Uses of Class
org.biomoby.shared.MobyException

Packages that use MobyException

ca.ucalgary.seahawk.services
de.mpg.mpiz_koeln.featureClient
org.biomoby.client	The components used for developing Moby clients.
org.biomoby.client.rdf.builder	Provides the classes that are necessary for creating BioMoby RDF documents.
org.biomoby.registry.definitions.types
org.biomoby.registry.meta
org.biomoby.registry.properties	Provides classes and interfaces that help utilize property and configuration files.
org.biomoby.registry.rdfagent.util
org.biomoby.registry.sync
org.biomoby.registry.sync.handler
org.biomoby.service	It contains general components that can be used by those writing code for Moby services.
org.biomoby.service.dashboard
org.biomoby.service.dashboard.data
org.biomoby.service.dashboard.renderers
org.biomoby.service.generator
org.biomoby.shared	It contains components that are used from more than one (other) packages.
org.biomoby.shared.data	The package org.biomoby.shared.data allows you to easily build MOBY data instances for sending to services, or querying the registry.
org.biomoby.shared.datatypes	The package org.biomoby.shared.datatypes contains containers for basic Biomoby data types (a basic parent class MobyObject and all Biomoby primitive types).
org.biomoby.shared.extended
org.biomoby.shared.parser	The package org.biomoby.shared.parser contains classes for parsing Biomoby data from an XML format (a Biomoby XML envelope) into Java objects, and back to XML.
org.biomoby.w3c.addressing
org.omg.lsae.notifications
org.omg.lsae.sax
org.soap
org.soap.sax
org.w3c.addressing.sax

Uses of MobyException in ca.ucalgary.seahawk.services

Methods in ca.ucalgary.seahawk.services that throw MobyException

MobyDataObject	MobyComplexBuilder.apply(Matcher matcher)
MobyDataObject	MobyComplexBuilder.apply(Matcher matcher, byte[] data)
MobyDataObject	MobyComplexBuilder.applyXPath(Object result, NamespaceContext nsContext)
String[]	MobyComplexBuilder.evaluateIterativeRule(Matcher matcher, String result, String whitespaceMode, String encodingMode, byte[] data)
MobyDataServiceAssocInstance	MobyClient.getServices(MobyDataObject mdo)
MobyDataServiceAssocInstance[]	MobyClient.getServices(MobyDataObject[] mdos)
MobyDataServiceAssocInstance	MobyClient.getServices(MobyDataObjectSet mdos)
MobyDataServiceAssocInstance[]	MobyClient.getServices(MobyDataObjectSet[] mdoss)
MobyDataServiceAssocInstance[]	MobyClient.getServices(Node n) Performs the moby object creation and service association together (XPath rules).
MobyDataServiceAssocInstance[]	MobyClient.getServices(String s) Performs the moby object creation and service association together (regex rules).
MobyDataServiceAssocInstance[]	MobyClient.getServices(URL u) Performs the moby object creation and service association together (url_regex rules).

Constructors in ca.ucalgary.seahawk.services that throw MobyException

MobyClient()
Nullary constructor that differs significantly in behaviour from the one-arg c-tor: it uses the registry from SeahawkOptions, or if not available, the RegistryCache default registry.

MobyClient(Registry reg)
Constructor specifying a particular registry to use.

Uses of MobyException in de.mpg.mpiz_koeln.featureClient

Methods in de.mpg.mpiz_koeln.featureClient that throw MobyException

void	FeatureClient.setCentral(String url, String uri) Sets the central to be used.

Constructors in de.mpg.mpiz_koeln.featureClient that throw MobyException

FeatureClient()
Creates a new FeatureClient instance default the central in Canada.

