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 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 index(OntologyDocument ontologyDocument) throws IntactSolrException { index(ontologyDocument, new DefaultDocumentFilter()); }
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; }
public void indexOntology(OntologyIterator ontologyIterator) { indexOntology(ontologyIterator, new DefaultDocumentFilter()); }
public void indexObo(String ontologyName, URL oboUrl) throws IntactSolrException { indexObo(ontologyName, oboUrl, new DefaultDocumentFilter()); }
public void index(OntologyDocument ontologyDocument, DocumentFilter documentFilter) throws IntactSolrException { if (documentFilter != null && !documentFilter.accept(ontologyDocument)) { return; } SolrInputDocument doc = createSolrInputDocument(ontologyDocument); try { solrServer.add(doc); } catch (Exception e) { throw new IntactSolrException("Problem adding ontology document to SOLR server: "+ontologyDocument, e); } }
commitSolr(false); numberDoc = 0; commitSolr(false);
private SolrInputDocument createSolrInputDocument(OntologyDocument ontologyDocument) { SolrInputDocument doc = new SolrInputDocument(); String uniqueKey = ontologyDocument.getOntology() + "_" + ontologyDocument.getParentId() + "_" + ontologyDocument.getChildId() + "_" + ontologyDocument.getRelationshipType(); addField(doc, OntologyFieldNames.ID, uniqueKey, false); addField(doc, OntologyFieldNames.ONTOLOGY, ontologyDocument.getOntology(), false); addField(doc, OntologyFieldNames.PARENT_ID, ontologyDocument.getParentId(), false); addField(doc, OntologyFieldNames.PARENT_NAME, ontologyDocument.getParentName(), true); addField(doc, OntologyFieldNames.CHILD_ID, ontologyDocument.getChildId(), false); addField(doc, OntologyFieldNames.CHILD_NAME, ontologyDocument.getChildName(), true); addField(doc, OntologyFieldNames.RELATIONSHIP_TYPE, ontologyDocument.getRelationshipType(), false); addField(doc, OntologyFieldNames.CYCLIC, ontologyDocument.isCyclicRelationship(), false); for (String synonym : ontologyDocument.getParentSynonyms()) { addField(doc, OntologyFieldNames.PARENT_SYNONYMS, synonym, false); } for (String synonym : ontologyDocument.getChildSynonyms()) { addField(doc, OntologyFieldNames.CHILDREN_SYNONYMS, synonym, false); } return doc; }
public void indexOntology(OntologyIterator ontologyIterator) { indexOntology(ontologyIterator, new DefaultDocumentFilter()); }
public void indexObo(OntologyMapping[] ontologyMappings) throws IntactSolrException { indexObo(ontologyMappings, new DefaultDocumentFilter()); }
public void index(OntologyDocument ontologyDocument, DocumentFilter documentFilter) throws IntactSolrException { if (documentFilter != null && !documentFilter.accept(ontologyDocument)) { return; } SolrInputDocument doc = createSolrInputDocument(ontologyDocument); try { solrServer.add(doc); } catch (Exception e) { int numberOfTries = 1; boolean isSuccessful = false; while (numberOfTries <= this.numberOfTries && !isSuccessful){ try { solrServer.add(doc); isSuccessful = true; } catch (Exception e2) { numberOfTries++; } } if (!isSuccessful){ throw new IntactSolrException("Problem adding ontology document to SOLR server: "+ontologyDocument, e); } } }
public void indexOntology(OntologyIterator ontologyIterator, DocumentFilter documentFilter) { Iterator<SolrInputDocument> iter = new SolrInputDocumentIterator(ontologyIterator, documentFilter); try { solrServer.add(iter); } catch (Throwable e) { throw new IntactSolrException("Problem indexing documents using iterator", e); } commitSolr(true); }
private SolrInputDocument createSolrInputDocument(OntologyDocument ontologyDocument) { SolrInputDocument doc = new SolrInputDocument(); String uniqueKey = ontologyDocument.getOntology() + "_" + ontologyDocument.getParentId() + "_" + ontologyDocument.getChildId() + "_" + ontologyDocument.getRelationshipType(); addField(doc, OntologyFieldNames.ID, uniqueKey, false); addField(doc, OntologyFieldNames.ONTOLOGY, ontologyDocument.getOntology(), false); addField(doc, OntologyFieldNames.PARENT_ID, ontologyDocument.getParentId(), false); addField(doc, OntologyFieldNames.PARENT_NAME, ontologyDocument.getParentName(), true); addField(doc, OntologyFieldNames.CHILD_ID, ontologyDocument.getChildId(), false); addField(doc, OntologyFieldNames.CHILD_NAME, ontologyDocument.getChildName(), true); //addField(doc, OntologyFieldNames.RELATIONSHIP_TYPE, ontologyDocument.getRelationshipType(), false); //addField(doc, OntologyFieldNames.CYCLIC, ontologyDocument.isCyclicRelationship(), false); for (String synonym : ontologyDocument.getParentSynonyms()) { addField(doc, OntologyFieldNames.PARENT_SYNONYMS, synonym, false); } for (String synonym : ontologyDocument.getChildSynonyms()) { addField(doc, OntologyFieldNames.CHILDREN_SYNONYMS, synonym, false); } return doc; }
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 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, 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) throws IntactSolrException { indexObo(ontologyName, oboUrl, new DefaultDocumentFilter()); }
public void index(OntologyDocument ontologyDocument) throws IntactSolrException { index(ontologyDocument, 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); }