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A

AbstractCSVAnnotationsExtension - Class in org.phenotips.vocabulary
AbstractCSVAnnotationsExtension() - Constructor for class org.phenotips.vocabulary.AbstractCSVAnnotationsExtension
 
append(String, Object) - Method in interface org.phenotips.vocabulary.VocabularyInputTerm
Generic property setter, additive.

C

count(Map<String, ?>) - Method in interface org.phenotips.vocabulary.Vocabulary
Get the number of terms that match a specific query.
createReplacementCore(Vocabulary) - Method in interface org.phenotips.vocabulary.SolrVocabularyResourceManager
Copy the Solr configuration file in a separate temporary directory, then register this temporary core with the Solr server.

D

data - Variable in class org.phenotips.vocabulary.AbstractCSVAnnotationsExtension
Data read from the source file.
discardReplacementCore(Vocabulary) - Method in interface org.phenotips.vocabulary.SolrVocabularyResourceManager
Delete the temporary core, if one was already created by SolrVocabularyResourceManager.createReplacementCore(Vocabulary).

E

extendQuery(SolrQuery, Vocabulary) - Method in class org.phenotips.vocabulary.AbstractCSVAnnotationsExtension
 
extendQuery(SolrQuery, Vocabulary) - Method in interface org.phenotips.vocabulary.VocabularyExtension
Called for each query on the vocabulary, this method modifies the query terms by changing, adding or removing fields.
extendTerm(VocabularyInputTerm, Vocabulary) - Method in class org.phenotips.vocabulary.AbstractCSVAnnotationsExtension
 
extendTerm(VocabularyInputTerm, Vocabulary) - Method in interface org.phenotips.vocabulary.VocabularyExtension
Called for each term during vocabulary reindexing, this method modifies the parsed terms by changing, adding or removing fields.

