Release 1.0.6

build.gradle

@@ -9,7 +9,7 @@ plugins {
 }
 
 group = 'org.radarbase'
-version = '1.0.5'
+version = '1.0.6'
 
 application {
     mainClass = 'org.radarbase.redcap.webapp.GrizzlyServer'

src/integration-test/kotlin/org/radarbase/redcap/EntryPointTest.kt

@@ -34,7 +34,7 @@ class EntryPointTest {
         val subject: Subject? =
             mpClient.getSubject(URL(REDCAP_URL), REDCAP_PROJECT_ID, REDCAP_RECORD_ID_2)
         Assert.assertNotNull(subject)
-        Assert.assertEquals(Integer.valueOf(REDCAP_RECORD_ID_2), subject?.externalId)
+        Assert.assertEquals(REDCAP_RECORD_ID_2.toString(), subject?.externalId)
         Assert.assertEquals(
             "$WORK_PACKAGE-$MP_PROJECT_ID-$MP_PROJECT_LOCATION-$REDCAP_RECORD_ID_2",
             subject?.humanReadableIdentifier

src/integration-test/kotlin/org/radarbase/redcap/integration/IntegratorTest.kt

@@ -105,7 +105,7 @@ class IntegratorTest {
 
         assertNotNull(subject)
         assertEquals(
-            Integer.valueOf(REDCAP_RECORD_ID_2),
+            REDCAP_RECORD_ID_2.toString(),
             subject?.externalId
         )
         assertEquals(

src/integration-test/kotlin/org/radarbase/redcap/managementportal/MpClientTest.kt

@@ -15,8 +15,8 @@ import java.net.URL
 @FixMethodOrder(MethodSorters.NAME_ASCENDING)
 class MpClientTest {
     private var project: Project? = null
-    private val testAttributes: Map<String, String> =
-        HashMap()
+    private val emptyAttributes: Map<String, String> = HashMap()
+    private val attributes: Map<String, String> = mapOf("group" to "test")
 
     @Before
     @Throws(IOException::class, TokenException::class)
@@ -42,7 +42,7 @@ class MpClientTest {
         }
         mpClient.createSubject(
             URL(IntegrationUtils.REDCAP_URL), project!!, IntegrationUtils.REDCAP_RECORD_ID_1,
-            IntegrationUtils.WORK_PACKAGE + IntegrationUtils.REDCAP_RECORD_ID_1, testAttributes
+            IntegrationUtils.WORK_PACKAGE + IntegrationUtils.REDCAP_RECORD_ID_1, emptyAttributes
         )
         val subject =
             mpClient.getSubject(
@@ -51,7 +51,7 @@ class MpClientTest {
             )
         Assert.assertNotNull(subject)
         Assert.assertEquals(
-            Integer.valueOf(IntegrationUtils.REDCAP_RECORD_ID_1),
+            IntegrationUtils.REDCAP_RECORD_ID_1.toString(),
             subject!!.externalId
         )
         Assert.assertEquals(
@@ -69,7 +69,27 @@ class MpClientTest {
         // This should throw exception since subject already exists
         mpClient.createSubject(
             URL(IntegrationUtils.REDCAP_URL), project!!, IntegrationUtils.REDCAP_RECORD_ID_1,
-            IntegrationUtils.WORK_PACKAGE + IntegrationUtils.REDCAP_RECORD_ID_1, testAttributes
+            IntegrationUtils.WORK_PACKAGE + IntegrationUtils.REDCAP_RECORD_ID_1, emptyAttributes
         )
     }
+
+    @Test
+    @Throws(IOException::class, URISyntaxException::class)
+    fun updateSubjectTest() {
+        if (project == null) {
+            projectTest()
+        }
+        val subject =
+            mpClient.getSubject(
+                URL(IntegrationUtils.REDCAP_URL), IntegrationUtils.REDCAP_PROJECT_ID,
+                IntegrationUtils.REDCAP_RECORD_ID_1
+            )
+        subject?.addAttributes(attributes)
+        val newSubject = mpClient.updateSubject(subject!!)
+
+        Assert.assertNotNull(newSubject)
+        Assert.assertEquals(subject, newSubject)
+        Assert.assertEquals(subject.attributes, newSubject.attributes)
+        Assert.assertEquals(subject.sources, newSubject.sources)
+    }
 }

src/main/kotlin/org/radarbase/redcap/config/RedCapManager.kt

@@ -97,7 +97,7 @@ object RedCapManager {
      * @throws NoSuchElementException In case the [URL] does not contain any characters
      */
     @Throws(MalformedURLException::class, NoSuchElementException::class)
-    fun getRecordUrl(redCapUrl: URL, projectId: Int, recordId: Int): URL {
+    fun getRecordUrl(redCapUrl: URL, projectId: Int, recordId: Int): String {
         val redCapInfo = getRedCapInfo(redCapUrl, projectId)
         var redCap = redCapInfo.url.toString()
 
