A B C D E F G H I J L M N O P R S T U V W X Z

A

AbstractJob - Class in org.soaplab.services

A convenient parent of other Job's implementations.

add(PropertiesBag) - Method in class org.soaplab.services.metadata.AnalysisDef

add(PropertiesBag) - Method in class org.soaplab.services.metadata.ParamDef

addConfigPropertyFile(String) - Static method in class org.soaplab.services.Config

Add new configuration properties from a property file.

addConfigXMLFile(String) - Static method in class org.soaplab.services.Config

Add new configuration properties from an XML file.

addProperties(PropertiesBag) - Method in class org.soaplab.services.metadata.PropertiesBag

Add new properties to this bag.

addValue(String) - Method in class org.soaplab.services.cmdline.NamedValues

Add a single value to the data representing user inputs.

Analysis - Interface in org.soaplab.share

An interface to a service (usually a web service, but nothing precludes to have, for example, a REST implementtaion of such service), accessing and controlling an analysis.

ANALYSIS_DESCRIPTION - Static variable in interface org.soaplab.share.SoaplabConstants

A property name for an analysis description.

ANALYSIS_EMBOSS - Static variable in interface org.soaplab.share.SoaplabConstants

A property name for an analysis.

ANALYSIS_EVENT - Static variable in interface org.soaplab.services.events.EventConstants

ANALYSIS_HELP_URL - Static variable in interface org.soaplab.share.SoaplabConstants

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

ANALYSIS_INSTALLATION - Static variable in interface org.soaplab.share.SoaplabConstants

A property name for an analysis installation.

ANALYSIS_MODULE - Static variable in interface org.soaplab.share.SoaplabConstants

A property name for an analysis module.

ANALYSIS_NAME - Static variable in interface org.soaplab.share.SoaplabConstants

A property name for an analysis name.

ANALYSIS_SUPPLIER - Static variable in interface org.soaplab.share.SoaplabConstants

A property name for an analysis supplier.

ANALYSIS_TYPE - Static variable in interface org.soaplab.share.SoaplabConstants

A property name for an analysis type.

ANALYSIS_VERSION - Static variable in interface org.soaplab.share.SoaplabConstants

A property name for an analysis version.

AnalysisDef - Class in org.soaplab.services.metadata

A structure with general description of an analysis (details about all analysis input/output data are not here, but in ParamDef structures).

AnalysisDef() - Constructor for class org.soaplab.services.metadata.AnalysisDef

AnalysisEvent - Class in org.soaplab.services.events

A base (immutable) class for all events coming from a running analysis.

AnalysisEvent(Object, String) - Constructor for class org.soaplab.services.events.AnalysisEvent

A constructor taking a general message carried on by this event, and the source of this event.

AnalysisEvent(String) - Constructor for class org.soaplab.services.events.AnalysisEvent

A constructor taking a general message carried on by this event.

AnalysisInstallation - Class in org.soaplab.services.metadata

A container holding data about an analysis.

AnalysisInstallation() - Constructor for class org.soaplab.services.metadata.AnalysisInstallation

Constructors

AnalysisInstallation(Properties) - Constructor for class org.soaplab.services.metadata.AnalysisInstallation

AnalysisInstallation(String, String) - Constructor for class org.soaplab.services.metadata.AnalysisInstallation

AnalysisInventory - Interface in org.soaplab.services

An interface that has to be implemented by classes providing lists of available analyses.

AnalysisList - Interface in org.soaplab.share

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

analysisSpec2Map(MetadataAccessor) - Static method in class org.soaplab.services.metadata.MetadataUtils

Convert a set of Analysis attributes into a Map (as defined and used, for example, by Analysis in Soaplab.

APP_NAME - Static variable in class org.soaplab.services.metadata.AnalysisInstallation

appName - Variable in class org.soaplab.services.metadata.AnalysisDef

B

BASE_PARAMETER - Static variable in class org.soaplab.services.metadata.ParamDef

BOOLEXP - Static variable in class org.soaplab.services.metadata.CondDef

BOOLEXP_ERROR - Static variable in class org.soaplab.services.metadata.CondDef

bools - Variable in class org.soaplab.services.metadata.ChoiceParamDef

C

canBeRepeatable() - Method in class org.soaplab.services.metadata.ParamDef

This method does nothing much here but it's supposed to be overritten.

canBeRepeatable() - Method in class org.soaplab.services.metadata.StdParamDef

Return true if this parameter is allowed to be repeated.

category - Variable in class org.soaplab.services.metadata.AnalysisDef

CATEGORY - Static variable in class org.soaplab.services.metadata.AnalysisInstallation

characters(char[], int, int) - Method in class org.soaplab.services.metadata.MetadataAccessorXML

characters()

checkMetadata() - Method in class org.soaplab.services.metadata.MetadataAccessorXML

Check if loaded metadata contains all necessary tags.

CHOICE_LIST_PARAMETER - Static variable in class org.soaplab.services.metadata.ParamDef

CHOICE_PARAMETER - Static variable in class org.soaplab.services.metadata.ParamDef

ChoiceParamDef - Class in org.soaplab.services.metadata

A data structure defining a 'boolean' or 'radio-group' parameter.

ChoiceParamDef() - Constructor for class org.soaplab.services.metadata.ChoiceParamDef

choiceType - Variable in class org.soaplab.services.metadata.ChoiceParamDef

cleanReport() - Method in class org.soaplab.services.Reporter

Clean-up all so far reported messages.

CmdLineJob - Class in org.soaplab.services.cmdline

An abstract parent of jobs that need to create any kind of command line (from metadata and from the user real inputs).

COND_OWNER_CLIENT - Static variable in class org.soaplab.services.metadata.CondDef

COND_OWNER_N_A - Static variable in class org.soaplab.services.metadata.CondDef

COND_OWNER_SERVER - Static variable in class org.soaplab.services.metadata.CondDef

CondDef - Class in org.soaplab.services.metadata

CondDef() - Constructor for class org.soaplab.services.metadata.CondDef

Constructors

conds - Variable in class org.soaplab.services.metadata.AnalysisDef

conds - Variable in class org.soaplab.services.metadata.ParamDef

Config - Class in org.soaplab.services

An abstract class giving access to the global Soaplab configuration.

Config() - Constructor for class org.soaplab.services.Config

createAndRun(SoaplabMap) - Method in interface org.soaplab.share.Analysis

A convenient combination of methods createJob(org.soaplab.share.SoaplabMap) and run.

createAndRunNotifiable(SoaplabMap, String) - Method in interface org.soaplab.share.Analysis

The same as createAndRun(org.soaplab.share.SoaplabMap) with addition of the channel notification negotiation.

createArg(Map<String, Object>, Job) - Method in interface org.soaplab.services.cmdline.Parameter

Return an array that can be directly used on the command-line.

createdFor - Variable in class org.soaplab.services.metadata.ParamDef

createEnv(Map<String, Object>, Job) - Method in interface org.soaplab.services.cmdline.Parameter

Return properties that represent an "environment" of the analysis that is going to be started.

createIO(Map<String, Object>, Job) - Method in interface org.soaplab.services.cmdline.Parameter

Create an array of data containers that kept (usually local) data whose references are mentioned on the command-line - for that see method Parameter.createArg(java.util.Map, org.soaplab.services.Job), or are not mentioned anywhere (e.g.

createJob(SoaplabMap) - Method in interface org.soaplab.share.Analysis

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

createMapEntry() - Method in class org.soaplab.share.ObjectFactory

Create an instance of MapEntry

createNamedArg(Map<String, Object>, Job) - Method in interface org.soaplab.services.cmdline.Parameter

Return a structure similar to the arguments for a command-line (as returned by createArg) but slightly more general.

createSoaplabMap() - Method in class org.soaplab.share.ObjectFactory

Create an instance of SoaplabMap

createValue() - Method in class org.soaplab.share.ObjectFactory

Create an instance of Value

D

DATA_HELP - Static variable in interface org.soaplab.share.SoaplabConstants

A property name of a parameter attribute.

DATA_PROMPT - Static variable in interface org.soaplab.share.SoaplabConstants

A property name of a data attribute.

DATA_TYPE - Static variable in interface org.soaplab.share.SoaplabConstants

A property name of a parameter attribute.

DataAdaptor - Interface in org.soaplab.services.adaptor

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

DEFAULT_CATEGORY - Static variable in class org.soaplab.services.metadata.AnalysisInstallation

DEFAULT_FOR_DIRECT - Static variable in interface org.soaplab.share.SoaplabConstants

A property name of a data input.

