A C D F G I J M O P Q R S T W X

A

ANALYSIS_DESCRIPTION - Static variable in interface org.embl.ebi.SoaplabShare.AnalysisWS

A property name for an analysis description.

ANALYSIS_HELP_URL - Static variable in interface org.embl.ebi.SoaplabShare.AnalysisWS

A property name for an analysis URL with a detailed help.

ANALYSIS_INSTALLATION - Static variable in interface org.embl.ebi.SoaplabShare.AnalysisWS

A property name for an analysis installation.

ANALYSIS_NAME - Static variable in interface org.embl.ebi.SoaplabShare.AnalysisWS

A property name for an analysis name.

ANALYSIS_SUPPLIER - Static variable in interface org.embl.ebi.SoaplabShare.AnalysisWS

A property name for an analysis supplier.

ANALYSIS_TYPE - Static variable in interface org.embl.ebi.SoaplabShare.AnalysisWS

A property name for an analysis type.

ANALYSIS_VERSION - Static variable in interface org.embl.ebi.SoaplabShare.AnalysisWS

A property name for an analysis version.

AnalysisFactoryWS - Interface in org.embl.ebi.SoaplabShare

An interface to a Web Service that produces a list of available analyses, and provides pointers to them.

AnalysisWS - Interface in org.embl.ebi.SoaplabShare

An interface to a Web Service accessing and controlling an analysis (an analysis is a remote program, mostly a command-line program).

C

createAndRun(Map) - Method in interface org.embl.ebi.SoaplabShare.AnalysisWS

A convenient combination of methods AnalysisWS.createJob(java.util.Map) and run.

createAndRunNotifiable(Map, String) - Method in interface org.embl.ebi.SoaplabShare.AnalysisWS

The same as AnalysisWS.createAndRun(java.util.Map) with addition of the channel notification negotiation.

createJob(Map) - Method in interface org.embl.ebi.SoaplabShare.AnalysisWS

Prepare a job with given input data but do not start it.

D

DATA_HELP - Static variable in interface org.embl.ebi.SoaplabShare.AnalysisWS

A property name of a data attribute.

DATA_PROMPT - Static variable in interface org.embl.ebi.SoaplabShare.AnalysisWS

A property name of a data attribute.

DATA_SEMANTIC_TYPE - Static variable in interface org.embl.ebi.SoaplabShare.AnalysisWS

A property name of a data attribute.

DATA_SEMANTIC_TYPE_2 - Static variable in interface org.embl.ebi.SoaplabShare.AnalysisWS

A property name of a data attribute.

DATA_SYNTAX_TYPE - Static variable in interface org.embl.ebi.SoaplabShare.AnalysisWS

A property name of a data attribute.

DataAdaptPlugIn - Interface in org.embl.ebi.analysis

An interface for adapting (changing, filtering) analysis data.

DEBUG - Static variable in interface org.embl.ebi.SoaplabServer.gowlab.RunPlugIn

Property name.

describe() - Method in interface org.embl.ebi.SoaplabShare.AnalysisWS

Return an XML string containing metadata describing this analysis service.

destroy(String) - Method in interface org.embl.ebi.SoaplabShare.AnalysisWS

Release related resources, including results.

F

FAULT_NOT_FOUND - Static variable in interface org.embl.ebi.SoaplabShare.AnalysisWS

A fault string.

FAULT_NOT_IMPLEMENTED - Static variable in interface org.embl.ebi.SoaplabShare.AnalysisWS

A fault string.

FAULT_NOT_RUNNABLE - Static variable in interface org.embl.ebi.SoaplabShare.AnalysisWS

A fault string.

FAULT_NOT_RUNNING - Static variable in interface org.embl.ebi.SoaplabShare.AnalysisWS

A fault string.

FAULT_NOT_TERMINATED - Static variable in interface org.embl.ebi.SoaplabShare.AnalysisWS

A fault string.

FAULT_NOT_VALID_INPUTS - Static variable in interface org.embl.ebi.SoaplabShare.AnalysisWS

A fault string.

FAULT_NOTIFY_UNACCEPTED - Static variable in interface org.embl.ebi.SoaplabShare.AnalysisWS

A fault string.

FAULT_UNKNOWN_NAME - Static variable in interface org.embl.ebi.SoaplabShare.AnalysisWS

A fault string.

fetch(HTTPConnection, URI, NVPair[], NVPair[]) - Method in interface org.embl.ebi.SoaplabServer.gowlab.RunPlugIn

Send given data to a site using given connection, wait for an answer, and store results into given Result Manager.

fetch(HTTPConnection, URI, NVPair[], NVPair[]) - Method in class org.embl.ebi.SoaplabServer.gowlab.RunPlugInBaseImpl

Must be implemented by sub-classes.

fetch(HTTPConnection, URI, NVPair[], NVPair[]) - Method in class org.embl.ebi.SoaplabServer.gowlab.RunPlugInDefaultImpl

Send given data to a site using given connection, wait for an answer, and store results into given Result Manager.

fetch(HTTPConnection, URI, NVPair[], NVPair[]) - Method in class org.embl.ebi.SoaplabServer.gowlab.RunPlugInExternalImpl

Fetching data by calling an external program given in the constructor.

