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/* Copyright (c) 2009 Peter Troshin
*
* JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0
*
* This library is free software; you can redistribute it and/or modify it under the terms of the
* Apache License version 2 as published by the Apache Software Foundation
*
* This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without
* even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache
* License for more details.
*
* A copy of the license is in apache_license.txt. It is also available here:
* @see: http://www.apache.org/licenses/LICENSE-2.0.txt
*
* Any republication or derived work distributed in source code form
* must include this copyright and license notice.
*/
package compbio.ws.client;
import java.io.BufferedReader;
import java.io.Closeable;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.FileReader;
import java.io.IOException;
import java.io.OutputStream;
import java.net.MalformedURLException;
import java.net.URL;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.logging.Level;
import java.util.logging.Logger;
import javax.xml.namespace.QName;
import javax.xml.ws.Service;
import javax.xml.ws.WebServiceException;
import compbio.data.msa.MsaWS;
import compbio.data.sequence.Alignment;
import compbio.data.sequence.ClustalAlignmentUtil;
import compbio.data.sequence.FastaSequence;
import compbio.data.sequence.SequenceUtil;
import compbio.metadata.JobSubmissionException;
import compbio.metadata.Limit;
import compbio.metadata.LimitsManager;
import compbio.metadata.Option;
import compbio.metadata.Preset;
import compbio.metadata.PresetManager;
import compbio.metadata.ResultNotAvailableException;
import compbio.metadata.RunnerConfig;
import compbio.metadata.WrongParameterException;
/**
* A command line client for JAva Bioinformatics Analysis Web Services
*
* @author pvtroshin
* @version 1.0
*/
public class Jws2Client {
/*
* 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());
final static String pseparator = "=";
// Parameters for required command line options
final static String hostkey = "-h";
final static String servicekey = "-s";
// Actions
final static String inputkey = "-i";
final static String paramList = "-parameters";
final static String presetList = "-presets";
final static String limitList = "-limits";
// Options
final static String paramFile = "-f";
final static String outputkey = "-o";
final static String parameterkey = "-p";
final static String presetkey = "-r";
//JABAWS version 1.0 service name
static final String qualifiedServiceName = "http://msa.data.compbio/01/01/2010/";
/**
* Searches the command line keys in the array of parameters
*
* @param cmd
* command line options
* @return true is the list of Parameters is requested, false otherwise
*/
private boolean listParameters(String[] cmd) {
return keyFound(cmd, paramList);
}
/**
* Check whether presetList is set in the command line
*
* @param cmd
* command line options
* @return true if presetList is found, false otherwise
*/
boolean listPresets(String[] cmd) {
return keyFound(cmd, presetList);
}
/**
* Returns {@code Preset} by its name
*
* @see Preset
* @param <T>
* @param msaws
* @param presetName
* @return Return a Preset by its optionName
*/
<T> Preset<T> getPreset(MsaWS<T> msaws, String presetName) {
assert presetName != null;
PresetManager<T> presets = getPresetList(msaws);
if (presets == null) {
System.out
.println("No presets are supported by the service! Ignoring -r directive!");
return null;
}
Preset<T> pre = presets.getPresetByName(presetName);
if (pre == null) {
System.out.println("Cannot find preset: " + presetName
+ " WARN: ignoring -r directive!");
}
return pre;
}
/**
* Extracts preset name from the command line is any
*
* @param cmd
* command line options
* @return presetName or null if no presets is defined
*/
String getPresetName(String[] cmd) {
String preset = null;
for (int i = 0; i < cmd.length; i++) {
String presetPrm = cmd[i];
if (presetPrm.trim().toLowerCase().startsWith(
presetkey + pseparator)) {
preset = presetPrm.substring(presetPrm.indexOf(pseparator) + 1);
break;
}
}
return preset;
}
/**
* Checks whether limitList parameter is in the command line
*
* @param cmd
* - command line options
* @return true if it is, false otherwise
*/
boolean listLimits(String[] cmd) {
return keyFound(cmd, limitList);
}
/**
* Checks whether the key is in the command line
*
* @param cmd
* @param key
* @return true if it is, false otherwise
*/
boolean keyFound(String[] cmd, String key) {
assert cmd != null && cmd.length > 0;
assert key != null;
for (int i = 0; i < cmd.length; i++) {
String listPresets = cmd[i];
if (listPresets.trim().equalsIgnoreCase(key)) {
return true;
}
}
return false;
}
/**
