org.obolibrary.robot

Class IOHelper

java.lang.Object

org.obolibrary.robot.IOHelper

public class IOHelper
extends Object

Provides convenience methods for working with ontology and term files.

Author:

James A. Overton

Constructor Summary

Constructors

Constructor and Description
IOHelper() Create a new IOHelper with the default prefixes.
IOHelper(boolean defaults) Create a new IOHelper with or without the default prefixes.
IOHelper(File file) Create a new IOHelper with prefixes from a file.
IOHelper(Map<String,Object> map) Create a new IOHelper with the specified prefixes.
IOHelper(String path) Create a new IOHelper with prefixes from a file path.

Method Summary

Modifier and Type	Method and Description
void	addBaseNamespace(String baseNamespace) Add a base namespace to the IOHelper.
void	addBaseNamespaces(String baseNamespacePath) Add a set of base namespaces to the IOHelper from file.
void	addPrefix(String combined) Add a prefix mapping as a single string "foo: http://example.com#".
void	addPrefix(String prefix, String target) Add a prefix mapping to the current JSON-LD context, as a prefix string and target string.
void	addPrefixes(com.github.jsonldjava.core.Context context1) Given a Context, add the prefix mappings to the current JSON-LD context.
void	addPrefixes(String prefixPath) Given a path to a JSON-LD prefix file, add the prefix mappings in the file to the current JSON-LD context.
void	addPrefixesAndSave(org.semanticweb.owlapi.model.OWLOntology ontology, File outputFile, List<String> addPrefixes) Deprecated. replaced by saveOntology(OWLOntology, OWLDocumentFormat, IRI, Map, boolean)
static String	cellToA1(int rowNum, int colNum) Convert a row index and column index for a cell to A1 notation.
protected static boolean	cleanTDB(String tdbDir) Given a directory containing TDB mappings, remove the files and directory.
org.semanticweb.owlapi.model.IRI	createIRI(String term) Given a term string, use the current prefixes to create an IRI.
org.semanticweb.owlapi.model.IRI	createIRI(String term, boolean qName) Given a term string, use the current prefixes to create an IRI.
Set<org.semanticweb.owlapi.model.IRI>	createIRIs(Set<String> terms) Given a set of term identifier strings, return a set of IRIs.
static org.semanticweb.owlapi.model.OWLLiteral	createLiteral(String value) Create an OWLLiteral.
static org.semanticweb.owlapi.model.OWLLiteral	createTaggedLiteral(String value, String lang) Create an OWLLiteral with a language tag.
org.semanticweb.owlapi.model.OWLLiteral	createTypedLiteral(String value, org.semanticweb.owlapi.model.IRI type) Create a typed OWLLiteral.
org.semanticweb.owlapi.model.OWLLiteral	createTypedLiteral(String value, String type) Create a typed OWLLiteral.
Set<String>	extractTerms(String input) Extract a set of term identifiers from an input string by removing comments, trimming lines, and removing empty lines.
Set<String>	getBaseNamespaces() Get the base namespaces.
com.github.jsonldjava.core.Context	getContext() Get a copy of the current context.
String	getContextString() Return the current prefixes as a JSON-LD string.
com.github.jsonldjava.core.Context	getDefaultContext() Get a copy of the default context.
static org.semanticweb.owlapi.model.OWLDocumentFormat	getFormat(String formatName) Given the name of a file format, return an instance of it.
Map<String,String>	getPrefixes() Get a copy of the current prefix map.
org.semanticweb.owlapi.util.DefaultPrefixManager	getPrefixManager() Get a prefix manager with the current prefixes.
Boolean	getXMLEntityFlag() Get the useXMLEntities flag.
File	guessCatalogFile(File ontologyFile) Try to guess the location of the catalog.xml file.
org.semanticweb.owlapi.model.OWLOntology	loadOntology(File ontologyFile) Load an ontology from a File, using a catalog file if available.
org.semanticweb.owlapi.model.OWLOntology	loadOntology(File ontologyFile, boolean useCatalog) Load an ontology from a File, with option to use a catalog file.
org.semanticweb.owlapi.model.OWLOntology	loadOntology(File ontologyFile, File catalogFile) Load an ontology from a File, with optional catalog File.
org.semanticweb.owlapi.model.OWLOntology	loadOntology(InputStream ontologyStream) Load an ontology from an InputStream, without a catalog file.
org.semanticweb.owlapi.model.OWLOntology	loadOntology(InputStream ontologyStream, String catalogPath) Load an ontology from an InputStream with a catalog file.
org.semanticweb.owlapi.model.OWLOntology	loadOntology(org.semanticweb.owlapi.model.IRI ontologyIRI) Given an ontology IRI, load the ontology from the IRI.
org.semanticweb.owlapi.model.OWLOntology	loadOntology(org.semanticweb.owlapi.model.IRI ontologyIRI, String catalogPath) Given an IRI and a path to a catalog file, load the ontology from the IRI with the catalog.
org.semanticweb.owlapi.model.OWLOntology	loadOntology(String ontologyPath) Load an ontology from a String path, using a catalog file if available.
org.semanticweb.owlapi.model.OWLOntology	loadOntology(String ontologyPath, boolean useCatalog) Load an ontology from a String path, with option to use catalog file.
