Merge Staging into Main branch

.github/workflows/compile-test.yml

@@ -1,6 +1,10 @@
 name: Test and Compile
 on:
   workflow_dispatch:
+    inputs:
+      dockerTag:
+        description: If set, docker img is built and tagged accordingly
+        required: false
   push:
 
 jobs:
@@ -37,7 +41,7 @@ jobs:
   Build-and-Deploy:
     name: "Build and Push Docker Image"
     runs-on: ubuntu-latest
-    if: github.ref_name == 'main'
+    if: contains(fromJSON('["main", "develop", "redlink", "staging"]'), github.ref_name) || github.event.inputs.dockerTag != ''
     needs:
       - Compile-and-Test
     steps:
@@ -47,18 +51,34 @@ jobs:
         with:
           distribution: 'temurin'
           java-version: 17
+      - name: Generate additional Docker-Tags
+        run: |
+          TAGS=${BRANCH}
+          if [ "$BRANCH" == "$MAIN_BRANCH" ]; then
+            TAGS="latest,$TAGS"
+          fi
+          if [ -n "$EVENT_PARAM" ]; then
+            TAGS="$EVENT_PARAM"
+          fi
+          echo "Generated Docker-Tags: $TAGS"
+          echo "TAGS=$TAGS" >> "$GITHUB_ENV"
+        env:
+          BRANCH: ${{ github.ref_name }}
+          MAIN_BRANCH: ${{ github.event.repository.default_branch }}
+          EVENT_PARAM: ${{ github.event.inputs.dockerTag }}
       - name: Build JIB container and publish to GitHub Packages
-        run: ./mvnw -B -U
-          --no-transfer-progress
-          clean verify jib:build
-          -Drevision=${{github.run_number}}
-          -Dchangelist=
-          -Dsha1=.${GITHUB_SHA:0:7}
-          -Dquick
-          -Ddocker.namespace=${DOCKER_NAMESPACE,,}
-          -Djib.to.tags=latest
-          -Djib.to.auth.username=${{ github.actor }}
-          -Djib.to.auth.password=${{ secrets.GITHUB_TOKEN }}
+        run:
+          ./mvnw -B -U
+            --no-transfer-progress
+            clean verify jib:build
+            -Drevision=${{github.run_number}}
+            -Dchangelist=
+            -Dsha1=.${GITHUB_SHA:0:7}
+            -Dquick
+            -Ddocker.namespace=${DOCKER_NAMESPACE,,}
+            -Djib.to.tags=${TAGS}
+            -Djib.to.auth.username=${{ github.actor }}
+            -Djib.to.auth.password=${{ secrets.GITHUB_TOKEN }}
         env:
           DOCKER_NAMESPACE: ghcr.io/${{ github.repository_owner }}
 
@@ -70,4 +90,4 @@ jobs:
         uses: actions/upload-artifact@v4
         with:
           name: Event File
-          path: ${{ github.event_path }}
+          path: ${{ github.event_path }}

pom.xml

@@ -27,8 +27,8 @@
         <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
 
         <java.version>17</java.version>
-        <spring-boot.version>3.1.2</spring-boot.version>
-        <testcontainers.version>1.19.0</testcontainers.version>
+        <spring-boot.version>3.3.1</spring-boot.version>
+        <testcontainers.version>1.19.8</testcontainers.version>
 
         <docker.namespace>more-project</docker.namespace>
 
@@ -74,14 +74,20 @@
             <artifactId>spring-boot-starter-actuator</artifactId>
         </dependency>
 
+        <!-- Cache -->
+        <dependency>
+            <groupId>org.springframework.boot</groupId>
+            <artifactId>spring-boot-starter-cache</artifactId>
+        </dependency>
+
         <!-- Persistence -->
         <dependency>
             <groupId>org.springframework.boot</groupId>
             <artifactId>spring-boot-starter-data-jdbc</artifactId>
         </dependency>
         <dependency>
             <groupId>org.flywaydb</groupId>
-            <artifactId>flyway-core</artifactId>
+            <artifactId>flyway-database-postgresql</artifactId>
         </dependency>
         <dependency>
             <groupId>org.postgresql</groupId>
@@ -98,7 +104,7 @@
         <dependency>
             <groupId>io.swagger.core.v3</groupId>
             <artifactId>swagger-annotations</artifactId>
-            <version>2.2.16</version>
+            <version>2.2.22</version>
         </dependency>
         <dependency>
             <groupId>jakarta.validation</groupId>
@@ -112,13 +118,13 @@
         <dependency>
             <groupId>net.sf.biweekly</groupId>
             <artifactId>biweekly</artifactId>
-            <version>0.6.7</version>
+            <version>0.6.8</version>
         </dependency>
 
