Merge pull request #726 from FEMR/temr-dev-michael

Refactoring and testing

app/femr/business/services/system/EncounterService.java

@@ -18,12 +18,15 @@
 */
 package femr.business.services.system;
 
+import femr.business.services.core.ISessionService;
+import femr.common.dtos.CurrentUser;
 import io.ebean.ExpressionList;
 import io.ebean.Query;
 import com.google.inject.Inject;
 import com.google.inject.name.Named;
 import femr.business.helpers.QueryProvider;
 import femr.business.services.core.IEncounterService;
+import femr.business.services.core.ISessionService;
 import femr.common.IItemModelMapper;
 import femr.common.dtos.ServiceResponse;
 import femr.common.models.*;
@@ -46,6 +49,7 @@ public class EncounterService implements IEncounterService {
     private final IRepository<IChiefComplaint> chiefComplaintRepository;
     private final IPatientRepository patientRepository;
     private final IEncounterRepository patientEncounterRepository;
+    private final ISessionService sessionService;
     private final IRepository<IPatientEncounterTabField> patientEncounterTabFieldRepository;
     private final IRepository<ITabField> tabFieldRepository;
     private final IUserRepository userRepository;
@@ -56,6 +60,7 @@ public class EncounterService implements IEncounterService {
     public EncounterService(IRepository<IChiefComplaint> chiefComplaintRepository,
                             IPatientRepository patientRepository,
                             IEncounterRepository patientEncounterRepository,
+                            ISessionService sessionService,
                             IRepository<IPatientEncounterTabField> patientEncounterTabFieldRepository,
                             IRepository<ITabField> tabFieldRepository,
                             IUserRepository userRepository,
@@ -65,6 +70,7 @@ public EncounterService(IRepository<IChiefComplaint> chiefComplaintRepository,
         this.chiefComplaintRepository = chiefComplaintRepository;
         this.patientRepository = patientRepository;
         this.patientEncounterRepository = patientEncounterRepository;
+        this.sessionService = sessionService;
         this.patientEncounterTabFieldRepository = patientEncounterTabFieldRepository;
         this.tabFieldRepository = tabFieldRepository;
         this.userRepository = userRepository;
@@ -77,7 +83,7 @@ public EncounterService(IRepository<IChiefComplaint> chiefComplaintRepository,
      */
     @Override
     public ServiceResponse<PatientEncounterItem> createPatientEncounter(int patientId, int userId, Integer tripId, String ageClassification, List<String> chiefComplaints) {
-
+        System.out.println("Create Patient Encounter");
         ServiceResponse<PatientEncounterItem> response = new ServiceResponse<>();
 
         try {
@@ -98,8 +104,9 @@ public ServiceResponse<PatientEncounterItem> createPatientEncounter(int patientI
             if (patientAgeClassification != null)
                 patientAgeClassificationId = patientAgeClassification.getId();
 
-            IPatientEncounter newPatientEncounter = patientEncounterRepository.createPatientEncounter(patientId, dateUtils.getCurrentDateTime(), nurseUser.getId(), patientAgeClassificationId, tripId);
-
+            CurrentUser currentUserSession = sessionService.retrieveCurrentUserSession();
+            String languageCode = currentUserSession.getLanguageCode();
+            IPatientEncounter newPatientEncounter = patientEncounterRepository.createPatientEncounter(patientId, dateUtils.getCurrentDateTime(), nurseUser.getId(), patientAgeClassificationId, tripId, languageCode);
             List<IChiefComplaint> chiefComplaintBeans = new ArrayList<>();
             Integer chiefComplaintSortOrder = 0;
             for (String cc : chiefComplaints) {

app/femr/data/daos/core/IEncounterRepository.java

@@ -17,7 +17,7 @@ public interface IEncounterRepository {
      * @param tripId id of the trip, may be null
      * @return the new patient encounter or null if an error happens
      */
-    IPatientEncounter createPatientEncounter(int patientID, DateTime date, int userId, Integer patientAgeClassificationId, Integer tripId);
+    IPatientEncounter createPatientEncounter(int patientID, DateTime date, int userId, Integer patientAgeClassificationId, Integer tripId, String languageCode);
 
     /**
      * Deletes a patient's encounter. this is a soft delete

app/femr/data/daos/system/EncounterRepository.java

@@ -41,7 +41,7 @@ public EncounterRepository(Provider<IMissionTrip> missionTripProvider,
      * {@inheritDoc}
      */
     @Override
-    public IPatientEncounter createPatientEncounter(int patientID, DateTime date, int userId, Integer patientAgeClassificationId, Integer tripId){
+    public IPatientEncounter createPatientEncounter(int patientID, DateTime date, int userId, Integer patientAgeClassificationId, Integer tripId, String languageCode){
 
         IPatientEncounter patientEncounter = patientEncounterProvider.get();
 
