Package org.obolibrary.robot

Class IOHelper

  • public class IOHelper
extends Object
    Provides convenience methods for working with ontology and term files.
    Author:
    James A. Overton

    • Constructor Summary

      Constructors 
      Constructor 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​(String path)
      Create a new IOHelper with prefixes from a file path.
      IOHelper​(Map<String,​Object> map)
      Create a new IOHelper with the specified prefixes.

    • Method Summary

      All Methods Static Methods Instance Methods Concrete Methods Deprecated Methods 
      Modifier and Type Method 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)
      Deprecated.
      replaced by createIRI(String)
      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, String type)
      Create a typed OWLLiteral.
      org.semanticweb.owlapi.model.OWLLiteral createTypedLiteral​(String value, org.semanticweb.owlapi.model.IRI 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.
      static boolean isValidCURIE​(CharSequence s)
      Determine if a string is a CURIE.
      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​(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.
      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​(org.semanticweb.owlapi.model.OWLOntologyManager manager, org.semanticweb.owlapi.io.OWLOntologyDocumentSource source)
      Given an ontology manager and a document source, load the ontology from the source using the manager.
      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 org.apache.jena.query.Dataset openTDBDataset​(String tdbDir)
      Given a path to a TDB directory, load the TDB as a Dataset.
      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, String ontologyPath)
      Save an ontology to a String path.
      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, 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, 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.
      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​(String jsonString)
      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 setPrefixes​(Map<String,​Object> map)
      Set the current prefix map.
      void setStrict​(Boolean strict)
      Set "strict" value.
      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, Writer writer, 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.

    • 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

      • setStrict

        public void setStrict​(Boolean strict)
        Set "strict" value. If true, any loadOntology method will fail on unparsed triples or OWLAPI "strict" parsing issues.
        Parameters:
        strict - boolean value

      • 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

      • loadOntology

        public org.semanticweb.owlapi.model.OWLOntology loadOntology​(org.semanticweb.owlapi.model.OWLOntologyManager manager,
                                                             org.semanticweb.owlapi.io.OWLOntologyDocumentSource source)
                                                      throws IOException,
                                                             org.semanticweb.owlapi.model.OWLOntologyCreationException
        Given an ontology manager and a document source, load the ontology from the source using the manager. Log unparsed triples, or throw exception if strict=true.
        Parameters:
        manager - OWLOntologyManager with IRI mappers to use
        source - OWLOntologyDocumentSource to load from
        Returns:
        a new ontology object, with a new OWLManager
        Throws:
        IOException - on problem with unparsed triples if strict=true
        org.semanticweb.owlapi.model.OWLOntologyCreationException - on problem loading ontology document

      • 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

      • openTDBDataset

        public static org.apache.jena.query.Dataset openTDBDataset​(String tdbDir)
        Given a path to a TDB directory, load the TDB as a Dataset.
        Parameters:
        tdbDir - path to existing TDB directory
        Returns:
        Dataset or null

      • 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 or null

      • createIRI

        @Deprecated
public org.semanticweb.owlapi.model.IRI createIRI​(String term,
                                                  boolean qName)
        Deprecated.
        replaced by createIRI(String)
        Given a term string, use the current prefixes to create an IRI.
        Parameters:
        term - the term to convert to an IRI
        qName - if true, validate that the IRI expands to a QName
        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 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

      • isValidCURIE

        public static boolean isValidCURIE​(CharSequence s)
        Determine if a string is a CURIE. Note that a valid CURIE is not always a valid QName. Adapted from:
        Parameters:
        s - Character sequence to check
        Returns:
        true if valid CURIE
        See Also:
        XMLUtils.isQName(CharSequence)

      • 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