✅ Fix the tests w.r.t updated schema repository functionality.

srdc · Aug 26, 2024 · ad44b11 · ad44b11
1 parent b57beff
commit ad44b11
Show file tree

Hide file tree

Showing 7 changed files with 14 additions and 14 deletions.
diff --git a/tofhir-engine/src/main/scala/io/tofhir/engine/util/FileUtils.scala b/tofhir-engine/src/main/scala/io/tofhir/engine/util/FileUtils.scala
@@ -52,7 +52,6 @@ object FileUtils {
 
   object FileExtensions extends Enumeration {
     type FileExtensions = Value
-    final val StructureDefinition = Value(".StructureDefinition")
     final val CSV = Value(".csv")
     final val JSON = Value(".json")
   }

diff --git a/...r/src/main/scala/io/tofhir/server/repository/mapping/ProjectMappingFolderRepository.scala b/...r/src/main/scala/io/tofhir/server/repository/mapping/ProjectMappingFolderRepository.scala
@@ -193,8 +193,8 @@ class ProjectMappingFolderRepository(mappingRepositoryFolderPath: String, projec
    * @return
    */
   private def getFileForMapping(projectId: String, fhirMapping: FhirMapping): Future[File] = {
-    val projectFuture: Future[Option[Project]] = projectFolderRepository.getProject(projectId)
-    projectFuture.map(project => {
+    projectFolderRepository.getProject(projectId).map(project => {
+      if (project.isEmpty) throw new IllegalStateException(s"This should not be possible. ProjectId: $projectId does not exist in the project folder repository.")
       val file: File = FileUtils.getPath(mappingRepositoryFolderPath, project.get.id, getFileName(fhirMapping.id)).toFile
       // If the project folder does not exist, create it
       if (!file.getParentFile.exists()) {

diff --git a/tofhir-server/src/main/scala/io/tofhir/server/repository/schema/SchemaFolderRepository.scala b/tofhir-server/src/main/scala/io/tofhir/server/repository/schema/SchemaFolderRepository.scala
@@ -243,8 +243,8 @@ class SchemaFolderRepository(schemaRepositoryFolderPath: String, projectFolderRe
    */
   private def initMap(schemaRepositoryFolderPath: String): mutable.Map[String, mutable.Map[String, SchemaDefinition]] = {
     val schemaDefinitionMap = mutable.Map[String, mutable.Map[String, SchemaDefinition]]()
-    logger.info(s"Initializing the Schema Repository from path $schemaRepositoryFolderPath.")
     val schemaFolder = FileUtils.getPath(schemaRepositoryFolderPath).toFile
+    logger.info(s"Initializing the Schema Repository from path ${schemaFolder.getAbsolutePath}.")
     if (!schemaFolder.exists()) {
       schemaFolder.mkdirs()
     }

diff --git a/tofhir-server/src/test/resources/application.conf b/tofhir-server/src/test/resources/application.conf
@@ -3,7 +3,7 @@ tofhir {
 
   # A path to a file/directory from where any File system readings should use within the mappingjob definition.
   # e.g., FileSystemSourceSettings.dataFolderPath or LocalFhirTerminologyServiceSettings.folderPath
-  context-path = "conf"
+  context-path = "test-conf"
 
   mappings = {
     repository = { # The repository where the mapping definition are kept.

diff --git a/tofhir-server/src/test/scala/io/tofhir/server/endpoint/MappingExecutionEndpointTest.scala b/tofhir-server/src/test/scala/io/tofhir/server/endpoint/MappingExecutionEndpointTest.scala
@@ -415,7 +415,7 @@ class MappingExecutionEndpointTest extends BaseEndpointTest with OnFhirTestConta
       val projects: JArray = TestUtil.getProjectJsonFile(toFhirEngineConfig)
       (projects.arr.find(p => (p \ "id").extract[String] == projectId).get \ "schemas").asInstanceOf[JArray].arr.length shouldEqual expectedSchemaCount
       // check schema folder is created
-      FileUtils.getPath(toFhirEngineConfig.schemaRepositoryFolderPath, projectId, s"${otherObservationSourceSchema.id}${FileExtensions.StructureDefinition}${FileExtensions.JSON}").toFile should exist
+      FileUtils.getPath(toFhirEngineConfig.schemaRepositoryFolderPath, projectId, s"${otherObservationSourceSchema.id}${FileExtensions.JSON}").toFile should exist
     }
   }
 