@@ -57,7 +57,7 @@ public IPatientEncounter createPatientEncounter(int patientID, DateTime date, in
                 patientEncounter.setPatientAgeClassification(Ebean.getReference(patientAgeClassificationProvider.get().getClass(), patientAgeClassificationId));
             if (tripId != null)
                 patientEncounter.setMissionTrip(Ebean.getReference(missionTripProvider.get().getClass(), tripId));
-
+            patientEncounter.setLanguageCode(languageCode);
             Ebean.save(patientEncounter);
         }catch (Exception ex){
 

app/femr/ui/controllers/BackEndControllerHelper.java

@@ -1,17 +1,8 @@
 package femr.ui.controllers;
 
-import femr.util.translation.TranslationServer;
-import femr.util.translation.TranslationJson;
 
 import java.io.*;
-import java.net.MalformedURLException;
 import java.util.ArrayList;
-import java.net.HttpURLConnection;
-import java.net.URL;
-
-import com.fasterxml.jackson.databind.ObjectMapper;
-import org.json.JSONArray;
-import org.json.JSONObject;
 
 
 public class BackEndControllerHelper  {
@@ -52,25 +43,4 @@ public static ArrayList<String> executeSpeedTestScript(String absPath) {
 
     return speedInfo;
   }
-
-  public static String translate(String arg, String from, String to) {
-      String output = "";
-      try {
-        output = TranslationServer.makeServerRequest(arg, from, to);
-
-        //parse translation from JSON
-        ObjectMapper mapper = new ObjectMapper();
-        TranslationJson api = mapper.readValue(output, TranslationJson.class);
-        output = api.translatedText;
-
-      } catch(MalformedURLException e){
-        System.out.println("Malformed URL Exception");
-        System.out.println(e.getMessage());
-      } catch(IOException e){
-        System.out.println("IOException for parsing JSON");
-        System.out.println(e.getMessage());
-      }
-      return output;
-    }
-
 }

app/femr/ui/controllers/MedicalController.java

@@ -1,5 +1,6 @@
 package femr.ui.controllers;
 
+import com.fasterxml.jackson.databind.ObjectMapper;
 import com.google.inject.Inject;
 import controllers.AssetsFinder;
 import femr.business.services.core.*;
@@ -19,6 +20,8 @@
 import femr.util.DataStructure.Mapping.TabFieldMultiMap;
 import femr.util.DataStructure.Mapping.VitalMultiMap;
 import femr.util.stringhelpers.StringUtils;
+import femr.util.translation.TranslationJson;
+import femr.util.translation.TranslationServer;
 import femr.util.translation.TranslationResponseMap;
 import play.data.Form;
 import play.data.FormFactory;
@@ -260,10 +263,11 @@ public Result editGet(int patientId) {
     }
 
     public Result translateGet() {
-        String text = request().getQueryString("text");
+        String jsonText = request().getQueryString("text");
+        int patientId = Integer.parseInt(request().getQueryString("patientId"));
+
         //Harrison Shu
-        CurrentUser currentUserSession = sessionService.retrieveCurrentUserSession();
-        String toLanguage = currentUserSession.getLanguageCode();
+        String toLanguage = sessionService.retrieveCurrentUserSession().getLanguageCode();
 
         // retrieve current patient encounter encounter
         int patientId = Integer.parseInt(request().getQueryString("patientId"));
@@ -280,17 +284,32 @@ public Result translateGet() {
         return ok(responseMapObject.getResponseJson());
     }
 
-    public String translate(String text, String fromLanguage, String toLanguage) {
+
+//    Calls Python Script to translate
+    private String translate(String jsonText, String fromLanguage, String toLanguage) {
         String data = "";
         try {
-            data = BackEndControllerHelper.translate(text, fromLanguage, toLanguage);
+            data = TranslationServer.makeServerRequest(jsonText, fromLanguage, toLanguage);
+            data = parseJsonResponse(data);
         } catch (Exception e) {
             e.printStackTrace();
         }
         return data;
     }
 
 
+    public String parseJsonResponse(String jsonResponse){
+        try{
+            ObjectMapper mapper = new ObjectMapper();
+            TranslationJson api = mapper.readValue(jsonResponse, TranslationJson.class);
+            jsonResponse = api.translatedText;
+            return jsonResponse;
+        } catch(Exception e){
+            System.out.println(e.getMessage());
+            throw new RuntimeException();
+        }
+    }
+
     /**
      * Get the populated partial view that represents 1 row of new prescription fields
      * - meant to be an AJAX call

app/femr/util/translation/TranslationServer.java

@@ -4,69 +4,49 @@
 import javax.inject.Singleton;
 import java.io.*;
 import java.net.HttpURLConnection;
-import java.net.MalformedURLException;
 import java.net.URL;
 import java.net.URLConnection;
-import java.nio.file.Files;
-import java.nio.file.Paths;
 import java.util.Scanner;
-import java.net.URLEncoder;
 import java.nio.charset.StandardCharsets;
 
 @Singleton
 public class TranslationServer {
     @Inject
     public TranslationServer(){
-        this.start();
+        start(timeout);
     }
 
     private static int portNumber = -1;
+    private static final String timeout = "600";
 
