#180: Observation Groups for the MORE Study Manager Backend

pom.xml

@@ -40,8 +40,7 @@
 
         <java.version>17</java.version>
         <spring-boot.version>3.5.5</spring-boot.version>
-        <testcontainers.version>1.21.3</testcontainers.version>
-
+        <testcontainers.version>2.0.2</testcontainers.version>
         <docker.namespace>more-project</docker.namespace>
 
         <start-class>io.redlink.more.studymanager.Application</start-class>
@@ -404,20 +403,20 @@
     <dependencyManagement>
         <dependencies>
             <dependency>
-                <groupId>org.springframework.boot</groupId>
-                <artifactId>spring-boot-dependencies</artifactId>
-                <version>${spring-boot.version}</version>
+                <groupId>org.testcontainers</groupId>
+                <artifactId>testcontainers-bom</artifactId>
+                <version>${testcontainers.version}</version>
                 <type>pom</type>
                 <scope>import</scope>
             </dependency>
-
             <dependency>
-                <groupId>org.testcontainers</groupId>
-                <artifactId>testcontainers-bom</artifactId>
-                <version>${testcontainers.version}</version>
+                <groupId>org.springframework.boot</groupId>
+                <artifactId>spring-boot-dependencies</artifactId>
+                <version>${spring-boot.version}</version>
                 <type>pom</type>
                 <scope>import</scope>
             </dependency>
+
             <dependency>
                 <groupId>co.elastic.clients</groupId>
                 <artifactId>elasticsearch-java</artifactId>

studymanager-observation/src/main/java/io/redlink/more/studymanager/component/observation/lime/LimeSurveyObservation.java

@@ -37,12 +37,14 @@ public LimeSurveyObservation(MoreObservationSDK sdk, C properties, LimeSurveyReq
     public void activate(){
         String surveyId = checkAndGetSurveyId();
 
+        //FIXME: This creates a LIME survey user for every participant, regardless if the Observation is relevant to the participant
         Set<Integer> participantIds = sdk.participantIds(MorePlatformSDK.ParticipantFilter.ALL);
+        //FIXME: Check for the expected keys (token and limeUrl) and not just if any properties are present!
         participantIds.removeIf(id -> sdk.getPropertiesForParticipant(id).isPresent());
         limeSurveyRequestService.activateParticipants(participantIds, surveyId)
                 .forEach(data ->
                     sdk.setPropertiesForParticipant(
-                            Integer.parseInt(data.firstname()),
+                            Integer.parseInt(data.firstname()), //NOTE: both the firstname and lastname are set to the participantId
                             new ObservationProperties(
                                     Map.of("token", data.token(),
                                             "limeUrl", limeSurveyRequestService.getBaseUrl())

studymanager-observation/src/main/java/io/redlink/more/studymanager/component/observation/lime/LimeSurveyObservationFactory.java

@@ -46,11 +46,13 @@ public class LimeSurveyObservationFactory<C extends LimeSurveyObservation<P>, P
 
     public LimeSurveyObservationFactory() {}
 
-    public LimeSurveyObservationFactory(
+    //FIXME: Try to get rid of constructors only used by UnitTests to Mock the LimeSurveyRequestService
+    LimeSurveyObservationFactory(
             ComponentFactoryProperties properties, LimeSurveyRequestService limeSurveyRequestService) {
         this.componentProperties = properties;
         this.limeSurveyRequestService = limeSurveyRequestService;
     }
+
     @Override
     public LimeSurveyObservationFactory<C, P> init(ComponentFactoryProperties componentProperties){
         this.componentProperties = componentProperties;

studymanager-services/pom.xml

@@ -139,17 +139,17 @@
         </dependency>
         <dependency>
             <groupId>org.testcontainers</groupId>
-            <artifactId>junit-jupiter</artifactId>
+            <artifactId>testcontainers-junit-jupiter</artifactId>
             <scope>test</scope>
         </dependency>
         <dependency>
             <groupId>org.testcontainers</groupId>
-            <artifactId>postgresql</artifactId>
+            <artifactId>testcontainers-postgresql</artifactId>
             <scope>test</scope>
         </dependency>
         <dependency>
             <groupId>org.testcontainers</groupId>
-            <artifactId>elasticsearch</artifactId>
+            <artifactId>testcontainers-elasticsearch</artifactId>
             <scope>test</scope>
         </dependency>
         <dependency>

studymanager-services/src/main/java/io/redlink/more/studymanager/exception/NotFoundException.java

