- * @param msaws\r
- * web service proxy\r
- * @return List of options supported by a web service\r
- */\r
- <T> List<Option<T>> getParametersList(MsaWS<T> msaws) {\r
- assert msaws != null;\r
- return msaws.getRunnerOptions().getArguments();\r
- }\r
-\r
- /**\r
- * Returns an objects from which the list of presets supported by web\r
- * service <T> can be obtained\r
- * \r
- * @param <T>\r
- * web service type\r
- * @param msaws\r
- * web service proxy\r
- * @return PresetManager, object which operates on presets\r
- */\r
- <T> PresetManager<T> getPresetList(MsaWS<T> msaws) {\r
- assert msaws != null;\r
- PresetManager<T> presetman = msaws.getPresets();\r
- return presetman;\r
- }\r
-\r
- /**\r
- * Returns a list of limits supported by web service Each limit correspond\r
- * to a particular preset.\r
- * \r
- * @param <T>\r
- * web service type\r
- * @param msaws\r
- * web service proxy\r
- * @return List of limits supported by a web service\r
- */\r
- <T> List<Limit<T>> getLimits(MsaWS<T> msaws) {\r
- assert msaws != null;\r
- LimitsManager<T> lmanger = msaws.getLimits();\r
-\r
- return lmanger != null ? lmanger.getLimits() : null;\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.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
- * service name.\r
- * \r
- * @param args\r
- * Usage: <Class or Jar file name> -h=host_and_context\r
- * -s=serviceName ACTION [OPTIONS]\r
- * \r
- * -h=<host_and_context> - a full URL to the JWS2 web server\r
- * including context path e.g. http://10.31.1.159:8080/ws\r
- * \r
- * -s=<ServiceName> - one of [MafftWS, MuscleWS, ClustalWS,\r
- * TcoffeeWS, ProbconsWS] ACTIONS:\r
- * \r
- * -i=<inputFile> - full path to fasta formatted sequence file,\r
- * from which to align sequences\r
- * \r
- * -parameters - lists parameters supported by web service\r
- * \r
- * -presets - lists presets supported by web service\r
- * \r
- * -limits - lists web services limits Please note that if input\r
- * file is specified other actions are ignored\r
- * \r
- * OPTIONS: (only for use with -i action):\r
- * \r
- * -r=<presetName> - name of the preset to use\r
- * \r
- * -o=<outputFile> - full path to the file where to write an\r
- * alignment -f=<parameterInputFile> - the name of the file with\r
- * the list of parameters to use. Please note that -r and -f\r
- * options cannot be used together. Alignment is done with either\r
- * preset or a parameters from the file, but not both!\r
- * \r
- */\r
- public static void main(String[] args) {\r
-\r
- if (args == null) {\r
- printUsage(1);\r
+ return alignment;\r
}\r
- if (args.length < 2) {\r
- System.out.println("Host and service names are required!");\r
- printUsage(1);\r
- }\r
-\r
- try {\r
- new Jws2Client(args);\r
- } catch (IOException e) {\r
- log.log(Level.SEVERE, "IOException in client! " + e.getMessage(), e\r
- .getCause());\r
- System.err.println("Cannot write output file! Stack trace: ");\r
- e.printStackTrace();\r
+ \r
+ /**\r
+ * Starts command line client, if no parameter are supported print help. Two\r
+ * parameters are required for successful call the JWS2 host name and a\r
+ * service name.\r
+ * \r
+ * @param args\r
+ * Usage: <Class or Jar file name> -h=host_and_context\r
+ * -s=serviceName ACTION [OPTIONS]\r
+ * \r
+ * -h=<host_and_context> - a full URL to the JWS2 web server\r
+ * including context path e.g. http://10.31.1.159:8080/ws\r
+ * \r
+ * -s=<ServiceName> - one of [MafftWS, MuscleWS, ClustalWS,\r
+ * TcoffeeWS, ProbconsWS] ACTIONS:\r
+ * \r
+ * -i=<inputFile> - full path to fasta formatted sequence file,\r
+ * from which to align sequences\r
+ * \r
+ * -parameters - lists parameters supported by web service\r
+ * \r
+ * -presets - lists presets supported by web service\r
+ * \r
+ * -limits - lists web services limits Please note that if input\r
+ * file is specified other actions are ignored\r
+ * \r
+ * OPTIONS: (only for use with -i action):\r
+ * \r
+ * -r=<presetName> - name of the preset to use\r
+ * \r
+ * -o=<outputFile> - full path to the file where to write an\r
+ * alignment -f=<parameterInputFile> - the name of the file with\r
+ * the list of parameters to use. Please note that -r and -f\r
+ * options cannot be used together. Alignment is done with either\r
+ * preset or a parameters from the file, but not both!\r
+ * \r
+ */\r
+ public static void main(String[] args) {\r
+ if (args == null) {\r
+ System.out.println(Constraints.help_text);\r
+ System.exit(1);\r
+ }\r
+ if (args.length < 2) {\r
+ System.err.println("Host (-h=<host>, e.g. -h=http://www.compbio.dundee.ac.uk/jabaws) and service (-s=<ServiceName>, e.g. -s=Jpred) are required!");\r
+ System.out.println(Constraints.help_text);\r
+ System.exit(1);\r
+ }\r
+ try {\r
+ new Jws2Client(args);\r
+ } catch (IOException e) {\r
+ log.log(Level.SEVERE, "IOException in client! " + e.getMessage(), e.getCause());\r
+ System.err.println("Cannot write output file! Stack trace: ");\r
+ e.printStackTrace();\r
+ }\r
}\r
- }\r
}\r
git://source.jalview.org / jabaws.git / blobdiff