Uses of MobyException in org.biomoby.client

Methods in org.biomoby.client that throw MobyException

static String	Taverna.buildWorkflow(ServicesEdge[] edges, String mobyEndpoint, Properties props) Creates a workflow definition (an XML string known as 'scufl' or 'xscufl') from the set of graph edges.
String	CentralImpl.call(String methodName, String inputXML)
String	BaseCmdLineClient.callRemoteService(String xmlInput) Call either a local class implementing a service, or pass it to the superclass that does a real (usual) SOAP call to a service (or first to a registry and then to a service).
String	ExtendedProtocolClient.callRemoteService(String xmlInput) Call either a local class implementing a service, or pass it to the superclass that does a real (usual) SOAP call to a service (or first to a registry and then to a service).
String	BaseClient.callRemoteService(String xmlInput) Call a SOAP-based BioMoby service.
String	MobyRequest.convertMOBYDataToMOBYRequest(MobyContentInstance data) Creates an XML representation of the data, renamed to fit the needs of the service if necessary, and adding any secondary parameter default values if not already specified in the incoming data.
String	MobyRequest.convertMOBYDataToMOBYRequest(MobyDataInstance data)
Element	MobyRequest.decodeSOAPMessage(Element n, StringBuffer contentsXMLOutput, String inputXML)
Element	MobyRequest.decodeSOAPMessage(Element n, StringBuffer contentsXMLOutput, String inputXML, boolean async) Isolates the MOBY Data from the SOAP message returned by the remote service host.
MobyService[]	CentralImpl.extractServices(String xml) Extract one or more MobyService objects from the given XML piece.
String	BaseCmdLineClient.fillRequest()
String	BaseClient.fillRequest() Create raw XML input.
boolean	BaseCmdLineClient.fillRequest(MobyJob request, MobyPackage inputContext)
abstract boolean	BaseClient.fillRequest(MobyJob request, MobyPackage inputContext) Crate data (fill them into 'request') for one Moby job (query).
boolean	BaseCmdLineClient.fillRequest(MobyPackage mobyInput, int jobCount)
boolean	BaseClient.fillRequest(MobyPackage mobyInput, int jobCount) Fill the whole 'mobyInput' - put there any number of jobs (queries) as you wish (you do not need to follow the 'jobCount' hint suggesting how many jobs should be put there).
MobyService[]	CentralImpl.findService(MobyService pattern)
MobyService[]	CentralImpl.findService(MobyService pattern, String[] keywords)
MobyService[]	CentralImpl.findService(MobyService pattern, String[] keywords, boolean includeChildrenServiceTypes, boolean includeParentDataTypes) All 'findService' methods end up here.
MobyService[]	CentralImpl.findService(String serviceType)
MobyService[]	CentralImpl.findService(String[] keywords)
MobyDataType	CentralImpl.getDataType(String dataTypeName) Parses and imports the following XML.
Map	CentralDigestCachedImpl.getDataTypeNames()
Map	CentralDigestCachedSimpleImpl.getDataTypeNames()
Map	CentralImpl.getDataTypeNames() Parses and imports the following XML.
Map	CentralImpl.getDataTypeRelationships(String dataTypeName) Parses and imports the following XML.
String[]	CentralImpl.getDataTypeRelationships(String dataTypeName, String relationshipType) Parses and imports the following XML.
MobyDataType[]	CentralDigestCachedImpl.getDataTypes()
MobyDataType[]	CentralDigestImpl.getDataTypes()
MobyDataType[]	CentralDigestCachedSimpleImpl.getDataTypes()
MobyDataType[]	CentralImpl.getDataTypes()
static CentralImpl	CentralImpl.getDefaultCentral() Using this method to get a Central object will ensure that other parts of the org.biomoby.shared class hierarchy that implicitly check the registry will use the same cache.
static CentralImpl	CentralImpl.getDefaultCentral(Registry reg)
MobyNamespace[]	CentralDigestCachedImpl.getFullNamespaces()
MobyNamespace[]	CentralDigestImpl.getFullNamespaces()
MobyNamespace[]	CentralDigestCachedSimpleImpl.getFullNamespaces()
MobyNamespace[]	CentralImpl.getFullNamespaces() Parses and imports the following XML.
MobyServiceType[]	CentralDigestImpl.getFullServiceTypes()
Map	CentralImpl.getNamespaces() Deprecated. Replaced by CentralImpl.getFullNamespaces() that gives more information for the same price.
MobyContentInstance	MobyRequest.getOutput()
String[]	CentralImpl.getProviders() Parses and imports the following XML.
InputStream	CentralImpl.getResource(String resourceName)
MobyResourceRef[]	CentralImpl.getResourceRefs() Parses and imports the following XML.
MobyServiceLocator	BaseCmdLineClient.getServiceLocator()
abstract MobyServiceLocator	BaseClient.getServiceLocator() Return characteristics of a BioMoby service that will be called, and that reveal where to find such service.
Map<String,String>	CentralImpl.getServiceNames() Deprecated. Replaced by CentralImpl.getServiceNamesByAuthority(). The reason is that this method returns a random result if there are more services with the same name but belonging to different authorities.
Map	CentralDigestCachedImpl.getServiceNamesByAuthority()
Map	CentralDigestCachedSimpleImpl.getServiceNamesByAuthority()
Map	CentralImpl.getServiceNamesByAuthority() Parses and imports the following XML.
MobyService[]	CentralDigestCachedImpl.getServices()
MobyService[]	CentralDigestImpl.getServices()
MobyService[]	CentralDigestCachedSimpleImpl.getServices()
Map	CentralImpl.getServicesByAuthority() Similar to CentralImpl.getServiceNamesByAuthority() but the resulting Map contains slightly more.
String[]	CentralImpl.getServiceTypeRelationships(String serviceTypeName, boolean expand) Parses and imports the following XML.
Map<String,String>	CentralImpl.getServiceTypes() Parses and imports the following XML.
String	CentralImpl.getServiceWSDL(String serviceName)
String	CentralImpl.getServiceWSDL(String serviceName, String authority)
String	BaseCmdLineClient.interceptRequest(String xmlInput)
String	BaseClient.interceptRequest(String xmlInput)
MobyContentInstance	MobyRequest.invokeService() The main method of the class.
static Document	CentralImpl.loadDocument(InputStream input) Loads a DOM Document from an InputStream.
void	BaseClient.process() The main method that packs input data, invokes a BioMoby service and uses its response.
void	BaseClient.process(int jobCount) The main method that packs input data, invokes a BioMoby service and uses its response.
void	CentralImpl.registerDataType(MobyDataType dataType)
void	CentralImpl.registerNamespace(MobyNamespace namespace)
void	CentralImpl.registerService(MobyService service)
void	CentralImpl.registerServiceType(MobyServiceType serviceType)
void	MobyRequest.setInput(MobyContentInstance data) Sets the input data for the MOBY service request.
void	MobyRequest.setInput(MobyDataInstance datum) Convenience method to run services that take one argument.
void	MobyRequest.setInput(MobyDataInstance[] data) Takes the data in the array, with their current articleNames, as input for the service
void	MobyRequest.setInput(MobyDataInstance datum, String paramName) Convenience method to run services that take one named argument.
void	MobyRequest.setSecondaryInput(Collection<MobyDataSecondaryInstance> secondaryData) Same functionality as setSecondaryInput(MobyDataSecondaryInstance[])
void	MobyRequest.setSecondaryInput(MobyDataSecondaryInstance[] secondaryData) This method will assign the provided secondary parameters to all primary input data currently in this object.
void	CentralImpl.unregisterDataType(MobyDataType dataType) B
void	CentralImpl.unregisterNamespace(MobyNamespace namespace)
void	CentralImpl.unregisterService(MobyService service)
void	CentralImpl.unregisterServiceType(MobyServiceType serviceType)
void	CentralDigestCachedSimpleImpl.updateCache(String id) Update the indicated part of the cache.
boolean	BaseCmdLineClient.useResponse(MobyJob response, MobyPackage responseContext)
abstract boolean	BaseClient.useResponse(MobyJob response, MobyPackage responseContext) Process a single job returned from a BioMoby service.
void	BaseCmdLineClient.useResponse(MobyPackage mobyResponse)
void	BaseClient.useResponse(MobyPackage mobyResponse) A high-level processing.
boolean	BaseCmdLineClient.useResponse(String xmlResponse)
boolean	BaseClient.useResponse(String xmlResponse) A raw-level processing.