@@ -107,6 +107,6 @@ object RedCapManager {
 
         redCap = "$redCap$PROJECT_ID$projectId$RECORD_ID$recordId" +
                 "$EVENT_ID${redCapInfo.enrolmentEvent}$PAGE_NAME${redCapInfo.integrationForm}"
-        return URL(redCap)
+        return URL(redCap).toString()
     }
 }

src/main/kotlin/org/radarbase/redcap/managementportal/MpClient.kt

@@ -129,15 +129,16 @@ open class MpClient @Inject constructor(private val httpClient: OkHttpClient) {
         val radarSubjectId = UUID.randomUUID().toString()
         val subject = Subject(
             subjectId = radarSubjectId,
-            externalId = recordId,
+            externalId = recordId.toString(),
             externalLink = RedCapManager.getRecordUrl(
                 redcapUrl,
                 project.redCapId!!,
                 recordId
             ),
             project = project,
             humanReadableId = humanReadableId,
-            attributes = attributes
+            attributes = attributes,
+            sources = listOf()
         )
         val request =
             getBuilder(Properties.subjectEndPoint).post(
@@ -182,26 +183,23 @@ open class MpClient @Inject constructor(private val httpClient: OkHttpClient) {
                 recordId
             )
         ).get().build()
-
         return performRequest(
             request = request,
             onSuccess = { response ->
-                val subjects =
-                    Subject.subjects(
-                        response
-                    )
-                if (subjects.size == 0) {
-                    LOGGER.info("Subject is not present")
+                val subjects = Subject.subjects(response)
+                    .filter { it.externalId.toString() == recordId.toString() }
+                if (subjects.isEmpty()) {
+                    LOGGER.info("Subject with externalId $recordId is not present")
                     return@performRequest null
                 }
+
                 check(subjects.size <= 1) {
-                    ("More than 1 subjects exist with same "
-                            + "externalId in the same Project")
+                    "More than one subject exists with the same externalId ($recordId) in the same project"
                 }
-                subjects[0]
+                subjects.first()
             },
             onError = {
-                LOGGER.info("Subject is not present")
+                LOGGER.info("Failed to retrieve subject with externalId $recordId")
                 null
             },
             errorMessage = "Subject could not be retrieved"
@@ -264,6 +262,7 @@ open class MpClient @Inject constructor(private val httpClient: OkHttpClient) {
                 .addPathSegment(projectName)
                 .addPathSegment("subjects")
                 .addQueryParameter("externalId", recordId.toString())
+                .addQueryParameter("size", Int.MAX_VALUE.toString())
                 .build()
             return subjectUrl.toUrl()
         }

src/main/kotlin/org/radarbase/redcap/managementportal/Organization.kt

@@ -3,6 +3,9 @@ package org.radarbase.redcap.managementportal
 import com.fasterxml.jackson.core.JsonParser
 import com.fasterxml.jackson.databind.DeserializationContext
 import com.fasterxml.jackson.databind.JsonDeserializer
+import com.fasterxml.jackson.core.JsonGenerator
+import com.fasterxml.jackson.databind.JsonSerializer
+import com.fasterxml.jackson.databind.SerializerProvider
 import com.fasterxml.jackson.databind.ObjectMapper
 import com.fasterxml.jackson.databind.JsonNode
 import com.fasterxml.jackson.databind.annotation.JsonDeserialize
@@ -33,4 +36,17 @@ class OrganizationDeserializer : JsonDeserializer<Organization>() {
             }
         }
     }
+}
+
+class OrganizationSerializer : JsonSerializer<Organization>() {
+    override fun serialize(value: Organization, gen: JsonGenerator, serializers: SerializerProvider) {
+        when (value) {
+            is Organization.StringOrganization -> {
+                gen.writeString(value.value)
+            }
+            is Organization.ObjectOrganization -> {
+                gen.writeObject(value.value)
+            }
+        }
+    }
 }

