Package net.bioclipse.managers

Class RDFManager

java.lang.Object

net.bioclipse.managers.RDFManager

public class RDFManager
extends Object

Bioclipse manager that provides functionality around the Resource Description Framework standard. It allows creating in memory and on disk triple stores, creating on content, and IO functionality.

Field Summary

Fields

Modifier and Type	Field	Description
static final Integer	CONNECT_TIME_OUT
static final Integer	READ_TIME_OUT

Constructor Summary

Constructors

Constructor	Description
RDFManager(String workspaceRoot)	Creates a new RDFManager.

Method Summary

Modifier and Type	Method	Description
void	addDataProperty(net.bioclipse.rdf.business.IRDFStore store, String subject, String property, String value)	Creates a new RDF data triple in the given triple store.
void	addObjectProperty(net.bioclipse.rdf.business.IRDFStore store, String subject, String property, String object)	Creates a new RDF object triple in the given triple store.
void	addPrefix(net.bioclipse.rdf.business.IRDFStore store, String prefix, String namespace)	Adds a prefix definition to the given triple store.
void	addPropertyInLanguage(net.bioclipse.rdf.business.IRDFStore store, String subject, String property, String value, String language)	Creates a new RDF data triple in the given triple store.
void	addTypedDataProperty(net.bioclipse.rdf.business.IRDFStore store, String subject, String property, String value, String dataType)	Creates a new RDF data triple in the given triple store.
List<String>	allOwlEquivalentClass(net.bioclipse.rdf.business.IRDFStore store, String resourceURI)	Lists all resources that are owl:equivalentClass as the given resource.
List<String>	allOwlSameAs(net.bioclipse.rdf.business.IRDFStore store, String resourceURI)	Lists all resources that are owl:sameAs as the given resource.
String	asRDFN3(net.bioclipse.rdf.business.IRDFStore store)	Serializes the triples in the triple store as Notation3.
String	asString(org.apache.jena.shex.ShexReport report)	Converts a ShexReport into a String.
String	asTurtle(net.bioclipse.rdf.business.IRDFStore store)	Serializes the triples in the triple store as Turtle.
net.bioclipse.rdf.business.IRDFStore	createInMemoryStore()	Creates a triple store that is fully stored in memory.
net.bioclipse.rdf.business.IRDFStore	createInMemoryStore(boolean ontologyModel)	Creates an ontology triple store that is fully stored in memory.
net.bioclipse.rdf.business.IRDFStore	createStore(String tripleStoreDirectoryPath)	Creates a triple store that is fully stored on disk.
List<String>	getForPredicate(net.bioclipse.rdf.business.IRDFStore store, String resourceURI, String predicate)	Lists all resources or literals for the resource and predicate.
net.bioclipse.rdf.business.IRDFStore	importFile(net.bioclipse.rdf.business.IRDFStore store, String rdfFile, String format)	Reads a RDF file in the given format from the workspace and stores the triples in the given triple store.
net.bioclipse.rdf.business.IRDFStore	importFromStream(net.bioclipse.rdf.business.IRDFStore store, InputStream stream, String format)	Reads RDF triples from an InputStream in the given format and stores the triples in the given triple store.
net.bioclipse.rdf.business.IRDFStore	importFromString(net.bioclipse.rdf.business.IRDFStore store, String rdfContent, String format)	Reads RDF triples from an String in the given format and stores the triples in the given triple store.
net.bioclipse.rdf.business.IRDFStore	importURL(net.bioclipse.rdf.business.IRDFStore store, String url)	Reads RDF triples from a URL and stores the triples in the given triple store.
net.bioclipse.rdf.business.IRDFStore	importURL(net.bioclipse.rdf.business.IRDFStore store, String url, Map<String,String> extraHeaders)	Reads RDF triples from a URL and stores the triples in the given triple store, with additional HTTP headers.
net.bioclipse.core.domain.IStringMatrix	processSPARQLXML(byte[] queryResults, String originalQuery)	Processes XML returned by a remote SPARQL end point.
long	size(net.bioclipse.rdf.business.IRDFStore store)	Returns the number of RDF triples in the triple store.
net.bioclipse.core.domain.StringMatrix	sparql(net.bioclipse.rdf.business.IRDFStore store, String queryString)	Queries a local RDF triple store.
net.bioclipse.core.domain.StringMatrix	sparqlRemote(String serviceURL, String sparqlQueryString)	Queries a remote SPARQL end point.
org.apache.jena.shex.ShexReport	validateAllOfType(net.bioclipse.rdf.business.IRDFStore store, String shexFile, String shapeURI, String type)	Validates triples according to some shape expression in ShEx format.

