How to use

indexObo

method

in

uk.ac.ebi.intact.dataexchange.psimi.solr.ontology.OntologyIndexer

public void indexOntologies(OntologyMapping[] ontologyMappings) throws IntactSolrException {
  if (ontologySolrServer == null) {
    throw new IllegalStateException("To index an ontology, an ontology SolrServer must be passed to the constructor");
  }
  
  if (log.isInfoEnabled()) log.info("Indexing ontologies: "+ Arrays.asList(ontologyMappings));
  
  OntologyIndexer ontologyIndexer = new OntologyIndexer(ontologySolrServer);
  ontologyIndexer.indexObo(ontologyMappings);
}

public void indexOntologies(OntologyMapping[] ontologyMappings) throws IntactSolrException {
  if (ontologySolrServer == null) {
    throw new IllegalStateException("To index an ontology, an ontology SolrServer must be passed to the constructor");
  }
  
  if (log.isInfoEnabled()) log.info("Indexing ontologies: "+ Arrays.asList(ontologyMappings));
  
  OntologyIndexer ontologyIndexer = new OntologyIndexer(ontologySolrServer);
  ontologyIndexer.indexObo(ontologyMappings);
}

public void indexObo(String ontologyName, URL oboUrl) throws IntactSolrException {
  indexObo(ontologyName, oboUrl, new DefaultDocumentFilter());
}

public void indexObo(OntologyMapping[] ontologyMappings) throws IntactSolrException {
  indexObo(ontologyMappings, new DefaultDocumentFilter());
}

public void indexObo(String ontologyName, URL oboUrl) throws IntactSolrException {
  indexObo(ontologyName, oboUrl, new DefaultDocumentFilter());
}

public void indexObo(OntologyMapping[] ontologyMappings) throws IntactSolrException {
  indexObo(ontologyMappings, new DefaultDocumentFilter());
}

public void indexObo(OntologyMapping[] ontologyMappings, DocumentFilter documentFilter) throws IntactSolrException {
  for (OntologyMapping om : ontologyMappings) {
    indexObo(om.getName(), om.getUrl(), documentFilter);
  }
}

public void indexObo(OntologyMapping[] ontologyMappings, DocumentFilter documentFilter) throws IntactSolrException {
  for (OntologyMapping om : ontologyMappings) {
    indexObo(om.getName(), om.getUrl(), documentFilter);
  }
}

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;
}