compbio.ws.client

Class WSTester

java.lang.Object

compbio.ws.client.WSTester

public class WSTester
extends java.lang.Object

Class for testing web services

Version:

1.5 February 2013

Author:

pvtroshin

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	clustalRNAAlignment
private static java.lang.String	FAILED Status strings
static java.lang.String	fastaAlignment
static java.lang.String	fastaInput1record
static java.lang.String	fastaInput2records Test sequences to be used as input for WS
static java.lang.String	fastaRNAAlignment
private java.lang.String	hostname
private static java.lang.String	OK
private static java.lang.String	UNSUPPORTED
private java.io.PrintWriter	writer

Constructor Summary

Constructors

Constructor and Description
WSTester(java.lang.String hostname, java.io.PrintWriter writer) Construct an instance of JABAWS tester

Method Summary

Modifier and Type	Method and Description
private <T> boolean	checkService(JABAService wservice, Services service) Call most of web services functions and check the output
boolean	checkService(Services service) Test JABA web service
private JABAService	connect(java.lang.String host, Services service) Connects to a web service by the host and the service name web service type
private static java.util.List<FastaSequence>	loadAlignment() Converting input to a form accepted by WS
private static java.util.List<FastaSequence>	loadRNAAlignment() Converting input to a form accepted by WS
private static java.util.List<FastaSequence>	loadSeqs(int nLines) Converting input to a form accepted by WS
static <T> void	main(java.lang.String[] args) Test JWS2 web services
private <T> boolean	presetAlign(MsaWS<T> msaws, java.util.List<Preset<T>> presets) Calls alignment with preset
(package private) static void	printUsage() Prints usage
private void	reportException(java.lang.Exception e)
private void	reportResults(Services serv, boolean succeed)
private <T> boolean	testDefaultAlignment(MsaWS<T> msaws, Services service) Align using default settings
private <T> boolean	testDefaultAnalyse(java.util.List<FastaSequence> fastalist, SequenceAnnotation<T> wsproxy, Preset<T> preset, java.util.List<Option<T>> customOptions)
private <T> void	testMetadata(Metadata<T> msaws)
private <T> boolean	testMsaWS(MsaWS<T> msaws, Services service)
private <T> boolean	testSequenceAnnotationWS(SequenceAnnotation<T> wservice, Services service)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

fastaInput2records

public static final java.lang.String fastaInput2records

Test sequences to be used as input for WS

See Also:

Constant Field Values

fastaInput1record

public static final java.lang.String fastaInput1record

See Also:

Constant Field Values

fastaAlignment

public static final java.lang.String fastaAlignment

See Also:

Constant Field Values

fastaRNAAlignment

public static final java.lang.String fastaRNAAlignment

See Also:

Constant Field Values

clustalRNAAlignment

public static final java.lang.String clustalRNAAlignment

See Also:

Constant Field Values

FAILED

private static final java.lang.String FAILED

Status strings

See Also:

Constant Field Values

OK

private static final java.lang.String OK

See Also:

Constant Field Values

UNSUPPORTED

private static final java.lang.String UNSUPPORTED

See Also:

Constant Field Values

writer

private final java.io.PrintWriter writer

hostname

private final java.lang.String hostname

Constructor Detail

WSTester

public WSTester(java.lang.String hostname,
                java.io.PrintWriter writer)

Construct an instance of JABAWS tester

Parameters:

hostname - - fully qualified host and context name of JABAWS e.g. http://nanna.cluster.lifesci.dundee.ac.uk:8080/jaba

writer - a PrintWriter instance to writer test log to.

Method Detail

loadSeqs

private static java.util.List<FastaSequence> loadSeqs(int nLines)

Converting input to a form accepted by WS

Returns:

List of FastaSequence records

loadAlignment

private static java.util.List<FastaSequence> loadAlignment()

Converting input to a form accepted by WS

Returns:

List of FastaSequence records

loadRNAAlignment

private static java.util.List<FastaSequence> loadRNAAlignment()

Converting input to a form accepted by WS

Returns:

List of FastaSequence records with aligned RNA sequences

printUsage

static void printUsage()

Prints usage

presetAlign

private <T> boolean presetAlign(MsaWS<T> msaws,
                                java.util.List<Preset<T>> presets)
                         throws UnsupportedRuntimeException

Calls alignment with preset

Type Parameters:

T -

Parameters:

msaws -

presets - list of the Preset

Throws:

UnsupportedRuntimeException

testMsaWS

private <T> boolean testMsaWS(MsaWS<T> msaws,
                              Services service)
                       throws java.lang.Exception

Throws:

java.lang.Exception

checkService

private <T> boolean checkService(JABAService wservice,
                                 Services service)

Call most of web services functions and check the output

Type Parameters:

T - web service type

Parameters:

msaws -

Throws:

UnsupportedRuntimeException - is thrown if the connection to a web service was made, but the web service is not functional. e.g. when native executable does not exists for a server platform

testSequenceAnnotationWS

private <T> boolean testSequenceAnnotationWS(SequenceAnnotation<T> wservice,
                                             Services service)
                                      throws java.lang.Exception

Throws:

java.lang.Exception

testDefaultAnalyse

private <T> boolean testDefaultAnalyse(java.util.List<FastaSequence> fastalist,
                                       SequenceAnnotation<T> wsproxy,
                                       Preset<T> preset,
                                       java.util.List<Option<T>> customOptions)
                                throws java.lang.Exception

Throws:

java.lang.Exception

reportException

private void reportException(java.lang.Exception e)

testMetadata

private <T> void testMetadata(Metadata<T> msaws)
                       throws UnsupportedRuntimeException

Throws:

UnsupportedRuntimeException

testDefaultAlignment

private <T> boolean testDefaultAlignment(MsaWS<T> msaws,
                                         Services service)
                                  throws java.lang.Exception

Align using default settings

Type Parameters:

T -

Parameters:

msaws -

Throws:

UnsupportedRuntimeException

java.lang.Exception

main

public static <T> void main(java.lang.String[] args)
                     throws java.io.IOException

Test JWS2 web services

Type Parameters:

T - web service type

Parameters:

args - -h= -s= which is optional. If service name is not provided then all known JWS2 web services are tested

Throws:

java.io.IOException

connect

private JABAService connect(java.lang.String host,
                            Services service)
                     throws javax.xml.ws.WebServiceException,
                            java.net.ConnectException

Connects to a web service by the host and the service name web service type

Parameters:

host - the fully qualified name of JABAWS server including JABAWS context name e.g http://nanna.cluster.lifesci.dundee.ac.uk:8080/jaba

service - the name of the JABAWS service to connect to

Returns:

JABAService

Throws:

javax.xml.ws.WebServiceException

java.net.ConnectException - if fails to connect to the service on the host

checkService

public boolean checkService(Services service)
                     throws java.net.ConnectException,
                            javax.xml.ws.WebServiceException

Test JABA web service

Parameters:

service - the service to test

Returns:

true if the service works as expected, false otherwise

Throws:

javax.xml.ws.WebServiceException

java.net.ConnectException

reportResults

private void reportResults(Services serv,
                           boolean succeed)