Package psidev.psi.mi.jami.bridges.fetcher

Interface CvTermFetcher<C extends CvTerm>

    • Method Detail

      • fetchByIdentifier

        C fetchByIdentifier​(String termIdentifier,
                    String miOntologyName)
             throws BridgeFailedException
        Uses the identifier and the name of the database to search for a complete form of the cvTerm.
        Parameters:
        termIdentifier - The identifier for the CvTerm to fetch.
        miOntologyName - The name of the ontology to search for. Eg, psi-mi, psi-mod, go. Must not be Null.
        Returns:
        A full cvTerm which matches the search term or null if one cannot be found.
        Throws:
        BridgeFailedException - if any.

      • fetchByIdentifier

        C fetchByIdentifier​(String termIdentifier,
                    CvTerm ontologyDatabase)
             throws BridgeFailedException
        Uses the identifier and a cvTerm denoting the database to search to fetch a complete from of the term.
        Parameters:
        termIdentifier - The identifier for the CvTerm to fetch
        ontologyDatabase - The cvTerm of the ontology to search for.
        Returns:
        A fully enriched cvTerm which matches the search term or null if one cannot be found.
        Throws:
        BridgeFailedException - if any.

      • fetchByName

        C fetchByName​(String searchName,
              String miOntologyName)
       throws BridgeFailedException
        Uses the name of the term and the name of the database to search for a complete form of the term.
        Parameters:
        searchName - A full or short name for the term to be searched for.
        miOntologyName - The ontology to search for the term in.
        Returns:
        A fully enriched cvTerm which matches the search term or null if one cannot be found.
        Throws:
        BridgeFailedException - if any.

      • fetchByName

        Collection<C> fetchByName​(String searchName)
                   throws BridgeFailedException
        Uses the name of the term and the name of the database to search for a complete form of the term.

        If the term can not be resolved to a database, then this method may return null.

        Parameters:
        searchName - A full or short name for the term to be searched for.
        Returns:
        A fully enriched cvTerm which matches the search term or null if one cannot be found.
        Throws:
        BridgeFailedException - if any.

      • fetchByIdentifiers

        Collection<C> fetchByIdentifiers​(Collection<String> termIdentifiers,
                                 String miOntologyName)
                          throws BridgeFailedException
        Uses the identifier and the name of the database to search for a complete form of the cvTerm.
        Parameters:
        termIdentifiers - The identifier for the CvTerm to fetch and the corresponding ontology database name.
        miOntologyName - The name of the ontology to search for the names in.
        Returns:
        A fully enriched cvTerm which matches the search term or null if one cannot be found.
        Throws:
        BridgeFailedException - if any.

      • fetchByIdentifiers

        Collection<C> fetchByIdentifiers​(Collection<String> termIdentifiers,
                                 CvTerm ontologyDatabase)
                          throws BridgeFailedException
        Uses the identifier and a cvTerm denoting the database to search to fetch a complete from of the term.
        Parameters:
        termIdentifiers - The identifier for the CvTerms to fetch.
        ontologyDatabase - The name of the ontology to search for the terms in.
        Returns:
        A fully enriched cvTerm which matches the search term or null if one cannot be found.
        Throws:
        BridgeFailedException - if any.

      • fetchByNames

        Collection<C> fetchByNames​(Collection<String> searchNames,
                           String miOntologyName)
                    throws BridgeFailedException
        Uses the name of the term and the name of the database to search for a complete form of the term.
        Parameters:
        searchNames - A full or short name for the term to be searched for.
        miOntologyName - The name of the database to search for the names in.
        Returns:
        A fully enriched cvTerm which matches the search term or null if one cannot be found.
        Throws:
        BridgeFailedException - if any.

      • fetchByNames

        Collection<C> fetchByNames​(Collection<String> searchNames)
                    throws BridgeFailedException
        Finds the CvTerms which match the exact names provided.

        If the a term found by the search can not be resolved to a database, this method may return null.

        Parameters:
        searchNames - A collection full or short names for the term to be searched for.
        Returns:
        A collection of cvTerms which matched a search term.
        Throws:
        BridgeFailedException - if any.