From e9caea5b097e1f2e4ca4e12dee46c3dbd6973d45 Mon Sep 17 00:00:00 2001
From: Pim van Nierop <pim@thehyve.nl>
Date: Fri, 3 May 2024 12:29:17 +0200
Subject: [PATCH 01/10] Implement ObservationsListDto return type

---
 data-dashboard-backend/dev/dashboard.yml      |  4 +-
 .../datadashboard/api/api/ObservationDto.kt   |  9 ++
 ...riableListDto.kt => ObservationListDto.kt} |  4 +-
 .../datadashboard/api/api/VariableDto.kt      | 37 -------
 .../api/domain/ObservationRepository.kt       | 28 +++---
 .../api/domain/mapper/Extensions.kt           | 24 +----
 .../api/domain/model/Observation.kt           | 51 +++++-----
 .../api/domain/model/Variable.kt              | 67 -------------
 .../enhancer/DashBoardApiEnhancerFactory.kt   |  4 +-
 .../api/resource/ObservationResource.kt       |  9 +-
 .../api/service/ObservationService.kt         |  9 +-
 .../changes/20220309-create-database.xml      | 64 +++++-------
 .../changes/20220321-insert-mock-data.xml     | 36 ++-----
 .../changes/20220321-observations.csv         |  9 ++
 .../api/DashboardIntegrationTest.kt           | 20 ++--
 .../api/resource/ObservationResourceTest.kt   | 98 +++++++++++++++++++
 .../api/service/ObservationServiceTest.kt     | 75 ++++++++++++++
 17 files changed, 287 insertions(+), 261 deletions(-)
 rename data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/api/{VariableListDto.kt => ObservationListDto.kt} (90%)
 delete mode 100644 data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/api/VariableDto.kt
 delete mode 100644 data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/domain/model/Variable.kt
 create mode 100644 data-dashboard-backend/src/main/resources/db/changelog/changes/20220321-observations.csv
 create mode 100644 data-dashboard-backend/src/test/java/org/radarbase/datadashboard/api/resource/ObservationResourceTest.kt
 create mode 100644 data-dashboard-backend/src/test/java/org/radarbase/datadashboard/api/service/ObservationServiceTest.kt

diff --git a/data-dashboard-backend/dev/dashboard.yml b/data-dashboard-backend/dev/dashboard.yml
index 14e86c6..c2e0cc5 100644
--- a/data-dashboard-backend/dev/dashboard.yml
+++ b/data-dashboard-backend/dev/dashboard.yml
@@ -5,13 +5,13 @@ service:
 
 auth:
   managementPortal:
-    url: http://localhost:8080/managementportal
+    url: http://127.0.0.1:8080/managementportal
     clientId: data_dashboard_api
     clientSecret: data_dashboard_api_secret
   jwtResourceName: res_DataDashboardAPI
 
 database:
-  url: jdbc:postgresql://localhost:5432/data
+  url: jdbc:postgresql://127.0.0.1:5432/data
   user: radarbase
   password: radarbase
   dialect: org.hibernate.dialect.PostgreSQLDialect
diff --git a/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/api/ObservationDto.kt b/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/api/ObservationDto.kt
index 3317c15..73ddc03 100644
--- a/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/api/ObservationDto.kt
+++ b/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/api/ObservationDto.kt
@@ -23,6 +23,15 @@ data class ObservationDto(
     /** Unique observation ID. */
     val id: Long?,
 
+    /** Unique identifier of study subject. */
+    val subject: String?,
+
+    /** Unique identifier of the kafka topic. */
+    val topic: String?,
+
+    /** Category of the observation (optional). */
+    val category: String?,
+
     /** Date or date-time of the observation. */
     val date: String?,
 
diff --git a/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/api/VariableListDto.kt b/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/api/ObservationListDto.kt
similarity index 90%
rename from data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/api/VariableListDto.kt
rename to data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/api/ObservationListDto.kt
index 761a397..85eb17b 100644
--- a/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/api/VariableListDto.kt
+++ b/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/api/ObservationListDto.kt
@@ -19,6 +19,6 @@
 package org.radarbase.datadashboard.api.api
 
 /** List of variables. */
-data class VariableListDto(
-    val variables: List<VariableDto>,
+data class ObservationListDto(
+    val observations: List<ObservationDto>,
 )
diff --git a/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/api/VariableDto.kt b/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/api/VariableDto.kt
deleted file mode 100644
index 7997a5f..0000000
--- a/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/api/VariableDto.kt
+++ /dev/null
@@ -1,37 +0,0 @@
-/*
- *
- *  *  Copyright 2024 The Hyve
- *  *
- *  *  Licensed under the Apache License, Version 2.0 (the "License");
- *  *  you may not use this file except in compliance with the License.
- *  *  You may obtain a copy of the License at
- *  *
- *  *    http://www.apache.org/licenses/LICENSE-2.0
- *  *
- *  *  Unless required by applicable law or agreed to in writing, software
- *  *  distributed under the License is distributed on an "AS IS" BASIS,
- *  *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- *  *  See the License for the specific language governing permissions and
- *  *  limitations under the License.
- *
- */
-
-package org.radarbase.datadashboard.api.api
-
-import org.radarbase.datadashboard.api.domain.model.Variable
-
-/** A variable, describing a type of observations. */
-data class VariableDto(
-    /** Unique ID. */
-    val id: Long?,
-    /** Canonical name of the variable. */
-    val name: String,
-    /** Data type of observations for this variable. */
-    val type: String?,
-    /** Category to group variables with. */
-    val category: String?,
-    /** Observations that are selected for this variable. */
-    val observations: List<ObservationDto>?,
-    /** Date type of observations. */
-    val dateType: Variable.DateType? = Variable.DateType.LOCAL_DATE,
-)
diff --git a/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/domain/ObservationRepository.kt b/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/domain/ObservationRepository.kt
index 0a15ebd..5db3759 100644
--- a/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/domain/ObservationRepository.kt
+++ b/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/domain/ObservationRepository.kt
@@ -20,30 +20,26 @@ package org.radarbase.datadashboard.api.domain
 
 import jakarta.inject.Provider
 import jakarta.persistence.EntityManager
-import jakarta.persistence.Tuple
 import jakarta.ws.rs.core.Context
+import org.radarbase.datadashboard.api.domain.model.Observation
 import org.radarbase.jersey.hibernate.HibernateRepository
 import org.slf4j.LoggerFactory
 
-
 class ObservationRepository(
     @Context em: Provider<EntityManager>,
 ) : HibernateRepository(em) {
 
-    fun getObservations(topicId: String, subjectId: String): List<Map<String, Any>> {
-        logger.debug("Get observations of topic {} and subject {}", topicId, subjectId)
-        val rows: List<Any?> = transact {
-            createNativeQuery(
-                "SELECT * FROM ${topicId} o WHERE o.userId = '${subjectId}' ORDER BY o.timestamp DESC",
-                Tuple::class.java
-            ).resultList
-        }
-        // Create a list of maps from the rows.
-        return rows.map { row ->
-            (row as Tuple).elements.associate {
-                // Column name is the key, value is the database value.
-                it.alias to row.get(it.alias)
-            }
+    fun getObservations(topicId: String, subjectId: String): List<Observation> {
+        logger.debug("Get observations in topic {} of subject {}", topicId, subjectId)
+
+        return transact {
+            createQuery(
+                "SELECT o FROM Observation o WHERE o.subject = :subjectId AND o.topic = :topicId ORDER BY o.date DESC",
+                Observation::class.java,
+            ).apply {
+                setParameter("subjectId", subjectId)
+                setParameter("topicId", topicId)
+            }.resultList
         }
     }
 
diff --git a/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/domain/mapper/Extensions.kt b/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/domain/mapper/Extensions.kt
index 5086efd..dc31d71 100644
--- a/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/domain/mapper/Extensions.kt
+++ b/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/domain/mapper/Extensions.kt
@@ -19,13 +19,14 @@
 package org.radarbase.datadashboard.api.domain.mapper
 
 import org.radarbase.datadashboard.api.api.ObservationDto
-import org.radarbase.datadashboard.api.api.VariableDto
 import org.radarbase.datadashboard.api.domain.model.Observation
-import org.radarbase.datadashboard.api.domain.model.Variable
 import java.time.Duration
 
 fun Observation.toDto(): ObservationDto = ObservationDto(
     id = id,
+    subject = subject,
+    topic = topic,
+    category = category,
     date = date?.toString(),
     period = if (date != null && endDate != null) {
         Duration.between(date, endDate).toString()
@@ -35,22 +36,3 @@ fun Observation.toDto(): ObservationDto = ObservationDto(
     value = valueNumeric ?: valueTextual,
 )
 
-fun Map.Entry<Variable, List<Observation>>.toDto(): VariableDto {
-    val (variable, observations) = this
-    return variable.toDto(
-        observations
-            .sortedBy { it.date }
-            .map { it.toDto() },
-    )
-}
-
-fun Variable.toDtoWithoutObservations(): VariableDto = toDto(null)
-
-fun Variable.toDto(observations: List<ObservationDto>?): VariableDto = VariableDto(
-    id = id,
-    name = name,
-    type = type,
-    category = category,
-    observations = observations,
-    dateType = dateType,
-)
diff --git a/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/domain/model/Observation.kt b/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/domain/model/Observation.kt
index 2120053..f464445 100644
--- a/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/domain/model/Observation.kt
+++ b/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/domain/model/Observation.kt
@@ -24,48 +24,55 @@ import java.util.*
 
 @Entity
 @Table(name = "observation")
-class Observation(
+data class Observation(
     @GeneratedValue(strategy = GenerationType.IDENTITY)
     @Column(updatable = false, nullable = false)
     @Id
-    val id: Long?,
-    @Column(name = "subject_id")
-    val subjectId: String,
-    @ManyToOne
-    @JoinColumn(name = "variable_id")
-    val variable: Variable,
-    val date: ZonedDateTime?,
+    val id: Long,
+
+    @Column(nullable = false)
+    @Id
+    val subject: String,
+
+    @Column(nullable = false)
+    @Id
+    val topic: String,
+
+    @Id
+    val category: String,
+
+    @Column(nullable = false)
+    @Id
+    val variable: String,
+
+    @Column(nullable = false)
+    @Id
+    val date: ZonedDateTime,
+
     @Column(name = "end_date")
     val endDate: ZonedDateTime?,
+
     @Column(name = "value_textual")
     val valueTextual: String?,
+
     @Column(name = "value_numeric")
     val valueNumeric: Double?,
+
 ) {
     override fun equals(other: Any?): Boolean {
         if (this === other) return true
         if (javaClass != other?.javaClass) return false
 
         other as Observation
-        if (id != null && other.id != null) {
-            return id == other.id
-        }
-
-        return subjectId == other.subjectId &&
+        return subject == other.subject &&
+            topic == other.topic &&
+            category == other.category &&
             variable == other.variable &&
             date == other.date &&
             endDate == other.endDate
     }
 
