Merge pull request #173 from MORE-Platform/develop

Merge develop branch into main pull request
MORE-Platform · Oct 14, 2024 · 8dc5fa7 · 8dc5fa7
2 parents 24969ed + 82a43a1
commit 8dc5fa7
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diff --git a/.github/workflows/compile-test.yml b/.github/workflows/compile-test.yml
@@ -14,7 +14,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Set up JDK 17
-        uses: actions/setup-java@v3
+        uses: actions/setup-java@v4
         with:
           distribution: 'temurin'
           java-version: 17
@@ -47,7 +47,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Set up JDK 17
-        uses: actions/setup-java@v3
+        uses: actions/setup-java@v4
         with:
           distribution: 'temurin'
           java-version: 17

diff --git a/pom.xml b/pom.xml
@@ -27,8 +27,8 @@
         <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
 
         <java.version>17</java.version>
-        <spring-boot.version>3.3.1</spring-boot.version>
-        <testcontainers.version>1.19.8</testcontainers.version>
+        <spring-boot.version>3.3.4</spring-boot.version>
+        <testcontainers.version>1.20.2</testcontainers.version>
 
         <docker.namespace>more-project</docker.namespace>
 
@@ -104,7 +104,7 @@
         <dependency>
             <groupId>io.swagger.core.v3</groupId>
             <artifactId>swagger-annotations</artifactId>
-            <version>2.2.22</version>
+            <version>2.2.25</version>
         </dependency>
         <dependency>
             <groupId>jakarta.validation</groupId>
@@ -124,7 +124,7 @@
         <dependency>
             <groupId>co.elastic.clients</groupId>
             <artifactId>elasticsearch-java</artifactId>
-            <version>8.13.4</version>
+            <version>8.14.3</version>
         </dependency>
         <dependency>
             <groupId>com.fasterxml.jackson.core</groupId>
@@ -140,7 +140,7 @@
         <dependency>
             <groupId>net.logstash.logback</groupId>
             <artifactId>logstash-logback-encoder</artifactId>
-            <version>7.4</version>
+            <version>8.0</version>
             <scope>runtime</scope>
         </dependency>
 
@@ -228,7 +228,7 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-surefire-plugin</artifactId>
-                <version>3.2.5</version>
+                <version>3.3.1</version>
             </plugin>
             <plugin>
                 <groupId>org.springframework.boot</groupId>
@@ -315,7 +315,7 @@
             <plugin>
                 <groupId>org.openapitools</groupId>
                 <artifactId>openapi-generator-maven-plugin</artifactId>
-                <version>6.6.0</version>
+                <version>7.7.0</version>
                 <executions>
                     <execution>
                         <id>data-api</id>
@@ -360,6 +360,19 @@
                     <generateModelTests>false</generateModelTests>
                     <generateSupportingFiles>false</generateSupportingFiles>
 
+                    <typeMappings>
+                        <typeMapping>string+date-time=Instant</typeMapping>
+                        <typeMapping>string+time=LocalTime</typeMapping>
+                    </typeMappings>
+                    <schemaMappings>
+                        <schemaMapping>Instant=java.time.Instant</schemaMapping>
+                        <schemaMapping>LocalTime=java.time.LocalTime</schemaMapping>
+                    </schemaMappings>
+                    <importMappings>
+                        <importMapping>Instant=java.time.Instant</importMapping>
+                        <importMapping>LocalTime=java.time.LocalTime</importMapping>
+                    </importMappings>
+
                     <configOptions>
                         <useSpringBoot3>true</useSpringBoot3>
                         <sourceFolder>src</sourceFolder>
@@ -368,6 +381,7 @@
                         <useTags>true</useTags>
                         <openApiNullable>false</openApiNullable>
                         <skipDefaultInterface>true</skipDefaultInterface>
+                        <requestMappingMode>api_interface</requestMappingMode>
                     </configOptions>
                 </configuration>
             </plugin>

diff --git a/src/main/java/io/redlink/more/data/controller/ExternalDataApiV1Controller.java b/src/main/java/io/redlink/more/data/controller/ExternalDataApiV1Controller.java
@@ -68,8 +68,8 @@ public ResponseEntity<Void> storeExternalBulk(String moreApiToken, EndpointDataB
             Interval interval = externalService.getIntervalForObservation(apiRoutingInfo.studyId(), apiRoutingInfo.observationId(), participantId);
 
             endpointDataBulkDTO.getDataPoints().stream()
-                .map(datapoint -> datapoint.getTimestamp().toInstant())
-                .map(timestamp -> timestamp.isBefore(interval.getStart()) || timestamp.isAfter(interval.getEnd()))
+                .map(ExternalDataDTO::getTimestamp)
+                .map(timestamp -> !(timestamp.isBefore(interval.getStart()) || timestamp.isAfter(interval.getEnd())))
                 .filter(v -> v)
                 .findFirst()
                 .orElseThrow(BadRequestException::TimeFrame);

diff --git a/src/main/java/io/redlink/more/data/controller/transformer/BaseTransformers.java b/src/main/java/io/redlink/more/data/controller/transformer/BaseTransformers.java
@@ -4,8 +4,6 @@
 package io.redlink.more.data.controller.transformer;
 
 import java.time.Instant;
-import java.time.OffsetDateTime;
-import java.time.ZoneOffset;
 
 public final class BaseTransformers {
 
@@ -16,14 +14,4 @@ public static Long toVersionTag(Instant modified) {
         return modified.toEpochMilli();
     }
 