org.semanticweb.owlapi.model.OWLOntology	loadOntology(String ontologyPath, String catalogPath) Load an ontology from a String path, with optional catalog file.
static org.apache.jena.query.Dataset	loadToTDBDataset(String inputPath, String tdbDir) Given a path to an RDF/XML or TTL file and a RDF language, load the file as the default model of a TDB dataset backed by a directory to improve processing time.
static org.semanticweb.owlapi.util.DefaultPrefixManager	makePrefixManager(Map<String,String> prefixes) Make an OWLAPI DefaultPrefixManager from a map of prefixes.
static com.github.jsonldjava.core.Context	parseContext(String jsonString) Load a map of prefixes from the "@context" of a JSON-LD string.
Set<org.semanticweb.owlapi.model.IRI>	parseTerms(String input) Parse a set of IRIs from a space-separated string, ignoring '#' comments.
static List<List<String>>	readCSV(InputStream stream) Read comma-separated values from a stream to a list of lists of strings.
static List<List<String>>	readCSV(Reader reader) Read comma-separated values from a reader to a list of lists of strings.
static List<List<String>>	readCSV(String path) Read comma-separated values from a path to a list of lists of strings.
static List<List<String>>	readTable(String path) Read a table from a path to a list of lists of strings.
static List<List<String>>	readTSV(InputStream stream) Read tab-separated values from a stream to a list of lists of strings.
static List<List<String>>	readTSV(Reader reader) Read tab-separated values from a reader to a list of lists of strings.
static List<List<String>>	readTSV(String path) Read tab-separated values from a path to a list of lists of strings.
void	saveContext(File file) Write the current context as a JSON-LD file.
void	saveContext(String path) Write the current context as a JSON-LD file.
org.semanticweb.owlapi.model.OWLOntology	saveOntology(org.semanticweb.owlapi.model.OWLOntology ontology, File ontologyFile) Save an ontology to a File.
org.semanticweb.owlapi.model.OWLOntology	saveOntology(org.semanticweb.owlapi.model.OWLOntology ontology, org.semanticweb.owlapi.model.IRI ontologyIRI) Save an ontology to an IRI, using the file extension to determine the format.
org.semanticweb.owlapi.model.OWLOntology	saveOntology(org.semanticweb.owlapi.model.OWLOntology ontology, org.semanticweb.owlapi.model.OWLDocumentFormat format, File ontologyFile) Save an ontology in the given format to a file.
org.semanticweb.owlapi.model.OWLOntology	saveOntology(org.semanticweb.owlapi.model.OWLOntology ontology, org.semanticweb.owlapi.model.OWLDocumentFormat format, File ontologyFile, boolean checkOBO) Save an ontology in the given format to a file, with the option to ignore OBO document checks.
org.semanticweb.owlapi.model.OWLOntology	saveOntology(org.semanticweb.owlapi.model.OWLOntology ontology, org.semanticweb.owlapi.model.OWLDocumentFormat format, org.semanticweb.owlapi.model.IRI ontologyIRI) Save an ontology in the given format to an IRI.
org.semanticweb.owlapi.model.OWLOntology	saveOntology(org.semanticweb.owlapi.model.OWLOntology ontology, org.semanticweb.owlapi.model.OWLDocumentFormat format, org.semanticweb.owlapi.model.IRI ontologyIRI, boolean checkOBO) Save an ontology in the given format to an IRI, with the option to ignore OBO document checks.
org.semanticweb.owlapi.model.OWLOntology	saveOntology(org.semanticweb.owlapi.model.OWLOntology ontology, org.semanticweb.owlapi.model.OWLDocumentFormat format, org.semanticweb.owlapi.model.IRI ontologyIRI, Map<String,String> addPrefixes, boolean checkOBO) Save an ontology in the given format to an IRI, with option to add prefixes and option to ignore OBO document checks.
org.semanticweb.owlapi.model.OWLOntology	saveOntology(org.semanticweb.owlapi.model.OWLOntology ontology, org.semanticweb.owlapi.model.OWLDocumentFormat format, String ontologyPath, boolean checkOBO) Save an ontology in the given format to a path, with the option to ignore OBO document checks.
org.semanticweb.owlapi.model.OWLOntology	saveOntology(org.semanticweb.owlapi.model.OWLOntology ontology, String ontologyPath) Save an ontology to a String path.
void	setContext() Set an empty context.
void	setContext(com.github.jsonldjava.core.Context context) Set the current JSON-LD context to the given context.
void	setContext(Map<String,Object> map) Set the current JSON-LD context to the given map.
void	setContext(String jsonString) Set the current JSON-LD context to the given context.
void	setPrefixes(Map<String,Object> map) Set the current prefix map.
void	setXMLEntityFlag(Boolean entityFlag) Set whether or not XML entities will be swapped into URIs in saveOntology XML output formats.
static void	writeTable(List<String[]> table, File file, char separator) Write a table from a list of arrays.
static void	writeTable(List<String[]> table, String path) Write a table from a list of arrays.
static void	writeTable(List<String[]> table, Writer writer, char separator) Write a table from a list of arrays.

