Update tracing and appointments logic (#30)

* update tracing and appointments logic

* Update AppointmentRegisterDao.kt

android/engine/src/main/java/org/smartregister/fhircore/engine/data/local/register/dao/AppointmentRegisterDao.kt

@@ -16,9 +16,13 @@
 
 package org.smartregister.fhircore.engine.data.local.register.dao
 
+import ca.uhn.fhir.rest.gclient.TokenClientParam
 import ca.uhn.fhir.rest.param.ParamPrefixEnum
 import com.google.android.fhir.FhirEngine
 import com.google.android.fhir.logicalId
+import com.google.android.fhir.search.Operation
+import com.google.android.fhir.search.filter.TokenParamFilterCriterion
+import com.google.android.fhir.search.has
 import com.google.android.fhir.search.search
 import java.util.Calendar
 import javax.inject.Inject
@@ -44,7 +48,7 @@ import org.smartregister.fhircore.engine.domain.model.RegisterData
 import org.smartregister.fhircore.engine.domain.repository.RegisterDao
 import org.smartregister.fhircore.engine.domain.util.PaginationConstant
 import org.smartregister.fhircore.engine.util.DefaultDispatcherProvider
-import org.smartregister.fhircore.engine.util.LOGGED_IN_PRACTITIONER
+import org.smartregister.fhircore.engine.util.SharedPreferenceKey
 import org.smartregister.fhircore.engine.util.SharedPreferencesHelper
 import org.smartregister.fhircore.engine.util.extension.asReference
 import org.smartregister.fhircore.engine.util.extension.extractAge
@@ -65,7 +69,10 @@ constructor(
 ) : RegisterDao {
 
   private val currentPractitioner by lazy {
-    sharedPreferencesHelper.read<Practitioner>(key = LOGGED_IN_PRACTITIONER, decodeWithGson = true)
+    sharedPreferencesHelper.read(
+      key = SharedPreferenceKey.PRACTITIONER_ID.name,
+      defaultValue = null
+    )
   }
 
   private fun Appointment.patientRef() =
@@ -85,7 +92,6 @@ constructor(
     return fhirEngine
       .search<Appointment> {
         filter(Appointment.STATUS, { value = of(Appointment.AppointmentStatus.BOOKED.toCode()) })
-        filter(Appointment.DATE, { value = of(DateTimeType.today()) })
       }
       .map { it.resource }
       .count {
@@ -116,6 +122,7 @@ constructor(
     page: Int = -1
   ): List<Appointment> {
     filters as AppointmentRegisterFilter
+    val patientTypeFilterTag = applicationConfiguration().patientTypeFilterTagViaMetaCodingSystem
     val searchResults =
       fhirEngine.search<Appointment> {
         if (!loadAll) count = PaginationConstant.DEFAULT_PAGE_SIZE
@@ -139,33 +146,31 @@ constructor(
           }
         )
 
-        //        if (filters.myPatients && currentPractititoner != null)
-        //          filter(Appointment.PRACTITIONER, { value =
-        // currentPractititoner!!.referenceValue() })
-        //
-        //        filters.patientCategory?.let {
-        //          val paramQueries: List<(TokenParamFilterCriterion.() -> Unit)> =
-        //            it.flatMap { healthStatus ->
-        //              val coding: Coding =
-        //                Coding().apply {
-        //                  system = "https://d-tree.org"
-        //                  code = healthStatus.name.lowercase().replace("_", "-")
-        //                }
-        //              val alternativeCoding: Coding =
-        //                Coding().apply {
-        //                  system = "https://d-tree.org"
-        //                  code = healthStatus.name.lowercase()
-        //                }
-        //
-        //              return@flatMap listOf<Coding>(coding, alternativeCoding).map<
-        //                Coding, TokenParamFilterCriterion.() -> Unit> { c -> { value = of(c) } }
-        //            }
-        //
-        //          has<Patient>(Appointment.PATIENT){
-        //            filter(TokenClientParam("_tag"), *paramQueries.toTypedArray(), operation =
-        // Operation.OR)
-        //          }
-        //        }
+        if (filters.myPatients && currentPractitioner != null)
+          filter(Appointment.PRACTITIONER, { value = currentPractitioner!! })
+
+        filters.patientCategory?.let {
+          val paramQueries: List<(TokenParamFilterCriterion.() -> Unit)> =
+            it.flatMap { healthStatus ->
+              val coding: Coding =
+                Coding().apply {
+                  system = patientTypeFilterTag
+                  code = healthStatus.name.lowercase().replace("_", "-")
+                }
+              val alternativeCoding: Coding =
+                Coding().apply {
+                  system = patientTypeFilterTag
+                  code = healthStatus.name.lowercase()
+                }
+
+              return@flatMap listOf<Coding>(coding, alternativeCoding).map<
+                Coding, TokenParamFilterCriterion.() -> Unit> { c -> { value = of(c) } }
+            }
+
+          has<Patient>(Appointment.PATIENT) {
+            filter(TokenClientParam("_tag"), *paramQueries.toTypedArray(), operation = Operation.OR)
+          }
+        }
 