-    override fun hashCode(): Int = Objects.hash(subjectId, variable, date)
-
-    override fun toString(): String = "Observation(" +
-        "id=$id, " +
-        "variable=$variable, " +
-        "date=$date, " +
-        "endDate=$endDate, " +
-        "valueTextual=${valueTextual.toPrintString()}, " +
-        "valueNumeric=$valueNumeric)"
+    override fun hashCode(): Int = Objects.hash(subject, variable, date)
 
     companion object {
         internal fun String?.toPrintString() = if (this != null) "'$this'" else "null"
diff --git a/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/domain/model/Variable.kt b/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/domain/model/Variable.kt
deleted file mode 100644
index 104bcf8..0000000
--- a/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/domain/model/Variable.kt
+++ /dev/null
@@ -1,67 +0,0 @@
-/*
- *
- *  *  Copyright 2024 The Hyve
- *  *
- *  *  Licensed under the Apache License, Version 2.0 (the "License");
- *  *  you may not use this file except in compliance with the License.
- *  *  You may obtain a copy of the License at
- *  *
- *  *    http://www.apache.org/licenses/LICENSE-2.0
- *  *
- *  *  Unless required by applicable law or agreed to in writing, software
- *  *  distributed under the License is distributed on an "AS IS" BASIS,
- *  *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- *  *  See the License for the specific language governing permissions and
- *  *  limitations under the License.
- *
- */
-
-package org.radarbase.datadashboard.api.domain.model
-
-import org.radarbase.datadashboard.api.domain.model.Observation.Companion.toPrintString
-import jakarta.persistence.*
-
-@Entity
-@Table(name = "variable")
-class Variable(
-    @GeneratedValue(strategy = GenerationType.IDENTITY)
-    @Id
-    val id: Long?,
-    val name: String,
-    val type: String?,
-    val category: String?,
-    @OneToMany(mappedBy = "variable", fetch = FetchType.LAZY)
-    val observations: List<Observation>,
-    @Enumerated(EnumType.STRING)
-    @Column(name = "date_type")
-    val dateType: DateType? = DateType.LOCAL_DATE,
-) {
-    enum class DateType {
-        LOCAL_DATE, ZONED_DATE, LOCAL_DATE_TIME, ZONED_DATE_TIME,
-    }
-
-    override fun equals(other: Any?): Boolean {
-        if (this === other) return true
-        if (javaClass != other?.javaClass) return false
-
-        other as Variable
-
-        if (id != null && other.id != null) {
-            return id == other.id
-        }
-
-        return name == other.name &&
-            type == other.type &&
-            category == other.category &&
-            dateType == other.dateType
-    }
-
-    override fun hashCode(): Int = name.hashCode()
-
-    override fun toString(): String = "Variable(" +
-        "id=$id, " +
-        "name='$name', " +
-        "type=${type.toPrintString()}, " +
-        "category=${category.toPrintString()}, " +
-        "dateType=$dateType)"
-}
diff --git a/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/enhancer/DashBoardApiEnhancerFactory.kt b/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/enhancer/DashBoardApiEnhancerFactory.kt
index af24ae3..7dec3d3 100644
--- a/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/enhancer/DashBoardApiEnhancerFactory.kt
+++ b/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/enhancer/DashBoardApiEnhancerFactory.kt
@@ -20,7 +20,6 @@ package org.radarbase.datadashboard.api.enhancer
 
 import org.radarbase.datadashboard.api.config.DashboardApiConfig
 import org.radarbase.datadashboard.api.domain.model.Observation
-import org.radarbase.datadashboard.api.domain.model.Variable
 import org.radarbase.jersey.enhancer.EnhancerFactory
 import org.radarbase.jersey.enhancer.Enhancers
 import org.radarbase.jersey.enhancer.JerseyResourceEnhancer
@@ -40,8 +39,7 @@ class DashBoardApiEnhancerFactory(
         HibernateResourceEnhancer(
             config.database.copy(
                 managedClasses = listOf(
-                    Observation::class.jvmName,
-                    Variable::class.jvmName
+                    Observation::class.jvmName
                 ),
             ),
         ),
diff --git a/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/resource/ObservationResource.kt b/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/resource/ObservationResource.kt
index 6f18fd1..34616fc 100644
--- a/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/resource/ObservationResource.kt
+++ b/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/resource/ObservationResource.kt
@@ -23,12 +23,12 @@ import jakarta.ws.rs.*
 import jakarta.ws.rs.container.ContainerRequestContext
 import jakarta.ws.rs.core.Context
 import jakarta.ws.rs.core.Response
-import org.radarbase.datadashboard.api.api.VariableListDto
 import org.radarbase.datadashboard.api.service.ObservationService
 import org.radarbase.auth.authorization.Permission
+import org.radarbase.datadashboard.api.api.ObservationDto
+import org.radarbase.datadashboard.api.api.ObservationListDto
 import org.radarbase.jersey.auth.Authenticated
 import org.radarbase.jersey.auth.NeedsPermission
-import org.radarbase.jersey.auth.filter.RadarSecurityContext
 
 @Path("subject/{subjectId}/topic/{topicId}")
 @Resource
@@ -36,8 +36,7 @@ import org.radarbase.jersey.auth.filter.RadarSecurityContext
 @Consumes("application/json")
 @Authenticated
 class ObservationResource(
-    @Context private val observationService: ObservationService,
-    @Context private val request: ContainerRequestContext
+    @Context private val observationService: ObservationService
 ) {
     @GET
     @Path("observations")
@@ -45,7 +44,7 @@ class ObservationResource(
     fun getObservations(
         @PathParam("subjectId") subjectId: String,
         @PathParam("topicId") topicId: String
-    ): List<Map<String, Any>> {
+    ): ObservationListDto {
 //        if (request.securityContext != null && request.securityContext is RadarSecurityContext) {
 //            val userName = (request.securityContext as RadarSecurityContext).userPrincipal
 //            if (!subjectId.equals(userName)) throw NotFoundException("Subjects can only access their own data.")
diff --git a/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/service/ObservationService.kt b/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/service/ObservationService.kt
index 7fe9047..5086be2 100644
--- a/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/service/ObservationService.kt
+++ b/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/service/ObservationService.kt
@@ -19,14 +19,17 @@
 package org.radarbase.datadashboard.api.service
 
 import jakarta.ws.rs.core.Context
-import org.radarbase.datadashboard.api.api.VariableListDto
+import org.radarbase.datadashboard.api.api.ObservationListDto
 import org.radarbase.datadashboard.api.domain.ObservationRepository
 import org.radarbase.datadashboard.api.domain.mapper.toDto
 
 class ObservationService(
     @Context private val observationRepository: ObservationRepository
 ) {
-    fun getObservations(topicId: String, subjectId: String): List<Map<String, Any>> {
-        return  this.observationRepository.getObservations(topicId, subjectId)
+    fun getObservations(topicId: String, subjectId: String): ObservationListDto {
+        val result = this.observationRepository.getObservations(topicId, subjectId)
+        return ObservationListDto(
+            result.map { it.toDto() },
+        )
     }
 }
diff --git a/data-dashboard-backend/src/main/resources/db/changelog/changes/20220309-create-database.xml b/data-dashboard-backend/src/main/resources/db/changelog/changes/20220309-create-database.xml
index c879c52..61c14aa 100644
--- a/data-dashboard-backend/src/main/resources/db/changelog/changes/20220309-create-database.xml
+++ b/data-dashboard-backend/src/main/resources/db/changelog/changes/20220309-create-database.xml
@@ -21,53 +21,35 @@
     xmlns="http://www.liquibase.org/xml/ns/dbchangelog"
     xsi:schemaLocation="http://www.liquibase.org/xml/ns/dbchangelog
     https://www.liquibase.org/xml/ns/dbchangelog/dbchangelog-4.6.xsd">
+    <property name="autoIncrement" value="true" dbms="h2,mysql,postgresql,oracle,mssql"/>
 
-    <changeSet id="Create topic tables" author="pim" context="dev">
-        <comment>Create topic tables</comment>
-        <createTable tableName="android_phone_battery_level">
-            <column name="timestamp" type="DATETIME"/>
-            <column name="projectId" type="VARCHAR">
-                <constraints nullable="false" primaryKey="true"/>
+    <changeSet id="Create observation tables" author="pim">
+        <createTable tableName="observation">
+            <column name="id" type="bigint" autoIncrement="${autoIncrement}">
+                <constraints primaryKey="true" nullable="false"/>
             </column>
-            <column name="userId" type="VARCHAR">
-                <constraints nullable="false" primaryKey="true"/>
+            <column name="subject" type="varchar(255)">
+                <constraints primaryKey="true" nullable="false"/>
             </column>
-            <column name="sourceId" type="VARCHAR">
-                <constraints nullable="false" primaryKey="true"/>
+            <column name="topic" type="varchar(255)">
+                <constraints primaryKey="true" nullable="false"/>
             </column>
-            <column name="time" type="DATETIME">
-                <constraints nullable="false" primaryKey="true"/>
+            <column name="category" type="varchar(255)"/>
+            <column name="variable" type="varchar(255)">
+                <constraints primaryKey="true" nullable="false"/>
             </column>
-            <column name="timeReceived" type="DATETIME"/>
-            <column name="batteryLevel" type="INT"/>
-            <column name="isPlugged" type="boolean"/>
-            <column name="status" type="VARCHAR"/>
-        </createTable>
-
-        <createTable tableName="android_phone_relative_location">
-            <column name="timestamp" type="DATETIME"/>
-            <column name="projectId" type="VARCHAR">
-                <constraints nullable="false" primaryKey="true"/>
-            </column>
-            <column name="userId" type="VARCHAR">
-                <constraints nullable="false" primaryKey="true"/>
-            </column>
-            <column name="sourceId" type="VARCHAR">
-                <constraints nullable="false" primaryKey="true"/>
+            <column name="date" type="timestamp with time zone">
+                <constraints primaryKey="true" nullable="false"/>
             </column>
-            <column name="time" type="DATETIME">
-                <constraints nullable="false" primaryKey="true"/>
-            </column>
-            <column name="timeReceived" type="DATETIME"/>
-            <column name="offsetReference" type="INT"/>
-            <column name="provider" type="VARCHAR"/>
-            <column name="latitude" type="DOUBLE"/>
-            <column name="longitude" type="DOUBLE"/>
-            <column name="altitude" type="INT"/>
-            <column name="accuracy" type="INT"/>
-            <column name="speed" type="INT"/>
-            <column name="bearing" type="INT"/>
+            <column name="end_date" type="timestamp with time zone"/>
+            <column name="value_numeric" type="double"/>
+            <column name="value_textual" type="clob"/>
         </createTable>
-    </changeSet>
 