Methods inherited from class java.lang.Object

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

Constructor Detail

IOHelper

public IOHelper()
         throws IOException

Create a new IOHelper with the default prefixes.

Throws:

IOException - on problem getting default context

IOHelper

public IOHelper(boolean defaults)
         throws IOException

Create a new IOHelper with or without the default prefixes.

Parameters:

defaults - false if defaults should not be used

Throws:

IOException - on problem getting default context

IOHelper

public IOHelper(Map<String,Object> map)
         throws IOException

Create a new IOHelper with the specified prefixes.

Parameters:

map - the prefixes to use

Throws:

IOException - on issue parsing map

IOHelper

public IOHelper(String path)
         throws IOException

Create a new IOHelper with prefixes from a file path.

Parameters:

path - to a JSON-LD file with a @context

Throws:

IOException - on issue parsing JSON-LD file as context

IOHelper

public IOHelper(File file)
         throws IOException

Create a new IOHelper with prefixes from a file.

Parameters:

file - a JSON-LD file with a @context

Throws:

IOException - on issue reading file or setting context from file

Method Detail

addPrefixesAndSave

@Deprecated
public void addPrefixesAndSave(org.semanticweb.owlapi.model.OWLOntology ontology,
                                           File outputFile,
                                           List<String> addPrefixes)
                                    throws IOException

Deprecated. replaced by saveOntology(OWLOntology, OWLDocumentFormat, IRI, Map, boolean)

Given an ontology, a file, and a list of prefixes, save the ontology to the file and include the prefixes in the header.

Parameters:

ontology - OWLOntology to save

outputFile - File to save ontology to

addPrefixes - List of prefixes to add ("foo: http://foo.bar/")

Throws:

IOException - On issue parsing list of prefixes or saving file

cleanTDB

protected static boolean cleanTDB(String tdbDir)

Given a directory containing TDB mappings, remove the files and directory. If successful, return true.

