Load resources like Questionnaire, StructureMap,PlanDefinition from r…

…esources folder when using appId with `/debug` (#3065) * Update loading on resources locally * Load SMS, PD and Qs locally from configJson * Add resources to DB * Run spotlessApply * Update resources to DB * Fix resource addition to DB * Fix some resources not updated * Add tests for loading local resources * Add docs * Fix spotless errors * Beautify docs * Fix coverage * Test exception --------- Co-authored-by: SebaMutuku <[email protected]> Co-authored-by: Sebastian <[email protected]>
opensrp · Jun 1, 2024 · ee6d05e · ee6d05e
1 parent f64baa8
commit ee6d05e
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Showing 12 changed files with 359 additions and 108 deletions.
diff --git a/...ne/src/main/java/org/smartregister/fhircore/engine/configuration/ConfigurationRegistry.kt b/...ne/src/main/java/org/smartregister/fhircore/engine/configuration/ConfigurationRegistry.kt
@@ -18,7 +18,9 @@ package org.smartregister.fhircore.engine.configuration
 
 import android.content.Context
 import android.database.SQLException
+import ca.uhn.fhir.context.ConfigurationException
 import ca.uhn.fhir.context.FhirContext
+import ca.uhn.fhir.parser.DataFormatException
 import com.google.android.fhir.FhirEngine
 import com.google.android.fhir.db.ResourceNotFoundException
 import com.google.android.fhir.get
@@ -38,7 +40,6 @@ import kotlinx.coroutines.withContext
 import kotlinx.serialization.json.Json
 import okhttp3.RequestBody.Companion.toRequestBody
 import okio.ByteString.Companion.decodeBase64
-import org.apache.commons.lang3.StringUtils
 import org.hl7.fhir.r4.model.Base
 import org.hl7.fhir.r4.model.Binary
 import org.hl7.fhir.r4.model.Bundle
@@ -298,7 +299,7 @@ constructor(
     }
   }
 
-  private suspend fun populateConfigurationsMap(
+  suspend fun populateConfigurationsMap(
     context: Context,
     composition: Composition,
     loadFromAssets: Boolean,
@@ -308,21 +309,33 @@ constructor(
     if (loadFromAssets) {
       retrieveAssetConfigs(context, appId).forEach { fileName ->
         // Create binary config from asset and add to map, skip composition resource
-        // Use file name as the key. Conventionally navigation configs MUST end with
-        // "_config.<extension>"
+        // Use file name as the key. Conventionally configs MUST end with _config.<extension>"
         // File names in asset should match the configType/id (MUST be unique) in the config JSON
+        // Resource configs are saved to the database
         if (!fileName.equals(String.format(COMPOSITION_CONFIG_PATH, appId), ignoreCase = true)) {
-          val configKey =
-            fileName
-              .lowercase(Locale.ENGLISH)
-              .substring(
-                fileName.indexOfLast { it == '/' }.plus(1),
-                fileName.lastIndexOf(CONFIG_SUFFIX),
-              )
-              .camelCase()
-
           val configJson = context.assets.open(fileName).bufferedReader().readText()
-          configsJsonMap[configKey] = configJson
+          if (fileName.contains(RESOURCES_PATH)) {
+            try {
+              val resource = configJson.decodeResourceFromString<Resource>()
+              if (resource.resourceType != null) {
+                addOrUpdate(resource)
+              }
+            } catch (configurationException: ConfigurationException) {
+              Timber.e("Error parsing FHIR resource", configurationException)
+            } catch (dataFormatException: DataFormatException) {
+              Timber.e("Error parsing FHIR resource", dataFormatException)
+            }
+          } else {
+            val configKey =
+              fileName
+                .lowercase(Locale.ENGLISH)
+                .substring(
+                  fileName.indexOfLast { it == '/' }.plus(1),
+                  fileName.lastIndexOf(CONFIG_SUFFIX),
+                )
+                .camelCase()
+            configsJsonMap[configKey] = configJson
+          }
         }
       }
     } else {
@@ -422,14 +435,17 @@ constructor(
             } else {
               val chunkedResourceIdList = entry.value.chunked(MANIFEST_PROCESSOR_BATCH_SIZE)
 