Constructors in org.biomoby.client that throw MobyException

CentralCachedCallsImpl()
Default constructor.

CentralCachedCallsImpl(String endpoint)
Constructor allowing to specify which Moby Registry to use.

CentralCachedCallsImpl(String endpoint, String namespace)
Constructor allowing to specify which Moby Registry and what namespace to use.

CentralDigestCachedImpl()
The same as calling CentralDigestCachedImpl(null)

CentralDigestCachedImpl(String cacheDir)
Create an instance that will access a default Moby registry and will cache results in the 'cacheDir' directory.

CentralDigestCachedImpl(String endpoint, String namespace)
Create an instance that will access a specific Moby registry and will cache results in the default cache directory.

CentralDigestCachedImpl(String endpoint, String namespace, String cacheDir)
Create an instance that will access a Moby registry defined by its 'endpoint' and 'namespace', and will cache results in the 'cacheDir' directory.

CentralDigestCachedSimpleImpl(String cacheDir)
Create an instance that will access a default Moby registry and will cache results in the 'cacheDir' directory.

CentralDigestCachedSimpleImpl(String endpoint, String namespace, String cacheDir)
Create an instance that will access a Moby registry defined by its 'endpoint' and 'namespace', and will cache results in the 'cacheDir' directory.

CentralDigestImpl()
Default constructor.

CentralDigestImpl(String endpoint)
Constructor allowing to specify which Moby Registry to use.

CentralDigestImpl(String endpoint, String namespace)
Constructor allowing to specify which Moby Registry and what namespace to use.

CentralImpl()
Default constructor.

CentralImpl(String endpoint)
Constructor allowing to specify which Moby Registry to use.

CentralImpl(String endpoint, String namespace)
Constructor allowing to specify which Moby Registry and what namespace to use.

GraphsServlet(String mobyEndpoint, String mobyNamespace)
A real constructor that is called when it is known what Moby registry we are going to serve for.

Uses of MobyException in org.biomoby.client.rdf.builder

Constructors in org.biomoby.client.rdf.builder that throw MobyException

ServiceInstanceRDF()
Default Constructor: Uses the default mobycentral

ServiceInstanceRDF(Registry reg)
Constructor:

Uses of MobyException in org.biomoby.registry.definitions.types

Methods in org.biomoby.registry.definitions.types that throw MobyException

static void	JObjectsSqlImpl.main(String[] args)
static void	JNamespacesSqlImpl.main(String[] args)
static void	JServicesSqlImpl.main(String[] args)

Constructors in org.biomoby.registry.definitions.types that throw MobyException

JNamespacesSqlImpl()

JObjectsSqlImpl()

JServicesSqlImpl()

Uses of MobyException in org.biomoby.registry.meta

Methods in org.biomoby.registry.meta that throw MobyException

static URL	Registry.findResourceURL(Registry reg, String resourceName) Learn the RDF location for resources of the registry.
Registry	RegistriesList.get(String synonym)
Registry	Registries.get(String synonym) Return an object with properties of a given BioMoby registry.

Uses of MobyException in org.biomoby.registry.properties

Methods in org.biomoby.registry.properties that throw MobyException

static Map	MobyCentralConfig.getMobyCentral() A method that retrieves the mySQL connection details for the database mobycentral.
static Map	MobyCentralConfig.getMobyNamespace() A method that retrieves the mySQL connection details for the database mobynamespace.
static Map	MobyCentralConfig.getMobyObject() A method that retrieves the mySQL connection details for the database mobyobject.
static Map	MobyCentralConfig.getMobyRelationship() A method that retrieves the mySQL connection details for the database mobyrelationship.
static Map	MobyCentralConfig.getMobyService() A method that retrieves the mySQL connection details for the database mobyservice.
static void	MobyCentralConfig.main(String[] args) a brief test application that outputs the information obtained by calling each of the methods in this class.