-    public static Instant toInstant(OffsetDateTime dateTime) {
-        if (dateTime == null)
-            return null;
-        return dateTime.toInstant();
-    }
-
-    public static OffsetDateTime toOffsetDateTime(Instant instant) {
-        if (instant == null) return null;
-        return instant.atOffset(ZoneOffset.UTC);
-    }
 }
diff --git a/src/main/java/io/redlink/more/data/controller/transformer/DataTransformer.java b/src/main/java/io/redlink/more/data/controller/transformer/DataTransformer.java
@@ -26,13 +26,14 @@ public static List<DataPoint> createDataPoints(DataBulkDTO bulk) {
     }
 
     public static DataPoint createDataPoint(ObservationDataDTO dataPoint, Instant recordingTime) {
+        Instant dateTime = dataPoint.getTimestamp();
         return new DataPoint(
                 dataPoint.getDataId(),
                 dataPoint.getObservationId(),
                 dataPoint.getObservationType(),
                 dataPoint.getObservationType(),
                 recordingTime,
-                BaseTransformers.toInstant(dataPoint.getTimestamp()),
+                dateTime,
                 dataPoint.getDataValue());
     }
 
@@ -44,13 +45,14 @@ public static List<DataPoint> createDataPoints(EndpointDataBulkDTO bulk, ApiRout
     }
 
     public static DataPoint createDataPoint(ExternalDataDTO dataPoint, ApiRoutingInfo routingInfo, Instant recordingTime, Integer observationId) {
+        Instant dateTime = dataPoint.getTimestamp();
         return new DataPoint(
                 UUID.randomUUID().toString(),
                 observationId.toString(),
                 routingInfo.observationType(),
                 routingInfo.observationType(),
                 recordingTime,
-                BaseTransformers.toInstant(dataPoint.getTimestamp()),
+                dateTime,
                 dataPoint.getDataValue());
     }
 }
diff --git a/src/main/java/io/redlink/more/data/controller/transformer/ParticipantTransformer.java b/src/main/java/io/redlink/more/data/controller/transformer/ParticipantTransformer.java
@@ -18,7 +18,7 @@ public static ParticipantDTO toDTO(Participant participant) {
                 participant.alias(),
                 ParticipantStatusDTO.fromValue(participant.status()),
                 toGroupDto(participant),
-                BaseTransformers.toOffsetDateTime(participant.start())
+                participant.start()
         );
     }
 

diff --git a/src/main/java/io/redlink/more/data/controller/transformer/StudyTransformer.java b/src/main/java/io/redlink/more/data/controller/transformer/StudyTransformer.java
@@ -84,9 +84,11 @@ public static ObservationDTO toDTO(Observation observation, Instant start, Insta
     }
 
     public static ObservationScheduleDTO toObservationScheduleDTO(Range<Instant> schedule) {
+        Instant instant = schedule.getMaximum();
+        Instant instant1 = schedule.getMinimum();
         return new ObservationScheduleDTO()
-                .start(BaseTransformers.toOffsetDateTime(schedule.getMinimum()))
-                .end(BaseTransformers.toOffsetDateTime(schedule.getMaximum()))
+                .start(instant1)
+                .end(instant)
                 ;
     }
 

diff --git a/src/main/java/io/redlink/more/data/repository/NotificationRepository.java b/src/main/java/io/redlink/more/data/repository/NotificationRepository.java
@@ -11,16 +11,17 @@
 import com.fasterxml.jackson.core.JsonProcessingException;
 import com.fasterxml.jackson.databind.ObjectMapper;
 import io.redlink.more.data.api.app.v1.model.PushNotificationDTO;
+import java.sql.ResultSet;
+import java.sql.SQLException;
+import java.sql.Timestamp;
+import java.time.Instant;
+import java.util.List;
+import java.util.Map;
+import java.util.Optional;
 import org.springframework.jdbc.core.RowMapper;
 import org.springframework.jdbc.core.namedparam.NamedParameterJdbcTemplate;
 import org.springframework.stereotype.Component;
 
-import java.sql.ResultSet;
-import java.sql.SQLException;
-import java.time.OffsetDateTime;
-import java.time.ZoneOffset;
-import java.util.*;
-
 @Component
 public class NotificationRepository {
 
@@ -68,10 +69,10 @@ private static RowMapper<PushNotificationDTO> getRowMapper() {
         };
     }
 
-    private static OffsetDateTime getTimestamp(ResultSet rs) {
+    private static Instant getTimestamp(ResultSet rs) {
         try {
             return Optional.ofNullable(rs.getTimestamp("timestamp"))
-                    .map(d -> d.toInstant().atOffset(ZoneOffset.UTC))
+                    .map(Timestamp::toInstant)
                     .orElse(null);
         } catch (SQLException e) {
             return null;