DEFAULT_JOB_FACTORY_CLASS - Static variable in class org.soaplab.services.Config

A default name for a class representing a Job factory.

DEFAULT_MODULE - Static variable in class org.soaplab.services.metadata.AnalysisInstallation

DefaultDeserializer - Class in org.soaplab.services.events

A default implementation of the EventDeserializer that recognizes standard Soaplab events.

DefaultDeserializer() - Constructor for class org.soaplab.services.events.DefaultDeserializer

DefaultEventListener - Class in org.soaplab.services.events

A default implementation of an EventListener interface.

DefaultEventListener() - Constructor for class org.soaplab.services.events.DefaultEventListener

DefaultMetadataAccessorFactory - Class in org.soaplab.services.metadata

A default implementation of the MetadataAccessorFactory interface.

DefaultMetadataAccessorFactory() - Constructor for class org.soaplab.services.metadata.DefaultMetadataAccessorFactory

defaultValue - Variable in class org.soaplab.services.metadata.InputPropertyDef

DESC - Static variable in class org.soaplab.services.metadata.AnalysisInstallation

describe() - Method in interface org.soaplab.services.metadata.MetadataAccessor

Return the whole metadata in the raw format.

describe() - Method in class org.soaplab.services.metadata.MetadataAccessorXML

describe() - Method in interface org.soaplab.share.Analysis

Return an XML string containing metadata describing this analysis service.

deserialize(Object, String) - Method in class org.soaplab.services.events.DefaultDeserializer

deserialize(Object, File) - Method in class org.soaplab.services.events.DefaultDeserializer

deserialize(Object, String) - Method in interface org.soaplab.services.events.EventDeserializer

Create an object representing an event from 'xmlEvent'.

deserialize(Object, File) - Method in interface org.soaplab.services.events.EventDeserializer

Create an object representing an event from XML stored in given file.

destroy() - Method in class org.soaplab.services.AbstractJob

Destroy resources related to this job.

destroy() - Method in interface org.soaplab.services.Job

Destroy resources related to this job.

destroy(String) - Method in interface org.soaplab.share.Analysis

Release related resources, including results.

dflt - Variable in class org.soaplab.services.metadata.ParamDef

DIRECT_DATA_SUFFIX - Static variable in interface org.soaplab.share.SoaplabConstants

A suffix added to the input property representing direct data.

DT_FORMAT - Static variable in interface org.soaplab.share.SoaplabConstants

A string defining a full date-time format, used in reports

E

EMPTY_IODATA - Static variable in class org.soaplab.services.cmdline.CmdLineJob

EMPTY_LIST - Static variable in class org.soaplab.services.cmdline.CmdLineJob

EMPTY_NAMED - Static variable in class org.soaplab.services.cmdline.CmdLineJob

EMPTY_PROPS - Static variable in class org.soaplab.services.cmdline.CmdLineJob

endDocument() - Method in class org.soaplab.services.metadata.MetadataAccessorXML

endDocument()

endElement(String, String, String) - Method in class org.soaplab.services.metadata.MetadataAccessorXML

endElement()

ENVAR - Static variable in class org.soaplab.services.metadata.ParamDef

equals(Object) - Method in class org.soaplab.services.metadata.AnalysisInstallation

equals()

error(String) - Method in class org.soaplab.services.Reporter

Add an error message to the 'report' result.

EVALUATOR - Static variable in class org.soaplab.services.metadata.CondDef

EventConstants - Interface in org.soaplab.services.events

A collection of constants used Soaplab events in XML format.

EventDeserializer - Interface in org.soaplab.services.events

An interface whose implementations can re-create Soaplab events (Java objects) from their XML representation.

EventListener - Interface in org.soaplab.services.events

An interface for listening to the Soaplab events.

EventManager - Class in org.soaplab.services.events

An inter-mediator between individual jobs and all event listeners.

EventManager() - Constructor for class org.soaplab.services.events.EventManager

exists(String) - Method in class org.soaplab.services.metadata.AnalysisDef

exists(String) - Method in class org.soaplab.services.metadata.CondDef

exists(String) - Method in class org.soaplab.services.metadata.ParamDef

exists(String) - Method in class org.soaplab.services.metadata.PropertiesBag

Returns true if an option defined by a 'key' is present and has a non-empty value.

F

FALSEVALUE - Static variable in class org.soaplab.services.metadata.ParamDef

FAULT_INTERNAL_ERROR - Static variable in interface org.soaplab.share.SoaplabConstants

A fault string.

FAULT_NOT_ACCEPTABLE_INPUTS - Static variable in interface org.soaplab.share.SoaplabConstants

A fault string.

FAULT_NOT_FOUND - Static variable in interface org.soaplab.share.SoaplabConstants

A fault string.

FAULT_NOT_IMPLEMENTED - Static variable in interface org.soaplab.share.SoaplabConstants

A fault string.

FAULT_NOT_RUNNABLE - Static variable in interface org.soaplab.share.SoaplabConstants

A fault string.

FAULT_NOT_RUNNING - Static variable in interface org.soaplab.share.SoaplabConstants

A fault string.

FAULT_NOT_TERMINATED - Static variable in interface org.soaplab.share.SoaplabConstants

A fault string.

FAULT_NOT_VALID_INPUTS - Static variable in interface org.soaplab.share.SoaplabConstants

A fault string.

FAULT_NOTIFY_UNACCEPTED - Static variable in interface org.soaplab.share.SoaplabConstants

A fault string.

FAULT_UNKNOWN_NAME - Static variable in interface org.soaplab.share.SoaplabConstants

A fault string.

file - Variable in class org.soaplab.services.metadata.AnalysisDef

FILE_EXT - Static variable in interface org.soaplab.share.SoaplabConstants

A property name of a data output.

FOR_DIRECT_DATA - Static variable in class org.soaplab.services.metadata.CondDef

FOR_URL_DATA - Static variable in class org.soaplab.services.metadata.CondDef

format(int) - Method in class org.soaplab.services.metadata.ChoiceParamDef

As toString() with but indentations.

format(int) - Method in class org.soaplab.services.metadata.CondDef

As toString() but with indentations.

format(int) - Method in class org.soaplab.services.metadata.InputPropertyDef

As toString() but with indentations.

format(int) - Method in class org.soaplab.services.metadata.IOParamDef

As toString() but with indentations.

format(int) - Method in class org.soaplab.services.metadata.ListDef

As toString() but with indentations.

format(int) - Method in class org.soaplab.services.metadata.ListItemDef

As toString() but with indentations.

format(int) - Method in class org.soaplab.services.metadata.OutputPropertyDef

As toString() but with indentations.

format(int) - Method in class org.soaplab.services.metadata.ParamDef

As toString() but with indentations.

format(int) - Method in class org.soaplab.services.metadata.PropertiesBag

As toString() but with indentations.

format(int) - Method in class org.soaplab.services.metadata.RepeatableDef

As toString() but with indentations.

format(int) - Method in class org.soaplab.services.metadata.StdParamDef

As toString() but with indentations.

FORMAT_DIRECT - Static variable in class org.soaplab.services.metadata.IOParamDef

FORMAT_UNSPECIFIED - Static variable in class org.soaplab.services.metadata.IOParamDef

FORMAT_URL - Static variable in class org.soaplab.services.metadata.IOParamDef

formatAndLog(Throwable, Log) - Static method in exception org.soaplab.share.SoaplabException

Format given exception 'e' depending on how serious it it.

formatSource() - Method in class org.soaplab.services.events.AnalysisEvent

Return a stringified version of this event's source.

found(String, String) - Method in class org.soaplab.services.metadata.PropertiesBag

Returns true if an option indicated by 'key' is found within this bag AND is equal to a given value.

fromMap(Map<String, Object>) - Static method in class org.soaplab.share.SoaplabMap

fromMaps(Map<String, Object>[]) - Static method in class org.soaplab.share.SoaplabMap

fromStringMap(Map<String, String>) - Static method in class org.soaplab.share.SoaplabMap

FULL - Static variable in class org.soaplab.services.metadata.ListDef

G

get() - Static method in class org.soaplab.services.Config

The main method returning a configuration object.

get(String) - Method in class org.soaplab.services.metadata.AnalysisDef

get(String) - Method in class org.soaplab.services.metadata.CondDef

get(String) - Method in class org.soaplab.services.metadata.ParamDef

get(String, int) - Method in class org.soaplab.services.metadata.ParamDef

Several extensions to the convenience methods accessing 'options'.

get(String) - Method in class org.soaplab.services.metadata.RepeatableDef

Convenient methods for accessing 'options'

get(String) - Method in class org.soaplab.share.SoaplabMap

getAnalysisDef() - Method in interface org.soaplab.services.metadata.MetadataAccessor