         filters.reasonCode?.let {
           val codeableConcept =
@@ -184,7 +189,8 @@ constructor(
     return searchResults.map { it.resource }.filter {
       val patientAssignmentFilter =
         !filters.myPatients ||
-          (it.practitionerRef()?.reference == currentPractitioner?.asReference()?.reference)
+          (it.practitionerRef()?.reference ==
+            currentPractitioner?.asReference(ResourceType.Practitioner)?.reference)
       val patientCategoryFilter =
         filters.patientCategory == null || (patientCategoryMatches(it, filters.patientCategory))
 
@@ -195,7 +201,8 @@ constructor(
         it.hasStart() &&
         patientAssignmentFilter &&
         patientCategoryFilter &&
-        appointmentReasonFilter
+        appointmentReasonFilter &&
+        it.patientRef() != null
     }
   }
 

android/engine/src/main/java/org/smartregister/fhircore/engine/data/local/register/dao/HomeTracingRegisterDao.kt

@@ -46,5 +46,10 @@ constructor(
     sharedPreferencesHelper
   ) {
 
-  override val tracingCoding: Coding = Coding("https://d-tree.org", "home-tracing", "Home Tracing")
+  override val tracingCoding: Coding = taskCode
+
+  companion object {
+    val taskCode: Coding =
+      Coding("https://d-tree.org/fhir/contact-tracing", "home-tracing", "Home Tracing")
+  }
 }

android/engine/src/main/java/org/smartregister/fhircore/engine/data/local/register/dao/PhoneTracingRegisterDao.kt

@@ -46,6 +46,10 @@ constructor(
     sharedPreferencesHelper
   ) {
 
-  override val tracingCoding: Coding =
-    Coding("https://d-tree.org", "phone-tracing", "Phone Tracing")
+  override val tracingCoding: Coding = taskCode
+
+  companion object {
+    val taskCode: Coding =
+      Coding("https://d-tree.org/fhir/contact-tracing", "phone-tracing", "Phone Tracing")
+  }
 }

android/engine/src/main/java/org/smartregister/fhircore/engine/data/local/register/dao/TracingRegisterDao.kt

@@ -56,7 +56,7 @@ import org.smartregister.fhircore.engine.domain.model.RegisterData
 import org.smartregister.fhircore.engine.domain.repository.RegisterDao
 import org.smartregister.fhircore.engine.domain.util.PaginationConstant
 import org.smartregister.fhircore.engine.util.DefaultDispatcherProvider
-import org.smartregister.fhircore.engine.util.LOGGED_IN_PRACTITIONER
+import org.smartregister.fhircore.engine.util.SharedPreferenceKey
 import org.smartregister.fhircore.engine.util.SharedPreferencesHelper
 import org.smartregister.fhircore.engine.util.extension.asDdMmmYyyy
 import org.smartregister.fhircore.engine.util.extension.asReference
@@ -94,7 +94,10 @@ constructor(
     patient.extractOfficialIdentifier() ?: HivRegisterDao.ResourceValue.BLANK
 
   private val currentPractitioner by lazy {
-    sharedPreferencesHelper.read<Practitioner>(key = LOGGED_IN_PRACTITIONER, decodeWithGson = true)
+    sharedPreferencesHelper.read(
+      key = SharedPreferenceKey.PRACTITIONER_ID.name,
+      defaultValue = null
+    )
   }
 
   private val filtersForValidTask: BaseSearch.() -> Unit = {
@@ -125,6 +128,7 @@ constructor(
     page: Int = -1
   ): List<Pair<Patient, Iterable<Task>>> {
     filters as TracingRegisterFilter
+    val filterFilter = applicationConfiguration().patientTypeFilterTagViaMetaCodingSystem
     val patients: List<Patient> =
       fhirEngine
         .search<Patient> {
@@ -139,12 +143,12 @@ constructor(
               it.flatMap { healthStatus ->
                 val coding: Coding =
                   Coding().apply {
-                    system = "https://d-tree.org"
+                    system = filterFilter
                     code = healthStatus.name.lowercase().replace("_", "-")
                   }
                 val alternativeCoding: Coding =
                   Coding().apply {
-                    system = "https://d-tree.org"
+                    system = filterFilter
                     code = healthStatus.name.lowercase()
                   }
 
