In preparation for Spring Boot 2.2.6:

Replaced System.out println and logger.info with logger.debug. Updated org.mousephenotype.cda.db.utilities.H2Function Updated org.springframework.data.domain.PageRequest.PageRequest (constructor changed) Replaced org.springframework.hateoas Resources class with CollectionModel Replaced org.springframework.hateoas.hal.Jackson2HalModule with org.springframework.hateoas.mediatype.hal.Jackson2HalModule
mpi2 · Apr 22, 2020 · 0046b82 · 0046b82
1 parent be2c233
commit 0046b82
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Showing 8 changed files with 21 additions and 19 deletions.
diff --git a/data-model-db/src/test/java/org/mousephenotype/cda/db/utilities/H2Function.java b/data-model-db/src/test/java/org/mousephenotype/cda/db/utilities/H2Function.java
@@ -24,7 +24,7 @@ public class H2Function {
     @SuppressWarnings("rawtypes")
     public static int removeDateDifference() {
         try {
-            Field field = Function.class.getDeclaredField("FUNCTIONS");
+            Field field = Function.class.getDeclaredField("FUNCTIONS_BY_NAME");
             field.setAccessible(true);
             ((Map)field.get(null)).remove("DATEDIFF");
         } catch (Exception e) {
@@ -38,4 +38,4 @@ public static long dateDifference(Date date1, Date date2) {
         Objects.nonNull(date2);
         return ChronoUnit.DAYS.between(date1.toLocalDate(), date2.toLocalDate());
     }
-}
+}
diff --git a/data-model-db/src/test/java/org/mousephenotype/cda/db/utilities/ImpressUtilsTest.java b/data-model-db/src/test/java/org/mousephenotype/cda/db/utilities/ImpressUtilsTest.java
@@ -28,6 +28,7 @@
 import org.mousephenotype.cda.db.pojo.Parameter;
 import org.mousephenotype.cda.db.repositories.ParameterRepository;
 import org.mousephenotype.cda.enumerations.ObservationType;
+import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.ApplicationContext;
@@ -49,7 +50,7 @@
 @ContextConfiguration(classes = {UtilitiesTestConfig.class})
 public class ImpressUtilsTest {
 
-    private final org.slf4j.Logger logger = LoggerFactory.getLogger(this.getClass());
+    private final Logger logger = LoggerFactory.getLogger(this.getClass());
 
     @Autowired
     private ApplicationContext context;

diff --git a/data-model/src/test/java/org/mousephenotype/cda/utilities/DateUtilsTest.java b/data-model/src/test/java/org/mousephenotype/cda/utilities/DateUtilsTest.java
@@ -95,12 +95,11 @@ public void testZonedDateTimeParsingWithMilliseconds() {
                 new DateExpectedOutput("2012-12-12T12:12:01.123", "2012-12-12T12:12:01.123Z[UTC]"),
                 new DateExpectedOutput("2012-12-12 12:12:01.123Z", "2012-12-12T12:12:01.123Z[UTC]"),
                 new DateExpectedOutput("2012-12-12T 12:12:01.123Z", "2012-12-12T12:12:01.123Z[UTC]")
-
         );
 
         for (DateExpectedOutput input : inputs) {
 
-            System.out.println("Testing Date format: " + input.dateString);
+            logger.debug("Testing Date format: " + input.dateString);
 