Return a general description of an analysis.

getAnalysisDef() - Method in class org.soaplab.services.metadata.MetadataAccessorXML

Methods of AnalysisMetadataAccessor interface Most of these public methods are synchronized in order to prevent returning uncomplete data if the parsing of metadata is in progress.

getAnalysisType() - Method in interface org.soaplab.share.Analysis

Return attributes describing this analysis.

getAppName() - Method in class org.soaplab.services.metadata.AnalysisInstallation

getAuthority() - Method in interface org.soaplab.services.AnalysisInventory

Return an identifier of this list.

getAvailableAnalyses() - Method in interface org.soaplab.share.AnalysisList

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

getAvailableAnalysesInCategory(String) - Method in interface org.soaplab.share.AnalysisList

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

getAvailableAnalysesWithDescription() - Method in interface org.soaplab.share.AnalysisList

Return the same list as by method AnalysisList.getAvailableAnalyses() but now enriched by short description for each analysis.

getAvailableCategories() - Method in interface org.soaplab.share.AnalysisList

Return an array of names of all available categories.

getBinaryArray() - Method in class org.soaplab.share.Value

Gets the value of the binaryArray property.

getCategory() - Method in class org.soaplab.services.metadata.AnalysisInstallation

Access methods

getCharacteristics(String) - Method in interface org.soaplab.share.Analysis

Returning job's time characteristics.

getCompletedSteps() - Method in class org.soaplab.services.events.StepProgressEvent

Get the number of completed steps.

getConfigFiles() - Static method in class org.soaplab.services.Config

getCreated() - Method in class org.soaplab.services.AbstractJob

Job created - returns number of millis from the BOE.

getCreated() - Method in interface org.soaplab.services.Job

Job created - returns number of seconds from the BOE.

getDefinition() - Method in interface org.soaplab.services.cmdline.Parameter

Return a definition of this parameter.

getDesc() - Method in class org.soaplab.services.metadata.AnalysisInstallation

getDescription() - Method in interface org.soaplab.services.storage.PersistentStorage

Return a (human-readable) description of this persistent storage.

getDeserializer() - Static method in class org.soaplab.services.events.DefaultDeserializer

Find available deserializer, create its instance and return it.

getElapsed() - Method in class org.soaplab.services.AbstractJob

Job time elapsed - returns number in milliseconds.

getElapsed() - Method in interface org.soaplab.services.Job

Job time elapsed - returns number in milliseconds.

getEnded() - Method in class org.soaplab.services.AbstractJob

Job ended - returns number of millis from the BOE.

getEnded() - Method in interface org.soaplab.services.Job

Job ended - returns number of seconds from the BOE.

getEntries() - Method in class org.soaplab.share.SoaplabMap

Gets the value of all entries.

getFaultInfo() - Method in exception org.soaplab.share.SoaplabException

getFullName() - Method in class org.soaplab.services.metadata.AnalysisInstallation

Return a name consisting from both category and application name.

getId() - Method in class org.soaplab.services.AbstractJob

Return this job identity (an ID).

getId() - Method in class org.soaplab.services.cmdline.NamedValues

Return an ID of a parameter whose data this container keeps.

getId() - Method in interface org.soaplab.services.Job

Get this job ID.

getInputDefs() - Method in interface org.soaplab.services.metadata.MetadataAccessor

Return a slightly simplified version of what is returned by MetadataAccessor.getParamDefs() - and only for input data and options.

getInputDefs() - Method in class org.soaplab.services.metadata.MetadataAccessorXML

getInputSpec() - Method in interface org.soaplab.share.Analysis

Return information about all possible data inputs.

getInstance(String) - Method in class org.soaplab.services.metadata.DefaultMetadataAccessorFactory

getInstance(String) - Method in interface org.soaplab.services.metadata.MetadataAccessorFactory

getInt(String, int, String, Object) - Static method in class org.soaplab.services.Config

Almost the same functionality as getString method - see there details about parameters - except that it expects property value to be an integer.

getInt(String) - Method in class org.soaplab.services.metadata.AnalysisDef

getInt(String) - Method in class org.soaplab.services.metadata.CondDef

getInt(String) - Method in class org.soaplab.services.metadata.ParamDef

getInt(String, int) - Method in class org.soaplab.services.metadata.ParamDef

getInt(String) - Method in class org.soaplab.services.metadata.PropertiesBag

Return an integer value of the option indicated by 'key'.

getIOFormatAsString() - Method in class org.soaplab.services.metadata.IOParamDef

getIOTypeAsString() - Method in class org.soaplab.services.metadata.IOParamDef

getJobDir() - Method in class org.soaplab.services.AbstractJob

The job directory is created in a SANDBOX (see more in getSandbox()).

getJobDir() - Method in interface org.soaplab.services.Job

Create (unless it already exists) and return a new directory which will become a working directory for this job.

getJobProperties() - Method in class org.soaplab.services.Reporter

getJobProperties(String) - Method in interface org.soaplab.services.storage.PersistentStorage

Return known properties of the given job.

getJobState(String) - Method in interface org.soaplab.services.storage.PersistentStorage

This is as close to re-creating a stored job as possible.

getKey() - Method in class org.soaplab.share.MapEntry

Gets the value of the key property.

getLastEvent() - Method in class org.soaplab.services.AbstractJob

getLastEvent() - Method in interface org.soaplab.services.Job

Get the last event.

getLastEvent(String) - Method in interface org.soaplab.share.Analysis

Return the last event which happened to the given job.

getList() - Method in interface org.soaplab.services.AnalysisInventory

Return a list of available analysis, with basic properties.

getMatchingProperties(String, String, Object) - Static method in class org.soaplab.services.Config

Get all properties contained in the configuration whose keys (names) match the specified prefix.

getMessage() - Method in class org.soaplab.services.events.AnalysisEvent

Get the main contents of this event.

getMessage() - Method in class org.soaplab.share.SoaplabExceptionBean

getMetadataAccessor() - Method in class org.soaplab.services.AbstractJob

Get metadata accessor.

getMetadataAccessor() - Method in interface org.soaplab.services.Job

Get metadata accessor.

getModule() - Method in class org.soaplab.services.metadata.AnalysisInstallation

getNewState() - Method in class org.soaplab.services.events.StateChangeEvent

Get the new state as reported by this event.

getNotificationDescriptor(String) - Method in interface org.soaplab.share.Analysis

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

getObjectValue() - Method in class org.soaplab.share.MapEntry

getOutputDefs() - Method in interface org.soaplab.services.metadata.MetadataAccessor

Return a slightly simplified version of what is returned by MetadataAccessor.getParamDefs() - and only for output data.

getOutputDefs() - Method in class org.soaplab.services.metadata.MetadataAccessorXML

getParamDefs() - Method in interface org.soaplab.services.metadata.MetadataAccessor

Return description of all parameters for an analysis.

getParamDefs() - Method in class org.soaplab.services.metadata.MetadataAccessorXML

getPath() - Method in class org.soaplab.services.metadata.TagTracer

Gets contents of the whole stack.

getPercentage() - Method in class org.soaplab.services.events.PercentProgressEvent

Get the percentage.

getPreviousState() - Method in class org.soaplab.services.events.StateChangeEvent

Get the previous state as reported by this event.

getReporter() - Method in class org.soaplab.services.AbstractJob

Get reporter.

getReporter() - Method in interface org.soaplab.services.Job

Get reporter.

getResult(String, String) - Method in interface org.soaplab.services.storage.PersistentStorage

Find in this persistent storage the given result for the given job and return them back.

getResults() - Method in class org.soaplab.services.AbstractJob

Return all (available) results.

getResults(String[]) - Method in class org.soaplab.services.AbstractJob

Return all wanted (and available) results.

getResults() - Method in interface org.soaplab.services.Job

Return all (available) results.

getResults(String[]) - Method in interface org.soaplab.services.Job

Return all wanted (and available) results.

getResults() - Method in class org.soaplab.services.Reporter

Retrieve and return all available results, set so far.

getResults(String[]) - Method in class org.soaplab.services.Reporter

getResults(String) - Method in interface org.soaplab.services.storage.PersistentStorage

Find in this persistent storage all results for the given job and return them back.

getResults(String) - Method in interface org.soaplab.share.Analysis

Return all (available) results from the given job.

getResultsInfo() - Method in class org.soaplab.services.AbstractJob

getResultsInfo() - Method in interface org.soaplab.services.Job

getResultsInfo() - Method in class org.soaplab.services.Reporter

getResultsInfo(String) - Method in interface org.soaplab.services.storage.PersistentStorage

