Upload FHIR resources

efsity/src/main/java/org/smartregister/Main.java

@@ -20,7 +20,8 @@
       ValidateFhirResourcesCommand.class,
       TranslateCommand.class,
       QuestionnaireResponseGeneratorCommand.class,
-      ValidateFileStructureCommand.class
+      ValidateFileStructureCommand.class,
+      PublishFhirResourcesCommand.class
     })
 public class Main implements Runnable {
   public static void main(String[] args) {

efsity/src/main/java/org/smartregister/command/PublishFhirResourcesCommand.java

@@ -0,0 +1,242 @@
+package org.smartregister.command;
+
+import org.apache.http.HttpResponse;
+import org.apache.http.client.methods.HttpPost;
+import org.apache.http.entity.StringEntity;
+import org.apache.http.impl.client.CloseableHttpClient;
+import org.apache.http.impl.client.HttpClients;
+import org.json.JSONObject;
+import org.smartregister.domain.FctFile;
+import org.smartregister.fhircore_tooling.BuildConfig;
+import org.smartregister.util.FctUtils;
+import picocli.CommandLine;
+
+import java.io.*;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.text.SimpleDateFormat;
+import java.util.*;
+
+@CommandLine.Command(name = "publish")
+public class PublishFhirResourcesCommand implements Runnable{
+
+    @CommandLine.Option(
+            names = {"-i", "--input"},
+            description = "path of the file or folder to publish")
+    String projectFolder;
+
+    @CommandLine.Option(
+            names = {"-bu", "--fhir-base-url"},
+            description = "fhir server base url")
+    String fhirBaseUrl;
+
+    @CommandLine.Option(
+            names = {"-at", "--access-token"},
+            description = "access token for fhir server")
+    String accessToken;
+
+    @CommandLine.Option(
+            names = {"-e", "--env"},
+            description = "path to env.properties file")
+    String propertiesFile;
+
+    @Override
+    public void run() {
+        long start = System.currentTimeMillis();
+        if(propertiesFile != null && !propertiesFile.isBlank()){
+            try(InputStream inputProperties = new FileInputStream(propertiesFile)){
+                Properties properties = new Properties();
+                properties.load(inputProperties);
+                setProperties(properties);
+            } catch (IOException e) {
+                throw new RuntimeException(e);
+            }
+        }
+        try {
+            publishResources();
+            stateManagement();
+        } catch (IOException e) {
+            throw new RuntimeException(e);
+        }
+        FctUtils.printCompletedInDuration(start);
+    }
+
+    void setProperties(Properties properties){
+        if (projectFolder == null || projectFolder.isBlank()){
+            if (properties.getProperty("projectFolder") != null){
+                projectFolder = properties.getProperty("projectFolder");
+            } else {
+                throw new NullPointerException("The projectFolder is missing");
+            }
+        }
+        if (fhirBaseUrl == null || fhirBaseUrl.isBlank()){
+            if (properties.getProperty("fhirBaseUrl") != null){
+                fhirBaseUrl = properties.getProperty("fhirBaseUrl");
+            } else {
+                throw new NullPointerException("The fhirBaseUrl is missing");
+            }
+        }
+        if (accessToken == null || accessToken.isBlank()){
+            if (properties.getProperty("accessToken") != null){
+                accessToken = properties.getProperty("accessToken");
+            } else {
+                throw new NullPointerException("The accessToken is missing");
+            }
+        }
+    }
+
+    void publishResources() throws IOException {
+        ArrayList<String> resourceFiles = getResourceFiles(projectFolder);
+        ArrayList<JSONObject> resourceObjects = new ArrayList<>();
+        for(String f: resourceFiles){
+            FctFile inputFile = FctUtils.readFile(f);
+            // TODO check if file contains valid fhir resource
+            JSONObject resourceObject = buildResourceObject(inputFile);
+            resourceObjects.add(resourceObject);
+        }
+
+        // build the bundle
+        JSONObject bundle = new JSONObject();
+        bundle.put("resourceType", "Bundle");
+        bundle.put("type", "transaction");
+        bundle.put("entry",resourceObjects);
+        FctUtils.printToConsole("Full Payload to POST: ");
+        FctUtils.printToConsole(bundle.toString());
+
+        postRequest(bundle.toString(), accessToken);
+    }
+
+    ArrayList<String> getResourceFiles(String pathToFolder) throws IOException {
+        ArrayList<String> filesArray = new ArrayList<>();
+        Path projectPath = Paths.get(pathToFolder);
+        if (Files.isDirectory(projectPath)){
+            Files.walk(projectPath).forEach(path -> getFiles(filesArray, path.toFile()));
+        } else if (Files.isRegularFile(projectPath)) {
