org.phenotips.vocabulary

Interface VocabularyExtension

All Known Implementing Classes:

AbstractCSVAnnotationsExtension

@Unstable(value="New API introduced in 1.3, it may still change")
 @Role
public interface VocabularyExtension

Allows extending a base vocabulary with additional annotations. A vocabulary extension can support one or more base vocabularies, identified by the isVocabularySupported(org.phenotips.vocabulary.Vocabulary) method. Every time one of the supported vocabularies is reindexed, first indexingStarted(org.phenotips.vocabulary.Vocabulary) is called, so that the extension can prepare its needed resources, if any. Then, for each term parsed from its source the extendTerm(org.phenotips.vocabulary.VocabularyInputTerm, org.phenotips.vocabulary.Vocabulary) method is called, and new fields can be added to it. Once all the terms have been indexed, indexingEnded(org.phenotips.vocabulary.Vocabulary) is called, and any resources can be freed.

Since:

1.3M1

Version:

$Id: f0bdab50f77346747214cdb8aa03421bcca4226a $

Method Summary

Modifier and Type	Method and Description
void	extendQuery(org.apache.solr.client.solrj.SolrQuery query, Vocabulary vocabulary) Called for each query on the vocabulary, this method modifies the query terms by changing, adding or removing fields.
void	extendTerm(VocabularyInputTerm term, Vocabulary vocabulary) Called for each term during vocabulary reindexing, this method modifies the parsed terms by changing, adding or removing fields.
default String	getAnnotationSource() Specifies the annotation source URL.
default String	getName() The official name of the vocabulary extension.
void	indexingEnded(Vocabulary vocabulary) Called when a vocabulary reindex is done, so that this extension can clean up its resources, if any.
void	indexingStarted(Vocabulary vocabulary) Called when a vocabulary reindex begins, so that this extension can prepare its needed resources, if any.
boolean	isVocabularySupported(Vocabulary vocabulary) Checks if a vocabulary is supported by this extension.

Method Detail

isVocabularySupported

boolean isVocabularySupported(Vocabulary vocabulary)

Checks if a vocabulary is supported by this extension. This extension's other methods will only be called when indexing a supported vocabulary.

Parameters:

vocabulary - the vocabulary to check

Returns:

true if the target vocabulary is supported, false if not and this extension should no longer be invoked when processing that vocabulary

indexingStarted

void indexingStarted(Vocabulary vocabulary)

Called when a vocabulary reindex begins, so that this extension can prepare its needed resources, if any. This method is called only for supported vocabularies.

Parameters:

vocabulary - the vocabulary being indexed

extendTerm

void extendTerm(VocabularyInputTerm term,
                Vocabulary vocabulary)

Called for each term during vocabulary reindexing, this method modifies the parsed terms by changing, adding or removing fields. This method is called only for supported vocabularies .

Parameters:

term - the parsed term which can be altered

vocabulary - the the vocabulary being indexed

indexingEnded

void indexingEnded(Vocabulary vocabulary)

Called when a vocabulary reindex is done, so that this extension can clean up its resources, if any. This method is called only for supported vocabularies.

Parameters:

vocabulary - the vocabulary that was indexed

extendQuery

void extendQuery(org.apache.solr.client.solrj.SolrQuery query,
                 Vocabulary vocabulary)

Called for each query on the vocabulary, this method modifies the query terms by changing, adding or removing fields.

Parameters:

query - the query to process

vocabulary - the the vocabulary being queried

getAnnotationSource

default String getAnnotationSource()

Specifies the annotation source URL. This can be either a web (http) link, a network file, a local file:/// reference, a classpath resource, or any other URL format that can be read by the JVM.

Returns:

a valid annotation source URL

getName

default String getName()

The official name of the vocabulary extension.

Returns:

a string, for example The Disease HPO negative annotations