Return properties associated with all results from the given job.

getResultsInfo(String) - Method in interface org.soaplab.share.Analysis

getResultSpec() - Method in interface org.soaplab.share.Analysis

Return information about all possible results.

getServiceLocation(String) - Method in interface org.soaplab.share.AnalysisList

Return a location of a web service representing given analysis.

getServiceName() - Method in interface org.soaplab.services.metadata.MetadataAccessor

Return a name of a service providing this analysis.

getServiceName() - Method in class org.soaplab.services.metadata.MetadataAccessorXML

getServiceName() - Method in interface org.soaplab.services.protocol.ProtocolToolkit

Return name of service which was called by the current request.

getSingleBinary() - Method in class org.soaplab.share.Value

Gets the value of the singleBinary property.

getSingleString() - Method in class org.soaplab.share.Value

getSomeResults(String, String[]) - Method in interface org.soaplab.share.Analysis

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

getSource() - Method in class org.soaplab.services.events.AnalysisEvent

Get the event source (which may be null).

getStarted() - Method in class org.soaplab.services.AbstractJob

Job started - returns number of millis from the BOE.

getStarted() - Method in interface org.soaplab.services.Job

Job started - returns number of seconds from the BOE.

getState() - Method in class org.soaplab.services.Reporter

Return a container with job status.

getStatus() - Method in class org.soaplab.services.AbstractJob

getStatus() - Method in interface org.soaplab.services.Job

Get job status.

getStatus(String) - Method in interface org.soaplab.share.Analysis

Return a string describing the current job status.

getStr(String) - Method in class org.soaplab.services.metadata.PropertiesBag

Return a string value of the option indicated by 'key'.

getString(String, String, String, Object) - Static method in class org.soaplab.services.Config

Get a string associated with the given configuration key, or - if not found - get the given default value (which still may be null).

getStringArray() - Method in class org.soaplab.share.Value

Gets the value of the stringArray property.

getStrings(String, String, String, Object) - Static method in class org.soaplab.services.Config

Almost the same functionality as getString method - see there details about parameters.

getStrippedName() - Method in class org.soaplab.services.metadata.IOParamDef

Return the beginning of its own name, stripped of the endings indicating the 'ioFormat' type.

getTag() - Method in class org.soaplab.services.cmdline.NamedValues

Return a tag (qualifier) for this parameter (without any prefixes, such as minus sign or slash - even if such character is define din the parameter metadata).

getTimeRemaining() - Method in class org.soaplab.services.events.TimeProgressEvent

Get the remaining time (in 100 nanoseconds).

getTimestamp() - Method in class org.soaplab.services.events.AnalysisEvent

Get the event timestamp.

getTotalSteps() - Method in class org.soaplab.services.events.StepProgressEvent

Get the number of total steps.

getValue() - Method in class org.soaplab.share.MapEntry

Gets the value of the value property.

getValue() - Method in class org.soaplab.share.Value

Get a value kept in this instance.

getValues() - Method in class org.soaplab.services.cmdline.NamedValues

Return a list of data values representing user inputs.

getXMLDesc() - Method in class org.soaplab.services.metadata.AnalysisInstallation

H

handleAnalysisEvent(AnalysisEvent) - Method in class org.soaplab.services.events.DefaultEventListener

handleAnalysisEvent(AnalysisEvent) - Method in interface org.soaplab.services.events.EventListener

This method is called when a general event is sent, or its subclass that is not explicitly known to this interface.

handleAnalysisEvent(AnalysisEvent) - Method in class org.soaplab.services.events.EventManager

handleEvent(AnalysisEvent) - Method in class org.soaplab.services.events.EventManager

Broadcast an event to all event listeners.

handleHeartbeatProgressEvent(HeartbeatProgressEvent) - Method in class org.soaplab.services.events.DefaultEventListener

handleHeartbeatProgressEvent(HeartbeatProgressEvent) - Method in interface org.soaplab.services.events.EventListener

This method is called when a "heart-beat" event is sent.

handleHeartbeatProgressEvent(HeartbeatProgressEvent) - Method in class org.soaplab.services.events.EventManager

handlePercentProgressEvent(PercentProgressEvent) - Method in class org.soaplab.services.events.DefaultEventListener

handlePercentProgressEvent(PercentProgressEvent) - Method in interface org.soaplab.services.events.EventListener

This method is called when a "percent progress" event is sent.

handlePercentProgressEvent(PercentProgressEvent) - Method in class org.soaplab.services.events.EventManager

handleStateChangeEvent(StateChangeEvent) - Method in class org.soaplab.services.events.DefaultEventListener

handleStateChangeEvent(StateChangeEvent) - Method in interface org.soaplab.services.events.EventListener

This method is called when a "state-changed" event is sent.

handleStateChangeEvent(StateChangeEvent) - Method in class org.soaplab.services.events.EventManager

handleStepProgressEvent(StepProgressEvent) - Method in class org.soaplab.services.events.DefaultEventListener

handleStepProgressEvent(StepProgressEvent) - Method in interface org.soaplab.services.events.EventListener

This method is called when a "step progress" event is sent.

handleStepProgressEvent(StepProgressEvent) - Method in class org.soaplab.services.events.EventManager

handleTimeProgressEvent(TimeProgressEvent) - Method in class org.soaplab.services.events.DefaultEventListener

handleTimeProgressEvent(TimeProgressEvent) - Method in interface org.soaplab.services.events.EventListener

This method is called when a "time progress" event is sent.

handleTimeProgressEvent(TimeProgressEvent) - Method in class org.soaplab.services.events.EventManager

HEARTBEAT_PROGRESS - Static variable in interface org.soaplab.services.events.EventConstants

HeartbeatProgressEvent - Class in org.soaplab.services.events

A class representing an event that indicates that the underlying service/analysis/job is still in progress.

HeartbeatProgressEvent() - Constructor for class org.soaplab.services.events.HeartbeatProgressEvent

A usual constructor, taking nothing.

HeartbeatProgressEvent(Object, String) - Constructor for class org.soaplab.services.events.HeartbeatProgressEvent

The most general constructor, taking a message, and the event source.

I

id - Variable in class org.soaplab.services.metadata.ParamDef

IGNORED_RESULT - Static variable in interface org.soaplab.share.SoaplabConstants

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

INPUT_ADAPTOR - Static variable in class org.soaplab.services.metadata.IOParamDef

An option name.

INPUT_ALLOWED_VALUES - Static variable in interface org.soaplab.share.SoaplabConstants

A property name of a data input.

INPUT_DEFAULT_VALUE - Static variable in interface org.soaplab.share.SoaplabConstants

A property name of a data input.

INPUT_FORMAT - Static variable in interface org.soaplab.share.SoaplabConstants

A property name of a data input.

INPUT_MANDATORY - Static variable in interface org.soaplab.share.SoaplabConstants

A property name of a data input.

INPUT_NAME - Static variable in interface org.soaplab.share.SoaplabConstants

A property name of a data input.

INPUT_TYPE - Static variable in interface org.soaplab.share.SoaplabConstants

A property name of a data input.

InputPropertyDef - Class in org.soaplab.services.metadata

InputPropertyDef() - Constructor for class org.soaplab.services.metadata.InputPropertyDef

Constructor

inputSpec2Map(MetadataAccessor) - Static method in class org.soaplab.services.metadata.MetadataUtils

Convert a set of InputPropertyDef's into a Map (as defined and used, for example, by Analysis in Soaplab.

INTERFACE - Static variable in interface org.soaplab.share.SoaplabConstants

interface used by the client

INTERNAL_ERROR - Static variable in class org.soaplab.services.AbstractJob

IO_PARAMETER - Static variable in class org.soaplab.services.metadata.ParamDef

ioFormat - Variable in class org.soaplab.services.metadata.IOParamDef

IOParamDef - Class in org.soaplab.services.metadata

A data structure defining input/output types of an analysis tools.

