@Test public void testImplicitSpecies() throws Exception { NormalizerStats stats = normalize(2); try (Transaction tx = beginTx()) { NameUsage fam = getUsageByTaxonId("5"); NameUsage tulostoma = getUsageByTaxonId("6"); NameUsage tulostomaEx = getUsageByTaxonId("100"); assertEquals(tulostoma.getKey(), tulostomaEx.getParentKey()); NameUsage tulostomaExEx = getUsageByTaxonId("101"); assertEquals(tulostoma.getKey(), tulostomaExEx.getParentKey()); NameUsage tulostomaExRid = getUsageByTaxonId("102"); assertEquals(tulostoma.getKey(), tulostomaExRid.getParentKey()); NameUsage tulostomafake1 = getUsageByTaxonId("301"); assertEquals(fam.getKey(), tulostomafake1.getParentKey()); NameUsage tulostomafake2 = getUsageByTaxonId("302"); assertEquals(fam.getKey(), tulostomafake2.getParentKey()); } System.out.println(stats); assertEquals(14, stats.getCount()); assertEquals(7, stats.getDepth()); assertEquals(14, stats.getCountByOrigin(Origin.SOURCE)); assertEquals(1, stats.getRoots()); assertEquals(0, stats.getSynonyms()); }
private void normalize() throws NormalizationFailedException { LOG.info("Start processing explicit relations ..."); int counter = 0; Transaction tx = dao.getNeo().beginTx(); try { for (Node n : dao.getNeo().getAllNodes()) { setupRelation(n); counter++; relationMeter.mark(); tx = renewTx(tx); if (counter % 10000 == 0) { LOG.debug("Processed relations for {} nodes", counter); checkInterrupted(); } } } finally { tx.success(); tx.close(); } applyDenormedClassification(); cleanupRelations(); LOG.info("Relation setup completed, {} nodes processed. Setup rate: {}", counter, relationMeter.getMeanRate()); }
Normalizer extends ImportDb implements Runnable { private void normalize() throws NormalizationFailedException { LOG.info("Start processing explicit relations ..."); int counter = 0; Transaction tx = dao.getNeo().beginTx(); try { for (Node n : dao.getNeo().getAllNodes()) { setupRelation(n); counter++; relationMeter.mark(); tx = renewTx(tx); if (counter % 10000 == 0) { LOG.debug("Processed relations for {} nodes", counter); checkInterrupted(); } } } finally { tx.success(); tx.close(); } applyDenormedClassification(); cleanupRelations(); LOG.info("Relation setup completed, {} nodes processed. Setup rate: {}", counter, relationMeter.getMeanRate()); } }
Normalizer extends ImportDb implements Runnable { private void normalize() throws NormalizationFailedException { LOG.info("Start processing explicit relations ..."); int counter = 0; Transaction tx = dao.getNeo().beginTx(); try { for (Node n : dao.getNeo().getAllNodes()) { setupRelation(n); counter++; relationMeter.mark(); tx = renewTx(tx); if (counter % 10000 == 0) { LOG.debug("Processed relations for {} nodes", counter); checkInterrupted(); } } } finally { tx.success(); tx.close(); } applyDenormedClassification(); cleanupRelations(); LOG.info("Relation setup completed, {} nodes processed. Setup rate: {}", counter, relationMeter.getMeanRate()); } private  Normalizer(UUID datasetKey, UsageDao dao, File dwca, int batchSize,
                     MetricRegistry registry, Map<String, UUID> constituents, IdLookup lookup); }
Normalizer extends ImportDb implements Runnable { private void normalize() throws NormalizationFailedException { LOG.info("Start processing explicit relations ..."); int counter = 0; Transaction tx = dao.getNeo().beginTx(); try { for (Node n : dao.getNeo().getAllNodes()) { setupRelation(n); counter++; relationMeter.mark(); tx = renewTx(tx); if (counter % 10000 == 0) { LOG.debug("Processed relations for {} nodes", counter); checkInterrupted(); } } } finally { tx.success(); tx.close(); } applyDenormedClassification(); cleanupRelations(); LOG.info("Relation setup completed, {} nodes processed. Setup rate: {}", counter, relationMeter.getMeanRate()); } private  Normalizer(UUID datasetKey, UsageDao dao, File dwca, int batchSize,
                     MetricRegistry registry, Map<String, UUID> constituents, IdLookup lookup); static Normalizer create(NormalizerConfiguration cfg, UUID datasetKey, MetricRegistry registry,
                                  Map<String, UUID> constituents, IdLookup lookup); static Normalizer create(UUID datasetKey, UsageDao dao, File dwca, IdLookup lookup, int batchSize); static Normalizer create(NormalizerConfiguration cfg, UUID datasetKey); static Normalizer create(NormalizerConfiguration cfg, MetricRegistry registry, UUID datasetKey); void run(); void run(boolean closeDao); NormalizerStats getStats(); }
Normalizer extends ImportDb implements Runnable { private void normalize() throws NormalizationFailedException { LOG.info("Start processing explicit relations ..."); int counter = 0; Transaction tx = dao.getNeo().beginTx(); try { for (Node n : dao.getNeo().getAllNodes()) { setupRelation(n); counter++; relationMeter.mark(); tx = renewTx(tx); if (counter % 10000 == 0) { LOG.debug("Processed relations for {} nodes", counter); checkInterrupted(); } } } finally { tx.success(); tx.close(); } applyDenormedClassification(); cleanupRelations(); LOG.info("Relation setup completed, {} nodes processed. Setup rate: {}", counter, relationMeter.getMeanRate()); } private  Normalizer(UUID datasetKey, UsageDao dao, File dwca, int batchSize,
                     MetricRegistry registry, Map<String, UUID> constituents, IdLookup lookup); static Normalizer create(NormalizerConfiguration cfg, UUID datasetKey, MetricRegistry registry,
                                  Map<String, UUID> constituents, IdLookup lookup); static Normalizer create(UUID datasetKey, UsageDao dao, File dwca, IdLookup lookup, int batchSize); static Normalizer create(NormalizerConfiguration cfg, UUID datasetKey); static Normalizer create(NormalizerConfiguration cfg, MetricRegistry registry, UUID datasetKey); void run(); void run(boolean closeDao); NormalizerStats getStats();  }