feedback, remove more audits and exception catching

src/main/java/gov/nih/nci/evs/api/controller/BaseController.java

@@ -2,7 +2,6 @@
 
 import gov.nih.nci.evs.api.model.Audit;
 import gov.nih.nci.evs.api.service.ElasticOperationsService;
-import gov.nih.nci.evs.api.service.ElasticQueryService;
 import gov.nih.nci.evs.api.util.TerminologyUtils;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -23,9 +22,6 @@ public class BaseController {
   /* The terminology utils */
   @Autowired TerminologyUtils termUtils;
 
-  /** The elastic query service. */
-  @Autowired ElasticQueryService elasticQueryService;
-
   /** The elastic operations service. */
   @Autowired ElasticOperationsService elasticOperationsService;
 

src/main/java/gov/nih/nci/evs/api/model/Audit.java

@@ -426,9 +426,6 @@ public static void addAudit(
       String details,
       String logLevel)
       throws Exception {
-    operationsService.deleteQuery(
-        "terminology:" + terminology + " AND logLevel:" + logLevel + " AND details:" + details,
-        ElasticOperationsService.AUDIT_INDEX);
     Audit audit = new Audit(type, terminology, null, new Date(), process, details, logLevel);
     operationsService.index(audit, ElasticOperationsService.AUDIT_INDEX, Audit.class);
   }

src/main/java/gov/nih/nci/evs/api/service/AbstractStardogLoadServiceImpl.java

@@ -198,7 +198,7 @@ private void loadConceptsRealTime(
           "loadConceptsRealTime",
           terminology.getTerminology(),
           "No concepts found!",
-          "warning");
+          "WARN");
       return;
     }
 
@@ -252,7 +252,7 @@ private void loadConceptsRealTime(
                           "loadConceptsRealTime",
                           terminology.getTerminology(),
                           "Error handling history for concept " + c.getCode(),
-                          "error");
+                          "ERROR");
                     } catch (Exception e1) {
                       logger.error(e1.getMessage(), e1);
                     }
@@ -338,7 +338,7 @@ private void loadConceptsRealTime(
               "loadConceptsRealTime",
               terminology.getTerminology(),
               "UNABLE TO DELETE INDEX: " + NCIT_MAPS_TO + mapset.getKey() + " NOT FOUND!",
-              "warning");
+              "WARN");
         }
         Collections.sort(
             mapset.getValue().getMaps(),
@@ -545,7 +545,7 @@ public void addExtraSubsets(List<Concept> existingSubsets, Terminology terminolo
             "addExtraSubsets",
             terminology.getTerminology(),
             "Subset " + subsetCode + " not found as a concept, skipping.",
-            "warning");
+            "WARN");
         continue;
       }
 
@@ -577,7 +577,7 @@ public void addExtraSubsets(List<Concept> existingSubsets, Terminology terminolo
                 + ": "
                 + newSubsets.get(subsetCode)
                 + " not found, skipping.",
-            "warning");
+            "WARN");
         continue;
       }
 
@@ -627,13 +627,15 @@ public void addExtraSubsets(List<Concept> existingSubsets, Terminology terminolo
         // index subsetConcept
         operationsService.index(subsetConcept, terminology.getIndexName(), Concept.class);
       }
-      Audit.addAudit(
-          operationsService,
-          "Missing Subset Concepts",
-          "addExtraSubsets",
-          terminology.getTerminology(),
-          "Concepts " + missingConcepts + " not found for new subset " + subsetCode + ".",
-          "warning");
+      if (missingConcepts.size() > 0) {
+        Audit.addAudit(
+            operationsService,
+            "Missing Subset Concepts",
+            "addExtraSubsets",
+            terminology.getTerminology(),
+            "Concepts " + missingConcepts + " not found for new subset " + subsetCode + ".",
+            "WARN");
+      }
       // explicitly set leaf since it defaults to false
       newSubsetEntry.setLeaf(!newSubsets.containsValue(newSubsetEntry.getCode()));
       // add extra relevant properties to new subset

src/main/java/gov/nih/nci/evs/api/service/BaseLoaderService.java

@@ -210,7 +210,7 @@ public Set<String> cleanStaleIndexes(final Terminology terminology) throws Excep
         logger.warn("Deleting concepts index {} failed!", indexName);
         Audit.addAudit(
             operationsService,
-            "warning",
+            "WARN",
             "cleanStaleIndexes",
             terminology.getTerminology(),
             "Deleting concepts index " + objectIndexName + " failed!",
@@ -355,7 +355,7 @@ public void checkLoadStatus(int total, Terminology term) throws Exception {
         Thread.sleep(2000);
       } catch (InterruptedException e) {
         logger.error("Error while checking load status: sleep interrupted - " + e.getMessage(), e);
-        throw new Exception(e);
+        throw e;
       }
 
       if (attempts == 15) {

src/main/java/gov/nih/nci/evs/api/service/LoaderServiceImpl.java

@@ -210,6 +210,7 @@ public static void main(String[] args) throws Exception {
       Date endDate = new Date();
       termAudit.setEndDate(endDate);
       termAudit.setElapsedTime(endDate.getTime() - startDate.getTime());
+      termAudit.setLogLevel("INFO");
       logger.info("Audit: {}", termAudit.toString());
       // only add new audit if something major has actually happened
       if (termAudit.getElapsedTime() > 10000) {
@@ -224,7 +225,7 @@ public static void main(String[] args) throws Exception {
           e.getStackTrace()[0].getClassName(),
           cmd.getOptionValue("t"),
           e.getMessage(),
-          "error");
+          "ERROR");
       int exitCode =
           SpringApplication.exit(
               app,