G

get(String) - Method in class org.phenotips.vocabulary.script.OntologyScriptService
Deprecated.
get(String) - Method in class org.phenotips.vocabulary.script.VocabularyScriptService
Retrieve a vocabulary given its identifier.
get(String) - Method in interface org.phenotips.vocabulary.VocabularyTerm
Generic property access.
getAliases() - Method in interface org.phenotips.vocabulary.Vocabulary
A vocabulary has an official name, but it can also have other aliases, for example the Human Phenotype Ontology is known both as HP, which is the official prefix for its terms, HPO, which is its acronym, or the lowercase hpo.
getAncestors() - Method in interface org.phenotips.vocabulary.VocabularyTerm
Returns the ancestors (both direct and indirect ancestors) of this term.
getAncestorsAndSelf() - Method in interface org.phenotips.vocabulary.VocabularyTerm
Returns the ancestors (both direct and indirect ancestors) of this term and the term itself.
getAnnotationSource() - Method in interface org.phenotips.vocabulary.VocabularyExtension
Specifies the annotation source URL.
getAvailableCategories() - Method in interface org.phenotips.vocabulary.VocabularyManager
Retrieves a list of category names that are available for use with VocabularyManager.getVocabularies(String).
getAvailableVocabularies() - Method in class org.phenotips.vocabulary.script.VocabularyScriptService
Retrieves a list of vocabulary ids that are available for use with getVocabulary(String).
getAvailableVocabularies() - Method in interface org.phenotips.vocabulary.VocabularyManager
Retrieves a list of vocabulary ids that are available for use with VocabularyManager.getVocabulary(String).
getCitation() - Method in interface org.phenotips.vocabulary.Vocabulary
Get the citation for the vocabulary.
getContainer() - Method in interface org.phenotips.vocabulary.SolrCoreContainerHandler
Gets the Solr core container.
getDefaultSourceLocation() - Method in interface org.phenotips.vocabulary.Vocabulary
Get the default location where the sources for this vocabulary can be fetched from.
getDescription() - Method in interface org.phenotips.vocabulary.VocabularyTerm
The human-readable term description, usually a longer phrase or paragraph that describes the term.
getDistance(String, String) - Method in interface org.phenotips.vocabulary.Vocabulary
Find the distance between two terms identified by their term identifiers, if this is a structured ontology that supports computing such a distance.
getDistance(VocabularyTerm, VocabularyTerm) - Method in interface org.phenotips.vocabulary.Vocabulary
Find the distance between two terms, if this is a structured ontology that supports computing such a distance.
getDistanceTo(VocabularyTerm) - Method in interface org.phenotips.vocabulary.VocabularyTerm
Find the distance to another term in the same vocabulary, if the owner vocabulary is a structured ontology that supports computing such a distance.
getExtensions() - Method in interface org.phenotips.vocabulary.Vocabulary
Get the list of VocabularyExtensions that extend a base vocabulary with additional annotations.
getId() - Method in interface org.phenotips.vocabulary.VocabularyTerm
The (mandatory) term identifier, in the format <vocabulary prefix>:<term id>, for example HP:0002066 or MIM:260540.
getIdentifier() - Method in interface org.phenotips.vocabulary.Vocabulary
The identifier of the vocabulary, used internally to differentiate between different vocabularies and different implementations of the same vocabulary.
getName() - Method in interface org.phenotips.vocabulary.Vocabulary
The official name of the vocabulary.
getName() - Method in interface org.phenotips.vocabulary.VocabularyExtension
The official name of the vocabulary extension.
getName() - Method in interface org.phenotips.vocabulary.VocabularyTerm
The short human-readable term name, for example Gait ataxia.
getOntologiesVersions() - Method in class org.phenotips.vocabulary.listeners.PatientVocabularyVersionRecorder
Modify this function to add more version types.
getOntology(String) - Method in class org.phenotips.vocabulary.script.OntologyScriptService
Deprecated.
getParents() - Method in interface org.phenotips.vocabulary.VocabularyTerm
Returns the parents (direct ancestors) of this term.
getRelocation(String) - Method in interface org.phenotips.vocabulary.VocabularySourceRelocationService
get the XObject of type PhenoTips.VocabularySourceRelocationClass with the value for the original property equal to the value of the original argument, and if not null, return the value of the relocation property.
getReplacementSolrConnection(Vocabulary) - Method in interface org.phenotips.vocabulary.SolrVocabularyResourceManager
Get the temporary Solr core used for a vocabulary during reindexing.
getRowItem(CSVRecord, int) - Method in class org.phenotips.vocabulary.AbstractCSVAnnotationsExtension
Helper method that gets the cell on the specified column, as string, if it exists, without throwing exceptions.
getSolrConnection(Vocabulary) - Method in interface org.phenotips.vocabulary.SolrVocabularyResourceManager
Get the Solr core used for a vocabulary.
getSourceLocation() - Method in interface org.phenotips.vocabulary.Vocabulary
Get the location where the sources for this vocabulary can be fetched from.
getSupportedCategories() - Method in interface org.phenotips.vocabulary.Vocabulary
Reports the categories of terms supported by this vocabulary.
getTargetVocabularyIds() - Method in class org.phenotips.vocabulary.AbstractCSVAnnotationsExtension
Specifies the vocabularies targeted by this extension.
getTerm(String) - Method in interface org.phenotips.vocabulary.Vocabulary
Access an individual term from the vocabulary, identified by its term identifier.
getTermCache(Vocabulary) - Method in interface org.phenotips.vocabulary.SolrVocabularyResourceManager
Get the cache instance created for handling vocabulary terms.
getTerms(Collection<String>) - Method in interface org.phenotips.vocabulary.Vocabulary
Access a list of terms from the vocabulary, identified by their term identifiers.
getTranslatedDescription() - Method in interface org.phenotips.vocabulary.VocabularyTerm
The human-readable term description, translated in the current locale if a translation is available, usually a longer phrase or paragraph that describes the term.
getTranslatedName() - Method in interface org.phenotips.vocabulary.VocabularyTerm
The short human-readable term name, translated in the current locale if a translation is available, for example Marcha atáxica if the current user is browsing in Spanish.
getTranslatedValues(String) - Method in interface org.phenotips.vocabulary.VocabularyTerm
Generic translated property access.
getVersion() - Method in interface org.phenotips.vocabulary.Vocabulary
Get the available version of the vocabulary.
getVocabularies(String) - Method in interface org.phenotips.vocabulary.VocabularyManager
Retrieve a set of Vocabulary objects that fall under the provided vocabulary category.
getVocabulary(String) - Method in class org.phenotips.vocabulary.script.VocabularyScriptService
Retrieve a vocabulary given its identifier.
getVocabulary(String) - Method in interface org.phenotips.vocabulary.VocabularyManager
Retrieve a vocabulary given its identifier.
getVocabulary() - Method in interface org.phenotips.vocabulary.VocabularyTerm
Returns the vocabulary where this term is defined.
getWebsite() - Method in interface org.phenotips.vocabulary.Vocabulary
Get the website url for the vocabulary.