@@ -155,8 +159,11 @@ constructor(
             filter(TokenClientParam("_tag"), *paramQueries.toTypedArray(), operation = Operation.OR)
           }
 
-          if (filters.isAssignedToMe) {
-            filter(Patient.GENERAL_PRACTITIONER, { value = currentPractitioner!!.referenceValue() })
+          if (filters.isAssignedToMe && currentPractitioner != null) {
+            filter(
+              Patient.GENERAL_PRACTITIONER,
+              { value = currentPractitioner?.asReference(ResourceType.Practitioner)?.reference }
+            )
           }
         }
         .map { it.resource }
@@ -298,8 +305,9 @@ constructor(
           .patientTypeFilterTagViaMetaCodingSystem
       val tasks = validTasks(patient)
 
-      val attempt = tracingRepository.getTracingAttempt(patient)
+      val attempt = tracingRepository.getTracingAttempt(patient, tasks)
       var dueData = getDueDate(it)
+
       if (dueData == null) {
         tasks.minOfOrNull { task -> task.authoredOn }?.let { date -> dueData = date }
       }
@@ -354,7 +362,7 @@ constructor(
         subjectType = ResourceType.Patient,
         subjectParam = CarePlan.SUBJECT
       )
-      .filter { carePlan -> carePlan.status.equals(CarePlan.CarePlanStatus.ACTIVE) }
+      .filter { carePlan -> carePlan.status == CarePlan.CarePlanStatus.ACTIVE }
 
   suspend fun Patient.activeConditions() =
     defaultRepository.patientConditions(this.logicalId).filter { condition ->
@@ -364,6 +372,7 @@ constructor(
   suspend fun Patient.practitioners(): List<Practitioner> {
     return generalPractitioner.mapNotNull {
       try {
+        if (it.reference == null) return@mapNotNull null
         val id = it.reference.replace("Practitioner/", "")
         fhirEngine.get(ResourceType.Practitioner, id) as Practitioner
       } catch (e: Exception) {
@@ -427,6 +436,7 @@ constructor(
       tracingRepository
         .getTracingAttempt(list = listResource)
         .copy(reasons = tasks.mapNotNull { task -> task.reasonCode?.codingFirstRep?.code })
+
     val oldestTaskDate = tasks.minOfOrNull { it.authoredOn }
     return RegisterData.TracingRegisterData(
       logicalId = this.logicalId,

android/engine/src/main/java/org/smartregister/fhircore/engine/data/local/tracing/TracingRepository.kt

@@ -22,12 +22,12 @@ import com.google.android.fhir.logicalId
 import com.google.android.fhir.search.Operation
 import com.google.android.fhir.search.Order
 import com.google.android.fhir.search.search
+import com.google.android.fhir.testing.jsonParser
 import java.util.Date
 import javax.inject.Inject
 import org.hl7.fhir.r4.model.CodeableConcept
 import org.hl7.fhir.r4.model.Coding
 import org.hl7.fhir.r4.model.Encounter
-import org.hl7.fhir.r4.model.IdType
 import org.hl7.fhir.r4.model.ListResource
 import org.hl7.fhir.r4.model.Observation
 import org.hl7.fhir.r4.model.Patient
@@ -38,7 +38,9 @@ import org.smartregister.fhircore.engine.domain.model.TracingHistory
 import org.smartregister.fhircore.engine.domain.model.TracingOutcome
 import org.smartregister.fhircore.engine.domain.model.TracingOutcomeDetails
 import org.smartregister.fhircore.engine.domain.util.PaginationConstant
+import org.smartregister.fhircore.engine.util.extension.extractLogicalIdUuid
 import org.smartregister.fhircore.engine.util.extension.referenceValue
+import timber.log.Timber
 
 class TracingRepository @Inject constructor(val fhirEngine: FhirEngine) {
   suspend fun getTracingHistory(
@@ -237,13 +239,14 @@ class TracingRepository @Inject constructor(val fhirEngine: FhirEngine) {
       .firstOrNull()
   }
 