-              chunkedResourceIdList.forEach { parentIt ->
+              chunkedResourceIdList.forEach { sectionComponents ->
                 Timber.d(
-                  "Fetching config resource ${entry.key}: with ids ${StringUtils.join(parentIt,",")}",
+                  "Fetching config resource ${entry.key}: with ids ${sectionComponents.joinToString(",")}",
                 )
                 processCompositionManifestResources(
-                  entry.key,
-                  parentIt.map { sectionComponent -> sectionComponent.focus.extractId() },
-                  patientRelatedResourceTypes,
+                  resourceType = entry.key,
+                  resourceIdList =
+                    sectionComponents.map { sectionComponent ->
+                      sectionComponent.focus.extractId()
+                    },
+                  patientRelatedResourceTypes = patientRelatedResourceTypes,
                 )
               }
             }
@@ -622,7 +638,7 @@ constructor(
     this.apply {
       url =
         url
-          ?: "${openSrpApplication?.getFhirServerHost().toString()?.trimEnd { it == '/' }}/${this.referenceValue()}"
+          ?: """${openSrpApplication?.getFhirServerHost()?.toString()?.trimEnd { it == '/' }}/${this.referenceValue()}"""
     }
 
   fun writeToFile(resource: Resource): File {
@@ -811,13 +827,14 @@ constructor(
     const val TYPE_REFERENCE_DELIMITER = "/"
     const val DEFAULT_COUNT = 200
     const val PAGINATION_NEXT = "next"
+    const val RESOURCES_PATH = "resources/"
 
     /**
      * The list of resources whose types can be synced down as part of the Composition configs.
      * These are hardcoded as they are not meant to be easily configurable to avoid config vs data
      * sync issues
      */
-    val FILTER_RESOURCE_LIST =
+    private val FILTER_RESOURCE_LIST =
       listOf(
         ResourceType.Questionnaire.name,
         ResourceType.StructureMap.name,

diff --git a/...s/configs/app/patient_profile_config.json → .../app/profiles/patient_profile_config.json b/...s/configs/app/patient_profile_config.json → .../app/profiles/patient_profile_config.json
diff --git a/...onfigs/app/household_register_config.json → .../registers/household_register_config.json b/...onfigs/app/household_register_config.json → .../registers/household_register_config.json
diff --git a/.../configs/app/patient_register_config.json → ...pp/registers/patient_register_config.json b/.../configs/app/patient_register_config.json → ...pp/registers/patient_register_config.json
diff --git a/android/engine/src/test/assets/configs/app/resources/questionnaire/sample_questionnaire.json b/android/engine/src/test/assets/configs/app/resources/questionnaire/sample_questionnaire.json
@@ -0,0 +1,87 @@
+{
+  "resourceType": "Questionnaire",
+  "id": "3440",
+  "language": "en",
+  "name": "G6PD Test Photo Result",
+  "title": "G6PD Test Photo Result",
+  "status": "active",
+  "subjectType": [
+    "Patient"
+  ],
+  "publisher": "ONA-Systems",
+  "useContext": [
+    {
+      "code": {
+        "system": "http://hl7.org/fhir/codesystem-usage-context-type.html",
+        "code": "focus"
+      },
+      "valueCodeableConcept": {
+        "coding": [
+          {
+            "system": "http://fhir.ona.io",
+            "code": "000002",
+            "display": "G6PD Test Photo Results"
+          }
+        ]
+      }
+    }
+  ],
+  "extension": [
+    {
+      "url": "http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-targetStructureMap",
+      "valueCanonical": "https://fhir.labs.smartregister.org/StructureMap/5875"
+    },
+    {
+      "url": "http://hl7.org/fhir/StructureDefinition/cqf-library",
+      "valueCanonical": "Library/46831"
+    },
+    {
+      "url": "http://hl7.org/fhir/StructureDefinition/cqf-library",
+      "valueCanonical": "Library/46823"
+    }
+  ],
+  "item": [
+    {
+      "extension": [
+        {
+          "url": "http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-observationExtract",
+          "valueBoolean": true
+        }
+      ],
+      "linkId": "result_type",
+      "code": [
+        {
+          "system": "http://fhir.ona.io",
+          "code": "000001",
+          "display": "G6PD Result Type"
+        }
+      ],
+      "text": "G6PD Result Type",
+      "type": "choice",
+      "required": true,
+      "answerOption": [
+        {
+          "valueCoding": {
+            "system": "http://snomed.info/sct",
+            "code": "410680006",
+            "display": "Number"
+          }
+        },
+        {
+          "valueCoding": {
+            "system": "http://snomed.info/sct",
+            "code": "405358009",
+            "display": "Error"
+          }
+        },
+        {
+          "valueCoding": {
+            "system": "http://snomed.info/sct",
+            "code": "385432009",
+            "display": "N/A"
+          }
+        }
+      ]
+    }
+  ]
+}
diff --git a/android/engine/src/test/java/org/smartregister/fhircore/engine/app/fakes/Faker.kt b/android/engine/src/test/java/org/smartregister/fhircore/engine/app/fakes/Faker.kt
@@ -103,7 +103,7 @@ object Faker {
           context = ApplicationProvider.getApplicationContext<HiltTestApplication>(),
           openSrpApplication =
             object : OpenSrpApplication() {
-              override fun getFhirServerHost(): URL? {
+              override fun getFhirServerHost(): URL {
                 return URL("http://my_test_fhirbase_url/fhir/")
               }
             },