How to use

indexOntology

method

in

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

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;
}