G

getAnalysisType() - Method in interface org.embl.ebi.SoaplabShare.AnalysisWS

Return attributes describing this analysis.

getAvailableAnalyses() - Method in interface org.embl.ebi.SoaplabShare.AnalysisFactoryWS

Return an array of names of all available analyses, regardless which category they belong to.

getAvailableAnalysesInCategory(String) - Method in interface org.embl.ebi.SoaplabShare.AnalysisFactoryWS

Return an array of names of all available analyses from the given category.

getAvailableCategories() - Method in interface org.embl.ebi.SoaplabShare.AnalysisFactoryWS

Return an array of names of all available categories.

getCharacteristics(String) - Method in interface org.embl.ebi.SoaplabShare.AnalysisWS

A convenient method combining together methods AnalysisWS.getCreated(java.lang.String), AnalysisWS.getStarted(java.lang.String), AnalysisWS.getEnded(java.lang.String) and AnalysisWS.getElapsed(java.lang.String).

getCreated(String) - Method in interface org.embl.ebi.SoaplabShare.AnalysisWS

Return a creation time of the given job.

getElapsed(String) - Method in interface org.embl.ebi.SoaplabShare.AnalysisWS

Return the elapsed time of the execution of the given job (in milliseconds).

getEnded(String) - Method in interface org.embl.ebi.SoaplabShare.AnalysisWS

Return time when the given job ended.

getInputSpec() - Method in interface org.embl.ebi.SoaplabShare.AnalysisWS

Return information about all possible data inputs.

getLastEvent(String) - Method in interface org.embl.ebi.SoaplabShare.AnalysisWS

Return the last event which happened to the given job.

getNotificationDescriptor(String) - Method in interface org.embl.ebi.SoaplabShare.AnalysisWS

Return an XML string describing location and available protocol (or even protocols) of a notification channel which will have messages regarding given job.

getResults(String) - Method in interface org.embl.ebi.SoaplabShare.AnalysisWS

Return all (available) results from the given job.

getResultSpec() - Method in interface org.embl.ebi.SoaplabShare.AnalysisWS

Return information about all possible results.

getServiceLocation(String) - Method in interface org.embl.ebi.SoaplabShare.AnalysisFactoryWS

Return a location of a web service representing given analysis.

getSomeResults(String, String[]) - Method in interface org.embl.ebi.SoaplabShare.AnalysisWS

Return named (and available) results from the given job.

getStarted(String) - Method in interface org.embl.ebi.SoaplabShare.AnalysisWS

Return time when the given job started.

getStatus(String) - Method in interface org.embl.ebi.SoaplabShare.AnalysisWS

Return a string describing the current job status.

I

INPUT_ALLOWED_VALUES - Static variable in interface org.embl.ebi.SoaplabShare.AnalysisWS

A property name of a data input.

INPUT_DEFAULT_VALUE - Static variable in interface org.embl.ebi.SoaplabShare.AnalysisWS

A property name of a data input.

INPUT_MANDATORY - Static variable in interface org.embl.ebi.SoaplabShare.AnalysisWS

A property name of a data input.

INPUT_NAME - Static variable in interface org.embl.ebi.SoaplabShare.AnalysisWS

A property name of a data input.

INPUT_TYPE - Static variable in interface org.embl.ebi.SoaplabShare.AnalysisWS

A property name of a data input.

J

JOB_COMPLETED - Static variable in interface org.embl.ebi.SoaplabShare.AnalysisWS

A job status: Job has completed execution.

JOB_CREATED - Static variable in interface org.embl.ebi.SoaplabShare.AnalysisWS

A job status: Job has been created but not yet executed.

JOB_RUNNING - Static variable in interface org.embl.ebi.SoaplabShare.AnalysisWS

A job status: Job is running.

JOB_TERMINATED_BY_ERROR - Static variable in interface org.embl.ebi.SoaplabShare.AnalysisWS

A job status: Job was terminated due to an error.

JOB_TERMINATED_BY_REQUEST - Static variable in interface org.embl.ebi.SoaplabShare.AnalysisWS

A job status: Job was terminated by user request.

M

METHOD_GET - Static variable in interface org.embl.ebi.SoaplabServer.gowlab.RunPlugIn

An allowed value of the property RunPlugIn.PREFERRED_METHOD.

METHOD_POST - Static variable in interface org.embl.ebi.SoaplabServer.gowlab.RunPlugIn

An allowed value of the property RunPlugIn.PREFERRED_METHOD.

O

org.embl.ebi.SoaplabShare - package org.embl.ebi.SoaplabShare

P

PREFERRED_METHOD - Static variable in interface org.embl.ebi.SoaplabServer.gowlab.RunPlugIn

Property name.

process(String, InputStream, OutputStream) - Method in interface org.embl.ebi.analysis.DataAdaptPlugIn

Read 'source' data, adapt them, and create the result back.

process(String, InputStream, OutputStream, Map) - Method in interface org.embl.ebi.analysis.DataAdaptPlugIn

The same as process but you may specified additional requirements in the properties.

