Update indexer orders

Author: oblodgett

agr_indexer/src/main/java/org/alliancegenome/indexer/Main.java

@@ -68,18 +68,7 @@ public static void main(String[] args) {
 			log.info("Args[" + i + "]: " + args[i]);
 		}
 
-		ExecutorService parallelExecutor = Executors.newFixedThreadPool(10);
 		ExecutorService sequentialExecutor = Executors.newFixedThreadPool(1);
-
-		for (String type : parallelMap.keySet()) {
-			if (argumentSet.size() == 0 || argumentSet.contains(type)) {
-				log.info("Running Parallel for: " + type);
-				parallelExecutor.execute(indexers.get(type));
-				//indexers.get(type).start();
-			} else {
-				log.info("Not Starting: " + type);
-			}
-		}
 
 		for (String type : sequentialMap.keySet()) {
 			if (argumentSet.size() == 0 || argumentSet.contains(type)) {
@@ -90,29 +79,41 @@ public static void main(String[] args) {
 				log.info("Not Starting: " + type);
 			}
 		}
-
-		parallelExecutor.shutdown();
-		while (!parallelExecutor.isTerminated()) {
+		sequentialExecutor.shutdown();
+		while (!sequentialExecutor.isTerminated()) {
 			try {
 				Thread.sleep(1000);
 			} catch (InterruptedException e) {
 				ExceptionCatcher.report(e);
 				e.printStackTrace();
 			}
 		}
-		log.info("Finished Running Curation Indexers");
-		sequentialExecutor.shutdown();
-		while (!sequentialExecutor.isTerminated()) {
+		log.info("Finished Running Sequential Indexers");
+		
+		
+		ExecutorService parallelExecutor = Executors.newFixedThreadPool(10);
+		
+		for (String type : parallelMap.keySet()) {
+			if (argumentSet.size() == 0 || argumentSet.contains(type)) {
+				log.info("Running Parallel for: " + type);
+				parallelExecutor.execute(indexers.get(type));
+				//indexers.get(type).start();
+			} else {
+				log.info("Not Starting: " + type);
+			}
+		}
+		parallelExecutor.shutdown();
+		while (!parallelExecutor.isTerminated()) {
 			try {
 				Thread.sleep(1000);
 			} catch (InterruptedException e) {
 				ExceptionCatcher.report(e);
 				e.printStackTrace();
 			}
 		}
-		log.info("Finished Running Neo4j Indexers");
+		log.info("Finished Running Parallel Indexers");
 
-		log.debug("Waiting for Indexers to finish");
+		log.debug("Waiting for ALL Indexers to finish");
 		for (Indexer i : indexers.values()) {
 			try {
 				if (i.isAlive()) {

agr_indexer/src/main/java/org/alliancegenome/indexer/TestSpeciesOrder.java

@@ -30,7 +30,7 @@ public static void main(String[] args) throws Exception {
 			String taxonCurie = species.getTaxon() != null ? species.getTaxon().getCurie() : "null";
 			Integer order = species.getPhylogeneticOrder();
 			String fullName = species.getFullName();
-			System.out.println("  " + fullName + " | taxon: " + taxonCurie + " | phylogeneticOrder: " + order);
+			System.out.println(fullName + " | taxon: " + taxonCurie + " | phylogeneticOrder: " + order);
 
 			if (species.getTaxon() != null && order != null) {
 				String taxonIdPart = taxonCurie.replace("NCBITaxon:", "");
@@ -41,15 +41,15 @@ public static void main(String[] args) throws Exception {
 		System.out.println("\n=== Species order lookup map ===");
 		speciesOrderLookup.entrySet().stream()
 			.sorted(Map.Entry.comparingByValue())
-			.forEach(e -> System.out.println("  " + e.getKey() + " -> " + e.getValue()));
+			.forEach(e -> System.out.println(e.getKey() + " -> " + e.getValue()));
 
 		// Test buildSpeciesOrder for a specific taxon (e.g. Xenopus laevis 8355)
 		String testTaxon = args.length > 0 ? args[0] : "NCBITaxon:8355";
 		System.out.println("\n=== buildSpeciesOrder for " + testTaxon + " ===");
 		HashMap<String, Integer> speciesOrder = buildSpeciesOrder(speciesOrderLookup, testTaxon);
 		speciesOrder.entrySet().stream()
 			.sorted(Map.Entry.comparingByValue())
-			.forEach(e -> System.out.println("  " + e.getKey() + " -> " + e.getValue()));
+			.forEach(e -> System.out.println(e.getKey() + " -> " + e.getValue()));
 