src/main/kotlin/org/radarbase/redcap/managementportal/Project.kt

@@ -3,6 +3,7 @@ package org.radarbase.redcap.managementportal
 import com.fasterxml.jackson.annotation.JsonIgnore
 import com.fasterxml.jackson.annotation.JsonProperty
 import com.fasterxml.jackson.databind.annotation.JsonDeserialize
+import com.fasterxml.jackson.databind.annotation.JsonSerialize
 import com.fasterxml.jackson.databind.DeserializationFeature
 import com.fasterxml.jackson.databind.ObjectMapper
 import com.fasterxml.jackson.module.kotlin.KotlinModule
@@ -32,7 +33,12 @@ import org.radarbase.redcap.managementportal.Organization
 data class Project(
     @JsonProperty("id") val id: Int,
     @JsonProperty("projectName") val projectName: String,
-    @JsonProperty("organization") @JsonDeserialize(using = OrganizationDeserializer::class) val organization: Organization,
+
+    @JsonProperty("organization") 
+    @JsonDeserialize(using = OrganizationDeserializer::class) 
+    @JsonSerialize(using = OrganizationSerializer::class)
+    val organization: Organization,
+
     @JsonProperty("location") val location: String = "",
     @JsonProperty("attributes") val attributes: Map<String, String> = emptyMap()
 ) {

src/main/kotlin/org/radarbase/redcap/managementportal/Subject.kt

@@ -31,19 +31,20 @@ import java.net.URL
 /**
  * Constructor.
  * @param subjectId [String] representing Management Portal Subject identifier
- * @param externalId [Integer] representing the REDCap Record identifier
- * @param externalLink [URL] pointing the REDCap integration form / instrument
+ * @param externalId [String] representing the REDCap Record identifier
+ * @param externalLink [String] pointing the REDCap integration form / instrument
  * @param project [Project] associated with the subject
  * @param attributes [Map] of key,value pairs
  */
 data class Subject(
     @JsonProperty("id") val mpId: Long?,
     @JsonProperty("login") val subjectId: String,
-    @JsonProperty("externalId") val externalId: Int? = null,
-    @JsonProperty("externalLink") val externalLink: URL? = null,
+    @JsonProperty("externalId") val externalId: String? = null,
+    @JsonProperty("externalLink") val externalLink: String? = null,
     @JsonProperty("project") var project: Project? = null,
     @JsonProperty("attributes") val attributes: MutableMap<String, String> = mutableMapOf(),
-    @JsonProperty("status") val status: String = SubjectStatus.ACTIVATED.toString()
+    @JsonProperty("status") val status: String = SubjectStatus.ACTIVATED.toString(),
+    @JsonProperty("sources") val sources: List<JsonNode>
 ) {
     enum class SubjectStatus {
         DEACTIVATED, ACTIVATED, DISCONTINUED, INVALID
@@ -57,32 +58,42 @@ data class Subject(
     var operationStatus: SubjectOperationStatus =
         SubjectOperationStatus.NOOP
 
-
     /**
      * Constructor.
      * @param subjectId [String] representing Management Portal Subject identifier
      * @param externalId [Integer] representing the REDCap Record identifier
-     * @param externalLink [URL] pointing the REDCap integration form / instrument
+     * @param  [URL] pointing the REDCap integration form / instrument
      * @param project [Project] associated with the subject
      * @param humanReadableId [String] representing the value associated with
      * [.HUMAN_READABLE_IDENTIFIER_KEY]
      */
     constructor(
-        subjectId: String, externalId: Int, externalLink: URL, project: Project,
-        humanReadableId: String
+        subjectId: String,
+        externalId: String,
+        externalLink: String,
+        project: Project,
+        humanReadableId: String,
+        sources: List<JsonNode>
     ) : this(
-        null, subjectId, externalId, externalLink, project,
-        mutableMapOf<String, String>(Pair(HUMAN_READABLE_IDENTIFIER_KEY, humanReadableId))
+        null,
+        subjectId,
+        externalId,
+        externalLink,
+        project,
+        mutableMapOf(Pair(HUMAN_READABLE_IDENTIFIER_KEY, humanReadableId)),
+        SubjectStatus.ACTIVATED.toString(),
+        sources
     )
 
     constructor(
         subjectId: String,
-        externalId: Int,
-        externalLink: URL,
+        externalId: String,
+        externalLink: String,
         project: Project,
         humanReadableId: String,
-        attributes: Map<String, String>
-    ) : this(subjectId, externalId, externalLink, project, humanReadableId) {
+        attributes: Map<String, String>,
+        sources: List<JsonNode>
+    ) : this(subjectId, externalId, externalLink, project, humanReadableId, sources) {
         addAttributes(attributes)
     }