Methods inherited from class java.lang.Object

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

Field Details

CONNECT_TIME_OUT

public static final Integer CONNECT_TIME_OUT

READ_TIME_OUT

public static final Integer READ_TIME_OUT

Constructor Details

RDFManager

public RDFManager(String workspaceRoot)

Creates a new RDFManager.

Parameters:

workspaceRoot - location of the workspace, e.g. "."

Method Details

createInMemoryStore

public net.bioclipse.rdf.business.IRDFStore createInMemoryStore()

Creates a triple store that is fully stored in memory.

Returns:

a triple store as IRDFStore object

createStore

public net.bioclipse.rdf.business.IRDFStore createStore(String tripleStoreDirectoryPath)

Creates a triple store that is fully stored on disk.

Returns:

a triple store as IRDFStore object

createInMemoryStore

public net.bioclipse.rdf.business.IRDFStore createInMemoryStore(boolean ontologyModel)

Creates an ontology triple store that is fully stored in memory.

Returns:

a triple store as IRDFStore object

addPrefix

public void addPrefix(net.bioclipse.rdf.business.IRDFStore store,
 String prefix,
 String namespace)
               throws net.bioclipse.core.business.BioclipseException

Adds a prefix definition to the given triple store.

Parameters:

store - an IRDFStore object

prefix - the prefix

namespace - the RDF namespace

Throws:

net.bioclipse.core.business.BioclipseException

getForPredicate

public List<String> getForPredicate(net.bioclipse.rdf.business.IRDFStore store,
 String resourceURI,
 String predicate)
                             throws net.bioclipse.core.business.BioclipseException

Lists all resources or literals for the resource and predicate.

Parameters:

store - an IRDFStore object

resourceURI - subject of the triples

predicate - predicate of the triples

Returns:

List of objects (resources and literals).

Throws:

net.bioclipse.core.business.BioclipseException

allOwlSameAs

public List<String> allOwlSameAs(net.bioclipse.rdf.business.IRDFStore store,
 String resourceURI)
                          throws IOException,
net.bioclipse.core.business.BioclipseException,
org.eclipse.core.runtime.CoreException

Lists all resources that are owl:sameAs as the given resource.

Parameters:

store - the IRDFStore store where the identical classes are looked up

resourceURI - the resource to find the links for

Returns:

All matching resources.

Throws:

IOException

net.bioclipse.core.business.BioclipseException

org.eclipse.core.runtime.CoreException

allOwlEquivalentClass

public List<String> allOwlEquivalentClass(net.bioclipse.rdf.business.IRDFStore store,
 String resourceURI)
                                   throws IOException,
net.bioclipse.core.business.BioclipseException,
org.eclipse.core.runtime.CoreException

Lists all resources that are owl:equivalentClass as the given resource.

Parameters:

store - the IRDFStore store where the equivalent classes are looked up

resourceURI - the resource to find the links for

Returns:

All matching resources.

Throws:

IOException

net.bioclipse.core.business.BioclipseException

org.eclipse.core.runtime.CoreException

addObjectProperty

public void addObjectProperty(net.bioclipse.rdf.business.IRDFStore store,
 String subject,
 String property,
 String object)
                       throws net.bioclipse.core.business.BioclipseException

Creates a new RDF object triple in the given triple store.

