Package org.incenp.obofoundry.kgcl

Class KGCLHelper

java.lang.Object

org.incenp.obofoundry.kgcl.KGCLHelper

public class KGCLHelper
extends Object

A class providing static helper methods to work with KGCL.

Constructor Summary

Constructors

Constructor	Description
KGCLHelper()

Method Summary

Modifier and Type	Method	Description
static void	apply(List<org.incenp.obofoundry.kgcl.model.Change> changeset, IPatcher patcher, boolean noPartialApply, List<RejectedChange> rejects)	Applies a KGCL changeset using the provided patcher object.
static void	apply(List<org.incenp.obofoundry.kgcl.model.Change> changeset, org.semanticweb.owlapi.model.OWLOntology ontology, org.semanticweb.owlapi.reasoner.OWLReasoner reasoner, boolean noPartialApply)	Applies a KGCL changeset to an ontology.
static void	apply(List<org.incenp.obofoundry.kgcl.model.Change> changeset, org.semanticweb.owlapi.model.OWLOntology ontology, org.semanticweb.owlapi.reasoner.OWLReasoner reasoner, boolean noPartialApply, List<RejectedChange> rejects)	Applies a KGCL changeset to an ontology.
static void	apply(List<org.incenp.obofoundry.kgcl.model.Change> changeset, org.semanticweb.owlapi.model.OWLOntology ontology, org.semanticweb.owlapi.reasoner.OWLReasoner reasoner, boolean noPartialApply, List<RejectedChange> rejects, boolean provisional)	Applies a KGCL changeset to an ontology.
static List<org.incenp.obofoundry.kgcl.model.Change>	extractPendingChanges(org.semanticweb.owlapi.model.OWLOntology ontology, ZonedDateTime before)	Gets the "pending" (provisional) changes that are stored as KGCL annotations in the ontology,
static List<org.incenp.obofoundry.kgcl.model.Change>	parse(File kgcl, Map<String,String> prefixMap, List<KGCLSyntaxError> errors, ILabelResolver labelResolver)	Parses KGCL from a file and collects syntax errors.
static List<org.incenp.obofoundry.kgcl.model.Change>	parse(File kgcl, org.semanticweb.owlapi.model.PrefixManager prefixManager)	Parses KGCL from a file.
static List<org.incenp.obofoundry.kgcl.model.Change>	parse(File kgcl, org.semanticweb.owlapi.model.PrefixManager prefixManager, List<KGCLSyntaxError> errors)	Parses KGCL from a file and collects syntax errors.
static List<org.incenp.obofoundry.kgcl.model.Change>	parse(File kgcl, org.semanticweb.owlapi.model.PrefixManager prefixManager, List<KGCLSyntaxError> errors, ILabelResolver labelResolver)	Parses KGCL from a file and collects syntax errors.
static List<org.incenp.obofoundry.kgcl.model.Change>	parse(String kgcl, Map<String,String> prefixMap, List<KGCLSyntaxError> errors, ILabelResolver labelResolver)	Parses KGCL from a string and collects syntax errors.
static List<org.incenp.obofoundry.kgcl.model.Change>	parse(String kgcl, org.semanticweb.owlapi.model.PrefixManager prefixManager)	Parses KGCL from a string.
static List<org.incenp.obofoundry.kgcl.model.Change>	parse(String kgcl, org.semanticweb.owlapi.model.PrefixManager prefixManager, List<KGCLSyntaxError> errors)	Parses KGCL from a string and collects syntax errors.
static List<org.incenp.obofoundry.kgcl.model.Change>	parse(String kgcl, org.semanticweb.owlapi.model.PrefixManager prefixManager, List<KGCLSyntaxError> errors, ILabelResolver labelResolver)	Parses KGCL from a string and collects syntax errors.
static List<org.incenp.obofoundry.kgcl.model.Change>	parseYAML(File kgcl, Map<String,String> prefixMap)	Parses a changeset serialised in YAML form.
static List<org.incenp.obofoundry.kgcl.model.Change>	parseYAML(File kgcl, org.semanticweb.owlapi.model.PrefixManager prefixManager)	Parses a changeset serialised in YAML form.

Methods inherited from class java.lang.Object

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

Constructor Detail

KGCLHelper

public KGCLHelper()

Method Detail

parse

public static List<org.incenp.obofoundry.kgcl.model.Change> parse(String kgcl,
                                                                  org.semanticweb.owlapi.model.PrefixManager prefixManager)

Parses KGCL from a string.