IOParamDef() - Constructor for class org.soaplab.services.metadata.IOParamDef

A default constructor.

ioType - Variable in class org.soaplab.services.metadata.IOParamDef

is(String) - Method in class org.soaplab.services.metadata.AnalysisDef

Convenient methods for accessing 'options'

is(String) - Method in class org.soaplab.services.metadata.CondDef

Convenient methods for accessing 'options'

is(String) - Method in class org.soaplab.services.metadata.ParamDef

Convenient methods for accessing 'options'

is(String, int) - Method in class org.soaplab.services.metadata.ParamDef

is(String) - Method in class org.soaplab.services.metadata.PropertiesBag

Returns true if an option defined by a 'key' is present and has a true value.

is(String, int) - Method in class org.soaplab.services.metadata.PropertiesBag

Returns true if an option defined by a 'key' is present and has a true value.

is(String[]) - Method in class org.soaplab.services.metadata.TagTracer

Compares the contents of the current stack with the given list of tag names.

isDataReferenceSafe(String, ParamDef) - Method in class org.soaplab.services.AbstractJob

Check if the 'dataRef' (which is a file name or a URL) is safe for this job.

isDataReferenceSafe(String, ParamDef) - Method in interface org.soaplab.services.Job

Check if the 'dataRef' (which is a file name or a URL) is safe for this job.

isDirectData() - Method in class org.soaplab.services.metadata.IOParamDef

Return true if this definition represents direct data (and not reference nor unspecified data).

isEnabled(String, boolean, String, Object) - Static method in class org.soaplab.services.Config

Almost the same functionality as getString method - see there details about parameters - except that it expects property value to be a boolean.

isInput() - Method in class org.soaplab.services.metadata.IOParamDef

Return true if this definition represents an input (either a regular or a standard input).

isOlderThan(AnalysisEvent) - Method in class org.soaplab.services.events.AnalysisEvent

Compare this event with the 'newEvent'.

isOutput() - Method in class org.soaplab.services.metadata.IOParamDef

Return true if this definition represents an output (either a regular or a standard stream).

isRecreated() - Method in class org.soaplab.services.AbstractJob

isRecreated() - Method in interface org.soaplab.services.Job

Checks if the job is re-created

isReferenceData() - Method in class org.soaplab.services.metadata.IOParamDef

Return true if this definition represents reference data (and not direct nor unspecified data).

isRegularInput() - Method in class org.soaplab.services.metadata.IOParamDef

Return true if this definition represents a regular input (which excludes the standard input).

isRegularOutput() - Method in class org.soaplab.services.metadata.IOParamDef

Return true if this definition represents a regular output (which excludes the standard output and standard error output).

isSink() - Method in interface org.soaplab.services.storage.PersistentStorage

Return 'true' if this storage allows only setting data (jobs, state, results, etc.) but never returns them back.

isStandardStream() - Method in class org.soaplab.services.metadata.IOParamDef

Return true if this definition represents any of the standard streams.

isStderr() - Method in class org.soaplab.services.metadata.IOParamDef

Return true if this definition represents a standard error.

isStdin() - Method in class org.soaplab.services.metadata.IOParamDef

Return true if this definition represents a standard input.

isStdout() - Method in class org.soaplab.services.metadata.IOParamDef

Return true if this definition represents a standard output.

items - Variable in class org.soaplab.services.metadata.ListDef

J

Job - Interface in org.soaplab.services

An interface defining a job.

JOB_COMPLETED - Static variable in interface org.soaplab.share.SoaplabConstants

A job status: Job has completed execution.

JOB_CREATED - Static variable in interface org.soaplab.share.SoaplabConstants

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

JOB_REMOVED - Static variable in interface org.soaplab.share.SoaplabConstants

A job status: Job was removed.

JOB_RUNNING - Static variable in interface org.soaplab.share.SoaplabConstants

A job status: Job is running.

JOB_TERMINATED_BY_ERROR - Static variable in interface org.soaplab.share.SoaplabConstants

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

JOB_TERMINATED_BY_REQUEST - Static variable in interface org.soaplab.share.SoaplabConstants

A job status: Job was terminated by user request.

JOB_TIMEOUT_FOR_TERMINATE_CALLS - Static variable in interface org.soaplab.share.SoaplabConstants

Maximum waiting time for job terminate calls to return, 20 secs.

JOB_UNKNOWN - Static variable in interface org.soaplab.share.SoaplabConstants

A job status: An unknown one.

JUST_ONE - Static variable in class org.soaplab.services.metadata.ChoiceParamDef

Types of radiogroups (grouping together several boolean options).

L

launcher - Variable in class org.soaplab.services.metadata.AnalysisDef

level - Variable in class org.soaplab.services.metadata.ListItemDef

LIST_SERVICE_NAME - Static variable in interface org.soaplab.share.SoaplabConstants

A Soaplab2 list service name used in WSDL etc.

LIST_SERVICE_PORT_NAME - Static variable in interface org.soaplab.share.SoaplabConstants

A Soaplab2 port name for the list service used in WSDL etc.

ListDef - Class in org.soaplab.services.metadata

A data structure defining a static list of string values, possibly hierarchically nested (like a 'menu' structure').

ListDef() - Constructor for class org.soaplab.services.metadata.ListDef

Constructor.

ListItemDef - Class in org.soaplab.services.metadata

A data structure defining an item of a static list.

ListItemDef() - Constructor for class org.soaplab.services.metadata.ListItemDef

Constructor.

listJobs() - Method in interface org.soaplab.services.storage.PersistentStorage

Return names (job Ids) of all jobs still available from this storage handler.

lists - Variable in class org.soaplab.services.metadata.StdParamDef

LSF_ARCH - Static variable in class org.soaplab.services.Config

A property name.

LSF_ENABLED - Static variable in class org.soaplab.services.Config

A property name.

LSF_PROJECT - Static variable in class org.soaplab.services.Config

A property name.

LSF_QUEUENAME - Static variable in class org.soaplab.services.Config

A property name.

M

mandatory - Variable in class org.soaplab.services.metadata.InputPropertyDef

MANDATORY - Static variable in class org.soaplab.services.metadata.ParamDef

MapEntry - Class in org.soaplab.share

A container for a key-value pair used in SoaplabMap.

MapEntry() - Constructor for class org.soaplab.share.MapEntry

MapEntry(String, Object) - Constructor for class org.soaplab.share.MapEntry

maxRep - Variable in class org.soaplab.services.metadata.RepeatableDef

Maximum number of repetitions.

MESSAGE - Static variable in interface org.soaplab.services.events.EventConstants

MetadataAccessor - Interface in org.soaplab.services.metadata

An interface to get metadata describing behaviour, and possibly even look-and-feel, for any analysis.

MetadataAccessorFactory - Interface in org.soaplab.services.metadata

An interface for a factory creating instances of AnalysisMetadataAccessor for individual services.

MetadataAccessorXML - Class in org.soaplab.services.metadata

A default implementation of MetadataAccessor interface that reads service metadata from XML files.

MetadataAccessorXML(String) - Constructor for class org.soaplab.services.metadata.MetadataAccessorXML

A real constructor.

MetadataUtils - Class in org.soaplab.services.metadata

Some static pieces of code for dealing with analysis metadata.

MetadataUtils() - Constructor for class org.soaplab.services.metadata.MetadataUtils

method - Variable in class org.soaplab.services.metadata.AnalysisDef

METHOD - Static variable in class org.soaplab.services.metadata.ParamDef

MIME_TYPE - Static variable in interface org.soaplab.share.SoaplabConstants

A property name of a data output.

minRep - Variable in class org.soaplab.services.metadata.RepeatableDef

Minimum number of repetitions.

module - Variable in class org.soaplab.services.metadata.AnalysisDef

MODULE - Static variable in class org.soaplab.services.metadata.AnalysisInstallation

N

name - Variable in class org.soaplab.services.metadata.InputPropertyDef

name - Variable in class org.soaplab.services.metadata.ListDef

name - Variable in class org.soaplab.services.metadata.OutputPropertyDef

NamedValues - Class in org.soaplab.services.cmdline

A container for parameter name, parameter tag and its value, or values.

NamedValues(String) - Constructor for class org.soaplab.services.cmdline.NamedValues

Constructor - a parameter ID is needed (in most cases).

NamedValues() - Constructor for class org.soaplab.services.cmdline.NamedValues

Constructor - a container without parameter ID (used when a service metadata have a global METHOD template).

NEW_STATE - Static variable in interface org.soaplab.services.events.EventConstants

NODE - Static variable in class org.soaplab.services.metadata.ListItemDef

NODISPLAY - Static variable in class org.soaplab.services.metadata.ParamDef

O

ObjectFactory - Class in org.soaplab.share

This object contains factory methods for each Java content interface and Java element interface generated in the org.soaplab.share package.

ObjectFactory() - Constructor for class org.soaplab.share.ObjectFactory

Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: org.soaplab.share

ONE_OR_MORE - Static variable in class org.soaplab.services.metadata.ChoiceParamDef

options - Variable in class org.soaplab.services.metadata.AnalysisDef

options - Variable in class org.soaplab.services.metadata.CondDef

options - Variable in class org.soaplab.services.metadata.ParamDef

options - Variable in class org.soaplab.services.metadata.RepeatableDef

ORDERING - Static variable in class org.soaplab.services.metadata.ParamDef

org.soaplab.services.events - package org.soaplab.services.events

org.soaplab.services.metadata - package org.soaplab.services.metadata

org.soaplab.share - package org.soaplab.share

OUTPUT_ADAPTOR - Static variable in class org.soaplab.services.metadata.IOParamDef

An option name.