H

hasCategory(String) - Method in interface org.phenotips.vocabulary.VocabularyManager
Returns true iff the provided category name is valid, false otherwise.
hasVocabulary(String) - Method in interface org.phenotips.vocabulary.VocabularyManager
Returns true iff the provided vocabulary identifier is valid, false otherwise.

I

ID_KEY - Static variable in class org.phenotips.vocabulary.AbstractCSVAnnotationsExtension
 
indexingEnded(Vocabulary) - Method in class org.phenotips.vocabulary.AbstractCSVAnnotationsExtension
 
indexingEnded(Vocabulary) - Method in interface org.phenotips.vocabulary.VocabularyExtension
Called when a vocabulary reindex is done, so that this extension can clean up its resources, if any.
indexingStarted(Vocabulary) - Method in class org.phenotips.vocabulary.AbstractCSVAnnotationsExtension
 
indexingStarted(Vocabulary) - Method in interface org.phenotips.vocabulary.VocabularyExtension
Called when a vocabulary reindex begins, so that this extension can prepare its needed resources, if any.
isVocabularySupported(Vocabulary) - Method in class org.phenotips.vocabulary.AbstractCSVAnnotationsExtension
 
isVocabularySupported(Vocabulary) - Method in interface org.phenotips.vocabulary.VocabularyExtension
Checks if a vocabulary is supported by this extension.

L

logger - Variable in class org.phenotips.vocabulary.AbstractCSVAnnotationsExtension
Logging helper object.

O

onEvent(Event, Object, Object) - Method in class org.phenotips.vocabulary.listeners.PatientVocabularyVersionRecorder
 
OntologyScriptService - Class in org.phenotips.vocabulary.script
Deprecated.
OntologyScriptService() - Constructor for class org.phenotips.vocabulary.script.OntologyScriptService
Deprecated.
 
org.phenotips.vocabulary - package org.phenotips.vocabulary
 
org.phenotips.vocabulary.listeners - package org.phenotips.vocabulary.listeners
 
org.phenotips.vocabulary.script - package org.phenotips.vocabulary.script
 

P

PatientVocabularyVersionRecorder - Class in org.phenotips.vocabulary.listeners
Store the used vocabulary versions (in the form name:String, version:String) in the patient record.
PatientVocabularyVersionRecorder() - Constructor for class org.phenotips.vocabulary.listeners.PatientVocabularyVersionRecorder
Default constructor, sets up the listener name and the list of events to subscribe to.
processCSVRecordRow(CSVRecord, Vocabulary) - Method in class org.phenotips.vocabulary.AbstractCSVAnnotationsExtension
Processes and caches the row data.

R

reindex(String) - Method in interface org.phenotips.vocabulary.Vocabulary
Reindex the whole vocabulary, fetching the source from the specified location.
relocationService - Variable in class org.phenotips.vocabulary.AbstractCSVAnnotationsExtension
 
replaceCore(Vocabulary) - Method in interface org.phenotips.vocabulary.SolrVocabularyResourceManager
Copy new index data from the temporary core to the main index location.
resolveTerm(String) - Method in class org.phenotips.vocabulary.script.OntologyScriptService
Deprecated.
resolveTerm(String) - Method in class org.phenotips.vocabulary.script.VocabularyScriptService
Retrieve a term from its owner vocabulary.
resolveTerm(String) - Method in interface org.phenotips.vocabulary.VocabularyManager
Retrieve a term from its owner vocabulary.