@@ -28,6 +28,9 @@ public static NotFoundException Study(long id) {
     public static NotFoundException StudyGroup(long studyId, int studyGroupId) {
         return new NotFoundException("StudyGroup", studyId + "/" + studyGroupId);
     }
+    public static NotFoundException ObservationGroup(long studyId, int observationGroupId) {
+        return new NotFoundException("ObservationGroup", studyId + "/" + observationGroupId);
+    }
 
     public static NotFoundException Participant(long studyId, int participantId) {
         return new NotFoundException("Participant", studyId + "/" + participantId);

studymanager-services/src/main/java/io/redlink/more/studymanager/model/Intervention.java

@@ -21,6 +21,7 @@ public class Intervention {
     private ScheduleEvent schedule;
     private Instant created;
     private Instant modified;
+    private Integer observationGroupId;
 
     public Long getStudyId() {
         return studyId;
@@ -67,6 +68,15 @@ public Intervention setStudyGroupId(Integer studyGroupId) {
         return this;
     }
 
+    public Integer getObservationGroupId() {
+        return observationGroupId;
+    }
+
+    public Intervention setObservationGroupId(Integer observationGroupId) {
+        this.observationGroupId = observationGroupId;
+        return this;
+    }
+
     public ScheduleEvent getSchedule() {
         return schedule;
     }

studymanager-services/src/main/java/io/redlink/more/studymanager/model/Observation.java

@@ -27,6 +27,7 @@ public class Observation {
     private Instant modified;
     private Boolean hidden;
     private Boolean noSchedule = false;
+    private Integer observationGroupId;
 
     public Long getStudyId() {
         return studyId;
@@ -91,6 +92,15 @@ public Observation setStudyGroupId(Integer studyGroupId) {
         return this;
     }
 
+    public Integer getObservationGroupId() {
+        return observationGroupId;
+    }
+
+    public Observation setObservationGroupId(Integer observationGroupId) {
+        this.observationGroupId = observationGroupId;
+        return this;
+    }
+
     public ObservationProperties getProperties() {
         return properties;
     }

studymanager-services/src/main/java/io/redlink/more/studymanager/model/ObservationGroup.java

@@ -0,0 +1,76 @@
+/*
+ * Copyright LBI-DHP and/or licensed to LBI-DHP under one or more
+ * contributor license agreements (LBI-DHP: Ludwig Boltzmann Institute
+ * for Digital Health and Prevention -- A research institute of the
+ * Ludwig Boltzmann Gesellschaft, Österreichische Vereinigung zur
+ * Förderung der wissenschaftlichen Forschung).
+ * Licensed under the Elastic License 2.0.
+ */
+package io.redlink.more.studymanager.model;
+
+import io.redlink.more.studymanager.model.scheduler.Duration;
+
+import java.time.Instant;
+
+public class ObservationGroup {
+    private Long studyId;
+    private Integer observationGroupId;
+    private String title;
+    private String purpose;
+    private Instant created;
+    private Instant modified;
+
+    public Long getStudyId() {
+        return studyId;
+    }
+
+    public ObservationGroup setStudyId(Long studyId) {
+        this.studyId = studyId;
+        return this;
+    }
+
+    public Integer getObservationGroupId() {
+        return observationGroupId;
+    }
+
+    public ObservationGroup setObservationGroupId(Integer observationGroupId) {
+        this.observationGroupId = observationGroupId;
+        return this;
+    }
+
+    public String getTitle() {
+        return title;
+    }
+
+    public ObservationGroup setTitle(String title) {
+        this.title = title;
+        return this;
+    }
+
+    public String getPurpose() {
+        return purpose;
+    }
+
+    public ObservationGroup setPurpose(String purpose) {
+        this.purpose = purpose;
+        return this;
+    }
+
+    public Instant getCreated() {
+        return created;
+    }
+
+    public ObservationGroup setCreated(Instant created) {
+        this.created = created;
+        return this;
+    }
+
+    public Instant getModified() {
+        return modified;
+    }
+
+    public ObservationGroup setModified(Instant modified) {
+        this.modified = modified;
+        return this;
+    }
+}

studymanager-services/src/main/java/io/redlink/more/studymanager/model/Participant.java

@@ -8,6 +8,9 @@
  */
 package io.redlink.more.studymanager.model;
 import java.time.Instant;
+import java.util.Collection;
+import java.util.HashSet;
+import java.util.Set;
 
 public class Participant {
     private Long studyId;
@@ -19,6 +22,7 @@ public class Participant {
     private Instant modified;
     private Instant start;
     private String registrationToken;
+    private Set<Integer> observationGroupIds = new HashSet<>();
 
     public Long getStudyId() {
         return this.studyId;
@@ -92,6 +96,27 @@ public Participant setStudyGroupId(Integer studyGroupId) {
         return this;
     }
 