Parameters:

kgcl - The KGCL instructions to parse.

prefixManager - A prefix manager to expand CURIEs into IRIs. May be null.

Returns:

A KGCL changeset.

parse

public static List<org.incenp.obofoundry.kgcl.model.Change> parse(String kgcl,
                                                                  org.semanticweb.owlapi.model.PrefixManager prefixManager,
                                                                  List<KGCLSyntaxError> errors)

Parses KGCL from a string and collects syntax errors.

Parameters:

kgcl - The KGCL instructions to parse.

prefixManager - A prefix manager to expand CURIEs into IRIs. May be null.

errors - A list that will collect any syntax error encountered when parsing. If null, errors will be ignored.

Returns:

A KGCL changeset.

parse

public static List<org.incenp.obofoundry.kgcl.model.Change> parse(String kgcl,
                                                                  org.semanticweb.owlapi.model.PrefixManager prefixManager,
                                                                  List<KGCLSyntaxError> errors,
                                                                  ILabelResolver labelResolver)

Parses KGCL from a string and collects syntax errors. This method allows the use of labels in place of identifiers.

Parameters:

kgcl - The KGCL instructions to parse.

prefixManager - A prefix manager to expand CURIEs into IRIS. May be null.

errors - A list that will collect any syntax error encountered when parsing. If null, errors will be ignored.

labelResolver - A helper object to resolve labels into identifiers. May be null, in which case any use of a label where an identifier is normally expected would result in a syntax error.

Returns:

A KGCL changeset.

parse

public static List<org.incenp.obofoundry.kgcl.model.Change> parse(String kgcl,
                                                                  Map<String,String> prefixMap,
                                                                  List<KGCLSyntaxError> errors,
                                                                  ILabelResolver labelResolver)

Parses KGCL from a string and collects syntax errors.

Parameters:

kgcl - The KGCL instructions to parse.

prefixMap - A map of prefix names to prefix IRIs.

errors - A list that will collect any syntax error encountered when parsing. If null, errors will be ignored.

labelResolver - A helper object to resolve labels into identifiers. May be null, in which case any use of a label where an identifier is normally expected would result in an error.

Returns:

A KGCL changeset.

parse

public static List<org.incenp.obofoundry.kgcl.model.Change> parse(File kgcl,
                                                                  org.semanticweb.owlapi.model.PrefixManager prefixManager)
                                                           throws IOException

Parses KGCL from a file.

Parameters:

kgcl - The file to parse.

prefixManager - A prefix manager to expand CURIEs into IRIs. May be null.

Returns:

A KGCL changeset.

Throws:

IOException - If any non-KGCL I/O error occurs.

parse

public static List<org.incenp.obofoundry.kgcl.model.Change> parse(File kgcl,
                                                                  org.semanticweb.owlapi.model.PrefixManager prefixManager,
                                                                  List<KGCLSyntaxError> errors)
                                                           throws IOException

Parses KGCL from a file and collects syntax errors.

Parameters:

kgcl - The file to parse.

prefixManager - A prefix manager to expand CURIEs into IRIs. May be null.

errors - A list that will collect any syntax error encountered when parsing. If null, errors will be ignored.

Returns:

A KGCL changeset.

Throws:

IOException - If any non-KGCL I/O error occurs.

parse

public static List<org.incenp.obofoundry.kgcl.model.Change> parse(File kgcl,
                                                                  org.semanticweb.owlapi.model.PrefixManager prefixManager,
                                                                  List<KGCLSyntaxError> errors,
                                                                  ILabelResolver labelResolver)
                                                           throws IOException

Parses KGCL from a file and collects syntax errors. This method allows the use of labels in place of identifiers.

Parameters:

kgcl - The file to parse.

prefixManager - A prefix manager to expand CURIEs into IRIs. May be null.

errors - A list that will collect any syntax error encountered when parsing. If null, errors will be ignored.

labelResolver - A helper object to resolve labels into identifiers. May be null, in which case any use of a label where an identifier is normally expected would result in a syntax error.

Returns:

A KGCL changeset.

Throws:

IOException - If any non-KGCL I/O error occurs.

parse

public static List<org.incenp.obofoundry.kgcl.model.Change> parse(File kgcl,
                                                                  Map<String,String> prefixMap,
                                                                  List<KGCLSyntaxError> errors,
                                                                  ILabelResolver labelResolver)
                                                           throws IOException

Parses KGCL from a file and collects syntax errors.