Parameters:

tdbDir - directory to remove

Returns:

boolean indicating success

guessCatalogFile

public File guessCatalogFile(File ontologyFile)

Try to guess the location of the catalog.xml file. Looks in the directory of the given ontology file for a catalog file.

Parameters:

ontologyFile - the

Returns:

the guessed catalog File; may not exist!

loadOntology

public org.semanticweb.owlapi.model.OWLOntology loadOntology(String ontologyPath)
                                                      throws IOException

Load an ontology from a String path, using a catalog file if available.

Parameters:

ontologyPath - the path to the ontology file

Returns:

a new ontology object, with a new OWLManager

Throws:

IOException - on any problem

loadOntology

public org.semanticweb.owlapi.model.OWLOntology loadOntology(String ontologyPath,
                                                             boolean useCatalog)
                                                      throws IOException

Load an ontology from a String path, with option to use catalog file.

Parameters:

ontologyPath - the path to the ontology file

useCatalog - when true, a catalog file will be used if one is found

Returns:

a new ontology object, with a new OWLManager

Throws:

IOException - on any problem

loadOntology

public org.semanticweb.owlapi.model.OWLOntology loadOntology(String ontologyPath,
                                                             String catalogPath)
                                                      throws IOException

Load an ontology from a String path, with optional catalog file.

Parameters:

ontologyPath - the path to the ontology file

catalogPath - the path to the catalog file

Returns:

a new ontology object, with a new OWLManager

Throws:

IOException - on any problem

loadOntology

public org.semanticweb.owlapi.model.OWLOntology loadOntology(File ontologyFile)
                                                      throws IOException

Load an ontology from a File, using a catalog file if available.

Parameters:

ontologyFile - the ontology file to load

Returns:

a new ontology object, with a new OWLManager

Throws:

IOException - on any problem

loadOntology

public org.semanticweb.owlapi.model.OWLOntology loadOntology(File ontologyFile,
                                                             boolean useCatalog)
                                                      throws IOException

Load an ontology from a File, with option to use a catalog file.

Parameters:

ontologyFile - the ontology file to load

useCatalog - when true, a catalog file will be used if one is found

Returns:

a new ontology object, with a new OWLManager

Throws:

IOException - on any problem

loadOntology

public org.semanticweb.owlapi.model.OWLOntology loadOntology(File ontologyFile,
                                                             File catalogFile)
                                                      throws IOException

Load an ontology from a File, with optional catalog File.

Parameters:

ontologyFile - the ontology file to load

catalogFile - the catalog file to use

Returns:

a new ontology object, with a new OWLManager

Throws:

IOException - on any problem

loadOntology

public org.semanticweb.owlapi.model.OWLOntology loadOntology(InputStream ontologyStream)
                                                      throws IOException

Load an ontology from an InputStream, without a catalog file.

Parameters:

ontologyStream - the ontology stream to load

Returns:

a new ontology object, with a new OWLManager

Throws:

IOException - on any problem

loadOntology

public org.semanticweb.owlapi.model.OWLOntology loadOntology(InputStream ontologyStream,
                                                             String catalogPath)
                                                      throws IOException

Load an ontology from an InputStream with a catalog file.

Parameters:

ontologyStream - the ontology stream to load

catalogPath - the catalog file to use or null

Returns:

a new ontology object, with a new OWLManager

Throws:

IOException - on any problem

loadOntology

public org.semanticweb.owlapi.model.OWLOntology loadOntology(org.semanticweb.owlapi.model.IRI ontologyIRI)
                                                      throws IOException

Given an ontology IRI, load the ontology from the IRI.

Parameters:

ontologyIRI - the ontology IRI to load

Returns:

a new ontology object, with a new OWLManager

Throws:

IOException - on any problem

loadOntology

public org.semanticweb.owlapi.model.OWLOntology loadOntology(org.semanticweb.owlapi.model.IRI ontologyIRI,
                                                             String catalogPath)
                                                      throws IOException

Given an IRI and a path to a catalog file, load the ontology from the IRI with the catalog.