+    public Participant setObservationGroupIds(Set<Integer> observationGroupIds) {
+        this.observationGroupIds = observationGroupIds == null ? new HashSet<>() : observationGroupIds;
+        return this;
+    }
+
+    public Set<Integer> getObservationGroupIds() {
+        return observationGroupIds;
+    }
+
+    public Participant addObservationGroupId(Integer observationGroupId) {
+        if(observationGroupIds != null) {
+            this.observationGroupIds.add(observationGroupId);
+        }
+        return this;
+    }
+
+    public Participant removeObservationGroupId(Integer observationGroupId) {
+        this.observationGroupIds.remove(observationGroupId);
+        return this;
+    }
+
     public Instant getCreated() {
         return created;
     }

studymanager-services/src/main/java/io/redlink/more/studymanager/model/StudyImportExport.java

@@ -10,11 +10,13 @@
 
 import java.util.List;
 import java.util.Map;
+import java.util.Set;
 
 public class StudyImportExport {
 
     private Study study;
     private List<StudyGroup> studyGroups;
+    private List<ObservationGroup> observationGroups;
     private List<Observation> observations;
     private List<Intervention> interventions;
     private List<ParticipantInfo> participants;
@@ -40,6 +42,15 @@ public StudyImportExport setStudyGroups(List<StudyGroup> studyGroups) {
         return this;
     }
 
+    public List<ObservationGroup> getObservationGroups() {
+        return observationGroups;
+    }
+
+    public StudyImportExport setObservationGroups(List<ObservationGroup> observationGroups) {
+        this.observationGroups = observationGroups;
+        return this;
+    }
+
     public List<Observation> getObservations() {
         return observations;
     }
@@ -95,6 +106,7 @@ public StudyImportExport setIntegrations(List<IntegrationInfo> integrations) {
     }
 
     public record ParticipantInfo(
-            Integer groupId
+            Integer groupId,
+            Set<Integer> observationGroupIds
     ) {}
 }

studymanager-services/src/main/java/io/redlink/more/studymanager/repository/InterventionRepository.java

@@ -24,21 +24,22 @@
 import org.springframework.jdbc.core.namedparam.NamedParameterJdbcTemplate;
 import org.springframework.stereotype.Component;
 
+import java.util.Collection;
 import java.util.List;
 
 import static io.redlink.more.studymanager.repository.RepositoryUtils.getValidNullableIntegerValue;
 
 @Component
 public class InterventionRepository {
 
-    private static final String INSERT_INTERVENTION = "INSERT INTO interventions(study_id,intervention_id,title,purpose,study_group_id,schedule) VALUES (:study_id,(SELECT COALESCE(MAX(intervention_id),0)+1 FROM interventions WHERE study_id = :study_id),:title,:purpose,:study_group_id,:schedule::jsonb) RETURNING *";
-    private static final String IMPORT_INTERVENTION = "INSERT INTO interventions(study_id,intervention_id,title,purpose,study_group_id,schedule) VALUES (:study_id,:intervention_id,:title,:purpose,:study_group_id,:schedule::jsonb) RETURNING *";
+    private static final String INSERT_INTERVENTION = "INSERT INTO interventions(study_id,intervention_id,title,purpose,study_group_id,schedule,observation_group_id) VALUES (:study_id,(SELECT COALESCE(MAX(intervention_id),0)+1 FROM interventions WHERE study_id = :study_id),:title,:purpose,:study_group_id,:schedule::jsonb,:observation_group_id) RETURNING *";
+    private static final String IMPORT_INTERVENTION = "INSERT INTO interventions(study_id,intervention_id,title,purpose,study_group_id,schedule,observation_group_id) VALUES (:study_id,:intervention_id,:title,:purpose,:study_group_id,:schedule::jsonb,:observation_group_id) RETURNING *";
     private static final String GET_INTERVENTION_BY_IDS = "SELECT * FROM interventions WHERE study_id = ? AND intervention_id = ?";
     private static final String LIST_INTERVENTIONS = "SELECT * FROM interventions WHERE study_id = ?";
-    private static final String LIST_INTERVENTIONS_FOR_GROUP = "SELECT * FROM interventions WHERE study_id = :study_id AND (study_group_id IS NULL OR study_group_id = :study_group_id)";
+    private static final String LIST_INTERVENTIONS_FOR_GROUP = "SELECT * FROM interventions WHERE study_id = :study_id AND (study_group_id IS NULL OR study_group_id = :study_group_id) AND (observation_group_id IS NULL OR observation_group_id = ANY(:observation_group_ids::INT[]))";
     private static final String DELETE_INTERVENTION_BY_IDS = "DELETE FROM interventions WHERE study_id = ? AND intervention_id = ?";
     private static final String DELETE_ALL = "DELETE FROM interventions";
-    private static final String UPDATE_INTERVENTION = "UPDATE interventions SET title=:title, study_group_id=:study_group_id, purpose=:purpose, schedule=:schedule::jsonb WHERE study_id=:study_id AND intervention_id=:intervention_id";
+    private static final String UPDATE_INTERVENTION = "UPDATE interventions SET title=:title, study_group_id=:study_group_id, purpose=:purpose, schedule=:schedule::jsonb, observation_group_id=:observation_group_id WHERE study_id=:study_id AND intervention_id=:intervention_id";
     private static final String CREATE_ACTION = "INSERT INTO actions(study_id,intervention_id,action_id,type,properties) VALUES (:study_id,:intervention_id,(SELECT COALESCE(MAX(action_id),0)+1 FROM actions WHERE study_id = :study_id AND intervention_id=:intervention_id),:type,:properties::jsonb) RETURNING *";
     private static final String IMPORT_ACTION = "INSERT INTO actions(study_id,intervention_id,action_id,type,properties) VALUES (:study_id,:intervention_id,:action_id,:type,:properties::jsonb) RETURNING *";
     private static final String GET_ACTION_BY_IDS = "SELECT * FROM actions WHERE study_id=? AND intervention_id=? AND action_id=?";
@@ -60,7 +61,7 @@ public Intervention insert(Intervention intervention) {
         try {
             return namedTemplate.queryForObject(INSERT_INTERVENTION, interventionToParams(intervention), getInterventionRowMapper());
         } catch (DataIntegrityViolationException e) {
-            throw new BadRequestException("Study group " + intervention.getStudyGroupId() + " does not exist on study " + intervention.getStudyId());
+            throw new BadRequestException("Unable to insert Invervention because it refers an not existing group (Study group " + intervention.getStudyGroupId() + " and/or Observation group " + intervention.getObservationGroupId() + " does not exist on study " + intervention.getStudyId());
         }
     }
 
