org.biomoby.service
Class MobyServlet

java.lang.Object
  javax.servlet.GenericServlet
      javax.servlet.http.HttpServlet
          org.biomoby.service.MobyServlet

All Implemented Interfaces:

Serializable, Remote, javax.servlet.Servlet, javax.servlet.ServletConfig

Direct Known Subclasses:

ConvertAAtoFASTA_AA, FromFastaToDNASequence, LegacyService

@mobyService(name="MobyServlet",
             type="Testing",
             provider="moby.ucalgary.ca",
             author="gordonp@ucalgary.ca",
             in={},
             out={},
             description="No-operation base service implementation")
public class MobyServlet
extends javax.servlet.http.HttpServlet
implements Remote

This the base implementation of a MOBY servlet that can be easily extended to provide a meaningful service (by overriding processRequest()). Please see the documentation on how to use this servlet.

See Also:

Serialized Form

Field Summary

static String	ADMIN_MODE
static int	INIT_OUTPUT_BUFFER_SIZE
static String	MOBY_AUTHORITATIVE_PARAM
static String	MOBY_CENTRAL_URL_PARAM
static String	MOBY_CONTACT_PARAM
static String	MOBY_INPUT_PARAM
static String	MOBY_OUTPUT_PARAM
static String	MOBY_PROVIDER_URI_PARAM
static String	MOBY_SECONDARYINPUT_PARAM
static String	MOBY_SERVICE_DESC_PARAM
static String	MOBY_SERVICENAME_PARAM
static String	MOBY_SERVICETYPE_PARAM
static String	MODE_HTTP_PARAM
static String	RDF_MODE

Constructor Summary

MobyServlet()

Method Summary

MobyService	createServiceFromConfig(javax.servlet.http.HttpServletRequest request)
void	destroy() By default, this method does nothing.
void	doGet(javax.servlet.http.HttpServletRequest request, javax.servlet.http.HttpServletResponse response)
void	doPost(javax.servlet.http.HttpServletRequest request, javax.servlet.http.HttpServletResponse response)
Central	getCentralImpl() Returns the Moby Central server that the service is associated with, based on the web.xml and the servlet annotation.
MobyContentInstance	getMobyContents(javax.servlet.http.HttpServletRequest request)
String	getServiceName() Reads the service name from the mobyService annotation.
void	init() If you override this method, be sure to call super.init()
void	log(String msg)
void	log(String msg, Exception ex)
static void	main(String[] args) Expects one argument, an example MOBY XML input file or URL.
void	processRequest(MobyDataJob request, MobyDataJob result) The real worker method: implementing classes must override this method to do something useful.
void	processRequests(MobyContentInstance requestContents, MobyContentInstance resultContents) By default, this method will sequentially execute the individual jobs from the request payload (processRequest).
void	setCoCInitParameter(String param, String value)
static void	setMainTerminationExit(boolean b) Determines whether call to main() that terminate on error should call System.exit() or not.
static MobyPrimaryData	stringToPrimaryDataTemplate(String spec, Map<String,MobyDataTypeTemplate> runTimeTemplates) Strings have the form name:objectType:namespace, with ":namespace" optional If the input is expected to be a Collection, then the syntax is name:Collection(objectType):namespace
static MobySecondaryData	stringToSecondaryDataTemplate(String template) Strings have the form name:paramType:default:spec where spec depends on the parameter type.
static void	validateArguments(MobyDataJob job, MobyService service, String errMessagePrefix) Throws an exception if the data in the job does not match the input spec of the service.

Methods inherited from class javax.servlet.http.HttpServlet

service

Methods inherited from class javax.servlet.GenericServlet

getInitParameter, getInitParameterNames, getServletConfig, getServletContext, getServletInfo, getServletName, init, log

Methods inherited from class java.lang.Object

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

Field Detail

MOBY_CENTRAL_URL_PARAM

public static final String MOBY_CENTRAL_URL_PARAM

See Also:

Constant Field Values

MOBY_AUTHORITATIVE_PARAM

public static final String MOBY_AUTHORITATIVE_PARAM

See Also:

Constant Field Values

MOBY_CONTACT_PARAM

public static final String MOBY_CONTACT_PARAM

See Also:

Constant Field Values

MOBY_SERVICE_DESC_PARAM

public static final String MOBY_SERVICE_DESC_PARAM

See Also:

Constant Field Values

MOBY_PROVIDER_URI_PARAM

public static final String MOBY_PROVIDER_URI_PARAM

See Also:

Constant Field Values

MOBY_SERVICETYPE_PARAM

public static final String MOBY_SERVICETYPE_PARAM

See Also:

Constant Field Values

MOBY_SERVICENAME_PARAM

public static final String MOBY_SERVICENAME_PARAM

See Also:

Constant Field Values

MOBY_INPUT_PARAM

public static final String MOBY_INPUT_PARAM

See Also:

Constant Field Values

MOBY_SECONDARYINPUT_PARAM

public static final String MOBY_SECONDARYINPUT_PARAM

See Also:

Constant Field Values

MOBY_OUTPUT_PARAM

public static final String MOBY_OUTPUT_PARAM

See Also:

