Cleaning up diagnostic output.

Author: piotrszul

fhir-server/src/main/java/au/csiro/pathling/aggregate/AggregateExecutor.java

@@ -73,9 +73,6 @@ public AggregateExecutor(@Nonnull final QueryConfiguration configuration,
   public AggregateResponse execute(@Nonnull final AggregateRequest query) {
     final ResultWithExpressions resultWithExpressions = buildQuery(
         query);
-    resultWithExpressions.getDataset().explain();
-    resultWithExpressions.getDataset().show(1_000, false);
-
     // Translate the result into a response object to be passed back to the user.
     return buildResponse(resultWithExpressions);
   }
@@ -105,8 +102,8 @@ private AggregateResponse buildResponse(
   @Nonnull
   @SuppressWarnings("unchecked")
   private Function<Row, AggregateResponse.Grouping> mapRowToGrouping(
-          @Nonnull final List<EvaluatedPath> aggregations, @Nonnull final List<EvaluatedPath> groupings,
-          @Nonnull final List<EvaluatedPath> filters) {
+      @Nonnull final List<EvaluatedPath> aggregations, @Nonnull final List<EvaluatedPath> groupings,
+      @Nonnull final List<EvaluatedPath> filters) {
     return row -> {
       final List<Optional<Type>> labels = new ArrayList<>();
       final List<Optional<Type>> results = new ArrayList<>();

fhir-server/src/main/java/au/csiro/pathling/search/SearchExecutor.java

@@ -230,8 +230,6 @@ public List<IBaseResource> getResources(final int theFromIndex, final int theToI
         .of(subjectResource.toCode());
     requireNonNull(encoder);
     reportQueryPlan(resources);
-    resources.explain();
-
     return resources.as(encoder).collectAsList();
   }
 

fhir-server/src/test/java/au/csiro/pathling/aggregate/AggregateQueryExecutorTest.java

@@ -99,7 +99,6 @@ void simpleQueryWithLabels() {
     assertArrayEquals(new String[]{"patient_gender", "patient_count"},
         result.columns());
     assertThat(result)
-        .debugAllRows()
         .hasRows(spark, "responses/AggregateQueryExecutorTest/simpleQuery.tsv");
   }
 
@@ -116,7 +115,6 @@ void simpleQueryWithNoLabels() {
     final Dataset<Row> result = executor.buildQuery(request).getDataset();
     //assertTrue(Stream.of(result.columns()).allMatch(Strings::looksLikeAlias));
     assertThat(result)
-        .debugAllRows()
         .hasRows(spark, "responses/AggregateQueryExecutorTest/simpleQuery.tsv");
   }
 

fhir-server/src/test/java/au/csiro/pathling/extract/ExtractQueryTest.java

@@ -169,7 +169,6 @@ void multiplePolymorphicResolves() {
 
     final Dataset<Row> result = executor.buildQuery(request, ProjectionConstraint.FLAT);
     assertThat(result)
-        .debugAllRows()
         .hasRows(spark, "responses/ExtractQueryTest/multiplePolymorphicResolves.tsv");
   }
 
@@ -469,7 +468,6 @@ void structuredResult() {
     );
 
     assertThat(result)
-        .debugAllRows()
         .hasRows(spark, "responses/ExtractQueryTest/structuredResult.tsv");
   }
 

fhir-server/src/test/java/au/csiro/pathling/fhirpath/parser/ParserTest.java

@@ -589,7 +589,6 @@ void testDesignationFunctionWithNoLanguage() {
     assertThatResultOf(ResourceType.CONDITION,
         "code.coding.designation(http://terminology.hl7.org/CodeSystem/designation-usage|display)")
         .selectOrderedResult()
-        .debugAllRows()
         .hasRows(spark, "responses/ParserTest/testDesignationFunctionWithNoLanguage.tsv");
   }
 

fhir-server/src/test/resources/logback-test.xml

@@ -22,7 +22,7 @@
       <pattern>[%level] %logger{36} - %msg%n</pattern>
     </encoder>
   </appender>
-  <logger level="DEBUG" name="au.csiro"/>
+  <logger level="INFO" name="au.csiro"/>
   <logger level="ERROR" name="org.apache.hadoop.metrics2"/>
   <logger level="ERROR" name="org.apache.spark.sql.execution.CacheManager"/>
   <logger level="ERROR" name="org.apache.spark.sql.catalyst.util.SparkStringUtils"/>

fhirpath/src/main/java/au/csiro/pathling/fhirpath/execution/DataRootResolver.java

@@ -23,9 +23,11 @@
 import java.util.stream.Collectors;
 import java.util.stream.Stream;
 import lombok.Value;
+import lombok.extern.slf4j.Slf4j;
 import org.hl7.fhir.r4.model.Enumerations.ResourceType;
 
 @Value
+@Slf4j
 public class DataRootResolver {
 
   ResourceType subjectResource;
@@ -108,7 +110,7 @@ public void collectDataRoots(@Nonnull final DataRoot currentRoot,
       }
     } else if (headPath instanceof Paths.ExternalConstantPath ecp) {
       // we do not need to do anything here
-      System.out.println("External constant path" + ecp);
+      log.debug("External constant path: {}", ecp);
       if ("resource".equals(ecp.getName()) || "rootResource".equals(ecp.getName())) {
         // this root should already be addded here
         collectDataRoots(ResourceRoot.of(subjectResource), fhirPath.suffix(), FhirPath.nullPath(),

fhirpath/src/main/java/au/csiro/pathling/fhirpath/function/provider/ResolverFunctions.java

@@ -28,9 +28,7 @@ public static ResourceCollection reverseResolve(@Nonnull final ResourceCollectio
     final ReverseResolveRoot root = ReverseResolveRoot.ofResource(input.getResourceType(),
         childResourceType, childPath);
 
-    log.info("Reverse resolve root: {}", root);
-    System.out.println("Reverse resolve root: " + root);
-
+    log.debug("Reverse resolve root: {}", root);
     return evaluationContext.resolveReverseJoin(input, subjectPath.toExpression());
   }
 

fhirpath/src/test/java/au/csiro/pathling/extract/ExtractTest.java

@@ -64,8 +64,6 @@ void simple() {
         ), Collections.emptyList(), Optional.empty());
 
     final Dataset<Row> result = executor.buildQuery(request);
-    result.show();
-
     final Dataset<Row> expected = DatasetBuilder.of(spark)
         .withColumn("id", DataTypes.StringType)
         .withColumn("given_name", DataTypes.StringType)

fhirpath/src/test/java/au/csiro/pathling/fhirpath/column/DefaultRepresentationTest.java

@@ -66,7 +66,6 @@ void check() {
       for (int i = 0; i < result.size(); i++) {
         assertTrue(result.getBoolean(i), "Test " + i + " failed: " + tests.get(i));
       }
-      System.out.println(result);
     }
   }
 
@@ -116,13 +115,6 @@ void testSingular() {
         .assertEquals(13, valueOf(13).singular())
         .assertEquals("a", arrayOfOne("a").singular())
         .check();
-
-    // final SparkException ex = assertThrows(SparkException.class, () ->
-    //     spark.range(1).select(
-    //         ColumnHelpers.singular(functions.array(functions.lit("a"), functions.lit("b")))
-    //     ).collect());
-    // System.out.println(ex.getCause().getMessage());
-
   }
 
   @Test