Parameters:

store - the IRDFStore store where the triple is added

subject - the RDF Subject of the triple

property - the RDF Predicate of the triple

object - the RDF Object of the triple

Throws:

net.bioclipse.core.business.BioclipseException

addDataProperty

public void addDataProperty(net.bioclipse.rdf.business.IRDFStore store,
 String subject,
 String property,
 String value)
                     throws net.bioclipse.core.business.BioclipseException

Creates a new RDF data triple in the given triple store.

Parameters:

store - the IRDFStore store where the triple is added

subject - the RDF Subject of the triple

property - the RDF Predicate of the triple

value - the RDF Literal string

Throws:

net.bioclipse.core.business.BioclipseException

addTypedDataProperty

public void addTypedDataProperty(net.bioclipse.rdf.business.IRDFStore store,
 String subject,
 String property,
 String value,
 String dataType)
                          throws net.bioclipse.core.business.BioclipseException

Creates a new RDF data triple in the given triple store.

Parameters:

store - the IRDFStore store where the triple is added

subject - the RDF Subject of the triple

property - the RDF Predicate of the triple

value - the RDF Literal string

dataType - the data type of the RDF Literal

Throws:

net.bioclipse.core.business.BioclipseException

addPropertyInLanguage

public void addPropertyInLanguage(net.bioclipse.rdf.business.IRDFStore store,
 String subject,
 String property,
 String value,
 String language)
                           throws net.bioclipse.core.business.BioclipseException

Creates a new RDF data triple in the given triple store.

Parameters:

store - the IRDFStore store where the triple is added

subject - the RDF Subject of the triple

property - the RDF Predicate of the triple

value - the RDF Literal string

language - the language of the RDF Literal

Throws:

net.bioclipse.core.business.BioclipseException

sparqlRemote

public net.bioclipse.core.domain.StringMatrix sparqlRemote(String serviceURL,
 String sparqlQueryString)

Queries a remote SPARQL end point.

Parameters:

serviceURL - the URL of the SPARQL end point

sparqlQueryString - the SPARQL query

Returns:

an StringMatrix object with results

processSPARQLXML

public net.bioclipse.core.domain.IStringMatrix processSPARQLXML(byte[] queryResults,
 String originalQuery)
                                                         throws net.bioclipse.core.business.BioclipseException

Processes XML returned by a remote SPARQL end point.

Parameters:

queryResults - the search results as a byte array of the returned XML

originalQuery - the original SPARQL query that gave the results

Returns:

a matrix with SPARQL results

Throws:

net.bioclipse.core.business.BioclipseException

sparql

public net.bioclipse.core.domain.StringMatrix sparql(net.bioclipse.rdf.business.IRDFStore store,
 String queryString)
                                              throws IOException,
net.bioclipse.core.business.BioclipseException,
org.eclipse.core.runtime.CoreException

Queries a local RDF triple store.

Parameters:

store - the RDF triples store to query

queryString - the SPARQL query

Returns:

an StringMatrix object with results

Throws:

IOException

net.bioclipse.core.business.BioclipseException

org.eclipse.core.runtime.CoreException

size

public long size(net.bioclipse.rdf.business.IRDFStore store)
          throws net.bioclipse.core.business.BioclipseException

Returns the number of RDF triples in the triple store.

Parameters:

store - an IRDFStore object

Returns:

the number of triples

Throws:

net.bioclipse.core.business.BioclipseException

importFile

public net.bioclipse.rdf.business.IRDFStore importFile(net.bioclipse.rdf.business.IRDFStore store,
 String rdfFile,
 String format)
                                                throws IOException,
net.bioclipse.core.business.BioclipseException,
org.eclipse.core.runtime.CoreException

Reads a RDF file in the given format from the workspace and stores the triples in the given triple store.

Parameters:

store - IRDFStore to put the triples in

rdfFile - location of the RDF file

format - format of the RDF file (e.g. "RDF/XML", "TURTLE", or "N3")

Returns:

an RDF store with the content of the loaded RDF file

Throws:

IOException

net.bioclipse.core.business.BioclipseException

org.eclipse.core.runtime.CoreException

importFromStream

public net.bioclipse.rdf.business.IRDFStore importFromStream(net.bioclipse.rdf.business.IRDFStore store,
 InputStream stream,
 String format)
                                                      throws IOException,
net.bioclipse.core.business.BioclipseException,
org.eclipse.core.runtime.CoreException

Reads RDF triples from an InputStream in the given format and stores the triples in the given triple store.