* Attempt to construct the URL object from the string
*
* @param urlstr
* @return true if it succeed false otherwise
*/
public static boolean validURL(String urlstr) {
try {
if (urlstr == null || urlstr.trim().length() == 0) {
return false;
}
new URL(urlstr);
} catch (MalformedURLException e) {
return false;
}
return true;
}
/**
* Extracts service name from the command line
*
* @param cmd
* command line options
* @return service name or null if it is not defined
*/
public static String getServiceName(String[] cmd) {
for (int i = 0; i < cmd.length; i++) {
String serv = cmd[i];
if (serv.trim().toLowerCase().startsWith(servicekey + pseparator)) {
return serv.substring(serv.indexOf(pseparator) + 1);
}
}
return null;
}
/**
* Extracts host name from the command line
*
* @param cmd
* command line options
* @return host name or null if it is not defined
*/
public static String getHost(String[] cmd) {
for (int i = 0; i < cmd.length; i++) {
String host = cmd[i];
if (host.trim().toLowerCase().startsWith(hostkey + pseparator)) {
return host.substring(host.indexOf(pseparator) + 1);
}
}
return null;
}
/**
* Checks -i options and return the File if one was provided, null otherwise
*
* @param cmd
* @param key
* @param mustExist
* @return
* @throws IOException
*/
File getFile(String[] cmd, String key, boolean mustExist)
throws IOException {
assert key != null && key.trim().length() != 0;
for (int i = 0; i < cmd.length; i++) {
String filename = cmd[i];
filename = filename.trim();
if (filename.toLowerCase().startsWith(key + pseparator)) {
filename = filename.substring((key + pseparator).length());
File file = new File(filename);
if (mustExist && !file.exists()) {
System.out.println(key + " file " + file.getAbsolutePath()
+ " does not exist");
return null;
}
if (!mustExist && !file.exists()) {
file.createNewFile();
}
if (!file.canRead()) {
System.out.println("Cannot read " + key + " file "
+ file.getAbsolutePath());
return null;
}
return file;
}
}
return null;
}
/**
* Connects to the service and do the job as requested, if something goes
* wrong reports or/and prints usage help.
*
* @param <T>
* web service type
* @param cmd
* command line options
* @throws IOException
*/
<T> Jws2Client(String[] cmd) throws IOException {
String hostname = getHost(cmd);
if (hostname == null) {
System.out.println("Host name is not provided!");
printUsage(1);
}
if (!validURL(hostname)) {
System.out.println("Host name is not valid!");
printUsage(1);
}
String serviceName = getServiceName(cmd);
if (serviceName == null) {
System.out.println("Service name is no provided!");
printUsage(1);
}
Services service = Services.getService(serviceName);
if (service == null) {
System.out.println("Service " + serviceName
+ " is no supported! Valid values are: "
+ Arrays.toString(Services.values()));
printUsage(1);
}
File inputFile = getFile(cmd, inputkey, true);
File outFile = getFile(cmd, outputkey, false);
File parametersFile = getFile(cmd, paramFile, true);
String presetName = getPresetName(cmd);
MsaWS<T> msaws = connect(hostname, service);
Preset<T> preset = null;
if (presetName != null) {
preset = getPreset(msaws, presetName);
}
List<Option<T>> customOptions = null;
if (parametersFile != null) {
List<String> prms = loadParameters(parametersFile);
customOptions = processParameters(prms, msaws.getRunnerOptions());
}
Alignment alignment = null;
if (inputFile != null) {
alignment = align(inputFile, msaws, preset, customOptions);
OutputStream outStream = null;
if (outFile != null) {
outStream = getOutStream(outFile);
} else {
// this stream is going to be closed later which is fine as
// std.out will not be
outStream = System.out;
}
writeOut(outStream, alignment);
// stream is closed in the method no need to close it here
}
boolean listParameters = listParameters(cmd);
if (listParameters) {
System.out.println(getParametersList(msaws));
}
boolean listPreset = listPresets(cmd);
if (listPreset) {
System.out.println(getPresetList(msaws));
}
boolean listLimits = listLimits(cmd);
if (listLimits) {
System.out.println(getLimits(msaws));
}
log.fine("Disconnecting...");
((Closeable) msaws).close();
log.fine("Disconnected successfully!");
}
/**
* Load parameters from file
*
* @throws IOException
*/
List<String> loadParameters(File paramsfile) throws IOException {
assert paramsfile != null && paramsfile.exists();
BufferedReader reader = new BufferedReader(new FileReader(paramsfile));
String line = null;
ArrayList<String> params = new ArrayList<String>();
while ((line = reader.readLine()) != null) {
line = line.trim();
if (line.length() == 0)
continue;
params.add(line);
}
return params;
}
/**
* Converts options supplied via parameters file into {@code Option} objects
*
* @param <T>
* web service type
* @param params
