Add project and source to Observation objects

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
 

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?,
 

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

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(),

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,

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")
@@ -43,14 +43,15 @@ class ObservationResource(
     @Path("observations")
     @NeedsPermission(Permission.MEASUREMENT_READ)
     fun getObservations(
+        @PathParam("projectId") projectId: String,
         @PathParam("subjectId") subjectId: String,
         @PathParam("topicId") topicId: String
     ): ObservationListDto {
         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 observationService.getObservations(projectId = projectId, subjectId = subjectId, topicId = topicId)
         }
         return ObservationListDto(emptyList())
     }

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() },
         )

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>

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

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()

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() },
@@ -75,24 +72,46 @@ 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))
     }
 
     @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
+        )
+    }
+
 }

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
+        )
+    }
+
 }