Q

query2data(String) - Static method in class org.embl.ebi.SoaplabServer.gowlab.RunPlugInBaseImpl

A utility converting a query string (xxx=yyy&kkk=lll) into form-elements data.

R

removeHtml(String) - Static method in class org.embl.ebi.SoaplabServer.gowlab.RunPlugInBaseImpl

A utility removing HTML tags from 'input'.

RESULT_NAME - Static variable in interface org.embl.ebi.SoaplabShare.AnalysisWS

A property name of a data output (a result).

RESULT_NAMES - Static variable in interface org.embl.ebi.SoaplabServer.gowlab.RunPlugIn

Property name.

RESULT_TYPE - Static variable in interface org.embl.ebi.SoaplabShare.AnalysisWS

A property name of a data output (a result).

run(String) - Method in interface org.embl.ebi.SoaplabShare.AnalysisWS

Start an underlying analysis and return immediately, without waiting for its completion.

runAndWaitFor(Map) - Method in interface org.embl.ebi.SoaplabShare.AnalysisWS

Block the client until the underlying running analysis is completed and return immediately all results.

runNotifiable(String, String) - Method in interface org.embl.ebi.SoaplabShare.AnalysisWS

The same as AnalysisWS.run(java.lang.String) with addition of the channel notification negotiation.

RunPlugIn - Interface in org.embl.ebi.SoaplabServer.gowlab

An interface defining behaviour of Gowlab-aware plugins that are able to fetch data from remote web sites.

RunPlugInBaseImpl - Class in org.embl.ebi.SoaplabServer.gowlab

An abstract implementation of RunPlugIn interface, serving as a "utility" class for those wishing to extend it by a real implementation.

RunPlugInBaseImpl() - Constructor for class org.embl.ebi.SoaplabServer.gowlab.RunPlugInBaseImpl

RunPlugInDefaultImpl - Class in org.embl.ebi.SoaplabServer.gowlab

A default implementation of RunPlugIn interface.

RunPlugInDefaultImpl() - Constructor for class org.embl.ebi.SoaplabServer.gowlab.RunPlugInDefaultImpl

RunPlugInExternalImpl - Class in org.embl.ebi.SoaplabServer.gowlab

An extension of a default implementation of RunPlugIn interface that invokes an external program to fetch data.

RunPlugInExternalImpl(String) - Constructor for class org.embl.ebi.SoaplabServer.gowlab.RunPlugInExternalImpl

RunPlugInXSLTImpl - Class in org.embl.ebi.SoaplabServer.gowlab

An extension of a default implementation of RunPlugIn interface that converts resonse data by an XSLT stylesheet.

RunPlugInXSLTImpl(String, String) - Constructor for class org.embl.ebi.SoaplabServer.gowlab.RunPlugInXSLTImpl

Main constructor.

S

SERVICE_NAME - Static variable in interface org.embl.ebi.SoaplabServer.gowlab.RunPlugIn

Property name.

setEventManager(EventManager) - Method in interface org.embl.ebi.SoaplabServer.gowlab.RunPlugIn

Set an Event Manager where this instance will report about the fetching.

setEventManager(EventManager) - Method in class org.embl.ebi.SoaplabServer.gowlab.RunPlugInBaseImpl

setProperties(Properties) - Method in interface org.embl.ebi.SoaplabServer.gowlab.RunPlugIn

Set additional properties that can be useful during fetching data.

setProperties(Properties) - Method in class org.embl.ebi.SoaplabServer.gowlab.RunPlugInBaseImpl

setResultManager(ResultManager) - Method in interface org.embl.ebi.SoaplabServer.gowlab.RunPlugIn

Set a Result Manager where this instance will store fetched data, and where it will report about a success or failure.

setResultManager(ResultManager) - Method in class org.embl.ebi.SoaplabServer.gowlab.RunPlugInBaseImpl

SOAPLAB_SERVICE_NAME_DELIMITER - Static variable in interface org.embl.ebi.SoaplabShare.AnalysisFactoryWS

A string that delimits category name from a service name.

SoaplabException - Exception in org.embl.ebi.SoaplabShare

Just a renamed Exception - to get more specific error messages.

SoaplabException() - Constructor for exception org.embl.ebi.SoaplabShare.SoaplabException

SoaplabException(String) - Constructor for exception org.embl.ebi.SoaplabShare.SoaplabException

T

terminate(String) - Method in interface org.embl.ebi.SoaplabShare.AnalysisWS

Terminate the running analysis, identified by its job ID.

W

waitFor(String) - Method in interface org.embl.ebi.SoaplabShare.AnalysisWS

Block the client until the underlying running analysis is completed.

X

XSLT_DIR - Static variable in interface org.embl.ebi.SoaplabServer.gowlab.RunPlugIn

Property name.

XSLT_FILE - Static variable in interface org.embl.ebi.SoaplabServer.gowlab.RunPlugIn

Property name.

A C D F G I J M O P Q R S T W X