+        <createIndex tableName="observation" indexName="idx_observation_subject_in_topic">
+            <column name="subject"/>
+            <column name="topic"/>
+        </createIndex>
+
+    </changeSet>
 </databaseChangeLog>
diff --git a/data-dashboard-backend/src/main/resources/db/changelog/changes/20220321-insert-mock-data.xml b/data-dashboard-backend/src/main/resources/db/changelog/changes/20220321-insert-mock-data.xml
index 5ef108d..4a4c0f5 100644
--- a/data-dashboard-backend/src/main/resources/db/changelog/changes/20220321-insert-mock-data.xml
+++ b/data-dashboard-backend/src/main/resources/db/changelog/changes/20220321-insert-mock-data.xml
@@ -22,38 +22,14 @@
     xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
     xsi:schemaLocation="http://www.liquibase.org/xml/ns/dbchangelog https://www.liquibase.org/xml/ns/dbchangelog/dbchangelog-4.9.xsd">
 
-    <changeSet id="Add mock data for phone battery level" author="pim" context="dev">
+    <changeSet id="Add mock data for observations" author="pim" context="dev">
         <loadData
-            file="db/changelog/changes/20220321-android_phone_battery_level.csv"
+            file="db/changelog/changes/20220321-observations.csv"
             separator=";"
-            tableName="android_phone_battery_level"
-            usePreparedStatements="true"
-        >
-            <column name="projectId" type="STRING"/>
-            <column name="userId" type="STRING"/>
-            <column name="sourceId" type="STRING"/>
-            <column name="status" type="STRING"/>
+            tableName="observation"
+            usePreparedStatements="true">
+            <column name="value_numeric" type="NUMERIC"/>
+            <column name="value_textual" type="STRING"/>
         </loadData>
     </changeSet>
-
-    <changeSet id="Add mock data for phone relative location" author="pim" context="dev">
-        <loadData
-            file="db/changelog/changes/20220321-android_phone_relative_location.csv"
-            separator=";"
-            tableName="android_phone_relative_location"
-            usePreparedStatements="true"
-        >
-            <column name="projectId" type="STRING"/>
-            <column name="userId" type="STRING"/>
-            <column name="sourceId" type="STRING"/>
-            <column name="provider" type="STRING"/>
-            <column name="latitude" type="NUMERIC"/>
-            <column name="longitude" type="NUMERIC"/>
-            <column name="altitude" type="NUMERIC"/>
-            <column name="accuracy" type="NUMERIC"/>
-            <column name="speed" type="NUMERIC"/>
-            <column name="bearing" type="NUMERIC"/>
-        </loadData>
-    </changeSet>
-
 </databaseChangeLog>
diff --git a/data-dashboard-backend/src/main/resources/db/changelog/changes/20220321-observations.csv b/data-dashboard-backend/src/main/resources/db/changelog/changes/20220321-observations.csv
new file mode 100644
index 0000000..c7f744e
--- /dev/null
+++ b/data-dashboard-backend/src/main/resources/db/changelog/changes/20220321-observations.csv
@@ -0,0 +1,9 @@
+subject;topic;category;variable;value_numeric;value_textual;date;end_date
+sub-1;questionnaire_answer;baseline_questions;Perceived_Pain_Score;5;NULL;2021-02-20 00:00:00;NULL
+sub-1;questionnaire_answer;followup_questions;Name_Of_Physician;NULL;Dr.J.Adams;2021-02-20 00:00:00;NULL
+sub-2;questionnaire_answer;baseline_questions;Perceived_Pain_Score;2;NULL;2021-02-20 00:00:00;NULL
+sub-2;questionnaire_answer;followup_questions;Name_Of_Physician;NULL;Dr.G.Washington;2022-05-20 00:00:00;NULL
+sub-1;phone_battery_level;NULL;batteryLevel;5;NULL;2021-02-20 00:00:00;NULL
+sub-1;phone_battery_level;NULL;status;NULL;CHARGING;2021-02-20 00:00:00;NULL
+sub-2;phone_battery_level;NULL;batteryLevel;10;NULL;2021-02-20 00:00:00;NULL
+sub-2;phone_battery_level;NULL;status;NULL;FULL;2021-02-20 00:00:00;NULL
diff --git a/data-dashboard-backend/src/test/java/org/radarbase/datadashboard/api/DashboardIntegrationTest.kt b/data-dashboard-backend/src/test/java/org/radarbase/datadashboard/api/DashboardIntegrationTest.kt
index c493544..07ea8a5 100644
--- a/data-dashboard-backend/src/test/java/org/radarbase/datadashboard/api/DashboardIntegrationTest.kt
+++ b/data-dashboard-backend/src/test/java/org/radarbase/datadashboard/api/DashboardIntegrationTest.kt
@@ -28,15 +28,15 @@ import org.glassfish.jersey.test.ServletDeploymentContext
 import org.glassfish.jersey.test.grizzly.GrizzlyWebTestContainerFactory
 import org.glassfish.jersey.test.spi.TestContainerFactory
 import org.junit.jupiter.api.Assertions
-import org.junit.jupiter.api.Disabled
 import org.junit.jupiter.api.Test
 import org.radarbase.datadashboard.api.config.DashboardApiConfig
+import org.radarbase.datadashboard.api.resource.ObservationResource
 import org.radarbase.jersey.auth.AuthValidator
 import org.radarbase.jersey.auth.disabled.DisabledAuthValidator
 import org.radarbase.jersey.config.ConfigLoader
 
 
-class DashboardIntegrationTest : JerseyTest() {
+class DashboardIntegrationTest: JerseyTest() {
 
     lateinit var disabledAuthValidator: DisabledAuthValidator
 
@@ -49,6 +49,7 @@ class DashboardIntegrationTest : JerseyTest() {
                 bind(disabledAuthValidator).to(AuthValidator::class.java).ranked(1)
             }
         })
+        resourceConfig.register(ObservationResource::class.java)
         return resourceConfig
     }
 
@@ -69,22 +70,17 @@ class DashboardIntegrationTest : JerseyTest() {
     }
 
     @Test
-    @Disabled("Manageportal authentication does not yet work (always code 200 returned)")
     fun testGetObservationsNoToken() {
-        val response =
-            target("subject/f09c03f1-617d-4c2b-b093-4936f75092fa/topic/android_phone_battery_level/observations").request()
-                .get()
+        val response = target("subject/sub-1/topic/phone_battery_level/observations").request().get()
         Assertions.assertEquals(401, response.status)
     }
 
     @Test
     fun testGetObservationsWithToken() {
-        val response =
-            target("subject/f09c03f1-617d-4c2b-b093-4936f75092fa/topic/android_phone_battery_level/observations")
-                .request()
-                .header(HttpHeaders.AUTHORIZATION, "Bearer " + "... encoded token ...")
-                .get()
-        val a = response.readEntity(String::class.java)
+        val response = target("subject/sub-1/topic/phone_battery_level/observations")
+            .request()
+            .header(HttpHeaders.AUTHORIZATION, "Bearer " + "... encoded token ...")
+            .get()
         Assertions.assertEquals(200, response.status)
     }
 
