Package org.obolibrary.robot

Class MeasureOperation

java.lang.Object

org.obolibrary.robot.MeasureOperation

public class MeasureOperation
extends Object

Compute metrics for the ontology.

Author:

Nicolas Matentzoglu

Constructor Summary

Constructors

Constructor	Description
MeasureOperation()

Method Summary

Modifier and Type	Method	Description
static MeasureResult	getMetrics(org.semanticweb.owlapi.model.OWLOntology ontology, String metricsType, CURIEShortFormProvider curieShortFormProvider)	Compute metrics for a given ontology.
static MeasureResult	getMetrics(org.semanticweb.owlapi.model.OWLOntology ontology, org.semanticweb.owlapi.reasoner.OWLReasonerFactory rf, String metricsType, CURIEShortFormProvider curieShortFormProvider)	Run the metrics command using the reasoner factory.
static boolean	maybeWriteResult(MeasureResult result, String format, File output)	If a result set has results, write to the output stream and return true.
static void	measure(org.semanticweb.owlapi.model.OWLOntology ontology, org.semanticweb.owlapi.reasoner.OWLReasonerFactory rf, String metricsType, String format, File output, Map<String,String> prefixes)	Running the measure command
static void	writeResult(MeasureResult result, String format, File output)	Write a model to an output stream.

Methods inherited from class java.lang.Object

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

Constructor Detail

MeasureOperation

public MeasureOperation()

Method Detail

maybeWriteResult

public static boolean maybeWriteResult(MeasureResult result,
                                       String format,
                                       File output)
                                throws IOException

If a result set has results, write to the output stream and return true. Otherwise return false.

Parameters:

result - the results to write

format - the name of the file format to write the results to

output - the file to write to

Returns:

true if there were results, false otherwise

Throws:

IOException - if writing file failed

measure

public static void measure(org.semanticweb.owlapi.model.OWLOntology ontology,
                           org.semanticweb.owlapi.reasoner.OWLReasonerFactory rf,
                           String metricsType,
                           String format,
                           File output,
                           Map<String,String> prefixes)
                    throws IOException

Running the measure command

Parameters:

ontology - input ontology

rf - reasoner factory to be used for reasoning metrics

metricsType - The type of metrics that should be generated, like 'essential', 'extended' or all

format - the name of the file format to write the results to

output - the file to write to

prefixes - prefix map to be used for computing metrics

Throws:

IOException - if writing file failed

getMetrics

public static MeasureResult getMetrics(org.semanticweb.owlapi.model.OWLOntology ontology,
                                       String metricsType,
                                       CURIEShortFormProvider curieShortFormProvider)

Compute metrics for a given ontology.

Parameters:

ontology - Ontology to run metrics

metricsType - what kind of metrics to harvest

curieShortFormProvider - Shortformprovider to be used for computation of CURIEs

Returns:

Metrics, if successful

getMetrics

public static MeasureResult getMetrics(org.semanticweb.owlapi.model.OWLOntology ontology,
                                       org.semanticweb.owlapi.reasoner.OWLReasonerFactory rf,
                                       String metricsType,
                                       CURIEShortFormProvider curieShortFormProvider)

Run the metrics command using the reasoner factory. Note: when the reasoner factory is passed, it is assumed that reasoner metrics should be harvested. For example: both reasoner-all, and all will collect the same metrics: all metrics, plus the (simple) reasoner metrics.

Parameters:

ontology - Ontology to run metrics

rf - reasoner factory, in case reasoner metrics should be collected

metricsType - what kind of metrics to harvest

curieShortFormProvider - short form provider

Returns:

Metrics, if successful

writeResult

public static void writeResult(MeasureResult result,
                               String format,
                               File output)
                        throws IOException

Write a model to an output stream.

Parameters:

result - results of the metrics operation

format - the language to write in (if null, TTL)

output - the output stream to write to

Throws:

IOException - on problem writing to output