* @param options
* @return List of Options of type T
*/
<T> List<Option<T>> processParameters(List<String> params,
RunnerConfig<T> options) {
List<Option<T>> chosenOptions = new ArrayList<Option<T>>();
for (String param : params) {
String oname = null;
if (isParameter(param)) {
oname = this.getParamName(param);
} else {
oname = param;
}
Option<T> o = options.getArgumentByOptionName(oname);
if (o == null) {
System.out.println("WARN ignoring unsuppoted parameter: "
+ oname);
continue;
}
if (isParameter(param)) {
try {
o.setValue(getParamValue(param));
} catch (WrongParameterException e) {
System.out
.println("Problem setting value for the parameter: "
+ param);
e.printStackTrace();
}
}
chosenOptions.add(o);
}
return chosenOptions;
}
String getParamName(String fullName) {
assert isParameter(fullName);
return fullName.substring(0, fullName.indexOf(pseparator));
}
String getParamValue(String fullName) {
assert isParameter(fullName);
return fullName.substring(fullName.indexOf(pseparator) + 1);
}
boolean isParameter(String param) {
return param.contains(pseparator);
}
OutputStream getOutStream(File file) {
assert file != null && file.exists();
try {
return new FileOutputStream(file);
} catch (FileNotFoundException e) {
e.printStackTrace();
}
return null;
}
/**
* Outputs clustal formatted alignment into the file represented by the
* outStream
*
* @param outStream
* @param align
* the alignment to output
*/
void writeOut(OutputStream outStream, Alignment align) {
try {
ClustalAlignmentUtil.writeClustalAlignment(outStream, align);
} catch (IOException e) {
System.err
.println("Problems writing output file! Stack trace is below: ");
e.printStackTrace();
} finally {
if (outStream != null) {
try {
outStream.close();
} catch (IOException ignored) {
// e.printStackTrace();
}
}
}
}
/**
* Connects to a web service by the host and the service name
*
* @param <T>
* web service type
* @param host
* @param service
* @return MsaWS<T>
* @throws WebServiceException
*/
public static <T> MsaWS<T> connect(String host, Services service)
throws WebServiceException {
URL url = null;
log.log(Level.FINE, "Attempt to connect...");
try {
url = new URL(host + "/" + service.toString() + "?wsdl");
} catch (MalformedURLException e) {
e.printStackTrace();
// ignore as the host name is already verified
}
QName qname = new QName(qualifiedServiceName, service.toString());
Service serv = Service.create(url, qname);
MsaWS<T> msaws = serv.getPort(new QName(qualifiedServiceName, service
+ "Port"), MsaWS.class);
log.log(Level.FINE, "Connected successfully!");
return msaws;
}
/**
* Align sequences from the file using MsaWS
*
* @param <T>
* web service type e.g. Clustal
* @param file
* to write the resulting alignment to
* @param msaws
* MsaWS required
* @param preset
* Preset to use optional
* @param customOptions
* file which contains new line separated list of options
* @return Alignment
*/
static <T> Alignment align(File file, MsaWS<T> msaws, Preset<T> preset,
List<Option<T>> customOptions) {
FileInputStream instream = null;
List<FastaSequence> fastalist = null;
Alignment alignment = null;
try {
instream = new FileInputStream(file);
fastalist = SequenceUtil.readFasta(instream);
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!");
}
if (customOptions != null) {
jobId = msaws.customAlign(fastalist, customOptions);
} else if (preset != null) {
jobId = msaws.presetAlign(fastalist, preset);
} else {
jobId = msaws.align(fastalist);
}
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:");
e.printStackTrace();
} catch (JobSubmissionException e) {
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:");
e.printStackTrace();
} catch (InterruptedException ignored) {
// ignore and propagate an interruption
Thread.currentThread().interrupt();
} catch (WrongParameterException e) {
e.printStackTrace();
} finally {
if (instream != null) {
try {
instream.close();
} catch (IOException ignored) {
// ignore
}
}
}
return alignment;
}
/**
* Returns a list of options supported by web service
*
* @param <T>
* web service type
* @param msaws
* web service proxy
* @return List of options supported by a web service
*/
<T> List<Option<T>> getParametersList(MsaWS<T> msaws) {
assert msaws != null;
return msaws.getRunnerOptions().getArguments();
}
/**
* Returns an objects from which the list of presets supported by web
* service <T> can be obtained
*
* @param <T>
* web service type
* @param msaws
* web service proxy
* @return PresetManager, object which operates on presets
*/
<T> PresetManager<T> getPresetList(MsaWS<T> msaws) {
assert msaws != null;
PresetManager<T> presetman = msaws.getPresets();
return presetman;
}
/**
* Returns a list of limits supported by web service Each limit correspond
* to a particular preset.