-    //Takes a string, a from code and a to code, and returns the translatedtext
-    public static String makeServerRequest(String text, String from, String to) throws MalformedURLException {
-        if(serverNotRunning()){
-            start();
-            while(serverNotRunning()); //block
+    public static int getPortFromLog(String logPath, Boolean wait){
+        int portNumber = 0;
+        try{
+            File log = new File(logPath);
+            Scanner s = new Scanner(log);
+            if(wait){
+                while(log.length() == 0);
+            }
+            if (s.hasNext()) {
+                portNumber = Integer.parseInt(s.nextLine().split(": ")[1]);
+            }
+            s.close();
         }
-        //Build GET request argument, replacing spaces and newlines
-        String response = "";
-        try {
-            // Harrison Shu
-            // Encode the URL String parameter before creating URL to allow arabic and hebrew to be in the URL
-            String encodedText = URLEncoder.encode(text, StandardCharsets.UTF_8.toString());
-
-            //Make GET request
-            URL url = new URL("http://localhost:" + portNumber +"/?text=" +
-                    encodedText + "&from=" + from + "&to=" + to);
-            HttpURLConnection con = (HttpURLConnection) url.openConnection();
-            con.setRequestMethod("GET");
-            con.connect();
-
-            //read response from server
-            BufferedReader in = new BufferedReader(new InputStreamReader(con.getInputStream()));
-            response = in.readLine();
-            in.close();
-
-            con.disconnect();
-        } catch(IOException e){
-            return makeServerRequest(text, from, to);
+        catch(FileNotFoundException e){
+            return portNumber;
         }
-        return response;
+        catch(Exception e){
+            System.out.println("Problem retrieving port number from log");
+            throw new RuntimeException(e);
+        }
+        return portNumber;
     }
-    public static boolean serverNotRunning(){
+    public static boolean serverNotRunning(String logPath){
         //initial value of portNumber
         if(portNumber == -1){
-            File log = new File("translator/server.log");
-            try {
-                Scanner s = new Scanner(log);
-                if(s.hasNext()){
-                    portNumber = Integer.parseInt(s.nextLine().split(": ")[1]);
-                }
-                else{
-                    return true;
-                }
-            } catch (FileNotFoundException e) {
-                throw new RuntimeException(e);
+            portNumber = getPortFromLog(logPath, false);
+            if(portNumber == 0){
+                return true;
             }
         }
         try{
@@ -79,33 +59,63 @@ public static boolean serverNotRunning(){
             return true;
         }
     }
-    public static void start(){
+    public static String makeServerRequest(String jsonString, String from, String to) {
+        String logPath = "translator/server.log";
+        if(serverNotRunning(logPath)){
+            start(timeout);
+            while(serverNotRunning(logPath)); //block
+        }
+
+        String response;
+        try {
+            byte[] json = jsonString.getBytes(StandardCharsets.UTF_8);
+            int length = json.length;
+
+            //Make POST request
+            URL url = new URL("http://localhost:" + portNumber + "/?from=" + from + "&to=" + to);
+            HttpURLConnection con = (HttpURLConnection) url.openConnection();
+            con.setRequestMethod("POST");
+            con.setDoOutput(true);
+            con.setFixedLengthStreamingMode(length);
+            con.setRequestProperty("Content-Type", "application/json; charset=UTF-8");
+            con.connect();
+
+            try(OutputStream os = con.getOutputStream()) {
+                os.write(json);
+            }
+
+            //read response from server
+            BufferedReader in = new BufferedReader(new InputStreamReader(con.getInputStream()));
+            response = in.readLine();
+            in.close();
+
+            con.disconnect();
+        } catch(IOException e){
+            System.out.println(e.getMessage());
+            return "Translation Unavailable";
+        }
+        return response;
+    }
+    public static void start(String timeout) {
         System.out.println("Starting translation server...");
 
-        if(serverNotRunning()){
-            File log = new File("translator/server.log");
-            String absPath = "translator/server.py";
+        String logPath = "translator/server.log";
+        String absPath = "translator/server.py";
+        if(serverNotRunning(logPath)){
+            File log = new File(logPath);
             try {
-                ProcessBuilder pb = new ProcessBuilder("python", absPath);
+                log.createNewFile();
+                ProcessBuilder pb = new ProcessBuilder("python", absPath, timeout);
                 pb.redirectOutput(log);
                 pb.redirectErrorStream(true);
                 pb.start();
-
             } catch (IOException e) {
                 System.out.println("An I/O error has occurred.");
                 System.out.println(e.getMessage());
             }
 
-            try {
-                Scanner s = new Scanner(log);
-                //Wait for server.log to be written to (port number)
-                while(log.length() == 0);
-                portNumber = Integer.parseInt(s.nextLine().split(": ")[1]);
-                s.close();
-            } catch (FileNotFoundException e) {
-                System.out.println("A FileNotFound error has occurred.");
-                System.out.println(e.getMessage());
-            }
+            portNumber = getPortFromLog(logPath, true);
+
         }
         System.out.println("Translation server running!");
     }