Parameters:

ontologyIRI - the ontology IRI to load

catalogPath - the catalog file to use or null

Returns:

a new ontology object, with a new OWLManager

Throws:

IOException - on any problem

loadToTDBDataset

public static org.apache.jena.query.Dataset loadToTDBDataset(String inputPath,
                                                             String tdbDir)
                                                      throws org.apache.jena.shared.JenaException

Given a path to an RDF/XML or TTL file and a RDF language, load the file as the default model of a TDB dataset backed by a directory to improve processing time. Return the new dataset.

WARNING - this creates a directory at given tdbDir location!

Parameters:

inputPath - input path of RDF/XML or TTL file

tdbDir - location to put TDB mappings

Returns:

Dataset instantiated with triples

Throws:

org.apache.jena.shared.JenaException - if TDB directory can't be written to

getFormat

public static org.semanticweb.owlapi.model.OWLDocumentFormat getFormat(String formatName)
                                                                throws IllegalArgumentException

Given the name of a file format, return an instance of it.

Suported formats:

• OBO as 'obo'
• RDFXML as 'owl'
• Turtle as 'ttl'
• OWLXML as 'owx'
• Manchester as 'omn'
• OWL Functional as 'ofn'

Parameters:

formatName - the name of the format

Returns:

an instance of the format

Throws:

IllegalArgumentException - if format name is not recognized

saveOntology

public org.semanticweb.owlapi.model.OWLOntology saveOntology(org.semanticweb.owlapi.model.OWLOntology ontology,
                                                             String ontologyPath)
                                                      throws IOException

Save an ontology to a String path.

Parameters:

ontology - the ontology to save

ontologyPath - the path to save the ontology to

Returns:

the saved ontology

Throws:

IOException - on any problem

saveOntology

public org.semanticweb.owlapi.model.OWLOntology saveOntology(org.semanticweb.owlapi.model.OWLOntology ontology,
                                                             File ontologyFile)
                                                      throws IOException

Save an ontology to a File.

Parameters:

ontology - the ontology to save

ontologyFile - the file to save the ontology to

Returns:

the saved ontology

Throws:

IOException - on any problem

saveOntology

public org.semanticweb.owlapi.model.OWLOntology saveOntology(org.semanticweb.owlapi.model.OWLOntology ontology,
                                                             org.semanticweb.owlapi.model.IRI ontologyIRI)
                                                      throws IOException

Save an ontology to an IRI, using the file extension to determine the format.

Parameters:

ontology - the ontology to save

ontologyIRI - the IRI to save the ontology to

Returns:

the saved ontology

Throws:

IOException - on any problem

saveOntology

public org.semanticweb.owlapi.model.OWLOntology saveOntology(org.semanticweb.owlapi.model.OWLOntology ontology,
                                                             org.semanticweb.owlapi.model.OWLDocumentFormat format,
                                                             File ontologyFile)
                                                      throws IOException

Save an ontology in the given format to a file.

Parameters:

ontology - the ontology to save

format - the ontology format to use

ontologyFile - the file to save the ontology to

Returns:

the saved ontology

Throws:

IOException - on any problem

saveOntology

public org.semanticweb.owlapi.model.OWLOntology saveOntology(org.semanticweb.owlapi.model.OWLOntology ontology,
                                                             org.semanticweb.owlapi.model.OWLDocumentFormat format,
                                                             File ontologyFile,
                                                             boolean checkOBO)
                                                      throws IOException

Save an ontology in the given format to a file, with the option to ignore OBO document checks.

Parameters:

ontology - the ontology to save

format - the ontology format to use

ontologyFile - the file to save the ontology to

checkOBO - if false, ignore OBO document checks

Returns:

the saved ontology

Throws:

IOException - on any problem

saveOntology

public org.semanticweb.owlapi.model.OWLOntology saveOntology(org.semanticweb.owlapi.model.OWLOntology ontology,
                                                             org.semanticweb.owlapi.model.OWLDocumentFormat format,
                                                             org.semanticweb.owlapi.model.IRI ontologyIRI)
                                                      throws IOException

Save an ontology in the given format to an IRI.

