Validate FHIR Resources before publishing.

fixes #87
onaio · Dec 21, 2023 · 530e31f · 530e31f
1 parent 38478f6
commit 530e31f
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Showing 3 changed files with 28 additions and 10 deletions.
diff --git a/efsity/README.md b/efsity/README.md
@@ -98,6 +98,7 @@ $ fct publish -e /path/to/env.properties
 -bu or --fhir-base-url : The base url of the FHIR server to post resources to
 -at or --access-token : Access token to grant access to the FHIR server
  -e or --env : A properties file that contains the neessary variables
+ -vr or --validate-resources : (Optional) whether to validate FHIR resources before publishing or not. Optional boolean - default is `true`
 ```
 You can either pass your variables on the CLI or include them in the properties file. Variables passed on CLI
 take precedence over anything in the properties file.

diff --git a/efsity/src/main/java/org/smartregister/command/PublishFhirResourcesCommand.java b/efsity/src/main/java/org/smartregister/command/PublishFhirResourcesCommand.java
@@ -1,5 +1,7 @@
 package org.smartregister.command;
 
+import net.jimblackler.jsonschemafriend.GenerationException;
+import net.jimblackler.jsonschemafriend.ValidationException;
 import org.apache.http.HttpResponse;
 import org.apache.http.client.methods.HttpPost;
 import org.apache.http.entity.StringEntity;
@@ -41,6 +43,13 @@ public class PublishFhirResourcesCommand implements Runnable{
             description = "path to env.properties file")
     String propertiesFile;
 
+    @CommandLine.Option(
+      names = {"-vr", "--validate-resource"},
+      description =
+        "-vr or --validate-resource - (Optional) whether to validate FHIR resources before publishing or not. Optional boolean - default is `true`",
+      required = false)
+    private String validateResource = "true";
+
     @Override
     public void run() {
         long start = System.currentTimeMillis();
@@ -56,7 +65,7 @@ public void run() {
         try {
             publishResources();
             stateManagement();
-        } catch (IOException e) {
+        } catch (IOException | ValidationException | GenerationException e) {
             throw new RuntimeException(e);
         }
         FctUtils.printCompletedInDuration(start);
@@ -86,12 +95,20 @@ void setProperties(Properties properties){
         }
     }
 
-    void publishResources() throws IOException {
+    void publishResources() throws IOException, ValidationException, GenerationException {
         ArrayList<String> resourceFiles = getResourceFiles(projectFolder);
         ArrayList<JSONObject> resourceObjects = new ArrayList<>();
+        boolean validateResourceBoolean = Boolean.parseBoolean(validateResource);
+
         for(String f: resourceFiles){
+            if (validateResourceBoolean) {
+                FctUtils.printInfo(String.format("Validating file \u001b[35m%s\u001b[0m", f));
+                ValidateFhirResourcesCommand.validateFhirResources(f);
+            } else {
+                FctUtils.printInfo("Publishing Without Validation");
+            }
+
             FctFile inputFile = FctUtils.readFile(f);
-            // TODO check if file contains valid fhir resource
             JSONObject resourceObject = buildResourceObject(inputFile);
             resourceObjects.add(resourceObject);
         }
@@ -107,7 +124,7 @@ void publishResources() throws IOException {
         postRequest(bundle.toString(), accessToken);
     }
 
-    ArrayList<String> getResourceFiles(String pathToFolder) throws IOException {
+    static ArrayList<String> getResourceFiles(String pathToFolder) throws IOException {
         ArrayList<String> filesArray = new ArrayList<>();
         Path projectPath = Paths.get(pathToFolder);
         if (Files.isDirectory(projectPath)){
@@ -118,7 +135,7 @@ ArrayList<String> getResourceFiles(String pathToFolder) throws IOException {
         return filesArray;
     }
 
-    void getFiles(ArrayList<String> filesArray, File file){
+    static void getFiles(ArrayList<String> filesArray, File file){
         if (file.isFile()) {
             filesArray.add(file.getAbsolutePath());
         }

diff --git a/efsity/src/main/java/org/smartregister/command/ValidateFhirResourcesCommand.java b/efsity/src/main/java/org/smartregister/command/ValidateFhirResourcesCommand.java
@@ -42,7 +42,7 @@ public class ValidateFhirResourcesCommand implements Runnable {
       names = {"-s", "--schema"},
       description = "configs schema"
   )
-  private String configSchema;
+  private static String configSchema;
 
   @Override
   public void run() {
@@ -55,7 +55,7 @@ public void run() {
     }
   }
 
-  private void validateFhirResources(String inputFilePath) throws IOException, ValidationException, GenerationException {
+  public static void validateFhirResources(String inputFilePath) throws IOException, ValidationException, GenerationException {
 
     long start = System.currentTimeMillis();
 
@@ -119,7 +119,7 @@ private void validateFhirResources(String inputFilePath) throws IOException, Val
     }
   }
 
-  private int validateResource(FhirValidator validator, IBaseResource resource) {
+  private static int validateResource(FhirValidator validator, IBaseResource resource) {
 
     ValidationResult result = validator.validateWithResult(resource);
 
@@ -146,12 +146,12 @@ private int validateResource(FhirValidator validator, IBaseResource resource) {
     }
   }
 
-  boolean isConfigFile(FctFile inputFile){
+  static boolean isConfigFile(FctFile inputFile){
     JSONObject resource = new JSONObject(inputFile.getContent());
     return resource.has("configType");
   }
 
-  int validateConfig(FctFile configFile) throws GenerationException, ValidationException {
+  static int validateConfig(FctFile configFile) throws GenerationException, ValidationException {
     SchemaStore schemaStore = new SchemaStore();
     Schema schema = schemaStore.loadSchema(new File(String.valueOf(Paths.get(configSchema))));