@@ -76,7 +77,8 @@ public Intervention importIntervention(Long studyId, Intervention intervention)
                     "Error during import of intervention " +
                             intervention.getInterventionId() +
                             "for study " +
-                            intervention.getStudyId()
+                            intervention.getStudyId() +
+                            "(" + e.getClass().getSimpleName() + ": " + e.getMessage() + ")"
             );
         }
     }
@@ -85,10 +87,14 @@ public List<Intervention> listInterventions(Long studyId) {
         return template.query(LIST_INTERVENTIONS, getInterventionRowMapper(), studyId);
     }
 
-    public List<Intervention> listInterventionsForGroup(Long studyId, Integer groupId) {
+    public List<Intervention> listInterventionsForGroup(Long studyId, Integer groupId){
+        return listInterventionsForGroup(studyId, groupId, List.of());
+    }
+    public List<Intervention> listInterventionsForGroup(Long studyId, Integer groupId, Collection<Integer> observationGroupIds) {
         return namedTemplate.query(LIST_INTERVENTIONS_FOR_GROUP,
                 new MapSqlParameterSource("study_id", studyId)
-                        .addValue("study_group_id", groupId),
+                        .addValue("study_group_id", groupId)
+                        .addValue("observation_group_ids", observationGroupIds == null ? new Integer[0] : observationGroupIds.toArray(new Integer[0])),
                 getInterventionRowMapper()
         );
     }
@@ -190,7 +196,8 @@ private static MapSqlParameterSource interventionToParams(Intervention intervent
                 .addValue("title", intervention.getTitle())
                 .addValue("purpose", intervention.getPurpose())
                 .addValue("study_group_id", intervention.getStudyGroupId())
-                .addValue("schedule", MapperUtils.writeValueAsString(intervention.getSchedule()));
+                .addValue("schedule", MapperUtils.writeValueAsString(intervention.getSchedule()))
+                .addValue("observation_group_id", intervention.getObservationGroupId());
     }
 
     private static MapSqlParameterSource triggerToParams(Long studyId, Integer interventionId, Trigger trigger) {
@@ -235,6 +242,7 @@ private static RowMapper<Intervention> getInterventionRowMapper() {
                 .setSchedule(MapperUtils.readValue(rs.getString("schedule"), Event.class))
                 .setStudyGroupId(getValidNullableIntegerValue(rs, "study_group_id"))
                 .setCreated(RepositoryUtils.readInstant(rs,"created"))
-                .setModified(RepositoryUtils.readInstant(rs,"modified"));
+                .setModified(RepositoryUtils.readInstant(rs,"modified"))
+                .setObservationGroupId(getValidNullableIntegerValue(rs, "observation_group_id"));
         }
 }