improves reporting for when a type coercion in neo goes wrong

see #34

src/main/java/ebi/spot/neo4j2owl/N2OLog.java

@@ -33,6 +33,13 @@ public void log(Object msg) {
     public void error(Object msg) {
         //log.error(msg.toString());
         System.err.println("ERROR: "+msg + " " + getTimePassed());
+        errorInterpreter(msg.toString());
+    }
+
+    private void errorInterpreter(String msg) {
+        if(msg.contains("Property values can only be of primitive types or arrays thereof")) {
+            System.err.println("Debugging assistant: This error often (not always!) occurs in conjunction with the dynamic type coercing function (example: properties with more than 1 datatype associated with it in the ontology, say 200 Boolean values and 10 String values, get coerced to Boolean). Search the log the the 'Typing report for' the property for more information.");
+        }
     }
 
     public void info(Object msg) {

src/main/java/ebi/spot/neo4j2owl/importer/N2ONeoCSVLoader.java

@@ -109,10 +109,13 @@ private String computeDatatype(String h) {
             return dt_config.get();
         } else {
             Optional<String> dt_counter = this.relationTypeCounter.computeTypeForRelation(h);
+            String explanation = this.relationTypeCounter.getExplanationForTyping(h);
             if(dt_counter.isPresent()) {
-                return dt_counter.get();
+                String dt = dt_counter.get();
+                log.info(h+ " relation was assigned to the '"+dt+"' datatype." );
+                log.info(explanation);
+                return dt;
             } else {
-                String explanation = this.relationTypeCounter.getExplanationForTyping(h);
                 log.warning("Cant decide datatype of annotation property. Ambiguous typing for "+h+": "+explanation);
             }
         }

src/main/java/ebi/spot/neo4j2owl/importer/N2OUtils.java

@@ -27,25 +27,14 @@ public class N2OUtils {
     private static  final OWLDataFactory df = OWLManager.getOWLDataFactory();
     private static final DLSyntaxObjectRenderer ren = new DLSyntaxObjectRenderer();
 
-    public static <T> T inTx(GraphDatabaseService db, Callable<T> callable) {
-        try {
-            return inTxFuture(DEFAULT, db, callable).get();
-        } catch (RuntimeException e) {
-            throw e;
-        } catch (Exception e) {
-            throw new RuntimeException("Error executing in separate transaction: "+e.getMessage(), e);
-        }
-    }
 
-    public static Set<String> getLabels(OWLEntity c, OWLOntology o) {
-        Set<String> labels = new HashSet();
-        Iterator var3 = EntitySearcher.getAnnotations(c, o, df.getRDFSLabel()).iterator();
+    static Set<String> getLabels(OWLEntity c, OWLOntology o) {
+        Set<String> labels = new HashSet<>();
 
-        while(var3.hasNext()) {
-            OWLAnnotation a = (OWLAnnotation)var3.next();
+        for (OWLAnnotation a : EntitySearcher.getAnnotations(c, o, df.getRDFSLabel())) {
             OWLAnnotationValue value = a.getValue();
             if (value instanceof OWLLiteral) {
-                String val = ((OWLLiteral)value).getLiteral();
+                String val = ((OWLLiteral) value).getLiteral();
                 labels.add(val);
             }
         }
@@ -70,6 +59,7 @@ public static Object extractValueFromOWLAnnotationValue(OWLAnnotationValue aval)
             } else {
                 return literal.getLiteral();
             }
+            // "xsd:long", literal.getDatatypePrefixedName()
         }
         return "neo4j2owl_UnknownValue";
     }
@@ -85,21 +75,6 @@ public static void writeToFile(File dir, Map<String, List<String>> dataout, Stri
         }
     }
 
-
-    public static <T> Future<T> inTxFuture(ExecutorService pool, GraphDatabaseService db, Callable<T> callable) {
-        try {
-            return pool.submit(() -> {
-                try (Transaction tx = db.beginTx()) {
-                    T result = callable.call();
-                    tx.success();
-                    return result;
-                }
-            });
-        } catch (Exception e) {
-            throw new RuntimeException("Error executing in separate transaction", e);
-        }
-    }
-
     public final static ExecutorService DEFAULT = createDefaultPool();
 
     public static ExecutorService createDefaultPool() {

src/main/java/ebi/spot/neo4j2owl/importer/RelationTypeCounter.java

@@ -49,10 +49,13 @@ String getExplanationForTyping(String rel) {
             Map<String, Integer> ctm = mapCounter.get(rel);
             int sum = ctm.values().stream().mapToInt(Integer::intValue).sum();
             if(sum>0) {
+                if(ctm.keySet().size()!=1) {
+                    s.append("STRONG WARNING: More than one type recorded, ambiguous typing! ");
+                }
                 for (String type : ctm.keySet()) {
                     Integer ct = ctm.get(type);
                     double d = ((double) ct) / sum;
-                    s.append(type).append(": ").append(ctm.get(type)).append(" (").append(String.format("%.2f", d)).append(");");
+                    s.append(type).append(": ").append(ctm.get(type)).append(" (").append(String.format("%.2f", d)).append("); ");
                 }
             } else {
                 s.append("No typing information recorded.");

src/test/java/ebi/spot/neo4j2owl/N2OProcedureTest.java

@@ -52,10 +52,10 @@ private void runSmallTest(String ontologyUrl, String configUrl) throws KernelExc
 
         Result importResult = db.execute(call);
         Map<String, Object> resMap = importResult.next();
-        assertEquals(28L, resMap.get("elementsLoaded"));
-        assertEquals(9L, resMap.get("classesLoaded"));
+        assertEquals(32L, resMap.get("elementsLoaded"));
+        assertEquals(12L, resMap.get("classesLoaded"));
         assertEquals("", resMap.get("extraInfo"));
-        assertEquals(9L, db.execute("MATCH (n:Class) RETURN count(n) AS count").next().get("count"));
+        assertEquals(12L, db.execute("MATCH (n:Class) RETURN count(n) AS count").next().get("count"));
         db.shutdown();
     }
 
@@ -93,10 +93,10 @@ public void owl2Export() throws Exception {
         Result exportResult = db.execute("CALL ebi.spot.neo4j2owl.exportOWL()");
         Map<String,Object> resMapExport = exportResult.next();
 
-        assertEquals(28L, resMap.get("elementsLoaded"));
-        assertEquals(9L, resMap.get("classesLoaded"));
+        assertEquals(32L, resMap.get("elementsLoaded"));
+        assertEquals(12L, resMap.get("classesLoaded"));
         assertEquals("", resMap.get("extraInfo"));
-        assertEquals(9L, db.execute("MATCH (n:Class) RETURN count(n) AS count").next().get("count"));
+        assertEquals(12L, db.execute("MATCH (n:Class) RETURN count(n) AS count").next().get("count"));
 
         String ontologyString = (String)resMapExport.get("o");
         OWLOntologyManager man1 = OWLManager.createOWLOntologyManager();