Constant Field Values

MODE_HTTP_PARAM

public static final String MODE_HTTP_PARAM

See Also:

Constant Field Values

RDF_MODE

public static final String RDF_MODE

See Also:

Constant Field Values

ADMIN_MODE

public static final String ADMIN_MODE

See Also:

Constant Field Values

INIT_OUTPUT_BUFFER_SIZE

public static final int INIT_OUTPUT_BUFFER_SIZE

See Also:

Constant Field Values

Constructor Detail

MobyServlet

public MobyServlet()

Method Detail

doGet

public void doGet(javax.servlet.http.HttpServletRequest request,
                  javax.servlet.http.HttpServletResponse response)
           throws javax.servlet.ServletException,
                  IOException

Overrides:

doGet in class javax.servlet.http.HttpServlet

Throws:

javax.servlet.ServletException

IOException

doPost

public void doPost(javax.servlet.http.HttpServletRequest request,
                   javax.servlet.http.HttpServletResponse response)
            throws javax.servlet.ServletException,
                   IOException

Overrides:

doPost in class javax.servlet.http.HttpServlet

Throws:

javax.servlet.ServletException

IOException

getMobyContents

public MobyContentInstance getMobyContents(javax.servlet.http.HttpServletRequest request)
                                    throws Exception

Throws:

Exception

validateArguments

public static void validateArguments(MobyDataJob job,
                                     MobyService service,
                                     String errMessagePrefix)
                              throws Exception

Throws an exception if the data in the job does not match the input spec of the service.

Throws:

Exception

log

public void log(String msg)

Overrides:

log in class javax.servlet.GenericServlet

log

public void log(String msg,
                Exception ex)

init

public void init()

If you override this method, be sure to call super.init()

Overrides:

init in class javax.servlet.GenericServlet

getCentralImpl

public Central getCentralImpl()

Returns the Moby Central server that the service is associated with, based on the web.xml and the servlet annotation. If the servlet hasn't been initialized yet (init() hasn't been called), null will be returned.

setCoCInitParameter

public void setCoCInitParameter(String param,
                                String value)

createServiceFromConfig

public MobyService createServiceFromConfig(javax.servlet.http.HttpServletRequest request)
                                    throws Exception

Throws:

Exception

getServiceName

public String getServiceName()

Reads the service name from the mobyService annotation.

stringToSecondaryDataTemplate

public static MobySecondaryData stringToSecondaryDataTemplate(String template)
                                                       throws Exception

Strings have the form name:paramType:default:spec where spec depends on the parameter type. Currently, these are the valid paramTypes and their specs:

• Integer: blank or [,max] or [min,] or [min,max]
• Float: blank or [,max] or [min,] or [min,max]
• String: blank or [choice1,choice2,...]
• DateTime: blank or [,max] or [min,] or [min,max]
• Boolean: blank

e.g. db:String:nr:[nr,nt,est,swissprot] e.g. filter:Boolean:true e.g. hits:Integer:100:[0,]

Throws:

Exception

stringToPrimaryDataTemplate

public static MobyPrimaryData stringToPrimaryDataTemplate(String spec,
                                                          Map<String,MobyDataTypeTemplate> runTimeTemplates)
                                                   throws Exception

Strings have the form name:objectType:namespace, with ":namespace" optional If the input is expected to be a Collection, then the syntax is name:Collection(objectType):namespace

Throws:

Exception

destroy

public void destroy()

By default, this method does nothing. If any additional resources were allocated in an override of init(), they should be freed in an override of this method.

Specified by:

destroy in interface javax.servlet.Servlet

Overrides:

destroy in class javax.servlet.GenericServlet

processRequests

public void processRequests(MobyContentInstance requestContents,
                            MobyContentInstance resultContents)
                     throws Exception

By default, this method will sequentially execute the individual jobs from the request payload (processRequest). Override this method if you want to implement some division-of-labour scheme.

Parameters:

resultContents - is a Map prepopulated with pairs for the response

Throws:

Exception

processRequest

public void processRequest(MobyDataJob request,
                           MobyDataJob result)
                    throws Exception

The real worker method: implementing classes must override this method to do something useful. By default, nothing is done. If a ServiceException is thrown in this method, it is copied verbatim into the MOBY response. Any other exceptions thrown will be automatically wrapped in a ServiceException of severity ERROR and type INTERNAL_PROCESSING_ERROR. To add any other type of non-fatal error (e.g. a WARN), call addException() explicitly, rather than throwing a Java Exception which stops the job's execution.

Parameters:

request - the request to process, with params guaranteed to be of the type specified in the mobyService annotation, or values overriding the annjotation in a WAR file's WEB-INF/web.xml

Throws:

Exception

setMainTerminationExit

public static void setMainTerminationExit(boolean b)

Determines whether call to main() that terminate on error should call System.exit() or not. This is the default behaviour, and should generally be switched only for unit testing purposes.

main

public static void main(String[] args)
                 throws Exception

Expects one argument, an example MOBY XML input file or URL. processRequest() is then called for every job in the input data, and the results are printed to the screen.

Throws:

Exception