src/main/java/gov/nih/nci/evs/api/service/SparqlQueryManagerServiceImpl.java

@@ -524,7 +524,6 @@ public List<Concept> getConcepts(
             log.info("      finish main");
           } catch (final Exception e) {
             log.error("Unexpected error on main", e);
-            auditError(e, "getConcepts");
             exceptions.add(e);
           }
         });
@@ -538,7 +537,6 @@ public List<Concept> getConcepts(
             log.info("      finish roles");
           } catch (final Exception e) {
             log.error("Unexpected error on roles", e);
-            auditError(e, "getConcepts");
             exceptions.add(e);
           }
         });
@@ -552,7 +550,6 @@ public List<Concept> getConcepts(
             log.info("      finish inverse roles");
           } catch (final Exception e) {
             log.error("Unexpected error on inverse roles", e);
-            auditError(e, "getConcepts");
             exceptions.add(e);
           }
         });
@@ -566,20 +563,14 @@ public List<Concept> getConcepts(
             log.info("      finish axioms");
           } catch (final Exception e) {
             log.error("Unexpected error on axioms", e);
-            auditError(e, "getConcepts");
             exceptions.add(e);
           }
         });
     // Shutdown executor
     executor.shutdown();
 
     // Wait up to 10 min for processes to stop
-    try {
-      executor.awaitTermination(10, TimeUnit.MINUTES);
-    } catch (final InterruptedException e) {
-      auditError(e, "getConcepts");
-      throw new RuntimeException(e);
-    }
+    executor.awaitTermination(10, TimeUnit.MINUTES);
 
     if (axiomMap.isEmpty()) {
       // This likely occurs if the 10 minute awaitTermination isn't long enough
@@ -2448,12 +2439,7 @@ public List<Concept> getAllConceptsWithCode(final Terminology terminology) throw
     final String queryPrefix = queryBuilderService.constructPrefix(terminology);
     final String query = queryBuilderService.constructQuery("all.concepts.with.code", terminology);
     String res = null;
-    try {
-      res = restUtils.runSPARQL(queryPrefix + query, getQueryURL());
-    } catch (final Exception e) {
-      auditError(e, "getAllConceptsWithCode");
-      e.printStackTrace();
-    }
+    res = restUtils.runSPARQL(queryPrefix + query, getQueryURL());
 
     final ObjectMapper mapper = new ObjectMapper();
     mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
@@ -2489,12 +2475,7 @@ public List<Concept> getAllConceptsWithoutCode(final Terminology terminology) th
     final String query =
         queryBuilderService.constructQuery("all.concepts.without.code", terminology);
     String res = null;
-    try {
-      res = restUtils.runSPARQL(queryPrefix + query, getQueryURL());
-    } catch (final Exception e) {
-      auditError(e, "getAllConceptsWithoutCode");
-      e.printStackTrace();
-    }
+    res = restUtils.runSPARQL(queryPrefix + query, getQueryURL());
 
     final ObjectMapper mapper = new ObjectMapper();
     mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
@@ -2577,29 +2558,20 @@ private void getSubsetsHelper(
   /* see superclass */
   @Override
   public List<AssociationEntry> getAssociationEntries(
-      final Terminology terminology, final Concept association) {
+      final Terminology terminology, final Concept association) throws Exception {
     final String queryPrefix = queryBuilderService.constructPrefix(terminology);
     final String query =
         queryBuilderService.constructQuery(
             "association.entries", terminology, association.getCode());
     String res = null;
-    try {
-      res = restUtils.runSPARQL(queryPrefix + query, getQueryURL());
-    } catch (final Exception e1) {
-      auditError(e1, "getAssociationEntries");
-      e1.printStackTrace();
-    }
+    res = restUtils.runSPARQL(queryPrefix + query, getQueryURL());
+
     final ObjectMapper mapper = new ObjectMapper();
     mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
     final List<AssociationEntry> entries = new ArrayList<>();
     Sparql sparqlResult = null;
-    try {
-      sparqlResult = mapper.readValue(res, Sparql.class);
-    } catch (final Exception e) {
-      log.error("Mapper could not read value in Association Entries");
-      auditError(e, "getAssociationEntries");
-      e.printStackTrace();
-    }
+    sparqlResult = mapper.readValue(res, Sparql.class);
+
     if (sparqlResult != null) {
       final Bindings[] bindings = sparqlResult.getResults().getBindings();
       for (final Bindings b : bindings) {
@@ -2647,11 +2619,7 @@ private List<String> getIgnoreSourceUrls() {
     return Collections.emptyList();
   }
 
-  private void auditError(Exception e, String function) {
-    try {
-      Audit.addAudit(operationsService, "Exception", function, null, e.getMessage(), "error");
-    } catch (Exception e1) {
-      log.error("Error adding audit", e1);
-    }
+  private void auditError(Exception e, String function) throws Exception {
+    Audit.addAudit(operationsService, "Exception", function, null, e.getMessage(), "ERROR");
   }
 }