S

search(String, String, int) - Method in class org.phenotips.vocabulary.script.VocabularyScriptService
Suggest the terms that best match the user's input, in all vocabularies supporting the target category of terms.
search(Map<String, ?>) - Method in interface org.phenotips.vocabulary.Vocabulary
Generic search method, which looks for terms that match the specified term properties.
search(Map<String, ?>, Map<String, String>) - Method in interface org.phenotips.vocabulary.Vocabulary
Generic search method, which looks for terms that match the specified meta-properties.
search(String) - Method in interface org.phenotips.vocabulary.Vocabulary
Suggest the terms that best match the user's input.
search(String, int, String, String) - Method in interface org.phenotips.vocabulary.Vocabulary
Suggest the terms that best match the user's input.
search(String, String, int, String, String) - Method in interface org.phenotips.vocabulary.Vocabulary
Suggest the terms that best match the user's input, in a specific sub-category of this vocabulary.
search(String, String, int) - Method in interface org.phenotips.vocabulary.VocabularyManager
Suggest the terms that best match the user's input, in all vocabularies supporting the target category of terms.
set(String, Object) - Method in interface org.phenotips.vocabulary.VocabularyInputTerm
Generic property setter.
setDescription(String) - Method in interface org.phenotips.vocabulary.VocabularyInputTerm
Sets the human-readable term description, usually a longer phrase or paragraph that describes the term.
setId(String) - Method in interface org.phenotips.vocabulary.VocabularyInputTerm
Sets the (mandatory) term identifier.
setName(String) - Method in interface org.phenotips.vocabulary.VocabularyInputTerm
Sets the short human-readable term name.
setParents(Set<VocabularyTerm>) - Method in interface org.phenotips.vocabulary.VocabularyInputTerm
Sets the parents (direct ancestors) of this term.
setupCSVParser(Vocabulary) - Method in class org.phenotips.vocabulary.AbstractCSVAnnotationsExtension
Sets up a CSV parser so that it accepts the format of the input file, and has names for each column of interest.
size() - Method in interface org.phenotips.vocabulary.Vocabulary
Get the size (i.e.
SolrCoreContainerHandler - Interface in org.phenotips.vocabulary
Provides access to the configured Solr instance.
SolrVocabularyResourceManager - Interface in org.phenotips.vocabulary
Provides methods for initializing the resources needed by vocabularies stored in a Solr index.

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toJSON() - Method in interface org.phenotips.vocabulary.VocabularyTerm
Serialize all the known information about this term as a JSON object.

V

Vocabulary - Interface in org.phenotips.vocabulary
Provides access to a vocabulary, such as the HUGO Gene Nomenclature, or the Human Phenotype Ontology.
VocabularyExtension - Interface in org.phenotips.vocabulary
Allows extending a base vocabulary with additional annotations.
VocabularyInputTerm - Interface in org.phenotips.vocabulary
A vocabulary term that has been parsed from a vocabulary source during reindexing, exposing the already parsed fields and allowing new fields to be added.
VocabularyManager - Interface in org.phenotips.vocabulary
Provides access to the available vocabularies and their terms.
VocabularyScriptService - Class in org.phenotips.vocabulary.script
Provides access to the available vocabularies and their terms to public scripts.
VocabularyScriptService() - Constructor for class org.phenotips.vocabulary.script.VocabularyScriptService
 
VocabularySourceRelocationService - Interface in org.phenotips.vocabulary
Provides methods for accessing the location of the vocabulary source files to reindex vocabulary from a different location.
VocabularyTerm - Interface in org.phenotips.vocabulary
A term from a Vocabulary.
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