Uses of MobyException in org.biomoby.registry.rdfagent.util

Methods in org.biomoby.registry.rdfagent.util that throw MobyException

boolean	CentralDataAccess.decrementErrorCountForURL(String signatureURL)
boolean	CentralDataAccessImpl.decrementErrorCountForURL(String signatureURL)
boolean	CentralDataAccess.deleteErrorCountForURL(String signatureURL)
boolean	CentralDataAccessImpl.deleteErrorCountForURL(String signatureURL)
Connection	DBConnector.getConnection()
int	CentralDataAccess.getErrorCountForURL(String signatureURL)
int	CentralDataAccessImpl.getErrorCountForURL(String signatureURL)
boolean	CentralDataAccess.incrementErrorCountForURL(String signatureURL, int errorCode)
boolean	CentralDataAccessImpl.incrementErrorCountForURL(String signatureURL, int errorCode)
boolean	CentralDataAccess.insertErrorCountForURL(String signatureURL, int errorCode)
boolean	CentralDataAccessImpl.insertErrorCountForURL(String signatureURL, int errorCode)

Constructors in org.biomoby.registry.rdfagent.util that throw MobyException

CentralDataAccessImpl()
Default Constructor

DBConnector()
Constructor

Uses of MobyException in org.biomoby.registry.sync

Methods in org.biomoby.registry.sync that throw MobyException

static CentralDigestImpl	CentralFactory.getLocalCentral() Returns the local central.
static CentralDigestImpl	CentralFactory.getMasterCentral() Returns the master central.
static void	CentralFactory.init(Properties configuration) Initialise the master and the local centrals.
void	MobySynchronizeImpl.updateDatatypes()
void	MobySynchronize.updateDatatypes() Synchronize the dataypes between the local and master central
void	MobySynchronizeImpl.updateNamespaces()
void	MobySynchronize.updateNamespaces() Synchronize the namespaces between the local and master central
void	AbstractMobySynchronize.updateRegistry(Properties configuration) Updates the local registry.
void	MobySynchronizeImpl.updateServices()
void	MobySynchronize.updateServices() Synchronize the services between the local and master central
void	MobySynchronizeImpl.updateServiceTypes()
void	MobySynchronize.updateServiceTypes() Synchronize the servicetypes between the local and master central

Constructors in org.biomoby.registry.sync that throw MobyException

AbstractMobySynchronize()

MobySynchronizeImpl()

Uses of MobyException in org.biomoby.registry.sync.handler

Constructors in org.biomoby.registry.sync.handler that throw MobyException

AbstractMobyHandler(String authority)

DataTypeHandler(String authority)

NamespaceHandler(String authority)

ServiceHandler(String authority)

ServiceTypeHandler(String authority)

Uses of MobyException in org.biomoby.service

Methods in org.biomoby.service that throw MobyException

MobyPackage	BaseService.prepareOutput(MobyPackage mobyInput) Return a package that has the same number of jobs (and named the same) as the given input.
abstract void	BaseService.processIt(MobyJob request, MobyJob response, MobyPackage outputContext) A job-level processing: This is the main method to be overriden by a service provider!
void	BaseService.processIt(MobyPackage mobyInput, MobyPackage mobyOutput) A high-level processing.

Uses of MobyException in org.biomoby.service.dashboard

Methods in org.biomoby.service.dashboard that throw MobyException

String	RegistryModel.callRegistry(String methodName, File inputXML) Call the given method (on worker) with data given in 'inputXML'.
void	RegistrationServiceSubPanel.checkAndCallAgent()
void	RegistrationServiceTypeSubPanel.checkAndRegister(boolean realRegistration)
void	RegistrationPanel.checkAndRegister(boolean realRegistration) Should be overwritten by sub-panels.
void	RegistrationDataTypeSubPanel.checkAndRegister(boolean realRegistration)
void	RegistrationNamespaceSubPanel.checkAndRegister(boolean realRegistration)
void	RegistrationServiceSubPanel.checkAndRegister(boolean realRegistration)
HashSet	RegistryModel.findInDataTypes(String searchText) Return a HashSet filled with names of data types that have somewhere given 'searchText'.
HashSet	RegistryModel.findInNamespaces(String searchText) Return a HashSet filled with names of namespaces that have somewhere given 'searchText'.
Set<String>	RegistryModel.findInServices(String searchText) Return a Set filled with names of services that have somewhere given 'searchText'.
Set<String>	RegistryModel.findInServiceTypes(String searchText) Return a Set filled with names of service types that have somewhere given 'searchText'.
String	RegistryModel.getCacheInfoFormatted()
MobyDataType	RegistryModel.getDataType(String dataTypeName)
MobyDataType[]	RegistryModel.getDataTypes(Object initiator) Fetch data types (from a cache or from a registry).
MobyNamespace	RegistryModel.getNamespace(String namespace)
MobyNamespace[]	RegistryModel.getNamespaces(Object initiator) Fetch namespaces (from a cache or from a registry).
String	RegistryModel.getRegisterDataTypeXML(MobyDataType dataType)
String	RegistryModel.getRegisterNamespaceXML(MobyNamespace namespace)
String	RegistryModel.getRegisterServiceTypeXML(MobyServiceType serviceType)
String	RegistryModel.getRegisterServiceXML(MobyService service)
MobyService	RegistryModel.getService(String combinedServiceName)
MobyService[]	RegistryModel.getServices(Object initiator) Fetch services (from a cache or from a registry).
MobyServiceType	RegistryModel.getServiceType(String serviceTypeName)
MobyServiceType[]	RegistryModel.getServiceTypes(Object initiator) Fetch service types (from a cache or from a registry).
void	AntModel.mosesAll() Deal both with Moses-generated datatypes and skeletons - in an appropriate order.
void	AntModel.mosesCleanDatatypes() Remove generated datatypes.
void	AntModel.mosesCleanSkeletons() Remove generated skeletons
void	AntModel.mosesDatatypes() Deal with Moses-generated datatypes.
void	AntModel.mosesDeploy() Deploy selected services to a server (Tomcat/Axis).
void	AntModel.mosesSkeletons() Deal with Moses-generated skeletons.
void	AntModel.mosesUndeploy() Undeploy selected services to a server (Tomcat/Axis).
void	RegistryModel.registerDataType(MobyDataType dataType)
void	RegistryModel.registerNamespace(MobyNamespace namespace)
void	RegistryModel.registerService(MobyService service)
void	RegistryModel.registerServiceType(MobyServiceType serviceType)
void	RegistryModel.reloadDataTypesCache()
void	RegistryModel.reloadNamespacesCache()
void	RegistryModel.reloadServicesCache()
void	RegistryModel.reloadServiceTypesCache()
void	UnitTestingServiceCallermodel.runIt(DataContainer data) Call a service.
void	ServiceCallerModel.runIt(DataContainer data) Call a service.
void	RegistryModel.unRegisterDataType(MobyDataType dataType)
void	RegistryModel.unRegisterNamespace(MobyNamespace namespace)
void	RegistryModel.unRegisterService(MobyService service)
void	RegistryModel.unRegisterServiceType(MobyServiceType serviceType)
void	RegistryModel.updateDataTypesCache()
void	RegistryModel.updateNamespacesCache()
void	RegistryModel.updateServicesCache()
void	RegistryModel.updateServiceTypesCache()