*
* @param <T>
* web service type
* @param msaws
* web service proxy
* @return List of limits supported by a web service
*/
<T> List<Limit<T>> getLimits(MsaWS<T> msaws) {
assert msaws != null;
LimitsManager<T> lmanger = msaws.getLimits();
return lmanger != null ? lmanger.getLimits() : null;
}
/**
* Prints Jws2Client usage information to standard out
*
* @param exitStatus
*/
static void printUsage(int exitStatus) {
System.out.println();
System.out.println("Usage: <Class or Jar file name> " + hostkey
+ pseparator + "host_and_context " + servicekey + pseparator
+ "serviceName ACTION [OPTIONS] ");
System.out.println();
System.out
.println(hostkey
+ pseparator
+ "<host_and_context> - a full URL to the JWS2 web server including context path e.g. http://10.31.1.159:8080/ws");
System.out.println(servicekey + pseparator + "<ServiceName> - one of "
+ Arrays.toString(Services.values()));
System.out.println();
System.out.println("ACTIONS: ");
System.out
.println(inputkey
+ pseparator
+ "<inputFile> - full path to fasta formatted sequence file, from which to align sequences");
System.out.println(paramList
+ " - lists parameters supported by web service");
System.out.println(presetList
+ " - lists presets supported by web service");
System.out.println(limitList + " - lists web services limits");
System.out
.println("Please note that if input file is specified other actions are ignored");
System.out.println();
System.out.println("OPTIONS (only for use with -i action):");
System.out.println(presetkey + pseparator
+ "<presetName> - name of the preset to use");
System.out
.println(outputkey
+ pseparator
+ "<outputFile> - full path to the file where to write an alignment");
System.out
.println("-f=<parameterInputFile> - the name of the file with the list of parameters to use.");
System.out
.println("Please note that -r and -f options cannot be used together. "
+ "Alignment is done with either preset or a parameters from the file, but not both!");
System.exit(exitStatus);
}
/**
* Starts command line client, if no parameter are supported print help. Two
* parameters are required for successfull call the JWS2 host name and a
* service name.
*
* @param args
* Usage: <Class or Jar file name> -h=host_and_context
* -s=serviceName ACTION [OPTIONS]
*
* -h=<host_and_context> - a full URL to the JWS2 web server
* including context path e.g. http://10.31.1.159:8080/ws
*
* -s=<ServiceName> - one of [MafftWS, MuscleWS, ClustalWS,
* TcoffeeWS, ProbconsWS] ACTIONS:
*
* -i=<inputFile> - full path to fasta formatted sequence file,
* from which to align sequences
*
* -parameters - lists parameters supported by web service
*
* -presets - lists presets supported by web service
*
* -limits - lists web services limits Please note that if input
* file is specified other actions are ignored
*
* OPTIONS: (only for use with -i action):
*
* -r=<presetName> - name of the preset to use
*
* -o=<outputFile> - full path to the file where to write an
* alignment -f=<parameterInputFile> - the name of the file with
* the list of parameters to use. Please note that -r and -f
* options cannot be used together. Alignment is done with either
* preset or a parameters from the file, but not both!
*
*/
public static void main(String[] args) {
if (args == null) {
printUsage(1);
}
if (args.length < 2) {
System.out.println("Host and service names are required!");
printUsage(1);
}
try {
new Jws2Client(args);
} catch (IOException e) {
log.log(Level.SEVERE, "IOException in client! " + e.getMessage(), e
.getCause());
System.err.println("Cannot write output file! Stack trace: ");
e.printStackTrace();
}
}
}
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