             ZonedDateTime actualDate =
                     ZonedDateTime.parse(input.dateString,
@@ -109,4 +108,4 @@ public void testZonedDateTimeParsingWithMilliseconds() {
             assertEquals(input.expectedDate, actualDate.toString());
         }
     }
-}
+}
diff --git a/dependencies/pom.xml b/dependencies/pom.xml
@@ -19,8 +19,7 @@
     <parent>
         <groupId>org.springframework.boot</groupId>
         <artifactId>spring-boot-starter-parent</artifactId>
-        <version>2.1.8.RELEASE</version>
-<!--        <version>2.2.6.RELEASE</version>-->
+        <version>2.2.6.RELEASE</version>
         <relativePath />
         <!-- lookup parent from repository -->
     </parent>

diff --git a/...rc/test/java/org/mousephenotype/cda/loads/common/SeriesParameterObservationUtilsTest.java b/...rc/test/java/org/mousephenotype/cda/loads/common/SeriesParameterObservationUtilsTest.java
@@ -20,6 +20,8 @@
 import org.junit.Test;
 import org.junit.runner.RunWith;
 import org.mousephenotype.dcc.exportlibrary.datastructure.core.procedure.ProcedureMetadata;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.boot.test.context.SpringBootTest;
 import org.springframework.test.context.junit4.SpringRunner;
 
@@ -35,6 +37,8 @@
 @SpringBootTest(classes = SeriesParameterObservationUtilsTestConfig.class)
 public class SeriesParameterObservationUtilsTest extends TestCase {
 
+	private final Logger logger = LoggerFactory.getLogger(this.getClass());
+
 	private SeriesParameterObservationUtils utils;
 
     @PostConstruct
@@ -69,7 +73,7 @@ public void testTimeStringParsing() {
 
    		for (String value : variousTimeValues) {
 
-   			System.out.println("Testing date format: " + value);
+   			logger.debug("Testing date format: " + value);
 
    			String testDateString = utils.getParsedIncrementValue(value);
    			assertTrue(testDateString.equals(finalDateString));

diff --git a/web/src/main/java/uk/ac/ebi/phenotype/service/RestConfiguration.java b/web/src/main/java/uk/ac/ebi/phenotype/service/RestConfiguration.java
@@ -1,16 +1,16 @@
 package uk.ac.ebi.phenotype.service;
-import java.util.Arrays;
 
+import com.fasterxml.jackson.databind.DeserializationFeature;
+import com.fasterxml.jackson.databind.ObjectMapper;
 import org.springframework.boot.web.client.RestTemplateBuilder;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.hateoas.MediaTypes;
-import org.springframework.hateoas.hal.Jackson2HalModule;
+import org.springframework.hateoas.mediatype.hal.Jackson2HalModule;
 import org.springframework.http.converter.json.MappingJackson2HttpMessageConverter;
 import org.springframework.web.client.RestTemplate;
 
-import com.fasterxml.jackson.databind.DeserializationFeature;
-import com.fasterxml.jackson.databind.ObjectMapper;
+import java.util.Arrays;
 
 @Configuration
 public class RestConfiguration {

diff --git a/web/src/main/java/uk/ac/ebi/phenotype/stats/model/StatsResources.java b/web/src/main/java/uk/ac/ebi/phenotype/stats/model/StatsResources.java
@@ -1,13 +1,11 @@
 package uk.ac.ebi.phenotype.stats.model;
 
+import org.springframework.hateoas.CollectionModel;
+
 import java.util.ArrayList;
 import java.util.List;
 
-import org.springframework.hateoas.Resources;
-
-import uk.ac.ebi.phenotype.stats.model.Statistics;
-
-public class StatsResources extends Resources<Statistics> {
+public class StatsResources extends CollectionModel<Statistics> {
 
 private List<Statistics> stats;
 

diff --git a/web/src/main/java/uk/ac/ebi/phenotype/web/dao/ReferenceServiceImpl.java b/web/src/main/java/uk/ac/ebi/phenotype/web/dao/ReferenceServiceImpl.java
@@ -157,6 +157,7 @@ private PageRequest getPageRequest(int start, int length, String orderBy, String
         Sort.Direction direction = Sort.Direction.DESC;
         if(sortOrder.equals("ASC"))
             direction = Sort.Direction.ASC;
-        return new PageRequest(page, length, direction, orderBy);
+
+        return PageRequest.of(page, length, direction, orderBy);
     }
 }