diff --git a/data-dashboard-backend/src/test/java/org/radarbase/datadashboard/api/resource/ObservationResourceTest.kt b/data-dashboard-backend/src/test/java/org/radarbase/datadashboard/api/resource/ObservationResourceTest.kt
new file mode 100644
index 0000000..fdcd68c
--- /dev/null
+++ b/data-dashboard-backend/src/test/java/org/radarbase/datadashboard/api/resource/ObservationResourceTest.kt
@@ -0,0 +1,98 @@
+/*
+ *
+ *  *  Copyright 2024 The Hyve
+ *  *
+ *  *  Licensed under the Apache License, Version 2.0 (the "License");
+ *  *  you may not use this file except in compliance with the License.
+ *  *  You may obtain a copy of the License at
+ *  *
+ *  *    http://www.apache.org/licenses/LICENSE-2.0
+ *  *
+ *  *  Unless required by applicable law or agreed to in writing, software
+ *  *  distributed under the License is distributed on an "AS IS" BASIS,
+ *  *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ *  *  See the License for the specific language governing permissions and
+ *  *  limitations under the License.
+ *
+ */
+
+package org.radarbase.datadashboard.api.resource
+
+import jakarta.ws.rs.core.Application
+import org.glassfish.hk2.utilities.binding.AbstractBinder
+import org.glassfish.jersey.server.ResourceConfig
+import org.glassfish.jersey.test.JerseyTest
+import org.junit.jupiter.api.Assertions.assertEquals
+import org.junit.jupiter.api.BeforeEach
+import org.junit.jupiter.api.Test
+import org.mockito.Mock
+import org.mockito.Mockito.`when`
+import org.mockito.MockitoAnnotations
+import org.radarbase.datadashboard.api.api.ObservationListDto
+import org.radarbase.datadashboard.api.domain.mapper.toDto
+import org.radarbase.datadashboard.api.domain.model.Observation
+import org.radarbase.datadashboard.api.service.ObservationService
+import java.time.ZonedDateTime
+
+class ObservationResourceTest: JerseyTest() {
+
+
+    @Mock
+    lateinit var observationService: ObservationService
+
+    private lateinit var observationListDto: ObservationListDto
+    private val subjectId = "sub-1"
+    private val topicId = "topic-1"
+
+    override fun configure(): Application {
+        // Initialize all defined Mockito mocks (with @Mock annotation).
+        MockitoAnnotations.openMocks(this)
+        // Configure the Jersey Application.
+        val resourceConfig = ResourceConfig(ObservationResource::class.java)
+        // Register the ObservationService mock for dependency injection (needed by ObservationResource).
+        resourceConfig.register(object : AbstractBinder() {
+            override fun configure() {
+                bind(observationService).to(ObservationService::class.java)
+            }
+        })
+        return resourceConfig
+    }
+
+    @BeforeEach
+    fun init() {
+        // Create some fake observations that are returned by the service.
+        val obs1 = Observation(id = 1L, subject = subjectId, topic = "topic-1", category = "category-1", variable = "variable-1", date = ZonedDateTime.now(), valueTextual = "value1", valueNumeric = null, endDate = null)
+        val obs2 = Observation(id = 2L, subject = subjectId, topic = "topic-1", category = "category-1", variable = "variable-1", date = ZonedDateTime.now(), valueTextual = "value1", valueNumeric = null, endDate = null)
+        val obs3 = Observation(id = 3L, subject = subjectId, topic = "topic-1", category = "category-1", variable = "variable-1", date = ZonedDateTime.now(), valueTextual = "value1", valueNumeric = null, endDate = null)
+        val obs4 = Observation(id = 4L, subject = subjectId, topic = "topic-1", category = "category-1", variable = "variable-1", date = ZonedDateTime.now(), valueTextual = "value1", valueNumeric = null, endDate = null)
+        val observations: List<Observation> = listOf(obs1, obs2, obs3, obs4)
+        // Create Dto that should be returned by the ObservationService.
+        observationListDto = ObservationListDto(
+            observations.map { it.toDto() },
+        )
+    }
+
+    @Test
+    fun testGetObservations() {
+        // Instruct the mock to return the fake observations when called.
+        `when`(observationService.getObservations(subjectId = subjectId, topicId = topicId)).thenReturn(observationListDto)
+        // Make the call to the REST endpoint.
+        val response = target("subject/sub-1/topic/topic-1/observations").request().get()
+        // Expect the http response to be OK and the same as the expected DTO.
+        assertEquals(200, response.status)
+        assertEquals(observationListDto, response.readEntity(ObservationListDto::class.java))
+    }
+
+    @Test
+    fun testGetObservations_failNoSubjectId() {
+        val response = target("subject//topic/topic-1/observations").request().get()
+        assertEquals(404, response.status)
+    }
+
+    @Test
+    fun testGetObservations_failNoTopicId() {
+        val response = target("subject/sub-1/topic//observations").request().get()
+        assertEquals(404, response.status)
+    }
+
+}
\ No newline at end of file
diff --git a/data-dashboard-backend/src/test/java/org/radarbase/datadashboard/api/service/ObservationServiceTest.kt b/data-dashboard-backend/src/test/java/org/radarbase/datadashboard/api/service/ObservationServiceTest.kt
new file mode 100644
index 0000000..5fb1e1d
--- /dev/null
+++ b/data-dashboard-backend/src/test/java/org/radarbase/datadashboard/api/service/ObservationServiceTest.kt
@@ -0,0 +1,75 @@
+/*
+ *
+ *  *  Copyright 2024 The Hyve
+ *  *
+ *  *  Licensed under the Apache License, Version 2.0 (the "License");
+ *  *  you may not use this file except in compliance with the License.
+ *  *  You may obtain a copy of the License at
+ *  *
+ *  *    http://www.apache.org/licenses/LICENSE-2.0
+ *  *
+ *  *  Unless required by applicable law or agreed to in writing, software
+ *  *  distributed under the License is distributed on an "AS IS" BASIS,
+ *  *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ *  *  See the License for the specific language governing permissions and
+ *  *  limitations under the License.
+ *
+ */
+
+package org.radarbase.datadashboard.api.service
+
+import org.junit.jupiter.api.Assertions.assertEquals
+import org.junit.jupiter.api.Test
+import org.mockito.Mock
+import org.mockito.Mockito.`when`
+import org.mockito.MockitoAnnotations
+import org.radarbase.datadashboard.api.api.ObservationListDto
+import org.radarbase.datadashboard.api.domain.ObservationRepository
+import org.radarbase.datadashboard.api.domain.mapper.toDto
+import org.radarbase.datadashboard.api.domain.model.Observation
+import java.time.ZonedDateTime
+
+class ObservationServiceTest {
+
+    val subjectId = "sub-1"
+
+    // Create a Mockito mock of the ObservationRepository. This is instantiated in the init block.
+    @Mock
+    private lateinit var observationRepository: ObservationRepository
+
+    private val observationService: ObservationService
+
+    init {
+        // Initialize all Mockito mocks.
+        MockitoAnnotations.openMocks(this)
+        observationService = ObservationService(observationRepository)
+    }
+
+    /** This test does not test much (only whether the service calls the repository).
+     *  I made it mainly to document how to write a test with mocking.
+     * */
+    @Test
+    fun test_getObservations1() {
+
+        // Create some fake observations that are returned by the repository.
+        // Each observation is linked to a Variable.
+        val obs1 = Observation(id = 1L, subject = subjectId, topic = "topic-1", category = "category-1", variable = "variable-1", date = ZonedDateTime.now(), valueTextual = "value1", valueNumeric = null, endDate = null)
+        val obs2 = Observation(id = 2L, subject = subjectId, topic = "topic-1", category = "category-1", variable = "variable-1", date = ZonedDateTime.now(), valueTextual = "value1", valueNumeric = null, endDate = null)
+        val obs3 = Observation(id = 3L, subject = subjectId, topic = "topic-1", category = "category-1", variable = "variable-1", date = ZonedDateTime.now(), valueTextual = "value1", valueNumeric = null, endDate = null)
+        val obs4 = Observation(id = 4L, subject = subjectId, topic = "topic-1", category = "category-1", variable = "variable-1", date = ZonedDateTime.now(), valueTextual = "value1", valueNumeric = null, endDate = null)
+        val observations = listOf(obs1, obs2, obs3, obs4)
+
+        // Mock the repository to return the fake observations.
+        `when`(observationRepository.getObservations(subjectId = subjectId, topicId = "topic-1")).thenReturn(observations)
+
+        // Call the ObservationService (class under test) to get the observations.
+        val result = observationService.getObservations(subjectId = subjectId, topicId = "topic-1")
+
+        // Check if the result is as expected (observations transformed to ObservationListDto).
+        val expectedDto = ObservationListDto(
+            observations.map { it.toDto() }
+        )
+        assertEquals(expectedDto, result)
+    }
+
+}
\ No newline at end of file

From dba5437a25159050be3eacf58605e97f40171819 Mon Sep 17 00:00:00 2001
From: Pim van Nierop <pim@thehyve.nl>
Date: Fri, 3 May 2024 12:41:24 +0200
Subject: [PATCH 02/10] Enable check of user

---
 .../api/resource/ObservationResource.kt       | 22 ++++++++++++-------
 1 file changed, 14 insertions(+), 8 deletions(-)

diff --git a/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/resource/ObservationResource.kt b/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/resource/ObservationResource.kt
index 34616fc..9770b9c 100644
--- a/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/resource/ObservationResource.kt
+++ b/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/resource/ObservationResource.kt
@@ -22,13 +22,13 @@ import jakarta.annotation.Resource
 import jakarta.ws.rs.*
 import jakarta.ws.rs.container.ContainerRequestContext
 import jakarta.ws.rs.core.Context
-import jakarta.ws.rs.core.Response
 import org.radarbase.datadashboard.api.service.ObservationService
 import org.radarbase.auth.authorization.Permission
-import org.radarbase.datadashboard.api.api.ObservationDto
 import org.radarbase.datadashboard.api.api.ObservationListDto
 import org.radarbase.jersey.auth.Authenticated
 import org.radarbase.jersey.auth.NeedsPermission
+import org.radarbase.jersey.auth.filter.RadarSecurityContext
+import org.slf4j.LoggerFactory
 
 @Path("subject/{subjectId}/topic/{topicId}")
 @Resource
@@ -36,7 +36,8 @@ import org.radarbase.jersey.auth.NeedsPermission
 @Consumes("application/json")
 @Authenticated
 class ObservationResource(
-    @Context private val observationService: ObservationService
+    @Context private val observationService: ObservationService,
+    @Context private val request: ContainerRequestContext
 ) {
     @GET
     @Path("observations")
@@ -45,11 +46,16 @@ class ObservationResource(
         @PathParam("subjectId") subjectId: String,
         @PathParam("topicId") topicId: String
     ): ObservationListDto {
-//        if (request.securityContext != null && request.securityContext is RadarSecurityContext) {
-//            val userName = (request.securityContext as RadarSecurityContext).userPrincipal
-//            if (!subjectId.equals(userName)) throw NotFoundException("Subjects can only access their own data.")
+        if (request.securityContext != null && request.securityContext is RadarSecurityContext) {
+            val userName = (request.securityContext as RadarSecurityContext).userPrincipal
+            log.info("User $userName is accessing observations for $subjectId")
+            if (!subjectId.equals(userName)) throw NotFoundException("Subjects can only request their own observations.")
             return observationService.getObservations(topicId, subjectId)
-//        }
-//        return emptyList()
+        }
+        return ObservationListDto(emptyList())
+    }
+
+    companion object {
+        private val log = LoggerFactory.getLogger(ObservationResource::class.java)
     }
 }

From 614f1b76c2d1d0437bc99283d9cafffe78a0c1c8 Mon Sep 17 00:00:00 2001
From: Pim van Nierop <pim@thehyve.nl>
Date: Fri, 3 May 2024 12:57:47 +0200
Subject: [PATCH 03/10] Only create tables when running in dev mode

---
 .../resources/db/changelog/changes/20220309-create-database.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/data-dashboard-backend/src/main/resources/db/changelog/changes/20220309-create-database.xml b/data-dashboard-backend/src/main/resources/db/changelog/changes/20220309-create-database.xml
index 61c14aa..41c6b51 100644
--- a/data-dashboard-backend/src/main/resources/db/changelog/changes/20220309-create-database.xml
+++ b/data-dashboard-backend/src/main/resources/db/changelog/changes/20220309-create-database.xml
@@ -23,7 +23,7 @@
     https://www.liquibase.org/xml/ns/dbchangelog/dbchangelog-4.6.xsd">
     <property name="autoIncrement" value="true" dbms="h2,mysql,postgresql,oracle,mssql"/>
 