Parameters:

ontology - the ontology to save

format - the ontology format to use

ontologyIRI - the IRI to save the ontology to

Returns:

the saved ontology

Throws:

IOException - on any problem

saveOntology

public org.semanticweb.owlapi.model.OWLOntology saveOntology(org.semanticweb.owlapi.model.OWLOntology ontology,
                                                             org.semanticweb.owlapi.model.OWLDocumentFormat format,
                                                             String ontologyPath,
                                                             boolean checkOBO)
                                                      throws IOException

Save an ontology in the given format to a path, with the option to ignore OBO document checks.

Parameters:

ontology - the ontology to save

format - the ontology format to use

ontologyPath - the path to save the ontology to

checkOBO - if false, ignore OBO document checks

Returns:

the saved ontology

Throws:

IOException - on any problem

saveOntology

public org.semanticweb.owlapi.model.OWLOntology saveOntology(org.semanticweb.owlapi.model.OWLOntology ontology,
                                                             org.semanticweb.owlapi.model.OWLDocumentFormat format,
                                                             org.semanticweb.owlapi.model.IRI ontologyIRI,
                                                             boolean checkOBO)
                                                      throws IOException

Save an ontology in the given format to an IRI, with the option to ignore OBO document checks.

Parameters:

ontology - the ontology to save

format - the ontology format to use

ontologyIRI - the IRI to save the ontology to

checkOBO - if false, ignore OBO document checks

Returns:

the saved ontology

Throws:

IOException - on any problem

saveOntology

public org.semanticweb.owlapi.model.OWLOntology saveOntology(org.semanticweb.owlapi.model.OWLOntology ontology,
                                                             org.semanticweb.owlapi.model.OWLDocumentFormat format,
                                                             org.semanticweb.owlapi.model.IRI ontologyIRI,
                                                             Map<String,String> addPrefixes,
                                                             boolean checkOBO)
                                                      throws IOException

Save an ontology in the given format to an IRI, with option to add prefixes and option to ignore OBO document checks.

Parameters:

ontology - the ontology to save

format - the ontology format to use

ontologyIRI - the IRI to save the ontology to

addPrefixes - map of prefixes to add to header

checkOBO - if false, ignore OBO document checks

Returns:

the saved ontology

Throws:

IOException - on any problem

extractTerms

public Set<String> extractTerms(String input)

Extract a set of term identifiers from an input string by removing comments, trimming lines, and removing empty lines. A comment is a space or newline followed by a '#', to the end of the line. This excludes '#' characters in IRIs.

Parameters:

input - the String containing the term identifiers

Returns:

a set of term identifier strings

cellToA1

public static String cellToA1(int rowNum,
                              int colNum)

Convert a row index and column index for a cell to A1 notation.

Parameters:

rowNum - row index

colNum - column index

Returns:

A1 notation for cell location

createIRI

public org.semanticweb.owlapi.model.IRI createIRI(String term)

Given a term string, use the current prefixes to create an IRI.

Parameters:

term - the term to convert to an IRI

Returns:

the new IRI

createIRI

public org.semanticweb.owlapi.model.IRI createIRI(String term,
                                                  boolean qName)

Given a term string, use the current prefixes to create an IRI.

Parameters:

term - the term to convert to an IRI

qName - if true, check that the expanded IRI is a valid QName (if not, return null)

Returns:

the new IRI or null

createIRIs

public Set<org.semanticweb.owlapi.model.IRI> createIRIs(Set<String> terms)
                                                 throws IllegalArgumentException

Given a set of term identifier strings, return a set of IRIs.

Parameters:

terms - the set of term identifier strings

Returns:

the set of IRIs

Throws:

IllegalArgumentException - if term identifier is not a valid IRI

createLiteral

public static org.semanticweb.owlapi.model.OWLLiteral createLiteral(String value)

Create an OWLLiteral.

Parameters:

value - the lexical value

Returns:

a literal

createTaggedLiteral

public static org.semanticweb.owlapi.model.OWLLiteral createTaggedLiteral(String value,
                                                                          String lang)

Create an OWLLiteral with a language tag.

Parameters:

value - the lexical value

lang - the language tag

Returns:

a literal

createTypedLiteral

public org.semanticweb.owlapi.model.OWLLiteral createTypedLiteral(String value,
                                                                  String type)

Create a typed OWLLiteral.