Uses of MobyException in org.biomoby.service.dashboard.data

Methods in org.biomoby.service.dashboard.data that throw MobyException

void	DataContainer.setDataFromFile(File file) Fill this container by data from the given file.
void	ServiceInputPanel.setValues(String xml)

Uses of MobyException in org.biomoby.service.dashboard.renderers

Methods in org.biomoby.service.dashboard.renderers that throw MobyException

JComponent	Base64Image.getComponent(DataContainer data)
JComponent	TabCollectionRenderer.getComponent(DataContainer data)
JComponent	ICISPedigreeTree.getComponent(DataContainer data)
JComponent	BoxCollectionRenderer.getComponent(DataContainer data)
JComponent	XMLTreeRenderer.getComponent(DataContainer data)
JComponent	PlainText.getComponent(DataContainer data)
abstract JComponent	AbstractRenderer.getComponent(DataContainer data)
abstract JComponent	CollectionRenderer.getComponent(DataContainer data)
JComponent	Renderer.getComponent(DataContainer data) Return a JComponent displaying (rendering) given data.
boolean	Base64Image.save2File(DataContainer data, File file)
boolean	ICISPedigreeTree.save2File(DataContainer data, File file) Does not provide any file saving facility.
boolean	AbstractRenderer.save2File(DataContainer data, File file) Default implementation.
boolean	CollectionRenderer.save2File(DataContainer data, File file) It creates a separate file for each element of the collection in 'data' (it does nothing if 'data' is null, or if it does not contain a collection - an array).
boolean	Renderer.save2File(DataContainer data, File file) Save given data in the given file.

Constructors in org.biomoby.service.dashboard.renderers that throw MobyException

XMLTree(String text)
Build a new XMLTree from the supplied String containing XML.

XMLTree(String text, int textSizeLimit)
Build a new XMLTree from the supplied String containing XML.

Uses of MobyException in org.biomoby.service.generator

Methods in org.biomoby.service.generator that throw MobyException

abstract void	Generator.generate(Properties props) Generate "things" from a given Biomoby registry.
void	DataTypesGenerator.generate(Properties props) Generate classes for all data types from a given Biomoby registry.
void	ServicesGenerator.generate(Properties props) Generate classes for service(s) from a given Biomoby registry.
static File	Generator.makeDirs(String dirName, String packageName) Create all needed sub-directories - as required by given Java package name.

Constructors in org.biomoby.service.generator that throw MobyException

DataTypesGenerator(String cacheDir)

DataTypesGenerator(String registryEndpoint, String registryURI, String cacheDir)

Generator(String cacheDir)
Another constructor pointing to a cache directory where the retrieved data types are stored.

Generator(String registryEndpoint, String registryURI, String cacheDir)
Another constructor pointing to a cache directory and defining where is a Biomoby registry whoe data types will be generated.