-    <changeSet id="Create observation tables" author="pim">
+    <changeSet id="Create observation tables" author="pim" context="dev">
         <createTable tableName="observation">
             <column name="id" type="bigint" autoIncrement="${autoIncrement}">
                 <constraints primaryKey="true" nullable="false"/>

From a08d811adc8d8a8ba862606103b6f0ed85c7bdcf Mon Sep 17 00:00:00 2001
From: Pim van Nierop <pim@thehyve.nl>
Date: Fri, 3 May 2024 12:58:16 +0200
Subject: [PATCH 04/10] Publish docker images on GitHub and docker hub

---
 .github/workflows/docker-image.yml | 12 ++++++++----
 .github/workflows/release.yml      |  2 +-
 2 files changed, 9 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/docker-image.yml b/.github/workflows/docker-image.yml
index 21a4e0c..03d0bd8 100644
--- a/.github/workflows/docker-image.yml
+++ b/.github/workflows/docker-image.yml
@@ -1,8 +1,6 @@
 #See: https://docs.github.com/en/actions/publishing-packages/publishing-docker-images#publishing-images-to-github-packages
 name: Create and publish a Docker image
-on:
-  release:
-    types: [ published ]
+on: push
 env:
   REGISTRY: ghcr.io
   IMAGE_NAME: ${{ github.repository }}
@@ -20,11 +18,17 @@ jobs:
           registry: ${{ env.REGISTRY }}
           username: ${{ github.actor }}
           password: ${{ secrets.GITHUB_TOKEN }}
+      - name: Set environment variables
+        run: |
+          # Short name for current branch. For PRs, use target branch (base ref)
+          GIT_BRANCH=${GITHUB_BASE_REF:-${GITHUB_REF#refs/heads/}}
+          echo "GIT_BRANCH=$GIT_BRANCH" >> $GITHUB_ENV
       - name: Extract metadata (tags, labels) for Docker
         id: meta
         uses: docker/metadata-action@9ec57ed1fcdbf14dcef7dfbe97b2010124a938b7
         with:
-          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}-${{ env.GIT_BRANCH }}
+          tags: latest
       - name: Build and push Docker image
         uses: docker/build-push-action@f2a1d5e99d037542a71f64918e516c093c6f3fc4
         with:
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index f2fddaa..0cb936a 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -23,7 +23,7 @@ jobs:
         id: docker_meta
         uses: docker/metadata-action@v4
         with:
-          images: ${{ env.DOCKER_IMAGE }}
+          images: ${{ env.DOCKER_IMAGE }}-${{ env.GIT_BRANCH }}
           tags: |
             type=semver,pattern={{version}}
             type=semver,pattern={{major}}.{{minor}}

From 42e111429e502a81822d1d248fd803eead3a9dbf Mon Sep 17 00:00:00 2001
From: Pim van Nierop <pim@thehyve.nl>
Date: Fri, 3 May 2024 15:26:30 +0200
Subject: [PATCH 05/10] Add project and source to Observation objects

---
 README.md                                     |  2 +-
 .../datadashboard/api/api/ObservationDto.kt   |  6 +++
 .../api/domain/ObservationRepository.kt       |  7 ++--
 .../api/domain/mapper/Extensions.kt           |  2 +
 .../api/domain/model/Observation.kt           |  7 ++++
 .../api/resource/ObservationResource.kt       |  5 ++-
 .../api/service/ObservationService.kt         |  4 +-
 .../changes/20220309-create-database.xml      |  7 ++++
 .../changes/20220321-observations.csv         | 18 ++++-----
 .../api/DashboardIntegrationTest.kt           |  4 +-
 .../api/resource/ObservationResourceTest.kt   | 39 ++++++++++++++-----
 .../api/service/ObservationServiceTest.kt     | 33 +++++++++++-----
 12 files changed, 96 insertions(+), 38 deletions(-)

diff --git a/README.md b/README.md
index f6ac611..eb746b2 100644
--- a/README.md
+++ b/README.md
@@ -13,7 +13,7 @@ the data from the RADAR-base kafka service.[]\
 
 Data dashboard applications can use the APIs as follows.
 
-`GET */subject/{subjectId}/topic/{topicId}/observations`
+`GET */project/{projectId}/subject/{subjectId}/topic/{topicId}/observations`
 
 ## Installation
 
diff --git a/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/api/ObservationDto.kt b/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/api/ObservationDto.kt
index 73ddc03..eaf7d0b 100644
--- a/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/api/ObservationDto.kt
+++ b/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/api/ObservationDto.kt
@@ -23,9 +23,15 @@ data class ObservationDto(
     /** Unique observation ID. */
     val id: Long?,
 
+    /** Unique identifier of project. */
+    val project: String?,
+
     /** Unique identifier of study subject. */
     val subject: String?,
 
+    /** Unique identifier of the data source. */
+    val source: String?,
+
     /** Unique identifier of the kafka topic. */
     val topic: String?,
 
diff --git a/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/domain/ObservationRepository.kt b/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/domain/ObservationRepository.kt
index 5db3759..5f82150 100644
--- a/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/domain/ObservationRepository.kt
+++ b/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/domain/ObservationRepository.kt
@@ -29,14 +29,15 @@ class ObservationRepository(
     @Context em: Provider<EntityManager>,
 ) : HibernateRepository(em) {
 
-    fun getObservations(topicId: String, subjectId: String): List<Observation> {
-        logger.debug("Get observations in topic {} of subject {}", topicId, subjectId)
+    fun getObservations(projectId: String, subjectId: String, topicId: String): List<Observation> {
+        logger.debug("Get observations in topic {} of subject {} in project {}", topicId, subjectId, projectId)
 
         return transact {
             createQuery(
-                "SELECT o FROM Observation o WHERE o.subject = :subjectId AND o.topic = :topicId ORDER BY o.date DESC",
+                "SELECT o FROM Observation o WHERE o.project = :projectId AND o.subject = :subjectId AND o.topic = :topicId ORDER BY o.date DESC",
                 Observation::class.java,
             ).apply {
+                setParameter("projectId", projectId)
                 setParameter("subjectId", subjectId)
                 setParameter("topicId", topicId)
             }.resultList
diff --git a/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/domain/mapper/Extensions.kt b/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/domain/mapper/Extensions.kt
index dc31d71..9d99177 100644
--- a/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/domain/mapper/Extensions.kt
+++ b/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/domain/mapper/Extensions.kt
@@ -24,7 +24,9 @@ import java.time.Duration
 
 fun Observation.toDto(): ObservationDto = ObservationDto(
     id = id,
+    project = project,
     subject = subject,
+    source = source,
     topic = topic,
     category = category,
     date = date?.toString(),
diff --git a/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/domain/model/Observation.kt b/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/domain/model/Observation.kt
index f464445..cba018d 100644
--- a/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/domain/model/Observation.kt
+++ b/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/domain/model/Observation.kt
@@ -30,10 +30,17 @@ data class Observation(
     @Id
     val id: Long,
 
+    @Column(nullable = false)
+    @Id
+    val project: String,
+
     @Column(nullable = false)
     @Id
     val subject: String,
 
+    @Id
+    val source: String,
+
     @Column(nullable = false)
     @Id
     val topic: String,
diff --git a/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/resource/ObservationResource.kt b/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/resource/ObservationResource.kt
index 9770b9c..3e3d4b9 100644
--- a/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/resource/ObservationResource.kt
+++ b/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/resource/ObservationResource.kt
@@ -30,7 +30,7 @@ import org.radarbase.jersey.auth.NeedsPermission
 import org.radarbase.jersey.auth.filter.RadarSecurityContext
 import org.slf4j.LoggerFactory
 
-@Path("subject/{subjectId}/topic/{topicId}")
+@Path("project/{projectId}/subject/{subjectId}/topic/{topicId}")
 @Resource
 @Produces("application/json")
 @Consumes("application/json")
@@ -43,6 +43,7 @@ class ObservationResource(
     @Path("observations")
     @NeedsPermission(Permission.MEASUREMENT_READ)
     fun getObservations(
+        @PathParam("projectId") projectId: String,
         @PathParam("subjectId") subjectId: String,
         @PathParam("topicId") topicId: String
     ): ObservationListDto {
@@ -50,7 +51,7 @@ class ObservationResource(
             val userName = (request.securityContext as RadarSecurityContext).userPrincipal
             log.info("User $userName is accessing observations for $subjectId")
             if (!subjectId.equals(userName)) throw NotFoundException("Subjects can only request their own observations.")
-            return observationService.getObservations(topicId, subjectId)
+            return observationService.getObservations(projectId = projectId, subjectId = subjectId, topicId = topicId)
         }
         return ObservationListDto(emptyList())
     }
diff --git a/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/service/ObservationService.kt b/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/service/ObservationService.kt
index 5086be2..9f5874c 100644
--- a/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/service/ObservationService.kt
+++ b/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/service/ObservationService.kt
@@ -26,8 +26,8 @@ import org.radarbase.datadashboard.api.domain.mapper.toDto
 class ObservationService(
     @Context private val observationRepository: ObservationRepository
 ) {
-    fun getObservations(topicId: String, subjectId: String): ObservationListDto {
-        val result = this.observationRepository.getObservations(topicId, subjectId)
+    fun getObservations(projectId: String, subjectId: String, topicId: String): ObservationListDto {
+        val result = this.observationRepository.getObservations(projectId = projectId, topicId = topicId, subjectId = subjectId)
         return ObservationListDto(
             result.map { it.toDto() },
         )
diff --git a/data-dashboard-backend/src/main/resources/db/changelog/changes/20220309-create-database.xml b/data-dashboard-backend/src/main/resources/db/changelog/changes/20220309-create-database.xml
index 41c6b51..32c9ad9 100644
--- a/data-dashboard-backend/src/main/resources/db/changelog/changes/20220309-create-database.xml
+++ b/data-dashboard-backend/src/main/resources/db/changelog/changes/20220309-create-database.xml
@@ -28,9 +28,15 @@
             <column name="id" type="bigint" autoIncrement="${autoIncrement}">
                 <constraints primaryKey="true" nullable="false"/>
             </column>
+            <column name="project" type="varchar(255)">
+                <constraints primaryKey="true" nullable="false"/>
+            </column>
             <column name="subject" type="varchar(255)">
                 <constraints primaryKey="true" nullable="false"/>
             </column>
+            <column name="source" type="varchar(255)">
+                <constraints primaryKey="true" nullable="false"/>
+            </column>
             <column name="topic" type="varchar(255)">
                 <constraints primaryKey="true" nullable="false"/>
             </column>
@@ -47,6 +53,7 @@
         </createTable>
 