OutputPropertyDef - Class in org.soaplab.services.metadata

OutputPropertyDef() - Constructor for class org.soaplab.services.metadata.OutputPropertyDef

Constructors

OutputPropertyDef(String, String) - Constructor for class org.soaplab.services.metadata.OutputPropertyDef

outputSpec2Map(MetadataAccessor) - Static method in class org.soaplab.services.metadata.MetadataUtils

Convert a set of OutputPropertyDef's into a Map (as defined and used, for example, by Analysis in Soaplab).

OWNER - Static variable in class org.soaplab.services.metadata.CondDef

P

ParamDef - Class in org.soaplab.services.metadata

A general class defining a parameter for an analysis tool.

ParamDef() - Constructor for class org.soaplab.services.metadata.ParamDef

Constructor

Parameter - Interface in org.soaplab.services.cmdline

An interface defining a paramter of a Soaplab2 job, usualy a command-line parameter.

parseLauncher(MetadataAccessor, String, Object) - Static method in class org.soaplab.services.metadata.MetadataUtils

Find the 'launcher' directive in the given metadata, or in the configuration (using given 'serviceName' and the caller), and parse it into a list of two elements.

peek() - Method in class org.soaplab.services.metadata.TagTracer

Looks at the tag name at the top of this stack without removing it from the stack.

PERCENT_PROGRESS - Static variable in interface org.soaplab.services.events.EventConstants

PERCENTAGE - Static variable in interface org.soaplab.services.events.EventConstants

PercentProgressEvent - Class in org.soaplab.services.events

A class representing an event that reports the time percentage of the underlying service/analysis/job.

PercentProgressEvent(Object, String, float) - Constructor for class org.soaplab.services.events.PercentProgressEvent

The most general constructor, taking a message, percentage, and the event source.

PercentProgressEvent(String, float) - Constructor for class org.soaplab.services.events.PercentProgressEvent

A constructor taking a general message and percentage.

PercentProgressEvent(float) - Constructor for class org.soaplab.services.events.PercentProgressEvent

A usual constructor, taking just the percentage.

PersistentStorage - Interface in org.soaplab.services.storage

An interface defining how to store results, and other characteristics of service invocations ("jobs"), in more persistent way.

pop() - Method in class org.soaplab.services.metadata.TagTracer

Removes the tag name from the top of this stack and returns it.

possibleValues - Variable in class org.soaplab.services.metadata.InputPropertyDef

PREFIX_SYNONYM - Static variable in class org.soaplab.services.Config

A part of property names.

PREVIOUS_STATE - Static variable in interface org.soaplab.services.events.EventConstants

process(String, InputStream, OutputStream, Job) - Method in interface org.soaplab.services.adaptor.DataAdaptor

Read 'source' data, adapt them, and write them back into 'result'.

processFromList(String, List, Job) - Method in interface org.soaplab.services.adaptor.DataAdaptor

Read 'source' data, adapt them, and return them back.

PROP_ACCEPT_ANY_EXITCODE - Static variable in class org.soaplab.services.Config

A property name.

PROP_ADDTOPATH_DIR - Static variable in class org.soaplab.services.Config

A property name.

PROP_APPLIST_FILENAME - Static variable in class org.soaplab.services.Config

A property name.

PROP_BASE_DIR - Static variable in class org.soaplab.services.Config

A property name.

PROP_ENVAR - Static variable in class org.soaplab.services.Config

A property name.

PROP_EVENT_IGNORE_HEARBEAT - Static variable in class org.soaplab.services.Config

A property name.

PROP_EVENT_LOG_LEVEL - Static variable in class org.soaplab.services.Config

A property name.

PROP_JOBS_CLEANING_INTERVAL - Static variable in class org.soaplab.services.Config

A property name.

PROP_JOBS_TIMEOUT - Static variable in class org.soaplab.services.Config

A property name.

PROP_JOBS_WAITFOR_TIMEOUT - Static variable in class org.soaplab.services.Config

A property name.

PROP_KEEP_INPUTS - Static variable in class org.soaplab.services.Config

A property name.

PROP_LAUNCHER - Static variable in class org.soaplab.services.Config

A property name.

PROP_METADATA_DIR - Static variable in class org.soaplab.services.Config

A property name.

PROP_METADATA_FILE - Static variable in class org.soaplab.services.Config

A part of a property name.

PROP_RESULTS_DIR - Static variable in class org.soaplab.services.Config

A property name.

PROP_RESULTS_URL - Static variable in class org.soaplab.services.Config

A property name.

PROP_RESULTS_URL_DIR - Static variable in class org.soaplab.services.Config

A property name.

PROP_RESULTS_URL_IGNORE - Static variable in class org.soaplab.services.Config

A property name.

PROP_SANDBOX_DIR - Static variable in class org.soaplab.services.Config

A property name.

PROP_SCRIPTS_DIR - Static variable in class org.soaplab.services.Config

A property name.

PROP_SERVICES_CLEANING_INTERVAL - Static variable in class org.soaplab.services.Config

A property name.

PROP_SOAPLAB_CONFIGURATION - Static variable in class org.soaplab.services.Config

A property name.

PROP_SUPPLIER - Static variable in class org.soaplab.services.Config

A property name.

PROP_TOMCAT_HOST - Static variable in class org.soaplab.services.Config

A property name.

PROP_TOMCAT_PORT - Static variable in class org.soaplab.services.Config

A property name.

PROP_WORKING_DIR - Static variable in class org.soaplab.services.Config

A property name.

PropertiesBag - Class in org.soaplab.services.metadata

A simple extension of java.util.Hashtable bringing more methods for checking and retrieving properties.

PropertiesBag() - Constructor for class org.soaplab.services.metadata.PropertiesBag

An empty constructor.

PropertiesBag(String[]) - Constructor for class org.soaplab.services.metadata.PropertiesBag

Create a bag initialized with 'props'.

PropertiesBag(String, String) - Constructor for class org.soaplab.services.metadata.PropertiesBag

A convenient constructor for creating a bag with exactly one property.

ProtocolToolkit - Interface in org.soaplab.services.protocol

An interface providing basic features in distributed architecture environment that are dependent on the used protocol.

push(String) - Method in class org.soaplab.services.metadata.TagTracer

Pushes a tag name onto the top of this stack.

put(String, Object) - Method in class org.soaplab.share.SoaplabMap

R

RANGE_PARAMETER - Static variable in class org.soaplab.services.metadata.ParamDef

READONLY - Static variable in class org.soaplab.services.metadata.ParamDef

REGEXP - Static variable in class org.soaplab.services.metadata.CondDef

REGEXP_ERROR - Static variable in class org.soaplab.services.metadata.CondDef

REGULAR - Static variable in class org.soaplab.services.metadata.ListItemDef

REMAINING - Static variable in interface org.soaplab.services.events.EventConstants

REMOTE_IP - Static variable in interface org.soaplab.share.SoaplabConstants

IP address of the client

removeJob(String) - Method in interface org.soaplab.services.storage.PersistentStorage

Remove given job from this persistent storage.

removeJobs(String) - Method in interface org.soaplab.services.storage.PersistentStorage

Remove jobs from this persistent storage whose IDs contain the string specified by 'jobIdPattern'.

removeJobs(Date, Date) - Method in interface org.soaplab.services.storage.PersistentStorage

Remove jobs from this persistent storage that were last updated within given time interval.

repeat - Variable in class org.soaplab.services.metadata.StdParamDef

REPEAT_ERROR - Static variable in class org.soaplab.services.metadata.RepeatableDef

RepeatableDef - Class in org.soaplab.services.metadata

Structure defining how a parameter can be repeated.

RepeatableDef() - Constructor for class org.soaplab.services.metadata.RepeatableDef

report(String) - Method in class org.soaplab.services.Reporter

Add a message to the 'report' result.

report(String, String) - Method in class org.soaplab.services.Reporter

Add a property to the 'report' result.

report(String, File) - Method in class org.soaplab.services.Reporter

Add a contents of the given file to the 'report' result.

Reporter - Class in org.soaplab.services

An instance of a Reporter accompanies each "job" (an analysis invocation).