Parameters:

value - the lexical value

type - the type IRI string

Returns:

a literal

createTypedLiteral

public org.semanticweb.owlapi.model.OWLLiteral createTypedLiteral(String value,
                                                                  org.semanticweb.owlapi.model.IRI type)

Create a typed OWLLiteral.

Parameters:

value - the lexical value

type - the type IRI

Returns:

a literal

parseTerms

public Set<org.semanticweb.owlapi.model.IRI> parseTerms(String input)
                                                 throws IllegalArgumentException

Parse a set of IRIs from a space-separated string, ignoring '#' comments.

Parameters:

input - the string containing the IRI strings

Returns:

the set of IRIs

Throws:

IllegalArgumentException - if term identifier is not a valid IRI

parseContext

public static com.github.jsonldjava.core.Context parseContext(String jsonString)
                                                       throws IOException

Load a map of prefixes from the "@context" of a JSON-LD string.

Parameters:

jsonString - the JSON-LD string

Returns:

a map from prefix name strings to prefix IRI strings

Throws:

IOException - on any problem

addBaseNamespace

public void addBaseNamespace(String baseNamespace)

Add a base namespace to the IOHelper.

Parameters:

baseNamespace - namespace to add to bases.

addBaseNamespaces

public void addBaseNamespaces(String baseNamespacePath)
                       throws IOException

Add a set of base namespaces to the IOHelper from file. Each base namespace should be on its own line.

Parameters:

baseNamespacePath - path to base namespace file

Throws:

IOException - if file does not exist

getBaseNamespaces

public Set<String> getBaseNamespaces()

Get the base namespaces.

Returns:

set of base namespaces

getDefaultContext

public com.github.jsonldjava.core.Context getDefaultContext()
                                                     throws IOException

Get a copy of the default context.

Returns:

a copy of the current context

Throws:

IOException - if default context file cannot be read

getContext

public com.github.jsonldjava.core.Context getContext()

Get a copy of the current context.

Returns:

a copy of the current context

setContext

public void setContext()

Set an empty context.

setContext

public void setContext(com.github.jsonldjava.core.Context context)

Set the current JSON-LD context to the given context.

Parameters:

context - the new JSON-LD context

setContext

public void setContext(String jsonString)
                throws IOException

Set the current JSON-LD context to the given context.

Parameters:

jsonString - the new JSON-LD context as a JSON string

Throws:

IOException - on issue parsing JSON

setContext

public void setContext(Map<String,Object> map)
                throws IOException

Set the current JSON-LD context to the given map.

Parameters:

map - a map of strings for the new JSON-LD context

Throws:

IOException - on issue parsing JSON

setXMLEntityFlag

public void setXMLEntityFlag(Boolean entityFlag)

Set whether or not XML entities will be swapped into URIs in saveOntology XML output formats.

Parameters:

entityFlag - value to set

getXMLEntityFlag

public Boolean getXMLEntityFlag()

Get the useXMLEntities flag.

Returns:

boolean useXMLEntities flag

makePrefixManager

public static org.semanticweb.owlapi.util.DefaultPrefixManager makePrefixManager(Map<String,String> prefixes)

Make an OWLAPI DefaultPrefixManager from a map of prefixes.

Parameters:

prefixes - a map from prefix name strings to prefix IRI strings

Returns:

a new DefaultPrefixManager

getPrefixManager

public org.semanticweb.owlapi.util.DefaultPrefixManager getPrefixManager()

Get a prefix manager with the current prefixes.

Returns:

a new DefaultPrefixManager

addPrefix

public void addPrefix(String combined)
               throws IllegalArgumentException,
                      IOException

Add a prefix mapping as a single string "foo: http://example.com#".

Parameters:

combined - both prefix and target

Throws:

IllegalArgumentException - on malformed input

IOException - if prefix cannot be parsed

addPrefix

public void addPrefix(String prefix,
                      String target)
               throws IOException

Add a prefix mapping to the current JSON-LD context, as a prefix string and target string. Rebuilds the context.