         <createIndex tableName="observation" indexName="idx_observation_subject_in_topic">
+            <column name="project"/>
             <column name="subject"/>
             <column name="topic"/>
         </createIndex>
diff --git a/data-dashboard-backend/src/main/resources/db/changelog/changes/20220321-observations.csv b/data-dashboard-backend/src/main/resources/db/changelog/changes/20220321-observations.csv
index c7f744e..2d8302c 100644
--- a/data-dashboard-backend/src/main/resources/db/changelog/changes/20220321-observations.csv
+++ b/data-dashboard-backend/src/main/resources/db/changelog/changes/20220321-observations.csv
@@ -1,9 +1,9 @@
-subject;topic;category;variable;value_numeric;value_textual;date;end_date
-sub-1;questionnaire_answer;baseline_questions;Perceived_Pain_Score;5;NULL;2021-02-20 00:00:00;NULL
-sub-1;questionnaire_answer;followup_questions;Name_Of_Physician;NULL;Dr.J.Adams;2021-02-20 00:00:00;NULL
-sub-2;questionnaire_answer;baseline_questions;Perceived_Pain_Score;2;NULL;2021-02-20 00:00:00;NULL
-sub-2;questionnaire_answer;followup_questions;Name_Of_Physician;NULL;Dr.G.Washington;2022-05-20 00:00:00;NULL
-sub-1;phone_battery_level;NULL;batteryLevel;5;NULL;2021-02-20 00:00:00;NULL
-sub-1;phone_battery_level;NULL;status;NULL;CHARGING;2021-02-20 00:00:00;NULL
-sub-2;phone_battery_level;NULL;batteryLevel;10;NULL;2021-02-20 00:00:00;NULL
-sub-2;phone_battery_level;NULL;status;NULL;FULL;2021-02-20 00:00:00;NULL
+project;subject;source;topic;category;variable;value_numeric;value_textual;date;end_date
+project-1;sub-1;source-1;questionnaire_answer;baseline_questions;Perceived_Pain_Score;5;NULL;2021-02-20 00:00:00;NULL
+project-1;sub-1;source-1;questionnaire_answer;followup_questions;Name_Of_Physician;NULL;Dr.J.Adams;2021-02-20 00:00:00;NULL
+project-1;sub-2;source-1;questionnaire_answer;baseline_questions;Perceived_Pain_Score;2;NULL;2021-02-20 00:00:00;NULL
+project-1;sub-2;source-1;questionnaire_answer;followup_questions;Name_Of_Physician;NULL;Dr.G.Washington;2022-05-20 00:00:00;NULL
+project-1;sub-1;source-1;phone_battery_level;NULL;batteryLevel;5;NULL;2021-02-20 00:00:00;NULL
+project-1;sub-1;source-1;phone_battery_level;NULL;status;NULL;CHARGING;2021-02-20 00:00:00;NULL
+project-1;sub-2;source-1;phone_battery_level;NULL;batteryLevel;10;NULL;2021-02-20 00:00:00;NULL
+project-1;sub-2;source-1;phone_battery_level;NULL;status;NULL;FULL;2021-02-20 00:00:00;NULL
diff --git a/data-dashboard-backend/src/test/java/org/radarbase/datadashboard/api/DashboardIntegrationTest.kt b/data-dashboard-backend/src/test/java/org/radarbase/datadashboard/api/DashboardIntegrationTest.kt
index 07ea8a5..b73e411 100644
--- a/data-dashboard-backend/src/test/java/org/radarbase/datadashboard/api/DashboardIntegrationTest.kt
+++ b/data-dashboard-backend/src/test/java/org/radarbase/datadashboard/api/DashboardIntegrationTest.kt
@@ -71,13 +71,13 @@ class DashboardIntegrationTest: JerseyTest() {
 
     @Test
     fun testGetObservationsNoToken() {
-        val response = target("subject/sub-1/topic/phone_battery_level/observations").request().get()
+        val response = target("project/project-1/sub-1/topic/phone_battery_level/observations").request().get()
         Assertions.assertEquals(401, response.status)
     }
 
     @Test
     fun testGetObservationsWithToken() {
-        val response = target("subject/sub-1/topic/phone_battery_level/observations")
+        val response = target("project/project-1/subject/sub-1/topic/phone_battery_level/observations")
             .request()
             .header(HttpHeaders.AUTHORIZATION, "Bearer " + "... encoded token ...")
             .get()
diff --git a/data-dashboard-backend/src/test/java/org/radarbase/datadashboard/api/resource/ObservationResourceTest.kt b/data-dashboard-backend/src/test/java/org/radarbase/datadashboard/api/resource/ObservationResourceTest.kt
index fdcd68c..20122d9 100644
--- a/data-dashboard-backend/src/test/java/org/radarbase/datadashboard/api/resource/ObservationResourceTest.kt
+++ b/data-dashboard-backend/src/test/java/org/radarbase/datadashboard/api/resource/ObservationResourceTest.kt
@@ -36,11 +36,12 @@ import java.time.ZonedDateTime
 
 class ObservationResourceTest: JerseyTest() {
 
-
     @Mock
     lateinit var observationService: ObservationService
 
     private lateinit var observationListDto: ObservationListDto
+    private var observationId: Long = 1
+    private val projectId = "project-1"
     private val subjectId = "sub-1"
     private val topicId = "topic-1"
 
@@ -61,11 +62,7 @@ class ObservationResourceTest: JerseyTest() {
     @BeforeEach
     fun init() {
         // Create some fake observations that are returned by the service.
-        val obs1 = Observation(id = 1L, subject = subjectId, topic = "topic-1", category = "category-1", variable = "variable-1", date = ZonedDateTime.now(), valueTextual = "value1", valueNumeric = null, endDate = null)
-        val obs2 = Observation(id = 2L, subject = subjectId, topic = "topic-1", category = "category-1", variable = "variable-1", date = ZonedDateTime.now(), valueTextual = "value1", valueNumeric = null, endDate = null)
-        val obs3 = Observation(id = 3L, subject = subjectId, topic = "topic-1", category = "category-1", variable = "variable-1", date = ZonedDateTime.now(), valueTextual = "value1", valueNumeric = null, endDate = null)
-        val obs4 = Observation(id = 4L, subject = subjectId, topic = "topic-1", category = "category-1", variable = "variable-1", date = ZonedDateTime.now(), valueTextual = "value1", valueNumeric = null, endDate = null)
-        val observations: List<Observation> = listOf(obs1, obs2, obs3, obs4)
+        val observations: List<Observation> = listOf(createObservation(), createObservation(), createObservation(), createObservation())
         // Create Dto that should be returned by the ObservationService.
         observationListDto = ObservationListDto(
             observations.map { it.toDto() },
@@ -75,9 +72,9 @@ class ObservationResourceTest: JerseyTest() {
     @Test
     fun testGetObservations() {
         // Instruct the mock to return the fake observations when called.
-        `when`(observationService.getObservations(subjectId = subjectId, topicId = topicId)).thenReturn(observationListDto)
+        `when`(observationService.getObservations(projectId = projectId, subjectId = subjectId, topicId = topicId)).thenReturn(observationListDto)
         // Make the call to the REST endpoint.
-        val response = target("subject/sub-1/topic/topic-1/observations").request().get()
+        val response = target("project/project-1/subject/sub-1/topic/topic-1/observations").request().get()
         // Expect the http response to be OK and the same as the expected DTO.
         assertEquals(200, response.status)
         assertEquals(observationListDto, response.readEntity(ObservationListDto::class.java))
@@ -85,14 +82,36 @@ class ObservationResourceTest: JerseyTest() {
 
     @Test
     fun testGetObservations_failNoSubjectId() {
-        val response = target("subject//topic/topic-1/observations").request().get()
+        val response = target("project/project-1/subject//topic/topic-1/observations").request().get()
         assertEquals(404, response.status)
     }
 
     @Test
     fun testGetObservations_failNoTopicId() {
-        val response = target("subject/sub-1/topic//observations").request().get()
+        val response = target("project/project-1/subject/sub-1/topic//observations").request().get()
+        assertEquals(404, response.status)
+    }
+
+    @Test
+    fun testGetObservations_failNoProjectId() {
+        val response = target("project//subject/sub-1/topic/topic-1/observations").request().get()
         assertEquals(404, response.status)
     }
 
+    private fun createObservation(): Observation {
+        return Observation(
+            id = observationId,
+            project = "project-1",
+            subject = subjectId,
+            source = "source-1",
+            topic = "topic-1",
+            category = "category-1",
+            variable = "variable-1",
+            date = ZonedDateTime.now(),
+            valueTextual = "value1",
+            valueNumeric = null,
+            endDate = null
+        )
+    }
+
 }
\ No newline at end of file
diff --git a/data-dashboard-backend/src/test/java/org/radarbase/datadashboard/api/service/ObservationServiceTest.kt b/data-dashboard-backend/src/test/java/org/radarbase/datadashboard/api/service/ObservationServiceTest.kt
index 5fb1e1d..3d1b2f0 100644
--- a/data-dashboard-backend/src/test/java/org/radarbase/datadashboard/api/service/ObservationServiceTest.kt
+++ b/data-dashboard-backend/src/test/java/org/radarbase/datadashboard/api/service/ObservationServiceTest.kt
@@ -31,12 +31,15 @@ import java.time.ZonedDateTime
 
 class ObservationServiceTest {
 
-    val subjectId = "sub-1"
-
     // Create a Mockito mock of the ObservationRepository. This is instantiated in the init block.
     @Mock
     private lateinit var observationRepository: ObservationRepository
 