diff --git a/tofhir-server/src/test/scala/io/tofhir/server/endpoint/MetadataEndpointTest.scala b/tofhir-server/src/test/scala/io/tofhir/server/endpoint/MetadataEndpointTest.scala
@@ -6,6 +6,7 @@ import io.tofhir.server.endpoint.MetadataEndpoint
 import io.tofhir.server.model.Metadata
 import org.json4s.jackson.JsonMethods
 import io.tofhir.common.model.Json4sSupport.formats
+import io.tofhir.engine.config.ToFhirConfig
 
 import java.io.File
 
@@ -26,8 +27,8 @@ class MetadataEndpointTest extends BaseEndpointTest {
         metadata.repositoryNames.contexts shouldEqual "mapping-contexts"
         metadata.repositoryNames.jobs shouldEqual "mapping-jobs"
         metadata.repositoryNames.terminologySystems shouldEqual "terminology-systems"
-        metadata.archiving.erroneousRecordsFolder shouldEqual s"conf${File.separator}erroneous-records-folder"
-        metadata.archiving.archiveFolder shouldEqual s"conf${File.separator}archive-folder"
+        metadata.archiving.erroneousRecordsFolder shouldEqual s"${ToFhirConfig.engineConfig.contextPath}${File.separator}erroneous-records-folder"
+        metadata.archiving.archiveFolder shouldEqual s"${ToFhirConfig.engineConfig.contextPath}${File.separator}archive-folder"
         metadata.archiving.streamArchivingFrequency shouldEqual 5000
       }
     }

diff --git a/tofhir-server/src/test/scala/io/tofhir/server/endpoint/SchemaEndpointTest.scala b/tofhir-server/src/test/scala/io/tofhir/server/endpoint/SchemaEndpointTest.scala
@@ -39,7 +39,7 @@ class SchemaEndpointTest extends BaseEndpointTest with OnFhirTestContainer {
   ), sourceBinding = SqlSource(query = Some("select * from death"), preprocessSql = Some("select person_id, death_date, death_datetime, cause_source_value from test")))
 
 
-  // first schema schema to be created
+  // first schema to be created
   val schema1: SchemaDefinition = SchemaDefinition(url = "https://example.com/fhir/StructureDefinition/schema", `type` = "Ty", name = "name", description = Some("description"), rootDefinition = None, fieldDefinitions = None)
   // second schema to be created
   val schema2: SchemaDefinition = SchemaDefinition(url = "https://example.com/fhir/StructureDefinition/schema2", `type` = "Ty2", name = "name2", description = Some("description2"), rootDefinition = None, fieldDefinitions = None)
@@ -95,15 +95,15 @@ class SchemaEndpointTest extends BaseEndpointTest with OnFhirTestContainer {
         val projects: JArray = TestUtil.getProjectJsonFile(toFhirEngineConfig)
         (projects.arr.find(p => (p \ "id").extract[String] == projectId).get \ "schemas").asInstanceOf[JArray].arr.length shouldEqual 1
         // check schema folder is created
-        FileUtils.getPath(toFhirEngineConfig.schemaRepositoryFolderPath, projectId, s"${schema1.id}${FileExtensions.StructureDefinition}${FileExtensions.JSON}").toFile should exist
+        FileUtils.getPath(toFhirEngineConfig.schemaRepositoryFolderPath, projectId, s"${schema1.id}${FileExtensions.JSON}").toFile should exist
       }
       // create the second schema
       Post(s"/${webServerConfig.baseUri}/${ProjectEndpoint.SEGMENT_PROJECTS}/$projectId/${SchemaDefinitionEndpoint.SEGMENT_SCHEMAS}", HttpEntity(ContentTypes.`application/json`, writePretty(schema2))) ~> route ~> check {
         status shouldEqual StatusCodes.Created
         // validate that schema metadata file is updated
         val projects: JArray = TestUtil.getProjectJsonFile(toFhirEngineConfig)
         (projects.arr.find(p => (p \ "id").extract[String] == projectId).get \ "schemas").asInstanceOf[JArray].arr.length shouldEqual 2
-        FileUtils.getPath(toFhirEngineConfig.schemaRepositoryFolderPath, projectId, s"${schema2.id}${FileExtensions.StructureDefinition}${FileExtensions.JSON}").toFile should exist
+        FileUtils.getPath(toFhirEngineConfig.schemaRepositoryFolderPath, projectId, s"${schema2.id}${FileExtensions.JSON}").toFile should exist
       }
     }
 