         <dependency>
             <groupId>co.elastic.clients</groupId>
             <artifactId>elasticsearch-java</artifactId>
-            <version>8.10.2</version>
+            <version>8.13.4</version>
         </dependency>
         <dependency>
             <groupId>com.fasterxml.jackson.core</groupId>
@@ -127,7 +133,7 @@
         <dependency>
             <groupId>jakarta.json</groupId>
             <artifactId>jakarta.json-api</artifactId>
-            <version>2.1.2</version>
+            <version>2.1.3</version>
         </dependency>
 
         <!-- Logging -->
@@ -205,12 +211,12 @@
             <plugin>
                 <groupId>org.codehaus.mojo</groupId>
                 <artifactId>flatten-maven-plugin</artifactId>
-                <version>1.5.0</version>
+                <version>1.6.0</version>
             </plugin>
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-compiler-plugin</artifactId>
-                <version>3.11.0</version>
+                <version>3.13.0</version>
                 <configuration>
                     <source>${java.version}</source>
                     <target>${java.version}</target>
@@ -222,7 +228,7 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-surefire-plugin</artifactId>
-                <version>3.1.2</version>
+                <version>3.2.5</version>
             </plugin>
             <plugin>
                 <groupId>org.springframework.boot</groupId>
@@ -241,7 +247,7 @@
             <plugin>
                 <groupId>com.google.cloud.tools</groupId>
                 <artifactId>jib-maven-plugin</artifactId>
-                <version>3.3.2</version>
+                <version>3.4.3</version>
                 <executions>
                     <execution>
                         <id>jib-deploy</id>
@@ -375,7 +381,7 @@
                 <plugin>
                     <groupId>org.codehaus.mojo</groupId>
                     <artifactId>license-maven-plugin</artifactId>
-                    <version>2.2.0</version>
+                    <version>2.4.0</version>
                     <executions>
                         <execution>
                             <id>generate-third-party</id>

src/main/java/io/redlink/more/data/configuration/CachingConfiguration.java

@@ -0,0 +1,31 @@
+package io.redlink.more.data.configuration;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.cache.CacheManager;
+import org.springframework.cache.annotation.CacheEvict;
+import org.springframework.cache.annotation.EnableCaching;
+import org.springframework.cache.concurrent.ConcurrentMapCacheManager;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.scheduling.annotation.EnableScheduling;
+import org.springframework.scheduling.annotation.Scheduled;
+
+@Configuration
+@EnableCaching
+@EnableScheduling
+public class CachingConfiguration {
+
+    public static final String OBSERVATION_ENDINGS = "observationEndings";
+    private static final Logger LOGGER = LoggerFactory.getLogger(CachingConfiguration.class);
+    @Bean
+    public CacheManager cacheManager() {
+        return new ConcurrentMapCacheManager(OBSERVATION_ENDINGS);
+    }
+
+    @CacheEvict(allEntries = true, value = {OBSERVATION_ENDINGS})
+    @Scheduled(fixedDelay = 60 * 60 * 1000 ,  initialDelay = 5000)
+    public void reportCacheEvict() {
+        LOGGER.info("Flush Cache");
+    }
+}

src/main/java/io/redlink/more/data/configuration/SecurityConfig.java

@@ -58,6 +58,10 @@ public SecurityFilterChain filterChain(HttpSecurity http,
                     //External Data Gateway
                     req.requestMatchers("/api/v1/external/bulk")
                             .permitAll();
+                    req.requestMatchers("/api/v1/external/participants")
+                            .permitAll();
+                    req.requestMatchers("/api/v1/calendar/studies/*/calendar.ics")
+                            .permitAll();
                     // all other apis require credentials
                     req.requestMatchers("/api/v1/**")
                             .authenticated();
@@ -105,4 +109,4 @@ protected RequestRejectedHandler requestRejectedHandler() {
         return new HttpStatusRequestRejectedHandler(HttpStatus.I_AM_A_TEAPOT.value());
     }
 