+    private var observationId: Long = 1
+    private val projectId = "project-1"
+    private val subjectId = "sub-1"
+    private val topicId = "topic-1"
+
     private val observationService: ObservationService
 
     init {
@@ -53,17 +56,13 @@ class ObservationServiceTest {
 
         // Create some fake observations that are returned by the repository.
         // Each observation is linked to a Variable.
-        val obs1 = Observation(id = 1L, subject = subjectId, topic = "topic-1", category = "category-1", variable = "variable-1", date = ZonedDateTime.now(), valueTextual = "value1", valueNumeric = null, endDate = null)
-        val obs2 = Observation(id = 2L, subject = subjectId, topic = "topic-1", category = "category-1", variable = "variable-1", date = ZonedDateTime.now(), valueTextual = "value1", valueNumeric = null, endDate = null)
-        val obs3 = Observation(id = 3L, subject = subjectId, topic = "topic-1", category = "category-1", variable = "variable-1", date = ZonedDateTime.now(), valueTextual = "value1", valueNumeric = null, endDate = null)
-        val obs4 = Observation(id = 4L, subject = subjectId, topic = "topic-1", category = "category-1", variable = "variable-1", date = ZonedDateTime.now(), valueTextual = "value1", valueNumeric = null, endDate = null)
-        val observations = listOf(obs1, obs2, obs3, obs4)
+        val observations: List<Observation> = listOf(createObservation(), createObservation(), createObservation(), createObservation())
 
         // Mock the repository to return the fake observations.
-        `when`(observationRepository.getObservations(subjectId = subjectId, topicId = "topic-1")).thenReturn(observations)
+        `when`(observationRepository.getObservations(projectId = projectId, subjectId = subjectId, topicId = topicId)).thenReturn(observations)
 
         // Call the ObservationService (class under test) to get the observations.
-        val result = observationService.getObservations(subjectId = subjectId, topicId = "topic-1")
+        val result = observationService.getObservations(projectId = projectId, subjectId = subjectId, topicId = topicId)
 
         // Check if the result is as expected (observations transformed to ObservationListDto).
         val expectedDto = ObservationListDto(
@@ -72,4 +71,20 @@ class ObservationServiceTest {
         assertEquals(expectedDto, result)
     }
 
+    private fun createObservation(): Observation {
+        return Observation(
+            id = observationId,
+            project = "project-1",
+            subject = subjectId,
+            source = "source-1",
+            topic = "topic-1",
+            category = "category-1",
+            variable = "variable-1",
+            date = ZonedDateTime.now(),
+            valueTextual = "value1",
+            valueNumeric = null,
+            endDate = null
+        )
+    }
+
 }
\ No newline at end of file

From 674599b00281f37bfea26a2ca19de76efbc99514 Mon Sep 17 00:00:00 2001
From: Pim van Nierop <pim@thehyve.nl>
Date: Tue, 14 May 2024 13:16:07 +0200
Subject: [PATCH 06/10] Remove 'id' field from database schema

---
 .../radarbase/datadashboard/api/domain/mapper/Extensions.kt  | 1 -
 .../radarbase/datadashboard/api/domain/model/Observation.kt  | 5 -----
 .../db/changelog/changes/20220309-create-database.xml        | 3 ---
 .../datadashboard/api/resource/ObservationResourceTest.kt    | 1 -
 .../datadashboard/api/service/ObservationServiceTest.kt      | 1 -
 5 files changed, 11 deletions(-)

diff --git a/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/domain/mapper/Extensions.kt b/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/domain/mapper/Extensions.kt
index 9d99177..4a1a299 100644
--- a/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/domain/mapper/Extensions.kt
+++ b/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/domain/mapper/Extensions.kt
@@ -23,7 +23,6 @@ import org.radarbase.datadashboard.api.domain.model.Observation
 import java.time.Duration
 
 fun Observation.toDto(): ObservationDto = ObservationDto(
-    id = id,
     project = project,
     subject = subject,
     source = source,
diff --git a/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/domain/model/Observation.kt b/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/domain/model/Observation.kt
index cba018d..cae8c91 100644
--- a/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/domain/model/Observation.kt
+++ b/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/domain/model/Observation.kt
@@ -25,11 +25,6 @@ import java.util.*
 @Entity
 @Table(name = "observation")
 data class Observation(
-    @GeneratedValue(strategy = GenerationType.IDENTITY)
-    @Column(updatable = false, nullable = false)
-    @Id
-    val id: Long,
-
     @Column(nullable = false)
     @Id
     val project: String,
diff --git a/data-dashboard-backend/src/main/resources/db/changelog/changes/20220309-create-database.xml b/data-dashboard-backend/src/main/resources/db/changelog/changes/20220309-create-database.xml
index 32c9ad9..dc9154b 100644
--- a/data-dashboard-backend/src/main/resources/db/changelog/changes/20220309-create-database.xml
+++ b/data-dashboard-backend/src/main/resources/db/changelog/changes/20220309-create-database.xml
@@ -25,9 +25,6 @@
 
     <changeSet id="Create observation tables" author="pim" context="dev">
         <createTable tableName="observation">
-            <column name="id" type="bigint" autoIncrement="${autoIncrement}">
-                <constraints primaryKey="true" nullable="false"/>
-            </column>
             <column name="project" type="varchar(255)">
                 <constraints primaryKey="true" nullable="false"/>
             </column>
diff --git a/data-dashboard-backend/src/test/java/org/radarbase/datadashboard/api/resource/ObservationResourceTest.kt b/data-dashboard-backend/src/test/java/org/radarbase/datadashboard/api/resource/ObservationResourceTest.kt
index 20122d9..333fa1d 100644
--- a/data-dashboard-backend/src/test/java/org/radarbase/datadashboard/api/resource/ObservationResourceTest.kt
+++ b/data-dashboard-backend/src/test/java/org/radarbase/datadashboard/api/resource/ObservationResourceTest.kt
@@ -100,7 +100,6 @@ class ObservationResourceTest: JerseyTest() {
 
     private fun createObservation(): Observation {
         return Observation(
-            id = observationId,
             project = "project-1",
             subject = subjectId,
             source = "source-1",
diff --git a/data-dashboard-backend/src/test/java/org/radarbase/datadashboard/api/service/ObservationServiceTest.kt b/data-dashboard-backend/src/test/java/org/radarbase/datadashboard/api/service/ObservationServiceTest.kt
index 3d1b2f0..aab6da5 100644
--- a/data-dashboard-backend/src/test/java/org/radarbase/datadashboard/api/service/ObservationServiceTest.kt
+++ b/data-dashboard-backend/src/test/java/org/radarbase/datadashboard/api/service/ObservationServiceTest.kt
@@ -73,7 +73,6 @@ class ObservationServiceTest {
 
     private fun createObservation(): Observation {
         return Observation(
-            id = observationId,
             project = "project-1",
             subject = subjectId,
             source = "source-1",

From b990a8bfdf59efcb2bf9f255ea702f858ed8570a Mon Sep 17 00:00:00 2001
From: Pim van Nierop <pim@thehyve.nl>
Date: Tue, 14 May 2024 14:30:27 +0200
Subject: [PATCH 07/10] Fix linting errors

---
 .../datadashboard/api/api/ObservationDto.kt         |  2 --
 .../api/config/DashboardServiceConfig.kt            |  2 +-
 .../datadashboard/api/domain/mapper/Extensions.kt   |  5 ++---
 .../datadashboard/api/domain/model/Observation.kt   |  5 ++++-
 .../api/enhancer/DashBoardApiEnhancerFactory.kt     |  2 +-
 .../api/enhancer/DashboardApiEnhancer.kt            |  5 ++---
 .../api/resource/ObservationResource.kt             | 13 +++++++++----
 .../datadashboard/api/service/ObservationService.kt |  2 +-
 .../datadashboard/api/DashboardIntegrationTest.kt   |  4 +---
 .../api/resource/ObservationResourceTest.kt         |  7 +++----
 .../api/service/ObservationServiceTest.kt           |  8 +++-----
 11 files changed, 27 insertions(+), 28 deletions(-)

diff --git a/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/api/ObservationDto.kt b/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/api/ObservationDto.kt
index eaf7d0b..a461531 100644
--- a/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/api/ObservationDto.kt
+++ b/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/api/ObservationDto.kt
@@ -20,8 +20,6 @@ package org.radarbase.datadashboard.api.api
 
 /** Single observation or data point. */
 data class ObservationDto(
-    /** Unique observation ID. */
-    val id: Long?,
 
     /** Unique identifier of project. */
     val project: String?,
diff --git a/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/config/DashboardServiceConfig.kt b/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/config/DashboardServiceConfig.kt
index 4e08ba0..74149bb 100644
--- a/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/config/DashboardServiceConfig.kt
+++ b/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/config/DashboardServiceConfig.kt
@@ -40,4 +40,4 @@ data class DashboardServiceConfig(
         tokenExpiryTimeInMinutes = System.getenv("RADAR_DATA_DASHBOARD_TOKEN_EXPIRY_TIME_IN_MINUTES")?.toLong() ?: tokenExpiryTimeInMinutes,
         persistentTokenExpiryInMin = System.getenv("RADAR_DATA_DASHBOARD_PERSISTENT_TOKEN_EXPIRY_IN_MIN")?.toLong() ?: persistentTokenExpiryInMin,
     )
-}
\ No newline at end of file
+}
diff --git a/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/domain/mapper/Extensions.kt b/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/domain/mapper/Extensions.kt
index 4a1a299..c6b46d8 100644
--- a/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/domain/mapper/Extensions.kt
+++ b/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/domain/mapper/Extensions.kt
@@ -28,12 +28,11 @@ fun Observation.toDto(): ObservationDto = ObservationDto(
     source = source,
     topic = topic,
     category = category,
-    date = date?.toString(),
-    period = if (date != null && endDate != null) {
+    date = date.toString(),
+    period = if (endDate != null) {
         Duration.between(date, endDate).toString()
     } else {
         null
     },
     value = valueNumeric ?: valueTextual,
 )
-
diff --git a/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/domain/model/Observation.kt b/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/domain/model/Observation.kt
index cae8c91..2b4378e 100644
--- a/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/domain/model/Observation.kt
+++ b/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/domain/model/Observation.kt
@@ -18,7 +18,10 @@
 
 package org.radarbase.datadashboard.api.domain.model
 
-import jakarta.persistence.*
+import jakarta.persistence.Column
+import jakarta.persistence.Entity
+import jakarta.persistence.Id
+import jakarta.persistence.Table
 import java.time.ZonedDateTime
 import java.util.*
 
diff --git a/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/enhancer/DashBoardApiEnhancerFactory.kt b/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/enhancer/DashBoardApiEnhancerFactory.kt
index 7dec3d3..9eea113 100644
--- a/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/enhancer/DashBoardApiEnhancerFactory.kt
+++ b/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/enhancer/DashBoardApiEnhancerFactory.kt
@@ -39,7 +39,7 @@ class DashBoardApiEnhancerFactory(
         HibernateResourceEnhancer(
             config.database.copy(
                 managedClasses = listOf(
-                    Observation::class.jvmName
+                    Observation::class.jvmName,
                 ),
             ),
         ),
diff --git a/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/enhancer/DashboardApiEnhancer.kt b/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/enhancer/DashboardApiEnhancer.kt
index 42f8108..6e806b4 100644
--- a/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/enhancer/DashboardApiEnhancer.kt
+++ b/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/enhancer/DashboardApiEnhancer.kt
@@ -18,11 +18,11 @@
 
 package org.radarbase.datadashboard.api.enhancer
 
+import jakarta.inject.Singleton
+import org.glassfish.jersey.internal.inject.AbstractBinder
 import org.radarbase.datadashboard.api.config.DashboardApiConfig
 import org.radarbase.datadashboard.api.domain.ObservationRepository
 import org.radarbase.datadashboard.api.service.ObservationService
-import jakarta.inject.Singleton
-import org.glassfish.jersey.internal.inject.AbstractBinder
 import org.radarbase.jersey.enhancer.JerseyResourceEnhancer
 import org.radarbase.jersey.filter.Filters
 