Reporter(MetadataAccessor, PersistentStorage, EventManager) - Constructor for class org.soaplab.services.Reporter

The main constructor.

reset() - Method in class org.soaplab.services.metadata.TagTracer

Removes all elements fom the stack.

RESULT_DETAILED_STATUS - Static variable in interface org.soaplab.share.SoaplabConstants

A name for a specialized result.

RESULT_LENGTH - Static variable in interface org.soaplab.share.SoaplabConstants

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

RESULT_NAME - Static variable in interface org.soaplab.share.SoaplabConstants

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

RESULT_REPORT - Static variable in interface org.soaplab.share.SoaplabConstants

A name for a specialized result.

RESULT_SIZE - Static variable in interface org.soaplab.share.SoaplabConstants

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

RESULT_TYPE - Static variable in interface org.soaplab.share.SoaplabConstants

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

run() - Method in class org.soaplab.services.AbstractJob

The meat of Soaplab.

run() - Method in interface org.soaplab.services.Job

Run it.

run(String) - Method in interface org.soaplab.share.Analysis

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

runAndWaitFor(SoaplabMap) - Method in interface org.soaplab.share.Analysis

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

runNotifiable(String, String) - Method in interface org.soaplab.share.Analysis

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

S

sendEvent(AnalysisEvent) - Method in class org.soaplab.services.Reporter

Send an event to all event listeners.

SEPARATOR - Static variable in class org.soaplab.services.metadata.ListItemDef

SEPARATOR - Static variable in class org.soaplab.services.metadata.ParamDef

SERVER_CLASS - Static variable in class org.soaplab.services.metadata.ParamDef

SERVICE_NAME - Static variable in interface org.soaplab.share.SoaplabConstants

A Soaplab2 analysis service name used in WSDL etc.

SERVICE_PORT_NAME - Static variable in interface org.soaplab.share.SoaplabConstants

A Soaplab2 port name for the analsis service used in WSDL etc.

setDelimiter(String) - Method in class org.soaplab.services.metadata.AnalysisInstallation

Set a delimiter that is used to separate category and the real name of stored analysis.

setDetailedStatusResult() - Method in class org.soaplab.services.Reporter

Store 'detailed_status' result persistently.

setDocumentLocator(Locator) - Method in class org.soaplab.services.metadata.MetadataAccessorXML

setId(String) - Method in class org.soaplab.services.AbstractJob

Set this job ID.

setId(String) - Method in interface org.soaplab.services.Job

Set this job ID.

setInputs(Map<String, Object>) - Method in class org.soaplab.services.AbstractJob

Set input data into this job.

setInputs(Map<String, Object>) - Method in interface org.soaplab.services.Job

Set input data into this job.

setInputValue(String, Object) - Method in class org.soaplab.services.AbstractJob

Set an input value, given by its name.

setInputValue(String, Object) - Method in interface org.soaplab.services.Job

Set one input value.

setJob(Job) - Method in class org.soaplab.services.Reporter

Remember what job this reporter is serving.

setJob(Job) - Method in interface org.soaplab.services.storage.PersistentStorage

Store Job's state information to the persistent storage.

setJobProperties(Properties) - Method in class org.soaplab.services.Reporter

setJobProperties(String, Properties) - Method in interface org.soaplab.services.storage.PersistentStorage

Store properties for the given job.

setKey(String) - Method in class org.soaplab.share.MapEntry

Sets the value of the key property.

setMessage(String) - Method in class org.soaplab.share.SoaplabExceptionBean

setMetadataAccessor(MetadataAccessor) - Method in class org.soaplab.services.AbstractJob

Set metadata accessor.

setMetadataAccessor(MetadataAccessor) - Method in interface org.soaplab.services.Job

Set metadata accessor.

setProperties(Properties) - Method in class org.soaplab.services.metadata.AnalysisInstallation

Set properties.

setReporter(Reporter) - Method in class org.soaplab.services.AbstractJob

Set reporter.

setReporter(Reporter) - Method in interface org.soaplab.services.Job

Set reporter.

setReportResult() - Method in class org.soaplab.services.Reporter

Store 'report' result persistently.

setResult(String, Object) - Method in class org.soaplab.services.Reporter

It stores given result under given name.

setResult(Job, String, Object) - Method in interface org.soaplab.services.storage.PersistentStorage

Store result in the persistent storage.

setSharedAttributes(Map<String, Object>) - Method in class org.soaplab.services.AbstractJob

setSharedAttributes(Map<String, Object>) - Method in interface org.soaplab.services.Job

Shared attributes are any objects that are shared by more job instances.

setSingleBinary(byte[]) - Method in class org.soaplab.share.Value

Sets the value of the singleBinary property.

setSingleString(String) - Method in class org.soaplab.share.Value

setState(JobState) - Method in class org.soaplab.services.Reporter

Set the whole job state.

setTag(String) - Method in class org.soaplab.services.cmdline.NamedValues

Set a tag (qualifier).

setTimestamp(Date) - Method in class org.soaplab.services.events.AnalysisEvent

Set the event timestamp.

setValue(Value) - Method in class org.soaplab.share.MapEntry

Sets the value of the value property.

setValues(List<String>) - Method in class org.soaplab.services.cmdline.NamedValues

Set all values representing user inputs.

shown_as - Variable in class org.soaplab.services.metadata.ListItemDef

SLICE - Static variable in class org.soaplab.services.metadata.ListDef

slice - Variable in class org.soaplab.services.metadata.ListDef

SOAPLAB_CONFIG_FILENAME - Static variable in class org.soaplab.services.Config

A filename indicating a file containing Soaplab run-time properties.

SOAPLAB_NAMESPACE - Static variable in interface org.soaplab.share.SoaplabConstants

A Soaplab2 namespace used in WSDL etc.

SOAPLAB_SERVICE_NAME_DELIMITER - Static variable in interface org.soaplab.share.SoaplabConstants

A string that delimits category name from a service name.

SoaplabConstants - Interface in org.soaplab.share

A list of constants used to describe and to invoke analyses.

SoaplabException - Exception in org.soaplab.share

A general exception which can be used as a wrapper around other exceptions.

SoaplabException(String) - Constructor for exception org.soaplab.share.SoaplabException

A constructor specifying a reason for this exception.

SoaplabException(String, Throwable) - Constructor for exception org.soaplab.share.SoaplabException

A constructor allowing to chain exceptions.

SoaplabException(String, SoaplabExceptionBean) - Constructor for exception org.soaplab.share.SoaplabException

SoaplabException(String, SoaplabExceptionBean, Throwable) - Constructor for exception org.soaplab.share.SoaplabException

SoaplabExceptionBean - Class in org.soaplab.share

This class was generated by the JAX-WS RI.

SoaplabExceptionBean() - Constructor for class org.soaplab.share.SoaplabExceptionBean

SoaplabMap - Class in org.soaplab.share

A container for input and output data to/from Soaplab analysis services.

SoaplabMap() - Constructor for class org.soaplab.share.SoaplabMap

SPECIAL_TYPE - Static variable in class org.soaplab.services.metadata.IOParamDef

An option name.

splitName(String, String) - Static method in class org.soaplab.services.metadata.AnalysisInstallation

A static utility method: Split category and application name.

STANDARD_PARAMETER - Static variable in class org.soaplab.services.metadata.ParamDef

startDocument() - Method in class org.soaplab.services.metadata.MetadataAccessorXML

startDocument()

startElement(String, String, String, Attributes) - Method in class org.soaplab.services.metadata.MetadataAccessorXML

startElement()

STATE_CHANGED - Static variable in interface org.soaplab.services.events.EventConstants

StateChangeEvent - Class in org.soaplab.services.events

A class representing an event that characterizes a change of state of the underlying service/analysis/job.

StateChangeEvent(Object, String, String, String) - Constructor for class org.soaplab.services.events.StateChangeEvent

The most general constructor, taking a message, the two states, the old and new one, and an event source.

StateChangeEvent(String, String, String) - Constructor for class org.soaplab.services.events.StateChangeEvent

A constructor taking a general message and two states, the old and new one.

StateChangeEvent(String, String) - Constructor for class org.soaplab.services.events.StateChangeEvent

A usual constructor, taking just two states, the old and new one.

StdParamDef - Class in org.soaplab.services.metadata

A data structure defining a standard parameter.

StdParamDef() - Constructor for class org.soaplab.services.metadata.StdParamDef

STEP_PROGRESS - Static variable in interface org.soaplab.services.events.EventConstants

StepProgressEvent - Class in org.soaplab.services.events

A class representing an event that reports the numnber of total and completed steps for the underlying service/analysis/job.

StepProgressEvent(Object, String, int, int) - Constructor for class org.soaplab.services.events.StepProgressEvent

The most general constructor, taking a message, number of total and completed steps, and the event source.