+            filesArray.add(pathToFolder);
+        }
+        return filesArray;
+    }
+
+    void getFiles(ArrayList<String> filesArray, File file){
+        if (file.isFile()) {
+            filesArray.add(file.getAbsolutePath());
+        }
+    }
+
+    JSONObject buildResourceObject(FctFile inputFile){
+        JSONObject resource = new JSONObject(inputFile.getContent());
+        String resourceType = null;
+        String resourceID;
+        if(resource.has("resourceType")) {
+            resourceType = resource.getString("resourceType");
+        }
+        if(resource.has("id")){
+            resourceID = resource.getString("id");
+        } else {
+            resourceID = UUID.randomUUID().toString();
+        }
+
+        JSONObject request = new JSONObject();
+        request.put("method", "PUT");
+        request.put("url", resourceType + "/" + resourceID );
+
+        ArrayList<JSONObject> tags = new ArrayList<>();
+        JSONObject version = new JSONObject();
+        version.put("system", "https://smartregister.org/fct-release-version");
+        version.put("code", BuildConfig.RELEASE_VERSION);
+        tags.add(version);
+
+        JSONObject meta = new JSONObject();
+        meta.put("tag", tags);
+        resource.put("meta", meta);
+
+        JSONObject object = new JSONObject();
+        object.put("resource", resource);
+        object.put("request", request);
+
+        return object;
+    }
+
+    void postRequest(String payload, String accessToken) throws IOException {
+        CloseableHttpClient httpClient = HttpClients.createDefault();
+        HttpPost httpPost = new HttpPost(fhirBaseUrl);
+        httpPost.setHeader("Content-Type", "application/fhir+json");
+        httpPost.setHeader("Authorization", "Bearer " + accessToken);
+        httpPost.setEntity(new StringEntity(payload));
+        HttpResponse response = httpClient.execute(httpPost);
+
+        FctUtils.printToConsole("Response Status: " + response.getStatusLine().getStatusCode());
+        BufferedReader reader = new BufferedReader(new InputStreamReader(response.getEntity().getContent()));
+        String inputLine;
+        StringBuilder responseString = new StringBuilder();
+
+        while ((inputLine = reader.readLine()) != null) {
+            responseString.append(inputLine);
+        }
+        reader.close();
+        FctUtils.printToConsole("Response Content: " + responseString);
+    }
+
+    void stateManagement() throws IOException {
+        String pathToManifest;
+        if(Files.isDirectory(Paths.get(projectFolder))){
+            pathToManifest = projectFolder + "/.efsity/state.json";
+        } else {
+            pathToManifest = getProjectFolder(projectFolder);
+        }
+        File manifestFile = new File(pathToManifest);
+
+        // Create folder if it does not exist
+        if (Files.notExists(Paths.get(pathToManifest))){
+            if(manifestFile.getParentFile().mkdirs()){
+                if(manifestFile.createNewFile()){
+                    FctUtils.printToConsole("Manifest file created successfully");
+                }
+            }
+        }
+
+        // Set initial content
+        String initialContent;
+        if (manifestFile.length() != 0){
+            initialContent = FctUtils.readFile(pathToManifest).getContent();
+        } else {
+            initialContent = "[]";
+        }
+
+        JSONObject currentState = new JSONObject();
+        currentState.put("fctVersion", BuildConfig.RELEASE_VERSION);
+        currentState.put("url", fhirBaseUrl);
+        currentState.put("updated", updatedAt());
+        String finalString;
+        if (manifestFile.length() != 0){
+            finalString = initialContent.substring(0, initialContent.length() - 2) + ",\n" + currentState + "]";
+        } else {
+            finalString = initialContent.substring(0, initialContent.length() - 1) + currentState + "]";
+        }
+
+        FileWriter writer = new FileWriter(pathToManifest);
+        writer.write(finalString);
+        writer.flush();
+        writer.close();
+    }
+
+    String updatedAt(){
+        Date date = new Date(System.currentTimeMillis());
+        SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss.SSS");
+        sdf.setTimeZone(TimeZone.getTimeZone("UTC"));
+        return sdf.format(date);
+    }
+
+    // This function assumes the .efsity folder already exists in the project/parent folder
+    // and simply tries to find it
+    String getProjectFolder(String projectFolder){
+        File resourceFile = new File(projectFolder);
+        File parentFolder = resourceFile.getParentFile();
+        boolean check = new File(parentFolder, ".efsity").exists();
+        if (!check){
+            return getProjectFolder(parentFolder.toString());
+        }
+        return parentFolder.toString();
+    }
+}

efsity/src/test/java/org/smartregister/command/PublishFhirResourcesCommandTest.java