@@ -51,6 +51,5 @@ class DashboardApiEnhancer(
         bind(ObservationRepository::class.java)
             .to(ObservationRepository::class.java)
             .`in`(Singleton::class.java)
-
     }
 }
diff --git a/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/resource/ObservationResource.kt b/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/resource/ObservationResource.kt
index 3e3d4b9..ff6d948 100644
--- a/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/resource/ObservationResource.kt
+++ b/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/resource/ObservationResource.kt
@@ -19,12 +19,17 @@
 package org.radarbase.datadashboard.api.resource
 
 import jakarta.annotation.Resource
-import jakarta.ws.rs.*
+import jakarta.ws.rs.Consumes
+import jakarta.ws.rs.GET
+import jakarta.ws.rs.NotFoundException
+import jakarta.ws.rs.Path
+import jakarta.ws.rs.PathParam
+import jakarta.ws.rs.Produces
 import jakarta.ws.rs.container.ContainerRequestContext
 import jakarta.ws.rs.core.Context
-import org.radarbase.datadashboard.api.service.ObservationService
 import org.radarbase.auth.authorization.Permission
 import org.radarbase.datadashboard.api.api.ObservationListDto
+import org.radarbase.datadashboard.api.service.ObservationService
 import org.radarbase.jersey.auth.Authenticated
 import org.radarbase.jersey.auth.NeedsPermission
 import org.radarbase.jersey.auth.filter.RadarSecurityContext
@@ -37,7 +42,7 @@ import org.slf4j.LoggerFactory
 @Authenticated
 class ObservationResource(
     @Context private val observationService: ObservationService,
-    @Context private val request: ContainerRequestContext
+    @Context private val request: ContainerRequestContext,
 ) {
     @GET
     @Path("observations")
@@ -45,7 +50,7 @@ class ObservationResource(
     fun getObservations(
         @PathParam("projectId") projectId: String,
         @PathParam("subjectId") subjectId: String,
-        @PathParam("topicId") topicId: String
+        @PathParam("topicId") topicId: String,
     ): ObservationListDto {
         if (request.securityContext != null && request.securityContext is RadarSecurityContext) {
             val userName = (request.securityContext as RadarSecurityContext).userPrincipal
diff --git a/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/service/ObservationService.kt b/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/service/ObservationService.kt
index 9f5874c..e2bc479 100644
--- a/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/service/ObservationService.kt
+++ b/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/service/ObservationService.kt
@@ -24,7 +24,7 @@ import org.radarbase.datadashboard.api.domain.ObservationRepository
 import org.radarbase.datadashboard.api.domain.mapper.toDto
 
 class ObservationService(
-    @Context private val observationRepository: ObservationRepository
+    @Context private val observationRepository: ObservationRepository,
 ) {
     fun getObservations(projectId: String, subjectId: String, topicId: String): ObservationListDto {
         val result = this.observationRepository.getObservations(projectId = projectId, topicId = topicId, subjectId = subjectId)
diff --git a/data-dashboard-backend/src/test/java/org/radarbase/datadashboard/api/DashboardIntegrationTest.kt b/data-dashboard-backend/src/test/java/org/radarbase/datadashboard/api/DashboardIntegrationTest.kt
index b73e411..d1dd263 100644
--- a/data-dashboard-backend/src/test/java/org/radarbase/datadashboard/api/DashboardIntegrationTest.kt
+++ b/data-dashboard-backend/src/test/java/org/radarbase/datadashboard/api/DashboardIntegrationTest.kt
@@ -35,8 +35,7 @@ import org.radarbase.jersey.auth.AuthValidator
 import org.radarbase.jersey.auth.disabled.DisabledAuthValidator
 import org.radarbase.jersey.config.ConfigLoader
 
-
-class DashboardIntegrationTest: JerseyTest() {
+class DashboardIntegrationTest : JerseyTest() {
 
     lateinit var disabledAuthValidator: DisabledAuthValidator
 
@@ -85,5 +84,4 @@ class DashboardIntegrationTest: JerseyTest() {
     }
 
     // TODO add more tests that include the token validation.
-
 }
diff --git a/data-dashboard-backend/src/test/java/org/radarbase/datadashboard/api/resource/ObservationResourceTest.kt b/data-dashboard-backend/src/test/java/org/radarbase/datadashboard/api/resource/ObservationResourceTest.kt
index 333fa1d..a3e007e 100644
--- a/data-dashboard-backend/src/test/java/org/radarbase/datadashboard/api/resource/ObservationResourceTest.kt
+++ b/data-dashboard-backend/src/test/java/org/radarbase/datadashboard/api/resource/ObservationResourceTest.kt
@@ -34,7 +34,7 @@ import org.radarbase.datadashboard.api.domain.model.Observation
 import org.radarbase.datadashboard.api.service.ObservationService
 import java.time.ZonedDateTime
 
-class ObservationResourceTest: JerseyTest() {
+class ObservationResourceTest : JerseyTest() {
 
     @Mock
     lateinit var observationService: ObservationService
@@ -109,8 +109,7 @@ class ObservationResourceTest: JerseyTest() {
             date = ZonedDateTime.now(),
             valueTextual = "value1",
             valueNumeric = null,
-            endDate = null
+            endDate = null,
         )
     }
-
-}
\ No newline at end of file
+}
diff --git a/data-dashboard-backend/src/test/java/org/radarbase/datadashboard/api/service/ObservationServiceTest.kt b/data-dashboard-backend/src/test/java/org/radarbase/datadashboard/api/service/ObservationServiceTest.kt
index aab6da5..8c86c53 100644
--- a/data-dashboard-backend/src/test/java/org/radarbase/datadashboard/api/service/ObservationServiceTest.kt
+++ b/data-dashboard-backend/src/test/java/org/radarbase/datadashboard/api/service/ObservationServiceTest.kt
@@ -53,7 +53,6 @@ class ObservationServiceTest {
      * */
     @Test
     fun test_getObservations1() {
-
         // Create some fake observations that are returned by the repository.
         // Each observation is linked to a Variable.
         val observations: List<Observation> = listOf(createObservation(), createObservation(), createObservation(), createObservation())
@@ -66,7 +65,7 @@ class ObservationServiceTest {
 
         // Check if the result is as expected (observations transformed to ObservationListDto).
         val expectedDto = ObservationListDto(
-            observations.map { it.toDto() }
+            observations.map { it.toDto() },
         )
         assertEquals(expectedDto, result)
     }
@@ -82,8 +81,7 @@ class ObservationServiceTest {
             date = ZonedDateTime.now(),
             valueTextual = "value1",
             valueNumeric = null,
-            endDate = null
+            endDate = null,
         )
     }
-
-}
\ No newline at end of file
+}

From 3a1d7b5ebcf81d00c5de36ecaf88f17d3fbee8b3 Mon Sep 17 00:00:00 2001
From: Pim van Nierop <pim@thehyve.nl>
Date: Wed, 29 May 2024 10:27:21 +0200
Subject: [PATCH 08/10] Fix docker image name

---
 .github/workflows/release.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index 0cb936a..6bb4eb3 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -6,7 +6,7 @@ on:
     types: [published]
 
 env:
-  DOCKER_IMAGE: radarbase/data-dashboard-backend
+  DOCKER_IMAGE: radarbase/radar-data-dashboard-backend
 
 jobs:
   # Build and push tagged release docker image

From 68f176c35d26b4b886f7a4ec6a7d2bfd0de196f0 Mon Sep 17 00:00:00 2001
From: Pim van Nierop <pim@thehyve.nl>
Date: Wed, 29 May 2024 10:30:15 +0200
Subject: [PATCH 09/10] Remove 'category' from primary key colums

---
 .../org/radarbase/datadashboard/api/domain/model/Observation.kt  | 1 -
 1 file changed, 1 deletion(-)

diff --git a/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/domain/model/Observation.kt b/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/domain/model/Observation.kt
index 2b4378e..c642f31 100644
--- a/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/domain/model/Observation.kt
+++ b/data-dashboard-backend/src/main/java/org/radarbase/datadashboard/api/domain/model/Observation.kt
@@ -43,7 +43,6 @@ data class Observation(
     @Id
     val topic: String,
 
-    @Id
     val category: String,
 
     @Column(nullable = false)

From 93f56ac50d2ae230ef23eff6177b79150a390c17 Mon Sep 17 00:00:00 2001
From: Pim van Nierop <pim@thehyve.nl>
Date: Wed, 29 May 2024 10:31:12 +0200
Subject: [PATCH 10/10] Update docs

---
 README.md | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/README.md b/README.md
index eb746b2..ff0ce91 100644
--- a/README.md
+++ b/README.md
@@ -43,8 +43,7 @@ The OAuth client for authorizer-app-backend should have the following properties
 ```properties
 client-id:data_dashboard_api
 client-secret:Confidential
-grant-type:client_credentials
+grant-type:authorization_code,refresh_token
 resources:res_DataDashboardAPI
 scope:MEASUREMENT.READ
 ```
-