-  suspend fun getTracingAttempt(patient: Patient): TracingAttempt {
+  suspend fun getTracingAttempt(patient: Patient, tasks: List<Task>): TracingAttempt {
     val list = getPatientListResource(patient)
+    list?.let { Timber.e(jsonParser.encodeResourceToString(list)) }
     return list?.let { toTracingAttempt(it) }
       ?: TracingAttempt(
         historyId = null,
         lastAttempt = null,
-        numberOfAttempts = 0,
+        numberOfAttempts = if (tasks.isEmpty()) Int.MAX_VALUE else 0,
         outcome = "",
         reasons = listOf()
       )
@@ -260,62 +263,25 @@ class TracingRepository @Inject constructor(val fhirEngine: FhirEngine) {
       )
   }
 
-  private suspend fun toTracingAttempt(list: ListResource): TracingAttempt {
-    var lastAttempt: Encounter? = null
-    list
-      .entry
-      .map { it.item }
-      .filter { it.referenceElement.resourceType == ResourceType.Encounter.name }
-      .forEach { ref ->
-        val resourceId = IdType(ref.reference).idPart
-        kotlin
-          .runCatching { fhirEngine.get<Encounter>(resourceId) }
-          .onSuccess { enc ->
-            lastAttempt = maxOf(lastAttempt, enc, nullsFirst(compareBy { it.period?.start?.time }))
-          }
-          .onFailure { it.printStackTrace() }
-      }
-
-    val obs =
-      lastAttempt?.let {
-        fhirEngine.search<Observation> {
-          filter(Observation.ENCOUNTER, { value = it.referenceValue() })
-          filter(
-            Observation.CODE,
-            {
-              value =
-                of(
-                  CodeableConcept(
-                    Coding().apply {
-                      system = "https://d-tree.org"
-                      code = "tracing-outcome-conducted"
-                    }
-                  )
-                )
-            },
-            {
-              value =
-                of(
-                  CodeableConcept(
-                    Coding().apply {
-                      system = "https://d-tree.org"
-                      code = "tracing-outcome-unconducted"
-                    }
-                  )
-                )
-            },
-            operation = Operation.OR
-          )
-          count = 1
-        }
-      }
+  private fun toTracingAttempt(list: ListResource): TracingAttempt {
+    val lastAttempt: ListResource.ListEntryComponent? =
+      list
+        .entry
+        .filter { it.item.referenceElement.resourceType == ResourceType.Encounter.name }
+        .sortedByDescending { it.date }
+        .firstOrNull()
 
     val outcome =
-      obs
-        ?.map { it.resource }
-        ?.firstOrNull { it.hasValueCodeableConcept() }
-        ?.valueCodeableConcept
-        ?.text
+      lastAttempt?.let { _ ->
+        list.entry
+          .firstOrNull { entry ->
+            entry.flag.codingFirstRep.display ==
+              lastAttempt.item.reference.extractLogicalIdUuid() &&
+              entry.flag.codingFirstRep.code == "tracing-outcome"
+          }
+          ?.flag
+          ?.text
+      }
         ?: ""
 
     val attempts =
@@ -326,7 +292,7 @@ class TracingRepository @Inject constructor(val fhirEngine: FhirEngine) {
 
     return TracingAttempt(
       numberOfAttempts = attempts,
-      lastAttempt = lastAttempt?.period?.start,
+      lastAttempt = lastAttempt?.date,
       outcome = outcome,
       reasons = listOf(),
       historyId = list.logicalId

android/engine/src/main/java/org/smartregister/fhircore/engine/util/helper/TransformSupportServices.kt

@@ -28,6 +28,7 @@ import org.hl7.fhir.r4.model.Encounter
 import org.hl7.fhir.r4.model.EpisodeOfCare
 import org.hl7.fhir.r4.model.Group
 import org.hl7.fhir.r4.model.Immunization
+import org.hl7.fhir.r4.model.Observation
 import org.hl7.fhir.r4.model.Patient
 import org.hl7.fhir.r4.model.PlanDefinition
 import org.hl7.fhir.r4.model.ResourceFactory
@@ -72,6 +73,7 @@ class TransformSupportServices @Inject constructor(val simpleWorkerContext: Simp
       "PlanDefinition_Action" -> PlanDefinition.PlanDefinitionActionComponent()
       "Group_Characteristic" -> Group.GroupCharacteristicComponent()
       "Appointment_Participant" -> Appointment.AppointmentParticipantComponent()
+      "Observation_Component" -> Observation.ObservationComponentComponent()
       else -> ResourceFactory.createResourceOrType(name)
     }
   }