Package ubic.gemma.web.services

Class AbstractGemmaEndpoint

java.lang.Object

org.springframework.xml.transform.TransformerObjectSupport

org.springframework.ws.server.endpoint.AbstractDomPayloadEndpoint

ubic.gemma.web.services.AbstractGemmaEndpoint

All Implemented Interfaces:

org.springframework.ws.server.endpoint.PayloadEndpoint

Direct Known Subclasses:

ArrayDesignIdentifierByNameEndpoint, ArrayDesignUsedEndpoint, DEDVfromEEIDGeneIDEndpoint, DEDVRankEndpoint, DifferentialExpressionProbeResultEndpoint, ExperimentAnnotationEndpoint, ExperimentDEDVEndpoint, ExperimentIDbyTaxonEndpoint, ExperimentIdEndpoint, ExperimentNameEndpoint, ExperimentNumSamplesEndpoint, ExpressionExperimentSetIDsEndpoint, Gene2GOdescriptionEndpoint, Gene2GoTermEndpoint, Gene2ProbeEndpoint, GeneByNCBIIdEndpoint, GeneCoexpressionEndpoint, GeneCoexpressionSearchEndpoint, GeneDetailsByGeneIDEndpoint, GeneIDbyTaxonEndpoint, GeneIdEndpoint, GeneNameEndpoint, GeneOverlapEndpoint, GoTerm2GeneEndpoint, Probe2GeneEndpoint

public abstract class AbstractGemmaEndpoint
extends org.springframework.ws.server.endpoint.AbstractDomPayloadEndpoint

Abstracts out the security and a few constants.

Author:

gavin, klc

Field Summary

Fields

Modifier and Type	Field	Description
static String	DELIMITER
protected gemma.gsec.authentication.ManualAuthenticationService	manualAuthenticationService
static String	NAMESPACE_URI	Namespace of both request and response.
protected static String	REQUEST
protected static String	RESPONSE

Fields inherited from class org.springframework.xml.transform.TransformerObjectSupport

logger

Constructor Summary

Constructors

Constructor	Description
AbstractGemmaEndpoint()

Method Summary

Modifier and Type	Method	Description
protected boolean	authenticate()
protected Element	buildBadResponse(Document document, String msg)
protected Element	buildWrapper(Document document, Collection<String> values, String elementName)	Function to handle the constructing of output in xml format for returning the response to the client.
protected String	encode(Object[] data)
protected Collection<String>	getArrayValues(Element requestElement, String tagName)
protected String	getLastSingleNodeValue(Element requestElement, String tagName)	basically Delegates to getSingleNodeValue and returns the just the last value.
protected String	getNodeValue(Element requestElement, String tagName)
protected String	getOptionalNodeValue(Element requestElement, String tagName)
protected Collection<String>	getSingleNodeValue(Element requestElement, String tagName)	Function that handles the retrieval of xml input.
protected Document	readReport(InputStream is)	Looks to parse a previously generated xml report that was saved to disk.
protected Document	readReport(String filename)	uses the default path of gemmaData/datafile/xml/ to look for reports.
protected Document	readReport(String path, String fileName)
protected void	setLocalName(String localName)
void	setManualAuthenticationService(gemma.gsec.authentication.ManualAuthenticationService map)
protected void	writeReport(Element responseWrapper, Document document, String filename)	This method should/can only be used when the wrapper is manually built in the specific endpoints (ie.

Methods inherited from class org.springframework.ws.server.endpoint.AbstractDomPayloadEndpoint

createDocumentBuilder, createDocumentBuilderFactory, getDocumentElement, invoke, invokeInternal, setAlwaysTransform, setExpandEntityReferences, setNamespaceAware, setValidating

Methods inherited from class org.springframework.xml.transform.TransformerObjectSupport

createTransformer, getTransformerFactory, newTransformerFactory, setTransformerFactoryClass, transform

Methods inherited from class java.lang.Object

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

Field Detail

NAMESPACE_URI

public static final String NAMESPACE_URI

Namespace of both request and response.

DELIMITER

public static final String DELIMITER

See Also:

Constant Field Values

REQUEST

protected static final String REQUEST

See Also:

Constant Field Values

RESPONSE

protected static final String RESPONSE

See Also:

Constant Field Values

manualAuthenticationService

protected gemma.gsec.authentication.ManualAuthenticationService manualAuthenticationService

Constructor Detail

AbstractGemmaEndpoint

public AbstractGemmaEndpoint()

Method Detail

setManualAuthenticationService

public void setManualAuthenticationService(gemma.gsec.authentication.ManualAuthenticationService map)

authenticate

protected boolean authenticate()

buildBadResponse

protected Element buildBadResponse(Document document,
                                   String msg)

Parameters:

document - document

msg - msg

Returns:

Function to handle construction of output in xml for a bad response

buildWrapper

protected Element buildWrapper(Document document,
                               Collection<String> values,
                               String elementName)

Function to handle the constructing of output in xml format for returning the response to the client. Use this method for simple value returns such as single value or a single array of values. building Mapped values is not supported with this method. If values being passed in are null or contain no values, then a string msg will be returned

Parameters:

document - document

values - a collection of the values (in String format) to be returned to the client

elementName - element name

Returns:

element

encode

protected String encode(Object[] data)

Parameters:

data - data

Returns:

a string delimited representation of the objects array passed in.

getArrayValues

protected Collection<String> getArrayValues(Element requestElement,
                                            String tagName)

Parameters:

requestElement - erquest element

tagName - tag name

Returns:

A method written for array input from MATLAB clients. A more generic method to use is getNodeValues(). Column Arrays and Horizontal Arrays from MATLAB both work, but it must be passed in directly (i.e. EEArray.ee_ids)

getLastSingleNodeValue

protected String getLastSingleNodeValue(Element requestElement,
                                        String tagName)

basically Delegates to getSingleNodeValue and returns the just the last value.

Parameters:

requestElement - request element

tagName - tag name

Returns:

last value

getNodeValue

protected String getNodeValue(Element requestElement,
                              String tagName)

getOptionalNodeValue

protected String getOptionalNodeValue(Element requestElement,
                                      String tagName)

getSingleNodeValue

protected Collection<String> getSingleNodeValue(Element requestElement,
                                                String tagName)

Function that handles the retrieval of xml input. Use this method if there is only one value in the input but generically, this method can also store multiple input values as well. This will depend on how the xml is parsed by the client. OLDTODO Still need to test on different types of client requests.

Parameters:

requestElement - - xml request in node hierarchy

tagName - tag name

Returns:

a collection contain one string element

readReport

protected Document readReport(InputStream is)
                       throws IOException

Looks to parse a previously generated xml report that was saved to disk. Returns null if it fails to do so.

Parameters:

is - from an existing xml file

Returns:

An XML document

Throws:

IOException - IO problems

readReport

protected Document readReport(String filename)
                       throws IOException

uses the default path of gemmaData/datafile/xml/ to look for reports.

Parameters:

filename - needs the xml suffix

Returns:

document

Throws:

IOException - IO problems

readReport

protected Document readReport(String path,
                              String fileName)
                       throws IOException

Throws:

IOException

setLocalName

protected void setLocalName(String localName)

writeReport

protected void writeReport(Element responseWrapper,
                           Document document,
                           String filename)

This method should/can only be used when the wrapper is manually built in the specific endpoints (ie. not using the buildWrapper() in AbstractGemmaEndpoint).

Parameters:

responseWrapper - - Manually built wrapper

document - document

filename - - no xml extension is required