@@ -0,0 +1,90 @@
+package org.smartregister.command;
+
+import org.json.JSONObject;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.io.TempDir;
+import org.smartregister.domain.FctFile;
+import org.smartregister.util.FctUtils;
+
+import java.io.FileWriter;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.ArrayList;
+
+import static org.junit.jupiter.api.Assertions.*;
+
+public class PublishFhirResourcesCommandTest {
+
+    private PublishFhirResourcesCommand publishFhirResourcesCommand;
+
+    @TempDir
+    static Path tempDirectory;
+
+    @BeforeEach
+    void setUp(){
+        publishFhirResourcesCommand = new PublishFhirResourcesCommand();
+    }
+
+    @Test
+    void testGetResourceFiles() throws IOException {
+        // add folders and file to form sample project structure
+        Path testFolder = Files.createDirectory(tempDirectory.resolve("testFileFolder"));
+        Path projectFolder = Files.createDirectory(testFolder.resolve("testProject"));
+
+        // create 3 folders in projectFolder
+        Path questionnaireFolder = Files.createDirectory(projectFolder.resolve("questionnaires"));
+        Path plansFolder = Files.createDirectory(projectFolder.resolve("plan_definitions"));
+        Path structureMapsFolder = Files.createDirectory(projectFolder.resolve("structureMaps"));
+
+        // create a file in each of the folders above
+        Path questionnaireFile = Files.createFile(questionnaireFolder.resolve("patient_registration.json"));
+        Path planFile = Files.createFile(plansFolder.resolve("anc_visit.json"));
+        Path structureMapFile = Files.createFile(structureMapsFolder.resolve("pregnancy_screening.json"));
+
+        // get files in the folder
+        ArrayList<String> resourceFiles = publishFhirResourcesCommand.getResourceFiles(projectFolder.toString());
+
+        assertEquals(3, resourceFiles.size());
+        assertTrue(resourceFiles.contains(questionnaireFile.toString()));
+        assertTrue(resourceFiles.contains(planFile.toString()));
+        assertTrue(resourceFiles.contains(structureMapFile.toString()));
+    }
+
+    @Test
+    void testBuildResourceObject() throws IOException {
+        Path testFolder = Files.createDirectory(tempDirectory.resolve("testObjectFolder"));
+        Path resourceFile = Files.createFile(testFolder.resolve("group.json"));
+
+        String sampleResource = "{\n" +
+                "  \"resourceType\": \"Group\",\n" +
+                "  \"id\": \"548060c9-8e9b-4b0d-88e7-925e9348fdae\",\n" +
+                "  \"identifier\": [\n" +
+                "    {\n" +
+                "      \"use\": \"official\",\n" +
+                "      \"value\": \"548060c9-8e9b-4b0d-88e7-925e9348fdae\"\n" +
+                "    }\n" +
+                "  ],\n" +
+                "  \"active\": false,\n" +
+                "  \"name\": \"Test Group\"\n" +
+                "}";
+        FileWriter writer = new FileWriter(String.valueOf(resourceFile));
+        writer.write(sampleResource);
+        writer.flush();
+        writer.close();
+
+        FctFile testFile = FctUtils.readFile(resourceFile.toString());
+        JSONObject resourceObject = publishFhirResourcesCommand.buildResourceObject(testFile);
+
+        // assert that object has request
+        assertEquals(
+               "{\"method\":\"PUT\",\"url\":\"Group/548060c9-8e9b-4b0d-88e7-925e9348fdae\"}",
+               resourceObject.get("request").toString());
+
+        // assert object has meta with version tag
+        JSONObject resource = (JSONObject) resourceObject.get("resource");
+        assertTrue(resource.get("meta").toString()
+                .contains("{\"tag\":[{\"system\":\"https://smartregister.org/fct-release-version\",\"code\":\""));
+    }
+}