ca.ucalgary.services
Class ACDService

java.lang.Object
  javax.servlet.GenericServlet
      javax.servlet.http.HttpServlet
          org.biomoby.service.MobyServlet
              ca.ucalgary.services.LegacyService
                  ca.ucalgary.services.ACDService

All Implemented Interfaces:

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

public class ACDService
extends LegacyService

A servlet that will read in an EMBOSS ACD file (which describes the command-line usage of a program in the suite) and publishes it as a MOBY service. MOBY XML data is converted to regular input to EMBOSS input via an XSLT stylesheet. EMBOSS results are conveted to MOBY datatypes using some built-in heuristics.

See Also:

Serialized Form

Field Summary

static String	ACD_FILE_PARAM
static String	EMBOSS_ADV_PARAMS_PARAM
static String	EMBOSS_OUTPUT_PARAM
static String	EMBOSS_PARAMS_PARAM
static String	EMBOSS_ROOT_PARAM

Fields inherited from class ca.ucalgary.services.LegacyService

MOBY_RULES_DEFAULT_RESOURCE, MOBY_RULES_LOCATION_PARAM, TEXT_RULES_DEFAULT_RESOURCE, TEXT_RULES_LOCATION_PARAM

Fields inherited from class org.biomoby.service.MobyServlet

ADMIN_MODE, INIT_OUTPUT_BUFFER_SIZE, MOBY_AUTHORITATIVE_PARAM, MOBY_CENTRAL_URL_PARAM, MOBY_CONTACT_PARAM, MOBY_INPUT_PARAM, MOBY_OUTPUT_PARAM, MOBY_PROVIDER_URI_PARAM, MOBY_SECONDARYINPUT_PARAM, MOBY_SERVICE_DESC_PARAM, MOBY_SERVICENAME_PARAM, MOBY_SERVICETYPE_PARAM, MODE_HTTP_PARAM, RDF_MODE

Constructor Summary

ACDService()

Method Summary

void	configureServiceFromACDFile(MobyService service, File acdFile, boolean useAdvancedParams) Parses the ACD file and sets the MOBY signature parameters appropriately.
MobyService	createServiceFromConfig(javax.servlet.http.HttpServletRequest request) Determines the command-line program to execute when service requests come in, based on the values for the EMBOSS_ROOT_PARAM and ACD_FILE_PARAM parameters in the servlet configuration.
void	init() If you override this method, be sure to call super.init()
void	processRequest(MobyDataJob request, MobyDataJob result) Runs the command-line program specified by the servlet config, reformatting along the way.

Methods inherited from class org.biomoby.service.MobyServlet

destroy, doGet, doPost, getCentralImpl, getMobyContents, getServiceName, log, log, main, processRequests, setCoCInitParameter, setMainTerminationExit, stringToPrimaryDataTemplate, stringToSecondaryDataTemplate, validateArguments

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

EMBOSS_ROOT_PARAM

public static final String EMBOSS_ROOT_PARAM

See Also:

Constant Field Values

EMBOSS_PARAMS_PARAM

public static final String EMBOSS_PARAMS_PARAM

See Also:

Constant Field Values

EMBOSS_ADV_PARAMS_PARAM

public static final String EMBOSS_ADV_PARAMS_PARAM

See Also:

Constant Field Values

EMBOSS_OUTPUT_PARAM

public static final String EMBOSS_OUTPUT_PARAM

See Also:

Constant Field Values

ACD_FILE_PARAM

public static final String ACD_FILE_PARAM

See Also:

Constant Field Values

Constructor Detail

ACDService

public ACDService()

Method Detail

init

public void init()

Description copied from class: MobyServlet

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

Overrides:

init in class MobyServlet

processRequest

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

Runs the command-line program specified by the servlet config, reformatting along the way.

Overrides:

processRequest in class MobyServlet

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

createServiceFromConfig

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

Determines the command-line program to execute when service requests come in, based on the values for the EMBOSS_ROOT_PARAM and ACD_FILE_PARAM parameters in the servlet configuration.

Overrides:

createServiceFromConfig in class LegacyService

Throws:

Exception

configureServiceFromACDFile

public void configureServiceFromACDFile(MobyService service,
                                        File acdFile,
                                        boolean useAdvancedParams)
                                 throws Exception

Parses the ACD file and sets the MOBY signature parameters appropriately.

Throws:

Exception