Parameters:

prefix - the short prefix to add; should not include ":"

target - the IRI string that is the target of the prefix

Throws:

IOException - if prefix cannot be parsed

addPrefixes

public void addPrefixes(String prefixPath)
                 throws IOException

Given a path to a JSON-LD prefix file, add the prefix mappings in the file to the current JSON-LD context.

Parameters:

prefixPath - path to JSON-LD prefix file to add

Throws:

IOException - if the file does not exist or cannot be read

addPrefixes

public void addPrefixes(com.github.jsonldjava.core.Context context1)
                 throws IOException

Given a Context, add the prefix mappings to the current JSON-LD context.

Parameters:

context1 - Context to add

Throws:

IOException - if the Context cannot be set

getPrefixes

public Map<String,String> getPrefixes()

Get a copy of the current prefix map.

Returns:

a copy of the current prefix map

setPrefixes

public void setPrefixes(Map<String,Object> map)
                 throws IOException

Set the current prefix map.

Parameters:

map - the new map of prefixes to use

Throws:

IOException - on issue parsing map to context

getContextString

public String getContextString()
                        throws IOException

Return the current prefixes as a JSON-LD string.

Returns:

the current prefixes as a JSON-LD string

Throws:

IOException - on any error

saveContext

public void saveContext(String path)
                 throws IOException

Write the current context as a JSON-LD file.

Parameters:

path - the path to write the context

Throws:

IOException - on any error

saveContext

public void saveContext(File file)
                 throws IOException

Write the current context as a JSON-LD file.

Parameters:

file - the file to write the context

Throws:

IOException - on any error

readCSV

public static List<List<String>> readCSV(String path)
                                  throws IOException

Read comma-separated values from a path to a list of lists of strings.

Parameters:

path - file path to the CSV file

Returns:

a list of lists of strings

Throws:

IOException - on file or reading problems

readCSV

public static List<List<String>> readCSV(InputStream stream)
                                  throws IOException

Read comma-separated values from a stream to a list of lists of strings.

Parameters:

stream - the stream to read from

Returns:

a list of lists of strings

Throws:

IOException - on file or reading problems

readCSV

public static List<List<String>> readCSV(Reader reader)
                                  throws IOException

Read comma-separated values from a reader to a list of lists of strings.

Parameters:

reader - a reader to read data from

Returns:

a list of lists of strings

Throws:

IOException - on file or reading problems

readTSV

public static List<List<String>> readTSV(String path)
                                  throws IOException

Read tab-separated values from a path to a list of lists of strings.

Parameters:

path - file path to the CSV file

Returns:

a list of lists of strings

Throws:

IOException - on file or reading problems

readTSV

public static List<List<String>> readTSV(InputStream stream)
                                  throws IOException

Read tab-separated values from a stream to a list of lists of strings.

Parameters:

stream - the stream to read from

Returns:

a list of lists of strings

Throws:

IOException - on file or reading problems

readTSV

public static List<List<String>> readTSV(Reader reader)
                                  throws IOException

Read tab-separated values from a reader to a list of lists of strings.

Parameters:

reader - a reader to read data from

Returns:

a list of lists of strings

Throws:

IOException - on file or reading problems

readTable

public static List<List<String>> readTable(String path)
                                    throws IOException

Read a table from a path to a list of lists of strings.

Parameters:

path - file path to the CSV file

Returns:

a list of lists of strings

Throws:

IOException - on file or reading problems

writeTable

public static void writeTable(List<String[]> table,
                              String path)
                       throws IOException

Write a table from a list of arrays.

Parameters:

table - List of arrays to write

path - path to write to

Throws:

IOException - on file or writing problems

writeTable

public static void writeTable(List<String[]> table,
                              File file,
                              char separator)
                       throws IOException

Write a table from a list of arrays.

Parameters:

file - File to write to

table - List of arrays to write

separator - table separator

Throws:

IOException - on problem making Writer object or auto-closing CSVWriter

writeTable

public static void writeTable(List<String[]> table,
                              Writer writer,
                              char separator)
                       throws IOException

Write a table from a list of arrays.

Parameters:

writer - Writer object to write to

table - List of arrays to write

separator - table separator

Throws:

IOException - on problem auto-closing writer