@@ -160,7 +160,7 @@ class SchemaEndpointTest extends BaseEndpointTest with OnFhirTestContainer {
       }
       // update a schema with invalid id
       Put(s"/${webServerConfig.baseUri}/${ProjectEndpoint.SEGMENT_PROJECTS}/$projectId/${SchemaDefinitionEndpoint.SEGMENT_SCHEMAS}/123123", HttpEntity(ContentTypes.`application/json`, writePretty(schema2))) ~> route ~> check {
-        status shouldEqual StatusCodes.NotFound
+        status shouldEqual StatusCodes.BadRequest
       }
     }
 
@@ -172,7 +172,7 @@ class SchemaEndpointTest extends BaseEndpointTest with OnFhirTestContainer {
         val projects: JArray = TestUtil.getProjectJsonFile(toFhirEngineConfig)
         (projects.arr.find(p => (p \ "id").extract[String] == projectId).get \ "schemas").asInstanceOf[JArray].arr.length shouldEqual 1
         // check schema folder is deleted
-        FileUtils.getPath(toFhirEngineConfig.schemaRepositoryFolderPath, projectId, s"${schema1.id}${FileExtensions.StructureDefinition}${FileExtensions.JSON}").toFile shouldNot exist
+        FileUtils.getPath(toFhirEngineConfig.schemaRepositoryFolderPath, projectId, s"${schema1.id}${FileExtensions.JSON}").toFile shouldNot exist
       }
       // delete a schema with invalid id
       Delete(s"/${webServerConfig.baseUri}/${ProjectEndpoint.SEGMENT_PROJECTS}/$projectId/${SchemaDefinitionEndpoint.SEGMENT_SCHEMAS}/123123") ~> route ~> check {
@@ -468,7 +468,7 @@ class SchemaEndpointTest extends BaseEndpointTest with OnFhirTestContainer {
     "import StructureDefinition from a FHIR server" in {
       // settings to import a StructureDefinition named 'CustomPatient' from the onFHIR
       val schemaID = "CustomPatient"
-      val importSchemaSettings = ImportSchemaSettings(onFhirClient.getBaseUrl(),schemaID, None)
+      val importSchemaSettings = ImportSchemaSettings(onFhirClient.getBaseUrl(), schemaID, None)
       // import the StructureDefinition from onFHIR
       Post(s"/${webServerConfig.baseUri}/${ProjectEndpoint.SEGMENT_PROJECTS}/$projectId/${SchemaDefinitionEndpoint.SEGMENT_SCHEMAS}/${SchemaDefinitionEndpoint.SEGMENT_IMPORT}", HttpEntity(ContentTypes.`application/json`, writePretty(importSchemaSettings))) ~> route ~> check {
         status shouldEqual StatusCodes.OK