ServicesGenerator(String cacheDir)

ServicesGenerator(String registryEndpoint, String registryURI, String cacheDir)

Uses of MobyException in org.biomoby.shared

Methods in org.biomoby.shared that throw MobyException

String	Central.call(String methodName, String inputXML) Call Moby registry's method with given XML as input and return whatever you get back.
boolean	MobyUnitTest.compareOutputXML(String testXML) XML is assumed to be wellformed and valid.
boolean	MobyUnitTest.compareXmlWithXpath(String testXML)
static void	Utils.createFile(File file, String contents) Create a file and fill it with given contents.
static void	Utils.createFile(File file, StringBuffer contents) Create a file and fill it with given contents.
MobyService[]	Central.findService(MobyService pattern) Find services matching whatever is non-empty in the given 'pattern'.
MobyService[]	Central.findService(MobyService pattern, String[] keywords) Find service matching both all non-empty fields in the 'pattern' and the 'keywords'.
MobyService[]	Central.findService(MobyService pattern, String[] keywords, boolean includeChildrenServiceTypes, boolean includeParentDataTypes) Find service matching both all non-empty fields in the 'pattern' and the 'keywords', and take into account also the whole ontology tree.
MobyService[]	Central.findService(String serviceType) Find services of the given type and its sub-types.
MobyService[]	Central.findService(String[] keywords) Find services by given keywords.
MobyDataType	Central.getDataType(String dataTypeName) Get definition of the given data type.
Map<String,String>	Central.getDataTypeNames() Get the list of all registered data types.
Map<String,String>	Central.getDataTypeRelationships(String dataTypeName) Get all relationships of the given 'dataTypeName'.
String[]	Central.getDataTypeRelationships(String dataTypeName, String relationshipType) Get all relationships of type 'relationshipType' for the given 'dataTypeName'.
MobyDataType[]	CentralDigest.getDataTypes() Get definition of all known data types.
MobyDataType[]	Central.getDataTypes()
MobyNamespace[]	Central.getFullNamespaces() Get the list of all registered namespaces, with all their attributes.
MobyServiceType[]	CentralDigest.getFullServiceTypes() Get definition of all known service types.
static InputStream	Utils.getInputStream(URL url) Gets an InputStream on a URL
Map<String,String>	Central.getNamespaces() Deprecated. Replaced by Central.getFullNamespaces() that gives more information for the same price.
Map	MobyObjectDecompositionImpl.getObjectComposition(String name, String endpoint)
Map	MobyObjectDecomposition.getObjectComposition(String object, String mobyEndpoint) PRE:None.
String[]	Central.getProviders() Get the list of all providers (each provider is represented by an authority's URI.
InputStream	Central.getResource(String resourceName) First get (from a BioMoby registry) a URL for the given 'resourceName' and then retrieve a document from this URL.
MobyResourceRef[]	Central.getResourceRefs() Get URLs (and content types) of RDF documents describing various BioMoby ontologies.
Map<String,String>	Central.getServiceNames() Deprecated. Replaced by Central.getServiceNamesByAuthority(). The reason is that this method returns a random result if there are more services with the same name but belonging to different authorities.
Map<String,String[]>	Central.getServiceNamesByAuthority() Get a list of all authorities - and for each of them a list of their registered service names.
MobyService[]	CentralDigest.getServices() Get definition of all registered service instances.
String[]	Central.getServiceTypeRelationships(String serviceTypeName, boolean expand) Get all ISA relationships of the given 'serviceTypeName'.
Map<String,String>	Central.getServiceTypes() Get the list of all registered service types.
String	Central.getServiceWSDL(String serviceName) Get WSDL defining a service given by its name.
String	Central.getServiceWSDL(String serviceName, String authority) Get WSDL defining a service given by its name and its authority.
static void	MobyObjectDecompositionImpl.main(String[] args)
static String	Utils.readResource(String filename, Object resourceOwner) Find the resource with the given 'filename', read it and return it.
void	Central.registerDataType(MobyDataType dataType) Register new data type.
void	Central.registerNamespace(MobyNamespace namespace) Register new namespace.
void	Central.registerService(MobyService service) Register a new service.
void	Central.registerServiceType(MobyServiceType serviceType) Register new service type.
void	Central.unregisterDataType(MobyDataType dataType) Unregister given Moby data type.
void	Central.unregisterNamespace(MobyNamespace namespace) Unregister given Moby namespace.
void	Central.unregisterService(MobyService service) Unregister given Moby service.
void	Central.unregisterServiceType(MobyServiceType serviceType) Unregister given Moby service type.
void	CentralCached.updateCache(String id) Update the indicated part of a cache.

Uses of MobyException in org.biomoby.shared.data

Subclasses of MobyException in org.biomoby.shared.data

class

MobyServiceException

Methods in org.biomoby.shared.data that throw MobyException

void	MobyDataObject.addCrossReferences(Element e)
void	MobyDataObject.addCrossReferences(Element e, Registry reg)
void	MobyDataObject.addProvisionInfo(Element e)
static MobyDataInstance	MobyDataObject.createInstanceFromDOM(Element objectTag) This method creates a MobyDataObject of the appropriate subclass for a given input XML tree (e.g. base objects like MobyDataObject and MobyDataInt, or complex objects like MobyDataDateTime or MobyDataComposite, or even a MobyDataSecondaryInstance).
static MobyDataInstance	MobyDataObject.createInstanceFromDOM(Element objectTag, Registry registry)
static MobyDataObject	MobyDataObject.createInstanceFromString(String typeName, String value) Construct a primitive data type instance from a string value.
static MobyDataObject	MobyDataObject.createInstanceFromString(String typeName, String value, Registry registry)
static Collection<? extends MobyDataObject>	MobyDataObjectSet.getChildren(Element e, Registry registry)
void	MobyContentInstance.parseDataGroup(Element dataGroupTag, Registry registry)

Constructors in org.biomoby.shared.data that throw MobyException

MobyContentInstance(Element objectTag)
Builds a MobyContentInstance (i.e. one or more MOBY queries or responses) using a DOM-parsed XML MOBY envelope (i.e. the mobyContent tag).

