Package net.bioclipse.managers

Class WikidataManager

java.lang.Object

net.bioclipse.managers.WikidataManager

All Implemented Interfaces:

IBactingManager, net.bioclipse.managers.business.IBioclipseManager

public class WikidataManager
extends Object
implements IBactingManager

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.

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
List<String>	doi()	Lists the DOIs of the articles associated to this manager.
String	getEntityID(String doi)	Return a work with the given DOI, or throws an BioclipseException when it does not exist.
String	getEntityID(net.bioclipse.inchi.InChI inchi)	Returns the Wikidata entity ID for the molecule with the given InChI.
Map<String,String>	getEntityIDs(List<net.bioclipse.inchi.InChI> inchis)	Returns the Wikidata entity IDs for the molecules with the given InChIs.
Map<String,String>	getEntityIDsForDOIs(List<String> dois)	Returns the Wikidata entity IDs for the works with the given DOIs.
List<String>	getEntityIDsForType(String type)	Returns the Wikidata entity IDs for entities instance of a certain type (P31).
String	getManagerName()
net.bioclipse.core.domain.IMolecule	getMolecule(net.bioclipse.inchi.InChI inchi)	Return a molecule with the given InChI, or throws an BioclipseException when it does not exist.
boolean	hasMolecule(net.bioclipse.inchi.InChI inchi)	Return true if Wikidata contains a molecule with the given InChI.
boolean	isValidQIdentifier(String identifier)	Determines if an identifier is a valid Wikidata entity identifier, like Q5.

Methods inherited from class java.lang.Object

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

Constructor Details

WikidataManager

public WikidataManager(String workspaceRoot)

Creates a new WikidataManager.

Parameters:

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

Method Details

hasMolecule

public boolean hasMolecule(net.bioclipse.inchi.InChI inchi)
                    throws net.bioclipse.core.business.BioclipseException

Return true if Wikidata contains a molecule with the given InChI.

Parameters:

inchi - InChI of the molecule to check if it already exists in Wikidata

Throws:

net.bioclipse.core.business.BioclipseException

getEntityID

public String getEntityID(net.bioclipse.inchi.InChI inchi)
                   throws net.bioclipse.core.business.BioclipseException

Returns the Wikidata entity ID for the molecule with the given InChI.

Parameters:

inchi - InChI of the molecule to return Wikidata ID for

Throws:

net.bioclipse.core.business.BioclipseException

getEntityIDs

public Map<String,String> getEntityIDs(List<net.bioclipse.inchi.InChI> inchis)
                                throws net.bioclipse.core.business.BioclipseException

Returns the Wikidata entity IDs for the molecules with the given InChIs.

Parameters:

inchis - List of InChIs of the molecules to check if they already exists in Wikidata

Throws:

net.bioclipse.core.business.BioclipseException

getMolecule

public net.bioclipse.core.domain.IMolecule getMolecule(net.bioclipse.inchi.InChI inchi)
                                                throws net.bioclipse.core.business.BioclipseException

Return a molecule with the given InChI, or throws an BioclipseException when it does not exist.

Parameters:

inchi - InChI of the molecule to check if it already exists in Wikidata

Throws:

net.bioclipse.core.business.BioclipseException

getEntityID

public String getEntityID(String doi)
                   throws net.bioclipse.core.business.BioclipseException

Return a work with the given DOI, or throws an BioclipseException when it does not exist.

Parameters:

doi - DOI of the work to check if it already exists in Wikidata

Returns:

a String with the Q-id

Throws:

net.bioclipse.core.business.BioclipseException

getEntityIDsForDOIs

public Map<String,String> getEntityIDsForDOIs(List<String> dois)
                                       throws net.bioclipse.core.business.BioclipseException

Returns the Wikidata entity IDs for the works with the given DOIs.

Parameters:

dois - List of DOIs of the works to check if they already exists in Wikidata

Throws:

net.bioclipse.core.business.BioclipseException

getEntityIDsForType

public List<String> getEntityIDsForType(String type)
                                 throws net.bioclipse.core.business.BioclipseException

Returns the Wikidata entity IDs for entities instance of a certain type (P31).

Parameters:

type - identifier of a Wikidata item

Throws:

net.bioclipse.core.business.BioclipseException

isValidQIdentifier

public boolean isValidQIdentifier(String identifier)

Determines if an identifier is a valid Wikidata entity identifier, like Q5.

Parameters:

identifier - to test

Returns:

true, if the identifier is valid

getManagerName

public String getManagerName()

Specified by:

getManagerName in interface net.bioclipse.managers.business.IBioclipseManager

doi

public List<String> doi()

Description copied from interface: IBactingManager

Lists the DOIs of the articles associated to this manager.

Specified by:

doi in interface IBactingManager

Returns:

a List of String with DOIs