Merge remote-tracking branch 'd-tree-org/mwcore-dev' into mwcore-sdk-…

…upgrade
opensrp · Mar 5, 2024 · aaf28e6 · aaf28e6
2 parents 325371f + 133a40f
commit aaf28e6
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Showing 18 changed files with 187 additions and 142 deletions.
diff --git a/.github/workflows/ci-mwcore.yml b/.github/workflows/ci-mwcore.yml
@@ -12,6 +12,40 @@ env:
   CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
 jobs:
+  dataclerk:
+    runs-on: macos-latest
+    steps:
+      - name: Cancel Previous workflow runs
+        uses: styfle/[email protected]
+        with:
+          access_token: ${{ github.token }}
+
+      - name: Checkout 🛎️
+        uses: actions/checkout@v2
+        with:
+          fetch-depth: 2
+
+      - name: Set up JDK 17
+        uses: actions/setup-java@v1
+        with:
+          java-version: 17
+
+      - name: Decode google-services.json
+        run: echo $ENCODED_GOOGLE_SERVICES_JSON | base64 -d > android/quest/google-services.json
+        env:
+          ENCODED_GOOGLE_SERVICES_JSON: ${{ secrets.MWCORE_GOOGLE_SERVICES_JSON }}
+
+      - name: Grant execute permission for gradlew
+        run: chmod +x gradlew
+        working-directory: android
+
+      - name: Spotless check engine module
+        run: ./gradlew :dataclerk:spotlessCheck
+        working-directory: android
+
+      - name: Builds
+        run: ./gradlew :dataclerk:assembleDebug
+
   engine-tests:
     runs-on: macos-latest
     steps:
@@ -43,6 +77,9 @@ jobs:
         run: ./gradlew :engine:spotlessCheck
         working-directory: android
 
+      - name: Builds
+        run: ./gradlew :engine:assembleDebug
+
       # - name: Run Engine unit tests with Gradle
       #   run: ./gradlew :engine:clean && ./gradlew :engine:jacocoTestReport -x :engine:testReleaseUnitTest --stacktrace
       #   working-directory: android
@@ -83,6 +120,9 @@ jobs:
         run: ./gradlew :quest:spotlessCheck
         working-directory: android
 
+      - name: Builds
+        run: ./gradlew :quest:assembleMwcoreDevDebug
+
       # - name: Run Quest unit tests with Gradle
       #   run: ./gradlew :quest:clean && ./gradlew :quest:jacocoTestReportMwcoreDebug -x :quest:testMwcoreReleaseUnitTest --stacktrace
       #   working-directory: android

diff --git a/.../java/org/smartregister/fhircore/engine/data/local/register/dao/AppointmentRegisterDao.kt b/.../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 +146,36 @@ 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 =
@@ -186,7 +196,8 @@ constructor(
       .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))
 
@@ -197,7 +208,8 @@ constructor(
           it.hasStart() &&
           patientAssignmentFilter &&
           patientCategoryFilter &&
-          appointmentReasonFilter
+          appointmentReasonFilter &&
+          it.patientRef() != null
       }
   }
 

diff --git a/.../java/org/smartregister/fhircore/engine/data/local/register/dao/HomeTracingRegisterDao.kt b/.../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")
+  }
 }
diff --git a/...java/org/smartregister/fhircore/engine/data/local/register/dao/PhoneTracingRegisterDao.kt b/...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")
+  }
 }
diff --git a/...main/java/org/smartregister/fhircore/engine/data/local/register/dao/TracingRegisterDao.kt b/...main/java/org/smartregister/fhircore/engine/data/local/register/dao/TracingRegisterDao.kt
@@ -55,8 +55,7 @@ import org.smartregister.fhircore.engine.domain.model.ProfileData
 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.DispatcherProvider
-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 +93,10 @@ abstract class TracingRegisterDao(
     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 +127,7 @@ abstract class TracingRegisterDao(
     page: Int = -1,
   ): List<Pair<Patient, Iterable<Task>>> {
     filters as TracingRegisterFilter
+    val filterFilter = applicationConfiguration().patientTypeFilterTagViaMetaCodingSystem
     val patients: List<Patient> =
       fhirEngine
         .search<Patient> {
@@ -139,12 +142,12 @@ abstract class TracingRegisterDao(
               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()
                   }
 
@@ -159,8 +162,11 @@ abstract class TracingRegisterDao(
             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 }
@@ -310,8 +316,9 @@ abstract class TracingRegisterDao(
           .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 }
       }
@@ -367,7 +374,7 @@ abstract class TracingRegisterDao(
         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 ->
@@ -377,6 +384,7 @@ abstract class TracingRegisterDao(
   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) {
@@ -439,6 +447,7 @@ abstract class TracingRegisterDao(
       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,