Parameters:

kgcl - The file to parse.

prefixMap - A map of prefix names to prefix IRIs.

errors - A list that will collect any syntax error encountered when parsing. If null, errors will be ignored

labelResolver - A helper object to resolve labels into identifiers. May be null, in which case any use of a label where an identifier is normally expected would result in a syntax error.

Returns:

A KGCL changeset.

Throws:

IOException - If any non-KGCL I/O error occurs.

parseYAML

public static List<org.incenp.obofoundry.kgcl.model.Change> parseYAML(File kgcl,
                                                                      Map<String,String> prefixMap)
                                                               throws IOException

Parses a changeset serialised in YAML form.

Parameters:

kgcl - The YAML file from which to read the changeset. That file is expected to contain a list of KGCL change objects.

prefixMap - A map of prefix names to prefix IRIs. May be null.

Returns:

A KGCL changeset.

Throws:

IOException - If any error occurs. Note that, contrary to the methods that read from the KGCL controlled natural language, here this includes post-I/O errors caused by invalid KGCL contents within the source file.

parseYAML

public static List<org.incenp.obofoundry.kgcl.model.Change> parseYAML(File kgcl,
                                                                      org.semanticweb.owlapi.model.PrefixManager prefixManager)
                                                               throws IOException

Parses a changeset serialised in YAML form.

Parameters:

kgcl - The YAML file from which to read the changeset. That file is expected to contain a list of KGCL change objects.

prefixManager - A prefix manager to expand CURIEs into IRIs. May be null.

Returns:

A KGCL changeset.

Throws:

IOException - If any error occurs. Note that, contrary to the methods that read from the KGCL controlled natural language, here this includes post-I/O errors caused by invalid KGCL contents within the source file.

extractPendingChanges

public static List<org.incenp.obofoundry.kgcl.model.Change> extractPendingChanges(org.semanticweb.owlapi.model.OWLOntology ontology,
                                                                                  ZonedDateTime before)

Gets the "pending" (provisional) changes that are stored as KGCL annotations in the ontology,

Note that the annotations are removed during the process.

Parameters:

ontology - The ontology to extract pending changes from.

before - If not null, only changes older than the specified date are extracted.

Returns:

The list of pending changes.

apply

public static void apply(List<org.incenp.obofoundry.kgcl.model.Change> changeset,
                         org.semanticweb.owlapi.model.OWLOntology ontology,
                         org.semanticweb.owlapi.reasoner.OWLReasoner reasoner,
                         boolean noPartialApply)

Applies a KGCL changeset to an ontology.

Parameters:

changeset - The changeset to apply.

ontology - The ontology to apply it to.

reasoner - The reasoner to use.

noPartialApply - If true, changes will only be applied if they all can be applied.

apply

public static void apply(List<org.incenp.obofoundry.kgcl.model.Change> changeset,
                         org.semanticweb.owlapi.model.OWLOntology ontology,
                         org.semanticweb.owlapi.reasoner.OWLReasoner reasoner,
                         boolean noPartialApply,
                         List<RejectedChange> rejects)

Applies a KGCL changeset to an ontology.

Parameters:

changeset - The changeset to apply.

ontology - The ontology to apply it to.

reasoner - The reasoner to use.

noPartialApply - If true, changes will only be applied if they can all be applied.

rejects - A list that will collect the changes that cannot be applied. May be null.

apply

public static void apply(List<org.incenp.obofoundry.kgcl.model.Change> changeset,
                         org.semanticweb.owlapi.model.OWLOntology ontology,
                         org.semanticweb.owlapi.reasoner.OWLReasoner reasoner,
                         boolean noPartialApply,
                         List<RejectedChange> rejects,
                         boolean provisional)

Applies a KGCL changeset to an ontology.

Parameters:

changeset - The changeset to apply.

ontology - The ontology to apply it to.

reasoner - The reasoner to use,

noPartialApply - If true, changes will only be applied if they can all be applied.

rejects - A list that will collect the changes that cannot be applied. May be null.

provisional - If true, changes will be recorded in the ontology for later application, rather than applied directly.

apply

public static void apply(List<org.incenp.obofoundry.kgcl.model.Change> changeset,
                         IPatcher patcher,
                         boolean noPartialApply,
                         List<RejectedChange> rejects)

Applies a KGCL changeset using the provided patcher object.

Parameters:

changeset - The changeset to apply.

patcher - The patcher for the knowledge graph to modify.

noPartialApply - If true, changes will only be applied if they can all be applied.

rejects - A list that will collect the changes that cannot be applied. May be null.