-}
+}

src/main/java/io/redlink/more/data/controller/CalendarApiV1Controller.java

@@ -0,0 +1,28 @@
+package io.redlink.more.data.controller;
+
+import io.redlink.more.data.api.app.v1.webservices.CalendarApi;
+import io.redlink.more.data.service.CalendarService;
+import org.springframework.http.MediaType;
+import org.springframework.http.ResponseEntity;
+import org.springframework.stereotype.Controller;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RestController;
+
+@Controller
+@RestController
+@RequestMapping(value = "/api/v1", produces = MediaType.APPLICATION_JSON_VALUE)
+public class CalendarApiV1Controller implements CalendarApi {
+
+    private final CalendarService calendarService;
+
+    public CalendarApiV1Controller(CalendarService calendarService) {
+        this.calendarService = calendarService;
+    }
+
+    @Override
+    public ResponseEntity<String> getStudyCalendar(Long studyId) {
+        return ResponseEntity.of(
+                this.calendarService.getICalendarString(studyId)
+        );
+    }
+}

src/main/java/io/redlink/more/data/controller/DataApiV1Controller.java

@@ -56,16 +56,16 @@ public ResponseEntity<List<String>> storeBulk(DataBulkDTO dataBulkDTO) {
 
         final RoutingInfo routingInfo = userDetails.getRoutingInfo();
         try (LoggingUtils.LoggingContext ctx = LoggingUtils.createContext(userDetails.getRoutingInfo())) {
-            if (routingInfo.studyActive()) {
+            if (routingInfo.acceptData()) {
                 final List<String> storedIDs = elasticService.storeDataPoints(
                         DataTransformer.createDataPoints(dataBulkDTO), routingInfo);
                 return ResponseEntity.ok(storedIDs);
             } else {
                 final List<String> discardedIDs = dataBulkDTO.getDataPoints().stream()
                         .map(ObservationDataDTO::getDataId)
                         .toList();
-                LOG.info("Discarding {} observations because study_{} is not 'active'",
-                        discardedIDs.size(), routingInfo.studyId());
+                LOG.info("Discarding {} observations because study_{} or participant_{} is not 'active'",
+                        discardedIDs.size(), routingInfo.studyId(), routingInfo.participantId());
                 return ResponseEntity.ok(
                         discardedIDs
                 );

src/main/java/io/redlink/more/data/controller/ExternalDataApiV1Controller.java

@@ -10,10 +10,14 @@
 
 import io.redlink.more.data.api.app.v1.model.EndpointDataBulkDTO;
 import io.redlink.more.data.api.app.v1.model.ExternalDataDTO;
+import io.redlink.more.data.api.app.v1.model.ParticipantDTO;
 import io.redlink.more.data.api.app.v1.webservices.ExternalDataApi;
 import io.redlink.more.data.controller.transformer.DataTransformer;
+import io.redlink.more.data.controller.transformer.ParticipantTransformer;
+import io.redlink.more.data.exception.BadRequestException;
 import io.redlink.more.data.model.ApiRoutingInfo;
 import io.redlink.more.data.model.RoutingInfo;
+import io.redlink.more.data.model.scheduler.Interval;
 import io.redlink.more.data.service.ElasticService;
 import io.redlink.more.data.service.ExternalService;
 import io.redlink.more.data.util.LoggingUtils;
@@ -25,15 +29,14 @@
 import org.springframework.web.bind.annotation.RequestMapping;
 import org.springframework.web.bind.annotation.RestController;
 
-import java.util.Base64;
 import java.util.List;
-import java.util.Optional;
 
 @RestController
 @RequestMapping(value = "/api/v1", produces = MediaType.APPLICATION_JSON_VALUE)
 public class ExternalDataApiV1Controller implements ExternalDataApi {
 
-    private static final Logger LOG = LoggerFactory.getLogger(DataApiV1Controller.class);
+    private static final Logger LOG = LoggerFactory.getLogger(ExternalDataApiV1Controller.class);
+
     private final ExternalService externalService;
     private final ElasticService elasticService;
 