MobyContentInstance(Element objectTag, Registry registry)

MobyContentInstance(MobyDataInstance mdi, String paramName)
A convenience constructor when you want to create an envelope with just one object in it.

MobyDataBytes(Element element)
Construct the object using a DOM fragment.

MobyDataBytes(Element element, Registry registry)

MobyDataBytes(String name, byte[] data)
C-tor to use when you have binary data to encode

MobyDataBytes(String name, byte[] data, MobyDataType inputDataType)
C-tor to use when you have binary data to encode

MobyDataBytes(String name, byte[] data, Registry registry)

MobyDataBytes(String name, CharSequence data, MobyDataType inputDataType)
C-tor to use when you have received text-encoded binary.

MobyDataBytes(String name, URL resourceURL)
C-tor to use when you want to encode a resource, such as an image file.

MobyDataBytes(String name, URL resourceURL, MobyDataType inputDataType)
C-tor to use when you want to encode a resource, such as an image file.

MobyDataBytes(String name, URL resourceURL, Registry registry)

MobyDataComposite(Element element)
Construct the object using a DOM fragment.

MobyDataComposite(Element element, Registry registry)

MobyDataComposite(MobyDataType type, MobyNamespace namespace, String id, Object... memberStrings)
Instantiates a composite with a variable number of members using Java 1.5's varargs.

MobyDataObject(Element element)
Construct the object using a DOM fragment.

MobyDataObject(Element element, Registry registry)

MobyDataObjectSet(Element e)

MobyDataObjectSet(Element e, Registry registry)

MobyDataSecondaryInstance(Element objectTag)
Create an instance from XML input.

MobyDataXref(Element e)

MobyDataXref(Element e, Registry registry)

Uses of MobyException in org.biomoby.shared.datatypes

Methods in org.biomoby.shared.datatypes that throw MobyException

Class	MapDataTypesIfc.getClass(String dataTypeName)
Class	MapPrimitiveDataTypes.getClass(String dataTypeName) Return a class that represents given data type.
double	MobyFloat.getFloatValue() Return the value of this object as a numeric object (double).
long	MobyInteger.getIntValue() Return the value of this object as a numeric object (long).
void	MobyXref.setEvidenceCode(String code) Set an evidence code.
void	MobyObject.setValue(String value) Set a value of this object.
void	MobyDateTime.setValue(String value) Additionally to the same method in the superclass, it checks for a correct format.
void	MobyInteger.setValue(String value) Additionally to the same method in the superclass, it checks for numerical and integer value (its length is not limited - internaly it uses BigInteger object).
void	MobyBoolean.setValue(String value) Additionally to the same method in the superclass, it checks for boolean value - but it takes always everything, so no exception thrown.
void	MobyFloat.setValue(String value) Additionally to the same method in the superclass, it checks for numerical value (its length is not limited - internaly it uses BigDecimal object).
void	MobyObject.setValueXML(String value) Set a value of this object.

Uses of MobyException in org.biomoby.shared.extended

Methods in org.biomoby.shared.extended that throw MobyException

MobyDataType[]	DataTypeParser.getMobyDataTypesFromRDF()
MobyNamespace[]	NamespaceParser.getMobyNamespacesFromRDF()
MobyService[]	ServiceInstanceParser.getMobyServicesFromRDF()
MobyService[]	ServiceInstanceParser.getMobyServicesFromRDF(com.hp.hpl.jena.rdf.model.Model model)
MobyService[]	ServiceInstanceParser.getMobyServicesFromRDF(String rdf)
MobyServiceType[]	ServiceTypeParser.getMobyServiceTypesFromRDF()
static void	ServiceInstanceParser.main(String[] args)
static void	NamespaceParser.main(String[] args)
static void	DataTypeParser.main(String[] args)
static void	ServiceTypeParser.main(String[] args)
void	ServiceInstanceParser.setUrl(String url)
void	NamespaceParser.setUrl(String url)
void	DataTypeParser.setUrl(String url)
void	ServiceTypeParser.setUrl(String url)
void	ServiceInstanceParser.setUrl(URL url)
void	NamespaceParser.setUrl(URL url)
void	DataTypeParser.setUrl(URL url)
void	ServiceTypeParser.setUrl(URL url)

Constructors in org.biomoby.shared.extended that throw MobyException

DataTypeParser(String url)
Parameterized Constructor that takes in a string argument that is the url for the RDF document that describes the Data Type ontology.

DataTypeParser(URL url)
Parameterized Constructor that takes in a url for the RDF document that describes the Data Type ontology.

NamespaceParser(String url)
Parameterized Constructor that takes in a string argument that is the url for the RDF document that describes the Namespace ontology.

NamespaceParser(URL url)
Parameterized Constructor that takes in a url for the RDF document that describes the Namespace ontology.

ServiceInstanceParser(String url)
Parameterized Constructor that takes in a string argument that is the url for the RDF document that describes the service ontology.

ServiceInstanceParser(URL url)
Parameterized Constructor that takes in a url for the RDF document that describes the service ontology.

ServiceTypeParser(String url)
Parameterized Constructor that takes in a string argument that is the url for the RDF document that describes the Service Type ontology.