StepProgressEvent(String, int, int) - Constructor for class org.soaplab.services.events.StepProgressEvent

A constructor taking a general message and number of total and completed steps.

StepProgressEvent(int, int) - Constructor for class org.soaplab.services.events.StepProgressEvent

A usual constructor, taking just the number of total and completed steps.

STEPS_COMPLETED - Static variable in interface org.soaplab.services.events.EventConstants

T

TAG - Static variable in class org.soaplab.services.metadata.ParamDef

TAGSEPAR - Static variable in class org.soaplab.services.metadata.ParamDef

TagTracer - Class in org.soaplab.services.metadata

The class represents a stack of visited tags when parsing an XML source.

TagTracer() - Constructor for class org.soaplab.services.metadata.TagTracer

A default constructor.

terminate() - Method in class org.soaplab.services.AbstractJob

Terminate this running job.

terminate() - Method in interface org.soaplab.services.Job

Terminate this running job.

terminate(String) - Method in interface org.soaplab.share.Analysis

Terminate the running analysis, identified by its job ID.

TIME_CREATED - Static variable in interface org.soaplab.share.SoaplabConstants

A name of a property returned by AnalysisService.getCharacteristics().

TIME_ELAPSED - Static variable in interface org.soaplab.share.SoaplabConstants

A name of a property returned by AnalysisService.getCharacteristics().

TIME_ENDED - Static variable in interface org.soaplab.share.SoaplabConstants

A name of a property returned by AnalysisService.getCharacteristics().

TIME_PROGRESS - Static variable in interface org.soaplab.services.events.EventConstants

TIME_STARTED - Static variable in interface org.soaplab.share.SoaplabConstants

A name of a property returned by AnalysisService.getCharacteristics().

TimeProgressEvent - Class in org.soaplab.services.events

A class representing an event that reports the remaining time of the underlying service/analysis/job.

TimeProgressEvent(Object, String, long) - Constructor for class org.soaplab.services.events.TimeProgressEvent

The most general constructor, taking a message, remaining time (in 100 nanoseconds), and the event source.

TimeProgressEvent(String, long) - Constructor for class org.soaplab.services.events.TimeProgressEvent

A constructor taking a general message and , remaining time (in 100 nanoseconds).

TimeProgressEvent(long) - Constructor for class org.soaplab.services.events.TimeProgressEvent

A usual constructor, taking just the remaining time (in 100 nanoseconds).

TIMESTAMP - Static variable in interface org.soaplab.services.events.EventConstants

TIMESTAMP_FORMAT - Static variable in interface org.soaplab.services.events.EventConstants

toMap(SoaplabMap) - Static method in class org.soaplab.share.SoaplabMap

toMaps(SoaplabMap[]) - Static method in class org.soaplab.share.SoaplabMap

toString() - Method in class org.soaplab.services.events.AnalysisEvent

Return a stringified version of this event - in an XML format.

toString() - Method in class org.soaplab.services.metadata.AnalysisDef

toString() - Method in class org.soaplab.services.metadata.AnalysisInstallation

toString()

toString() - Method in class org.soaplab.services.metadata.ChoiceParamDef

toString() - Method in class org.soaplab.services.metadata.CondDef

toString() - Method in class org.soaplab.services.metadata.InputPropertyDef

toString() - Method in class org.soaplab.services.metadata.IOParamDef

toString() - Method in class org.soaplab.services.metadata.ListDef

toString() - Method in class org.soaplab.services.metadata.ListItemDef

toString() - Method in class org.soaplab.services.metadata.OutputPropertyDef

toString() - Method in class org.soaplab.services.metadata.ParamDef

toString() - Method in class org.soaplab.services.metadata.RepeatableDef

toString() - Method in class org.soaplab.services.metadata.StdParamDef

toStringMap(SoaplabMap) - Static method in class org.soaplab.share.SoaplabMap

toStringMaps(SoaplabMap[]) - Static method in class org.soaplab.share.SoaplabMap

TOTAL_STEPS - Static variable in interface org.soaplab.services.events.EventConstants

toXML() - Method in class org.soaplab.services.events.AnalysisEvent

Create an XML element representing this event.

toXML() - Method in class org.soaplab.services.events.HeartbeatProgressEvent

Create an XML element representing this event.

toXML() - Method in class org.soaplab.services.events.PercentProgressEvent

Create an XML element representing this event.

toXML() - Method in class org.soaplab.services.events.StateChangeEvent

Create an XML element representing this event.

toXML() - Method in class org.soaplab.services.events.StepProgressEvent

Create an XML element representing this event.

toXML() - Method in class org.soaplab.services.events.TimeProgressEvent

Create an XML element representing this event.

TRUEVALUE - Static variable in class org.soaplab.services.metadata.ParamDef

type - Variable in class org.soaplab.services.metadata.AnalysisDef

type - Variable in class org.soaplab.services.metadata.InputPropertyDef

type - Variable in class org.soaplab.services.metadata.ListDef

type - Variable in class org.soaplab.services.metadata.ListItemDef

type - Variable in class org.soaplab.services.metadata.OutputPropertyDef

type - Variable in class org.soaplab.services.metadata.ParamDef

TYPE_BINARY_ARRAY - Static variable in interface org.soaplab.share.SoaplabConstants

A name of an input or a result type.

TYPE_BINARY_SIMPLE - Static variable in interface org.soaplab.share.SoaplabConstants

A name of an input or a result type.

TYPE_BOOLEAN_SIMPLE - Static variable in interface org.soaplab.share.SoaplabConstants

A name of an input type.

TYPE_INPUT - Static variable in class org.soaplab.services.metadata.IOParamDef

Input/output types.

TYPE_OUTPUT - Static variable in class org.soaplab.services.metadata.IOParamDef

TYPE_STDERR - Static variable in class org.soaplab.services.metadata.IOParamDef

TYPE_STDIN - Static variable in class org.soaplab.services.metadata.IOParamDef

TYPE_STDOUT - Static variable in class org.soaplab.services.metadata.IOParamDef

TYPE_TEXT_ARRAY - Static variable in interface org.soaplab.share.SoaplabConstants

A name of an input or a result type.

TYPE_TEXT_SIMPLE - Static variable in interface org.soaplab.share.SoaplabConstants

A name of an input or a result type.

U

URL_RESULT_SUFFIX - Static variable in interface org.soaplab.share.SoaplabConstants

A suffix to a result name.

URL_SUFFIX - Static variable in interface org.soaplab.share.SoaplabConstants

A suffix added to the input property representing reference data.

USA_SUFFIX - Static variable in interface org.soaplab.share.SoaplabConstants

A suffix added to the input property representing reference and EMBOSS specific data.

USE_DEFAULTS - Static variable in class org.soaplab.services.metadata.ParamDef

V

validate(Map<String, Object>, Job, Object) - Method in interface org.soaplab.services.cmdline.Parameter

Verify value (or values, if they are repetitive) of this parameter.

value - Variable in class org.soaplab.services.metadata.ListItemDef

Value - Class in org.soaplab.share

A container for a value used in MapEntry (which is further used in SoaplabMap).

Value() - Constructor for class org.soaplab.share.Value

Value(Object) - Constructor for class org.soaplab.share.Value

VERIF_LEVEL_ABORT - Static variable in class org.soaplab.services.metadata.CondDef

VERIF_LEVEL_N_A - Static variable in class org.soaplab.services.metadata.CondDef

VERIF_LEVEL_NONE - Static variable in class org.soaplab.services.metadata.CondDef

VERIF_LEVEL_SILENT - Static variable in class org.soaplab.services.metadata.CondDef

VERIF_LEVEL_WARNING - Static variable in class org.soaplab.services.metadata.CondDef

VERLEVEL - Static variable in class org.soaplab.services.metadata.CondDef

VERSION - Static variable in class org.soaplab.services.metadata.TagTracer

Version and date of last update of this class.

W

waitFor() - Method in class org.soaplab.services.AbstractJob

Block and wait until job completes.

waitFor() - Method in interface org.soaplab.services.Job

Block and wait for completion.

waitFor(String) - Method in interface org.soaplab.share.Analysis

Block the client until the underlying running analysis is completed.

X

XML_DESC - Static variable in class org.soaplab.services.metadata.AnalysisInstallation

Z

ZERO_OR_MORE - Static variable in class org.soaplab.services.metadata.ChoiceParamDef

ZERO_OR_ONE - Static variable in class org.soaplab.services.metadata.ChoiceParamDef

A B C D E F G H I J L M N O P R S T U V W X Z