@@ -43,45 +46,45 @@ public ExternalDataApiV1Controller(ExternalService externalService, ElasticServi
     }
 
     @Override
-    public ResponseEntity<Void> storeExternalBulk(String moreApiToken, EndpointDataBulkDTO endpointDataBulkDTO) {
+    public ResponseEntity<List<ParticipantDTO>> listParticipants(String moreApiToken) {
         try {
-            String[] split = moreApiToken.split("\\.");
-            String[] primaryKey = new String(Base64.getDecoder().decode(split[0])).split("-");
+            ApiRoutingInfo apiRoutingInfo = externalService.getRoutingInfo(moreApiToken);
+            return ResponseEntity.ok(
+                    externalService.listParticipants(apiRoutingInfo.studyId(), apiRoutingInfo.studyGroupId())
+                            .stream()
+                            .map(ParticipantTransformer::toDTO)
+                            .toList()
+            );
+        } catch(IndexOutOfBoundsException | NumberFormatException e) {
+            throw new AccessDeniedException("Invalid Token");
+        }
+    }
 
-            Long studyId = Long.valueOf(primaryKey[0]);
-            Integer observationId = Integer.valueOf(primaryKey[1]);
+    @Override
+    public ResponseEntity<Void> storeExternalBulk(String moreApiToken, EndpointDataBulkDTO endpointDataBulkDTO) {
+        try {
+            ApiRoutingInfo apiRoutingInfo = externalService.getRoutingInfo(moreApiToken);
             Integer participantId = Integer.valueOf(endpointDataBulkDTO.getParticipantId());
-            Integer tokenId = Integer.valueOf(primaryKey[2]);
-            String secret = new String(Base64.getDecoder().decode(split[1]));
+            Interval interval = externalService.getIntervalForObservation(apiRoutingInfo.studyId(), apiRoutingInfo.observationId(), participantId);
 
-            final Optional<ApiRoutingInfo> apiRoutingInfo = externalService.getRoutingInfo(
-                    studyId,
-                    observationId,
-                    tokenId,
-                    secret);
-            if(apiRoutingInfo.isEmpty()) {
-                throw new AccessDeniedException("Invalid token");
-            }
-
-            externalService.validateTimeFrame(studyId, observationId,
-                    endpointDataBulkDTO.getDataPoints().stream().map(datapoint ->
-                            datapoint.getTimestamp().toInstant()
-                    ).toList());
+            endpointDataBulkDTO.getDataPoints().stream()
+                .map(datapoint -> datapoint.getTimestamp().toInstant())
+                .map(timestamp -> timestamp.isBefore(interval.getStart()) || timestamp.isAfter(interval.getEnd()))
+                .filter(v -> v)
+                .findFirst()
+                .orElseThrow(BadRequestException::TimeFrame);
 
-            final RoutingInfo routingInfo = new RoutingInfo(
-                    externalService.validateRoutingInfo(apiRoutingInfo.get(), participantId),
-                    participantId
-            );
+            final RoutingInfo routingInfo = externalService.validateAndCreateRoutingInfo(apiRoutingInfo, participantId);
             try (LoggingUtils.LoggingContext ctx = LoggingUtils.createContext(routingInfo)) {
-                if(routingInfo.studyActive()) {
+                if(routingInfo.acceptData()) {
                     elasticService.storeDataPoints(
-                            DataTransformer.createDataPoints(endpointDataBulkDTO, apiRoutingInfo.get(), observationId),
+                            DataTransformer.createDataPoints(endpointDataBulkDTO, apiRoutingInfo, apiRoutingInfo.observationId()),
                             routingInfo
                     );
                 } else {
                     final List<ExternalDataDTO> discardedIDs = endpointDataBulkDTO.getDataPoints();
-                    LOG.info("Discarding {} observations because study_{} is not 'active'",
-                            discardedIDs.size(), routingInfo.studyId());
+                    LOG.info("Discarding {} observations because either study_{} or participant_{} is not 'active'",
+                            discardedIDs.size(), routingInfo.studyId(), routingInfo.participantId());
                 }
                 return ResponseEntity.noContent().build();
             }