public void indexOntology(OntologyIterator ontologyIterator) throws IntactSolrException { if (ontologySolrServer == null) { throw new IllegalStateException("To index an ontology, an ontology SolrServer must be passed to the constructor"); } OntologyIndexer ontologyIndexer = new OntologyIndexer(ontologySolrServer); ontologyIndexer.indexOntology(ontologyIterator); }
public void indexOntology(OntologyIterator ontologyIterator) throws IntactSolrException { if (ontologySolrServer == null) { throw new IllegalStateException("To index an ontology, an ontology SolrServer must be passed to the constructor"); } OntologyIndexer ontologyIndexer = new OntologyIndexer(ontologySolrServer); ontologyIndexer.indexOntology(ontologyIterator); }
public void indexOntology(OntologyIterator ontologyIterator) { indexOntology(ontologyIterator, new DefaultDocumentFilter()); }
public void indexOntology(OntologyIterator ontologyIterator) { indexOntology(ontologyIterator, new DefaultDocumentFilter()); }
public void indexObo(String ontologyName, URL oboUrl, DocumentFilter documentFilter) throws IntactSolrException { OntologyIterator oboIterator; if ( log.isInfoEnabled() ) log.info( "Starting to index " + ontologyName + " from " + oboUrl ); try { oboIterator = new OboOntologyIterator(ontologyName, oboUrl); } catch (Throwable e) { throw new IntactSolrException("Problem creating OBO iterator for: "+ontologyName+" URL: "+oboUrl, e); } indexOntology(oboIterator, documentFilter); }
public void indexObo(String ontologyName, URL oboUrl, DocumentFilter documentFilter) throws IntactSolrException { OntologyIterator oboIterator; if ( log.isInfoEnabled() ) log.info( "Starting to index " + ontologyName + " from " + oboUrl ); try { oboIterator = new OboOntologyIterator(ontologyName, oboUrl); } catch (Throwable e) { throw new IntactSolrException("Problem creating OBO iterator for: "+ontologyName+" URL: "+oboUrl, e); } indexOntology(oboIterator, documentFilter); }
public void indexUniprotTaxonomy() throws IntactSolrException { OntologyIterator ontologyIterator; try { if ( log.isInfoEnabled() ) log.info( "Starting to index uniprot taxonomy" ); ontologyIterator = new UniprotTaxonomyOntologyIterator(); } catch (Throwable e) { throw new IntactSolrException("Problem creating default Uniprot taxonomy iterator", e); } indexOntology(ontologyIterator); }
public void indexUniprotTaxonomy() throws IntactSolrException { OntologyIterator ontologyIterator; try { if ( log.isInfoEnabled() ) log.info( "Starting to index uniprot taxonomy" ); ontologyIterator = new UniprotTaxonomyOntologyIterator(); } catch (Throwable e) { throw new IntactSolrException("Problem creating default Uniprot taxonomy iterator", e); } indexOntology(ontologyIterator); }
public RepeatStatus execute(StepContribution contribution, ChunkContext chunkContext) throws Exception { if (ontologiesSolrUrl == null) { throw new NullPointerException("ontologiesSolrUrl is null"); } HttpSolrServer ontologiesSolrServer = createSolrServer(); OntologyIndexer ontologyIndexer = new OntologyIndexer(ontologiesSolrServer); if (taxonomyOntologyMappings != null) { indexUniprotTaxonomy = true; } if (indexUniprotTaxonomy) { if (taxonomyOntologyMappings == null) { ontologyIndexer.indexUniprotTaxonomy(); } else { for (OntologyMapping om : taxonomyOntologyMappings) { ontologyIndexer.indexOntology(new UniprotTaxonomyOntologyIterator(om.getUrl())); } } } ontologyIndexer.indexObo(oboOntologyMappings.toArray(new OntologyMapping[oboOntologyMappings.size()])); long count = countDocs(ontologiesSolrServer); contribution.getExitStatus().addExitDescription("Total docs in index: "+count); ontologiesSolrServer.shutdown(); return RepeatStatus.FINISHED; }