Parameters:

store - IRDFStore to put the triples in

stream - the InputStream from which the triples are read

format - format of the RDF file (e.g. "RDF/XML", "TURTLE", or "N3")

Returns:

an RDF store with the content of the loaded RDF content

Throws:

IOException

net.bioclipse.core.business.BioclipseException

org.eclipse.core.runtime.CoreException

importFromString

public net.bioclipse.rdf.business.IRDFStore importFromString(net.bioclipse.rdf.business.IRDFStore store,
 String rdfContent,
 String format)
                                                      throws IOException,
net.bioclipse.core.business.BioclipseException,
org.eclipse.core.runtime.CoreException

Reads RDF triples from an String in the given format and stores the triples in the given triple store.

Parameters:

store - IRDFStore to put the triples in

rdfContent - the String from which the triples are read

format - format of the RDF file (e.g. "RDF/XML", "TURTLE", or "N3")

Returns:

an RDF store with the content of the loaded RDF content

Throws:

IOException

net.bioclipse.core.business.BioclipseException

org.eclipse.core.runtime.CoreException

importURL

public net.bioclipse.rdf.business.IRDFStore importURL(net.bioclipse.rdf.business.IRDFStore store,
 String url)
                                               throws IOException,
net.bioclipse.core.business.BioclipseException,
org.eclipse.core.runtime.CoreException

Reads RDF triples from a URL and stores the triples in the given triple store.

Parameters:

store - IRDFStore to put the triples in

url - the URL from which the triples are read

Returns:

an RDF store with the content of the loaded RDF file

Throws:

IOException

net.bioclipse.core.business.BioclipseException

org.eclipse.core.runtime.CoreException

importURL

public net.bioclipse.rdf.business.IRDFStore importURL(net.bioclipse.rdf.business.IRDFStore store,
 String url,
 Map<String,String> extraHeaders)
                                               throws IOException,
net.bioclipse.core.business.BioclipseException,
org.eclipse.core.runtime.CoreException

Reads RDF triples from a URL and stores the triples in the given triple store, with additional HTTP headers.

Parameters:

store - IRDFStore to put the triples in

url - the URL from which the triples are read

extraHeaders - the extra HTTP headers

Returns:

an RDF store with the content of the loaded RDF file

Throws:

IOException

net.bioclipse.core.business.BioclipseException

org.eclipse.core.runtime.CoreException

asRDFN3

public String asRDFN3(net.bioclipse.rdf.business.IRDFStore store)
               throws net.bioclipse.core.business.BioclipseException

Serializes the triples in the triple store as Notation3.

Parameters:

store - the IRDFStore

Returns:

a String with Notation3-formatted triples

Throws:

net.bioclipse.core.business.BioclipseException

asTurtle

public String asTurtle(net.bioclipse.rdf.business.IRDFStore store)
                throws net.bioclipse.core.business.BioclipseException

Serializes the triples in the triple store as Turtle.

Parameters:

store - the IRDFStore

Returns:

a String with Turtle-formatted triples

Throws:

net.bioclipse.core.business.BioclipseException

validateAllOfType

public org.apache.jena.shex.ShexReport validateAllOfType(net.bioclipse.rdf.business.IRDFStore store,
 String shexFile,
 String shapeURI,
 String type)

Validates triples according to some shape expression in ShEx format.

Parameters:

store - the IRDFStore

shexFile - the file with shape expressions

shapeURI - URI of the shape to test against

type - URI of the rdf:type of the resources to test

Returns:

the ShEx validation report as ShexReport

asString

public String asString(org.apache.jena.shex.ShexReport report)

Converts a ShexReport into a String.

Parameters:

report - the ShexReport

Returns:

String serialization of the report