A C D E G H I L O P R S T V

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AbstractCSVAnnotationsExtension - Class in org.phenotips.vocabulary

Implements VocabularyExtension to annotate VocabularyInputTerm from supported vocabularies with data from a tab- or comma-separated file.

AbstractCSVAnnotationsExtension() - Constructor for class org.phenotips.vocabulary.AbstractCSVAnnotationsExtension

append(String, Object) - Method in interface org.phenotips.vocabulary.VocabularyInputTerm

Generic property setter, additive.

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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.

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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).

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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.

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get(String) - Method in class org.phenotips.vocabulary.script.OntologyScriptService

Deprecated.

use $services.vocabularies.get instead

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.

use $services.vocabularies.getVocabulary instead

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.

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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.

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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.

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logger - Variable in class org.phenotips.vocabulary.AbstractCSVAnnotationsExtension

Logging helper object.

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onEvent(Event, Object, Object) - Method in class org.phenotips.vocabulary.listeners.PatientVocabularyVersionRecorder

OntologyScriptService - Class in org.phenotips.vocabulary.script

Deprecated.

use $services.vocabularies instead

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

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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.

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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.

use $services.vocabularies.resolveTerm instead

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.

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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.

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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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