ServiceTypeParser(URL url)
Parameterized Constructor that takes in a url for the RDF document that describes the Service Type ontology.

Uses of MobyException in org.biomoby.shared.parser

Subclasses of MobyException in org.biomoby.shared.parser

class

ServiceException A container for an exception raised by a service provider when something wrong has to be reported back to a client.

Methods in org.biomoby.shared.parser that throw MobyException

void	MobyJob.addData(MobyObject data) Create an un-named Simple object and add it as the last one in the current data elements.
void	MobyJob.addData(MobyObject data, String name) Create a named Simple object and add it as the last one in the current data elements.
void	MobyJob.addDataSet(MobyObject[] data) Create an un-named Collection object and add it as the last one in the current data elements.
void	MobyJob.addDataSet(MobyObject[] data, String name) Create a named Collection object and add it as the last one in the current data elements.
static MobyPackage	MobyPackage.createFromXML(Object xmlData) Constructing a MobyPackage object from XML.
static MobyPackage	MobyPackage.createFromXML(Object xmlData, Map<String,String> lowestKnownDataTypes) Constructing a MobyPackage object from XML.
static MobyPackage	MobyPackage.createFromXML(Object xmlData, String lowestKnownDataType) Constructing a MobyPackage object from XML.
String	MobyPackage.evaluateExceptions(org.apache.commons.logging.Log log, boolean throwException) Evaluate current exceptions.
MobyObject	MobyJob.getData() Find and return the first data element of type Simple (which may not be the first data element in this job).
MobyObject	MobyJob.getData(String name) Find and return a data element of a Simple type that is named by 'name'.
MobyObject	MobyJob.getData(String name, String dataTypeName) Find and return a data element of a Simple type that is named by 'name' and has data type 'dataTypeName'.
MobyObject[]	MobyJob.getDataSet() Find and return the first data element of type Collection (which may not be the first data element in this job).
MobyObject[]	MobyJob.getDataSet(int index) Find and return the 'index'-th data element, assuming that it is a Collection data element.
MobyObject[]	MobyJob.getDataSet(String name) Find and return a data element of a Collection type that is named by 'name'.
MobyObject[]	MobyJob.getDataSet(String name, String dataTypeName) Find and return a data element coming from a Collection type that is named by 'name' and has data type 'dataTypeName'.
MobyJob	MobyPackage.getJob(int index) Get back a job indicated by its order number.
String	MobyJob.getParameter(String name) Find a Parameter object named by 'name', and return its value.
static MapDataTypesIfc	MobyParser.loadB2JMapping() Load mapping class between Biomoby data types names and their Java representations.
MobyPackage	MobyParser.parse(InputStream xml) Parse the contents coming from the given input stream.
MobyPackage	MobyParser.parse(Reader xmlReader) Parse the contents coming from the given reader.
MobyPackage	MobyParser.parse(String xmlFilename) Parse the contents of the given file.
void	MobyJob.setData(MobyObject data) Create an un-named Simple object as the first data element.
void	MobyJob.setData(MobyObject data, String name) Create a named Simple object as the first data element.
void	MobyJob.setData(MobyObject data, String name, int index) Create a named Simple object and put it as the 'index'-th data element.
void	MobyJob.setDataSet(MobyObject[] data) Create an un-named Collection object as the first data element.
void	MobyJob.setDataSet(MobyObject[] data, String name) Create a named Collection object as the first data element.
void	MobyJob.setDataSet(MobyObject[] data, String name, int index) Create a named Collection object and put it as the 'index'-th data element.

Uses of MobyException in org.biomoby.w3c.addressing

Methods in org.biomoby.w3c.addressing that throw MobyException

static EndpointReference

EndpointReference.createFromXML(Object xmlData)

Uses of MobyException in org.omg.lsae.notifications

Methods in org.omg.lsae.notifications that throw MobyException

static AnalysisEvent[]

AnalysisEvent.createFromXML(Object xmlData)

Uses of MobyException in org.omg.lsae.sax

Methods in org.omg.lsae.sax that throw MobyException

AnalysisEvent[]	EventParser.parse(InputStream xml) Parse the contents coming from the given input stream.
AnalysisEvent[]	EventParser.parse(Reader xmlReader) Parse the contents coming from the given reader.
AnalysisEvent[]	EventParser.parse(String xmlFilename) Parse the contents of the given file.

Uses of MobyException in org.soap

Methods in org.soap that throw MobyException

static SOAPFault

SOAPFault.createFromXML(Object xmlData)

Uses of MobyException in org.soap.sax

Methods in org.soap.sax that throw MobyException

SOAPFault	SOAPFaultParser.parse(InputStream xml) Parse the contents coming from the given input stream.
SOAPFault	SOAPFaultParser.parse(Reader xmlReader) Parse the contents coming from the given reader.
SOAPFault	SOAPFaultParser.parse(String xmlFilename) Parse the contents of the given file.

Uses of MobyException in org.w3c.addressing.sax

Methods in org.w3c.addressing.sax that throw MobyException

EndpointReference	EndpointReferenceParser.parse(InputStream xml) Parse the contents coming from the given input stream.
EndpointReference	EndpointReferenceParser.parse(Reader xmlReader) Parse the contents coming from the given reader.
EndpointReference	EndpointReferenceParser.parse(String xmlFilename) Parse the contents of the given file.