 		System.out.println("\nDone.");
 	}

agr_indexer/src/main/java/org/alliancegenome/indexer/config/IndexerConfig.java

@@ -30,6 +30,9 @@ public enum IndexerConfig {
 
 	// Curation Indexers
 
+	// Run Sequentially -- typically take a lot of RAM or do consolidation in memory
+	ReleaseInfoIndexer("release", ReleaseInfoIndexer.class, 1, 1, 1, 1, 1, false),
+	
 	// Run Parallelly
 	ParalogyIndexer("paralogy", GeneToGeneParalogyIndexer.class, 4, 5000, 5000, 8, 1, true),
 	AffectedGenomicModelAnnotationIndexer("agmAnnotation", AGMAnnotationCurationIndexer.class, 4, 1500, 1500, 8, 1, true),
@@ -44,16 +47,13 @@ public enum IndexerConfig {
 	DiseaseSummaryIndexer("diseaseSummary", DiseaseSummaryCurationIndexer.class, 4, 1500, 1500, 4, 1, true),
 	TransgenicAlleleIndexer("transgenicAlleles", TransgenicAlleleCurationIndexer.class, 1, 3000, 1500, 8, 1, true),
 	GeneExpressionRibbonSummaryIndexer("geneExpressionRibbonSummary", GeneExpressionRibbonSummaryIndexer.class, 1, 1, 1, 1, 1, true),
-	ReleaseInfoIndexer("release", ReleaseInfoIndexer.class, 1, 1, 1, 1, 1, true),
-
-	// Run Sequentially -- typically take a lot of RAM or do consolidation in memory
-	DiseaseSearchResultIndexer("diseaseSearchResult", DiseaseSearchResultCurationIndexer.class, 8, 50, 50, 4, 1, false),
-	GOSearchResultCurationIndexer("goSearchResult", GOSearchResultCurationIndexer.class, 4, 1500, 1500, 4, 1, false),
-	AlleleSummaryIndexer("alleleSummary", AlleleSummaryCurationIndexer.class, 4, 1500, 1500, 4, 1, false),
-	GeneToGeneOrthologyIndexer("geneToGeneOrthology", GeneToGeneOrthologyIndexer.class, 4, 2500, 2500, 8, 1, false),
-	GeneMolecularInteractionIndexers("geneMolecularInteraction", GeneMolecularInteractionCurationIndexer.class, 4, 1500, 1500, 2, 1, false),
-	PhenotypeAnnotationIndexer("phenotypeAnnotation", PhenotypeAnnotationCurationIndexer.class, 4, 1500, 1500, 2, 1, false),
-	DiseaseAnnotationIndexer("diseaseAnnotation", DiseaseAnnotationCurationIndexer.class, 1, 1500, 1500, 2, 1, false),
+	DiseaseSearchResultIndexer("diseaseSearchResult", DiseaseSearchResultCurationIndexer.class, 8, 50, 50, 4, 1, true),
+	GOSearchResultCurationIndexer("goSearchResult", GOSearchResultCurationIndexer.class, 4, 1500, 1500, 4, 1, true),
+	AlleleSummaryIndexer("alleleSummary", AlleleSummaryCurationIndexer.class, 4, 1500, 1500, 4, 1, true),
+	GeneToGeneOrthologyIndexer("geneToGeneOrthology", GeneToGeneOrthologyIndexer.class, 4, 2500, 2500, 8, 1, true),
+	GeneMolecularInteractionIndexers("geneMolecularInteraction", GeneMolecularInteractionCurationIndexer.class, 4, 1500, 1500, 2, 1, true),
+	PhenotypeAnnotationIndexer("phenotypeAnnotation", PhenotypeAnnotationCurationIndexer.class, 4, 1500, 1500, 2, 1, true),
+	DiseaseAnnotationIndexer("diseaseAnnotation", DiseaseAnnotationCurationIndexer.class, 1, 1500, 1500, 2, 1, true),
 	;
 
 	private String typeName;